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PubMed2026

Cooperation and the evolution of bacterial niche breadth.

Bacteria exhibit varying niche breadths, with generalists thriving in diverse environments and specialists confined to specific habitats. Although genes for cooperative traits have been suggested to influence niche breadth evolution, their precise role remains unclear. We used a combination of phylogeny-based comparative methods to test causal hypotheses about the directionality of the relationship between genes for cooperation and bacterial niche breadth evolution across 25,785 species. Our results revealed 1) a positive correlation between the proportion of genes for cooperation and niche breadth; 2) genes for cooperation influenced niche breadth evolution, with a decreased proportion of such genes promoting niche contraction as the predominant evolutionary direction; and 3) genes for cooperation experience more frequent gain and loss within species rather than across species. These findings suggest a role of bacterial cooperation in influencing niche breadth evolution and maintaining the ecological versatility of bacteria. While our results are consistent with a simple relationship under the hypotheses tested, more complex causal scenarios are possible, including the role of factors that influence both cooperation and niche breadth.

Phylogeny↗
PubMed2024

Extreme elevational migration spurred cryptic speciation in giant hummingbirds.

The ecoevolutionary drivers of species niche expansion or contraction are critical for biodiversity but challenging to infer. Niche expansion may be promoted by local adaptation or constrained by physiological performance trade-offs. For birds, evolutionary shifts in migratory behavior permit the broadening of the climatic niche by expansion into varied, seasonal environments. Broader niches can be short-lived if diversifying selection and geography promote speciation and niche subdivision across climatic gradients. To illuminate niche breadth dynamics, we can ask how "outlier" species defy constraints. Of the 363 hummingbird species, the giant hummingbird (Patagona gigas) has the broadest climatic niche by a large margin. To test the roles of migratory behavior, performance trade-offs, and genetic structure in maintaining its exceptional niche breadth, we studied its movements, respiratory traits, and population genomics. Satellite and light-level geolocator tracks revealed an >8,300-km loop migration over the Central Andean Plateau. This migration included a 3-wk, ~4,100-m ascent punctuated by upward bursts and pauses, resembling the acclimatization routines of human mountain climbers, and accompanied by surging blood-hemoglobin concentrations. Extreme migration was accompanied by deep genomic divergence from high-elevation resident populations, with decisive postzygotic barriers to gene flow. The two forms occur side-by-side but differ almost imperceptibly in size, plumage, and respiratory traits. The high-elevation resident taxon is the world's largest hummingbird, a previously undiscovered species that we describe and name here. The giant hummingbirds demonstrate evolutionary limits on niche breadth: when the ancestral niche expanded due to evolution (or loss) of an extreme migratory behavior, speciation followed.

Animals↗
PubMed2026

Characteristics and assembly mechanisms of tobacco-associated bacteria in typical tobacco-planting regions across China.

INTRODUCTION: Plant-associated microbiota critically modulates host growth and environmental adaptation, yet assembly mechanisms, niche differentiation, and ecological strategies of bacterial communities inhabiting tobacco microhabitats remain poorly elucidated across geographical gradients. METHODS: Here, we systematically characterized bacterial microbiome assembly across five tobacco-associated niches (bulk soil, rhizosphere soil, root, stem, and leaf) from seven typical tobacco-planting regions using 16S rRNA amplicon sequencing, genome annotation, and niche breadth analysis. The independent and interactive effects of geographical location and host compartment on community structure, and further compared genomic traits, functional profiles, and life-history strategies between specialist and generalist bacterial populations were quantified. RESULTS: The results revealed a deterministic soil-plant continuum stratification of bacterial communities and diversity, with progressively simplified communities and decreasing alpha diversity from bulk soil to above-ground tissues, accompanied by progressive dominance of Proteobacteria. Geographical factors predominantly structured soil microbial communities via divergent edaphic properties, while host filtering acted as a universal dominant driver shaping endophytic microbiome assembly. Niche differentiation analysis demonstrated that niche-specialized bacterial ASVs overwhelmingly dominated all microhabitats and geographical sites, whereas generalist taxa only constituted auxiliary populations. Although specialist and generalist microbes exhibited highly conserved core genomic architectures and overall functional repertoires, they displayed distinct niche-specific functional divergence in metabolic pathways, stress resistance, and secondary metabolism across host compartments. Life-history strategy analysis further revealed that Y-strategist represented the core adaptive bacterial population, especially enriched in above-ground tobacco tissues. DISCUSSION: Our study establishes a hierarchical dual-filtering assembly model for tobacco microbiota, clarifies the ecological differentiation and functional adaptation of specialist and generalist bacteria, and provides fundamental insights into the assembly rules and adaptive mechanisms of crop-associated microbiomes for future microbial resource utilization and agricultural microbiome regulation.

biogeography↗
PubMed2026

Comparative Genomics Reveals Convergent Evolution Between Avivorous Bats (Ia io and Nyctalus aviator).

