The research combined descriptions of fresh and dried specimens with DNA sequence analysis. Macroscopic observations covered basidioma, habitat and associated vegetation, while microscopic measurements examined spores, basidia, cystidia and tissue structures. The researchers amplified and sequenced the nuclear ribosomal internal transcribed spacer and large-subunit regions and generated 20 nrITS and eight nrLSU sequences.

The combined nrITS and nrLSU dataset contained 77 sequences and 1,838 characters. Maximum-likelihood and Bayesian analyses produced the same tree topology. Four well-supported main clades were recovered within H. subgenus Hygrocybe, designated /acutoconica, /appalachianensis, /conica and /hypohaemacta, and the new taxa occurred in each of these lineages.

H. perdomoi was placed in the /acutoconica clade, H. jarabacoensis in the /appalachianensis clade, and H. citrinonigrescens, H. parabolica and H. xerophila in the /conica clade. H. pseudohypohaemacta and H. variecolor were assigned to the /hypohaemacta clade. The study used Hygroaster albellus and Hygroaster sp. identified as H. nodulisporus as outgroup taxa.

The seven new species were supported by combinations of macroscopic, microscopic and ribosomal-sequence differences. H. citrinonigrescens has a vivid lemon-yellow pileus and blackens strongly with age or handling. H. jarabacoensis has greenish to reddish-green coloration, a long stipe and strongly dimorphic spores and basidia. H. parabolica is small and orange-red, with a parabolic pileus and slow, faint blackening. H. perdomoi has slimy-viscid basidiomata and differs from H. acutoconica in size, surface features and spore shape.

H. pseudohypohaemacta has scarlet-red or orange coloration, a yellow pileus margin, a thick transparent glutinous layer on the stipe, and dimorphic spores and basidia. H. variecolor also has dimorphic spores and basidia, but differs in habitat, spore dimensions and shape, the rarity of pseudocystidia, and ribosomal-sequence divergence. The authors considered it possibly rare globally, but emphasized that it was represented by one collection and that further collections may reveal greater variation.

The new Florida variety, H. xerophila var. floridana, differs from the Dominican type variety in its redder pileus, larger macrospores, smaller microspores, geographic range and a single-nucleotide polymorphism in the ITS region. Despite these micromorphological differences, the Dominican and Florida collections did not separate clearly in the phylogenetic analyses and differed by only three nucleotides in nrITS, leading the authors to treat them as varieties of one species.

Several limitations constrain the findings. Some newly described species were represented by few collections, and the authors stated that additional material may clarify their variation. An unclassified Dominican specimen morphologically overlapping H. pseudohypohaemacta had a low genetic distance but a comparatively high proportion of gaps, so its taxonomic status remains uncertain pending further collections and sequences. The study also excluded previously published Belize sequences attributed to H. hypohaemacta because they showed high similarity to Termitomyces sequences and were interpreted as contaminants.

Subject of Research: Taxonomic and phylogenetic characterization of Hygrocybe subgenus Hygrocybe in the Dominican Republic

Article Title: The genus Hygrocybe subgenus Hygrocybe in the Dominican Republic: phylogeny, diversity, and description of seven novel species and one variety ( Agaricomycetes , Hygrocybaceae )

Article References: Dovana, F., Angelini, C., Lodge, D. J., Marchetti, M., & Vizzini, A. (2026). The genus Hygrocybe subgenus Hygrocybe in the Dominican Republic: phylogeny, diversity, and description of seven novel species and one variety (Agaricomycetes, Hygrocybaceae). IMA Fungus, 17, Article e195850. https://doi.org/10.3897/imafungus.17.195850

Image Credits: AI Generated

DOI: 10.3897/imafungus.17.195850

Keywords: Hygrocybe, waxcap fungi, fungal taxonomy, phylogenetics, ITS sequencing, LSU sequencing, mushroom morphology, Dominican Republic, Caribbean biodiversity, new species, genus, subgenus

The specimens were gathered during macrofungal fieldwork in the Yarlung Zangbo Grand Canyon National Nature Reserve in Xizang and border counties of Yunnan. Researchers examined macroscopic and microscopic features, including the cap, gills, stem, basidiospores, basidia, marginal elements and pileipellis. Dried material was mounted in 5% potassium hydroxide for microscopy, with Congo red used to facilitate observation, while scanning electron microscopy was used to examine spore ornamentation. The specimens were deposited in the Herbarium of Cryptogams of the Kunming Institute of Botany, Chinese Academy of Sciences.

DNA was extracted from the fruiting bodies, and the nuclear ribosomal internal transcribed spacer region, ITS, and nuclear ribosomal large subunit region, nrLSU, were amplified and sequenced. The dataset contained 64 sequences representing 22 species: eight newly generated sequences and 56 sequences downloaded from other sources. It included 54 ITS and 10 nrLSU sequences and produced a combined alignment of 1,555 characters, including gaps.

Maximum-likelihood and Bayesian phylogenetic analyses yielded similar tree topologies, and both new species clustered within section Telamonia. Section Tragani was selected as the outgroup. The authors considered the placements consistent with several diagnostic section-level traits, including weakly hygrophanous caps with dense fibrillose squamules, fibrous-scaly stems, white to dirty-white veils that can form a ring, moderately verrucose ellipsoid to amygdaliform spores, and a duplex pileipellis. Some placements had relatively low bootstrap support.

Cortinarius linzhiensis was represented by a holotype collected at 3,420 meters in a mixed forest of Quercus aquifolioides and Picea likiangensis var. linzhiensis in Lulang Town, Linzhi City, and by an additional specimen from Picea-dominated forest at 3,815 meters. Its medium-sized fruiting bodies have caps 40–90 millimeters wide that are light brown to dark brown, wrinkled, weakly hygrophanous and densely covered with fibrillose squamules. The cap margin can crack halfway up the cap and bears grayish-white, spiderweb-like veil remnants.

