Giddings Lesley-Ann, Kunstman Kevin, Moumen Bouziane, Asiama Laurent, Green Stefan, Delafont Vincent, Brockley Matthew, Samba-Louaka Ascel
Department of Chemistry, Smith College, Northampton, MA, United States.
Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, United States.
Front Microbiol. 2022 May 23;13:856908. doi: 10.3389/fmicb.2022.856908. eCollection 2022.
Protozoa play important roles in microbial communities, regulating populations predation and contributing to nutrient cycling. While amoebae have been identified in acid rock drainage (ARD) systems, our understanding of their symbioses in these extreme environments is limited. Here, we report the first isolation of the amoeba from an ARD environment as well as the genome sequence and annotation of an associated bacterium, strain Ely Copper Mine, from Ely Brook at the Ely Copper Mine Superfund site in Vershire, Vermont, United States. Fluorescent hybridization analysis showed this bacterium colonizing cells of sp. in addition to being outside of amoebal cells. This amoeba-resistant bacterium is Gram-negative with a genome size of 5.36 Mbp and GC content of 62.5%. The genome of the strain Ely Copper Mine encodes biosynthetic pathways for amino acids, carbohydrates, nucleic acids, and lipids. Genes involved in nitrate (1) and sulfate (7) reduction, metal (229) and antibiotic resistance (37), and secondary metabolite production (6) were identified. Notably, 26 hydrolases were identified by RAST as well as other biomass degradation genes, suggesting roles in carbon and energy cycling within the microbial community. The genome also contains type IV secretion system genes involved in amoebae resistance, revealing how this bacterium likely survives predation from sp. This genome analysis and the association of strain Ely Copper Mine with sp. provide insight into the functional roles of amoebae and bacteria within ARD environments.
原生动物在微生物群落中发挥着重要作用，调节种群数量、进行捕食并促进养分循环。虽然在酸性矿山排水（ARD）系统中已发现变形虫，但我们对它们在这些极端环境中的共生关系了解有限。在此，我们报告了首次从ARD环境中分离出变形虫，以及对来自美国佛蒙特州弗希尔市伊莱铜矿超级基金场地伊莱溪的相关细菌菌株伊莱铜矿的基因组序列和注释。荧光原位杂交分析表明，这种细菌除了存在于变形虫细胞外部，还定殖于变形虫细胞内。这种抗变形虫细菌为革兰氏阴性菌，基因组大小为5.36 Mbp，GC含量为62.5%。伊莱铜矿菌株的基因组编码了氨基酸、碳水化合物、核酸和脂质的生物合成途径。鉴定出了参与硝酸盐（1个）和硫酸盐（7个）还原、金属（229个）和抗生素抗性（37个）以及次级代谢产物产生（6个）的基因。值得注意的是，RAST鉴定出26种水解酶以及其他生物质降解基因，表明其在微生物群落中的碳和能量循环中发挥作用。该基因组还包含与抗变形虫有关的IV型分泌系统基因，揭示了这种细菌可能如何在变形虫的捕食中存活下来。这种基因组分析以及伊莱铜矿菌株与变形虫的关联，为深入了解ARD环境中变形虫和细菌的功能作用提供了线索。