Investigating the genetic basis of dietary specialization can provide insights into the evolution of niche breadth. In this study, we employed comparative genomics to investigate the adaptive mechanisms enabling two bat species (Nyctalus aviator and Ia io) to shift from insectivory to seasonal bird consumption (avivorous bats). Our findings revealed adaptation related to immune response and lipid metabolism in avivorous bat species. Avivorous bats exhibit strong positive selection and convergent evolution in immune-related genes, which are under heightened selective pressure compared to those of non-avivorous bats. These species also display significantly fewer endogenous retroviral elements. These findings emphasized the significance of immune-driven adaptive evolution in avivory. Additionally, our results showed that the dietary evolution of avivorous bats is accompanied by convergent evolution associated with the lipid metabolism. Notably, CEPT1, the upstream gene required for the activation of the PPAR pathway, underwent positive selection and convergence, which may have affected lipid metabolism. These adaptations may enable avivorous bat species to face the challenge of immune response and nutrition during dietary niche expansion. These findings not only provide comprehensive insights into the adaptive evolution driving the unique diet of avivorous bats but also offered novel perspectives on the molecular mechanisms underlying ecological niche evolution in a dietary context.

Animals↗
PubMed2026

Microplastic aging drives convergence of the plastisphere microbiome and resistome toward agricultural soils.

The degree of microplastic (MP) aging varies substantially in agricultural soils; however, how this common aging gradient influences the plastisphere microbiome and resistome remains largely unknown. We therefore collected polyethylene MPs from long‑term mulched farmlands and classified them into low‑aged plastispheres (LAPs) and high‑aged plastispheres (HAPs). Bacterial community dissimilarity to soil decreased progressively from LAPs to HAPs, accompanied by broadening niche breadth, increasing bacterial diversity, and a shift toward more stochastic community assembly. The diversity and abundance of antibiotic resistance genes (ARGs) declined significantly along the aging gradient, with clinically relevant high-risk ARGs (e.g., vanR, ugd, and aac(6')-I) decreasing by 53.34-84.01%. Furthermore, the ARG hosts shifted from Actinomycetota in LAPs to Pseudomonadota in soils. Variance partitioning showed that the carbonyl index uniquely explained 57.03% of the variation in plastisphere ARG profile distance toward soil, identifying MP aging as the primary driver of resistome convergence. Collectively, these findings demonstrate that natural MP aging drives a progressive convergence of the plastisphere resistome toward that of the surrounding soil, indicating that aged MPs may pose a reduced risk of antibiotic resistance compared to newly formed MPs. This convergence underscores the need to incorporate plastic aging into future risk assessment frameworks for plastisphere-associated ARGs.

Soil Microbiology↗
PubMed2026

Multi-omics reveal microbial functional traits and antifungal metabolites associated with lower Pseudogymnoascus destructans loads in bat cave soils.

White-nose syndrome, caused by Pseudogymnoascus destructans (Pd), is a major fungal disease threatening hibernating bats. Cave soils can serve as environmental reservoirs for Pd, yet the microbial and biochemical mechanisms underlying naturally low Pd burdens in some cave environments remain poorly understood. Here, we integrated soil microbiome profiling, metagenomics, metabolomics, multi-omics network analysis, and in vitro validation to investigate the ecological and functional basis of differential Pd loads in hibernating bat caves in Northeast China. The three caves shared cold, humid, and weakly acidic microenvironments, but differed significantly in electrical conductivity, soil water content, nutrient availability, and extracellular enzyme activities. Soil microbial communities showed significant inter-cave variation in composition, diversity, and niche breadth, with stochastic processes contributing substantially to community assembly. Environmental variables, particularly pH and Pd load, were important predictors of microbial community structure. Functional analyses revealed that the low-Pd Gezi Cave was enriched in genes associated with organic carbon degradation, nitrogen input and retention, and secondary metabolism. Metabolomic profiling further identified cave-specific metabolite signatures, among which Biochanin A, 4-Hydroxybenzaldehyde, Vanillin, and Arachidonic acid were negatively correlated with Pd loads. Integrated pathway and network analyses showed that differential genes and metabolites jointly mapped to secondary metabolite biosynthesis, aminobenzoate degradation, and flavonoid degradation pathways, forming a microbe-metabolite-functional gene coupling network involving key taxa such as Rhodococcus, Pseudorhodoplanes, and Rhodoplanes. In vitro assays confirmed that 4-Hydroxybenzaldehyde, Coumarin, and Vanillin inhibited Pd growth. Structural equation modelling further indicated that environmental heterogeneity was associated with variation in Pd loads through microbial functional attributes and metabolite profiles. These findings suggest that naturally low-Pd cave soils are associated with coordinated environmental filtering, microbial functional specialization, and antifungal metabolite production, providing mechanistic insight into microbial and biochemical constraints on Pd persistence in cave reservoirs.

