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1. Diversity of fungal microbiome obtained from plant rhizoplanes

   https://doi.org/10.1016/j.scitotenv.2023.164506  

   Lupini, Simone; Nguyen, Hang N; Morales, Demosthenes; House, Geoffrey L; Paudel, Sachin; Chain, Patrick SG; Rodrigues, Debora F (September 2023, Science of The Total Environment)

   Microbial communities, and their ecological importance, have been investigated in several habitats. However, so far, most studies could not describe the closest microbial interactions and their functionalities. This study investigates the co-occurring interactions between fungi and bacteria in plant rhizoplanes and their potential functions. The partnerships were obtained using fungal-highway columns with four plant-based media. The fungi and associated microbiomes isolated from the columns were identified by sequencing the ITS (fungi) and 16S rRNA genes (bacteria). Statistical analyses including Exploratory Graph and Network Analysis were used to visualize the presence of underlying clusters in the microbial communities and evaluate the metabolic functions associated with the fungal microbiome (PICRUSt2). Our findings characterize the presence of both unique and complex bacterial communities associated with different fungi. The results showed that Bacillus was associated as exo-bacteria in 80 % of the fungi but occurred as putative endo-bacteria in 15 %. A shared core of putative endo-bacterial genera, potentially involved in the nitrogen cycle was found in 80 % of the isolated fungi. The comparison of potential metabolic functions of the putative endo- and exo-communities highlighted the potential essential factors to establish an endosymbiotic relationship, such as the loss of pathways associated with metabolites obtained from the host while maintaining pathways responsible for bacterial survival within the hypha. 

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2. Effect of permafrost thaw on plant and soil fungal community in a boreal forest: Does fungal community change mediate plant productivity response?

   https://doi.org/10.1111/1365-2745.13139  

   Schütte, Ursel M.; Henning, Jeremiah A.; Ye, Yuzhen; Bowling, Annie; Ford, James; Genet, Hélène; Waldrop, Mark P.; Turetsky, Merritt R.; White, Jeffrey R.; Bever, James D.; et al (February 2019, Journal of Ecology)
3. Epigenetic regulation of nuclear processes in fungal plant pathogens

   https://doi.org/10.1371/journal.ppat.1011525  

   Kramer, H. Martin; Cook, David E.; Seidl, Michael F.; Thomma, Bart P.H.J. (August 2023, PLOS Pathogens)

   Ballou, Elizabeth (Ed.)

   Through the association of protein complexes to DNA, the eukaryotic nuclear genome is broadly organized into open euchromatin that is accessible for enzymes acting on DNA and condensed heterochromatin that is inaccessible. Chemical and physical alterations to chromatin may impact its organization and functionality and are therefore important regulators of nuclear processes. Studies in various fungal plant pathogens have uncovered an association between chromatin organization and expression of in planta - induced genes that are important for pathogenicity. This review discusses chromatin-based regulation mechanisms as determined in the fungal plant pathogen Verticillium dahliae and relates the importance of epigenetic transcriptional regulation and other nuclear processes more broadly in fungal plant pathogens. 

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4. Specificity in plant-mycorrhizal fungal relationships: prevalence, parameterization, and prospects

   https://doi.org/10.3389/fpls.2023.1260286  

   d’Entremont, Tyler W; Kivlin, Stephanie N (October 2023, Frontiers in Plant Science)

   Species interactions exhibit varying degrees of specialization, ranging from generalist to specialist interactions. For many interactions (e.g., plant-microbiome) we lack standardized metrics of specialization, hindering our ability to apply comparative frameworks of specificity across niche axes and organismal groups. Here, we discuss the concept of plant host specificity of arbuscular mycorrhizal (AM) fungi and ectomycorrhizal (EM) fungi, including the predominant theories for their interactions: Passenger, Driver, and Habitat Hypotheses. We focus on five major areas of interest in advancing the field of plant-mycorrhizal fungal host specificity: phylogenetic specificity, host physiology specificity, functional specificity, habitat specificity, and mycorrhizal fungal-mediated plant rarity. Considering the need to elucidate foundational concepts of specificity in this globally important symbiosis, we propose standardized metrics and comparative studies to enhance our understanding. We also emphasize the importance of analyzing global mycorrhizal data holistically to draw meaningful conclusions and suggest a shift toward single-species analyses to unravel the complexities underlying these associations. 

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5. The Costs and Benefits of Plant–Arbuscular Mycorrhizal Fungal Interactions

   https://doi.org/10.1146/annurev-arplant-102820-124504  

   Bennett, Alison E.; Groten, Karin (May 2022, Annual Review of Plant Biology)

   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. 

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