Evolution and networks in ancient and widespread symbioses between Mucoromycotina and liverworts

Phosphorus/nitrogen sensing and signaling in diverse root-fungus symbioses

Establishing mutualistic relationships between plants and fungi is crucial for overcoming nutrient deficiencies in plants. This review highlights the intricate nutrient sensing and uptake mechanisms used by plants in response to phosphate and nitrogen starvation, as well as their interactions with plant immunity. The coordination of transport systems in both host plants and fungal partners ensures efficient nutrient uptake and assimilation, contributing to the long-term maintenance of these mutualistic associations. It is also essential to understand the distinct responses of fungal partners to external nutrient levels and forms, as they significantly impact the outcomes of symbiotic interactions. Our review also highlights the importance of evolutionarily younger and newly discovered root-fungus associations, such as endophytic associations, which offer potential benefits for improving plant nutrition. Mechanistic insights into the complex dynamics of phosphorus and nitrogen sensing within diverse root-fungus associations can facilitate the identification of molecular targets for engineering symbiotic systems and developing plant phenotypes with enhanced nutrient use efficiency. Ultimately, this knowledge can inform tailored fertilizer management practices to optimize plant nutrition.

Can cardiolipins be used as a biomarker for arbuscular mycorrhizal fungi?

Specific biomarker molecules are increasingly being used for detection and quantification in plant and soil samples of arbuscular mycorrhizal (AM) fungi, an important and widespread microbial guild heavily implicated in transfers of nutrients and carbon between plants and soils and in the maintenance of soil physico-chemical properties. Yet, concerns have previously been raised as to the validity of a range of previously used approaches (e.g., microscopy, AM-specific fatty acids, sterols, glomalin-like molecules, ribosomal DNA sequences), justifying further research into novel biomarkers for AM fungal abundance and/or functioning. Here, we focused on complex polar lipids contained in pure biomass of Rhizophagus irregularis and in nonmycorrhizal and mycorrhizal roots of chicory (Cichorium intybus), leek (Allium porrum), and big bluestem (Andropogon gerardii). The lipids were analyzed by shotgun lipidomics using a high-resolution hybrid mass spectrometer. Size range between 1350 and 1550 Da was chosen for the detection of potential biomarkers among cardiolipins (1,3-bis(sn-3'-phosphatidyl)-sn-glycerols), a specific class of phospholipids. The analysis revealed a variety of molecular species, including cardiolipins containing one or two polyunsaturated fatty acids with 20 carbon atoms each, i.e., arachidonic and/or eicosapentaenoic acids, some of them apparently specific for the mycorrhizal samples. Although further verification using a greater variety of AM fungal species and samples from various soils/ecosystems/environmental conditions is needed, current results suggest the possibility to identify novel biochemical signatures specific for AM fungi within mycorrhizal roots. Whether they could be used for quantification of both root and soil colonization by the AM fungi merits further scrutiny.

Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned?

The first genome sequenced of a eukaryotic organism was for Saccharomyces cerevisiae, as reported in 1996, but it was more than 10 years before any of the zygomycete fungi, which are the early-diverging terrestrial fungi currently placed in the phyla Mucoromycota and Zoopagomycota, were sequenced. The genome for Rhizopus delemar was completed in 2008; currently, more than 1000 zygomycete genomes have been sequenced. Genomic data from these early-diverging terrestrial fungi revealed deep phylogenetic separation of the two major clades-primarily plant-associated saprotrophic and mycorrhizal Mucoromycota versus the primarily mycoparasitic or animal-associated parasites and commensals in the Zoopagomycota. Genomic studies provide many valuable insights into how these fungi evolved in response to the challenges of living on land, including adaptations to sensing light and gravity, development of hyphal growth, and co-existence with the first terrestrial plants. Genome sequence data have facilitated studies of genome architecture, including a history of genome duplications and horizontal gene transfer events, distribution and organization of mating type loci, rDNA genes and transposable elements, methylation processes, and genes useful for various industrial applications. Pathogenicity genes and specialized secondary metabolites have also been detected in soil saprobes and pathogenic fungi. Novel endosymbiotic bacteria and viruses have been discovered during several zygomycete genome projects. Overall, genomic information has helped to resolve a plethora of research questions, from the placement of zygomycetes on the evolutionary tree of life and in natural ecosystems, to the applied biotechnological and medical questions.

