Search Results (274)

Leccinum is an ecologically significant and taxonomically complex genus of ectomycorrhizal fungi widely distributed across boreal, temperate, Mediterranean, and selected tropical regions. Despite its ecological, nutritional, and applied importance, no comprehensive review has previously synthesized global knowledge on this genus. This work provides the first integrative assessment of Leccinum research, combining a bibliometric analysis of 293 peer-reviewed publications with an in-depth qualitative synthesis of ecological, biochemical, and environmental findings. Bibliometric results show increasing scientific attention since the mid-20th century, with major contributions from Europe, Asia, and North America, and dominant research themes spanning taxonomy, ecology, chemistry, and environmental sciences. The literature review highlights substantial advances in phylogenetic understanding, species diversity, and host specificity. Leccinum forms ectomycorrhizal associations with over 60 woody host genera, underscoring its functional importance in forest ecosystems. Nutritionally, Leccinum species are rich in proteins, carbohydrates, minerals, bioactive polysaccharides, phenolic compounds, and umami-related peptides, with demonstrated antioxidant, immunomodulatory, and antitumor activities. At the same time, the genus exhibits notable bioaccumulation capacity for heavy metals (particularly Hg, Cd, and Pb) and radionuclides, making it both a valuable food source and a sensitive environmental bioindicator. Applications in biotechnology, environmental remediation, forest restoration, and functional food development are emerging but remain insufficiently explored. Identified research gaps include the need for global-scale phylogenomic frameworks, expanded geographic sampling, standardized biochemical analyses, and deeper investigation into physiological mechanisms and applied uses. This review provides the first holistic synthesis of Leccinum, offering an integrated perspective on its taxonomy, ecology, nutritional composition, environmental significance, and practical applications. The findings serve as a foundation for future mycological, ecological, and biotechnological research on this diverse and understudied fungal genus. Full article

This paper explores the intersection of digital technologies, sustainable agriculture, and biodiversity conservation within the framework of the European Green Deal. The study investigates how intelligent agricultural practices—enabled by digital tools such as sensors, AI, and IoT—can enhance soil health and conserve agrobiodiversity. A systematic literature review was conducted to map out current research trajectories, identify the taxonomic focus areas in biodiversity monitoring, and assess the integration of digital tools. Results show a significant upward trend in publications linking digitalization and sustainability in agriculture. Findings highlight that pollinators and soil biota dominate monitoring focus, while technologies like remote sensing and AI show increasing adoption. The study concludes that intelligent agriculture offers a path toward ecological and economic resilience in rural landscapes, aligning with the EU’s green transition agenda. Full article

This study explores the intestinal microbiota of eight 18-month-old male alpacas from two distinct high-altitude regions in Peru: the Wet Puna (4200 m above sea level) and the Dry Puna (4900 m above sea level). Using 16S rRNA and 18S rRNA metabarcoding, microbial communities of bacteria, archaea, fungi, and protists were analyzed from the first compartment of the stomach (C1) to investigate the diversity, taxonomic composition, and correlations with hematological parameters. Significant differences in microbial diversity and composition were observed between regions, driven by dietary and environmental factors. The Wet Puna exhibited greater alpha diversity in bacterial and fungal communities, while beta diversity highlighted distinct microbial compositions. Key taxa, such as Prevotella ruminicola and Acetitomaculum, were associated with energy metabolism and host adaptation, whereas methanogenic archaea (Methanobrevibacter, Methanosphaera) dominated in the Dry Puna, reflecting adaptations to arid conditions. Correlations between microbial taxa and hematological variables, such as Acetitomaculum with red blood cell count and Eremoplastron with neutrophil percentage, emphasize the complex interplay between microbiota and host physiology. These findings contribute to understanding microbial adaptations in high-altitude livestock and provide practical insights for enhancing alpaca management and conservation strategies through tailored nutritional approaches and sustainable grazing practices. Full article

