蕨类植物与微生物

The aim of the study was to determine the still not completely described microbiome associated with the aquatic fern Azolla filiculoides. During the experiment, 58 microbial isolates (43 epiphytes and 15 endophytes) with different morphologies were obtained. We successfully identified 85% of microorganisms and assigned them to 9 bacterial genera: Achromobacter, Bacillus, Microbacterium, Delftia, Agrobacterium, and Alcaligenes (epiphytes) as well as Bacillus, Staphylococcus, Micrococcus, and Acinetobacter (endophytes). We also studied an A. filiculoides cyanobiont originally classified as Anabaena azollae; however, the analysis of its morphological traits suggests that this should be renamed as Trichormus azollae. Finally, the potential of the representatives of the identified microbial genera to synthesize plant growth-promoting substances such as indole-3-acetic acid (IAA), cellulase and protease enzymes, siderophores and phosphorus (P) and their potential of utilization thereof were checked. Delftia sp. AzoEpi7 was the only one from all the identified genera exhibiting the ability to synthesize all the studied growth promoters; thus, it was recommended as the most beneficial bacteria in the studied microbiome. The other three potentially advantageous isolates (Micrococcus sp. AzoEndo14, Agrobacterium sp. AzoEpi25 and Bacillus sp. AzoEndo3) displayed 5 parameters: IAA (excluding Bacillus sp. AzoEndo3), cellulase, protease, siderophores (excluding Micrococcus sp. AzoEndo14), as well as mineralization and solubilization of P (excluding Agrobacterium sp. AzoEpi25).

Bacteria communities associated with plants have been given increasing consideration because they are arguably beneficial to their host plants. To understand the ecological and evolutionary impact of these mutualistic associations, it is important to explore the vast unknown territory of bacterial genomic diversity and their functional contributions associated with the major branches of the tree-of-life. Arguably, this aim can be achieved by profiling bacterial communities by applying high throughput sequencing approaches, besides establishing model plant organisms to test key predictions. This study utilized the Illumina Miseq reads of bacterial 16S rRNA sequences to determine the bacterial diversity associated with the endosphere of the leaves of the highly specialized rock spleenwort Asplenium delavayi (Aspleniaceae). By documenting the bacterial communities associated with ferns collected in natural occurrence and cultivation, this study discovered the most species-rich bacterial communities associated with terrestrial ferns reported until now. Despite the substantial variations of species diversity and composition among accessions, a set of 28 bacterial OTUs was found to be shared among all accessions. Functional analyses recovered evidence to support the predictions that changes in bacterial community compositions correspond to functional differentiation. Given the ease of cultivating this species, Asplenium delavayi is introduced here as a model organism to explore the ecological and evolutionary benefits created by mutualistic associations between bacteria and ferns.

PREMISE Azolla is a genus of floating ferns that has closely evolved with a vertically transmitted obligate cyanobacterium endosymbiont-Anabaena azollae-that fixes nitrogen. There are also other lesser-known Azolla symbionts whose role and mode of transmission are unknown. METHODS We sequenced 112 Azolla specimens collected across the state of California and characterized their metagenomes to identify the common bacterial endosymbionts and assess their patterns of interaction. RESULTS Four genera were found across all samples, establishing that multiple Azolla endosymbionts were consistently present. We found varying degrees of cophylogenetic signal across these taxa as well as varying degrees of isolation by distance and of pseudogenation, which demonstrates that multiple processes underlie how this endosymbiotic community is constituted. We also characterized the entire Azolla leaf pocket microbiome. CONCLUSIONS These results show that the Azolla symbiotic community is complex and features members at potentially different stages of symbiosis evolution, further supporting the utility of the Azolla microcosm as a system for studying the evolution of symbioses.

… ferns and fern allies, are … microbiome, only few studies have been undertaken in this area, thereby creating a huge research gap. Hence, this review compiles pteridophyte microbiome …

Azolla is a floating fern that has closely evolved with a vertically transmitted obligate cyanobacterium endosymbiont—Anabaena azollae—that performs nitrogen fixation in specialized Azolla leaf pockets. This cyanobac-terium has a greatly reduced genome and appears to be in the “advanced” stages of symbiosis, potentially evolving into a nitrogen-fixing organelle. However, there are also other lesser-known inhabitants of the leaf pocket whose role and mode of transmission are unknown. We sequenced 112 Azolla specimens collected across the state of California and characterized their metagenomes in order to identify the common bacterial endosymbionts of the leaf pocket and assess their patterns of co-diversification. Four taxa were found across all samples, establishing that there are multiple endosymbionts that consistently inhabit the Azolla leaf pocket. We found varying degrees of co-diversification across these taxa as well as varying degrees of isolation by distance and of pseudogenation, which implies that the endosymbiotic community is transmitted by a mix of horizontal and vertical mechanisms, and that some members of the microbiome are more facultative symbionts than others. These results show that the Azolla symbiotic community is complex, featuring members at potentially different stages of symbiosis evolution, further supporting the utility of the Azolla microcosm as a system for studying the evolution of symbioses.

Abstract The microbiome is the synchronised congregation of millions of microbial cells in a particular ecosystem. The rhizospheric, phyllospheric, and endospheric microbial diversity of lower groups of plants like pteridophytes, which includes the Ferns and Fern Allies, have also given numerous alternative opportunities to achieve greener and sustainable agriculture. The broad-spectrum bioactivities of these microorganisms, including bioremediation of heavy metals (HMs) in contaminated soil, have been drawing the attention of agricultural researchers for the preparation of bioformulations for applications in climate-resilient and versatile agricultural production systems. Pteridophytes have an enormous capacity to absorb HMs from the soil. However, their direct application in the agricultural field for HM absorption seems infeasible. At the same time, utilisation of Pteridophyte-associated microbes having the capacity for bioremediation have been evaluated and can revolutionise agriculture in mining and mineral-rich areas. In spite of the great potential, this group of microbiomes has been less studied. Under these facts, this prospective review was carried out to summarise the basic and applied research on the potential of Pteridophyte microbiomes for soil bioremediation and other agricultural applications globally. Gaps have also been indicated to present scopes for future research programmes.

… Contrary to observations of a diverse, shared leaf pocket microbiome in wild Azolla ferns, … a persistent vertically-transmitted microbiome outside of the cyanobacterium Trichormus (syn. …

This study reports the analyses of the rhizospheric microbiome of the terrestrial mangrove fern Acrostichum aureum Linn. from the Indian Sunderbans. Samples were collected using standard protocols and 16S rRNA gene V3–V4 region amplicon sequencing was performed to identify the microbial communities prevalent in the rhizosphere. A total of 1,931,252 quality checked reads were assembled into 204,818 contigs and were analysed using QIIME to reveal the abundance of Proteobacteria, Acidobacteria and Planctomycetes. The data is available at the NCBI - Sequence Read Archive with accession number: SRX2660456. This is the first report of the rhizospheric microbiome belonging to a fern species.

