The origin and evolution of mycorrhizal symbioses: from palaeomycology to phylogenomics

Analysing diversification dynamics using barcoding data: The case of an obligate mycorrhizal symbiont

Analysing diversification dynamics is key to understanding the past evolutionary history of clades that led to present-day biodiversity patterns. While such analyses are widespread in well-characterized groups of species, they are much more challenging in groups for which diversity is mostly known through molecular techniques. Here, we use the largest global database on the small subunit (SSU) rRNA gene of Glomeromycotina, a subphylum of microscopic arbuscular mycorrhizal fungi that provide mineral nutrients to most land plants by forming one of the oldest terrestrial symbioses, to analyse the diversification dynamics of this clade in the past 500 million years. We perform a range of sensitivity analyses and simulations to control for potential biases linked to the nature of the data. We find that Glomeromycotina tend to have low speciation rates compared to other eukaryotes. After a peak of speciations between 200 and 100 million years ago, they experienced an important decline in speciation rates toward the present. Such a decline could be at least partially related to a shrinking of their mycorrhizal niches and to their limited ability to colonize new niches. Our analyses identify patterns of diversification in a group of obligate symbionts of major ecological and evolutionary importance and illustrate that short molecular markers combined with intensive sensitivity analyses can be useful for studying diversification dynamics in microbial groups.

The Costs and Benefits of Plant-Arbuscular Mycorrhizal Fungal Interactions

The symbiotic interaction between plants and arbuscular mycorrhizal (AM) fungi is often perceived as beneficial for both partners, though a large ecological literature highlights the context dependency of this interaction. Changes in abiotic variables, such as nutrient availability, can drive the interaction along the mutualism-parasitism continuum with variable outcomes for plant growth and fitness. However, AM fungi can benefit plants in more ways than improved phosphorus nutrition and plant growth. For example, AM fungi can promote abiotic and biotic stress tolerance even when considered parasitic from a nutrient provision perspective. Other than being obligate biotrophs, very little is known about the benefits AM fungi gain from plants. In this review, we utilize both molecular biology and ecological approaches to expand our understanding of the plant-AM fungal interaction across disciplines.

The mycorrhizal-induced growth promotion and insect resistance reduction in Populus alba × P. berolinensis seedlings: a multi-omics study

Arbuscular mycorrhizal (AM) fungi are an alternative to chemical insecticides or fertilizers, and there is an urgent need to extend the application of AM fungi to woody plants. This study aims to investigate the growth and resistance against the gypsy moth larvae (Lymantria dispar) in Glomus intraradices-colonized Populus alba × P. berolinensis seedlings, and to unravel the transcriptome and metabolome phenotypes recruited by AM fungus colonization that affect plant growth and insect resistance. Our results showed a positive mycorrhizal growth response, i.e., growth and biomass of mycorrhizal seedlings were enhanced. However, AM fungus inoculation reduced the resistance of poplar to gypsy moth larvae, as evidenced by the decreased carbon/nitrogen ratio in leaves, as well as the increased larval growth and shortened larval developmental duration. Transcriptome analysis revealed that in both auxin and gibberellin signaling transductions, all nodes were responsive to AM symbiosis and most differentially expressed genes belonging to effectors were up-regulated in mycorrhizal seedlings. Furthermore, the two key enzymes (4-coumarate-CoA ligase and trans-cinnamate 4-monooxygenase) involved in the synthesis of p-Coumaroyl-CoA, an initial metabolite in flavonoid biosynthesis and the first rate-limiting enzyme (chalcone synthase) in flavonoid biosynthesis, were down-regulated at the transcriptional level. Consistent with the transcriptome results, metabolome analysis found that the amounts of all differentially accumulated flavonoid compounds (e.g., catechin and quercetin) identified in mycorrhizal seedlings were decreased. Taken together, these findings highlight the diverse outcomes of AM fungi-host plant-insect interaction and reveal the regulatory network of the positive mycorrhizal growth response and mycorrhizal-induced reduction of insect resistance in poplar.

The liverwort Marchantia polymorpha, a model for all ages

The liverwort Marchantia polymorpha has been known to man for millennia due to its inclusion Greek herbals. Perhaps due to its familiarity and association with growth in, often, man-made disturbed habitats, it was readily used to address fundamental biological questions of the day, including elucidation of land plant life cycles in the late 18th century, the formulation of cell theory early in the 19th century and the discovery of the alternation of generations in land plants in the mid-19th century. Subsequently, Marchantia was used as model in botany classes. With the arrival of the molecular era, its organellar genomes, the chloroplast and mitochondrial, were some of the first to be sequenced from any plant. In the past two decades, molecular genetic tools have been applied such that genes may be manipulated seemingly at will. Here, are past, present, and some views to the future of Marchantia as a model.

Evolutionary transition to the ectomycorrhizal habit in the genomes of a hyperdiverse lineage of mushroom-forming fungi

The ectomycorrhizal (ECM) symbiosis has independently evolved from diverse types of saprotrophic ancestors. In this study, we seek to identify genomic signatures of the transition to the ECM habit within the hyperdiverse Russulaceae. We present comparative analyses of the genomic architecture and the total and secreted gene repertoires of 18 species across the order Russulales, of which 13 are newly sequenced, including a representative of a saprotrophic member of Russulaceae, Gloeopeniophorella convolvens. The genomes of ECM Russulaceae are characterized by a loss of genes for plant cell wall-degrading enzymes (PCWDEs), an expansion of genome size through increased transposable element (TE) content, a reduction in secondary metabolism clusters, and an association of small secreted proteins (SSPs) with TE 'nests', or dense aggregations of TEs. Some PCWDEs have been retained or even expanded, mostly in a species-specific manner. The genome of G. convolvens possesses some characteristics of ECM genomes (e.g. loss of some PCWDEs, TE expansion, reduction in secondary metabolism clusters). Functional specialization in ECM decomposition may drive diversification. Accelerated gene evolution predates the evolution of the ECM habit, indicating that changes in genome architecture and gene content may be necessary to prime the evolutionary switch.

