Wetland degradation alters rhizosphere habitats and resource availability, yet its effects on bacterial and fungal diversity and life-history strategies remain unclear. We examined Deyeuxia angustifolia rhizosphere communities across four wetland types in the Sanjiang Plain, China: marsh (ZZ), typical meadow (DC), slightly degraded (DN), and severely degraded (DS). We measured plant biomass and soil properties and analyzed microbial communities using 16 S rRNA gene and ITS amplicon sequencing, life-history strategy indices, and partial least-squares path modeling (PLS-PM). Bacterial and fungal community composition differed significantly among wetland types (P ≤ 0.001 and P = 0.006, respectively). Bacterial alpha diversity did not differ significantly, whereas fungal Shannon and ACE indices were lower in DN than in DC (P < 0.05). The relative abundances of Acidobacteriota and Archaeorhizomyces increased with degradation, whereas Pseudomonadota and Actinomycetota peaked in DC; Ascomycota dominated fungal communities. The bacterial oligotrophic-to-copiotrophic ratio was highest in ZZ, followed by DN, with both exceeding DC and DS (P < 0.05). The fungal ectomycorrhizal-to-saprotrophic ratio showed no significant differences. PLS-PM indicated that degradation was negatively associated with soil environmental conditions (P < 0.001), which were positively associated with the bacterial oligotrophic-to-copiotrophic ratio (P < 0.05) and negatively associated with fungal alpha diversity (P < 0.05). Overall, fungal diversity in the rhizosphere soil of Deyeuxia angustifolia differed significantly across the wetland degradation gradient. Bacterial life-history strategies showed a significant, non-linear shift among degradation stages, reflected in changes in the relative dominance of oligotrophic and copiotrophic taxa. These findings provide insight into how wetland microbial communities respond to degradation and may inform wetland restoration.
Bark beetles form varying associations with fungi, yet the mycobiomes of many deciduous phloem-feeding species are poorly studied and their ecological significance remains underexplored. Here, we used ITS2 metabarcoding to characterize the fungal communities of the beech bark beetles Ernoporicus fagi and Taphrorychus bicolor collected from 61 forest patches across six regions in Germany. Despite sampling two beetle species across an elevational gradient, experimental forest management treatments, and six regions, beetle species identity, treatment, and elevation explained little variation in beetle mycobiomes, and region showed only a weak effect that disappeared under closer inspection. However, we found mycobiome composition varied more consistently at the finer scale of individual forest sites, and geographic distance between patches had a weak but significant effect, suggesting that the fungal communities these bark beetles carry are shaped by local, patch-level factors rather than broader regional or host-related factors. The mycobiomes of both beetle species were largely similar and dominated by ubiquitous saprotrophs and yeasts.
The honey bee (Apis mellifera) colony is a superorganism, but its microbiota is known mostly from the worker hindgut. Direct comparison across studies and niches is confounded by different regions of the 16S rRNA gene, bioinformatic processing choices, and reference database used for taxonomic assignment. We reprocessed 4,586 short-read Illumina libraries from 37 BioProjects, and added 345 full-length (V1-V9) PacBio libraries of dissected worker and queen gut tissues as a reference. Sequences were processed using one set of filtering and reporting thresholds and one species-level reference database. Each library was processed twice, with and without read denoising. The two methods agreed on genus-level composition but denoised reads produced far fewer amplicon sequence variants per library and significantly lower alpha diversity. Species resolution was highly dependent on 16S rRNA gene region. Full-length reads named nearly every major genus to species, while some short regions named almost none. The superorganismal microbiota is comprised of both niche specialists, and generalists shared across multiple niches. We identified at least three abundant amplicon sequencing variants that lack species-level description. Contaminant reads were abundant throughout the dataset due to next generation sequencing of niches with low microbial biomass. Contaminants scaled inversely with bacterial load, dominating drone reproductive tissue, larvae, mouthparts, hive materials, control or lab reared worker guts and stored food. Thus, conclusions about honey bee microbiota and/or its integration with host information depend strongly on primer region, how sequencing error was handled, and the level of high-throughput sequencing contamination.
Abstract Early-life wheezing has been associated with microbial alterations along the gut-airway axis, yet few studies have examined bacterial communities in both compartments within the same children. This cross-sectional exploratory pilot study (n=25) characterized nasal and stool bacterial communities in children aged 1–4 years with recurrent wheeze and healthy controls using 16S rRNA gene metabarcoding. Across participants, nasal and stool bacteriomes were highly individualized and taxonomically diverse. Overall richness, evenness, and global community composition did not differ significantly between healthy controls and children with recurrent wheeze in either compartment. Nasal communities in the recurrent-wheeze group showed greater within-group dispersion, although the comparison did not reach the conventional significance threshold (p=0.054). Exploratory distance-based stratification identified a subgroup with nasal profiles farther from the healthy-control centroid; these profiles had lower richness and evenness, higher Moraxella abundance, and lower abundances of Prevotella spp., Alloprevotella , and Veillonella . No statistically supported genus-level differences were detected in stool samples. Community-assembly and co-occurrence analyses yielded group-specific descriptive patterns in both compartments. Different sets of cross-compartment correlations passed the multiple-testing threshold in healthy controls and children with recurrent wheeze, including correlations of stool Lactococcus with several nasal taxa in the recurrent-wheeze group. Because these analyses were performed in small groups, they are considered hypothesis-generating. These findings identify nasal microbial heterogeneity and exploratory differences in community organization in preschool children with recurrent wheeze, while providing no evidence for causal or Moraxella -driven effects. Larger longitudinal studies with functional measurements are required for validation.
High-mountain ecosystems are sentinels of global environmental change, yet the soil microbial communities of North Africa’s highest peak remain entirely unexplored. Here, we present the first comprehensive characterization of soil bacterial and fungal communities across a 3,600-meter elevational gradient on Mount Toubkal (500–4,165 m), Morocco, integrating next-generation sequencing (16 S rRNA and ITS1) with soil physicochemical and enzymatic analyses. Our findings reveal a fundamental divergence in biodiversity patterns: bacterial alpha diversity remained comparatively stable along the sampled transect, whereas fungal richness decreased toward higher elevations. Site-level analysis confirmed a negative association between fungal richness and elevation (ρ= -0.70, P = 0.036, n = 9). Fungal richness and Shannon diversity were positively associated with soil organic matter at the site level (ρ = 0.83, P = 0.005, and ρ = 0.77, P = 0.016, respectively), while bacterial richness was associated with available phosphorus, pH, and phosphatase activity. Bacterial and fungal community composition differed among the sampled elevation-sites. Actinobacteriota was the dominant bacterial phylum throughout the transect, while Ascomycota dominated fungal communities at most sites. Chytridiomycota became dominant specifically at 3,500 m. Bacterial and fungal community composition differed among sampled elevation-sites, although these patterns reflected both community-centroid and dispersion differences. Community dissimilarity increased with absolute elevation difference, indicating compositional turnover along the sampled transect. Microbial diversity and composition were associated with variation in soil organic matter, available phosphorus, and pH along the sampled transect. These findings establish the first soil-microbiome baseline across Mount Toubkal and expand current knowledge of microbial biogeography in North African mountain ecosystems.
