摘要
      沉积物中微生物群落对环境扰动的系统发育转换机制尚不清楚。在这项研究中，揭示了系统发育转换的分子机制，以及抗生素和抗生素抗性基因（ARGs）对微生物组合修饰的影响。我们通过高通量定量PCR和illumina测序，研究了306个ARGs、8个转座酶和4个整合子整合酶、细菌和真核生物多样性、21种抗生素和3种四环素副产物。与以分枝杆菌属为主的河口生态系统相比，淡水和河口生态系统主要由硫卵属主导，并由密切相关的物种定居（接近中心度=0.42对0.46）。细菌群落中86%的生态过程是由随机过程驱动的，而其余的是由确定性过程驱动的。与环境相关的抗生素浓度（0.15–32.53纳克/克）刺激了ARGs的增殖，这可能会调节微生物群落的组装。ARG的获得通过保护机制显著增加了真核生物的多样性（P＜0.001）。ARG与微生物群落表现出复杂的相互关系，节肢动物门和线虫门表现出最强的ARG获取潜力。这项研究为环境政策制定者了解抗生素的生态影响以及ARGs在调节微生物群落系统发育周转和营养转移机制中的作用提供了关键见解。
Abstract
The mechanisms of phylogenetic turnover of microbial communities to environmental perturbations in sediments remain unclear. In this study, the molecular mechanisms of phylogenetic turnover, and impact of antibiotics and antibiotic resistance genes (ARGs) on the modification of microbial assemblages were unravelled. We investigated 306 ARGs, 8 transposases, and 4 integron integrases, bacteria, and eukaryotic diversity through high-throughput quantitative PCR and illumina sequencing, 21 antibiotics and 3 tetracycline byproducts. The freshwater and estuary ecosystems were mainly dominated by genus Sulfurovum and colonised by closely related species compared with the estuary (closeness centrality = 0.42 vs. 0.46), which was dominated by genus Mycobacterium. Eighty-six percent of the ecological process in the bacterial community was driven by stochastic processes, while the rest was driven by deterministic processes. Environmental-related concentrations of antibiotics (0.15–32.53 ng/g) stimulated the proliferation of ARGs which potentially modulated the microbial community assembly. ARG acquisition significantly (P < 0.001) increased eukaryotic diversity through protection mechanisms. ARGs showed complex interrelationships with the microbial communities, and phylum arthropods and Nematea demonstrated the strongest ARG acquisition potential. This study provides key insights for environmental policymakers into understanding the ecological impact of antibiotics and the role of ARGs in modulating the phylogenetic turnover of microbial communities and trophic transfer mechanisms.

https://www.sciencedirect.com/science/article/abs/pii/S030147972202120X