Background Azolla is a small floating fern living in symbiosis with nitrogen-fixing cyanobacteria and provides a variety of important ecosystem benefits. Previous studies have presented that Azolla harbors diverse bacteria that may play a key role in host fitness and productivity. However, the characteristics of endophytic bacteria inhabiting the phyllosphere of different species of Azolla have not yet been fully understood. Results In this study, the 16S ribosomal DNA (rDNA) V5-V7 region of bacteria was determined by Illumina high-throughput sequencing platform to study the diversity and richness of endophytic bacterial communities in the phyllosphere of five Azolla species collected from different countries. A total of 1150 operational taxonomic units (OTUs) were detected for the endophytic bacteria community. According to the α diversity indices, the diversity of bacteria was ordered as Azolla imbricata  >  A. pinnata  >  A. filiculoides  >  A. mexicana  >  A. caroliniana . The PCoA results displayed that the bacterial communities of A. mexicana and A. caroliniana shared the highest similarity, followed by the similarity between A. pinnata and A. imbricata , and they were significantly distinct from the community of A. filiculoides . The dominant bacteria of Azolla mainly belonged to the phylum of Proteobacteria, followed by Actinobacteria, Chlorobillobacteria, and Firmicutes. In detail, the relative abundance of Proteobacteria in A. imbricata was 52.23%, whereas it was more than 80.00% in the other four species of Azolla . Notably, Herbaspirillum (45.91%, 44.08%) and Methylophilus (29.97%, 37.96%) were the main genera inhabiting A. mexicana and A. caroliniana respectively. Ferrovibrio (18.54%) and Rhizobium (16.68%) were the dominant genera inhabiting A. filiculoides . The group of unidentified genera (41.63%, 44.92%) consisted most of the bacteria in A. imbricata and A. pinnata respectively. Further analysis suggested that the significant different bacteria identified in LDA Effect Size analysis existed Azolla species-specific patterns. Conclusions In summary, all results suggested that the diversity and composition of the endophytic bacterial communities were different in Azolla species.

Summary Dinitrogen fixation by Nostoc azollae residing in specialized leaf pockets supports prolific growth of the floating fern Azolla filiculoides. To evaluate contributions by further microorganisms, the A. filiculoides microbiome and nitrogen metabolism in bacteria persistently associated with Azolla ferns were characterized. A metagenomic approach was taken complemented by detection of N2O released and nitrogen isotope determinations of fern biomass. Ribosomal RNA genes in sequenced DNA of natural ferns, their enriched leaf pockets and water filtrate from the surrounding ditch established that bacteria of A. filiculoides differed entirely from surrounding water and revealed species of the order Rhizobiales. Analyses of seven cultivated Azolla species confirmed persistent association with Rhizobiales. Two distinct nearly full‐length Rhizobiales genomes were identified in leaf‐pocket‐enriched samples from ditch grown A. filiculoides. Their annotation revealed genes for denitrification but not N2‐fixation. 15N2 incorporation was active in ferns with N. azollae but not in ferns without. N2O was not detectably released from surface‐sterilized ferns with the Rhizobiales. N2‐fixing N. azollae, we conclude, dominated the microbiome of Azolla ferns. The persistent but less abundant heterotrophic Rhizobiales bacteria possibly contributed to lowering O2 levels in leaf pockets but did not release detectable amounts of the strong greenhouse gas N2O.

The increasing volume of wastewater from fish farming poses a serious environmental threat. This study investigated a novel treatment method for butter catfish (Ompok bimaculatus) wastewater using a constructed wetland-microbial fuel cell (CW-MFC) integrated with the water fern Azolla microphylla. The system was effectiveness in removing pollutants like electrical conductivity (EC), total dissolved solids (TDS), ammonium, nitrate, nitrite, and phosphate was evaluated. Additionally, the electricity generation capabilities were measured. The CW-MFC system achieved significant removal rates: 67.65% for EC, 61.67% for TDS, 100% for ammonium, 75.00% for nitrate, 81.25% for nitrite, and 70.00% for phosphate. Furthermore, the system generated a maximum open-circuit voltage (OCV) of 690±90 mV, a current density (CD) of 7.29±0.43 mA/m³and a power density (PD) of 0.37±0.04 mW/m³. Analysis of the microbial community revealed a diverse root consortium dominated by bacterial genera including Phreatobacter, Emticicia and Rhodobacter, along with fungal genera such as Strelitziana, Ramularia, Cladosporium,Trichomerium, Cercospora, Erythrobasidium and Fusarium. These findings suggest that CW-MFC systems integrated with A. microphylla offer a promising approach for sustainable and efficient treatment of wastewater from catfish farming while simultaneously generating bioelectricity.

… to report only presence/ absence of fungal endophytes that might represent a kind of symbiosis. In most of the surveys focussing on pteridophytes used in our study, it becomes clear …

… In the present study, isolation of an endophytic fungus from fern roots was not invariably achieved, and it may well be that some of these failures were due to the presence of endophytes …

… in the pteridophytes and fungal endophyte … pteridophytes as well as to isolate and identify endophytic fungi from the same fronds. In this study, we have attempted to study endophytic …

… of fungal associations in pteridophytes is surprisingly patchy … fungal associations across pteridophytes and consider future … , hyphae in a range of pteridophytes, advocating a mutualistic …

… hyphomycetes as root endophytes in Pteridophytic plants. … Recent studies reveal their endophytic presence in plant roots… hyphomycetes as endophyte of the Pteridophytic plant roots. …

… This article describes the results of a light and electron microscopic study of the fungal endophytes and vascular anatomy in the rhizomes and gametophytes of Tmesipteris and Psilotum…

Arbuscular mycorrhizas (AM) are one of the most widespread types of symbiotic associations. Pteridophytes occupy an important position in the evolution of vascular plants. However, their mycorrhizal state remains poorly understood. The aim of this work was to describe the general mycorrhizal status and the occurrence of dark septate endophytes (DSE) in the pteridophytic flora of a Valdivian temperate forest in Patagonia, Argentina. First, the roots of nine terrestrial species representing six families were examined, and this information was then compared with other surveys concerning the occurrence of AM in other pteridophytic species within the same Valdivian temperate forest. AM were recorded in 98.6% of the samples analyzed in this work and all of them corresponded to the Paris‐type morphology. DSEs were also present within the roots of all terrestrial species. A comparison to published results in other ferns and lycophytes that have been studied in this Valdivian temperate forest (161 sporophytes, 21 species and 10 families) was made. Clear differences in colonization patterns between eusporangiate/leptosporangiate and epiphytic/terrestrial species became evident and are discussed.

… surveyed, this is the first study of endophytes bacterial isolates from pteridophytes in the country, and a lot more is needed in order to elaborate the role of endophytes from this plant. …

From the saprotrophs that decay plant material to the pathogens and mutualists that shape plant demography at local and regional scales, fungi are major drivers of tropical forest dynamics. Although endophytic fungi are abundant and diverse in many biomes, they reach their greatest diversity in tropical forests, where they can influence plant physiology, performance and survival. The number of quantitative studies regarding endophytes has increased dramatically in the past two decades, but general rules have not yet emerged regarding the biogeography, host affiliations, local or regional distributions, or phylogenetic diversity of endophytes in most tropical settings. Here, endophytic fungal communities associated with 18 species of eupolypod fern were compared among forest reserves in Panama, Costa Rica and Mexico. Molecular sequence data for >2000 isolates were used to determine the relationships of host taxonomy, forest (site), and environmental dissimilarity to endophyte community composition. Communities in related ferns differed significantly among forests, reflecting the interplay of geographic distance and environmental dissimilarity. Although the same phyla and classes of fungi were prevalent at each site, they differed in relative abundance. All sites were dominated by the same order (Xylariales), but sites differed in the phylogenetic clusteringvs.evenness of their endophyte communities. By addressing the relationship of endophyte communities to host taxonomy, geographic distance and environmental factors, this study complements previous work on angiosperms and contributes to a growing perspective on the factors shaping communities of ecologically important fungi in tropical forests.

Fern species belonging to the oldest vascular plants have been widely used as traditional medicines by indigenous communities especially in the humid regions of South East Asia for thousands of years. Fungal endophytic associations with ferns have been identified through various mechanisms, resulting in host ferns’ resistance to adverse conditions or growth enhancement. The highest potential of fungal endophytes to produce bioactive compounds and their biological properties has prompted research into endophytes associated with fern species. The purpose of this review is to provide an overview of the endophytic fungi isolated from fern plants with medicinal properties and highlight their potential as natural sources of novel bioactive compounds for agricultural and therapeutic applications. Further research is needed to investigate these fungal endophytes colonizing medicinal ferns in different ecological niches.

