Ecological features of microbial community linked to stochastic and deterministic assembly processes in acid mine drainage

• Published in: Applied and environmental microbiology 2024-12, p.e0102824
• Main Authors: Liu, Zhenghua, Jiang, Chengying, Yin, Zhuzhong, Ibrahim, Ibrahim Ahmed, Zhang, Teng, Wen, Jing, Zhou, Lei, Jiang, Guoping, Li, Liangzhi, Yang, Zhendong, Huang, Ye, Yang, Zhaoyue, Gu, Yabing, Meng, Delong, Yin, Huaqun
• Format: Article
• Language: English
• Subjects: Bacteriophages; Microbial Ecology
• ISSN: 0099-2240; 1098-5336; 1098-5336
• DOI: 10.1128/aem.01028-24

Ecological processes greatly shape microbial community assembly, but the driving factors remain unclear. Here, we compiled a metagenomic data set of microbial communities from global acid mine drainage (AMD) and explored the ecological features of microbial community linked to stochastic and deterministic processes from the perspective of species niche position, interaction patterns, gene functions, and viral infection. Our results showed that dispersal limitation (DL) (48.5%~93.5%) dominated the assembly of phylogenetic bin in AMD microbial community, followed by homogeneous selection (HoS) (3.1%~39.2%), heterogeneous selection (HeS) (1.4%~22.2%), and drift (DR) (0.2%~2.7%). The dominant process of dispersal limitation was significantly influenced by niche position in temperature ( = -0.518, = 0.007) and dissolved oxygen ( = 0.471, = 0.015). Network stability had a significantly negative correlation with the relative importance of dispersal limitation, while it had a positive correlation with selection processes, implying changes in network properties could be mediated by ecological processes. Furthermore, we found that ecological processes were mostly related to the gene functions of energy production and conversion (C), and amino acid transport and metabolism (E). Meanwhile, our results showed that the number of proviruses and viral genes involved in arsenic (As) resistance is negatively associated with the relative importance of ecological drift in phylogenetic bin assembly, implying viral infection might weaken ecological drift. Taken together, these results highlight that ecological processes are associated with ecological features at multiple levels, providing a novel insight into microbial community assembly in extremely acidic environments. Unraveling the forces driving community assemblage is a core issue in microbial ecology, but how ecological constraints impose stochasticity and determinism remains unknown. This study presents a comprehensive investigation to uncover the association of ecological processes with species niche position, interaction patterns, microbial metabolisms, and viral infections, which provides novel insights into community assembly in extreme environments.