The story began with a reanalysis of fungal DNA sequencing data from 291 Arabidopsis root samples collected at 18 sites across Europe. From more than 26 million sequenced reads targeting the fungal internal transcribed spacer region, the researchers identified 338 fungal sequence variants present in roots. Only five of these were reproducibly detected in more than 80 percent of the samples, defining a tiny multispecies core mycobiota. Among these five, one variant stood out: it was detected in 98 percent of root samples, and when the team cross-referenced it against 488 cultured fungal isolates from four of the sampling sites, 18 percent of those isolates matched it perfectly. The organism behind this ubiquitous signature was Plectosphaerella cucumerina.

To understand how widespread this fungus really is, the researchers queried the GlobalFungi database, a global repository of fungal occurrence data from environmental sequencing studies. Plectosphaerella sequences appeared in soil, mosses, topsoil, rhizosphere and root samples distributed across the planet, and the plants associated with these detections spanned a phylogenetically diverse array of monocot and dicot hosts. Among the five most prevalent root-associated fungal variants, Plectosphaerella showed the strongest enrichment at the soil–root interface, confirming that it is not merely a soil dweller but an active root colonizer with a host range that cuts across the plant tree of life.

With the ecological stage set, the team assembled a collection of 72 Plectosphaerella strains isolated from plants as diverse as mosses, grasses and flowering dicots, gathered from multiple continents. Using PacBio long-read sequencing, they generated high-quality genome assemblies ranging from 35.5 to 40.5 million base pairs. A phylogeny built from 5,466 single-copy genes revealed two subspecies and a small outgroup, with a burst of transposable elements in one subspecies. Yet the most important result was what the genomes did not show: when the researchers tested whether the host plant from which each strain had been isolated explained variation in the fungi’s repertoires of carbohydrate-active enzymes, proteases and candidate effectors, it did not. Fungal phylogeny accounted for roughly half of the variance in these gene families, but host identity had no detectable effect. The fungus, in other words, carries no signature of specialization on particular plants.

Functional assays reinforced this picture of a generalist. Most isolates, regardless of their host of origin, were detrimental to Arabidopsis seedlings grown in sterile culture, and two Arabidopsis-derived strains retained their harmful effects across 12 geographically diverse Arabidopsis accessions. All 72 isolates consumed carbon sources with nearly identical profiles, showing a particular aptitude for plant cell wall-derived monosaccharides. The modest genetic variation among strains therefore seemed unlikely to explain the fungus’s remarkable environmental and host flexibility on its own, pointing the investigators toward gene regulation rather than gene content as the decisive factor.

To test this, the researchers performed controlled recolonization experiments in which germ-free Arabidopsis, tomato and barley seedlings were inoculated with a single fungal strain originally isolated from Arabidopsis roots. The results were strikingly host-dependent. The fungus significantly reduced a combined index of plant survival and growth by 19.5 percent in Arabidopsis and 10.7 percent in tomato, both dicots, but had no measurable effect on barley, a monocot. Quantitative PCR showed that the fungus colonized the roots of all three species, including barley, but confocal microscopy revealed a crucial difference: in Arabidopsis, fungal hyphae penetrated deep into the peridermal and cortical cell layers, establishing extensive endophytic growth throughout the root system. In tomato, invasion was confined largely to the epidermal layer. In barley, hyphae clustered around root hairs but never entered the root interior, suggesting that the monocot’s immune system or structural barriers halt the fungus at the surface.

The transcriptomic explanation for this host specificity emerged when the team sequenced fungal gene expression inside the roots of all three plants. Of 3,399 fungal genes significantly regulated during root colonization compared with growth on inert membranes, most responded in a host-specific manner, revealing remarkable transcriptional plasticity. Genes involved in catabolism were disproportionately represented among the upregulated sets, and genes encoding carbohydrate-active enzymes, the molecular tools fungi use to dismantle plant cell walls, were strongly overrepresented among induced genes in every host condition. Crucially, the specific enzymes activated mirrored the cell wall chemistry of each host. In the pectin-rich walls of the two dicots, the fungus induced pectin-degrading enzymes; in barley, whose walls are dominated by xylans and mixed-linkage glucans, it switched on xylan-degrading enzymes instead. The fungus, it appears, reads the chemical composition of its host’s walls and tailors its enzymatic arsenal accordingly.