… studies on endophytes in bryophyte and pteridophyte cultures, and on endophytes and endosymbionts forming mycorrhizae on roots and shoots of various pteridophyte species, in vivo …

… Information on AM and SE fungal status of the Indian pteridophytes is very limited. Less than 150 species of pteridophytes have been examined for the presence of endorhizal fungal …

The morphology of a Glomus-like fungus-host interaction in chlorophyllous gametophytes and young apogamic sporophytes of Dryopteris muenchii A.R. Sm. was studied from ferns cultivated in laboratory, using soil as substrate. An aseptate fungus colonized the gametophytes tissue through the rhizoids, developing vesicles. The fungus penetrated the young sporophytes primary roots by developing appressoria. It spread forming inter- and intra-cellular hyphae through the epidermis and the outermost cortical cell layers, where it formed vesicles, hyphal coils-like and arbuscules. The fungus hyphae never colonized the gametophytesporophyte cellular junction. The fungal structures observed on D. muenchii during this study, are rather similar to those reported for the plant host-arbuscular mycorrhizal fungus (AMF) interaction, where the AMF described belonged to Phylum Glomeromycota. Therefore, this study is a contribution to the scarce knowledgement of the association between AMF and chlorophyllous gametophytes and young apogamic sporophytes of ferns.

Mucilage, a polysaccharide‐rich substance secreted by root cap and border cells, is a key mediator of plant–soil interactions. This review traces the evolutionary origins of root mucilage from ancestral secretion mechanisms in streptophyte algae to its diverse roles in modern vascular plants. We highlight how mucilage biosynthesis relies on conserved gene families involved in polysaccharide assembly, whose phylogenomic distribution suggests that components of this machinery were already present in algal ancestors. Combining genetic, functional, and ecological evidence, we infer a stepwise evolutionary trajectory in which mucilage initially facilitated hydration and anchorage, later supporting soil structuring, plant–microbe interactions, nutrient availability, root water uptake, and drought tolerance. Fossil and comparative evidence indicates that both the secretion of mucilage and its regulatory mechanisms are deeply conserved traits. By connecting ancestral molecular and physiological functions to modern ecological roles, we demonstrate that mucilage has been a critical adaptation enabling plants to colonize and thrive in terrestrial environments over geological timescales.

Mycorrhizal symbiosis is common among land plants including pteridophytes (monilophytes and lycophytes). In pteridophytes with diplohaplontic life cycle, mycorrhizal formations were …

… the rhizosphere of a fern in Mexico as well as for A. firma. … diversity of AMF spores in the rhizosphere of A. firma present … of AMF associated with the rhizosphere of a fern in Mexico as …

… of mycorrhizae -- arbuscular and orchid -- in the roots of fern or its allies collected in Korea. Neither the ectomycorrhizal … of fern species having arbuscular mycorrhizal structures, but not …

… of the most important forms of symbioses in the context of … of mycorrhizal symbioses in extinct plant groups. We report the first evidence of endomycorrhizal associations in the seed fern …

… to investigate mycorrhizal associations of a fern that appeared … , (2) whether mycorrhiza has any impact on sporophyte growth… Mycorrhiza of gametophytes and sporophytes of a few fern …

… That this symbiotic association may occur in still lower organisms than the ferns is shown in … the occurrence of this in the green prothallia of ferns quite readily understood. Whether in the …

Arbuscular mycorrhizal fungi (AMF) are amongst the most studied obligate plant symbionts and regularly found in terrestrial plants. However, global estimates of AMF abundance amongst all land plants are difficult because i) the mycorrhizal status of many non-commercial, wild plant species is still unknown, ii) numerous plant species engage in facultative symbiosis, meaning that they can, but do not always do, associate with mycorrhiza, and iii) mycorrhizal status can vary within families, genera, and species. To gain deeper insights to the distribution of the plant-AMF symbiosis we investigated the mycorrhizal status in some of the oldest lineages of extant vascular plants, Polypodiophytina (ferns) and lycophytes, in one of the hotspots of natural plant diversification, the tropical rainforest. Providing a new data set of AMF abundance for 82 fern species representing 19 families, we hypothesized that (1) AMF would be found in 60-80% of the studied plants and (2) plant species with AMF symbionts would be more abundant than non-mycorrhizal species. Both hypotheses were rejected while the following observations were made: (1) AMF occurred in 30.5% of studied species, representing 63% of the studied fern families, (2) AMF colonisation was not correlated with species abundance, (3) a small proportion of AMF-hosting ferns was epiphytic (6%) and (4) mycorrhization was inconsistent among different populations of the same species (facultative mycorrhization). While these observations align with previous studies on ferns, they emphasise that mycorrhization is not a taxonomic trait and underscore the challenges in estimating the global abundance of AMF. In addition, the occurrence of AMF in epiphytic plants and no net benefits of AMF for plant abundance indicate that the mycorrhization observed in this study likely comprises the commensalism to parasitism range of the symbiosis spectrum.

… to mycorrhizal ones. As a basis for future studies, we hypothesize that non-mycorrhizal fern … In turn, this raises the question why is it that not all fern species have mycorrhizal symbioses…

… Analysis of field root and soil samples from the ferns introduced and native range as well as … mycorrhizal colonization in the roots of L. microphyllum and the dependency on mycorrhizal …

… We studied the arbuscular mycorrhizal fungi (AMF) and dark septate fungi (DSF) in two lycopods and 23 ferns … This is the first report of the mycorrhizal status for 17 species. Arbuscular …

… of fern species sampled for mycorrhizae by about 1% (109) and that of genera by 6% (19). While knowledge of mycorrhizae among ferns … functional need for this symbiosis in the canopy …

… mycorrhizal symbiosis may be involved in As uptake by this fern. This is because arbuscular … Based on the results of this study, it can be concluded that the mycorrhizal status of ferns …

The establishment of mycorrhizal relationships between a fungus and a plant typically enhances nutrient and water uptake for the latter while securing a carbon source for the fungus. However, under a particular set of environmental conditions, such as low availability of light and abundant nutrients in the soil, the resources invested in the maintenance of the fungi surpass the benefits obtained by the host. In those cases, facultative mycorrhizal plants are capable of surviving without symbiosis. Facultative mycorrhization in ferns has been overlooked until now. The present study measured the response of Struthiopteris spicant L. Weiss, and its root-associated fungi to different levels of light and nutrient availability in terms of growth, mycorrhizal presence, and leaf nutrient content. This fern species exhibits a great tolerance to variable light, nutrient, and pH conditions, and it has been found with and without mycorrhizae. We conducted a greenhouse experiment with 80 specimens of S. spicant and three factors (Light, Phosphorus, and Nitrogen) resulting in eight treatments. We found a significant influence of the factor light on fungal community composition, plant biomass, and nutrient accumulation. Departing from a lack of colonization at the initial stage, plants showed a remarkable increment of more than 80% in the arbuscular mycorrhizal fungi (AMF) richness and abundance in their roots when grown under high light conditions, compared with the ones in low light. We also observed an upward trend of C:P and C:N ratios and the above- and belowground biomass production when AMF abundance increased. Furthermore, the compositional analysis of the whole fungal communities associated with S. spicant roots revealed clear differences among low-light and high-light treatments. This study is the first to investigate the importance of light and nutrient availability in determining fern-AMF relationships. We confirmed that Struthiopteris spicant is a facultative mycorrhizal plant. The composition and diversity of AMF found in the roots of this fern are strongly influenced by light and less by nutrient conditions. Our study shows that ferns respond very sensitively to changes in environmental factors, leading to shifts in the associated mycorrhizal communities.

