Microbial community divergence and environmental responses across multi-phase landfill environments.

Species-specific salinity adaptation mechanisms drive niche partitioning of nitrite-dependent anaerobic methane oxidation bacteria in a natural wetland gradient.

Co-occurrence bloom of lipophilic toxic-producers in a hotspot Chilean fjord: Fine-scale distribution, toxins and fate in shellfish.

Biofilm pre-colonization strengthening: A new strategy for low-inoculum and startup of partial nitritation/anammox process in integrated fixed-film activated sludge systems.

Soil salinization, a growing global issue threatening sustainable agriculture, can be mitigated by Plant Growth-Promoting Bacteria (PGPB) as a green strategy. PGPB primarily consist of plant growth-promoting rhizobacteria (PGPR) and plant growth-promoting endophytes (PGPE). Numerous studies have demonstrated that both types of bacteria can enhance plant performance under salt stress through various mechanisms that help maintain ion homoeostasis, improve osmotic adjustment, and enhance antioxidant defence. Although PGPR and PGPE share highly conserved core mechanisms, their distinct colonisation niches lead to functional divergence in efficacy, stability, and ecological roles. This review systematically summarises these conserved mechanisms for enhancing plant salt tolerance. Furthermore, it elaborates on their functional differences across various ecological niches and discusses the major challenges and future directions for the field application of these PGPB. Ultimately, this review aims to provide a theoretical foundation for the scientific deployment of PGPB in saline agroecosystems.

Carbon availability dictates the stability of nitrate-vanadium co-remediation in stratified biofilters.

The phyllosphere microbiome plays crucial roles in plant health, but evidence of 'cry for help' strategy in the face of pathogen attack in the phyllosphere remains limited, particularly for the microbiomes of distinct leaf ecological niches. We investigated whether foliar pathogen anthracnose (Colletotrichum lentis) influenced the assembly and functions of microbiomes in epiphytic and endophytic niches of the phyllosphere of common vetch (Vicia sativa) leaves. We also evaluated synthetic microbial communities (SynComs), including representatives of disease-associated strains, for pathogen protection. Anthracnose mediated the deterministic assembly process of epiphytic bacterial and endophytic fungal communities, and increased the complexity of bacterial co-occurrence networks. Iron competition and antifungal genes were also enriched in the epiphytic bacteria, which produce siderophores and degrade fungal cell walls to counteract pathogens. SynComs of beneficial epiphytic bacteria partially protect hosts by regulating bacterial interactions and inducing host immune responses. These findings suggest that disease drives the deterministic assembly of distinct phyllosphere microbiomes, their diversity and their function. Moreover, SynComs from the epiphytic niche can confer host plant disease resistance.

Microbial chitinases in the plant holobiont: ecological roles and structural determinants.

Genome-wide identification of adaptive genes for kiwifruit leaf surface and apoplast colonization in Pseudomonas syringae pv. actinidiae.

Integrative Single-Cell and Bulk Transcriptomics Analysis Reveals Cellular Heterogeneity, Immune Microenvironment Dynamics, and Prognostic Signatures in Oral Squamous Cell Carcinoma.

ABSTRACTEach species occupies a distinct ecological niche, defined by a specific set of environmental conditions and resource requirements necessary for its survival and reproduction. However, climate change is altering species distributions, predator–prey relationships, and resource partitioning between species, with these changes being pronounced in the Arctic. Stable isotope analysis of carbon (δ13C) and nitrogen (δ15N) has been widely used to estimate isotopic niches and quantify niche overlap among species using a two‐dimensional approach (2D). However, δ13C is not always sufficient to differentiate habitat and resource use among species due to minimal variation between end‐members. Incorporating sulfur stable isotopes (δ34S) can enhance resolution in such cases. Using an Arctic coastal food web as a model system, we used a three‐dimensional isotopic niche approach (3D: δ13C–δ15N–δ34S) with 664 individuals across 49 species spanning multiple taxonomic groups (invertebrates, fish, seabirds, and marine mammals) that utilize resources from benthic and pelagic habitats. We compared the traditional 2D isotopic niches with a 3D framework using nicheROVER to assess how the addition of a third dimension changes niche size estimates and probability of niche overlap between species. We found that several benthic‐associated species, including the common eider (Somateria mollissima) and various benthic invertebrates, tended to show greater changes in isotopic niche size with the addition of δ34S than pelagic‐associated species. In addition, niche overlap among benthic‐associated taxa generally decreased with the 3D approach, suggesting better resolution of habitat use and resource partitioning. This reflects the greater ecological diversity, foraging specialization, and more complex food web structure characteristic of benthic than pelagic ecosystems. We recommend incorporating δ34S for aquatic studies that involve benthic habitats and emphasize the value of multidimensional approaches to increase the resolution of ecological niche analysis.