The C. linzhiensis stem is dirty white, sometimes with a pale purple tint at the apex, and bears brown fibrillose squamules and a pale yellow ring. Its basidiospores measured (8–)8.5–10(–11) × 5.5–7(–7.5) micrometers, with a mean length-to-width ratio of 1.47 ± 0.08. The pileipellis has a weakly developed epicutis 15–45 micrometers thick. Phylogenetic analysis placed the species as sister to C. lijiangensis, although with moderate bootstrap support. By comparison, C. lijiangensis has a maroon cap and stem, an evanescent arachnoid annulus and a thicker epicutis of 140–230 micrometers.

The two C. linzhiensis collections differed by two nucleotide substitutions and insertion–deletion sites in their ITS sequences, as well as in cap color and pigmentation of the stem apex. The authors interpreted these differences as intraspecific variation associated with differences in altitude and host-forest environment rather than as diagnostic characters, and therefore treated the collections as conspecific.

Cortinarius pallidomarginatus was collected at 1,770 meters in a broad-leaved forest dominated by Castanopsis, Lithocarpus and Cyclobalanopsis in Houqiao Town, Tengchong City, Yunnan. Its 40–60-millimeter cap is weakly hygrophanous and reddish brown, with a white margin, reddish-brown spiderweb-like veil remnants and dense fibrillose squamules. Its gills are reddish brown, and its stem is light reddish brown. Basidiospores measured (8–)8.5–10 × (5.5–)6–7 micrometers, with a mean length-to-width ratio of 1.43 ± 0.06, and were brown in potassium hydroxide with moderately verrucose ornamentation.

Phylogenetic analysis placed C. pallidomarginatus in a sister clade to a misidentified C. torvus-like lineage, with low bootstrap support, and showed it as closely related to C. subionophyllus and C. ultimiionophyllus. Morphologically, its reddish-brown cap with a white margin distinguishes it from those two species, which have grayish-purplish-brown to ochraceous-brown caps without white margins. The analysis also exposed unresolved taxonomy within Telamonia: some sequences labeled C. torvus formed separate clades, including one clustering with C. tigrinipes, indicating possible misidentification or misapplication of the name.

Because many published reference species of section Telamonia lack publicly available sequences for the protein-coding loci RPB1, RPB2 and TEF1-α, the researchers selected ITS plus nrLSU for the primary reconstruction to maximize taxon coverage. Newly obtained sequences for the three protein-coding loci provided supplementary evidence for the independent evolutionary status of the new species. The conclusions remain bounded by a sample of only four specimens, relatively low bootstrap support for some placements, and limited availability of high-resolution reference sequences.

Subject of Research: Integrative taxonomy of two new Cortinarius section Telamonia species from southwestern China

Article Title: Integrative taxonomy reveals two new species of Cortinarius section Telamonia ( Cortinariaceae , Agaricales ) from southwestern China

Article References: Li, T.-S., Zhang, Y., Yang, Y.-Y., Guan, H.-B., Wu, F., & Zhao, Q. (2026). Integrative taxonomy reveals two new species of Cortinarius section Telamonia (Cortinariaceae, Agaricales) from southwestern China. MycoKeys, 138, 149-162. https://doi.org/10.3897/mycokeys.138.186765

Image Credits: AI Generated

DOI: 10.3897/mycokeys.138.186765

Keywords: Cortinarius, Telamonia, fungal taxonomy, new species, mushroom morphology, ITS sequencing, nrLSU sequencing, phylogenetics, Xizang, Yunnan, Integrative, taxonomy

Passal. & Sicoli. The paper is a taxonomic combination rather than a new field discovery or a fresh molecular analysis: it places an existing species within a genus delimited using morphological and molecular evidence. The species was originally described from southern Italy and subsequently reported from Belgium, while a later record was also made in Thailand.

When P. cladii-marisci was described, its placement in Psathyrella rested on a combination of macroscopic and microscopic characters. The reported basidiomata were small to medium-sized, thin, fragile and non-deliquescent, with grayish to pale clay-colored or deep brown surfaces. Lamellae formed the hymenium, and the basidiospores were described as smooth, truncated and dark.

Versiform hymenial cystidia occurred together with sphaeropedunculate and clavate cells along the gill edge. These features supported assignment to the broad genus concept of Psathyrella used at the time, but the authors now regard that concept as overly broad and superseded. The decisive taxonomic framework came from a 2020 study led by Wächter and Melzer, which combined morphological and molecular evidence to refine Psathyrella sensu lato.

That work divided the former broad concept into three genera: Britzelmayria , Candolleomyces and Olotia . Some species previously classified in Psathyrella were transferred to these newly delimited groups. A 2021 report on two new Candolleomyces species from China proposed a molecularly informed combination for the Italian taxon on the basis of internal transcribed spacer, or ITS, sequence analysis.

A subsequent Thai record was identified using morphology together with ITS and large-subunit, or LSU, ribosomal DNA evidence, further supporting recognition of the species within Candolleomyces . The new combination also corrects a problem in the name’s publication history. The earlier proposed Candolleomyces combination was based on Psathyrella cladium-mariscii , but that name had been invalidly published because its protologue did not cite an identifier issued by a recognized repository, as required under the relevant botanical naming rules.

The attempted combination was consequently invalid as well. In 2022, Sicoli and colleagues validly published Psathyrella cladii-marisci , integrating corrections to the original description with additional information from the European detection. By basing the present combination on that validly published name, the authors establish Candolleomyces cladii-marisci as the appropriate name under the revised generic classification.

The change therefore resolves both the broader placement of the species and the technical defect affecting the earlier name. The holotype documents the species’ type locality in Calabria, southern Italy. It was collected on 10 April 2018 by Antonio Biagio De Giuseppe and Giovanni Sicoli in a marsh at the base of cut culms of Cladium mariscus at the Orto Botanico Università della Calabria in Rende, Cosenza.