Plasma cell-free RNA (cfRNA) metagenomics is increasingly explored for blood-based pathogen detection, but the structure of the shared background “blood microbiome”, the reproducibility of reported signals, and the practical limits of this approach remain unclear. We performed a critical re-analysis and benchmarking (“stress test”) of host-filtered blood RNA sequencing data from two cohorts: a bacteriologically confirmed tuberculosis (TB) cohort (n = 51) previously used only to derive host cfRNA signatures, and a coronary artery disease (CAD) cohort (n = 16) previously reported to show a CAD-shifted “blood microbiome” enriched for periodontal taxa. Both datasets were processed with a unified pipeline combining stringent human read removal and taxonomic profiling using the latest versions of specialized tools Kraken2 and MetaPhlAn4. Across both cohorts, only a minority of non-host reads were classifiable; under strict host filtering, classified non-host reads comprised 7.3% (5.0–12.0%) in CAD and 21.8% (5.4–31.5%) in TB, still representing only a small fraction of total cfRNA. Classified non-host communities were dominated by recurrent, low-abundance taxa from skin, oral, and environmental lineages, forming a largely shared, low-complexity background in both TB and CAD. Background-derived bacterial signatures showed only modest separation between disease and control groups, with wide intra-group variability. Mycobacterium tuberculosis-assigned reads were detectable in many TB-positive samples but accounted for ≤0.001% of total cfRNA and occurred at similar orders of magnitude in a subset of TB-negative samples, precluding robust discrimination. Phylogeny-aware visualization confirmed that visually “enriched” taxa in TB-positive plasma arose mainly from background-associated clades rather than a distinct pathogen-specific cluster. Collectively, these findings provide a quantitative benchmark of the background-dominated regime and practical limits of plasma cfRNA metagenomics for pathogen detection, highlighting that practical performance is constrained more by a shared, low-complexity background and sparse pathogen-derived fragments than by large disease-specific shifts, underscoring the need for transparent host filtering, explicit background modeling, and integration with targeted or orthogonal assays. Full article

Long-term continuous cropping is a prevalent agricultural practice aimed at maximizing land use efficiency and crop yields, yet it often leads to severe soil degradation, nutrient imbalance, and microbial community disruption. Effective soil remediation strategies are urgently needed to restore soil health and ensure sustainable agricultural production. In this study, we investigated the impact of forest soil amendment on microbial community structure, diversity, and functional potential in long-term continuous cropping soils. Using metagenomic sequencing, we analyzed soils from natural forest (BK), forest soil-amended soils (BCP), and fields under continuous cropping for 15 years (CP15) and 30 years (CP30). Forest soil amendment significantly mitigated microbial diversity loss and structural degradation caused by prolonged monoculture. Alpha diversity analysis revealed that BCP restored microbial diversity to levels comparable to BK, while beta diversity and NMDS analyses showed that microbial community composition in BCP closely resembled that of forest soil. Taxonomic profiling indicated that forest soil amendment enriched beneficial taxa such as Actinobacterota and Acidobacteriota, reversing shifts observed in CP15 and CP30. Functionally, COG and KEGG annotations revealed that BCP soils exhibited higher abundances of genes involved in carbohydrate metabolism, energy production, and nutrient cycling. Notably, the amendment reduced antibiotic resistance genes and virulence factors, potentially improving the microbial risk profile of soil communities. These findings demonstrate that forest soil amendment effectively restores microbial community structure and functionality in degraded soils, providing a nature-based solution for sustainable agriculture. Full article

Next Generation Sequencing is a constantly evolving technology whose applicability is increasingly expanding into the field of routine food analysis. In this context, metabarcoding has proven to be a powerful tool for detecting food fraud due to its ability to taxonomically classify even highly fragmented DNA from processed products. While Illumina sequencing platforms, representing second-generation sequencing technologies, are widely used for such applications, fourth-generation sequencing devices such as Oxford Nanopore Technologies’ MinION offer advantages in terms of flexibility, scalability, and simplified handling. In this study, we evaluate the transferability of an established Illumina-based metabarcoding method for the detection of pistachio adulteration in processed foods to the MinION platform of Oxford Nanopore Technology. In more detail, we transferred the established method from Illumina on both MinION and Flongle flow cells to assess sequencing accuracy, quantification potential and practical aspects such as cost-efficiency and workflow. Our results highlight the applicability of the MinION sequencing platform as a reliable and cost-effective alternative to Illumina protocols for routine food authenticity testing, enabling faster processing and broader accessibility without significantly compromising accuracy. Full article

