Pineapple sett rot, caused by Thielaviopsis species, constrains sugarcane production worldwide. Mechanical planting systems facilitate pathogen infection through increased wounding of planting material, exacerbating disease incidence. In Florida's Everglades Agricultural Area, the recent transition from manual to mechanical planting has intensified pineapple sett rot problems, threatening the United States' most important sugarcane-growing region. This study characterized Thielaviopsis isolates from symptomatic sugarcane billets collected during the 2023-2024 Florida planting season to establish species identity, virulence, and baseline fungicide sensitivity. Phylogenetic analysis of concatenated ITS and tef1-α sequences confirmed all 93 isolates as Thielaviopsis ethacetica, representing the first molecular characterization from North American sugarcane. Phylogenetic analysis resolved the Florida population in study into the two previously described intraspecific lineages of T. ethacetica, one isolate assigned to the African lineage and 11 to the South American lineage; the latter exhibited intra-lineage polymorphism resolvable into at the least three subclades. MAT1-1 mating type idiomorphs were detected in 38.7% of isolates; MAT1-2 could not be confirmed due to primer amplification failure. Virulence testing on cultivars CP96-1252 and CPCL05-1201 revealed that all representative isolates were highly pathogenic, reducing survival by 50-98% and plant height by 64-96% at 38 days after inoculation. Among the tested cultivars, CPCL05-1201 displayed higher quantitative resistance to T. ethacetica. Baseline propiconazole sensitivity testing of 14 representative isolates spanning the phylogenetic diversity observed in the population showed uniform susceptibility, with EC₅₀ values from 0.0081 to 0.0115 μg/mL (mean = 0.0095 μg/mL, CV = 12.2%). These values were substantially lower than typical field application rates, suggesting strong propiconazole efficacy. These findings provide critical baseline data for proactive resistance management and breeding programs targeting pineapple sett rot in sugarcane.

Freshwater biodiversity is declining at a pace that outstrips the capacity of existing monitoring approaches both in temporal and spatial dimensions, highlighting the urgent need for rapid and scalable assessment and attribution of biodiversity states and changes. Here we present a global assessment and unified analysis of riverine fish biodiversity using environmental DNA collected from 1,818 sites across 113 river systems spanning 5 continents. We quantified species richness, functional redundancy, phylogenetic diversity and genetic sequence diversity, and related them to drainage characteristics. Our results showed that environmental DNA effectively captured global patterns of multi-faceted riverine fish biodiversity and disentangled the roles of climate and different aspects of human activities in shaping biodiversity-area relationships. The accumulation of biodiversity with catchment area was consistently enhanced in warmer climates, while human activities weakened this scaling. Further, species richness, functional and genetic sequence diversity exhibited stronger negative responses to human activities in larger catchments. In contrast, phylogenetic diversity was negatively affected by human activities, yet this effect diminished as catchment area increased, highlighting the facet-dependent nature of biodiversity responses to environmental gradients and catchment characteristics. Our findings demonstrate the power of environmental-DNA-based datasets for harmonized, multi-faceted biodiversity assessments, offering a scalable approach for detecting and attributing biodiversity change and informing conservation strategies under accelerating global change.

Extracellular vesicles (EVs) are membranous nanoparticles released by cells that help shape the extracellular environment, remove cellular waste, and mediate cell-to-cell communication. Their release is ubiquitous across kingdoms, species, and cell types, highlighting their functional importance. Nearly as evolutionarily widespread and heterogeneous is the release of viruses, which have evolved to co-opt the host's cellular machinery to facilitate their replication and spread within all branches of life. Nearly all viruses, enveloped or not, repurpose EVs to modulate infection dynamics, while EVs also play a crucial role in the host's response to infection. This review explores the interplay between EVs and viruses across the phylogenetic diversity of virus species. We urge virologists and EV biologists to look beyond a single infection model and learn from the unique concepts and shared commonalities observed between close, as well as distantly related viruses, whether they infect mammals, vertebrates, insects, plants, bacteria, or more. To facilitate these efforts, we provide a comprehensive, taxonomical overview of the current knowledge regarding DNA and RNA virus families, and discuss recurring motifs in EV release and function during infection.

Multidimensional diversity patterns and community assembly of wintering waterbirds in isolated lakes within an intensively farmed floodplain.