Predicting global numbers of teleomorphic ascomycetes

Sexual reproduction is the basic way to form high genetic diversity and it is beneficial in evolution and speciation of fungi. The global diversity of teleomorphic species in Ascomycota has not been estimated. This paper estimates the species number for sexual ascomycetes based on five different estimation approaches, viz. by numbers of described fungi, by fungus:substrate ratio, by ecological distribution, by meta-DNA barcoding or culture-independent studies and by previous estimates of species in Ascomycota. The assumptions were made with the currently most accepted, “2.2–3.8 million” species estimate and results of previous studies concluding that 90% of the described ascomycetes reproduce sexually. The Catalogue of Life, Species Fungorum and published research were used for data procurement. The average value of teleomorphic species in Ascomycota from all methods is 1.86 million, ranging from 1.37 to 2.56 million. However, only around 83,000 teleomorphic species have been described in Ascomycota and deposited in data repositories. The ratio between described teleomorphic ascomycetes to predicted teleomorphic ascomycetes is 1:22. Therefore, where are the undiscovered teleomorphic ascomycetes? The undescribed species are no doubt to be found in biodiversity hot spots, poorly-studied areas and species complexes. Other poorly studied niches include extremophiles, lichenicolous fungi, human pathogens, marine fungi, and fungicolous fungi. Undescribed species are present in unexamined collections in specimen repositories or incompletely described earlier species. Nomenclatural issues, such as the use of separate names for teleomorph and anamorphs, synonyms, conspecific names, illegitimate and invalid names also affect the number of described species. Interspecies introgression results in new species, while species numbers are reduced by extinctions.

The Waiting Room Hypothesis revisited by orchids: were orchid mycorrhizal fungi recruited among root endophytes?

BACKGROUND

As in most land plants, the roots of orchids (Orchidaceae) associate with soil fungi. Recent studies have highlighted the diversity of the fungal partners involved, mostly within Basidiomycotas. The association with a polyphyletic group of fungi collectively called rhizoctonias (Ceratobasidiaceae, Tulasnellaceae and Serendipitaceae) is the most frequent. Yet, several orchid species target other fungal taxa that differ from rhizoctonias by their phylogenetic position and/or ecological traits related to their nutrition out of the orchid roots (e.g. soil saprobic or ectomycorrhizal fungi). We offer an evolutionary framework for these symbiotic associations.

SCOPE

Our view is based on the 'Waiting Room Hypothesis', an evolutionary scenario stating that mycorrhizal fungi of land flora were recruited from ancestors that initially colonized roots as endophytes. Endophytes biotrophically colonize tissues in a diffuse way, contrasting with mycorrhizae by the absence of morphological differentiation and of contribution to the plant's nutrition. The association with rhizoctonias is probably the ancestral symbiosis that persists in most extant orchids, while during orchid evolution numerous secondary transitions occurred to other fungal taxa. We suggest that both the rhizoctonia partners and the secondarily acquired ones are from fungal taxa that have broad endophytic ability, as exemplified in non-orchid roots. We review evidence that endophytism in non-orchid plants is the current ecology of many rhizoctonias, which suggests that their ancestors may have been endophytic in orchid ancestors. This also applies to the non-rhizoctonia fungi that were secondarily recruited by several orchid lineages as mycorrhizal partners. Indeed, from our review of the published literature, they are often detected, probably as endophytes, in extant rhizoctonia-associated orchids.

CONCLUSION

The orchid family offers one of the best documented examples of the 'Waiting Room Hypothesis': their mycorrhizal symbioses support the idea that extant mycorrhizal fungi have been recruited among endophytic fungi that colonized orchid ancestors.

Evolution of the Mode of Nutrition in Symbiotic and Saprotrophic Fungi in Forest Ecosystems

In this review, we highlight the main insights that have been gathered from recent developments using large-scale genomics of fungal saprotrophs and symbiotrophs (including ectomycorrhizal and orchid and ericoid mycorrhizal fungi) inhabiting forest ecosystems. After assessing the goals and motivations underlying our approach, we explore our current understanding of the limits and future potential of using genomics to understand the ecological roles of these forest fungi. Comparative genomics unraveled the molecular machineries involved in lignocellulose decomposition in wood decayers, soil and litter saprotrophs, and mycorrhizal symbionts. They also showed that transitions from saprotrophy to mutualism entailed widespread losses of lignocellulose-degrading enzymes; diversification of novel, lineage-specific symbiosis-induced genes; and convergent evolution of genetic innovations that facilitate the accommodationof mutualistic symbionts within their plant hosts. We also identify the major questions that remain unanswered and propose new avenues of genome-based research to understand the role of soil fungi in sustainable forest ecosystems.

The Role of Plant-Associated Bacteria, Fungi, and Viruses in Drought Stress Mitigation

Drought stress is an alarming constraint to plant growth, development, and productivity worldwide. However, plant-associated bacteria, fungi, and viruses can enhance stress resistance and cope with the negative impacts of drought through the induction of various mechanisms, which involve plant biochemical and physiological changes. These mechanisms include osmotic adjustment, antioxidant enzyme enhancement, modification in phytohormonal levels, biofilm production, increased water and nutrient uptake as well as increased gas exchange and water use efficiency. Production of microbial volatile organic compounds (mVOCs) and induction of stress-responsive genes by microbes also play a crucial role in the acquisition of drought tolerance. This review offers a unique exploration of the role of plant-associated microorganisms-plant growth promoting rhizobacteria and mycorrhizae, viruses, and their interactions-in the plant microbiome (or phytobiome) as a whole and their modes of action that mitigate plant drought stress.