Probiotic and postbiotic compounds found in food influence gut microbiota to attenuate chronic metabolic diseases; however, the underlying mechanisms are not yet fully understood. This study employed a customized in vitro anaerobic pseudo-colon system (AMMR) to evaluate the impacts of Lactiplantibacillus plantarum (probiotic) and butyrate (postbiotic) on gut microbial composition and functionality, using human fecal samples. Metagenomic (16S rRNA) profiling and untargeted metabolomic (GC-MS) analysis were conducted after 48 h treatments. The results showed that butyrate supplementation markedly enhanced microbial diversity, inhibited opportunistic pathobionts (e.g., Enterococcus and Klebsiella), and selectively enriched butyrate producers (e.g., Lachnoclostridium), while diminishing the Firmicutes : Bacteroidetes ratio. It increased indole levels metabolically and redirected pathways towards amino acid synthesis and energy metabolism, while suppressing fatty acid formation. In contrast, L. plantarum exhibited modest alterations in microbial diversity while enhancing Bacteroides and Klebsiella and preserving elevated Enterococcus levels. It elevated saturated fatty acids (octanoic/capric acid) and enhanced amino acid catabolic pathways (valine/leucine) and redox regulators (taurine metabolism). Correlation analysis revealed that butyrate was associated with fiber-degrading microbes, whereas L. plantarum was associated with lactic acid bacteria, suggesting distinct ecological niches and interaction patterns. These findings collectively indicate that butyrate and L. plantarum elicit complementary microbial alterations, i.e., butyrate directly transforms the microbial structure and metabolism towards an anti-inflammatory phenotype, while L. plantarum largely influences via metabolic byproducts and niche adjustment. The complementary actions highlight the therapeutic potential of integrated probiotic-postbiotic approaches for the enhancement of gut health.

Tuberculosis remains one of the world's deadliest infectious diseases. The development of new therapies is limited by the absence of human-relevant models that reproduce the distinct lung niches encountered by Mycobacterium tuberculosis. Current macrophage or epithelial monocultures fail to predict how drugs act in the alveolar versus airway compartments, where intracellular and extracellular bacteria coexist and trigger different immune responses. Here, we introduce a dual human lung platform integrating alveolar macrophage-like cells and air-liquid interface airway epithelium. These models recapitulate key physiological features, including macrophage immunoregulatory programming, epithelial barrier function, mucociliary activity, and compartment-specific drug penetration. Benchmarking standard antibiotics, host-directed therapies, and antivirulence strategies revealed striking niche-dependent differences in antimicrobial and immunomodulatory activities. This system provides a powerful and accessible preclinical tool to evaluate antimicrobial and host-directed interventions in relevant human lung environments, helping bridge the gap between simplified in vitro assays and the complex biology of human tuberculosis.

Southern African hominin fossils traditionally attributed to Paranthropus robustus and Australopithecus africanus are differentiated from each other by their dentition and cranial architecture, but their postcranial anatomy has typically been regarded functionally as broadly similar (i.e., terrestrial bipedalism with some degree of arboreal locomotion). Testing the hypothesis of a similar locomotor repertoire between these two taxa has been complicated by a lack of postcranial fossils attributable to P. robustus. Here, we detail our comparative examination of the internal bone anatomy of a recently described c. 1.8 Ma P. robustus articulating femur and tibia, which suggests distinct patterns of joint loading and locomotor behavior. Our analysis of cortical bone in the hip and trabecular bone in the ankle, knee, and hip joints suggests that P. robustus habitually adopted a high frequency of ankle, knee, and hip flexion, as required for climbing, while Australopithecus from a c. 3.4 Ma level at the site of Sterkfontein displays a more modern human-like structural pattern across the lower limb joints consistent with comparatively more frequent terrestrial bipedalism. These results reveal that geologically younger P. robustus likely used arboreality more frequently than older Sterkfontein Australopithecus. Together with differences in masticatory behavior, this line of evidence indicates that these two hominin taxa occupied distinct ecological niches.