Cascade dam development is transforming freshwater ecosystems worldwide, yet the long-term responses of fish beta diversity to progressive hydrological disturbances remain poorly understood. We analyzed data from the upper reaches of the Yellow River on the Qinghai-Tibet Plateau spanning five decades (pre-1975 to 2023), across a 1983-km river corridor influenced by sequential cascade dams. We quantified temporal shifts in taxonomic, phylogenetic, and functional beta diversity and determined the contributions of species extinctions and introductions to multidimensional beta-diversity change. Although damming is generally expected to promote biotic homogenization by simplifying habitats and favoring widespread generalist or non-native species, thereby making communities more similar, our results revealed pervasive biotic differentiation, with communities becoming increasingly distinct across all diversity dimensions. Beta diversity followed a nonlinear trajectory, increasing sharply during early dam construction and stabilizing in later stages. Both native species extinctions and non-native introductions contributed to these patterns, but their relative importance shifted over time, with introductions showing a greater contribution at later stages. Non-native species, particularly those introduced from outside the Yellow River basin, exerted disproportionate effects on phylogenetic and functional beta diversity owing to their distinct evolutionary histories and ecological traits. Environmental predictors such as reservoir age, cumulative upstream reservoir capacity, and individual reservoir capacity were strongly associated with patterns in beta diversity, reflecting the cumulative and spatially structured effects of long-term hydrological modification. Our findings provide quantitative, multidimensional evidence that non-native species introductions can outweigh native species extinctions in shaping beta diversity under sequential disturbance. We highlight the importance of proactive management of non-native species and long-term, multidimensional biodiversity monitoring to detect postdisturbance dynamics and guide timely conservation interventions. Collectively, our results offer a framework for identifying and anticipating the cumulative ecological consequences of cascade dam development and other chronic ecosystem modifications in the Anthropocene.

Almond anthracnose, caused by Colletotrichum spp. has become an increasing threat in modern almond orchards in Portugal. This study aimed to characterize the genetic, phylogenetic, morphological and virulence diversity of Colletotrichum species associated with symptomatic and asymptomatic almond tree organs collected in the main producing regions of Portugal. A total of 112 isolates were obtained from fruits, leaves, flowers and branches, with most samples originating from the Alentejo region. Almond anthracnose in Portugal is caused by genetically and biologically heterogeneous Colletotrichum species dominated by C. godetiae, which exhibited high multilocus genetic diversity, with most isolates corresponding to unique haplotypes, indicating the coexistence of genetically distinct strains. Colletotrichum godetiae and C. acutatum were predominantly isolated from symptomatic organs in the field, whereas C. fioriniae, C. karsti and C. gloeosporioides were detected in asymptomatic organs; however, all species were able to cause disease. This study reports C. karsti and C. gloeosporioides on almond for the first time. This diversity suggests multiple introductions and/or ongoing diversification of Colletotrichum populations associated with almond. Differences in virulence among the representative isolates tested, combined with similar incubation and latency periods, indicate that the severity is related to post-penetration events. Moreover, disease prevalence, averaging 36%, was associated with rainfall during the period from fruit set to early fruit development, highlighting the strong influence of meteorological conditions on anthracnose outbreaks. These findings support targeted monitoring, risk assessment and integrated disease management under agricultural intensification and climatic variability.

Genome-informed monitoring and characterization of Escherichia coli, including shiga toxin-producing strains, in a river with diverse land uses.

Metagenomics-guided targeted isolation and mechanistic elucidation of haloalkaliphilic bisphenol A-degrading microorganisms.

We have retrieved approximately 9,000 protein sequences annotated as fungal acid phosphatase or phytase from the UniProtKB database. Following stringent quality filtering, a curated dataset comprising 3,058 high-confidence sequences was assembled. Phylogenetic analysis resolved these enzymes into eight distinct clades, representing distinct groups of fungal acid phosphatases: purple acid phosphatases, phytases, and groups containing both phytases and acid phosphatases annotations. Based on this classification, we have developed three representative protein profiles referred to as Prf-A-Fungal_phos, Prf-B-Fungal_phos, and Prf-C-Fungal_phos, each designed to capture the phylogenetic and functional diversity of these enzyme families. Heat-map analyses confirmed the breadth and high specificity of these profiles. Application of these profiles to public protein and metagenomic databases enabled the identification of hundreds of previously uncharacterized fungal proteins, with a broad taxonomic distribution and notable prevalence in the Ascomycota and Basidiomycota phyla. Functional validation through heterologous expression of selected candidates in Saccharomyces cerevisiae confirmed their phosphatase activity, supporting the accuracy of the in silico predictions. By integrating large-scale bioinformatics with experimental validation, this study provides robust tools for the discovery of novel fungal phosphatases and for investigation of their ecological roles in nutrient-limited environments.IMPORTANCEFungal acid phosphatases are critical enzymes in global phosphorus cycling, yet no dedicated bioinformatic tools exist to comprehensively identify and classify them across fungal diversity. Here, we present the first PROSITE generalized profiles specific to fungal acid phosphatases, derived from a curated data set of over 3,000 high-confidence sequences spanning eight phylogenetic groups. These profiles exhibit high specificity and sensitivity, enabling the detection of hundreds of previously uncharacterized proteins from public protein databases. Experimental expression of representative candidates in Saccharomyces cerevisiae confirmed their phosphatase activity, validating our in silico predictions. By bridging large-scale bioinformatics with functional validation, this study delivers robust resources to uncover novel fungal phosphatases and to explore their ecological roles in nutrient-limited environments. The developed profiles will advance metagenomic annotation, support soil and environmental microbiology research, and foster biotechnological innovation in sustainable phosphorus management.