… lycophytes and ferns, although mycorrhizae are believed to be crucial for the majority of land plants. We screened the degree of mycorrhizal colonization for all 75 fern species recorded …

… about the evolutionary significance of this symbiosis. These are: l) the … ferns growing under pure stands of ectomycorrhizal forest trees in New Zealand, were not observed on the ferns in …

… Of the biotic influences, mycorrhizae play an important role in … from the presence of mycorrhizal associates via a variety of … The influence of mycorrhizal symbioses extends beyond the …

… that Cheilanthes ferns are also mycorrhizal. Fungal presence … A field survey of mycorrhizal associations in ferns of Pakistan. … Mycorrhizal symbioses found in roots of fern and its relatives …

… Pteridophytes and Gymnosperms revealed the presence of N2-fixing micro-organisms in their phyllosphere. … in the phyllosphere of plants achieved by spraying bacterial suspension at …

The foliar surface forms one of the largest aboveground habitats on Earth and maintains plant-fungus relationships that greatly affect ecosystem functioning. Despite many studies with particular plant species, the foliar epiphytic mycobiome has not been studied across a large number of plant species from different taxa. Using high-throughput sequencing, we assessed epiphytic mycobiomes on leaf surfaces of 592 plant species in a botanical garden. Plants of angiosperms, gymnosperms, and pteridophytes were involved. Plant taxonomy, leaf side, growing environment, and evolutionary relationships were considered. We found that pteridophytes showed the higher fungal species diversity, stronger mutualistic fungal interactions, and a greater percentage of putative pathogens than gymnosperms and angiosperms. Plant taxonomic group, leaf side, and growing environment were significantly associated with the foliar epiphytic mycobiome, but the similarity of the mycobiomes among plants was not directly related to the distance of the host evolutionary tree. Our results provide a general understanding of the foliar fungal mycobiomes from pteridophytes to angiosperms. These findings will facilitate our understanding of foliar fungal epiphytes and their roles in plant communities and ecosystems. This article is protected by copyright. All rights reserved.

Phylosymbiosis, the congruence of microbiome composition with host phylogeny, is a valuable framework for investigating plant-microbe associations and their evolutionary ecology. This review assesses the prevalence of phylosymbiosis across the plant kingdom, elucidates the fundamental ecological and evolutionary processes contributing to its occurrence based on previous research and explores commonly used methods for identifying phylosymbiosis. We find that the presence of phylosymbiosis may be influenced by both phylogenetic distance and the taxonomic level at which host plants are examined, with the strength of associations potentially decreasing as the taxonomic scale becomes finer. Notably, the endophytic microbiome exhibits a stronger phylosymbiosis signal compared to the epiphytic or rhizosphere-associated microbiomes. The type of microorganisms (e.g., fungi and bacteria) can yield highly variable evidence for phylosymbiosis due to differences in colonization, transmission, or functional characteristics. We also outline how the four community assembly processes (dispersal, selection, diversification, drift) contribute to the establishment and maintenance of host-microbe phylosymbiosis. Furthermore, we highlight the diversity of methods employed to detect phylosymbiosis, which involves three key processes: constructing host phylogenies, assessing microbial data, and statistically evaluating the correlation between host phylogeny and microbial composition. Remarkably different methodologies across studies make comparisons between findings challenging. To advance our understanding, future research is expected to explore phylosymbiosis at lower taxonomic levels and investigate different microbial communities coexisting synergistically within the same host. Understanding the relative importance of community assembly processes in driving phylosymbiosis will be critical for gaining deeper insights into the ecology and evolution of host-microbe interactions.

Background: Azolla is a versatile aquatic fern that is rich in nutrients and possesses valuable antibacterial components, making it a useful green manure and medicinal raw plant material. However, the growth of Azolla is affected by microorganisms under different environmental conditions, the investigation on the interaction between microorganisms and Azolla is one of the crucial projects for Azollaexploration and application. Results: In this study, we cultivated two different Azolla species, Azolla imbricata (Aim) and Azolla pinnata (Api), under identical condition to investigate their respective incidence rates. Metagenome analysis of phyllosphere microorganisms was performed to uncover the interaction between Azollaand microorganisms. Our results revealed significantly higher incidence rates in Aim compared to Api. The microbiological community taxonomy showed a predominance of Proteobacteria phylum and Burkholderiales order, with higher proportions in the Aim group. Conversely, the Api group had higher proportions of Cyanobacteria phylum, Nostocales order, Nostocaceae family, and Trichormusgenus. Moreover, pathogenic bacteria exhibited a higher relative abundance in the Aim group. We further analyzed significant differences in KEGG pathways between the two groups and identified the top 10 enriched pathways. Additionally, according to the resistance gene analysis results, five resistant genes showed different patterns between Api and Aim groups. Expect AAC6-IIa, the other five resistant genes had a higher abundance in Aim than in Api. Conclusions: The greater disease susceptibility of Aim compared to Api may be linked to the microbial community structure of the two species. The variations in microbial community structure could be influenced by the antibacterial components present in Api, whereas Aim may lack or have lower levels of these antibacterial components.These findings provide insights into the microorganisms-Azolla interaction, aiding the development of strategies to enhance Azolla growth and utilization.

… Pteridophytes have an implausible ability to phytoremediate … on the usage of various pteridophytic species as potential … Bacterial AsV-reductase coded by arsC gene facilitates the …

Plant tissues harbor abundant endophytes, which are crucial for plant growth. Endophytes present in Alsophila spinulosa, which is enriched with medicinal components, have not been isolated and characterized yet. Here we employed meta-amplicon sequencing to identify endophytic species and examined their diversity in the leaves, petioles, roots and stems of A. spinulosa. Our findings revealed 1,247 operational taxonomic units (OTUs) for endophytic bacteria across 210 species and 476 OTUs for endophytic fungi across 222 species. Alpha diversity analysis showed the highest endophytic bacterial diversity in A. spinulosa roots, whereas fungal diversity was similar across the leaf, petiole and root tissues. Fungal diversity in the leaves and petioles was markedly higher than that in the stems. Furthermore, beta diversity analysis revealed similarities in the endophytic bacterial and fungal compositions between the leaves and petioles, whereas the compositions in roots and stems considerably differed from those in the leaves and petioles. At the genus level, the predominant endophytic bacteria were Methylobacterium-Methylorubrum and Pseudomonas, whereas the predominant endophytic fungi were Cutaneotrichosporon and Pseudofabraea. Linear discriminant analysis effect size revealed characteristic endophytic bacterial genera specific to each tissue type and characteristic endophytic fungal genera specifically in the leaves, petioles and roots. The co-occurrence network analysis indicated that the complexity of endophyte networks was the highest in the leaves and the lowest in the stems of A. spinulosa. Overall, this study elucidates the distribution patterns of endophytes in A. spinulosa across various tissues, offering valuable microbial resources for the development of natural products for medicinal application.

Chloromethane (CH3 Cl) is the most abundant halogenated volatile organic compound in the atmosphere and contributes to stratospheric ozone depletion. CH3 Cl has mainly natural sources such as emissions from vegetation. In particular, ferns have been recognized as strong emitters. Mitigation of CH3 Cl to the atmosphere by methylotrophic bacteria, a global sink for this compound, is likely underestimated and remains poorly characterized. We identified and characterized CH3 Cl-degrading bacteria associated with intact and living tree fern plants of the species Cyathea australis by stable isotope probing (SIP) with 13 C-labeled CH3 Cl combined with metagenomics. Metagenome assembled genomes (MAGs) related to Methylobacterium and Friedmanniella were identified as being involved in the degradation of CH3 Cl in the phyllosphere, i.e., the aerial parts of the tree fern, while a MAG related to Sorangium was linked to CH3 Cl degradation in the fern rhizosphere. The only known metabolic pathway for CH3 Cl degradation, via a methyltransferase system including the gene cmuA, was not detected in metagenomes or MAGs identified by SIP. Hence, a yet uncharacterized methylotrophic cmuA-independent pathway may drive CH3 Cl degradation in the investigated tree ferns. This article is protected by copyright. All rights reserved.