The plants had been transplanted from Lago dell’Aquila in Laureana di Borrello, Reggio Calabria. The site is specified at 39°21′25.05″ north, 16°13′44.57″ east and 220 metres above sea level, at the corner of a concrete tank maintained full of water. The holotype is deposited as CLU F302.

Subject of Research: Nomenclatural transfer of Psathyrella cladii-marisci to the morphologically and molecularly refined genus Candolleomyces

Article Title:  Candolleomyces cladii-marisci ( Psathyrellaceae ), a new combination

Article References: Passalacqua, N. G., & Sicoli, G. (2022). Candolleomyces cladii-marisci (Psathyrellaceae), a new combination. Italian Botanist, 14, 95-97. https://doi.org/10.3897/italianbotanist.14.96281

Image Credits: AI Generated

DOI: 10.3897/italianbotanist.14.96281

Keywords: fungal taxonomy, Candolleomyces, Psathyrella, Psathyrellaceae, new combination, ITS sequencing, LSU sequencing, botanical nomenclature, Cladium mariscus, wetland fungi, cladii-marisci, combination

The research team, led by Leonardo Zamora-Leiva of the Bionostra Chile Research Foundation together with colleagues at Universidad Andrés Bello and the University of Chile, sampled a trial established in 1998 at the Sugar Cane Research Institute in Santiago de Cuba. The experiment spans eleven fertilizer treatments varying nitrogen, phosphorus, and potassium, from plots receiving no nitrogen at all to those receiving very high doses of a single macronutrient. Because the fertilization regimes assigned to each plot have been maintained without interruption since the trial began, the soils sampled in 2022 carry the cumulative legacy of 24 years of continuous nutrient management, making the site an unusually clean natural laboratory for asking how sustained inputs shape the rhizosphere microbiome.

Using high-throughput sequencing of the bacterial 16S rRNA gene and the fungal internal transcribed spacer region, the researchers identified 421 bacterial and 471 fungal genera from 5,741 amplicon sequence variants across the treatments. The dominant bacterial phyla were Actinomycetota, Pseudomonadota, and Acidobacteriota, which together accounted for roughly 60 percent of relative abundance, while fungal communities were overwhelmingly dominated by Ascomycota, which exceeded 69 percent across all plots. These core lineages appeared in similar proportions regardless of whether a plot had been drenched in nitrogen for decades or left without it, and statistical tests for differences in alpha and beta diversity, along with differential abundance analyses using LEfSe and ANCOM-BC2, found no significant treatment effects on community composition.

The physicochemical data help explain why. Soil pH remained nearly constant across the site, ranging from 6.4 to 6.5 in potassium chloride and 7.7 to 7.9 in water, a stability the authors attribute to the massive buffering capacity conferred by consistently high reservoirs of exchangeable calcium and magnesium. Organic matter, available phosphorus, and potassium varied among plots, but those variations did not align with the theoretical fertilizer doses. The team argues that intense tropical rainfall and the leaching-prone clay matrix of sialitic soils, which are classified internationally as inceptisols or Cambisols, rapidly redistribute applied nutrients, homogenizing bulk soil chemistry and decoupling what farmers apply from what microbes actually experience.

Where the study becomes genuinely striking is in its network analysis. Rather than treating the bacterial and fungal datasets separately, the authors merged them into a single trans-domain co-occurrence network of 371 nodes and 747 edges, retaining only robust correlations with a Spearman coefficient above 0.6 and a false-discovery-rate-adjusted p-value below 0.01. The resulting architecture was highly modular, organized into 48 distinct structural modules, and overwhelmingly positive in sign: 99.8 percent of the correlations were cooperative or commensal rather than competitive. Fungal taxa, particularly Ascomycota and Basidiomycota, showed higher connectivity than bacteria, suggesting that fungi form the structural backbone of the rhizosphere interaction web in these soils.

Within that architecture, the vast majority of amplicon sequence variants, about 95 percent, behaved as peripheral nodes, while a small subset of highly connected connectors and module hubs, including taxa related to Pseudomonas, Steroidobacter, Gaiella, and Streptomyces, appeared to stabilize the whole system. A substantial fraction of the interacting taxa remained taxonomically unclassified, a reminder that tropical and Caribbean soil microorganisms are poorly represented in reference databases such as SILVA and UNITE. The authors suggest these unresolved lineages may include endemic or highly specialized microbes that contribute to the unique functioning of nutrient-leached tropical soils, and they call for expanding genomic reference databases to cover such environments.

The most ecologically revealing result came from an overlap analysis of which microbes appear under which fertilization regime. By intersecting presence-absence matrices across treatments, the team identified a universal core of 76 amplicon sequence variants shared across every nitrogen, phosphorus, and potassium gradient, a trans-domain alliance built on bacterial Bacillota and Pseudomonadota and fungal Ascomycota including genera such as Fusarium and Cladophialophora. This core appears to be the stable foundation of the sugarcane rhizosphere, resistant to profound nutritional fluctuations. Beyond it, each macronutrient recruited its own distinct satellite community: nitrogen variation recruited 18 exclusive specialists, predominantly fungal, while phosphorus addition recruited a much larger accessory cohort of 40 unique variants, heavily dominated by fungi including Talaromyces and various Basidiomycota. Potassium produced the most restricted response, with only six strict specialists.

This core-and-satellite assembly strategy has direct agronomic implications. Yield records from the trial show that fertilized plots consistently outperform unfertilized controls, but that yields plateau across a wide range of NPK doses, with the highest nitrogen treatments actually producing the lowest yields among fertilized plants. The new microbial data offer a possible explanation: once the universal core is in place, additional nutrients do not restructure the community but instead selectively recruit specialized accessory taxa to exploit available resources. Fertilization, in other words, may influence soil functioning by modulating specialized ecological niches rather than through broad taxonomic turnover, which is why diversity-based monitoring alone can miss the ecological consequences of management decisions.

