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Summary: The pathways regulated in ectomycorrhizal (EcM) plant hosts during the establishment of symbiosis are not as well understood when compared to the functional stages of this mutualistic interaction. Our study used the EcM host Eucalyptus grandis to elucidate symbiosis‐regulated pathways across the three phases of this interaction.Using a combination of RNA sequencing and metabolomics we studied both stage‐specific and core responses of E. grandis during colonization by Pisolithus microcarpus. Using exogenous manipulation of the abscisic acid (ABA), we studied the role of this pathway during symbiosis establishment.Despite the mutualistic nature of this symbiosis, a large number of disease signalling TIR‐NBS‐LRR genes were induced. The transcriptional regulation in E. grandis was found to be dynamic across colonization with a small core of genes consistently regulated at all stages. Genes associated to the carotenoid/ABA pathway were found within this core and ABA concentrations increased during fungal integration into the root. Supplementation of ABA led to improved accommodation of P. microcarpus into E. grandis roots.The carotenoid pathway is a core response of an EcM host to its symbiont and highlights the need to understand the role of the stress hormone ABA in controlling host–EcM fungal interactions. [ABSTRACT FROM AUTHOR]

Summary: Ectomycorrhizal (ECM) fungi are integral to boreal and temperate forest ecosystem functioning and nutrient cycling. ECM fungi, however, originate from diverse saprotrophic lineages and the impacts of genetic variation across species, and especially within a given ECM species, on function and interactions with the environment is not well understood. Here, we explore the extent of intra‐species variation between four isolates of the ECM fungus Pisolithus microcarpus, in terms of gene regulation, carbon metabolism and growth, and interactions with a host, Eucalyptus grandis. We demonstrate that, while a core response to the host is maintained by all of the isolates tested, they have distinct patterns of gene expression and carbon metabolism, resulting in the differential expression of isolate‐specific response pathways in the host plant. Together, these results highlight the importance of using a wider range of individuals within a species to understand the broader ecological roles of ECM fungi and their host interactions. [ABSTRACT FROM AUTHOR]

Armillaria root rot is a fungal disease that affects a wide range of trees and crops around the world. Despite being a widespread disease, little is known about the plant molecular responses towards the pathogenic fungi at the early phase of their interaction. With recent research highlighting the vital roles of metabolites in plant root–microbe interactions, we sought to explore the presymbiotic metabolite responses of Eucalyptus grandis seedlings towards Armillaria luteobuablina, a necrotrophic pathogen native to Australia. Using a metabolite profiling approach, we have identified threitol as one of the key metabolite responses in E. grandis root tips specific to A. luteobubalina that were not induced by three other species of soil‐borne microbes of different lifestyle strategies (a mutualist, a commensalist, and a hemi‐biotrophic pathogen). Using isotope labelling, threitol detected in the Armillaria‐treated root tips was found to be largely derived from the fungal pathogen. Exogenous application of d‐threitol promoted microbial colonization of E. grandis and triggered hormonal responses in root cells. Together, our results support a role of threitol as an important metabolite signal during eucalypt‐Armillaria interaction prior to infection thus advancing our mechanistic understanding on the earliest stage of Armillaria disease development. Comparative metabolomics of eucalypt roots interacting with a range of fungal lifestyles identified threitol enrichment as a specific characteristic of Armillaria pathogenesis. Our findings suggest that threitol acts as one of the earliest fungal signals promoting Armillaria colonization of roots. Comparative metabolomics of eucalypt roots interacting with different fungi identified threitol enrichment as a specific characteristic of Armillaria pathogenesis. Our findings suggest that threitol acts as one of the earliest fungal signals promoting Armillaria colonization of roots. [ABSTRACT FROM AUTHOR]

