宏基因组学揭示水生环境中抗性基因的丰度和组成：分层和地理的影响。
Metagenomic insights into the abundance and composition of resistance genes in aquatic environments: Influence of stratification and geography.
机构信息
Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK.
School of Agriculture, Ludong University, Yantai 264025, China.
出版信息
Environ Int. 2019 Jun;127:371-380. doi: 10.1016/j.envint.2019.03.062. Epub 2019 Apr 4.
A global survey was performed with 122 aquatic metagenomic DNA datasets (92 lake water and 30 seawater) obtained from the Sequence Read Archive (SRA). Antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) were derived from the dataset sequences via bioinformatic analysis. The relative abundances of ARGs and MRGs in lake samples were in the ranges ND (not detected)-1.34 × 10 and 1.22 × 10-1.98 × 10 copies per 16S rRNA, which were higher than those in seawater samples. Among ARGs, multidrug resistance genes and bacitracin resistance genes had high relative abundances in both lake and sea water samples. Multi-metal resistance genes, mercury resistance genes and copper resistance genes had the greatest relative abundance for MRGs. No significant difference was found between epilimnion and hypolimnion in abundance or the Shannon diversity index for ARGs and MRGs. Principal coordinates analysis and permutational multivariate analysis of variance (PERMANOVA) test showed that stratification and geography had significant influence on the composition of ARGs and MRGs in lakes (p < 0.05, PERMANOVA). Coastal seawater samples had significantly greater relative abundance and a higher Shannon index for both ARGs and MRGs than deep ocean and Antarctic seawater samples (p < 0.05, Kruskal-Wallis one-way ANOVA), suggesting that human activity may exert more selective pressure on ARGs and MRGs in coastal areas than those in deep ocean and Antarctic seawater.
本研究对从 Sequence Read Archive（SRA）获得的 122 个水生宏基因组 DNA 数据集（92 个湖水和 30 个海水）进行了全球调查。通过生物信息学分析，从数据集序列中获得了抗生素抗性基因（ARGs）和金属抗性基因（MRGs）。湖泊样本中 ARG 和 MRG 的相对丰度范围为 ND（未检出）-1.34×10 和 1.22×10-1.98×10 拷贝 16S rRNA，高于海水样本。在 ARGs 中，多药耐药基因和杆菌肽耐药基因在湖水和海水中的相对丰度较高。多金属耐药基因、汞耐药基因和铜耐药基因是 MRGs 中相对丰度最高的基因。湖水中 ARG 和 MRG 的丰度或 Shannon 多样性指数在表水层和底水层之间没有显著差异。主坐标分析和置换多元方差分析（PERMANOVA）检验表明，分层和地理位置对湖泊中 ARG 和 MRG 的组成有显著影响（p<0.05，PERMANOVA）。沿海海水样本中 ARGs 和 MRGs 的相对丰度和 Shannon 指数均显著高于深海和南极海水样本（p<0.05，Kruskal-Wallis 单向 ANOVA），表明人类活动可能对沿海地区的 ARGs 和 MRGs 施加了比深海和南极海水更大的选择性压力。
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