One gene rose above all others in this analysis: a single-copy gene encoding a secreted enzyme from glycoside hydrolase family 64, a candidate β-1,3-glucanase whose expression was induced more than 100-fold inside roots regardless of host species. Structural prediction placed it close to a biochemically characterized β-1,3-glucanase from a soil bacterium, an enzyme with strict specificity for β-1,3-linked glucose chains. These linkages occur in plant callose and mixed-linkage glucans, but they are also the principal immunogenic components of fungal cell walls, meaning the enzyme could serve the fungus in two ways: dismantling host defenses or masking its own wall from immune detection. When the researchers deleted the gene using CRISPR-Cas9 genome editing, confirmed by whole-genome resequencing to be a clean single insertion, the consequences were dramatic. Pathogenicity on Arabidopsis and tomato dropped by 62 to 77 percent, and root colonization fell by 18 to 24 percent, while growth in artificial media and colonization of barley were unaffected. The enzyme, in short, is a specific determinant of infection in the hosts the fungus can actually invade.

The evolutionary reach of this mechanism became apparent when the team surveyed 2,534 fungal genomes. GH64 genes are significantly enriched in plant saprotrophs, pathogens and endophytes, and multiple species in the destructive genus Colletotrichum carry a single copy. Deleting the orthologous gene in Colletotrichum incanum, a root pathogen from a different fungal family that diverged from Plectosphaerella long ago, reduced fungal load in Arabidopsis roots by 68.5 percent and increased plant shoot weight by 10 percent. Notably, the gene was dispensable for infection of Nicotiana benthamiana, consistent with its low expression in that host’s roots. Two independently evolved pathogens thus rely on the same enzyme family to infect the same host, demonstrating that host-induced carbohydrate-active enzymes can couple fungal virulence with multihost compatibility. Because core root fungi are normally held in check by bacterial commensals and plant immune metabolites in nature, the authors suggest that disease emerges when these restraints fail. The GH64 enzyme and its relatives now stand out as promising targets for protecting crops against broad-host-range root pathogens, and the study more broadly reframes fungal host range not as a fixed genomic property but as a dynamic regulatory capacity, unlocked one enzyme at a time by the chemical cues of whatever root the fungus encounters.

Subject of Research: Carbohydrate-active enzymes enabling multihost root infection by the fungus Plectosphaerella cucumerina

Article Title: Carbohydrate-active enzymes from a core root mycobiota member enable infection of multiple plant hosts

Article References: Raja-Kumar, R.-S., Mesny, F., Basak, A. K., Newfeld, J., Chesneau, G., Entila, F., Lee, T., Rigerte, L., Carvajal Acevedo, S., Hüttel, B., Crous, P. W., Maciá-Vicente, J. G., Stewart, H., Ryan, M., Fakhoury, A. M., Sacristán, S., Aitouguinane, M., Batisson, I., Dumontet, S., … Hacquard, S. (2026). Carbohydrate-active enzymes from a core root mycobiota member enable infection of multiple plant hosts. Nature Microbiology. https://doi.org/10.1038/s41564-026-02492-3

Image Credits: AI Generated

DOI: 10.1038/s41564-026-02492-3

Keywords: Plectosphaerella cucumerina, root microbiome, CAZymes, GH64, β-1,3-glucanase, plant pathology, Arabidopsis thaliana, Colletotrichum incanum, fungal genomics, cell wall degradation, host range, CRISPR gene editing

Soap Lake is a meromictic soda lake, meaning its water column is permanently stratified into two layers that never fully mix. The upper mixolimnion, extending to about 19 metres, is relatively warm, brackish and well oxygenated, while the lower monimolimnion, between 21 and 27 metres, is colder, anoxic, hypersaline and contains dissolved sulfide concentrations reported to exceed 150 millimolar. Superimposed on this vertical structure are steep gradients in salinity, redox potential and sulfur chemistry, created by waters enriched in sodium carbonate, bicarbonate and sulfate. These conditions are hostile to most life, yet they have fostered specialised microbial communities, and it is from the sulfidic depths that A. saponilacus was recovered. The lake’s geochemistry even resembles conditions hypothesised for ancient Martian basins and subsurface oceans on icy moons, making it a valuable analogue for astrobiology as well as a reservoir of extremophiles with industrial promise.

A. saponilacus belongs to the family Marinilabiliaceae within the phylum Bacteroidota, a lineage renowned for its sophisticated machinery for degrading complex polysaccharides. The new study began by mapping the bacterium’s metabolic breadth, culturing it anaerobically at 37 degrees Celsius in minimal medium supplemented with a panel of mono- and polysaccharides. The organism grew strongly on beta-glucan substrates, achieving its highest final culture densities on laminarin, a beta-1,3/1,6-glucan from algae, birchwood glucuronoxylan, tamarind xyloglucan and barley mixed-linkage beta-glucan. Growth was minimal or absent on pectin and gum arabic, indicating a lack of the enzymes or transporters needed to exploit those polymers. Among monosaccharides, glucose and xylose supported robust growth, consistent with the bacterium’s preference for glucose- and xylose-based carbohydrates.