Intrinsic waste component synergy: calcium-rich eggshell waste modulates fungal-bacterial microbiome toward selectively medium-chain fatty acid production.

Background: Eleutherine bulbosa (Mill.) Urb. (Iridaceae), popularly known as Dayak onion in Kalimantan, Indonesia, occupies a distinct niche within traditional Dayak ethnomedicine, where its bulbs are employed to treat conditions ranging from breast tumours and hypertension to infectious diarrhoea. Despite well over two decades of phytochemical characterisation, the plant remains largely absent from mainstream drug discovery pipelines, representing both a scientific gap and a translational opportunity. Objective: This systematic review consolidates available evidence on the phytochemistry, molecular pharmacology, toxicological profile, and pharmacokinetic properties of E. bulbosa, with particular emphasis on mechanistic detail, quantitative bioactivity data, and translational potential. Methods: A structured literature search was conducted across PubMed, Scopus, Web of Science, and Google Scholar, following PRISMA 2020 guidelines. Of 387 records screened, 78 studies met the inclusion criteria and were subjected to qualitative synthesis. Results: The plant's bulbs elaborate a distinctive array of naphthalene, naphthoquinone, and anthraquinone derivatives, among which eleutherin, isoeleutherin, eleutherol, and eleutherinol constitute the pharmacologically dominant scaffold. Documented bioactivities span anticancer (IC50 range 12–85 µg/mL against multiple cell lines), antibacterial (MIC as low as 7.8 µg/mL against MRSA), antifungal, antioxidant, anti-inflammatory, and antidiabetic effects. Molecular targets identified include caspase-3/-9, Bcl-2/Bax, NF-κB p65, PI3K/Akt, α-glucosidase, and tyrosinase. Acute toxicity studies in rodents indicate LD50 values generally exceeding 2000 mg/kg for crude extracts, suggesting a reasonable therapeutic window. Conclusions: E. bulbosa harbours a structurally privileged chemical space with multimodal pharmacological relevance. The near-complete absence of clinical data limited pharmacokinetic characterisation, and sparse structure-activity relationship studies define the principal gaps that must be addressed before rational drug development can proceed.

Birds and mammals exhibit extraordinary facial diversity, reflecting adaptations to distinct ecological niches and feeding strategies. While core face-building developmental programs are conserved and orchestrated by interactions between ectodermal organizers and the underlying mesenchyme, mechanisms driving facial shape variation remain poorly understood. Here, we integrate single-cell transcriptomic and chromatin accessibility profiling of mouse and chicken developing face to construct a comparative regulatory map. Although both ectodermal and mesenchymal populations display distinct regulatory features in each species, the mesenchyme exhibits markedly greater divergence, pointing to its central role in shaping facial morphology. We further reveal unexpected molecular complexity in the main face-shaping organizer, including a mouse-specific Shh/Wnt5a expression domain. At key morphogen loci (Bmp4, Fgf8, and Wnt5a), conserved and lineage-specific enhancers exhibit spatially restricted activity patterns that mirror divergent signaling domains. These findings demonstrate how cis-regulatory evolution modulates conserved developmental programs to generate morphological novelty, providing a valuable resource for studying vertebrate facial evolution.