The authors argue that trans-domain interaction networks provide crucial insights into how soils respond to long-term fertilization that are not evident from diversity or abundance data alone. In tropical sialitic soils, where leaching and rapid nutrient turnover render bulk chemistry erratic, physically protected rhizosphere microhabitats, formed by roots, fungal hyphae, and bacterial extracellular polymers, appear to act as ecological refuges that preserve microbial organization. Sustainable fertilization strategies, the study concludes, should aim to support these foundational microbial architectures while optimizing nutrient inputs, rather than assuming that more fertilizer simply means more of everything below ground. For sugarcane producers in Cuba and other tropical systems, the message is that the invisible network around the roots may matter as much as the nutrients themselves.

Subject of Research: Effects of long-term NPK fertilization regimes on sugarcane rhizosphere microbial diversity and bacterial-fungal co-occurrence networks in tropical sialitic soils

Article Title: Fertilizer regimes reshape microbial interaction networks without altering sugarcane rhizosphere diversity

Article References: Zamora-Leiva, L., Soto, J., Ramos-Tapia, I., & Paneque, M. (2026). Fertilizer regimes reshape microbial interaction networks without altering sugarcane rhizosphere diversity. SOIL, 12(2), 999-1019. https://doi.org/10.5194/soil-12-999-2026

Image Credits: AI Generated

DOI: 10.5194/soil-12-999-2026

Keywords: sugarcane, rhizosphere, soil microbiome, fertilization, co-occurrence networks, 16S rRNA, ITS sequencing, Ascomycota, nutrient leaching, inceptisols, tropical agriculture, soil ecology

The research focused on timber elements removed during the bridge’s most recent renovation in the autumn of 2025, when workers from the Skellefteå Municipality replaced roadway and frame sections that showed visible signs of rot. Because the bridge has been a state-protected architectural monument since 1994 and cannot be rebuilt, moved, or fundamentally altered, conservationists face a peculiar challenge: they must monitor and maintain a living piece of history without destroying the very fabric that makes it precious. Destructive sampling is severely restricted, which means that much of the internal damage to such structures historically went undetected until it became catastrophic.

Enter X-ray computed tomography, or CT scanning, the same non-invasive technology developed for medical diagnostics that has more recently transformed wood science. The team used a Microtec Mito scanner equipped with a cone-beam X-ray source to peer inside the removed bridge timbers at a spatial resolution of half a millimetre per voxel. What they saw was striking. In three-dimensional reconstructions processed with Python and visualised in 3D Slicer, intact wood could be clearly distinguished from decayed regions by density alone. Sound wood measured approximately 600 kilograms per cubic metre, while degraded zones dropped to around 450. In one particularly damaged specimen, the heartwood around the pith had decayed so completely that a central cavity had formed, and surrounding density fell to just 330 kilograms per cubic metre against roughly 520 in adjacent sound tissue.

The CT images did more than quantify the damage; they told a story about how it developed. Density gradients along the longitudinal sections suggested that decay had initiated at one end of the timbers and progressed inward, most likely accelerated by long-term moisture exposure. The scans even revealed an unexpected accomplice: a metal nail embedded deep within one timber, whose presence may have drawn moisture into the wood through suction from the end-grain, creating a localised microenvironment ideal for fungal colonisation. Crucially, the degraded regions corresponded to areas showing the classic fingerprints of brown rot, including cubical cracking, where the wood shrinks and fractures into small, brittle, cube-like chunks as its structural polymers are dismantled.

Brown rot is among the most destructive forms of fungal decay in conifer timber. Unlike white-rot fungi, which enzymatically degrade all major cell-wall components including the tough lignin, brown-rot fungi primarily depolymerise cellulose and hemicellulose through a combination of oxidative and enzymatic mechanisms, leaving behind modified lignin residues and wood that has lost most of its mechanical strength. Because this degradation often begins deep inside a beam long before any external symptom appears, traditional visual inspection frequently fails. The density loss documented by the Swedish team demonstrates precisely why non-destructive imaging is becoming indispensable for heritage structures: externally, some of these timbers showed only limited visible damage while harboring extensive internal deterioration.

To identify which organisms were responsible, the researchers turned to culture-based microbiology. Wood fragments were separated from timber sections 50 millimetres beyond visible damage edges, surface-sterilised with sodium hypochlorite and ethanol, and placed on malt extract agar in controlled laboratory chambers. In a clever methodological refinement, additional fragments were briefly flame-sterilised to suppress fast-growing surface moulds, a step that proved essential for recovering slow-growing decay fungi that would otherwise be overrun. The team also hunted microscopically for clamp connections, distinctive loop-like structures on hyphae that betray basidiomycete identity. The result was a library of 37 pure fungal cultures representing 17 species across 11 genera, identified by amplifying and Sanger-sequencing the internal transcribed spacer (ITS) region of fungal DNA and comparing the sequences against the GenBank database, with sequences deposited under accession numbers PZ161136 through PZ161152.

Most of the recovered species were saprotrophs, moulds, and wood-associated ascomycetes typical of weathered timber, including multiple species of Trichoderma and Penicillium, along with Aureobasidium pullulans, Mucor circinelloides, Apiospora arundinis, and Sydowia polyspora. These are largely secondary colonisers, opportunists exploiting the nutrient-rich niches created as decomposition advances. Trichoderma colonies, in particular, grew so aggressively in the laboratory that they blanketed culture plates within three to four days. But the headline discovery involved two basidiomycetes found in association with the brown-rot symptoms: Amyloporia xantha, isolated seven times and the most frequently recovered basidiomycete, and a single isolate of Crustoderma sp., which could not be pinned down to species level with the ITS marker alone.