To understand how the bacterium targets its preferred substrates, the researchers examined its polysaccharide utilisation loci, or PULs, the genetic systems that Bacteroidetes use to sense, bind and degrade polysaccharides at the cell surface. Genome analysis revealed 14 predicted PULs, four of which appeared tailored to beta-glucans. The team focused on PUL 10, which encodes an unusually rich complement of enzymes, including a glycoside hydrolase family 128 protein, two family 16 enzymes, and auxiliary glycosidases from families 43, 2, 31 and 97 likely involved in removing side-chain decorations. Reverse transcription quantitative PCR confirmed that the SusC/SusD-like transport genes within PUL 10 were strongly upregulated when the bacterium was grown on laminarin but not on xylan, while the equivalent pair from the xylan-targeting PUL 7 responded to xylan but not laminarin. This reciprocal pattern confirmed PUL 10 as the locus specifically dedicated to long-chain beta-glucan degradation.

With beta-glucan metabolism experimentally confirmed, the team mined the bacterium’s published proteome for enzymes with detergent relevance. Modern granular laundry and automatic dishwashing detergents operate at alkaline pH, typically between 9.5 and 11.0, and contain high carbonate and surfactant concentrations that inactivate most enzymes isolated from conventional mesophilic bacteria. Because enzymes secreted by A. saponilacus must function extracellularly in Soap Lake’s carbonate-rich, high-pH waters, the researchers prioritised predicted secreted, endo-acting proteins below 100 kilodaltons. From 3,564 encoded proteins, bioinformatic filtering narrowed the field to 190 enzymatic candidates and finally to a shortlist of 54 for heterologous production, spanning glycoside hydrolases, polysaccharide lyases, lipases, esterases, nucleases and proteases.

Three representative glycoside hydrolases were then expressed recombinantly in Escherichia coli and characterised biochemically in sodium carbonate buffer at pH 10. AsGH16, a multidomain family 16 enzyme carrying three carbohydrate-binding modules and a Por secretion system sorting domain, was confirmed as an endo-beta-1,3-glucanase that cleaves paramylon and yeast beta-glucan into laminaritriose, laminaribiose and glucose, with reduced activity on branched substrates due to steric hindrance. AsGH26, a family 26 enzyme, proved to be an endo-beta-1,4-mannanase active on ivory nut mannan, carob galactomannan and glucomannan. AsGH9, a family 9 enzyme from a separate PUL, showed activity on mixed-linkage lichenan and tamarind xyloglucan, releasing glucose and glucobiose. Notably, AsGH16 retained 60 percent of its activity at pH 9 to 10, and AsGH26 retained a striking 83.8 percent at pH 10, reflecting broadened pH-activity profiles rather than shifted optima, a hallmark of enzymes from environments with fluctuating pH.

AlphaFold3-based structural modelling revealed the molecular basis of this alkaline resilience. All three enzymes displayed an increased prevalence of negatively charged residues on their solvent-accessible surfaces, with folded net charges at pH 10 ranging from minus 7.46 to minus 10.98 per 100 amino acids, a conserved electronegativity thought to stabilise proteins in extreme alkalinity. Beyond surface charge, each enzyme appeared to employ a partially distinct stabilisation strategy. AsGH26 combined the highest hydrogen bond density, 104.7 per 100 residues, with the most tightly packed hydrophobic core and the smallest internal cavity volume. AsGH16 showed the most pronounced lysine depletion, at just 1.7 percent of its mature sequence, suggesting electrostatic strategies and core reinforcement can operate independently. AsGH9, the only enzyme with a disulfide bond, displayed weaker hydrophobic packing and a large internal cavity, consistent with its more neutral pH profile.

The decisive test came through the wash. In automated tergotometer trials mimicking real laundering conditions, each enzyme was spiked at just 2 parts per million into commercial detergents. AsGH16 added to a heavy-duty granular detergent at pH 10.5 delivered a statistically significant 10 percent improvement in make-up stain removal compared with a nil-enzyme control. AsGH26 improved removal of mannan-containing food stains, including chocolate pudding, chocolate ice cream, balsamic salad dressing and guar gum soils, in both heavy-duty liquid detergent at pH 8 and heavy-duty granular detergent at pH 10.5, with significant effects on chocolate stains in both matrices. AsGH9, meanwhile, tackled a different problem: soil redeposition. In multi-cycle washing with particulate carbon black, cotton fabrics washed with AsGH9 retained a whiteness index of minus 32.0, against minus 58.8 for detergent alone, a visible and quantifiable preservation of fabric whiteness across repeated washes.