Sea Level Rise (SLR) as a result of Climate change in combination with anthropogenically altered environment results in alterations in rapid land dynamics in forms of erosion and accretion; along with the associated alteration in species diversity, energy cycling and productivity, significantly in sensitive ecosystems such as river deltas. Geologically, interglacial periods follow bouts of glaciation and presently we are passing through one of those phases wherein, sea level rise (SLR) is being evidenced in case of the Ganga–Brahmaputra basin. It has become more than 100 m higher in the last 18,000 years. Over the years due to the loss of landmass as a rise in sea level, human population has migrated from the different parts of the Sunderban Biosphere Reserve area to specific islands of the Indian Sunderbans. This process of migration has resulted in the removal of forest cover. As a result, extensive loss of epiphytic ferns has occurred. In this work, we have evaluated the distribution of Drynaria across the Indian Sunderbans region from an ecological, biochemical and metagenomic perspective. Results indicate that anthropogenic influences results in gradual depletion of Drynaria abundance and thus can be used as an important indicator for understanding the effects of migration of human population.

… High-throughput sequencing, specifically pyrosequencing, has emerged as a cutting-edge tool for metagenomics and metagenetic analysis, offering a compelling alternative for …

Ferns are pioneer plants that can grow on waste slag in antimony mining areas. They can influence the abundance of soil microorganisms, but the mechanism by which they do so remains unclear. This study investigated the differential effects of Pteridium aquilinum on abundant (relative abundance >0.5 %) and rare (relative abundance <0.01 %) microbial taxa in waste slag. Our results showed that P. aquilinum colonization significantly reduced soil heavy metal concentrations (Sb: 66.08 %; Pb: 22.99 %; Hg: 15.15 %; Zn: 14.83 %; As: 7.39 %) and induced distinct restructuring of the microbial community. Among abundant bacterial taxa, P. aquilinum colonization significantly increased the relative abundances of Roseiarcus and Acidipila, while decreasing those of Aquabacterium, Conexibacter, Ferrithrix, Roseiarcus, Acidipila and Sulfobacillus. Notably, colonization by the fern resulted in the disappearance of rare phyla (Rokubacteria, Synergistetes, Euryarchaeota, and Spirochaetes), while promoting the emergence of rare genera (Fimbriimonadaceae, Babeliaceae, Acidisoma, Anaeromyxobacter, and Amycolatopsis). Redundancy analysis revealed strong correlations between these microbial community shifts and changes in heavy metal concentrations. These findings suggest that P. aquilinum colonization mediates both heavy metal remediation and microbial community succession in waste slag, particularly through the turnover of rare bacterial taxa. This work provides new insights into screening for functional rare bacteria through plant-soil-microbe interactions to improve waste slag management.

The diversity of plant-associated microbial communities is shaped by both host factors and the environment. Natural environmental gradients, specifically elevational ones, can serve as study systems to understand community and ecosystem responses to environmental changes, however the relationship between elevation and microbial diversity is not completely understood, especially in non-model systems such as wild plants. In this paper we explored the role of environmental factors in shaping the diversity and structure of the rhizosphere and phyllosphere of the cloud forest tree fern Cyathea fulva. Samples of phyllosphere, rhizosphere and soil were collected from 15 individual tree ferns across five forest plots along an elevation gradient ranging from 1978 to 2210 meters above sea level. Physicochemical soil data were collected, along with environmental data of all plots. Using 16S rRNA and ITS1 amplicon sequencing, we tested for differences in diversity and composition of bacterial and fungal communities and their potential abiotic drivers. We found that bacterial alpha diversity decreased with elevation in the phyllosphere and rhizosphere, but for fungi this pattern was only found in the rhizosphere. We also observed significant changes in community structure and composition with elevation in both the fungal and bacterial phyllosphere and rhizosphere. Our results suggest a close relationship between elevation and the overall microbial structure associated with tree ferns. We envision this information will help to further understand the dynamics between microbiota and wild plants, contributing to the conservation of necessary interactions for plants and ecosystems wellbeing.

… hypothesized that microscopy and shotgun metagenomic sequencing might reveal eukaryotic … Krona analysis of SSU (16S rDNA þ 18S rDNA) sequences filtered from the metagenomic …

… is determined by its metagenome and that, therefore, not only the fern but also associated microflora … (b) Sporophyte habit after 4 weeks with a 16 h light period with tube light (TL, which …

New pathways in plants and microbes Plants and microbes have interacted through evolution in ways that shaped diversity and helped plants colonize land. Delaux and Schornack review how insights from a range of plant and algal genomes reveal sustained use through evolution of ancient gene modules as well as emergence of lineage-specific specializations. Mosses, liverworts, and hornworts have layered innovation onto existing pathways to build new microbial interactions. Such innovations may be transferrable to crop plants with an eye toward building a more sustainable agriculture. Science, this issue p. eaba6605 BACKGROUND Microbial interactions have shaped plant diversity in terrestrial ecosystems. By forming mutually beneficial symbioses, microbes helped plants colonize land more than 450 million years ago. In parallel, omnipresent pathogens led to the emergence of innovative defense strategies. The evolution of plant-microbe interactions encompasses ancient conserved gene modules, recurrent concepts, and the fast-paced emergence of lineage-specific innovations. Microbes form communities on the surface or inside plant tissues and organs, and most intimately, microbes live within single plant cells. Intracellular colonization is established and controlled in part by plant genes that underpin general cell processes and defense mechanisms. To benefit from microbes, plants also evolved genetic modules for symbiosis support. These modules have been maintained despite the risk of getting hijacked by pathogens. ADVANCES The hundreds of land plant and algal genomes that are now available enable genome-wide comparisons of gene families associated with plant immunity and symbiosis. Reconstruction of gene phylogenies and large-scale comparative phylogenomic approaches have revealed an ancient subset of genes coevolving with the widespread arbuscular mycorrhiza symbiosis, the most ancient plant intracellular symbiosis, and with other types of more recently evolved intracellular symbioses in vascular and nonvascular plants. Intercellular symbiotic interactions formed with cyanobacteria or ectomycorrhizal fungi seem to repeatedly evolve through convergent, but not necessarily genetically conserved, mechanisms. Phylogenetic analyses revealed occurrence of candidate disease-resistance genes in green algae, as well as orthologs of flowering plant genes involved in symbiosis signaling and sensing microbial patterns. Yet, more research is needed to understand their functional conservation. The extent to which conserved symbiosis genes also fulfill often opposing roles during pathogen-plant interactions is being explored through studies of pathogen infections in plants capable of supporting symbiotic relationships. The development of plant-microbe systems in genetically tractable species covering the diversity of land plant lineages—including angiosperms and bryophytes, such as the liverwort Marchantia polymorpha—makes it possible to test hypotheses that emerge from phylogenetic analyses, linking genetic and functional conservation across land plants. Studies in bryophytes illustrate the range of possibilities for pathogen management: ancient genes, such as membrane receptors that perceive fungus-derived chitin; pathways with bryophyte clade–specific components, such as phenylpropanoid-derived auronidin stress metabolites; and jasmonate-like hormonal signaling for immunity. OUTLOOK Only a few plant-microbe interactions have been studied in depth, and those in only a few land plant lineages. Future investigations of interactions occurring across the diversity of plants may unravel new types of symbiotic or pathogenic interactions. The occurrence of microbe-sensing genes in streptophyte algae, harboring the closest algal relative to land plants, suggest the existence of overlooked and potentially ancient symbiotic associations. Genetically tractable plant-microbe model systems in diverse streptophyte algae, hornworts, liverworts, ferns, and the so far unsampled diversity of seed plants will enable dissection of the spectrum of molecular mechanisms that regulate the breadth of interactions occurring in plants. The actual function of the symbiotic genes present in bryophyte genomes also remains to be determined. Furthermore, our understanding of plant-microbe interactions will be enriched by more often combining evolutionary concepts with mechanistic studies. More efforts are needed to decipher the molecular changes that have enabled the emergence of new interactions, signaling pathways, and enzymatic specificities to support symbiosis and to protect against pathogens. Microbes manipulate plant processes, and complementary microbial studies are key to gaining a complete picture of plant-microbe evolution. Knowing the rules of engagement between distantly related plants and their microbes then helps genetic transplantation approaches into crops and the orthogonal engineering of bioprocesses aimed at achieving quantitative resistance against pathogens, improving phosphate uptake, or establishing nitrogen-fixing associations for efficient use in sustainable agriculture. Ancient friends and recent enemies shape plant evolution. Some pathogens such as oomycetes are able to infect a wide range of extant plant lineages, including bryophytes (left), and plant pathogen interactions often evolve at a fast pace. By contrast, some symbiotic interactions that look exactly as they do today can be found in the most ancient land plant fossils, here depicted as an illustration of the Rhynie chert fossil plant Aglaophyton major (right). Still, both types of plant-microbe interactions feature evolutionarily ancient as well as rapidly evolving aspects. Extending plant-microbe studies across diverse groups of plant lineages has enriched our understanding of these processes and their evolution. During 450 million years of diversification on land, plants and microbes have evolved together. This is reflected in today’s continuum of associations, ranging from parasitism to mutualism. Through phylogenetics, cell biology, and reverse genetics extending beyond flowering plants into bryophytes, scientists have started to unravel the genetic basis and evolutionary trajectories of plant-microbe associations. Protection against pathogens and support of beneficial, symbiotic, microorganisms are sustained by a blend of conserved and clade-specific plant mechanisms evolving at different speeds. We propose that symbiosis consistently emerges from the co-option of protection mechanisms and general cell biology principles. Exploring and harnessing the diversity of molecular mechanisms used in nonflowering plant-microbe interactions may extend the possibilities for engineering symbiosis-competent and pathogen-resilient crops.