The quality of human capital is pivotal to the promotion of economic growth and development. In this regard, the quality of education and of academic, practice-based research systems plays a crucial role. The authors conducted an analysis of the systemic framework for financing higher education and science in Poland, with a particular focus on the economic and financial situation of the 21 largest Polish universities from 2019 to 2024. In order to assess whether the current financial basis of these entities facilitates conducting research, bridges the gap between academia and industry, and thus supports their sustainable development, a taxonomic composite indicator and cluster analysis were employed. The results obtained indicated unfavourable trends in the domain of higher education and research and development (R&D) activity among Polish universities. These include, in particular, the exceeding of operating costs over operating revenues, the deterioration of financial results, insufficient funding from the state budget in relation to the scale of operations, and relatively high volatility of the economic and financial situation in subsequent years. Full article

This study investigates spatial and seasonal variation in the assemblages of benthic microgastropods (snails < 5–10 mm in length) within a poorly studied tropical bay. As these organisms are abundant, diverse and relatively easy to sample, with well-established taxonomy, they may prove a highly suitable group for ecological studies in such areas. Sediment samples were collected from three river basins in Camamu Bay, Brazil, during the wet and dry seasons. A total of 132 microgastropod species was recorded, demonstrating high diversity. The most abundant species were Eulithidium affine, Bittiolum varium, Cerithium atratum, Vitta virginea and Schwartziella bryerea. The least abundant species were Tenaturris gemma, Turbinella laevigata, Petaloconchus erectus, Parviturboides interruptus and Vitrinella cupidinensis. Statistical analysis revealed significant seasonal and spatial differences in diversity and assemblage composition, which correlated with environmental gradients. The results suggest that microgastropods are a suitable component of the biota for ecological and applied studies in marine sediments, particularly in remote tropical locations where full macrofaunal analysis may be challenging. Whilst further testing across impact gradients is needed, this approach offers a practical solution for ecological investigations in remote regions with limited taxonomic expertise and highlights microgastropods as a useful indicator taxon for impact biomonitoring in tropical marine sediments. Full article

Macroalgae provide key ecosystem services, forming habitats such as kelp and fucoid forests, rhodolith beds, and coralline reefs that sustain high biodiversity. However, multiple stressors, including climate change, harmful fishery practices, and pollution and coastal urbanization are driving macroalgal diversity loss and changing species composition and abundance. This study aims to assess macroalgal representativeness, richness and endemism in 16 Marine Protected Areas (MPAs), including four oceanic islands, and test if macroalgal assemblages in MPAs are distributed along a latitudinal gradient (0–29° S) in the Southwest Atlantic. To investigate the processes underlying community patterns, β-diversity was decomposition turnover and nestedness components. The complexity of taxonomic structure was measured by taxonomic distinctness. Overall, the studied MPAs comprised 695 macroalgal taxa, about 69% of Brazilian taxa, and 36% of the endemics. Rhodophyta were dominant (449 species) in most studied areas, except at Trindade and Martim Vaz Archipelago MPA, followed by Chlorophyta (158 species) and Ochrophyta (88 species). Macroalgal species composition in MPAs varied with latitude, and not with area size. They were continuously distributed across northeastern, eastern and southeastern Brazil and oceanic island ecoregions, between Fernando de Noronha (3° S) and São Paulo Litoral Norte (23° S) MPAs. Macroalgal diversity dissimilarity among MPAs was 92%, dominated by the turnover component (88%) and nestedness as a minor component (4%), indicating that dissimilarities are mainly driven by the replacement of species, rather than a gradual loss or gain of species. Effective protection of these MPAs should be prioritized as they harbor highly diverse, unique, and heterogeneous macroalgal assemblages along the SWA, surrounded by heavily impacted areas. Assessment of human impacts on macroalgal habitats in MPAs would contribute to defining effective management actions. Mid- and offshore shelf macroalgal habitats, particularly rhodolith beds, which harbor rare kelp species and mesophotic reefs, remain underprotected, and should be integrated into marine spatial planning for biodiversity conservation. Full article