Enzymes have already revolutionised laundering by enabling effective cleaning at lower temperatures, reducing energy demand and fossil fuel use. Yet the extreme alkalinity of modern detergent matrices has long limited which biocatalysts can be deployed, since most commercial enzymes derive from mesophilic organisms. Previous alkaliphilic cellulase producers, such as Bacillus strains KSM-19, KSM-64 and KSM-520, have been exploited for detergents but remain largely confined to cellulase activity. In contrast, A. saponilacus combines metabolic versatility across multiple complex carbon sources with a diverse repertoire of more than 50 predicted secreted enzymes, positioning it not only for detergent applications but potentially also for paper pulping, lignocellulosic biomass deconstruction and the treatment of alkaline industrial effluents, all processes where robust activity at high pH is prized.

The study’s authors conclude that Alkalitalea saponilacus stands as an excellent natural source of alkaline-stable, detergent-compatible enzymes, validated at every level from genome and gene expression through protein structure to in-wash performance. The compatibility of AsGH9, AsGH16 and AsGH26 with the surfactants, builders and carbonate concentrations of real formulations, together with their broad functional pH ranges, suggests these soda lake adaptations could soon find their way from one of Earth’s harshest aquatic environments into the washing machines of everyday consumers, while deeper exploration of the world’s soda lakes may yield further extremophilic catalysts waiting to be discovered.

Subject of Research: Alkaline-tolerant glycoside hydrolases from the soda lake bacterium Alkalitalea saponilacus with detergent biotechnology applications

Article Title: Exploration of Alkaliphilic Bacteria Alkalitalea saponilacus Identifies Glycoside Hydrolases With Biotechnological Potential

Article References: Exploration of Alkaliphilic Bacteria Alkalitalea saponilacus Identifies Glycoside Hydrolases With Biotechnological Potential. (n.d.). https://doi.org/10.1111/1751-7915.70448

Image Credits: AI Generated

DOI: 10.1111/1751-7915.70448

Keywords: Alkalitalea saponilacus, soda lakes, Soap Lake, extremophiles, glycoside hydrolases, CAZymes, alkaliphilic bacteria, detergent enzymes, polysaccharide utilisation loci, biotechnology, stain removal, protein stability

Lignocellulose is simultaneously one of the most abundant organic materials on Earth and one of the most stubborn to break down. Its two dominant carbohydrate components, cellulose and hemicellulose, differ sharply in architecture. Cellulose consists of long, linear chains of glucose that pack into crystalline microfibrils, while hemicellulose is a branched, chemically heterogeneous tangle of hexose and pentose sugars decorated with side groups such as arabinose and acetyl esters. Any organism hoping to feast on plant biomass must therefore deploy a correspondingly diverse arsenal of carbohydrate active enzymes, or CAZymes, including glycosyl hydrolases that cleave sugar backbones, carbohydrate esterases that strip off side groups, and carbohydrate-binding modules that tether the catalytic machinery to its insoluble target. Understanding which enzymes a bacterium makes, and when it makes them, is central to harnessing it for consolidated bioprocessing, a strategy in which a single organism both degrades biomass and ferments the resulting sugars into fuel.

To probe this capability, the team grew three strains of T. thermosaccharolyticum on a panel of carbohydrates ranging from simple hexoses and pentoses to complex hemicellulosic polysaccharides, then used liquid chromatography–tandem mass spectrometry to quantify the proteins each condition induced. The growth assays revealed a broad substrate palette, confirming that the species can metabolize a wide variety of sugars and oligosaccharides. But the proteomic data told a subtler story: the strains differed substantially in both the abundance of CAZymes they produced and their actual ability to grow on particular polysaccharides. This strain-to-strain variation matters for anyone hoping to select or engineer an industrial chassis, because the ability to digest a substrate on paper does not guarantee that a given isolate will express the right enzymatic toolkit at the right levels.

One of the clearest signals in the dataset emerged when the researchers compared global proteomic responses during growth on hexoses versus pentoses. Cells feeding on pentose sugars, the five-carbon building blocks liberated from hemicellulose, mounted a far stronger expression of proteins dedicated to handling hemicellulose-derived carbohydrates. The authors interpret this as a molecular reflection of structural reality: hemicellulose is more architecturally complex than cellulose, so liberating and metabolizing its sugars demands more enzymatic and transport machinery. For biorefinery design, this suggests that hemicellulose utilization is a distinct physiological program that can be studied, and potentially optimized, independently of cellulose degradation.