Amyloporia xantha is a well-recognised conifer-associated brown-rot fungus with a documented track record of degrading structural timber across northern Europe. Surveys in Norway have found this genus affecting roof and wall constructions, roof beams, and exterior structures, while a study of historic pre-1945 buildings in Styria, Austria, identified it in more than ten percent of cases, second only to the notorious dry-rot fungus Serpula. Its frequent recovery from the Lejonström timbers strongly suggests it is a principal driver of the bridge’s brown rot. The detection of Crustoderma adds an intriguing ecological wrinkle: many species in this genus are rare and of conservation interest, and the most frequently reported Swedish species, Crustoderma corneum, is classified as Near Threatened on the Swedish Red List. Its presence may reflect historic use of heartwood from old-growth forests rather than aggressive invasion, making the bridge something of an ecological time capsule as well as an engineering monument.

Phylogenetic analysis using Maximum Likelihood methods confirmed the picture, separating the ascomycetes, basidiomycetes, and the sole Mucoromycota representative into well-supported distinct lineages, with A. xantha and Crustoderma clustering together within the basidiomycete clade at 96 percent bootstrap support. The researchers acknowledge limitations: relying on a single culture medium likely favoured fast-growing species, and culture-independent metabarcoding could reveal slow-growing or unculturable inhabitants of historic timber. Still, the integrated approach of pairing CT-based structural assessment with molecular fungal identification offers a powerful template for heritage monitoring elsewhere.

The stakes are rising. Climate change is expected to increase temperatures, alter precipitation, and prolong periods of elevated wood moisture across northern environments, conditions that favour fungal growth and colonisation. The coastal climate of Västerbotten County, with relative humidity fluctuating between roughly 65 and 92 percent across the year, already provides ample opportunity for decay organisms. For the Lejonström bridge, which today looks much as it did in the 1870s and still carries automobile traffic, the study delivers both a warning and a toolkit: hidden decay is real, it is progressing, and X-ray tomography combined with fungal DNA sequencing can now catch it early enough to act. As the authors conclude, long-term surveillance of fungal-associated degradation will become increasingly vital for preserving wooden cultural heritage, and monitoring schedules should be tailored to each structure’s environmental exposure and conservation status rather than following a universal inspection interval.

Subject of Research: Brown-rot fungal decay and non-destructive CT monitoring of timber in the historic Lejonström bridge, Sweden

Article Title: Characterisation of brown-rot decay in the historic Lejonström bridge using X-ray tomography and molecular identification of associated fungi

Article References: Postovoitova, A., Lin, C.-F., Davydenko, K., Broman, O., Karlsson, O., & Myronycheva, O. (2026). Characterisation of brown-rot decay in the historic Lejonström bridge using X-ray tomography and molecular identification of associated fungi. npj Heritage Science, 14(1), Article 514. https://doi.org/10.1038/s40494-026-02998-3

Image Credits: AI Generated

DOI: 10.1038/s40494-026-02998-3

Keywords: brown rot, wood decay fungi, X-ray computed tomography, cultural heritage, Lejonström bridge, Amyloporia xantha, Crustoderma, ITS sequencing, Scots pine, timber conservation, mycology, Sweden

The problem CoMeDA addresses begins with the nature of sequencing data itself. When researchers sequence amplicons from a microbial community, the read counts they obtain are inherently compositional: the abundance of each taxon is only meaningful relative to the others, because sequencing depth constrains the total. A species that appears to double in abundance may simply have declined less than its neighbors. Ignoring this compositional structure, the authors note, can produce spurious results in downstream analyses, a pitfall that has been documented repeatedly in the compositional data analysis literature yet is still not consistently handled in widely used microbiome platforms.

Compounding the issue is the batch effect problem. Multi-cohort studies, which combine samples processed at different times, in different laboratories, or on different sequencing platforms, frequently carry technical variation that can masquerade as biological signal. If a disease cohort happens to be sequenced in a different batch than the healthy controls, apparent differences in microbial composition may reflect the sequencing run rather than the disease. Batch effects, if not properly addressed, can confound the very signals researchers are trying to detect. Despite the availability of multiple microbiome analysis platforms, the authors argue, these two analytical considerations have not always been incorporated together as central, user-accessible components of a workflow.

CoMeDA treats the compositional structure of metabarcoding data and batch effects as coordinated components of one analytical pipeline rather than as optional add-ons. The platform accepts both raw FASTQ files and pre-classified taxa tables, making it compatible with short-read and long-read sequencing technologies alike. That flexibility matters as long-read platforms such as PacBio gain traction in microbiome research, since many existing tools were built around short-read data. For the crucial first steps of quality control and taxonomic assignment, users can start from raw reads or jump in with an already classified table.

At the statistical core of the platform is the centered log-ratio transformation, applied as the default normalization strategy. CLR transformation is a standard technique in compositional data analysis: it converts relative abundance data into log-ratios relative to the geometric mean of all taxa in a sample, placing the data in a space where ordinary statistical operations are more defensible. Before the transformation can be applied, however, the platform must contend with zeros, the many taxa that were simply not observed in a given sample. CoMeDA performs zero handling through probabilistic estimation, replacing true zeros with small estimated values so that log-ratios remain computable without distorting the underlying structure.

Once the data are normalized, CoMeDA applies automated batch effect correction that removes technical variation while preserving biological signals. The balance is delicate: overcorrection can erase genuine differences between conditions, while undercorrection leaves artifacts in place. The authors evaluated the behavior of this automated strategy using simulated datasets and a mock community with known ground truth, allowing them to assess how well the correction distinguished technical noise from real biology. They also used these benchmarks to measure the contribution of individual analytical components and the accuracy of taxonomic classification within the pipeline.