Breeding disease-resistant varieties is one of the most effective and economical means to combat soilborne diseases in pulse crops. Commonalities between pathogenic and mutualistic microbe colonization strategies, however, raises the concern that reduced susceptibility to pathogens may simultaneously reduce colonization by beneficial microbes. We investigate here the degree of overlap in the transcriptional response of the Phytophthora medicaginis susceptible chickpea variety 'Sonali' to the early colonization stages of either Phytophthora, rhizobial bacteria or arbuscular mycorrhizal fungi. From a total of 6476 genes differentially expressed in Sonali roots during colonization by any of the microbes tested, 10.2% were regulated in a similar manner regardless of whether it was the pathogenic oomycete or a mutualistic microbe colonizing the roots. Of these genes, 49.7% were oppositely regulated under the same conditions in the moderately Phytophthora resistant chickpea variety 'PBA HatTrick'. Chickpea varieties with improved resistance to Phytophthora also displayed lower colonization by rhizobial bacteria and mycorrhizal fungi leading to an increased reliance on N and P from soil. Together, our results suggest that marker-based breeding in crops such as chickpea should be further investigated such that plant disease resistance can be tailored to a specific pathogen without affecting mutualistic plant:microbe interactions. [ABSTRACT FROM AUTHOR]

The plant hormones ethylene, jasmonic acid and salicylic acid have interconnecting roles during the response of plant tissues to mutualistic and pathogenic symbionts., We used morphological studies of transgenic- or hormone-treated Populus roots as well as whole-genome oligoarrays to examine how these hormones affect root colonization by the mutualistic ectomycorrhizal fungus Laccaria bicolor S238N., We found that genes regulated by ethylene, jasmonic acid and salicylic acid were regulated in the late stages of the interaction between L. bicolor and poplar. Both ethylene and jasmonic acid treatments were found to impede fungal colonization of roots, and this effect was correlated to an increase in the expression of certain transcription factors (e.g. ETHYLENE RESPONSE FACTOR1) and a decrease in the expression of genes associated with microbial perception and cell wall modification. Further, we found that ethylene and jasmonic acid showed extensive transcriptional cross-talk, cross-talk that was opposed by salicylic acid signaling., We conclude that ethylene and jasmonic acid pathways are induced late in the colonization of root tissues in order to limit fungal growth within roots. This induction is probably an adaptive response by the plant such that its growth and vigor are not compromised by the fungus. [ABSTRACT FROM AUTHOR]

Abstract: Ethylene is a central signalling agent in mediating plant defence against pathogens. Mutations to the ethylene receptor ETR1 have been shown to alter susceptibility of plants to mycotoxin-induced cell death. Using Fumonisin B1 (FB1) to induce cell death, we demonstrate that the receptor mutant ein4-1 has a reduced rate of necrosis, potentially due to an upregulation of ETHYLENE RESPONSE FACTOR1. Mutations in other ethylene receptors differentially affected the expression of genes in the jasmonic and salicylic acid defence pathways. Together these data indicate that ethylene receptors do not have redundant roles in mediating FB1-induced cell death. [Copyright &y& Elsevier]

Plant community biodiversity can be maintained, at least partially, by shifts in species interactions between facilitation and competition for resources as environmental conditions change. These interactions also drive ecosystem functioning, including productivity, and can promote over‐yielding‐ an ecosystem service prioritized in agro‐ecosystems, such as pastures, that occurs when multiple species together are more productive than the component species alone. Importantly, species interactions that can result in over‐yielding may shift in response to rising CO2 concentrations and changes in resource availability, and the consequences these shifts have on production is uncertain especially in the context of tropical mixed‐species grasslands.We examined the relative performance of two species pairs of tropical pasture grasses and legumes growing in monoculture and mixtures in a glasshouse experiment manipulating CO2. We investigated how over‐yielding can arise from nitrogen (N) niche partitioning and biotic facilitation using stable isotopes to differentiate soil N from biological N fixation (BNF) within N acquisition into above‐ground biomass for these two‐species mixtures.We found that N niche partitioning in species‐level use of soil N versus BNF drove species interactions in mixtures. Importantly partitioning and overyielding were generally reduced under elevated CO2. However, this finding was mixture‐dependent based on biomass of dominant species in mixtures and the strength of selection effects for the dominant species.This study demonstrates that rising atmospheric CO2 may alter niche partitioning between co‐occurring species, with negative implications for the over‐yielding benefits predicted for legume‐grass mixtures in working landscapes with tropical species. Furthermore, these changes in inter‐species interactions may have consequences for grassland composition that are not yet considered in larger‐scale projections for impacts of climate change and species distributions. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

