Grapevine health is influenced by microbiome composition, which is affected by region and several plant features such as cultivar, age and rootstock. Grapevine Trunk Diseases (GTDs) are caused by several wood-colonizing fungi, leading to imbalances in microbiome composition. Here, we performed next-generation sequencing of fungal and bacterial microbiomes present in trunk samples of ninety-seven symptomatic grapevines, from two cultivars (cv. Touriga Nacional and cv. Aragonez), collected in eight Portuguese wine-producing regions. The influence of wine-producing regions, grapevine genotype, rootstock, and age was analyzed. Results indicate that microbiome composition is largely influenced by region and cultivar, with more pronounced alterations in cv. Touriga Nacional. Furthermore, relationships between microbes were characterized, revealing that several genera could engage in competitive interactions with the pathogens. We postulate that environmental conditions associated to the wine-producing regions modulate trunk endosphere and microbiome composition. Plant cultivar, age and rootstock also influence the trunk microbiome assembly, leading to distinct taxa composition in the trunk, and also altered microbe relationships.

• Keywords
• Vitis vinifera L, Grapevine trunk diseases, Metabarcoding, Microbiome changes, Next generation sequencing, Trunk endosphere,
• MeSH
• Bacteria genetics   classification   isolation & purification   MeSH
• Genotype MeSH
• Fungi genetics   classification   isolation & purification   MeSH
• Microbiota * genetics   MeSH
• Plant Diseases * microbiology   genetics   MeSH
• Wine MeSH
• Vitis * microbiology   genetics   MeSH
• High-Throughput Nucleotide Sequencing MeSH
• Publication type
• Journal Article MeSH

UNLABELLED: Growing catch crops can improve soil health by enhancing microbial diversity, but their impact may be constrained by how they are managed. This study examined the effects of different catch crop species and soil cultivation methods on bacterial and fungal diversity, and total soil microbial biomass. A 3-year field experiment on Luvi-haplic Chernozem included two catch crop species and five mixtures (further catch crop species) and three cultivation methods (ploughing, reduced tillage and no tillage), resulting in 21 treatments (7 catch crop species x 3 soil cultivations). Soil samples (0–15 cm depth) were collected annually in autumn and spring since 2021 to 2024. Microbial biomass was assessed using the chloroform fumigation extraction method, while fungal and bacterial diversity was analysed by amplifying and sequencing the ITS2 region of rDNA and the V4 region of the 16 S rRNA gene for fungi and bacteria, respectively, via Illumina paired-end amplicon sequencing. Soil cultivation methods affected bacterial diversity, with reduced tillage showing higher diversity and evenness than ploughing, though neither differed from no-till. However, no effect was observed on fungal diversity, including AM fungi, or microbial biomass. Catch crop species did not significantly impact microbial diversity or biomass. Neither cultivation method nor catch crop species influenced the ratios of functional trophic groups, such as pathogens, saprotrophs or symbionts. This study underscores the critical role of soil management practices—especially reduced tillage—in promoting soil health, primarily through the enhancement of bacterial diversity. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-15255-7.

• Keywords
• Fungal and bacterial diversity, Microbial biomass, No-tillage, Ploughing, Reduced tillage, Trophic groups of microorganisms,
• Publication type
• Journal Article MeSH

As part of an ongoing study of marine fungi associated with seagrasses, we discovered a novel root-fungus symbiosis in the Indo-Pacific species Thalassodendronciliatum from Mauritius. Culturing its mycobionts yielded dozens of morphologically and genetically uniform isolates, all representing a previously unknown fungus. A second undescribed fungus was isolated from saline soils in Czechia. Phylogenetic analyses based on three rDNA markers confirmed both taxa as distinct, hitherto unknown lineages within the Lulworthiales, which are introduced here as Thalassodendromycespurpureus gen. et sp. nov. and Halomyrmapluriseptata gen. et sp. nov., respectively. Both species developed characteristic structures under culture conditions that enabled their morphological characterisation: T.purpureus forms distinctive clusters of dark brown monilioid hyphae, while H.pluriseptata is characterised by holoblastic conidiogenesis and solitary, dark brown, multicellular conidia. Thalassodendromyces clustered in a strongly supported clade with Spathulospora, a parasitic genus of the red macroalga Ballia, while the closest relatives of Halomyrma were identified as the asexual genera Halazoon and Halophilomyces (nom. inval. Art. 40.7). An analysis of published metabarcoding ITS rDNA data from environmental samples in the GlobalFungi database indicated that H.pluriseptata is widely distributed across temperate, subtropical, and tropical regions in the Northern and Southern Hemispheres. The species exhibits a strong preference for aquatic biomes, particularly marine and estuarine, with a few records in terrestrial ecosystems. In contrast, no record of T.purpureus was retrieved from GlobalFungi, suggesting narrower ecological specialisation, a close association with its seagrass host, and/or a restricted geographical range. Our findings expand the ecological and phylogenetic scope of the Lulworthiales, bridging marine and terrestrial fungal communities, and highlight seagrass roots as an important source of novel symbiotic marine fungi. Recent discoveries of the Lulworthiales in saline inland soils challenge their marine exclusivity and raise important questions about their ecological plasticity, dispersal mechanisms, and adaptive strategies. In light of current observations, we discuss the taxonomic challenges of the Spathulosporales and the lulworthialean fungi, integrating molecular and morphological perspectives. We address the importance of combining morphological and molecular approaches to accurately delineate new fungal taxa, as well as the value of environmental DNA metabarcoding for uncovering cryptic fungal diversity and enhancing our understanding of fungal distribution and ecological functions.