Hypertension (HTN) remains a leading global health burden and a key risk factor for cardiovascular disease. While the Dietary Approaches to Stop Hypertension (DASH) diet is an established strategy for blood pressure control, the interplay between dietary patterns and the oral microbiome in the etiology of HTN is not well understood. To investigate the independent and joint associations of genus-level oral microbiome composition and adherence to the DASH diet with hypertension in a nationally representative sample of US adults. We analyzed data from the 2009-2010 and 2011-2012 National Health and Nutrition Examination Survey (NHANES), including 5371 adults with complete oral microbiome, dietary, blood pressure, and covariate data. Genus-level oral microbiome profiles were derived from oral rinse samples using 16S rRNA sequencing and transformed with the centered log-ratio method. DASH adherence was assessed from 24-h dietary recalls using a validated score. Hypertension was defined as self-reported diagnosis, antihypertensive medication use, or measured blood pressure meeting 2017 American College of Cardiology/American Heart Association (ACC/AHA) criteria (systolic ≥130 mmHg or diastolic ≥80 mmHg). Analyses employed a multistage design: differential abundance testing to identify hypertension-associated genera; survey-weighted multivariable logistic regression to examine independent and joint associations, adjusting for demographic, lifestyle, and clinical covariates; subgroup analyses by sex, age, and microbial characteristics; and sensitivity analyses to assess robustness. Greater adherence to the DASH diet was associated with lower odds of hypertension [high vs. low tertile odds ratio (OR) ≈0.62; P < 0.005]. Several oral bacterial genera - Actinomyces, Rothia, Lactobacillus, and Veillonella - showed independent associations with increased hypertension risk (OR range: 1.302-1.468; P < 0.05). Higher Faith's Phylogenetic Diversity was inversely associated with hypertension (OR = 0.742; P = 0.037). Stratified analyses suggested effect modification: the protective DASH-hypertension association was strongest among individuals with low Lactobacillus abundance and intermediate microbial diversity and Rothia abundance, more pronounced in women, and attenuated in adults aged at least 60 years. Sensitivity analyses confirmed these patterns, highlighting the consistent risk associated with Actinomyces and the stability of joint DASH-microbiome associations. Genus-level oral microbiome composition and DASH dietary adherence were independently and jointly associated with hypertension risk. These results support a potential oral-dietary axis in cardiovascular risk and underscore the need for integrated microbiome-dietary approaches to hypertension prevention.

Akkermansia muciniphila, a commensal bacterium that represents 1-4% of the fecal microbiota in healthy adults, and can use mucin as a sole source of carbon and nitrogen, has attracted interest as soon as it was discovered due to the relationship between its abundance and various benefits, particularly pertaining to metabolic health. Especially noteworthy is the finding that A. muciniphila stimulates the proliferation and differentiation of intestinal stem cells, as part of tissue homeostasis and repair after biological, chemical, or physical injury. In this review, we discuss some of the evidence that supports the ability of A. muciniphila and of specific bacterial proteins to support the intestinal stem cell niche. The additional finding that some of these benefits are exerted during gestation on fetal stem cells, persist into adulthood, and influence crypt regeneration after injury, suggests that A. muciniphila may be part of the gestational environment that shapes the health of offspring. While most A. muciniphila health benefits were characterized using MucT (A. muciniphila ATCC BAA-835), the discovery of large phylogenetic and functional diversity within the Akkermansia genus galvanized efforts to compare different strains for their individual health profiles. Even closely related A. muciniphila strains may not always share the same health benefits, and sometimes the same strain may be beneficial or harmful depending on host-related factors, pointing towards the need to characterize health phenotypes at the strain level and in context of the host, and underscoring the ongoing gaps in defining the optimal formulation and safety profile of individual strains.

Restoring structural complexity in temperate forests increases bat and bird diversity.