Downstream, the platform offers a suite of analyses that all operate within the same compositional framework. Diversity assessment uses compositionally appropriate metrics, and significance testing draws on established methods including PERMANOVA, PERMDISP, and ANOSIM, alongside principal coordinates analysis for visualization. Differential abundance analysis incorporates effect size estimation, and the platform supports approaches such as linear discriminant analysis effect size, robust centered log-ratio methods, and interquartile log-ratio transformations. Co-occurrence network inference and functional prediction, the latter covering both bacterial and fungal communities with reference to resources such as the Kyoto Encyclopedia of Genes and Genomes, round out the workflow. Because every step follows the same compositional logic, the results are internally consistent in a way that pieced-together pipelines often are not.

One of the platform’s more distinctive features is the split-CLR transformation, designed for cross-dataset analyses. When researchers want to combine datasets with different compositional structures, for example to run cross-kingdom correlation analyses linking bacteria and fungi, or paired-condition analyses within the same subjects, directly merging the data can introduce spurious correlations. Split-CLR addresses this by transforming each dataset appropriately before integration, reducing the artificial associations that arise from naive combination. This capability is particularly relevant to studies of polymicrobial diseases, where bacterial-fungal interactions may be clinically important but statistically treacherous to assess.

To demonstrate the platform in practice, the authors reanalyzed three published datasets spanning different study designs and sequencing technologies. A multi-cohort gout dataset allowed them to test batch correction across cohorts, and the analysis recovered biologically coherent patterns while highlighting additional findings supported by the literature, including distinctions related to hyperuricemia. A pediatric Crohn’s disease dataset covering both bacterial and fungal communities exercised the cross-kingdom analysis capabilities. Finally, a PacBio long-read periodontitis dataset confirmed compatibility with long-read data. Across all three, CoMeDA recovered patterns consistent with the original publications while surfacing additional literature-supported findings, suggesting the integrated workflow can add value without discarding established results.

Accessibility is a stated design goal. The platform features an interactive web interface and requires no programming expertise, lowering the barrier for clinical researchers and experimentalists who lack bioinformatics support. The open-source release, published under a Creative Commons Attribution 4.0 license, includes the Docker image for local deployment, an option likely to appeal to institutions handling sensitive clinical data. As microbiome studies grow in scale and increasingly pool cohorts across laboratories, tools that treat compositionality and batch structure as first-class citizens, rather than afterthoughts, may become essential infrastructure. CoMeDA’s authors position their platform as a step in that direction: a compositionally coherent workflow in which normalization, batch correction, and downstream analysis follow a single, consistent analytical logic from raw reads to biological interpretation.

Subject of Research: An integrated web platform for compositional analysis and batch correction of metabarcoding data

Article Title: CoMeDA: an integrated platform for compositional analysis of metabarcoding data with batch correction

Article References: Lee, C.-Y., & Chang, T.-H. (2026). CoMeDA: an integrated platform for compositional analysis of metabarcoding data with batch correction. BMC Bioinformatics. https://doi.org/10.1186/s12859-026-06705-8

Image Credits: AI Generated

DOI: 10.1186/s12859-026-06705-8

Keywords: metabarcoding, microbiome, compositional data analysis, batch effect correction, 16S rRNA, ITS sequencing, CLR transformation, differential abundance, co-occurrence networks, cross-kingdom analysis, bioinformatics software, long-read sequencing

The research team, led by Shaokun Wang and Salman Zare of the Northwest Institute of Eco-Environment and Resources at the Chinese Academy of Sciences, working from the Urat Desert-grassland Research Station, set out to answer a deceptively simple question: how do different grazing intensities reshape the soil microbial communities of desert grasslands, and does the dominant vegetation type, shrubs versus grasses, change that answer? To find out, they sampled soils across six treatment combinations, pairing three grazing regimes, non-grazing, light grazing, and heavy grazing, with two vegetation types, shrub-dominated and grass-dominated plots, in the Inner Mongolian desert steppe.

The methodological backbone of the study was high-throughput sequencing of the 16S rRNA gene for bacteria and the internal transcribed spacer region for fungi, the standard molecular barcodes that allow ecologists to inventory entire microbial communities from a pinch of soil. Rather than stopping at a simple species list, the researchers also constructed co-occurrence networks, statistical maps in which microbial taxa are nodes and significant correlations between their abundances are edges. These networks offer a window into the potential ecological interactions, cooperation, competition, and shared habitat preferences, that structure life below ground, and their architecture is increasingly used as a proxy for ecosystem stability.

What the sequencing revealed first was a familiar cast of characters. The bacterial communities were dominated by the phyla Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, and Chloroflexi, a lineup typical of arid-land soils where rapid-growing copiotrophs and slow, resilient oligotrophs jostle for scarce carbon. On the fungal side, a single phylum, Ascomycota, overwhelmingly dominated, reflecting the capacity of many ascomycete lineages to tolerate drought, exploit plant litter, and persist in harsh, resource-poor conditions. But the real story emerged not from who was present, but from how many were present and how they were connected.

Across the board, heavy grazing eroded microbial diversity. Plots that had never been grazed supported the highest richness, the highest Shannon diversity, and the greatest phylogenetic diversity of soil microbes, meaning they harbored not just more species but a broader evolutionary spread of lineages. Light grazing occupied an intermediate position, while heavy grazing consistently produced the poorest communities. This pattern matters because diversity is widely treated as insurance: communities rich in species and evolutionary history are expected to buffer ecosystems against disturbance, maintain nutrient cycling under stress, and recover more readily after shocks. Stripping away that insurance in already marginal desert soils is a gamble with thin margins.

The network analysis delivered the study’s most striking and counterintuitive result. The most complex bacterial network appeared not in the untouched plots but under heavy grazing in the grass-dominated sites, where the network boasted 62,255 edges, a density of 0.0530, and a complexity index of 43.65. At first glance, that might sound like good news, as if heavy grazing somehow stimulated a richer web of microbial interactions. But the researchers found that this apparent complexity came bundled with reduced stability indicators. In other words, the network had become tangled and densely connected in a way that signals fragility rather than robustness, a crowded switchboard in which the failure of a few key nodes could cascade through the whole system.