Niche differentiation of Mucoromycotinian and Glomeromycotinian arbuscular mycorrhizal fungi along a 2-million-year soil chronosequence

Current literature suggests ecological niche differentiation between co-occurring Mucoromycotinian arbuscular mycorrhizal fungi (M-AMF) and Glomeromycotinian AMF (G-AMF), but experimental evidence is limited. We investigated the influence of soil age, water availability (wet and dry), and plant species (native Microlaena stipoides and exotic Trifolium subterraneum) on anatomical root colonisation and DNA profiles of M-AMF and G-AMF under glasshouse conditions. We grew seedlings of each species in soils collected from the four stages of a soil chronosequence, where pH decreases from the youngest to oldest stages, and phosphorus (P) is low in the youngest and oldest, but high in the intermediate stages. We scored the percentage of root length colonised and used DNA metabarcoding to profile fungal richness and community composition associated with treatment combinations. Soil age, water availability, and plant species were important influencers of root colonisation, although no M-AMF were visible following staining of M. stipoides roots. Soil age and host plant influenced fungal richness and community composition. However, response to soil age, potential host species, and water availability differed between M-AMF and G-AMF. Root colonisation of T. subterraneum by M-AMF and G-AMF was inversely correlated with soil P level. Community composition of M-AMF and G-AMF was structured by soil age and, to a lesser extent, plant species. Richness of M-AMF and G-AMF was negatively, and positively, correlated with available P, respectively. These findings are experimental evidence of ecological niche differentiation of M-AMF and G-AMF and invite further exploration into interactive effects of abiotic and biotic factors on their communities along successional trajectories.

Direct nitrogen, phosphorus and carbon exchanges between Mucoromycotina 'fine root endophyte' fungi and a flowering plant in novel monoxenic cultures

Most plants form mycorrhizal associations with mutualistic soil fungi. Through these partnerships, resources are exchanged including photosynthetically fixed carbon for fungal-acquired nutrients. Recently, it was shown that the diversity of associated fungi is greater than previously assumed, extending to Mucoromycotina fungi. These Mucoromycotina 'fine root endophytes' (MFRE) are widespread and generally co-colonise plant roots together with Glomeromycotina 'coarse' arbuscular mycorrhizal fungi (AMF). Until now, this co-occurrence has hindered the determination of the direct function of MFRE symbiosis. To overcome this major barrier, we developed new techniques for fungal isolation and culture and established the first monoxenic in vitro cultures of MFRE colonising a flowering plant, clover. Using radio- and stable-isotope tracers in these in vitro systems, we measured the transfer of 33 P, 15 N and 14 C between MFRE hyphae and the host plant. Our results provide the first unequivocal evidence that MFRE fungi are nutritional mutualists with a flowering plant by showing that clover gained both 15 N and 33 P tracers directly from fungus in exchange for plant-fixed C in the absence of other micro-organisms. Our findings and methods pave the way for a new era in mycorrhizal research, firmly establishing MFRE as both mycorrhizal and functionally important in terrestrial ecosystems.