The sky islands of Southwest China are biodiversity hotspots, where geographic isolation has led to allopatric diversification and cryptic speciation. Here, we integrated phylogenomics, molecular species delimitation, and morphometric analyses to assess the phylogenetic and morphological diversity of the small mammal family of talpid moles. Our findings strongly support recognizing geographically isolated populations as distinct species, highlighting that species diversity in Southwest China's sky islands is considerably underestimated. As traditional morphology-based methods struggled to detect these cryptic species due to morphological conservatism, we developed a deep learning model that analyzes cranial and mandible images using a hierarchical classification approach, to first differentiate genera and then species. This deep learning model achieved high accuracy (95% genus-level, 90% species-level) with identifying both known and cryptic species. Importantly, it uncovered previously overlooked diagnostic morphological characters thereby demonstrating the potential of deep learning methods to reveal hidden biodiversity within morphologically conserved species complexes, applicable broadly across diverse taxa.

Recent advances in genomic technologies have enabled detailed analyses of ancient microbiomes using dental calculus. While most studies have focused on European and North American populations, ancient Japanese oral microbiomes remain largely unexplored. Here, we analyzed dental calculus primarily from Edo period individuals (17th-19th centuries) to investigate the compositional, functional, and phylogenetic diversity of ancient oral microbiomes. Our results revealed clear differences between ancient and modern Japanese microbiomes, as well as phylogenetic divergence between the Final Jomon (ca. 1000 BCE) and Edo periods. We also identified regional variation in ancient oral microbiomes and clade-level diversity within the periodontitis-associated archaeon Methanobrevibacter oralis. Interestingly, individuals with traces of tooth blackening (ohaguro), a custom practiced by Edo period women, were all assigned to the same clade, suggesting cultural influences on the oral microbiome. These findings highlight the important role of human culture and demography in shaping the evolutionary dynamics of microbiomes.

ABSTRACTForest aboveground biomass (AGB) is crucial for maintaining global carbon balance, with its accumulation closely associated with biodiversity. However, the mechanisms by which these diversity effects take place, and which dimension of biodiversity that has the most prominent impact on AGB productivity remain insufficiently elucidated. We measured AGB, functional traits and evolutionary relatedness of the overstory and understory tree layers in a subtropical forest in Yunnan Province, China. We assessed predictive importance of functional and phylogenetic diversity indices on AGB across tree layers by using partial least squares (PLS) regression. Overstory exhibited greater AGB with tree species showing higher community‐weighted means of resource‐acquisitive traits (e.g., specific leaf area), as well as higher phylogenetic diversity. The understory AGB was mainly enhanced by conservative strategies (e.g., lower specific leaf area) as well as mean nearest taxon distance; and it was also increased by higher phylogenetic species richness and functional richness. Our results highlight the role of functional identity in regulating AGB. Notably, contrary to the results in previous Biodiversity and Ecosystem Function (BEF) studies where the influence of functional diversity was greater than phylogenetic diversity, we found that phylogenetic diversity is more capable of explaining the accumulation of AGB than functional diversity across tree strata. Our study thus underscores the significance of incorporating phylogenetic diversity into biodiversity and ecosystem function studies.

Forest conversion from natural forests to secondary forests and plantations has significantly altered wildlife habitats in subtropical regions. However, the drivers of disparities in bird and mammal multidimensional diversity between these forest types remain poorly understood. We analyzed a four-year camera-trapping dataset to compare the taxonomic, functional, and phylogenetic diversity and community structure of birds and mammals. Our results indicated that forest conversion impacts biodiversity differently across taxa. Birds exhibited higher taxonomic and phylogenetic diversity in secondary forests than in plantations. A similar pattern was also evident for birds among different stand types. However, mammals exhibited considerable taxonomic diversity but showed higher phylogenetic diversity and structure in secondary forests. A similar pattern was also evident for mammals among different stand types. Beta diversity revealed significant differences in bird taxonomic composition and mammal phylogenetic composition between secondary and plantation forests. Furthermore, elevation primarily influenced bird taxonomic diversity, phylogenetic diversity and structure in secondary forests, whereas mammal functional diversity, phylogenetic diversity and structure were more sensitive to elevational changes in both secondary and plantation forests. These findings reveal that birds and mammals respond distinctively to forest conversion. We emphasize that management strategies must be group-specific. For birds, we recommend prioritizing the preservation of secondary forests as biodiversity refugia and transforming structurally simplified plantations into complex habitats by retaining legacy trees and native understory vegetation. For mammals, conservation should prioritize landscape-scale connectivity by protecting continuous forest corridors along altitudinal gradients. Practically, this requires restricting further fragmentation of high-altitude habitats and restoring native vegetation in degraded corridors to facilitate dispersal and maintain the phylogenetic integrity of mammal communities.