… Understanding these intricate plant-microbe interactions is vital for advancing ecological restoration efforts and sustainable agricultural practices, especially in nutrient-poor soils. It …

… In this opinion article, we propose new hypotheses regarding the origin and evolution of mechanisms controlling efficient plant–microbe symbioses, highlighting the need for new plant …

Angiosperms represent most of plants that human cultivate, grow and eat. However, angiosperms are only one of five major land plant lineages. As a whole lineage, plants also include algal groups. All these clades represent a tremendous genetic diversity, that can be investigated to reveal the evolutionary history of any given mechanism. In this review, we describe the current model of the plant immune system, discuss its evolution based on the recent literature and propose future directions for the field. In angiosperms, plant-microbe interactions have been intensively studied, revealing essential cell surface and intracellular immune receptors, as well as metabolic and hormonal defence pathways. Exploring diversity at the genomic and functional levels demonstrated the conservation of theses pathways across land plants, and for some of them beyond plants. From the conserved mechanisms, lineage-specific variations have occurred leading to diversified reservoirs of immune mechanisms. In rare cases, this diversity has been harnessed and successfully transferred to other species, by integration of wild immune receptors or engineering of novel forms of receptors, for improved resistance to pathogens. We propose that exploring further the diversity of immune mechanisms in the whole plant lineage will reveal completely novel sources of resistance to be deployed in crops.

… studies provided lists of candidate genes and, more importantly, proved that comparative phylogenomics has the potential to strongly improve our understanding of plant–microbe …

ABSTRACT The Genetics Society Non-Seed Plant meeting brought together researchers embracing the diversity of plants and using emerging and established model systems covering hornworts, mosses, liverworts, lycophytes and ferns. This growing community of researchers is exploring fundamental questions on plant development, evolution and environmental responses. Highlights included cutting-edge work in bryophytes on meristem development, hormonal signalling and chromatin regulation, as well as advances in charophyte algae, illuminating the evolutionary origins of key plant traits. The meeting emphasized how non-seed plants, often overlooked in mainstream plant science, are now providing transformative insights into gene regulation, plant-environment interactions and crop improvement potential. These developments reflect a broader shift in plant biology, where diverse model systems are essential for reconstructing the evolutionary history of plants and addressing modern agricultural challenges.

Our planet is teeming with an astounding diversity of plants. In a mere single group of closely related species, tremendous diversity can be observed in their form and function - the colour of petals in flowering plants, the shape of the fronds in ferns, and the branching pattern of the gametophyte in mosses. Diversity can also be found in subtler traits, such as the resistance to pathogens or the ability to recruit symbiotic microbes from the environment. Plant traits can also be highly conserved - at the cellular and metabolic levels, entire biosynthetic pathways are present in all plant groups, and morphological characteristics such as vascular tissues have been conserved for hundreds of millions of years. The research community that seeks to understand these traits - both the diverse and the conserved - by taking an evolutionary point-of-view on plant biology is growing. Here, we summarize a subset of the different aspects of plant evolutionary biology, provide a guide for structuring comparative biology approaches and discuss the pitfalls that (plant) researchers should avoid when embarking on such studies.

The Pseudomonas syringae species complex harbors a diverse range of pathogenic bacteria that can infect hosts across the plant kingdom. However, much of our current understanding of P. syringae is centered on its infection of flowering plants. We took a comparative approach to understand how P. syringae infects evolutionarily divergent plants. We identified P. syringae isolates causing disease in the liverwort Marchantia polymorpha, the fern Ceratopteris richardii, and the flowering plant Nicotiana benthamiana, which last shared a common ancestor >500 million years ago. Phytotoxin-enriched phylogroup (PG) 2 isolates of P. syringae are virulent in non-flowering plants, relying on type-3 effectors and the lipopeptide phytotoxin syringomycin. Ectopic syringomycin promotes tissue necrosis, activates conserved stress-related genes, and enhances in planta bacterial growth of toxin-deficient PGs in Marchantia. Collectively, our research reveals a key role for syringomycin in promoting Pseudomonas colonization, which works alongside effectors to antagonize an exceptionally wide spectrum of land plants.

Herein, we report the presence of a plant paleocommunity, dominated by ferns of the family Osmundaceae, structurally preserved from the only known Mesozoic, fossiliferous geothermal deposits, from the La Matilde Formation (Middle-Upper Jurassic) in the Deseado Massif of Southern Patagonia, Argentina. A total of 13 siliceous chert blocks sampled in an area of approximately 250 m2, preserving a monotypic assemblage dominated by Osmundaceae embedded within its original swampy substrate, are documented. Additional Osmundaceae and fewer ferns and conifers are present in the stratigraphically continuous, adjacent chert levels. This association is comparable to those dominated by Osmundaceae in modern swampy settings, such as in high-altitude lagoons in the Paraná Forest in Northeastern Argentina. In addition, a diverse community of mutualistic, parasitic, and saprotrophic microorganisms associated with the ferns and conifers in the assemblage is present. These compositional, paleoenvironmental, and trophic characteristics of the Jurassic Osmundaceae suggest a possible case of ecological stasis, where Osmundaceae-dominated plant communities apparently persisted in swamps of comparable structures, functions, and physical characteristics for over 150 million years. This suggests that Osmundaceae formed similar communities in compatible settings in the Jurassic, becoming preserved in analogous configurations.

