27 Search Results

Fungal specialized metabolites are a major source of beneficial compounds that are routinely isolated, characterized, and manufactured as pharmaceuticals, agrochemical agents, and industrial chemicals. The production of these metabolites is encoded by biosynthetic gene clusters that are often silent under standard growth conditions. There are limited resources for characterizing the direct link between abiotic stimuli and metabolite production. Herein, we introduce a network analysis-based, data-driven algorithm comprising two routes to characterize the production of specialized fungal metabolites triggered by different exogenous compounds: the direct route and the auxiliary route. Both routes elucidate the influence of treatments on the production ofmore » specialized metabolites from experimental data. The direct route determines known and putative metabolites induced by treatments and provides additional insight over traditional comparison methods. The auxiliary route is specific for discovering unknown analytes, and further identification can be curated through online bioinformatic resources. We validated our algorithm by applying chitooligosaccharides and lipids at two different temperatures to the fungal pathogen Aspergillus fumigatus. After liquid chromatography–mass spectrometry quantification of significantly produced analytes, we used network centrality measures to rank the treatments’ ability to elucidate these analytes and confirmed their identity through fragmentation patterns or in silico spiking with commercially available standards. Later, we examined the transcriptional regulation of these metabolites through real-time quantitative polymerase chain reaction. Our data-driven techniques can complement existing metabolomic network analysis by providing an approach to track the influence of any exogenous stimuli on metabolite production. Our experimental-based algorithm can overcome the bottlenecks in elucidating novel fungal compounds used in drug discovery.« less

CO₂ release from forest soils (R_s) is a prominent flux in the global carbon cycle. Rs is derived from roots (autotrophic respiration, R_a) and microbial (heterotrophic) respiration and is highly dynamic, as it depends on edaphic and environmental conditions as well as root functional traits and microbial community composition. It is unclear how root functional traits affect root and microbial respiration rates; however, their consideration may help parse out the relative contributions of root and microbial respiration to R_s. At a temperate forest site, root systems of 3–4 functional root orders and their surrounding surface soil were carefully excavated andmore » placed into custom trays designed to repeatedly measure R_s in situ on eight temperate tree species that varied in their root functional strategies and mycorrhizal affinity. R_s was measured bi-weekly to monthly for nearly one year using a custom chamber attached to a gas exchange system. R_s varied over time, ranging from 0.3 to 12 µmol m^-2 s^-1. Comparable root systems of the same species were excised from the soil and specific root respiration rates (R_r) were measured. Rr ranged from 2.5 to 9.0 nmol g^-1 s^-1 and was negatively correlated with root tissue density and positively related to root tissue nitrogen concentration. Using R_r to estimate R_a, we estimate that R_a accounts for <10%, on average 2–3%, of R_s for individual root systems (averaging 1.2 g dry biomass) housed in surrounding soil (average 1.3 kg dry mass) in situ; thus, Ra was roughly 20 times greater than Rh per unit mass. The contribution of R_a peaked in the fall and coincided with leaf senescence of the forest canopy. A soil-sterilizing experimental treatment designed to help isolate R_a in situ reduced bacterial biomass and shifted fungal community composition, but there was no reduction in Rs of the in-situ root-soil tray systems. The relative R_a to R_s ratio increased with root functional strategies characterized by greater specific root length and tip abundance, but also to greater root tissue density. The ratio of R_a to R_s also increased with warmer soil temperatures and decreased slightly with increasing soil moisture. We discuss how incorporating root functional traits as modulators of the autotrophic contribution to R_s could be considered when modeling total soil CO₂ efflux from forests.« less

Soil hydraulic properties are often estimated based on laboratory data or pedotransfer functions dependent on soil physical properties, which often do not consider potential impacts of soil roots or fungal hyphae. Here, we first review current knowledge of how these soil biotic components affect hydraulic properties, then we conducted laboratory experiments to specifically test if the presence of roots and mycorrhizal fungi had a significant effect on the hydraulic properties of two soils with contrasting textures: Flint sand and Hamblen silt loam. Soil cores were seeded with (Panicum virgatum) and grown in a greenhouse over three separate growth periods. Themore » endophytic fungus Serendipita indica was injected as liquid inoculant into designated mycorrhizal cores. Saturated hydraulic conductivity (K_sat) measurements were made with a constant head permeameter, and soil water retention curves were obtained by the evaporation method, supplemented at the dry end for Hamblen silt loam with water activity meter data. Retention curve parameters were obtained by fitting the van Genuchten equation to the resulting measurements. Mean root volume ratios were higher in the mycorrhizal inoculated treatment than in the uninoculated treatment for both soils. For Flint sand, analysis of variance revealed that K_sat was reduced by the presence of roots as compared to bare soil. This was likely due to roots clogging soil pores. Results also indicated the presence of roots changed the shape of the water retention curve for Flint sand by increasing water content at saturation and by reducing the slope of the curve. These changes suggested roots created additional porosity and broadened the pore-size distribution. The presence of mycorrhizal fungi accentuated the root effects. The influence of roots and mycorrhizal fungi on hydraulic properties was less obvious for the Hamblen silt loam, as none of the treatments differed from each other at p < 0.05. The results highlight the necessity to consider the impact of root and fungal structures on models of soil hydraulic properties.« less