Fungal microbiomes associated with Lycopodiaceae during ecological succession

Lycopodiaceae species form an early-diverging plant family, characterized by achlorophyllous and subterranean gametophytes that rely on mycorrhizal fungi for their nutrition. Lycopodiaceae often emerge after a disturbance, like in the Hochfeld reserve (Alsace, France) where seven lycopod species appeared on new ski trails following a forest cut. Here, to better understand their ecological dynamic, we conducted a germination experiment of lycopod spores following an anthropogenic disturbance and examined their associated fungi. Only 12% of the samples germinated, and all gametophytes were abundantly colonized by a specific clade of Densosporaceae (Endogonales, Mucoromycotina), which were also present in the roots of lycopod sporophytes, but absent from the ungerminated spores and the roots of surrounding herbaceous plants, suggesting high mycorrhizal specificity in Lycopodiaceae. In addition, ungerminated spores were profusely parasitized by chytrid fungi, also present in the surrounding lycopod gametophytes and sporophytes, which might explain the low spore germination rate. Altogether, the requirement of specific mycorrhizal Mucoromycotina fungi and the high prevalence of parasites may explain why Lycopodiaceae are often rare pioneer species in temperate regions, limited to the first stages of ecological succession. This illustrates the primordial roles that belowground microbes play in aboveground plant dynamics.

The origin of a land flora

The origin of a land flora fundamentally shifted the course of evolution of life on earth, facilitating terrestrialization of other eukaryotic lineages and altering the planet's geology, from changing atmospheric and hydrological cycles to transforming continental erosion processes. Despite algal lineages inhabiting the terrestrial environment for a considerable preceding period, they failed to evolve complex multicellularity necessary to conquer the land. About 470 million years ago, one lineage of charophycean alga evolved complex multicellularity via developmental innovations in both haploid and diploid generations and became land plants (embryophytes), which rapidly diversified to dominate most terrestrial habitats. Genome sequences have provided unprecedented insights into the genetic and genomic bases for embryophyte origins, with some embryophyte-specific genes being associated with the evolution of key developmental or physiological attributes, such as meristems, rhizoids and the ability to form mycorrhizal associations. However, based on the fossil record, the evolution of the defining feature of embryophytes, the embryo, and consequently the sporangium that provided a reproductive advantage, may have been most critical in their rise to dominance. The long timeframe and singularity of a land flora were perhaps due to the stepwise assembly of a large constellation of genetic innovations required to conquer the terrestrial environment.

Structure and specialization of mycorrhizal networks in phylogenetically diverse tropical communities

BACKGROUND

The root mycobiome plays a fundamental role in plant nutrition and protection against biotic and abiotic stresses. In temperate forests or meadows dominated by angiosperms, the numerous fungi involved in root symbioses are often shared between neighboring plants, thus forming complex plant-fungus interaction networks of weak specialization. Whether this weak specialization also holds in rich tropical communities with more phylogenetically diverse sets of plant lineages remains unknown. We collected roots of 30 plant species in semi-natural tropical communities including angiosperms, ferns, and lycophytes, in three different habitat types on La Réunion island: a recent lava flow, a wet thicket, and an ericoid shrubland. We identified root-inhabiting fungi by sequencing both the 18S rRNA and the ITS2 variable regions. We assessed the diversity of mycorrhizal fungal taxa according to plant species and lineages, as well as the structure and specialization of the resulting plant-fungus networks.

RESULTS

The 18S and ITS2 datasets are highly complementary at revealing the root mycobiota. According to 18S, Glomeromycotina colonize all plant groups in all habitats forming the least specialized interactions, resulting in nested network structures, while Mucoromycotina (Endogonales) are more abundant in the wetland and show higher specialization and modularity compared to the former. According to ITS2, mycorrhizal fungi of Ericaceae and Orchidaceae, namely Helotiales, Sebacinales, and Cantharellales, also colonize the roots of most plant lineages, confirming that they are frequent endophytes. While Helotiales and Sebacinales present intermediate levels of specialization, Cantharellales are more specialized and more sporadic in their interactions with plants, resulting in highly modular networks.