• Keywords
• Dictyoconidia, Thalassodendron, holoblastic conidiogenesis, marine, monilioid, new taxa, phylogenetics, saprobic, symbiotic,
• Publication type
• Journal Article MeSH

BACKGROUND: Fine woody debris (FWD; deadwood < 10 cm diameter) is a crucial but often overlooked component of forest ecosystems. It provides habitat for microbial communities and enhances soil fertility through nutrient cycling. This role is especially important in managed forests, which typically have limited deadwood stocks. Climate change is increasing forest disturbances and expanding early successional forests with low canopy cover, yet the effects on microbial communities and related processes remain poorly understood. RESULTS: In a ten-year canopy manipulation experiment, we examined the decomposition of FWD of Fagus sylvatica and Abies alba. Increased canopy openness significantly decreased bacterial diversity in decomposing FWD and altered the community composition in surrounding soil. Decomposition time was the main factor shaping bacterial community structure in FWD, with tree species and canopy cover also contributing. We identified bacterial groups involved in carbohydrate degradation, fungal biomass breakdown, and nitrogen fixation. Importantly, bacterial communities in fully decomposed FWD remained distinct from soil communities. CONCLUSIONS: Deadwood decomposition and nutrient cycling are driven by complex ecological interactions. Microbial community dynamics are influenced by the interplay of FWD decomposition stage, tree species, and microclimatic conditions. Bacterial communities, although less frequently studied in this context, appear more stable over time than previously studied fungi. This stability may help sustain decomposition processes and nutrient turnover under the environmental variability associated with global change.

• Keywords
• Bacterial community, Canopy cover, Deadwood, Decomposition, Ecology, Fine woody debris, Microclimate, Succession, Temperate forest,
• Publication type
• Journal Article MeSH

Climate change is altering associations between plants and soil microbiota, threatening ecosystem functioning and stability. Predicting these effects requires understanding how concomitant changes in temperature and precipitation influence plant-soil microbiota associations. We identify the pathways via which temperature and precipitation shape prokaryote and fungal rhizosphere and root-associated networks of the perennial grass Festuca rubra in cold-climate ecosystems. We found that joint effects of temperature and precipitation are key in shaping plant-soil microbiota associations, with the start of the growing season as a critical mediating factor. Specifically, the start of the growing season is advanced by increasing temperature but delayed by increasing precipitation. This joint pathway particularly shaped rhizosphere organic matter degrading microbiota and root-associated putative plant pathotroph-saprotrophs and beneficial microbiota. We conclude that understanding local temperature, precipitation, and seasonal changes is crucial to accurately predict how the unique plant-microbiota interactions shaping cold-climate ecosystems are evolving with the ongoing change in climate.

• Keywords
• microbial co‐occurrence networks, precipitation, rhizosphere microbiome, root microbiome, seasonality, snow cover, temperature,
• MeSH
• Acclimatization physiology   MeSH
• Rain * MeSH
• Festuca growth & development   microbiology   MeSH
• Climate Change * MeSH
• Plant Roots microbiology   MeSH
• Microbiota * MeSH
• Soil chemistry   MeSH
• Soil Microbiology * MeSH
• Rhizosphere MeSH
• Plants * microbiology   MeSH
• Temperature * MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Soil MeSH