Pleurotus ostreatus, commonly known as the oyster mushroom, is increasingly recognized as a key agrobiotechnological resource within sustainable development frameworks due to its ecological adaptability, rich nutritional profile, and broad socioeconomic contributions. This review integrates agroecological, socioeconomic, and biotechnological dimensions to examine its taxonomic identity, resilience to diverse environmental conditions, and efficiency in organic waste bioconversion. The species plays a critical role in circular bioeconomy strategies by advancing environmental sustainability, improving food and nutrition security, and supporting rural livelihoods through accessible, low-cost cultivation practices. Additionally, P. ostreatus demonstrates significant nutraceutical and pharmacological properties, making it a promising candidate for innovative biotechnological applications. Drawing on global and local case studies, this review highlights the species’ capacity to strengthen resilient agroecological systems and inclusive approaches to public health and livelihoods. Promoting its cultivation further enhances community well-being by generating equitable economic opportunities, empowering small-scale producers, and fostering social cohesion through sustainable food networks and shared resource systems. According to Mexico’s agroecological conditions, P. ostreatus represents a potential alternative to generate socioeconomic and nutritional benefits for the population at large. Full article

Ex situ collections of rare and endangered plant species are crucial components of integrated conservation systems, as outlined in the Global Strategy for Plant Conservation. Plant tissue culture collections play an essential role in achieving conservation objectives, as they offer a means of propagating plant material for habitat restoration and other practical applications. This study analyzes existing tissue culture protocols for coastal plant species of the Baltic Sea region, reviewing micropropagation research spanning 25 families and 112 highly coastal-specific species. The analysis of 232 experimental studies showed that tissue culture studies have been conducted with 38 coastal-specific species of the Baltic Sea region, which is only 34% of the initially identified target species. Special attention in the field of tissue culture technology development should be paid to several highly coastal-specific species with great potential for practical use, such as Blysmus rufus, Bolboschoenus maritimus, Schoenoplectus tabernaemontani, Halimione spp., Cochlearia spp., Euphrasia spp., and Odontites spp. Comprehensive research on tissue cultures of coastal plant species is imperative to establish micropropagation protocols for underrepresented taxonomic groups. The research should prioritize functional studies with ecological relevance and the development of practical biotechnological approaches for commercial applications. Full article

Diagnoses are one of the most important ways that taxonomists make new taxa recognisable by others. A recent paper stated that diagnoses for newly described organisms should include both the characteristic(s) of the new taxon (providing state-specificity) and name the taxa with which they are compared (giving contrastiveness). I argue that the characteristics of the compared taxa should also be included such that the diagnostic features are not only contrastIVE but also overtly contrastED I surveyed 278 papers wherein 405 new insect genera were described. Forty-four genera did not have a formal diagnosis, among the rest, there was a total of 427 diagnoses because some genera had multiple diagnoses. Among these, 83 (19.4%) had one or more diagnostic states overtly contrasted and over one-eighth (13.9%) contrasted all of them. Unsurprisingly, diagnoses that overtly compared the new genus to others were significantly more likely to include characteristics that were contrasted than did diagnoses that were lists or combinations. I discuss how features should be contrasted in diagnoses. Full article