Although the heterogeneity and plasticity of fibroblasts are recognized hallmarks of tissue fibrosis, their specific contributions to renal fibrosis progression and the therapeutic validity of targeting key effector subsets remain key unanswered questions. Here, we revealed that diverse, functionally exclusive fibroblast subpopulations actively shape their local microenvironment. Pro-inflammatory fibroblasts (i-Fibs) construct immune-active areas, while pro-fibrotic fibroblasts (ECM-Fibs) generate fibrogenic zones. These two distinct microenvironments form a spatial mosaic, occupying mutually exclusive territories within the kidney tissue. We identified mechanotransduction as a signal governing the switch from i-Fibs to the pathogenic ECM-Fib phenotype. Through unbiased bioinformatics and genetic tools, we pinpointed CD248 as a specific cell-surface protein on this matrix-producing subset. Mechanistically, CD248, via its C-type lectin-like domain, senses the disordered matrix, promoting focal adhesion assembly and YAP nuclear translocation through an IQGAP1/ARF6-GTP-dependent axis, leading to a sustained feedback loop between aberrant matrix and myofibroblasts activation. A monoclonal antibody targeting CD248, IgG78, effectively interrupted this feedback loop, mitigating fibrogenesis both in vitro and in vivo in male mice. Collectively, this study established that fibroblast heterogeneity drives pathological niche specification in the fibrotic kidney and validated CD248 as a promising therapeutic target to counteract tissue fibrosis by disrupting aberrant mechanosignaling.

Background and ObjectiveDifferentiating neuromyelitis optica spectrum disorder (NMOSD) from multiple sclerosis (MS) is clinically difficult, especially when patients are seronegative for anti–aquaporin-4 immunoglobulin G (AQP4-IgG). Bile acids (BAs) function as important immunoregulatory metabolites, yet their metabolic signatures have not been profiled across NMOSD subtypes or compared with MS. We therefore profiled BA metabolism in NMOSD and MS to determine diagnostic utility.MethodsWe enrolled 112 NMOSD patients (32 AQP4-IgG seronegative, 80 AQP4-IgG seropositive), 50 MS patients, and 66 healthy controls. Targeted liquid chromatography–mass spectrometry quantified 15 bile acids, from which 71 derived metabolic indices were computed. Candidate biomarkers were identified using nested cross-validation combined with stability selection and integrated into diagnostic models evaluated under a pre-specified internal multi-level validation framework. Associations between BA profiles and neurological disability were assessed using Spearman correlation.ResultsSerum BA signatures differed markedly between NMOSD and MS. NMOSD showed a pronounced increase in primary conjugated BAs, whereas MS displayed enhanced secondary BA metabolism. Notably, AQP4-IgG seronegative NMOSD had significantly lower secondary BA concentrations than all other groups. A BA-based diagnostic model distinguished NMOSD from MS with an AUC of 0.874. When specifically differentiating AQP4-IgG–seronegative NMOSD from MS, deoxycholic acid (DCA) demonstrated strong discriminative potential (AUC 0.965), with internally consistent performance across resampling- and cross-validation–based robustness analyses. Disease-specific correlations between BA profiles and Expanded Disability Status Scale scores were also observed.ConclusionsSerum bile acid metabolomic profiling reveals disease- and subtype-specific signatures that may assist in the differential diagnosis of NMOSD and MS, particularly in AQP4-IgG–seronegative cases. Given the cross-sectional design, these findings should be interpreted as disease-associated metabolic signatures rather than causal mechanisms. DCA showed strong discriminatory performance; however, its clinical utility remains hypothesis-generating and requires replication in a fully independent external cohort.

Accurate deconvolution of bulk and spatial transcriptomes is essential for studying tissue architecture and disease, yet remains challenged by unmodeled differences in cellular RNA content and cross-source heterogeneity. We introduce CSsingle, a unified deconvolution framework that explicitly corrects for cell-type-specific RNA content differences using either External RNA Controls Consortium (ERCC) spike-ins or a computational estimator, while robustly harmonizing data across platforms. CSsingle employs an iteratively reweighted least-squares model initialized by marker-gene sectional linearity, enabling accurate inference of cell-type proportions from diverse single-cell references. In bulk data, CSsingle outperforms existing methods by correcting systematic errors, including neutrophil underestimation in blood and tumor purity underestimation in breast tumor. Applied to spatial transcriptomics, CSsingle enables fine-grained mapping of cellular organization in the developing human pancreas and reveals functionally distinct niches in colon cancer. By integrating cell size awareness with cross-platform robustness, CSsingle advances the integrative analysis of complex tissues.