The fungal genus Cryptococcus includes several life-threatening human pathogens as well as diverse saprobic species whose genome architecture, ecology, and evolutionary history remain less well characterized. Understanding how some lineages evolved into major pathogens remains a central challenge and may be advanced by comparisons with their nonpathogenic counterparts. Integrative approaches have become essential for delimiting species and reconstructing evolutionary relationships, particularly in lineages with cryptic diversity or extensive chromosomal rearrangements. Here, we formally characterize six Cryptococcus species representing distinct evolutionary lineages, comprising both newly discovered and previously recognized but unnamed taxa, through a combination of phylogenomic analyses, divergence metrics, chromosomal comparisons, mating assays, and phenotypic profiling. Among pathogenic taxa, we formally name Cryptococcus hyracis sp. nov., corresponding to the previously characterized VGV lineage within the C. gattii complex. In parallel, we describe five saprobic, nonpathogenic species isolated from fruit, soil, and bark beetle galleries, spanning four phylogenetic clades. We identify a strong ecological association with bark beetles for Cryptococcus porticicola sp. nov., the only newly described nonpathogenic species with multiple sequenced strains from diverse sites. In this species, we detect strain-level chromosomal variation and evidence of sexual reproduction, along with population-level signatures of recombination consistent with ongoing genetic exchange. Across the genus, chromosome-level comparisons reveal extensive structural variation, including species- and strain-specific rearrangements that may restrict gene flow. We also identify multiple instances of chromosome number reduction, often associated with centromere inactivation following interchromosomal rearrangements. Comparative metabolic profiling with Biolog phenotype microarrays reveals clade-level differentiation and distinct substrate preferences, which may reflect metabolic divergence and habitat-specific diversification. Notably, we confirm that thermotolerance is restricted to clinically relevant taxa. These findings refine the species-level taxonomy of Cryptococcus, broaden its known genomic and ecological diversity, and strengthen the framework for investigating speciation, adaptation, and the emergence of pathogenicity within the genus.

• Keywords
• Fungal speciation, chromosome evolution, comparative genomics, digital DNA–DNA hybridization, human fungal pathogens, rRNA architecture,
• Publication type
• Journal Article MeSH
• Preprint MeSH

Gradients in species diversity across elevations and latitudes have fascinated biologists for decades. While these gradients have been well documented for macroorganisms, there is limited consensus about their universality, shape and drivers for microorganisms, such as fungi, despite the importance of fungal diversity for ecosystem functions and services. We conducted a comprehensive survey of fungal species richness in forests across 17 elevational transects along a latitudinal gradient covering the continental scale of Europe. Diversity patterns along elevational and latitudinal gradients differed among fungal ecological guilds. Diversity of saprotrophs declined with elevation while ectomycorrhizal (ECM) fungal diversity peaked in mid-elevations. Moreover, the diversity of root endophytic fungi increased with latitude but did not change with elevation. Bayesian species distribution modeling suggests that fungal diversity is structured by deterministic rather than stochastic drivers. Importantly, ECM fungal diversity pattern persists even after accounting for the effects of environmental conditions. These results suggest that environmental conditions differentially shape the diversity of fungal guilds along elevational and latitudinal gradients, but this goes beyond soil and climatic factors in the case of ECM fungi. This study paves the way toward a better understanding of fungal diversity gradients across elevations and latitudes, with possible implications for macroecological theory, conservation and management.

• Keywords
• altitudinal and latitudinal gradients, biogeography, climate, ectomycorrhizal fungi, fungal diversity, join species distribution models, root endophytic fungi, saprotrophic fungi,
• MeSH
• Bayes Theorem MeSH
• Biodiversity * MeSH
• Fungi * physiology   MeSH
• Mycorrhizae physiology   MeSH
• Altitude * MeSH
• Geography MeSH
• Publication type
• Journal Article MeSH
• Geographicals
• Europe MeSH

Decomposition is a crucial process in terrestrial ecosystems, driving nutrient cycling and carbon storage dynamics. Considering the amount of fungal necromass produced in soils annually, its decomposition represents an important nutrient recycling process. Understanding the decomposition dynamics and associated microbial communities of fungal necromass is essential for elucidating ecosystem functioning, especially in environmentally sensitive regions such as the Arctic tundra, which remain under-explored. In a three-year field experiment conducted in the Svalbard archipelago, we investigated the decomposition of two types of fungal necromass with differing biochemical properties. We studied the decomposition rate, changes in chemical composition, and the succession of fungal and bacterial communities associated with the decaying fungal necromass. We discovered that up to 20% of fungal necromass remained even after three years of decomposition, indicating that the decomposition process was incomplete. Our results indicate the crucial role of Pseudogymnoascus in decomposing low-quality, highly melanized necromass with a high C:N ratio in Arctic soils, underscoring its importance in carbon cycling in the Arctic tundra. Notably, we observed dynamic changes in bacterial communities, with increasing richness over time and a shift from copiotrophic to oligotrophic species specializing in decomposing recalcitrant material. Our study indicates the strong potential that fungal necromass can play in carbon sequestration of arctic soils and reveals the distinct dynamics between rather stable fungal and rapidly changing bacterial communities associated with the decomposing fungal necromass in the Arctic tundra. These findings enhance our understanding of microbial succession during decomposition in extreme environments and highlight the potentially differing roles of fungi and bacteria in these processes.