Animals↗
PubMed2026

Cross-kingdom genomic variation in chicken gut microbiomes: insights from China's diverse local breeds.

BACKGROUND: The gut microbiome possesses substantial genetic diversity that supports microbial adaptation, but the genomic variation patterns across its prokaryotic and viral populations remain incompletely characterized. RESULTS: Through integrated metagenomic and metatranscriptomic analysis of ten indigenous chicken breeds from China, we recovered 1527 representative prokaryotic MAGs, 37,555 representative DNA viral contigs, and 1867 representative RNA viral contigs (primarily comprising Bacillota/Bacteroidota, Uroviricota, and Lenarviricota/Pisuviricota, respectively). By integrating complementary short-read and long-read metagenomics with metatranscriptomics, we identified structural variants (SVs) and single-nucleotide variants (SNVs) in these cross-kingdom genomes. Positive SV-SNV density correlations occurred consistently across all microbial groups, indicating coordinated mutational processes. DNA viruses exhibited the highest variant prevalence (86.9% SNVs, 47.7% SVs), with temperate phages accumulating significantly more variants than virulent phages. Functionally, prokaryotic variants accumulated in carbohydrate metabolism and amino acid metabolism, while viral variants demonstrated broad metabolic hijacking. Horizontal gene transfer (HGT) was characterized by a strong virus-associated signature (69.40% of 536 events) and marked by an asymmetric pattern, with phage-to-bacteria (P-to-B) flow alone constituting 37.50% of all events. Random forest analysis revealed a strong bidirectional predictive relationship between SV and SNV densities across prokaryotic, DNA viral, and RNA viral populations, suggesting coupled genomic instability. Niche breadth emerged as a major driver of SNVs across kingdoms and was positively correlated with variant density. In prokaryotes, HGT events significantly shaped variant patterns. For viruses, genomic GC content was an important factor and consistently showed a negative correlation with SNV density in both DNA and RNA viruses. CONCLUSIONS: These findings demonstrate that coordinated mutational processes and kingdom-specific intrinsic factors drive genomic variation, with viruses serving as key genetic exchange vectors in chicken gut ecosystems. Video Abstract.

Animals↗
PubMed2026

Effector loss and gain drives host range at a fitness cost.

Epidemic preparedness depends on tracking microbial evolution that drives shifts in ecological behaviors such as disease emergence. However, the genetic constraints mediating microbial emergence for generalist and specialist behaviors remain poorly described. Here, we addressed this question by combining comparative and functional genomics with phylogeny-based evolutionary analyses of the cereal pathogen Xanthomonas translucens. We show that a generalist X. translucens subgroup arose from a specialist ancestor, and the loss of a single effector gene, xopAL1, contributed to the generalist host expansion by promoting host jump from barley to wheat. Deleting barley-specialist X. translucens xopAL1 recapitulated the host jump to wheat and demonstrates risk across each globally distributed genetic lineage. However, this niche expansion via XopAL1 loss incurs a significant fitness cost to colonize barley. Moreover, the specialist lineage gained an additional effector gene, xopAJ, which enhanced virulence on barley while restricting oat infection, thereby reinforcing niche specialization. We further conducted transcriptomic analysis of wheat and determined that XopAL1 triggers a defense response that involves the reduction of photosynthetic processes. Our work provides an experimentally validated evolutionary framework to understand mechanisms of intergenera host jump. Overall, we demonstrate that single events of gene loss and gain shape ecological behaviors by creating a dynamic trade-off between niche breadth and specialization.

Triticum↗