Meta-analysis of the role of zinc in coordinating absorption of mineral elements in wheat seedlings

BACKGROUND

Zinc (Zn) is an important nutrient for human beings, which is also an essential micronutrient for crop growth. This study investigated the role of Zn in coordinating the mineral elements absorption in modern wheat (Triticum aestivum L.) cultivars with a new developed method.

RESULTS

A method was developed, and showed a robust capability to simultaneously investigate seven mineral elements uptake in wheat seedling. With this method, we found low Zn supply (<  1 μM) promoted the absorption of potassium (K), magnesium (Mg) and manganese (Mn) in wheat seedling, while high Zn supply (>  1 μM) significantly inhibited the absorption of these elements. Cultivars with the green genes (Rht-B1b and Rht-D1b) showed a higher uptake capability on ammonium (NH₄⁺), and cultivars with Rht-B1b allele can uptake more phosphors (P), K, calcium (Ca), Mn and Zn compared to cultivars with Rht-D1b. Further analysis indicated higher uptake capability of NH₄⁺ in cultivars contained Rhts was independent of Zn.

CONCLUSION

The key role of Zn in coordinating for mineral elements absorption was identified in modern wheat cultivars, providing the reference for Zn application in wheat. Meanwhile, this study provides a robust method for quantifying the absorption of mineral elements, which may be adopted into the broadly investigations on the coordinated nutrients absorption of plant.

Deciphering the Chitin Code in Plant Symbiosis, Defense, and Microbial Networks

Chitin is a structural polymer in many eukaryotes. Many organisms can degrade chitin to defend against chitinous pathogens or use chitin oligomers as food. Beneficial microorganisms like nitrogen-fixing symbiotic rhizobia and mycorrhizal fungi produce chitin-based signal molecules called lipo-chitooligosaccharides (LCOs) and short chitin oligomers to initiate a symbiotic relationship with their compatible hosts and exchange nutrients. A recent study revealed that a broad range of fungi produce LCOs and chitooligosaccharides (COs), suggesting that these signaling molecules are not limited to beneficial microbes. The fungal LCOs also affect fungal growth and development, indicating that the roles of LCOs beyond symbiosis and LCO production may predate mycorrhizal symbiosis. This review describes the diverse structures of chitin; their perception by eukaryotes and prokaryotes; and their roles in symbiotic interactions, defense, and microbe-microbe interactions. We also discuss potential strategies of fungi to synthesize LCOs and their roles in fungi with different lifestyles.

The plant microbiota: composition, functions, and engineering

Plants growing in nature live in association with beneficial, commensal, and pathogenic microbes, which make up the plant microbiota. The close interaction between plants and their microbiotas has raised fundamental questions about plant responses to these microbes and the identity of the main factors driving microbiota structure, diversity, and function in bulk soil, in the rhizosphere, and in the plant organs. Beneficial microorganisms have long been used as inoculants for crops; the current development of synthetic microbial communities and the identification of plant traits that respond to the microbiota form the basis for rational engineering of the plant microbiota to improve sustainable agriculture.

Facultative symbiosis with a saprotrophic soil fungus promotes potassium uptake in American sweetgum trees

Several species of soil free-living saprotrophs can sometimes establish biotrophic symbiosis with plants, but the basic biology of this association remains largely unknown. Here, we investigate the symbiotic interaction between a common soil saprotroph, Clitopilus hobsonii (Agaricomycetes), and the American sweetgum (Liquidambar styraciflua). The colonized root cortical cells were found to contain numerous microsclerotia-like structures. Fungal colonization led to increased plant growth and facilitated potassium uptake, particularly under potassium limitation (0.05 mM K⁺ ). The expression of plant genes related to potassium uptake was not altered by the symbiosis, but colonized roots contained the transcripts of three fungal genes with homology to K⁺ transporters (ACU and HAK) and channel (SKC). Heterologously expressed ChACU and ChSKC restored the growth of a yeast K⁺ -uptake-defective mutant. Upregulation of ChACU transcript under low K⁺ conditions (0 and 0.05 mM K⁺ ) compared to control (5 mM K⁺ ) was demonstrated in planta and in vitro. Colonized plants displayed a larger accumulation of soluble sugars under 0.05 mM K⁺ than non-colonized plants. The present study suggests reciprocal benefits of this novel tree-fungus symbiosis under potassium limitation mainly through an exchange of additional carbon and potassium between both partners.

Important innate differences in determining symbiotic responsiveness in host and non-hosts of arbuscular mycorrhiza

Genetic components that regulate arbuscular mycorrhizal (AM) interactions in hosts and non-hosts are not completely known. Comparative transcriptomic analysis was combined with phylogenetic studies to identify the factors that distinguish AM host from non-host. Mycorrhized host, non-mycorrhized host and non-host cultivars of tomato (Solanum lycopersicum) were subjected to RNA seq analysis. The top 10 differentially expressed genes were subjected to extensive in silico phylogenetic analysis along with 10 more candidate genes that have been previously reported for AM-plant interactions. Seven distantly related hosts and four non-hosts were selected to identify structural differences in selected gene/protein candidates. The screened genes/proteins were subjected to MEME, CODEML and DIVERGE analysis to identify evolutionary patterns that differentiate hosts from non-hosts. Based on the results, candidate genes were categorized as highly influenced (SYMRK and CCaMK), moderately influenced and minimally influenced by evolutionary constraints. We propose that the amino acid and nucleotide changes specific to non-hosts are likely to correspond to aberrations in functionality towards AM symbiosis. This study paves way for future research aimed at understanding innate differences in genetic make-up of AM hosts and non-hosts, in addition to the theory of gene losses from the "AM-symbiotic toolkit".