CONCLUSIONS

This study of the root mycobiome in tropical environments reinforces the idea that mycorrhizal fungal taxa are locally shared between co-occurring plants, including phylogenetically distant plants (e.g. lycophytes and angiosperms), where they may form functional mycorrhizae or establish endophytic colonization. Yet, we demonstrate that, irrespectively of the environmental variations, the level of specialization significantly varies according to the fungal lineages, probably reflecting the different evolutionary origins of these plant-fungus symbioses. Frequent fungal sharing between plants questions the roles of the different fungi in community functioning and highlights the importance of considering networks of interactions rather than isolated hosts.

Atmospheric pollution, soil nutrients and climate effects on Mucoromycota arbuscular mycorrhizal fungi

Fine root endophyte mycorrhizal fungi in the Endogonales (Mucoromycota arbuscular mycorrhizal fungi, M‐AMF) are now recognized as at least as important globally as Glomeromycota AMF (G‐AMF), yet little is known about the environmental factors which influence M‐AMF diversity and colonization, partly because they typically only co‐colonize plants with G‐AMF. Wild populations of Lycopodiella inundata predominantly form mycorrhizas with M‐AMF and therefore allow focussed study of M‐AMF environmental drivers. Using microscopic examination and DNA sequencing we measured M‐AMF colonization and diversity over three consecutive seasons and modelled interactions between these response variables and environmental data. Significant relationships were found between M‐AMF colonization and soil S, P, C:N ratio, electrical conductivity, and the previously overlooked micronutrient Mn. Estimated N deposition was negatively related to M‐AMF colonization. Thirty‐nine Endogonales Operational Taxonomic Units (OTUs) were identified in L. inundata roots, a greater diversity than previously recognized in this plant. Endogonales OTU richness correlated negatively with soil C:N while community composition was mostly influenced by soil P. This study provides first evidence that M‐AMF have distinct ecological preferences in response to edaphic variables also related to air pollution. Future studies require site‐level atmospheric pollution monitoring to guide critical load policy for mycorrhizal fungi in heathlands and grasslands.

Symbiosis and the Anthropocene

Recent human activity has profoundly transformed Earth biomes on a scale and at rates that are unprecedented. Given the central role of symbioses in ecosystem processes, functions, and services throughout the Earth biosphere, the impacts of human-driven change on symbioses are critical to understand. Symbioses are not merely collections of organisms, but co-evolved partners that arise from the synergistic combination and action of different genetic programs. They function with varying degrees of permanence and selection as emergent units with substantial potential for combinatorial and evolutionary innovation in both structure and function. Following an articulation of operational definitions of symbiosis and related concepts and characteristics of the Anthropocene, we outline a basic typology of anthropogenic change (AC) and a conceptual framework for how AC might mechanistically impact symbioses with select case examples to highlight our perspective. We discuss surprising connections between symbiosis and the Anthropocene, suggesting ways in which new symbioses could arise due to AC, how symbioses could be agents of ecosystem change, and how symbioses, broadly defined, of humans and “farmed” organisms may have launched the Anthropocene. We conclude with reflections on the robustness of symbioses to AC and our perspective on the importance of symbioses as ecosystem keystones and the need to tackle anthropogenic challenges as wise and humble stewards embedded within the system.

Cryptogamic ground covers as analogues for early terrestrial biospheres: Initiation and evolution of biologically mediated proto-soils

