Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany.
ISME J. 2021 Nov;15(11):3258-3270. doi: 10.1038/s41396-021-01003-y. Epub 2021 May 19.
Plasmids have the potential to transfer genetic traits within bacterial communities and thereby serve as a crucial tool for the rapid adaptation of bacteria in response to changing environmental conditions. Our knowledge of the environmental pool of plasmids (the metaplasmidome) and encoded functions is still limited due to a lack of sufficient extraction methods and tools for identifying and assembling plasmids from metagenomic datasets. Here, we present the first insights into the functional potential of the metaplasmidome of permafrost-affected active-layer soil-an environment with a relatively low biomass and seasonal freeze-thaw cycles that is strongly affected by global warming. The obtained results were compared with plasmid-derived sequences extracted from polar metagenomes. Metaplasmidomes from the Siberian active layer were enriched via cultivation, which resulted in a longer contig length as compared with plasmids that had been directly retrieved from the metagenomes of polar environments. The predicted hosts of plasmids belonged to Moraxellaceae, Pseudomonadaceae, Enterobacteriaceae, Pectobacteriaceae, Burkholderiaceae, and Firmicutes. Analysis of their genetic content revealed the presence of stress-response genes, including antibiotic and metal resistance determinants, as well as genes encoding protectants against the cold.
质粒具有在细菌群落中转移遗传特征的潜力，因此是细菌快速适应环境变化的重要工具。由于缺乏足够的提取方法和工具来从宏基因组数据集中识别和组装质粒，我们对质粒的环境库（元质粒组）和编码功能的了解仍然有限。在这里，我们首次深入了解了受永久冻土影响的活动层土壤（一种生物量相对较低且经历季节性冻融循环的环境，受全球变暖的强烈影响）中元质粒组的功能潜力。获得的结果与从极地宏基因组中提取的质粒衍生序列进行了比较。通过培养从西伯利亚活动层中富集元质粒组，与直接从极地环境的宏基因组中检索到的质粒相比，获得了更长的连续序列。预测的质粒宿主属于莫拉氏菌科、假单胞菌科、肠杆菌科、果胶杆菌科、伯克霍尔德氏菌科和厚壁菌门。对其遗传内容的分析表明存在应激反应基因，包括抗生素和金属抗性决定因素，以及编码抗寒保护剂的基因。