Irving T, Chakraborty S, Ané JM. Perception of lipo-chitooligosaccharides by the bioenergy crop Populus

Populus sp. is a developing feedstock for second-generation biofuel production. To ensure its success as a sustainable biofuel source, it is essential to capitalize on the ability of Populus sp. to associate with beneficial plant-associated microbes (e.g., mycorrhizal fungi) and engineer Populus sp. to associate with non-native symbionts (e.g., rhizobia). Here, we review recent research into the molecular mechanisms that control ectomycorrhizal associations in Populus sp. with particular emphasis on the discovery that ectomycorrhizal fungi produce lipochitooligosaccharides capable of activating the common symbiosis pathway. We also present new evidence that lipo-chitooligosaccharides produced by both ectomycorrhizal fungi and various species of rhizobia that do not associate with Populus sp. can induce nuclear calcium spiking in the roots of Populus sp. Thus, we argue Populus sp. already possesses the molecular machinery necessary for perceiving rhizobia, and the next step in engineering symbiosis with rhizobia should be focused on inducing bacterial accommodation and nodule organogenesis. The gene Nodule INception is central to these processes, and several putative orthologs are present in Populus sp. Manipulating the promoters of these genes to match that of plants in the nitrogen-fixing clade may be sufficient to introduce nodulation in Populus sp.

Saprotrophic fungal diversity predicts ectomycorrhizal fungal diversity along the timberline in the framework of island biogeography theory

Island biogeography theory (IBT) is one of the most fruitful paradigms in macroecology, positing positive species-area and negative species-isolation relationships for the distribution of organisms. Biotic interactions are also crucial for diversity maintenance on islands. In the context of a timberline tree species (Betula ermanii) as "virtual island", we surveyed ectomycorrhizal (EcM) fungal diversity along a 430-m vertical gradient on the top of Changbai Mountain, China, sampling fine roots and neighboring soils of B. ermanii. Besides elevation, soil properties and plant functional traits, endophytic and saprotrophic fungal diversity were assessed as candidate predictors to construct integrative models. EcM fungal diversity decreased with increasing elevation, and exhibited positive diversity to diameter at breast height and negative diversity to distance from forest edge relationships in both roots and soils. Integrative models further showed that saprotrophic fungal diversity was the strongest predictor of EcM fungal diversity, directly enhancing EcM fungal diversity in roots and soils. Our study supports IBT as a basic framework to explain EcM fungal diversity. The diversity-begets-diversity hypothesis within the fungal kingdom is more predictive for EcM fungal diversity within the IBT framework, which reveals a tight association between saprotrophic and EcM fungal lineages in the timberline ecosystem.

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.

Evidence for Niche Differentiation in the Environmental Responses of Co-occurring Mucoromycotinian Fine Root Endophytes and Glomeromycotinian Arbuscular Mycorrhizal Fungi

Fine root endophytes (FRE) were traditionally considered a morphotype of arbuscular mycorrhizal fungi (AMF), but recent genetic studies demonstrate that FRE belong within the subphylum Mucoromycotina, rather than in the subphylum Glomeromycotina with the AMF. These findings prompt enquiry into the fundamental ecology of FRE and AMF. We sampled FRE and AMF in roots of Trifolium subterraneum from 58 sites across temperate southern Australia. We investigated the environmental drivers of composition, richness, and root colonization of FRE and AMF by using structural equation modelling and canonical correspondence analyses. Root colonization by FRE increased with increasing temperature and rainfall but decreased with increasing phosphorus (P). Root colonization by AMF increased with increasing soil organic carbon but decreased with increasing P. Richness of FRE decreased with increasing temperature and soil pH. Richness of AMF increased with increasing temperature and rainfall but decreased with increasing soil aluminium (Al) and pH. Aluminium, soil pH, and rainfall were, in decreasing order, the strongest drivers of community composition of FRE; they were also important drivers of community composition of AMF, along with temperature, in decreasing order: rainfall, Al, temperature, and soil pH. Thus, FRE and AMF showed the same responses to some (e.g. soil P, soil pH) and different responses to other (e.g. temperature) key environmental factors. Overall, our data are evidence for niche differentiation among these co-occurring mycorrhizal associates.

Endophyte roles in nutrient acquisition, root system architecture development and oxidative stress tolerance

Plants associate with communities of microbes (bacteria and fungi) that play critical roles in plant development, nutrient acquisition and oxidative stress tolerance. The major share of plant microbiota is endophytes which inhabit plant tissues and help them in various capacities. In this article, we have reviewed what is presently known with regard to how endophytic microbes interact with plants to modulate root development, branching, root hair formation and their implications in overall plant development. Endophytic microbes link the interactions of plants, rhizospheric microbes and soil to promote nutrient solubilization and further vectoring these nutrients to the plant roots making the soil-plant-microbe continuum. Further, plant roots internalize microbes and oxidatively extract nutrients from microbes in the rhizophagy cycle. The oxidative interactions between endophytes and plants result in the acquisition of nutrients by plants and are also instrumental in oxidative stress tolerance of plants. It is evident that plants actively cultivate microbes internally, on surfaces and in soils to acquire nutrients, modulate development and improve health. Understanding this continuum could be of greater significance in connecting endophytes with the hidden half of the plant that can also be harnessed in applied terms to enhance nutrient acquisition through the development of favourable root system architecture for sustainable production under stress conditions.