Modern cryptogamic ground covers (CGCs), comprising assemblages of bryophytes (hornworts, liverworts, mosses), fungi, bacteria, lichens and algae, are thought to resemble early divergent terrestrial communities. However, limited in situ plant and other fossils in the rock record, and a lack of CGC-like soils reported in the pre-Silurian sedimentological record, have hindered understanding of the structure, composition and interactions within the earliest CGCs. A key question is how the earliest CGC-like organisms drove weathering on primordial terrestrial surfaces (regolith), leading to the early stages of soil development as proto-soils, and subsequently contributing to large-scale biogeochemical shifts in the Earth System. Here, we employed a novel qualitative, quantitative and multi-dimensional imaging approach through X-ray micro-computed tomography, scanning electron, and optical microscopy to investigate whether different combinations of modern CGC organisms from primordial-like settings in Iceland develop organism-specific soil forming features at the macro- and micro-scales. Additionally, we analysed CGCs growing on hard rocky substrates to investigate the initiation of weathering processes non-destructively in 3D. We show that thalloid CGC organisms (liverworts, hornworts) develop thin organic layers at the surface (<1 cm) with limited subsurface structural development, whereas leafy mosses and communities of mixed organisms form profiles that are thicker (up to ~ 7 cm), structurally more complex, and more organic-rich. We term these thin layers and profiles proto-soils. Component analyses from X-ray micro-computed tomography data show that thickness and structure of these proto-soils are determined by the type of colonising organism(s), suggesting that the evolution of more complex soils through the Palaeozoic may have been driven by a shift in body plan of CGC-like organisms from flattened and appressed to upright and leafy. Our results provide a framework for identifying CGC-like proto-soils in the rock record and a new proxy for understanding organism-soil interactions in ancient terrestrial biospheres and their contribution to the early stages of soil formation.

Mucoromycotina Fungi Possess the Ability to Utilize Plant Sucrose as a Carbon Source: Evidence From Gongronella sp. w5

Mucoromycotina is one of the earliest fungi to establish a mutualistic relationship with plants in the ancient land. However, the detailed information on their carbon supply from the host plants is largely unknown. In this research, a free-living Mucoromycotina called Gongronella sp. w5 (w5) was employed to explore its effect on Medicago truncatula growth and carbon source utilization from its host plant during the interaction process. W5 promoted M. truncatula growth and caused the sucrose accumulation in M. truncatula root tissue at 16 days post-inoculation (dpi). The transportation of photosynthetic product sucrose to the rhizosphere by M. truncatula root cells seemed accelerated by upregulating the SWEET gene. A predicted cytoplasmic invertase (GspInv) gene and a sucrose transporter (GspSUT1) homology gene in the w5 genome upregulated significantly at the transcriptional level during w5–M. truncatula interaction at 16 dpi, indicating the possibility of utilizing plant sucrose directly by w5 as the carbon source. Further investigation showed that the purified GspInv displayed an optimal pH of 5.0 and a specific activity of 3380 ± 26 U/mg toward sucrose. The heterologous expression of GspInv and GspSUT1 in Saccharomyces cerevisiae confirmed the function of GspInv as invertase and GspSUT1 as sugar transporter with high affinity to sucrose in vivo. Phylogenetic tree analysis showed that the ability of Mucoromycotina to utilize sucrose from its host plant underwent a process of “loss and gain.” These results demonstrated the capacity of Mucoromycotina to interact with extant land higher plants and may employ a novel strategy of directly up-taking and assimilating sucrose from the host plant during the interaction.

Archaeosporites rhyniensis gen. et sp. nov. (Glomeromycota, Archaeosporaceae) from the Lower Devonian Rhynie chert: a fungal lineage morphologically unchanged for more than 400 million years

BACKGROUND AND AIMS

Structurally preserved arbuscular mycorrhizas from the Lower Devonian Rhynie chert represent core fossil evidence of the evolutionary history of mycorrhizal systems. Moreover, Rhynie chert fossils of glomeromycotan propagules suggest that this lineage of arbuscular fungi was morphologically diverse by the Early Devonian; however, only a small fraction of this diversity has been formally described and critically evaluated.

METHODS

Thin sections, previously prepared by grinding wafers of chert from the Rhynie beds, were studied by transmitted light microscopy. Fossils corresponding to the description of Archaeospora spp. occurred in 29 slides, and were measured, photographed and compared with modern-day species in that genus.