This distinction between complexity and stability is the conceptual heart of the paper. Ecologists have long debated whether bigger, denser ecological networks are inherently more stable, and the evidence from Inner Mongolia argues emphatically that they are not. A network can be large and interconnected yet brittle, particularly when that structure arises as a stress response rather than as the product of a mature, well-buffered community. Under heavy grazing pressure, the loss of plant cover, the trampling and compaction of soil, and the depletion of carbon and nitrogen inputs appear to force microbes into a reorganized, densely correlated state, one that may reflect shared stress responses or disrupted niche partitioning rather than healthy mutualism. Complexity, the authors conclude, is not synonymous with stability.

Vegetation type turned out to be a critical modifier of these grazing effects. Shrub-dominated plots partially mitigated the damage that heavy grazing inflicted on the microbial communities. Shrubs, with their deeper roots, woody litter, and ability to trap windblown organic material, create fertile islands beneath their canopies that can sustain microbial populations even when livestock pressure is intense. Grass-dominated communities, by contrast, offered less protection, and it was precisely in the heavily grazed grass sites that the most complex yet least stable bacterial networks appeared. For land managers, this suggests that the composition of the plant community is not a backdrop to soil health but an active participant in it, capable of either cushioning or amplifying the impacts of grazing.

The statistical analyses reinforced how tightly the underground world is coupled to what happens above it. Mantel tests, which measure the correspondence between two distance matrices, revealed strong positive associations between microbial community composition and plant diversity, plant biomass, soil carbon, and soil nitrogen, with Mantel’s r exceeding 0.4 and p-values below 0.001. Pearson correlations painted a consistent picture at the level of individual variables. The message is that microbes are not passive residents of these soils; their diversity and their interaction networks track the plant community and the soil’s chemical fertility almost in lockstep. When grazing degrades plants and depletes carbon and nitrogen, the microbial world degrades with them, and the ecosystem services those microbes provide, decomposition, nutrient mineralization, soil aggregation, are likely to follow.

The practical implications stretch well beyond Inner Mongolia. Desert grasslands cover vast swaths of Central Asia and similar arid regions worldwide, and they support pastoral livelihoods that have persisted for millennia. Yet they are also among the ecosystems most vulnerable to degradation, and the soil microbes that underpin their functioning recover slowly, if at all, once lost. The study’s authors argue that their findings underscore the necessity of sustainable grazing management to preserve soil microbial resilience and ecosystem functioning. Concretely, that means keeping stocking rates within the carrying capacity of the land, rotating livestock to allow recovery periods, and paying particular attention to shrub-dominated patches, which appear to act as refugia for below-ground biodiversity. The invisible economy beneath the steppe, the new research makes clear, can only absorb so much before its tangled connections begin to fray, and once they do, the productivity and stability of the entire grassland hang in the balance.

Subject of Research: Effects of grazing intensity on soil microbial diversity and co-occurrence networks in Inner Mongolian desert grasslands

Article Title: Responses of soil microbial diversity and network complexity to the grazing intensities in grass and shrub dominated desert-grasslands of Inner Mongolia

Article References: Wang, S., Zhao, S., Zhao, X., Liu, L., Zare, S., Qu, H., Ma, X., & Yue, P. (2026). Responses of soil microbial diversity and network complexity to the grazing intensities in grass and shrub dominated desert-grasslands of Inner Mongolia. Plant and Soil. https://doi.org/10.1007/s11104-026-09069-3

Image Credits: AI Generated

DOI: 10.1007/s11104-026-09069-3

Keywords: soil microbiome, grazing intensity, desert grasslands, Inner Mongolia, co-occurrence networks, microbial diversity, 16S rRNA sequencing, ITS sequencing, network stability, shrub encroachment, soil carbon, ecosystem functioning

The dog was referred to the Veterinary Clinic of the Faculty of Veterinary Medicine at the University of Tehran with a striking dermatological picture. It lived outdoors under unsanitary conditions with regular exposure to vegetation and soil, and it presented with diffuse hair loss, marked redness, itching and scaling across the skin of its back. Crucially, there was no ulceration or open wound, no lethargy and no loss of appetite, so systemic illness seemed unlikely and a complete blood count was not performed. The owner declined a skin biopsy, which meant the team could not obtain histopathological evidence of fungal invasion, a detail that would later shape how carefully the conclusions had to be framed. Hair plucks and skin scrapings were collected from the affected areas under sterile conditions and sent to the laboratory for fungal examination.

The initial diagnostic workup followed the standard playbook for suspected dermatophytosis, the superficial fungal infection of keratinized skin that is usually caused by organisms such as Microsporum canis, Microsporum gypseum or Trichophyton mentagrophytes. A Wood’s lamp examination was negative, and a direct microscopic examination of material treated with 10 percent potassium hydroxide also failed to reveal fungal elements. But the story changed when the samples were cultured on Sabouraud Dextrose Agar. After incubation at 28 degrees Celsius, colonies emerged that were creamy-brown and powdery with a colorless reverse surface. Lactophenol cotton blue staining of the growth revealed thin, septate hyphae studded with large, round, warty conidia, a morphological signature that immediately suggested the team was not dealing with a routine dermatophyte.

Seeking to probe the organism’s thermal behavior, the researchers subcultured the colonies onto blood agar and incubated them at 37 degrees Celsius, close to mammalian body temperature, for five days. The fungus produced creamy, dome-shaped, mucoid colonies under these conditions, and Giemsa staining revealed round-to-oval yeast-like cells with budding and point attachments when viewed under oil immersion at 100 times magnification. This dimorphic tendency, the ability to alter its appearance under different growth conditions, added another layer of complexity to the identification. Morphology alone could not settle the question, particularly since members of the family Chaetomiaceae, to which Corynascus belongs, are notorious for overlapping phenotypic features among closely related species. The team therefore turned to the laboratory’s molecular arsenal.