Herein, we report the presence of a plant paleocommunity dominated by ferns of the family Osmundaceae embedded in siliceous chert blocks from the only known Mesozoic, fossiliferous geothermal deposits, from the La Matilde Formation (Middle-Upper Jurassic), in the Deseado Massif, southern Patagonia, Argentina. A total of 13 blocks sampled in an area of approximately 250 m2, which includes multiple structurally preserved, monotypic, in-situ, rhizomatous stems of Osmundaceae, embedded within their original swampy substrate are documented. Additional Osmundaceae and other ferns, and conifers are present in chert levels adjacent to the previous blocks. This mimics similar monotypic associations of Osmundaceae in high-altitude lagoons in northeastern Argentina in the middle of the Paraná Forest, suggesting that the fern assemblage found occupied similar open spaces in the Jurassic, becoming preserved in analogous configurations. In addition, observation of the preserved fern tissues and surrounding substrate revealed a variety of interacting microorganisms, which are comparable to those that make up the microbiological communities inhabiting modern osmundaceous environments. This finding reveals a case of ecological stasis, where members of the same fern family separated by more than 150 million years formed similar exclusive groupings of individuals in microecosystems of comparable structure and general characteristics.

Studying the effects of the microbiome on the development of different types of cancer has recently received increasing research attention. In this context, the microbial content of organs of the gastrointestinal tract has been proposed to play a potential role in the development of pancreatic cancer (PC). Proposed mechanisms for the pathogenesis of PC include persistent inflammation caused by microbiota leading to an impairment of antitumor immune surveillance and altered cellular processes in the tumor microenvironment. The limited available diagnostic markers that can currently be used for screening suggest the importance of microbial composition as a non-invasive biomarker that can be used in clinical settings. Samples including saliva, stool, and blood can be analyzed by 16 s rRNA sequencing to determine the relative abundance of specific bacteria. Studies have shown the potentially beneficial effects of prebiotics, probiotics, antibiotics, fecal microbial transplantation, and bacteriophage therapy in altering microbial diversity, and subsequently improving treatment outcomes. In this review, we summarize the potential impact of the microbiome in the pathogenesis of PC, and the role these microorganisms might play as biomarkers in the diagnosis and determining the prognosis of patients. We also discuss novel treatment methods being used to minimize or prevent the progression of dysbiosis by modulating the microbial composition. Emerging evidence is supportive of applying these findings to improve current therapeutic strategies employed in the treatment of PC.

We use open source human gut microbiome data to learn a microbial "language" model by adapting techniques from Natural Language Processing (NLP). Our microbial "language" model is trained in a self-supervised fashion (i.e., without additional external labels) to capture the interactions among different microbial taxa and the common compositional patterns in microbial communities. The learned model produces contextualized taxon representations that allow a single microbial taxon to be represented differently according to the specific microbial environment in which it appears. The model further provides a sample representation by collectively interpreting different microbial taxa in the sample and their interactions as a whole. We demonstrate that, while our sample representation performs comparably to baseline models in in-domain prediction tasks such as predicting Irritable Bowel Disease (IBD) and diet patterns, it significantly outperforms them when generalizing to test data from independent studies, even in the presence of substantial distribution shifts. Through a variety of analyses, we further show that the pre-trained, context-sensitive embedding captures meaningful biological information, including taxonomic relationships, correlations with biological pathways, and relevance to IBD expression, despite the model never being explicitly exposed to such signals.

In flowering plants, strigolactones (SLs) have dual functions as hormones that regulate growth and development, and as rhizosphere signaling molecules that induce symbiosis with arbuscular mycorrhizal (AM) fungi. Here, we report the identification of bryosymbiol (BSB), an SL from the bryophyte Marchantia paleacea. BSB is also found in vascular plants, indicating its origin in the common ancestor of land plants. BSB synthesis is enhanced at AM symbiosis permissive conditions and BSB deficient mutants are impaired in AM symbiosis. In contrast, the absence of BSB synthesis has little effect on the growth and gene expression. We show that the introduction of the SL receptor of Arabidopsis renders M. paleacea cells BSB-responsive. These results suggest that BSB is not perceived by M. paleacea cells due to the lack of cognate SL receptors. We propose that SLs originated as AM symbiosis-inducing rhizosphere signaling molecules and were later recruited as plant hormone. Strigolactones (SLs) regulate angiosperm development and promote symbiosis with arbuscular mycorrhizae. Here the authors show that bryosymbiol, an SL present in bryophytes and angiosperms, promotes AM symbiosis in Marchantia paleacea suggesting an ancestral function of SLs as rhizosphere signals.

… the occurrence and abundance of MLG in diverse monilophytes, and to define MLG structures … quantitative and qualitative variation occurring in xyloglucan throughout the monilophytes. …

Strigolactones (SLs) are an important class of carotenoid-derived signalling molecule in plants, which function both as exogenous signals in the rhizosphere and as endogenous plant hormones. In flowering plants, SLs are synthesized by a core pathway of four enzymes and are perceived by the DWARF14 (D14) receptor, leading to degradation of SMAX1-LIKE7 (SMXL7) target proteins in a manner dependent on the SCFMAX2 ubiquitin ligase. The evolutionary history of SLs is poorly understood, and it is not clear whether SL synthesis and signalling are present in all land plant lineages, nor when these traits evolved. We have utilized recently-generated genomic and transcriptomic sequences from across the land plant clade to resolve the origin of each known component of SL synthesis and signalling. We show that all enzymes in the core SL synthesis pathway originated at or before the base of land plants, consistent with the previously observed distribution of SLs themselves in land plant lineages. We also show that the late-acting enzyme LATERAL BRANCHING OXIDOREDUCTASE (LBO) may be considerably more ancient than previously thought. We perform a detailed phylogenetic analysis of SMXL proteins and show that specific SL target proteins only arose in flowering plants. We also assess diversity and protein structure in the SMXL family, identifying several previously unknown clades. Overall, our results suggest that SL synthesis is much more ancient than canonical SL signalling, consistent with the idea that SLs first evolved as rhizosphere signals and were only recruited much later as hormonal signals.

Strigolactones are an important class of plant signalling molecule with both external rhizospheric and internal hormonal functions in flowering plants. The past decade has seen staggering progress in strigolactone biology, permitting highly detailed understanding of their signalling, synthesis and biological roles - or so it seems. However, phylogenetic analyses show that strigolactone signalling mediated by the D14-SCFMAX2 -SMXL7 complex is only one of a number of closely related signalling pathways, and is much less ubiquitous in land plants than might be expected. The existence of closely related pathways, such as the KAI2-SMAX1 module, challenges many of our assumptions about strigolactones, and in particular emphasizes how little we understand about the specificity of strigolactone signalling with respect to related signalling pathways. In this review, we examine recent advances in strigolactone signalling, taking a holistic evolutionary view to identify the ambiguities and uncertainties in our understanding. We highlight that while we now have highly detailed molecular models for the core mechanism of D14-SMXL7 signalling, we still do not understand the ligand specificity of D14, the specificity of its interaction with SMXL7, nor the specificity of SMXL7 function. Our analysis thus identifies key areas requiring further study.