We aimed to identify genomic traits of transitions to ectomycorrhizal ecology within the Boletales by comparing the genomes of 21 symbiotrophic species with their saprotrophic brown-rot relatives. Gene duplication rate is constant along the backbone of Boletales phylogeny with large loss events in several lineages, while gene family expansion sharply increased in the late Miocene, mostly in the Boletaceae. Ectomycorrhizal Boletales have a reduced set of plant cell-wall-degrading enzymes (PCWDEs) compared with their brown-rot relatives. However, the various lineages retain distinct sets of PCWDEs, suggesting that, over their evolutionary history, symbiotic Boletales have become functionally diverse. A smaller PCWDE repertoire was found in Sclerodermatineae. The gene repertoire of several lignocellulose oxidoreductases (e.g. laccases) is similar in brown-rot and ectomycorrhizal species, suggesting that symbiotic Boletales are capable of mild lignocellulose decomposition. Transposable element (TE) proliferation contributed to the higher evolutionary rate of genes encoding effector-like small secreted proteins, proteases, and lipases. On the other hand, we showed that the loss of secreted CAZymes was not related to TE activity but to DNA decay. This study provides novel insights on our understanding of the mechanisms influencing the evolutionary diversification of symbiotic boletes., (© 2021 The Authors. New Phytologist © 2021 New Phytologist Foundation.)

Using the newly available genome for Eucalyptus grandis, we sought to determine the genome-wide traits that enable this host to form mutualistic interactions with ectomycorrhizal (ECM) Pisolithus sp. and to determine how future predicted concentrations of atmospheric carbon dioxide (CO2 ) will affect this relationship. We analyzed the physiological and transcriptomic responses of E. grandis during colonization by different Pisolithus sp. isolates under conditions of ambient (400 ppm) and elevated (650 ppm) CO2 to tease out the gene expression profiles associated with colonization status. We demonstrate that E. grandis varies in its susceptibility to colonization by different Pisolithus isolates in a manner that is not predictable by geographic origin or the internal transcribed spacer (ITS)-based phylogeny of the fungal partner. Elevated concentrations of CO2 alter the receptivity of E. grandis to Pisolithus, a change that is correlated to a dramatic shift in the transcriptomic profile of the root. These data provide a starting point for understanding how future environmental change may alter the signaling between plants and their ECM partners and is a step towards determining the mechanism behind previously observed shifts in Eucalypt-associated fungal communities exposed to elevated concentrations of atmospheric CO2 ., (© 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.)

Given recent technological advances, we are in a golden era of cell and whole organism research. With the availability of so many sequenced genomes, and the data that has been mined there-in, it is easy to gain the impression that all our work as scientists is complete. Instead, such work and results have now provided oceans of data, but with minimal functional information. We also do not have a full grasp on the working relationships within a number of different plant developmental pathways. This is especially true in the study of the symbiotic interaction between ectomycorrhizal fungi and their plant hosts. One of the current interests in symbiotic and pathogenic interactions between plants and fungi is the role of small, secreted proteins. What makes fungal small secreted proteins so interesting is that only a few of them share sequence homology to any other known proteins, but some may act as effectors modulating plant metabolism and development. Therefore, it is difficult to make predictions as to the action of these proteins without functional analysis. For this reason, we created a pipeline to analyze the role and function of these proteins. Typically, this involves transcriptional analysis of genes followed by protein localization, identification of protein-protein interactions, and functional analysis of the protein through heterologous expression in yeast among many other different procedures. Due to the physiology of mycorrhizal root tips, there are a number of unique challenges that must be overcome to properly study a fungal effector. Here, we outline some of the methods, and hopefully helpful tips, that we are currently using to pursue the study of different effectors in the Laccaria-Populus interaction.