Department of Biology, University of Central Arkansas, Conway, AR, 72035, USA.
Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.
Environ Microbiol. 2021 Jan;23(1):126-142. doi: 10.1111/1462-2920.15279. Epub 2020 Nov 3.
As predators of bacteria, amoebae select for traits that allow bacteria to become symbionts by surviving phagocytosis and exploiting the eukaryotic intracellular environment. Soil-dwelling social amoebae can help us answer questions about the natural ecology of these amoeba-bacteria symbioses along the pathogen-mutualist spectrum. Our objective was to characterize the natural bacterial microbiome of phylogenetically and morphologically diverse social amoeba species using next-generation sequencing of 16S rRNA amplicons directly from amoeba fruiting bodies. We found six phyla of amoeba-associated bacteria: Proteobacteria, Bacteroidetes, Actinobacteria, Chlamydiae, Firmicutes, and Acidobacteria. The most common associates of amoebae were classified to order Chlamydiales and genus Burkholderia-Caballeronia-Paraburkholderia. These bacteria were present in multiple amoeba species across multiple locations. While there was substantial intraspecific variation, there was some evidence for host specificity and differentially abundant taxa between different amoeba hosts. Amoebae microbiomes were distinct from the microbiomes of their soil habitat, and soil pH affected amoeba microbiome diversity. Alpha-diversity was unsurprisingly lower in amoebae samples compared with soil, but beta-diversity between amoebae samples was higher than between soil samples. Further exploration of social amoebae microbiomes may help us understand the roles of bacteria, host, and environment on symbiotic interactions and microbiome formation in basal eukaryotic organisms.
作为细菌的捕食者，变形虫通过存活吞噬作用并利用真核细胞内环境选择使细菌成为共生体的特征。土壤中存在的群居变形虫可以帮助我们回答有关这些变形虫-细菌共生体沿着病原体-共生体谱的自然生态学问题。我们的目标是使用直接从变形虫生殖体中扩增的 16S rRNA 扩增子对具有系统发育和形态多样性的群居变形虫物种的天然细菌微生物组进行特征描述。我们发现了六种与变形虫相关的细菌门：变形菌门、拟杆菌门、放线菌门、衣原体门、厚壁菌门和酸杆菌门。变形虫最常见的共生体被归类为衣原体目和伯克霍尔德氏菌-卡巴利奥尼亚菌-副伯克霍尔德氏菌属。这些细菌存在于多个地点的多种变形虫物种中。虽然存在大量的种内变异，但宿主特异性和不同变形虫宿主之间的差异丰度类群存在一些证据。变形虫微生物组与它们的土壤栖息地的微生物组不同，土壤 pH 值影响变形虫微生物组的多样性。与土壤相比，变形虫样本中的 alpha 多样性明显较低，但变形虫样本之间的 beta 多样性高于土壤样本之间的 beta 多样性。进一步探索群居变形虫微生物组可能有助于我们理解细菌、宿主和环境对共生相互作用和基础真核生物微生物组形成的作用。