Plants associate with nitrogen-fixing bacteria to secure nitrogen, which is generally the most limiting nutrient for plant growth. Endosymbiotic nitrogen-fixing associations are widespread among diverse plant lineages, ranging from microalgae to angiosperms, and are primarily one of three types: cyanobacterial, actinorhizal or rhizobial. The large overlap in the signaling pathways and infection components of arbuscular mycorrhizal, actinorhizal and rhizobial symbioses reflects their evolutionary relatedness. These beneficial associations are influenced by environmental factors and other microorganisms in the rhizosphere. In this review, we summarize the diversity of nitrogen-fixing symbioses, key signal transduction pathways and colonization mechanisms relevant to such interactions, and compare and contrast these interactions with arbuscular mycorrhizal associations from an evolutionary standpoint. Additionally, we highlight recent studies on environmental factors regulating nitrogen-fixing symbioses to provide insights into the adaptation of symbiotic plants to complex environments.

Strigolactones (SLs), lactone-containing carotenoid derivatives, function as signaling molecules in the rhizosphere, inducing symbiosis with arbuscular mycorrhizal. In addition, as a class of plant hormones, SLs control plant growth and development in flowering plants (angiosperms). Recent studies show that the ancestral function of SLs, which precede terrestrialization of plants, is as rhizosphere signaling molecules. SLs were then recruited as a class of plant hormones through the step-by-step acquisition of signaling components. The D14 gene encoding the SL receptor arose by gene duplication of KARRIKIN INSENSITIVE2 (KAI2), the receptor of karrikins and KAI2 ligand (KL), an unknown ligand, in the common ancestor of seed plants. KL signaling targets SMAX1, a repressor protein. On the other hand, the SL signaling targets SMXL78 subclade repressors, which arose by duplication of SMAX1 in angiosperms. Thus, gymnosperms contain the SL receptor D14 but not SMXL78, the SL signaling-specific repressor proteins. We studied two gymnosperm species, ginkgo (Ginkgo biloba) and Japanese umbrella pine (Sciadopitys verticillata), to clarify whether SLs are perceived and the signals are transduced in gymnosperms. We show that D14 and KAI2 of ginkgo and Japanese umbrella pine specifically perceive an SL analog and KL mimic, respectively. Furthermore, our results suggest that both SL signaling and KL signaling target SMAX1, and the specific localization of the receptor may result in the specificity of the signaling in gymnosperms.

… angiosperm SMAX1 clade I, where monilophyte clades may have emerged before angiosperm … Sub-clades of clade I (dark blue and yellow) represent monilophytes and gymnosperm …

Abstract Plants display a tremendous diversity of developmental and physiological features, resulting from gains and losses of functional innovations across the plant phylogeny. Among those, the most impactful have been undoubtedly the ones that allowed plant terrestrializations, the transitions from an aquatic to a terrestrial environment. Although the embryophyte terrestrialization has been particularly scrutinized, others occurred across the plant phylogeny with the involvement of mutualistic symbioses as a common theme. Here, we review the current pieces of evidence supporting that the repeated colonization of land by plants has been facilitated by interactions with mutualistic symbionts. In that context, we detail two of these mutualistic symbioses: the arbuscular mycorrhizal symbiosis in embryophytes and the lichen symbiosis in chlorophyte algae. We suggest that associations with bacteria should be revisited in that context, and we propose that overlooked symbioses might have facilitated the emergence of other land plant clades.

The emergence of plant hormone signaling pathways is deeply intertwined with land plant evolution. In angiosperms, two plant hormones, salicylic Acid (SA) and Jasmonates (JAs), play a key role in plant defense, where JAs-mediated defenses are typically activated in response to herbivores and necrotrophic pathogens, whereas SA is prioritized against hemi/biotrophic pathogens. Thus, studying the evolution of SA and JAs and their crosstalk is essential to understand the evolution of molecular plant-microbe interactions (EvoMPMI) in land plants. Recent advances in the evolution of SA and JAs biosynthesis, signaling, and crosstalk in land plants illustrated that the insight gained in angiosperms does not necessarily apply to non-seed plant lineages, where the receptors perceive different ligands and the hormones activate pathways independently on the canonical receptors. In this review, recent findings on the two main defense hormones (JAs and SA) in non-seed plants, including functional studies in the bryophyte model Marchantia polymorpha, will be discussed.

Summary Nucleotide‐binding domain and leucine‐rich repeat (NLR) proteins are important intracellular immune receptors that activate robust plant immune responses upon detecting pathogens. Canonical NLRs consist of a conserved tripartite architecture that includes a central regulatory nucleotide‐binding domain, C‐terminal leucine‐rich repeats, and variable N‐terminal domains that directly participate in immune execution. In flowering plants, the vast majority of NLR N‐terminal domains belong to the coiled‐coil, Resistance to Powdery Mildew 8, or Toll/interleukin‐1 receptor subfamilies, with recent structural and biochemical studies providing detailed mechanistic insights into their functions. In this insight review, we focus on the immune‐related biochemistries of known plant NLR N‐terminal domains and discuss the evolutionary diversity of atypical NLR domains in nonflowering plants. We further contrast these observations against the known diversity of NLR‐related receptors from microbes to metazoans across the tree of life.

Plant pathogenic Pseudomonas species naturally antagonize a diverse range of flowering plants. While emerging research demonstrates that isolates belonging to the P. syringae species complex colonize diverse hosts, the extent to which these bacteria naturally infect non-flowering plants like the model liverwort Marchantia polymorpha remains unclear. Here, we identify natural associations between Pseudomonas viridiflava and the liverwort Marchantia polymorpha. Pseudomonas bacteria isolated from diseased liverworts in the wild successfully re-infected M. polymorpha under pure culture conditions, producing high in planta bacterial densities and causing prominent tissue maceration. Comparative genomic analysis of Marchantia-associated P. viridiflava identified core virulence machinery like the type III secretion system (T3SS) and conserved effectors (AvrE and HopM1) that were essential for liverwort infection. Disease assays performed in Nicotiana benthamiana further confirmed that liverwort-associated P. viridiflava infect flowering plants in an effector-dependent manner. Our work highlights P. viridiflava as an effective broad host pathogen that relies on conserved virulence factors to manipulate evolutionarily divergent host plants.

Natural compounds isolated from macroalgae are promising, ecofriendly, and multifunctional bioinoculants, which have been tested and used in agriculture. Ulvans, for instance, one of the major polysaccharides present in Ulva spp. cell walls, have been tested for their plant growth-promoting properties as well as their ability to activate plant immune defense, on a large variety of crops. Recently, we have characterized for the first time an arabinogalactan protein-like (AGP-like) from Ulva lactuca, which exhibits several features associated to land plant AGPs. In land plant, AGPs were shown to play a role in several plant biological functions, including cell morphogenesis, reproduction, and plant-microbe interactions. Thus, isolated AGP-like proteins may be good candidates for either the plant growth-promoting properties or the activation of plant immune defense. Here, we have isolated an AGP-like enriched fraction from Ulva lactuca and we have evaluated its ability to (i) protect oilseed rape (Brassica napus) cotyledons against Leptosphaeria maculans, and (ii) its ability to activate immune responses. Preventive application of the Ulva AGP-like enriched fraction on oilseed rape, followed by cotyledon inoculation with the fungal hemibiotroph L. maculans, resulted in a major reduction of infection propagation. The noticed reduction correlated with an accumulation of H2O2 in treated cotyledons and with the activation of SA and ET signaling pathways in oilseed rape cotyledons. In parallel, an ulvan was also isolated from Ulva lactuca. Preventive application of ulvan also enhanced plant resistance against L. maculans. Surprisingly, reduction of infection severity was only observed at high concentration of ulvan. Here, no such significant changes in gene expression and H2O2 production were observed. Together, this study indicates that U. lactuca AGP-like glycoproteins exhibit promising elicitor activity and that plant eliciting properties of Ulva extract, might result not only from an ulvan-originated eliciting activities, but also AGP-like originated.