Researchers from across the four U.S. Department of Energy Bioenergy Research Centers engaged in a microbiome workshop that focused on identifying challenges and collaboration opportunities to better understand bioenergy-relevant plant–microbe interactions. The virtual workshop included hands-on educational sessions and a keynote address on current best practices in microbiome science and community microbiome standards, as well as breakout sessions aimed at identifying microbiome-related data and measurements that should be prioritized, opportunities for and barriers to integrating plant metabolites to microbiome research, and strategies for more effectively integrating microbiome data and processes into existing models. Based on participant discussion, key findings ofmore » the workshop were the need to prioritize scaling data sharing across BRCs and the broader research community and securing collaborative infrastructure in the areas of microbiome-ecosystem modeling and molecular plant-microbe interactions. This workshop review highlights additional main findings from this event, to encourage cross-site and more holistic meta-analyses while promoting wide scientific community engagement across plant microbiome sciences.« less

Arbuscular mycorrhizal symbiosis (AMS) is widespread mutualistic association between plants and fungi, which plays an essential role in nutrient exchange, enhancement in plant stress resistance, development of host, and ecosystem sustainability. Previous studies have shown that plant small secreted proteins (SSPs) are involved in beneficial symbiotic interactions. However, the role of SSPs in the evolution of AMS has not been well studied yet. In this study, we performed computational analysis of SSPs in 60 plant species and identified three AMS-specific ortholog groups containing SSPs only from at least 30% of the AMS species in this study and three AMS-preferential orthologmore » groups containing SSPs from both AMS and non-AMS species, with AMS species containing significantly more SSPs than non-AMS species. We found that independent lineages of monocot and eudicot plants contained genes in the AMS-specific ortholog groups and had significant expansion in the AMS-preferential ortholog groups. Also, two AMS-preferential ortholog groups showed convergent changes, between monocot and eudicot species, in gene expression in response to arbuscular mycorrhizal fungus Rhizophagus irregularis. Furthermore, conserved cis-elements were identified in the promoter regions of the genes showing convergent gene expression. We found that the SSPs, and their closely related homologs, in each of three AMS-preferential ortholog groups, had some local variations in the protein structural alignment. We also identified genes co-expressed with the Populus trichocarpa SSP genes in the AMS-preferential ortholog groups. This first plant kingdom-wide analysis on SSP provides insights on plant-AMS convergent evolution with specific SSP gene expression and local diversification of protein structures.« less

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)more » content, a reduction in secondary metabolism clusters, and an association of small secreted proteins (SSPs) with TE ‘nests’, or dense aggregations of TEs. Here, 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.« less

Significance Secondary metabolites (SMs) produced by fungi mediate ecological interactions, define fungal niches, and are of profound pharmacological importance to humans. Most work on SMs has focused on a small number of individuals from each species, not fully reflecting the importance of intraspecific diversity. We demonstrate that even in one of the best-studied model fungi, the carcinogen-producing Aspergillus flavus , more than 25% of SM-producing biosynthetic gene clusters (BGCs) are novel and/or show population-specific variants. These results support the finding that the organization of BGC diversity into population-specific patterns may sometimes result from ecologically important interactions and may inform evolutionarymore » and etiological inferences of SM capacities within a species. Importantly, our work also presents a vision of sources of potential pharmaceuticals.« less

Plant-microbe symbioses span a continuum from pathogenic to mutualistic with functional consequences for both organisms in the symbiosis. In order to increase sustainable food and fuel production in the future, it is imperative that we harness these symbioses. The tree genus Populus is an excellent model system for studies examining plant-microbe interactions due to the wealth of genomic information available and the molecular tools that have been developed to manipulate Populus-microbe symbioses. In this review, we highlight how Populus can serve as a model system to explore plant-microbe interactions. Specifically, highlighting research linking Populus-microbe interactions from the gene to themore » ecosystem level. We explore why Populus is an excellent model for perennial plant systems, the molecular underpinnings of Populus-microbe interactions, how host genetics influence microbial community composition, and how microbial communities vary at fine spatial scales and between Populus species. Further, we explore how the patterns of the microbiome may affect ecosystem level functions in managed and natural ecosystems. Understanding and manipulating these interactions in Populus has the potential to improve plant health and impact ecosystem sustainability and processes as Populus trees function as foundational species in many natural ecosystems and are also deployed in managed ecosystems for various agroforestry applications.« less

Fungi and plants interact in a myriad of ways. These interactions range from mutualism to parasitism, and yet, many plant species appear to use similar tools to deal with both. One recent observation is the role that small RNAs play in mediating the conversation between plant and fungus. Increasingly, many studies demonstrate these RNAs are pivotal modulators, reprogramming gene expression and cellular processes essential to the biogenesis of these inter-kingdom relationships.