This study investigated the effects of Rhodopseudomonas palustris (R. palustris) supplementation on the rumen microbiota of Leizhou goats and explored its potential mechanisms. Thirty healthy Leizhou goats of similar weight and age were selected and randomly assigned to five groups (six goats per group) using a completely randomized block design for a 75-day feeding trial. The control group (CONRF) was fed a basal diet, and the Photosynthetic Bacteria Medium (PBMRF) group was fed a basal diet + PBM solution. The low-concentration R. palustris (LRPRF), medium-concentration R. palustris (MRPRF), and high-concentration R. palustris (HRPRF) groups were fed a base diet supplemented with 20.0 mL, 40.0 mL, and 80.0 mL of R. palustris solution, respectively. All supplements were administered by mixing them into the feed. On day 75 of the trial, three goats were randomly selected from each group for slaughter and evisceration. Rumen contents were collected, immediately filtered, aliquoted, quick-frozen in liquid nitrogen, and stored at −80 °C for subsequent analysis of rumen microbial diversity. Rumen microbial community structure was analyzed using high-throughput sequencing. The results showed that R. palustris enriched unique operational taxonomic units (OTUs), particularly in the LRPRF group. At the phylum level, Firmicutes and Bacteroidota were dominant; Firmicutes and Euryarchaeota abundance increased, while Bacteroidota decreased in the experimental groups. In addition, Verrucomicrobiota abundance was significantly elevated (p < 0.05). At the genus level, Prevotella was predominant, whereas Selenomonas abundance was significantly reduced (p < 0.01). Meanwhile, compared to the CONRF, PBMRF, and LRPRF groups, the MRPRF and HRPRF groups exhibited higher relative abundances of Christensenellaceae_R-7 group and Anaeroplasma. LEfSe analysis revealed a greater number of differential taxa in the experimental groups compared with the control, including enrichment of beneficial bacteria, such as Lactobacillus, which may contribute to optimizing the rumen environment by regulating immune and metabolic functions. Functional prediction indicated that rumen microorganisms were mainly involved in carbohydrate and amino acid metabolism. In conclusion, supplementation with R. palustris can beneficially modulate rumen microbial composition and function and promote rumen absorption of nutrients and degradation of crude fiber. This study provides a theoretical basis for green goat farming practices. Full article

Bloodstream infections and sepsis necessitate rapid, sensitive, and clinically relevant diagnostics to minimize treatment delays and improve clinical outcomes. Next-generation sequencing enables culture-independent pathogen detection, antimicrobial resistance profiling, and genome-informed epidemiology. This narrative review integrates clinical evidence with practical workflows across three complementary approaches. We describe the use of plasma microbial cell-free DNA for broad organism detection and burden monitoring, as well as metagenomic next-generation sequencing of blood or plasma for unbiased pathogen discovery, including culture-negative and polymicrobial infections. Same-day Oxford Nanopore Technologies sequencing of positive blood culture broth is also discussed as a way to accelerate species identification, targeted resistance reporting, and infection-prevention decisions. We outline the sample-to-result steps, typical turnaround time (TAT), and stewardship-aligned decision points. Analytical reliability depends on effective reduction in human DNA background, stringent control of background and reagent-derived nucleic acids in low-biomass samples, and documented and validated bioinformatics workflows that are supported by curated taxonomic and resistance databases. Quantitative reports should adhere to validated thresholds and should be interpreted in the context of internal controls and clinical pretest probability. Ongoing challenges include variable correlation between genotype and phenotype for specific pathogen and antibiotic pairs, interpretation of low-level signals, and inconsistent regulatory and reimbursement environments. Advances in portable sequencing, faster laboratory and analytical workflows, and scaled liquid biopsy strategies may further reduce the TAT and expand access. Integrating these tools within One Health frameworks and global genomic surveillance programs could support early resistance detection and coordinated public health action, which could help to advance sepsis care toward more precise treatment and real-time infection control insights. Full article

DNA barcoding is an effective method for species identification, but its practical application, as implemented in the Barcode of Life Data System (BOLD), faces numerous challenges. In our work, we conducted an empirical test of this approach using butterflies of the Volga River region in eastern Europe as a model system. We demonstrate that DNA barcoding is a powerful tool for identifying species clusters of the local fauna studied. However, assigning the identified clusters to scientific species names using BOLD was problematic for more than half of the species analyzed. The reasons for these problems are numerous errors in (1) species and even (2) generic identifications of DNA barcodes in the BOLD database (30% and 26% of all problematic cases, respectively), (3) similarity of DNA barcodes in different species (22%), (4) unresolved taxonomic problems associated with the species names that BOLD suggests as identifications (18%), (5) anomalous barcodes (2%), and (6) incompleteness of the BOLD database (2%). Solving problems 1, 2 and 5 requires improving the DNA barcode curation system and minimization of the identification errors in the BOLD database. Problems 3 and 6 can be partly solved by accumulating DNA barcodes, especially barcodes of local faunas, since populations of different species with identical DNA barcodes often have non-overlapping areas. Problem 4 is the most difficult and requires further intensive taxonomic research to solve it. Full article