Soil P reduces mycorrhizal colonization while favors fungal pathogens: observational and experimental evidence in Bipinnula (Orchidaceae)

Little is known about the soil factors influencing root-associated fungal communities in Orchidaceae. Limited evidence suggests that soil nutrients may modulate the association with orchid mycorrhizal fungi (OMF), but their influence on non-mycorrhizal fungi remains unexplored. To study how nutrient availability affects mycorrhizal and non-mycorrhizal fungi associated with the orchid Bipinnula fimbriata, we conducted a metagenomic investigation within a large population with variable soil conditions. Additionally, we tested the effect of phosphorus (P) addition on fungal communities and mycorrhizal colonization. Soil P negatively correlated with the abundance of OMF, but not with the abundance of non-mycorrhizal fungi. After fertilization, increments in soil P negatively affected mycorrhizal colonization; however, they had no effect on OMF richness or composition. The abundance and richness of pathotrophs were negatively related to mycorrhizal colonization and then, after fertilization, the decrease in mycorrhizal colonization correlated with an increase in pathogen richness. Our results suggest that OMF are affected by soil conditions differently from non-mycorrhizal fungi. Bipinnula fimbriata responds to fertilization by altering mycorrhizal colonization rather than by switching OMF partners in the short term, and the influence of nutrients on OMF is coupled with indirect effects on the whole fungal community and potentially on plant's health.

Plant evolution driven by interactions with symbiotic and pathogenic microbes

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.

Biological nitrification inhibition in the rhizosphere: determining interactions and impact on microbially mediated processes and potential applications

Nitrification is the microbial conversion of reduced forms of nitrogen (N) to nitrate (NO3-), and in fertilized soils it can lead to substantial N losses via NO3- leaching or nitrous oxide (N2O) production. To limit such problems, synthetic nitrification inhibitors have been applied but their performance differs between soils. In recent years, there has been an increasing interest in the occurrence of biological nitrification inhibition (BNI), a natural phenomenon according to which certain plants can inhibit nitrification through the release of active compounds in root exudates. Here, we synthesize the current state of research but also unravel knowledge gaps in the field. The nitrification process is discussed considering recent discoveries in genomics, biochemistry and ecology of nitrifiers. Secondly, we focus on the 'where' and 'how' of BNI. The N transformations and their interconnections as they occur in, and are affected by, the rhizosphere, are also discussed. The NH4+ and NO3- retention pathways alternative to BNI are reviewed as well. We also provide hypotheses on how plant compounds with putative BNI ability can reach their targets inside the cell and inhibit ammonia oxidation. Finally, we discuss a set of techniques that can be successfully applied to solve unresearched questions in BNI studies.

Mycorrhizal fungi control phosphorus value in trade symbiosis with host roots when exposed to abrupt 'crashes' and 'booms' of resource availability

Biological market theory provides a conceptual framework to analyse trade strategies in symbiotic partnerships. A key prediction of biological market theory is that individuals can influence resource value - meaning the amount a partner is willing to pay for it - by mediating where and when it is traded. The arbuscular mycorrhizal symbiosis, characterised by roots and fungi trading phosphorus and carbon, shows many features of a biological market. However, it is unknown if or how fungi can control phosphorus value when exposed to abrupt changes in their trade environment. We mimicked an economic 'crash', manually severing part of the fungal network (Rhizophagus irregularis) to restrict resource access, and an economic 'boom' through phosphorus additions. We quantified trading strategies over a 3-wk period using a recently developed technique that allowed us to tag rock phosphate with fluorescing quantum dots of three different colours. We found that the fungus: compensated for resource loss in the 'crash' treatment by transferring phosphorus from alternative pools closer to the host root (Daucus carota); and stored the surplus nutrients in the 'boom' treatment until root demand increased. By mediating from where, when and how much phosphorus was transferred to the host, the fungus successfully controlled resource value.

The genome of Geosiphon pyriformis reveals ancestral traits linked to the emergence of the arbuscular mycorrhizal symbiosis

Arbuscular mycorrhizal fungi (AMF) (subphylum Glomeromycotina)¹ are among the most prominent symbionts and form the Arbuscular Mycorrhizal symbiosis (AMS) with over 70% of known land plants.^2,3 AMS allows plants to efficiently acquire poorly soluble soil nutrients⁴ and AMF to receive photosynthetically fixed carbohydrates. This plant-fungus symbiosis dates back more than 400 million years⁵ and is thought to be one of the key innovations that allowed the colonization of lands by plants.⁶ Genomic and genetic analyses of diverse plant species started to reveal the molecular mechanisms that allowed the evolution of this symbiosis on the host side, but how and when AMS abilities emerged in AMF remain elusive. Comparative phylogenomics could be used to understand the evolution of AMS.^7,8 However, the availability of genome data covering basal AMF phylogenetic nodes (Archaeosporales, Paraglomerales) is presently based on fragmentary protein coding datasets.⁹Geosiphon pyriformis (Archaeosporales) is the only fungus known to produce endosymbiosis with nitrogen-fixing cyanobacteria (Nostoc punctiforme) presumably representing the ancestral AMF state.^10-12 Unlike other AMF, it forms long fungal cells ("bladders") that enclose cyanobacteria. Once in the bladder, the cyanobacteria are photosynthetically active and fix nitrogen, receiving inorganic nutrients and water from the fungus. Arguably, G. pyriformis represents an ideal candidate to investigate the origin of AMS and the emergence of a unique endosymbiosis. Here, we aimed to advance knowledge in these questions by sequencing the genome of G. pyriformis, using a re-discovered isolate.

