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The effects of mowing and multi-level N fertilization on soil bacterial and fungal communities in a semiarid grassland are year-dependent
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Ectomycorrhizal effects on decomposition are highly dependent on fungal traits, climate, and litter properties: A model-based assessment
It has been proposed that competition between ectomycorrhizal (ECM) fungi and free-living saprotrophs for resources like nitrogen (N) slows decomposition and increases the soil carbon storage in ECM ecosystems compared to arbuscular (AM) ecosystems. However, empirical evidence for the generality of such ECM effects is equivocal, and confounding mechanisms have been proposed that affect the magnitude and direction of ECM effects on soil carbon. Here, for this work, we conduct a theoretical modeling experiment, where we explicitly incorporate mycorrhizal processes into the Carbon, Organisms, Rhizosphere, and Protection in the Soil Environment (CORPSE) model. We use the model to explore the conditions under which ECM N acquisition processes can induce stronger saprotrophic N limitation and result in slower decomposition rates and greater soil organic carbon accumulation compared to AM processes. We found that the ECM fungi more strongly inhibited decomposition when litter inputs were N-depleted and relatively recalcitrant and when ECM fungi possessed a strong capacity to mine N from both recalcitrant soil organic matter and microbial necromass. Climate and seasonality also played a role as the ECM competition effect was strongest at low mean annual temperatures and when litterfall peaked seasonally. Priming effects driven by high root exudation rates in ECM-dominated systems could overwhelm the competition effect and reduce soil carbon under some circumstances. The ECM effect on decomposition in our simulations was highly context dependent. Based on our model results, we expect to see a strong ECM competition effect in temperate deciduous and boreal forests with relatively recalcitrant litter inputs, and with ECM fungi that produce oxidases and necromass-degrading enzymes. However, even a relatively strong ECM competition effect on decomposition only increased soil organic carbon accumulation by ~10%.
Polysaccharide assemblies in fungal and plant cell walls explored by solid-state NMR
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Designing chimeric enzymes inspired by fungal cellulosomes
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CreA-mediated repression of gene expression occurs at low monosaccharide levels during fungal plant biomass conversion in a time and substrate dependent manner
Carbon catabolite repression enables fungi to utilize the most favourable carbon source in the environment, and is mediated by a key regulator, CreA, in most fungi. CreA-mediated regulation has mainly been studied at high monosaccharide concentrations, an uncommon situation in most natural biotopes. In nature, many fungi rely on plant biomass as their major carbon source by producing enzymes to degrade plant cell wall polysaccharides into metabolizable sugars. To determine the role of CreA when fungi grow in more natural conditions and in particular with respect to degradation and conversion of plant cell walls, we compared transcriptomes of a creA deletion and reference strain of the ascomycete Aspergillus niger during growth on sugar beet pulp and wheat bran. Transcriptomics, extracellular sugar concentrations and growth profiling of A. niger on a variety of carbon sources, revealed that also under conditions with low concentrations of free monosaccharides, CreA has a major effect on gene expression in a strong time and substrate composition dependent manner. In addition, we compared the CreA regulon from five fungi during their growth on crude plant biomass or cellulose. It showed that CreA commonly regulated genes related to carbon metabolism, sugar transport and plant cell wall degrading enzymes across different species. We therefore conclude that CreA has a crucial role for fungi also in adapting to low sugar concentrations as occurring in their natural biotopes, which is supported by the presence of CreA orthologs in nearly all fungi.
A SWEET surprise: Anaerobic fungal sugar transporters and chimeras enhance sugar uptake in yeast
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Genome-scale phylogeny and comparative genomics of the fungal order Sordariales
The order Sordariales is taxonomically diverse, and harbours many species with different lifestyles and large economic importance. Despite its importance, a robust genome-scale phylogeny, and associated comparative genomic analysis of the order is lacking. In this study, we examined whole-genome data from 99 Sordariales, including 52 newly sequenced genomes, and seven outgroup taxa. We inferred a comprehensive phylogeny that resolved several contentious relationships amongst families in the order, and cleared-up intrafamily relationships within the Podosporaceae. Extensive comparative genomics showed that genomes from the three largest families in the dataset (Chaetomiaceae, Podosporaceae and Sordariaceae) differ greatly in GC content, genome size, gene number, repeat percentage, evolutionary rate, and genome content affected by repeat-induced point mutations (RIP). All genomic traits showed phylogenetic signal, and ancestral state reconstruction revealed that the variation of the properties stems primarily from within-family evolution. Together, the results provide a thorough framework for understanding genome evolution in this important group of fungi.
Structure of the Repurposed Fungal Terpene Cyclase FlvF Implicated in the C?N Bond-Forming Reaction
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Plasmid Copy Number Engineering Accelerates Fungal Polyketide Discovery upon Unnatural Polyketide Biosynthesis
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Forest tree growth is linked to mycorrhizal fungal composition and function across Europe
Most trees form symbioses with ectomycorrhizal fungi (EMF) which influence access to growth-limiting soil resources. Mesocosm experiments repeatedly show that EMF species differentially affect plant development, yet whether these effects ripple up to influence the growth of entire forests remains unknown. Here we tested the effects of EMF composition and functional genes relative to variation in well-known drivers of tree growth by combining paired molecular EMF surveys with high-resolution forest inventory data across 15 European countries. We show that EMF composition was linked to a three-fold difference in tree growth rate even when controlling for the primary abiotic drivers of tree growth. Fast tree growth was associated with EMF communities harboring high inorganic but low organic nitrogen acquisition gene proportions and EMF which form contact versus medium-distance fringe exploration types. These findings suggest that EMF composition is a strong bio-indicator of underlying drivers of tree growth and/or that variation of forest EMF communities causes differences in tree growth. While it may be too early to assign causality or directionality, our study is one of the first to link fine-scale variation within a key component of the forest microbiome to ecosystem functioning at a continental scale.
Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes
Abstract The herbivore digestive tract is home to a complex community of anaerobic microbes that work together to break down lignocellulose. These microbiota are an untapped resource of strains, pathways and enzymes that could be applied to convert plant waste into sugar substrates for green biotechnology. We carried out more than 400 parallel enrichment experiments from goat faeces to determine how substrate and antibiotic selection influence membership, activity, stability and chemical productivity of herbivore gut communities. We assembled 719 high-quality metagenome-assembled genomes (MAGs) that are unique at the species level. More than 90% of these MAGs are from previously unidentified herbivore gut microorganisms. Microbial consortia dominated by anaerobic fungi outperformed bacterially dominated consortia in terms of both methane production and extent of cellulose degradation, which indicates that fungi have an important role in methane release. Metabolic pathway reconstructions from MAGs of 737 bacteria, archaea and fungi suggest that cross-domain partnerships between fungi and methanogens enabled production of acetate, formate and methane, whereas bacterially dominated consortia mainly produced short-chain fatty acids, including propionate and butyrate. Analyses of carbohydrate-active enzyme domains present in each anaerobic consortium suggest that anaerobic bacteria and fungi employ mostly complementary hydrolytic strategies. The division of labour among herbivore anaerobes to degrade plant biomass could be harnessed for industrial bioprocessing.
Above- and belowground fungal biodiversity of Populus trees on a continental scale
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Global hotspots of mycorrhizal fungal richness are poorly protected
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