Perhaps the most surprising finding concerned arabinose, a pentose that constitutes only a minor fraction of lignocellulose. Despite its modest abundance in plant biomass, arabinose drove elevated CAZyme production at levels comparable to those triggered by complex hemicellulose-derived carbohydrates. In other words, this seemingly minor sugar acts as a powerful regulatory cue, essentially telling the bacterium that hemicellulose is nearby and prompting it to ramp up its degradative apparatus. Such a counterintuitive response hints that T. thermosaccharolyticum uses arabinose as an environmental signal, a strategy that could be exploited to induce enzyme production in industrial fermentations without relying on expensive complex substrates.

The centerpiece of the study, however, is the identification of two polysaccharide utilization loci, or PULs, in this Gram-positive thermophile. PULs were first characterized in gut Bacteroidetes, where they appear as clustered gene sets that coordinate the sensing, import and stepwise degradation of specific polysaccharides. Finding analogous systems in a thermophilic Gram-positive anaerobe is notable; the authors report these as among the first such loci described in thermophilic anaerobes, and they term them gpPULs, for Gram-positive polysaccharide utilization loci. Each gpPUL bundles together the genes encoding CAZymes, sugar transporters and regulatory proteins needed to attack a particular class of hemicellulosic substrate, providing a self-contained module for polysaccharide harvesting.

By measuring proteomic responses across multiple carbohydrates and multiple strains simultaneously, the team could correlate specific enzyme and transporter expression patterns with growth outcomes, allowing them to delineate the boundaries and contents of the two gpPULs and to assign functions to genes whose roles had previously been uncertain. The loci include glycosyl hydrolases targeting xylan backbones, enzymes that process arabinose side chains, carbohydrate-binding modules that recognize the insoluble substrate, and transport systems that funnel the liberated oligosaccharides into the cell. Building on this map, the researchers constructed a model describing how T. thermosaccharolyticum deploys these components to degrade hemicellulose at elevated temperature, from initial substrate recognition through extracellular cleavage to intracellular sugar metabolism.

The thermophilic nature of the organism adds practical weight to these findings. Running industrial bioprocessing at high temperatures offers real advantages: reduced risk of contamination by mesophilic microbes, improved solubility and kinetics of substrates, and easier recovery of volatile products. A thermophile with a well-characterized, genetically defined system for hemicellulose degradation is therefore an attractive platform for consolidated bioprocessing of lignocellulosic feedstocks. Moreover, because the gpPULs are organized as discrete gene clusters, the authors suggest that the identified genes could be transferred into other species to extend their substrate ranges, a form of synthetic biology that could broaden the menu of biomass components that engineered microbes can convert into fuels and chemicals.

The work also speaks to questions beyond the bioreactor. Saccharolytic bacteria play significant roles in human health and in the cycling of carbon through the environment, and the regulatory logic uncovered here, in which minor sugars act as major inducers of degradative machinery, may illuminate how microbial communities partition plant material in soils and guts alike. As the authors note, the study advances understanding of saccharolytic species both in applied settings such as biofuel production and in the biosphere at large. With the genetic blueprints of two thermophilic gpPULs now in hand, researchers have a concrete starting point for engineering faster, more complete conversion of plant waste into renewable energy, turning one of nature’s most recalcitrant materials into a feedstock for the bioeconomy.

Subject of Research: Proteomic characterization of lignocellulosic carbohydrate utilization and polysaccharide utilization loci in the thermophilic bacterium Thermoanaerobacterium thermosaccharolyticum

Article Title: Proteomics and characterization of lignocellulosic carbohydrate utilization for Thermoanaerobacterium thermosaccharolyticum reveals two thermophilic Gram-positive polysaccharide utilization loci

Article References: Stephens, K., Davin, M. E., Giannone, R. J., Bomble, Y. J., Lynd, L. R., Holwerda, E. K., & Hettich, R. L. (2026). Proteomics and characterization of lignocellulosic carbohydrate utilization for Thermoanaerobacterium thermosaccharolyticum reveals two thermophilic Gram-positive polysaccharide utilization loci. Biotechnology for Biofuels and Bioproducts. https://doi.org/10.1186/s13068-026-02822-x

Image Credits: AI Generated

DOI: 10.1186/s13068-026-02822-x

Keywords: Thermoanaerobacterium thermosaccharolyticum, polysaccharide utilization loci, CAZymes, lignocellulose, hemicellulose, biofuels, proteomics, thermophilic anaerobe, consolidated bioprocessing, arabinose, sugar transporters, anaerobic fermentation