Dispersal of Arbuscular Mycorrhizal Fungi: Evidence and Insights for Ecological Studies

Dispersal is a critical ecological process that modulates gene flow and contributes to the maintenance of genetic and taxonomic diversity within ecosystems. Despite an increasing global understanding of the arbuscular mycorrhizal (AM) fungal diversity, distribution and prevalence in different biomes, we have largely ignored the main dispersal mechanisms of these organisms. To provide a geographical and scientific overview of the available data, we systematically searched for the direct evidence on the AM fungal dispersal agents (abiotic and biotic) and different propagule types (i.e. spores, extraradical hyphae or colonized root fragments). We show that the available data (37 articles) on AM fungal dispersal originates mostly from North America, from temperate ecosystems, from biotic dispersal agents (small mammals) and AM fungal spores as propagule type. Much lesser evidence exists from South American, Asian and African tropical systems and other dispersers such as large-bodied birds and mammals and non-spore propagule types. We did not find strong evidence that spore size varies across dispersal agents, but wind and large animals seem to be more efficient dispersers. However, the data is still too scarce to draw firm conclusions from this finding. We further discuss and propose critical research questions and potential approaches to advance the understanding of the ecology of AM fungi dispersal.

Hormones as go-betweens in plant microbiome assembly

The interaction of plants with complex microbial communities is the result of co-evolution over millions of years and contributed to plant transition and adaptation to land. The ability of plants to be an essential part of complex and highly dynamic ecosystems is dependent on their interaction with diverse microbial communities. Plant microbiota can support, and even enable, the diverse functions of plants and are crucial in sustaining plant fitness under often rapidly changing environments. The composition and diversity of microbiota differs between plant and soil compartments. It indicates that microbial communities in these compartments are not static but are adjusted by the environment as well as inter-microbial and plant-microbe communication. Hormones take a crucial role in contributing to the assembly of plant microbiomes, and plants and microbes often employ the same hormones with completely different intentions. Here, the function of hormones as go-betweens between plants and microbes to influence the shape of plant microbial communities is discussed. The versatility of plant and microbe-derived hormones essentially contributes to the creation of habitats that are the origin of diversity and, thus, multifunctionality of plants, their microbiota and ultimately ecosystems.

30 years of free-air carbon dioxide enrichment (FACE): What have we learned about future crop productivity and its potential for adaptation?

Free-air CO₂ enrichment (FACE) allows open-air elevation of [CO₂ ] without altering the microclimate. Its scale uniquely supports simultaneous study from physiology and yield to soil processes and disease. In 2005 we summarized results of then 28 published observations by meta-analysis. Subsequent studies have combined FACE with temperature, drought, ozone, and nitrogen treatments. Here, we summarize the results of now almost 250 observations, spanning 14 sites and five continents. Across 186 independent studies of 18 C₃ crops, elevation of [CO₂ ] by ca. 200 ppm caused a ca. 18% increase in yield under non-stress conditions. Legumes and root crops showed a greater increase and cereals less. Nitrogen deficiency reduced the average increase to 10%, as did warming by ca. 2°C. Two conclusions of the 2005 analysis were that C₄ crops would not be more productive in elevated [CO₂ ], except under drought, and that yield responses of C₃ crops were diminished by nitrogen deficiency and wet conditions. Both stand the test of time. Further studies of maize and sorghum showed no yield increase, except in drought, while soybean productivity was negatively affected by early growing season wet conditions. Subsequent study showed reduced levels of nutrients, notably Zn and Fe in most crops, and lower nitrogen and protein in the seeds of non-leguminous crops. Testing across crop germplasm revealed sufficient variation to maintain nutrient content under rising [CO₂ ]. A strong correlation of yield response under elevated [CO₂ ] to genetic yield potential in both rice and soybean was observed. Rice cultivars with the highest yield potential showed a 35% yield increase in elevated [CO₂ ] compared to an average of 14%. Future FACE experiments have the potential to develop cultivars and management strategies for co-promoting sustainability and productivity under future elevated [CO₂ ].

The genetic architecture of host response reveals the importance of arbuscular mycorrhizae to maize cultivation

Arbuscular mycorrhizal fungi (AMF) are ubiquitous in cultivated soils, forming symbiotic relationships with the roots of major crop species. Studies in controlled conditions have demonstrated the potential of AMF to enhance the growth of host plants. However, it is difficult to estimate the actual benefit in the field, not least because of the lack of suitable AMF-free controls. Here we implement a novel strategy using the selective incorporation of AMF-resistance into a genetic mapping population to evaluate maize response to AMF. We found AMF to account for about one-third of the grain production in a medium input field, as well as to affect the relative performance of different plant genotypes. Characterization of the genetic architecture of the host response indicated a trade-off between mycorrhizal dependence and benefit. We identified several QTL linked to host benefit, supporting the feasibility of breeding crops to maximize profit from symbiosis with AMF.

Fungal colonization associated with phenological stages of a photosynthetic terrestrial temperate orchid from the Southern Iberian Peninsula

Fungal endophytes, both mycorrhizal and non-mycorrhizal, are involved in the development of the life cycle of orchids, providing potential beneficial relationships. Here, we assess the succession of changes in the diversity of fungal symbionts associated with a terrestrial temperate orchid species, Anacamptis morio subsp. champagneuxii, over three phenological stages: developed leaves but no stem elongation, flowering, and fruiting. Fungi endophyte associated with roots were obtained by culture in sterile conditions. A total of 18 morphotypes-one Mortierellomycota, two Basidiomycota and 15 Ascomycota-were differentiated, and were also characterized using PCR and DNA sequencing techniques. Only three of the 18 OTUs are shared among the three phenological stages examined: Westerdykella sp., a member of Ceratobasidiaceae, and Fusarium oxysporum, representing a relative abundance of between 28% (fruiting) to 41% (flowering). Our research confirmed that fungal symbionts varied among the different phenological stages examined, the peak of endophyte diversity appearing in the flowering stage. The availability of a diverse mycobiota seems to be important for the survival of orchid plants because it may cover particular physiological needs, and knowledge concerning this mycobiota is of special relevance in the establishment of reliable conservation programmes.

Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.

Mycorrhizal symbioses have evolved repeatedly in diverse fungal lineages. A large phylogenomic analysis sheds light on genomic changes associated with transitions from saprotrophy to symbiosis, including divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.

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.

Keystone metabolites of crop rhizosphere microbiomes

The role of microbes in sustaining agricultural plant growth has great potential consequences for human prosperity. Yet we have an incomplete understanding of the basic function of rhizosphere microbial communities and how they may change under future stresses, let alone how these processes might be harnessed to sustain or improve crop yields. A reductionist approach may aid the generation and testing of hypotheses that can ultimately be translated to agricultural practices. With this in mind, we ask whether some rhizosphere microbial communities might be governed by 'keystone metabolites', envisioned here as microbially produced molecules that, through antibiotic and/or growth-promoting properties, may play an outsized role in shaping the development of the community spatiotemporally. To illustrate this point, we use the example of redox-active metabolites, and in particular phenazines, which are produced by many bacteria found in agricultural soils and have well-understood catalytic properties. Phenazines can act as potent antibiotics against a variety of cell types, yet they also can promote the acquisition of essential inorganic nutrients. In this essay, we suggest the ways these metabolites might affect microbial communities and ultimately agricultural productivity in two specific scenarios: firstly, in the biocontrol of beneficial and pathogenic fungi in increasingly arid crop soils and, secondly, through promotion of phosphorus bioavailability and sustainable fertilizer use. We conclude with specific proposals for future research.

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.

Reconstructing trait evolution in plant evo-devo studies

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 macroevolutionary dynamics of symbiotic and phenotypic diversification in lichens

Symbioses are evolutionarily pervasive and play fundamental roles in structuring ecosystems, yet our understanding of their macroevolutionary origins, persistence, and consequences is incomplete. We traced the macroevolutionary history of symbiotic and phenotypic diversification in an iconic symbiosis, lichens. By inferring the most comprehensive time-scaled phylogeny of lichen-forming fungi (LFF) to date (over 3,300 species), we identified shifts among symbiont classes that broadly coincided with the convergent evolution of phylogenetically or functionally similar associations in diverse lineages (plants, fungi, bacteria). While a relatively recent loss of lichenization in Lecanoromycetes was previously identified, our work instead suggests lichenization was abandoned far earlier, interrupting what had previously been considered a direct switch between trebouxiophycean and trentepohlialean algal symbionts. Consequently, some of the most diverse clades of LFF are instead derived from nonlichenized ancestors and re-evolved lichenization with Trentepohliales algae, a clade that also facilitated lichenization in unrelated lineages of LFF. Furthermore, while symbiont identity and symbiotic phenotype influence the ecology and physiology of lichens, they are not correlated with rates of lineage birth and death, suggesting more complex dynamics underly lichen diversification. Finally, diversification patterns of LFF differed from those of wood-rotting and ectomycorrhizal taxa, likely reflecting contrasts in their fundamental biological properties. Together, our work provides a timeline for the ecological contributions of lichens, and reshapes our understanding of symbiotic persistence in a classic model of symbiosis.

Chemotactic Host-Finding Strategies of Plant Endoparasites and Endophytes

Plants interact with microorganisms in the environment during all stages of their development and in most of their organs. These interactions can be either beneficial or detrimental for the plant and may be transient or long-term. In extreme cases, microorganisms become endoparastic or endophytic and permanently reside within a plant, while the host plant undergoes developmental reprogramming and produces new tissues or organs as a response to the invasion. Events at the cellular and molecular level following infection have been extensively described, however the mechanisms of how these microorganisms locate their plant hosts via chemotaxis remain largely unknown. In this review, we summarize recent findings concerning the signalling molecules that regulate chemotaxis of endoparasitic/endophytic bacteria, fungi, and nematodes. In particular, we will focus on the molecules secreted by plants that are most likely to act as guidance cues for microorganisms. These compounds are found in a wide range of plant species and show a variety of secondary effects. Interestingly, these compounds show different attraction potencies depending on the species of the invading organism, suggesting that cues perceived in the soil may be more complex than anticipated. However, what the cognate receptors are for these attractants, as well as the mechanism of how these attractants influence these organisms, remain important outstanding questions. Host-targeting marks the first step of plant-microorganism interactions, therefore understanding the signalling molecules involved in this step plays a key role in understanding these interactions as a whole.

Into the wild blueberry (Vaccinium angustifolium) rhizosphere microbiota

The ability of wild blueberries to adapt to their harsh environment is believed to be closely related to their symbiosis with ericoid mycorrhizal fungi, which produce enzymes capable of organic matter mineralization. Although some of these fungi have been identified and characterized, we still know little about the microbial ecology of wild blueberry. Our study aims to characterize the fungal and bacterial rhizosphere communities of Vaccinium angustifolium (the main species encountered in wild blueberry fields). Our results clearly show that the fungal order Helotiales was the most abundant taxon associated with V. angustifolium. Helotiales contains most of the known ericoid mycorrhizal fungi which are expected to dominate in such a biotope. Furthermore, we found the dominant bacterial order was the nitrogen-fixing Rhizobiales. The Bradyrhizobium genus, whose members are known to form nodules with legumes, was among the 10 most abundant genera in the bacterial communities. In addition, Bradyrhizobium and Roseiarcus sequences significantly correlated with higher leaf-nitrogen content. Overall, our data documented fungal and bacterial community structure differences in three wild blueberry production fields.

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.

