Elevation Matters More than Season in Shaping the Heterogeneity of Soil and Root Associated Ectomycorrhizal Fungal Community

Altitude and season represent two important environmental gradients that shape the structure of biome, including the heterogeneity of EcM fungi. Previous studies have separately considered the influences of altitude and season on EcM fungal communities, but the relative importance of altitude and season is still unknown.

Machine learning for exploring microbial inter-kingdom associations in Cystic Fibrosis and Bronchiectasis

Background: Cystic fibrosis (CF) and non-CF bronchiectasis (BX) are lung diseases characterised by severe chronic infections. Fungal and bacterial components of infection are both recognized. Recent molecular investigation of sputum from patients with CF and BX has revealed a complex mycobiome. However, little is known about how fungal and bacterial organisms interact or whether the interactions impact on disease outcomes. Methods: Quantitative PCR and next generation sequencing of ITS2 and 16S rRNA gene was carried out on 107 patients with CF and BX and defined clinical fungal infection status. Fungal and bacterial communities were explored using supervised and unsupervised machine learning to understand associations between fungal and bacterial communities and their relationship to disease. Results: Fungal and bacterial communities both had significantly higher biomass and lower diversity in CF compared to BX patients. Random forest modelling demonstrated that the fungal and bacterial communities were distinct between CF and BX patients. Within the CF group, bacterial communities contained no predictive signal for fungal disease status. Neither bacterial nor fungal community composition were predictive of the presence of CF pulmonary exacerbation (CFPE). Intra-kingdom correlations were far stronger than those between the two kingdoms. Dirichlet mixture components analysis identified two distinct clusters of bacteria related to the relative abundance of Pseudomonas. Fungal community composition contained no predictive signal for bacterial clusters. Conclusions: Clear changes in diversity were observed between patients with different clinical disease status. Although our results demonstrate that bacterial community composition differs in the presence of fungal disease, no direct relationship between bacterial and fungal OTUs was found.

The Influence of Residue Mixing on the Decomposition of Pepper Root Residues

(1) Background: Residue degradation plays a very important role in terrestrial ecosystems and residue mixing is the main factor affecting the degradation rates. However, in the agricultural systems, the effect of residue mixing on the degradation of pepper residues and the microbial community in pepper root residues is not clear. (2) Methods: In this study, we added different residues into soil by using double-layered nylon litterbags in culture bottles. The treatments including pepper root (P: Capsicum annuum L.), soybean [S: Glycine max (L.) Merr.] and maize (M: Zea mays L.) residue, as well as mixtures of soybean + pepper (SP), maize + pepper (MP), maize + soybean + pepper (MSP) mixtures. Litterbags were harvested after 7, 14, 28, and 56 days, respectively. Mass loss and nitrogen and phosphorus contents in pepper residue were quantified and bacterial and fungal community levels in pepper residues were analyzed using quantitative PCR and high throughput amplicon sequencing; (3) Results: The study showed that the mass loss and fungal community abundance of pepper root residue in mixtures were higher than P, except day 7. The phosphorus contents in MSP-P and MP-P were significantly lower than that for P at day 28 and day 56. Illumina MiSeq sequencing showed that the presence of maize residue significantly altered the microbial community composition of pepper root pepper. Day 56. (4) Conclusions: Our results suggest that residue mixing changed the microbial community abundance in pepper residue and promoted the degradation of pepper residues compared to pepper residue decomposition alone, especially for mixtures with soybean.