KEY RESULTS

Sessile propagules <85 µm in diameter, some still attached to a sporiferous saccule, were found in early land plant axes and the chert matrix; they developed, in a similar manner to extant Archaeospora, laterally or centrally within the saccule neck. Microscopic examination and comparison with extant fungi showed that, morphologically, the fossils share the characters used to circumscribe the genus Archaeospora (Glomeromycota; Archaeosporales; Archaeosporaceae).

CONCLUSIONS

The fossils can be assigned with confidence to the extant family Archaeosporaceae, but because molecular analysis is necessary to place organisms in these taxa to present-day genera and species, they are placed in a newly proposed fossil taxon, Archaeosporites rhyniensis.

Genomic and fossil windows into the secret lives of the most ancient fungi

Fungi have crucial roles in modern ecosystems as decomposers and pathogens, and they engage in various mutualistic associations with other organisms, especially plants. They have a lengthy geological history, and there is an emerging understanding of their impact on the evolution of Earth systems on a large scale. In this Review, we focus on the roles of fungi in the establishment and early evolution of land and freshwater ecosystems. Today, questions of evolution over deep time are informed by discoveries of new fossils and evolutionary analysis of new genomes. Inferences can be drawn from evolutionary analysis by comparing the genes and genomes of fungi with the biochemistry and development of their plant and algal hosts. We then contrast this emerging picture against evidence from the fossil record to develop a new, integrated perspective on the origin and early evolution of fungi.

Unique and common traits in mycorrhizal symbioses

Mycorrhizas are among the most important biological interkingdom interactions, as they involve ~340,000 land plants and ~50,000 taxa of soil fungi. In these mutually beneficial interactions, fungi receive photosynthesis-derived carbon and provide the host plant with mineral nutrients such as phosphorus and nitrogen in exchange. More than 150 years of research on mycorrhizas has raised awareness of their biology, biodiversity and ecological impact. In this Review, we focus on recent phylogenomic, molecular and cell biology studies to present the current state of knowledge of the origin of mycorrhizal fungi and the evolutionary history of their relationship with land plants. As mycorrhizas feature a variety of phenotypes, depending on partner taxonomy, physiology and cellular interactions, we explore similarities and differences between mycorrhizal types. During evolution, mycorrhizal fungi have refined their biotrophic capabilities to take advantage of their hosts as food sources and protective niches, while plants have developed multiple strategies to accommodate diverse fungal symbionts. Intimate associations with pervasive ecological success have originated at the crossroads between these two evolutionary pathways. Our understanding of the biological processes underlying these symbioses, where fungi act as biofertilizers and bioprotectors, provides the tools to design biotechnological applications addressing environmental and agricultural challenges.

The distribution and evolution of fungal symbioses in ancient lineages of land plants

An accurate understanding of the diversity and distribution of fungal symbioses in land plants is essential for mycorrhizal research. Here we update the seminal work of Wang and Qiu (Mycorrhiza 16:299-363, 2006) with a long-overdue focus on early-diverging land plant lineages, which were considerably under-represented in their survey, by examining the published literature to compile data on the status of fungal symbioses in liverworts, hornworts and lycophytes. Our survey combines data from 84 publications, including recent, post-2006, reports of Mucoromycotina associations in these lineages, to produce a list of at least 591 species with known fungal symbiosis status, 180 of which were included in Wang and Qiu (Mycorrhiza 16:299-363, 2006). Using this up-to-date compilation, we estimate that fewer than 30% of liverwort species engage in symbiosis with fungi belonging to all three mycorrhizal phyla, Mucoromycota, Basidiomycota and Ascomycota, with the last being the most widespread (17%). Fungal symbioses in hornworts (78%) and lycophytes (up to 100%) appear to be more common but involve only members of the two Mucoromycota subphyla Mucoromycotina and Glomeromycotina, with Glomeromycotina prevailing in both plant groups. Our fungal symbiosis occurrence estimates are considerably more conservative than those published previously, but they too may represent overestimates due to currently unavoidable assumptions.