• Keywords
• Arctic tundra, Bacterial communities, Decomposition, Fungal communities, Fungal necromass,
• Publication type
• Journal Article MeSH

BACKGROUND: Understanding the temporal variability of the microbiome is critical for translating associations of the microbiome with health and disease into clinical practice. The aim of this study is to assess the extent of temporal variability of the human urinary microbiota. A pair of urine samples were collected from study participants at 3-40-month interval. DNA was extracted and the bacterial V4 hypervariable region of the 16S rRNA gene was sequenced on the Illumina MiSeq platform. The alpha diversity of paired samples was analyzed using Chao1 and Shannon indices and PERMANOVA was used to test the factors influencing beta diversity. RESULTS: A total of 63 participants (43 men and 20 women with a mean age of 63.0 and 57.1 years, respectively) were included in the final analysis. An average of 152 ± 128 bacterial operational taxonomic units (OTUs) were identified in each urine sample from the entire cohort. There was an average of 41 ± 32 overlapping OTUs in each sample pair, accounting for 66.3 ± 29.4% of the relative abundance. There was a clear correlation between the number of overlapping OTUs and the relative abundance covered. The difference in Chao1 index between paired samples was statistically significant; the difference in Shannon index was not. Beta diversity did not differ significantly within the paired samples. Neither age nor sex of the participants influenced the variation in community composition. With a longer interval between the collections, the relative abundance covered by the overlapping OTUs changed significantly but not the number of OTUs. CONCLUSION: Our findings demonstrated that, while the relative abundance of dominant bacteria varied, repeated collections generally shared more than 60% of the bacterial community. Furthermore, we observed little variation in the alpha and beta diversity of the microbial community in human urine. These results help to understand the dynamics of human urinary microbiota and enable interpretation of future studies.

• Keywords
• 16S rRNA gene, Bacterial community, Next-generation sequencing, Stability, Urinary microbiota, Variability,
• MeSH
• Bacteria * classification   genetics   isolation & purification   MeSH
• Biodiversity MeSH
• Time Factors MeSH
• DNA, Bacterial genetics   MeSH
• Middle Aged MeSH
• Humans MeSH
• Microbiota * genetics   MeSH
• Urine * microbiology   MeSH
• Prospective Studies MeSH
• RNA, Ribosomal, 16S genetics   MeSH
• Sequence Analysis, DNA MeSH
• Check Tag
• Middle Aged MeSH
• Humans MeSH
• Male MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Observational Study MeSH
• Names of Substances
• DNA, Bacterial MeSH
• RNA, Ribosomal, 16S MeSH

Microbial diversity plays a crucial role in litter decomposition. However, the relationships between microbial diversity and substrate successional stage are the drivers of this decomposition. In this study, we experimentally manipulated microbial diversity and succession in post-mining soil. We used leaf litter samples from two forests of a post-mining site near Sokolov, Czech Republic: one alder plantation and one mixed forest with birch aspen and willow. Litter from each site was decomposed in the field for 3 and 12 months. The litter was X-ray sterilized and part of the litter was kept unsterilized to produce inoculum. Leaf litter samples of two different ages (3 and 12 months) from each site were each inoculated with litter of two different ages (3 and 12 months), using less and more diluted inoculum, producing two levels of microbial diversity. In each of these eight treatments, the bacterial community was then characterized by amplicon sequencing of the 16S rRNA gene and microbial respiration was used to assess the rate of decomposition. A significantly higher respiration (p < 0.05) was found for the litter inoculated with the higher level of microbial diversity. Higher respiration was also found for the younger litter compared to the older litter and both litter origins. This shows a reduction in microbial respiration with substrate age and inoculation diversity, suggesting that microbial diversity supports the decomposition of soil organic matter.

• Keywords
• bacteria, decomposition of soil organic matter, fungi, microbial biomass, microbial diversity, succession,
• Publication type
• Journal Article MeSH