Oak displays common local but specific distant gene regulation responses to different mycorrhizal fungi

BACKGROUND

Associations of tree roots with diverse symbiotic mycorrhizal fungi have distinct effects on whole plant functioning. An untested explanation might be that such effect variability is associated with distinct impacts of different fungi on gene expression in local and distant plant organs. Using a large scale transcriptome sequencing approach, we compared the impact of three ectomycorrhizal (EMF) and one orchid mycorrhizal fungi (OMF) on gene regulation in colonized roots (local), non-colonized roots (short distance) and leaves (long distance) of the Quercus robur clone DF159 with reference to the recently published oak genome. Since different mycorrhizal fungi form symbiosis in a different time span and variable extents of apposition structure development, we sampled inoculated but non-mycorrhizal plants, for which however markedly symbiotic effects have been reported. Local root colonization by the fungi was assessed by fungal transcript analysis.

RESULTS

The EMF induced marked and species specific effects on plant development in the analysed association stage, but the OMF did not. At local level, a common set of plant differentially expressed genes (DEG) was identified with similar patterns of responses to the three EMF, but not to the OMF. Most of these core DEG were down-regulated and correspond to already described but also new functions related to establishment of EMF symbiosis. Analysis of the fungal transcripts of two EMF in highly colonized roots also revealed onset of a symbiosis establishment. In contrast, in the OMF, the DEG were mainly related to plant defence. Already at short distances, high specificities in transcriptomic responses to the four fungi were detected, which were further enhanced at long distance in leaves, where almost no common DEG were found between the treatments. Notably, no correlation between phylogeny of the EMF and gene expression patterns was observed.

CONCLUSIONS

Use of clonal oaks allowed us to identify a core transcriptional program in roots colonized by three different EMF, supporting the existence of a common EMF symbiotic pathway. Conversely, the specific responses in non-colonized organs were more closely related to the specific impacts of the different of EMF on plant performance.

Cheating in arbuscular mycorrhizal mutualism: a network and phylogenetic analysis of mycoheterotrophy

Although mutualistic interactions are widespread and essential in ecosystem functioning, the emergence of uncooperative cheaters threatens their stability, unless there are some physiological or ecological mechanisms limiting interactions with cheaters. In this framework, we investigated the patterns of specialization and phylogenetic distribution of mycoheterotrophic cheaters vs noncheating autotrophic plants and their respective fungi, in a global arbuscular mycorrhizal network with> 25 000 interactions. We show that mycoheterotrophy evolved repeatedly among vascular plants, suggesting low phylogenetic constraints for plants. However, mycoheterotrophic plants are significantly more specialized than autotrophic plants, and they tend to be associated with specialized and closely related fungi. These results raise new hypotheses about the mechanisms (e.g. sanctions, or habitat filtering) that actually limit the interaction of mycoheterotrophic plants and their associated fungi with the rest of the autotrophic plants. Beyond mycorrhizal symbiosis, this unprecedented comparison of mycoheterotrophic vs autotrophic plants provides a network and phylogenetic framework to assess the presence of constraints upon cheating emergences in mutualisms.

Biological Control of Plant-Parasitic Nematodes by Filamentous Fungi Inducers of Resistance: Trichoderma, Mycorrhizal and Endophytic Fungi

Plant-parasitic-nematodes represent a major threat to the agricultural production of different crops worldwide. Due to the high toxicity of chemical nematicides, it is necessary to develop new control strategies against nematodes. In this respect, filamentous fungi can be an interesting biocontrol alternative. The genus Trichoderma, mycorrhizal and endophytic fungi are the main groups of filamentous fungi studied and used as biological control agents (BCAs) against nematodes as resistance inducers. They are able to reduce the damage caused by plant-parasitic nematodes directly by parasitism, antibiosis, paralysis and by the production of lytic enzymes. But they also minimize harm by space and resource-competition, by providing higher nutrient and water uptake to the plant, or by modifying the root morphology, and/or rhizosphere interactions, that constitutes an advantage for the plant-growth. Besides, filamentous fungi are able to induce resistance against nematodes by activating hormone-mediated (salicylic and jasmonic acid, strigolactones among others) plant-defense mechanisms. Additionally, the alteration of the transport of chemical defense components through the plant or the synthesis of plant secondary metabolites and different enzymes can also contribute to enhancing plant defenses. Therefore, the use of filamentous fungi of the mentioned groups as BCAs is a promising durable biocontrol strategy in agriculture against plant-parasitic nematodes.

Evaluation of secondary ions related to plant tissue using least absolute shrinkage and selection operator

With regard to life sciences, it is important to understand biological functions such as metabolic reactions at the cellular level. Time-of-flight secondary ion mass spectrometry (TOF-SIMS) that can provide chemical mappings at 100 nm lateral resolutions is useful for obtaining three-dimensional maps of biological molecules in cells and tissues. TOF-SIMS spectra generally contain several hundred to several thousand secondary ion peaks that provide detailed chemical information. In order to manage such a large number of peaks, data analysis methods such as multivariate analysis techniques have been applied to TOF-SIMS data of complex samples. However, the interpretation of the data analysis results is sometimes still difficult, especially for biological samples. In this study, TOF-SIMS data of resin-embedded plant samples were analyzed using one of the sparse modeling methods, least absolute shrinkage and selection operator (LASSO), to directly select secondary ions related to biological structures such as cell walls and nuclei. The same sample was measured by optical microscopy and the same measurement area as TOF-SIMS was extracted in order to prepare a target image for LASSO. The same area of the TOF-SIMS and microscope data were fused to evaluate the influence of the image fusion on the TOF-SIMS spectrum information using principal component analysis. Specifically, the authors examined onion mycorrhizal root colonized with Gigaspora margarita (an arbuscular mycorrhizal fungus). The results showed that by employing this approach using LASSO, important secondary ions from biological samples were effectively selected and could be clearly distinguished from the embedding resin.