Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms
Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms
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DOI：
10.1128/msystems.00299-20
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发表时间：
2020-07-01
期刊：
影响因子：
6.4
通讯作者：
McMahon, Katherine D.
中科院分区：
文献类型：
--
作者：
McDaniel, Elizabeth A.;Peterson, Benjamin D.;McMahon, Katherine D.
甲基汞是一种有效的生物积累神经毒素，由使无机汞甲基化的特定微生物产生。最近，各种厌氧细菌和古生菌产生的甲基汞与hgcAB基因有关。然而，由于培养的实验验证的甲基化子的数量有限，以及基于引物的分子方法的局限性，汞甲基化微生物的全部系统发育和代谢多样性尚未完全揭开。在这里，我们描述了通过hgcAB鉴定在公共可获得的分离基因组和超基因组组装基因组(MAG)以及新的淡水MAG中推测的汞甲基化微生物的系统发育多样性和代谢灵活性。我们证明了推测的汞甲基化子在系统发育上比以前所知的更加多样化，并且hgcAB在基因组中的分布很可能是由于几个独立的水平基因转移事件。我们鉴定的微生物具有不同的代谢能力，跨越碳固定、硫酸盐还原、固氮和金属抗性途径。我们在之前发表的一组永久冻土变位基因中发现了111个可能的汞甲基化基因，并证明了不同的甲基化类别可能对HGCA在不同深度的表达起到作用。总之，我们提供了一个框架，用于利用基因组分辨的元基因组学和元转录组学来阐明汞甲基化的微生物基础，以基于hgcAB的存在来识别可能的甲基化子，并描述它们在环境中的可能功能。重要的是，通过表征环境中甲基化子的系统发育多样性、代谢功能和活性来准确评估生物累积神经毒性甲基汞的产生，对于理解汞循环的限制至关重要。我们对甲基汞产生的大部分理解是基于三角洲蛋白细菌、菲尔米库特和Eurya chaeota中培养的厌氧微生物。下一代测序技术的进步使得能够对来自众多生态系统的各种和特征不佳的微生物进行大规模的独立于栽培的调查。我们使用基因组分辨的元基因组学和元转录组学来强调推测的汞甲基化子的巨大系统发育和代谢多样性，以及它们在融化永久冻土中的深度离散活动。这项工作强调了使用基因组分辨的元基因组学来调查特定汞影响生态系统的特定假定甲基化种群的重要性。
Methylmercury is a potent bioaccumulating neurotoxin that is produced by specific microorganisms that methylate inorganic mercury. Methylmercury production in diverse anaerobic bacteria and archaea was recently linked to the hgcAB genes. However, the full phylogenetic and metabolic diversity of mercury-methylating microorganisms has not been fully unraveled due to the limited number of cultured experimentally verified methylators and the limitations of primer-based molecular methods. Here, we describe the phylogenetic diversity and metabolic flexibility of putative mercury-methylating microorganisms by hgcAB identification in publicly available isolate genomes and metagenome-assembled genomes (MAGs) as well as novel freshwater MAGs. We demonstrate that putative mercury methylators are much more phylogenetically diverse than previously known and that hgcAB distribution among genomes is most likely due to several independent horizontal gene transfer events. The microorganisms we identified possess diverse metabolic capabilities spanning carbon fixation, sulfate reduction, nitrogen fixation, and metal resistance pathways. We identified 111 putative mercury methylators in a set of previously published permafrost metatranscriptomes and demonstrated that different methylating taxa may contribute to hgcA expression at different depths. Overall, we provide a framework for illuminating the microbial basis of mercury methylation using genome-resolved metagenomics and metatranscriptomics to identify putative methylators based upon hgcAB presence and describe their putative functions in the environment.IMPORTANCE Accurately assessing the production of bioaccumulative neurotoxic methylmercury by characterizing the phylogenetic diversity, metabolic functions, and activity of methylators in the environment is crucial for understanding constraints on the mercury cycle. Much of our understanding of methylmercury production is based on cultured anaerobic microorganisms within the Deltaproteobacteria, Firmicutes, and Euryarchaeota. Advances in next-generation sequencing technologies have enabled large-scale cultivation-independent surveys of diverse and poorly characterized microorganisms from numerous ecosystems. We used genome-resolved metagenomics and metatranscriptomics to highlight the vast phylogenetic and metabolic diversity of putative mercury methylators and their depth-discrete activities in thawing permafrost. This work underscores the importance of using genome-resolved metagenomics to survey specific putative methylating populations of a given mercury-impacted ecosystem.