Genomic DNA was extracted from the isolate using a commercial fungal DNA extraction kit, and the internal transcribed spacer region of ribosomal DNA, comprising the ITS1 spacer, the 5.8S rRNA gene and the ITS2 spacer, was amplified with the universal primers ITS1 and ITS4. The polymerase chain reaction protocol began with denaturation at 94 degrees Celsius for three minutes, followed by 37 cycles of denaturation for 30 seconds, annealing at 60 degrees Celsius for 30 seconds and extension at 72 degrees Celsius for 30 seconds, with a final extension of eight minutes. The roughly 600-base-pair amplicon was then sequenced, and the resulting sequence was deposited in GenBank under accession number PV082530, making it publicly available for future comparisons by researchers anywhere in the world.

The sequence told a clear story. BLAST analysis showed 99.36 percent nucleotide similarity to reference sequences of Corynascus verrucosus and 99.34 percent similarity to a reference sequence of Corynascus sepedonium, a closely related species whose ITS region differs only marginally. To resolve the placement further, the researchers aligned their sequence with reference data from GenBank and constructed a maximum likelihood phylogenetic tree in MEGA7 using the Kimura two-parameter model with 1000 bootstrap replicates. The Iranian isolate fell squarely within the broader Corynascus lineage and clustered tightly with C. verrucosus sequences from different geographic regions, while reference sequences annotated as Myceliophthora, including Myceliophthora sepedonium and Myceliophthora verrucosa, occupied the same larger assemblage. The tree was rooted with Amesia atrobrunnea as the outgroup, and the resulting topology was consistent with previously published taxonomic frameworks placing Corynascus within the family Chaetomiaceae.

The taxonomy behind that placement is itself a story of scientific revision. The genus Corynascus comprises seven recognized species, and its boundaries have shifted repeatedly over decades of study, from early work by von Klopotek in 1974 and Stchigel and colleagues in 2000, who described three new thermotolerant species, to a 2015 re-evaluation of Myceliophthora using morphological and multilocus phylogenetic data that affirmed Corynascus as a distinct genus. More recent comprehensive studies have supported that distinction using multigene analyses incorporating ITS, LSU, rpb2, tub2 and tef sequences. Meanwhile, members of the Myceliophthora lineage have attracted industrial attention for their production of thermostable enzymes, and C. verrucosus itself made headlines in 2020 when researchers documented it as a mycoendophyte of Croton bonplandianus and a potential source of bioactive metabolites active against multidrug-resistant pathogens and cancer cells. None of this industrial or pharmacological relevance implies pathogenicity, a distinction the authors are careful to draw.

Where might a pet dog have encountered such a fungus? Environmental studies of composting offer a suggestive clue. Research on organic waste and manure composting has documented substantial shifts in fungal community composition as physicochemical conditions change, with thermophilic and thermotolerant fungi, exactly the ecological guild to which many Corynascus species belong, flourishing in these habitats. Composting environments and similar organic-material settings may therefore serve as reservoirs of environmentally adapted fungal taxa. The Tehran patient’s outdoor lifestyle, unsanitary surroundings and regular contact with soil and vegetation provided ample opportunity for exposure. Still, the authors emphasize that phylogenetic relatedness does not imply shared biological function or pathogenic potential, and that genetic similarity alone should never be read as evidence of a shared disease-causing role.

The clinical narrative, however, lends weight to a genuine association rather than a chance contaminant. The same fungal species was recovered on three independent cultures from the lesion, no bacterial growth was detected, and mite infestation was excluded. The dog was treated with oral ketoconazole combined with ketoconazole shampoo, receiving four weekly medicated baths. The itching and redness resolved within about a month, hair regrowth followed, and a uniform coat had returned approximately six months after treatment began. Over a nine-month follow-up period, the original cutaneous signs never recurred. The combination of repeated isolation, exclusion of other pathogens, molecular identification and clinical improvement following antifungal therapy supports, though it does not prove, a causal link.

That caution about proof is the intellectual heart of the report. Because histopathological examination was never performed, tissue invasion by the fungus could not be demonstrated directly, and the authors explicitly frame the finding as an association rather than definitive evidence of causality. Their broader message concerns method: for uncommon environmental fungi recovered from veterinary specimens, accurate identification demands a polyphasic approach that integrates morphology, ITS sequencing and phylogenetic placement rather than relying on any single line of evidence. Molecular methods can rescue isolates that fail to produce characteristic reproductive structures in culture, but they carry their own biases and limited discriminatory power, as the near-identical ITS sequences of C. verrucosus and C. sepedonium illustrate. By expanding the documented occurrence of C. verrucosus to a canine cutaneous lesion, the case adds a small but genuinely novel data point to veterinary mycology and a reminder that the fungal world’s opportunists may be more numerous, and better camouflaged, than current diagnostics routinely reveal.

Subject of Research: A rare case of cutaneous infection by the environmental fungus Corynascus verrucosus in a Shih Tzu dog, identified through molecular and phylogenetic analysis.

Article Title: A Rare Case of Cutaneous Infection by Corynascus verrucosus in a Shih Tzu Dog: Molecular Identification and Phylogenetic Analysis

Article References: Ghahremani, M., Sharifzadeh, A., Ashrafi Tamai, I., & Faridfar, G. (2026). A Rare Case of Cutaneous Infection by Corynascus verrucosus in a Shih Tzu Dog: Molecular Identification and Phylogenetic Analysis. Veterinary Medicine and Science, 12(5), Article e71205. https://doi.org/10.1002/vms3.71205

Image Credits: AI Generated

DOI: 10.1002/vms3.71205

Keywords: Corynascus verrucosus, veterinary mycology, canine dermatology, fungal infection, ITS sequencing, phylogenetic analysis, Chaetomiaceae, dermatophytosis, Shih Tzu, molecular identification, environmental fungi, ketoconazole treatment