Active and abandoned metal and coal mines generate acidic, metal-laden water that pollutes downstream areas, commonly referred to as acid mine drainage (AMD). AMD is host to microbial communities, including acidophilic iron oxidizers. Microbially mediated iron oxidation is a desirable (bio)remediation strategy for AMD. Ferrovaceae are Fe-oxidizing bacteria observed in AMD globally and thus could be an asset for bioremediation strategies. To better understand the potential for Ferrovaceae to contribute to AMD bioremediation, we analyzed 240 genomes and metagenome-assembled genomes from Ferrovaceae, including sequences from AMD sites with high iron oxidation rates. Based on our analyses, the phylogenetic and physiological diversity of this group is greater than previously known. We found that while all taxa are likely capable of iron oxidation using a cyc-2 like protein, some may also be capable of iron oxidation using an Mto-like protein. We also identified Ferrovaceae that are likely capable of anoxygenic phototrophy. Our findings indicate that multiple Ferrovaceae populations co-occur and suggest that differences in physiology may promote niche differentiation along resource axes. Physiologically diverse iron oxidizer communities could support a more resilient microbial community, resulting in higher iron oxidation rates and potentially more efficient bioremediation, and thus our results also indicate that future studies that link taxonomy with iron oxidation activity are warranted.IMPORTANCEAcid mine drainage (AMD) pollutes watersheds worldwide. Microbial communities can be leveraged to improve AMD bioremediation because they drive biogeochemical processes in these ecosystems. In AMD streams, iron-oxidizing microbial populations remove iron from the AMD effluent by precipitating iron oxides, which absorb other metals. These communities vary across sites and differ in how rapidly they oxidize iron. The factors that contribute to iron oxidation rates are not well understood, making it difficult to design effective bioremediation strategies. Ferrovaceae populations are widespread in AMD globally, including in sites with exceptionally high rates of iron oxidation. To examine the potential for Ferrovaceae to be key components of bioremediation strategies, we examined the genomic content and functional potential of Ferrovaceae in publicly available metagenomic data sets. Our analysis uncovered several new species of Ferrovaceae as well as an expanded metabolic potential for this group. Comparative genomics suggests that functional diversity leads to co-occurrence of multiple Ferrovaceae species at the same sites. The presence of multiple iron-oxidizing taxa with distinct physiology could be beneficial for bioremediation strategies.

Spectacular Saga: Phylogenetics and phylogeography of the Indian spectacled cobra (Naja naja Linnaeus, 1758).

The green-algal genus Trebouxia (Trebouxiophyceae, Chlorophyta) is the most common photosynthetic symbiont of lichens, displaying high phylogenetic diversity, and worldwide distribution across all climate zones. These single-celled terrestrial algae are valuable systems to study diversification, environmental adaptation and species interactions, yet genomic resources remain limited. We present over 30 new chloroplast and mitochondrial genomes of Trebouxia species, extracted from PacBio metagenomes of diverse Umbilicaria lichens from multiple climate zones. The genomes represent previously identified operational taxonomic units (OTUs) Trebouxia jamesii (A03), T. sp. (A04), T. incrustata (A06), T. vagua (A10), T. sp. (S02), T. sp. (S03), T. sp. (S04), T. suecica (S05), T. sp. (S08), T. angustilobata (S09), T. simplex (S10), T. sp. (S20) and T. barrenoae (S28); a newly designated OTU T. sp. (A57), and several Single-Occurrence Sequences (SOS) from clades A, I, and S. Up to four Trebouxia OTUs were found within a single thallus. Organelle genomes vary considerably in size and structure. The consensus phylogenies from chloroplast (77 genes) and mitochondrial (32 genes) genes are largely congruent with the nuclear ITS tree, differing mainly in the derived clade S sections. All genes are under purifying selection, with mitochondrial genes exhibiting higher nucleotide diversity and hence phylogenetic resolution than chloroplast genes. Certain gene and protein features correlate with temperature variability, and some (such as GC content, arginine, and valine content) mirror findings in mycobiont nuclear genomes from the same samples and highlight shared signatures of environmental adaptation. We designed primers for new, variable phylogenetic markers, including chloroplast genes ftsH and rpoC1, and mitochondrial genes ATP1, ATP6, and ND6. Overall, this study advances our understanding of organelle genome evolution in Trebouxia and provides valuable resources for future ecological and evolutionary research.

Patterns and drivers of waterbird alpha and beta diversity are different between arid and humid regions of China