Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity
Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity
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DOI：
10.1186/s40168-019-0623-8
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发表时间：
2019-01-28
期刊：
影响因子：
15.5
通讯作者：
Golyshina, Olga V.
中科院分区：
文献类型：
--
作者：
Korzhenkov, Aleksei A.;Toshchakov, Stepan V.;Golyshina, Olga V.
背景：目前的观点认为，在低温酸性环境中，古细菌的丰度明显低于细菌。因此，这项对帕里斯山（英国安格尔西）微生物组的研究揭示了目前这一假设的普遍性。帕里斯山是一个历史上重要的铜矿，其酸性矿山排水（AMD）水流的特点是恒定的中等温度（8-18摄氏度），极低的pH值（1。7)结果：帕里斯山古菌宏基因组DNA和SSU rRNA扩增产物序列分析显示，该地区古菌中属于广古菌门的比例较高，约占总古菌门的10%。社区的67%。在这个门，潜在的新分支的热浆门是过度代表（58%），与最主要的组是“E-血浆”，旁边低丰度Cuniculiplasmataceae，“Ca。Micrarchaeota“和”陆地杂广古菌群“（TMEG）古菌，它们在遗传学上接近于Methanomassilicoccales，并与酸性/中等酸性环境中的对应物聚类。在沉积物中，古菌和热浆菌贡献了最高的V3-V4扩增子读数，与水体群落形成对比，其中变形菌，硝化螺菌，酸杆菌和放线菌超过古菌。培养的努力揭示了丰富的古菌序列密切相关的Cuniculiplasma divulgatum在富集培养建立从过滤部分的水样。未过滤样品的富集培养物显示存在Ferrimicrobium acidophilum、C. divulgatum，'Ca.嗜酸Mancarchaeum acidiphilum Mia 14 '，'Ca.结论：与预期相反，我们的研究表明，在这种极端酸性的矿山影响的环境中，古细菌的丰度很高。此外，古菌种群由一个特定的群体主导，这表明它们在功能上很重要。在这些微生物群中古细菌的流行及其空间分布模式代表了我们对嗜酸菌生态学的理解的一个新的重要进展。我们还展示了一个程序的具体富集的细胞壁缺陷的成员的古细菌组成的这个社会，虽然大部分的古细菌类群仍然是不可培养的。最后，我们确定了一个单独的集群，全球发生的嗜酸性成员TMEG，共同属于一个不同的顺序内热浆菌，但在生态系统中的功能作用尚不清楚。
Background: The current view suggests that in low-temperature acidic environments, archaea are significantly less abundant than bacteria. Thus, this study of the microbiome of Parys Mountain (Anglesey, UK) sheds light on the generality of this current assumption. Parys Mountain is a historically important copper mine and its acid mine drainage (AMD) water streams are characterised by constant moderate temperatures (8-18 degrees C), extremely low pH (1. 7) and high concentrations of soluble iron and other metal cations.Results: Metagenomic and SSU rRNA amplicon sequencing of DNA from Parys Mountain revealed a significant proportion of archaea affiliated with Euryarchaeota, which accounted for ca. 67% of the community. Within this phylum, potentially new clades of Thermoplasmata were overrepresented (58%), with the most predominant group being "E-plasma", alongside low-abundant Cuniculiplasmataceae, 'Ca. Micrarchaeota' and 'Terrestrial Miscellaneous Euryarchaeal Group' (TMEG) archaea, which were phylogenetically close to Methanomassilicoccales and clustered with counterparts from acidic/moderately acidic settings. In the sediment, archaea and Thermoplasmata contributed the highest numbers in V3-V4 amplicon reads, in contrast with the water body community, where Proteobacteria, Nitrospirae, Acidobacteria and Actinobacteria outnumbered archaea. Cultivation efforts revealed the abundance of archaeal sequences closely related to Cuniculiplasma divulgatum in an enrichment culture established from the filterable fraction of the water sample. Enrichment cultures with unfiltered samples showed the presence of Ferrimicrobium acidiphilum, C. divulgatum, 'Ca. Mancarchaeum acidiphilum Mia14', 'Ca. Micrarchaeota'-related and diverse minor (< 2%) bacterial metagenomic reads.Conclusion: Contrary to expectation, our study showed a high abundance of archaea in this extremely acidic mine-impacted environment. Further, archaeal populations were dominated by one particular group, suggesting that they are functionally important. The prevalence of archaea over bacteria in these microbiomes and their spatial distribution patterns represents a novel and important advance in our understanding of acidophile ecology. We also demonstrated a procedure for the specific enrichment of cell wall-deficient members of the archaeal component of this community, although the large fraction of archaeal taxa remained unculturable. Lastly, we identified a separate clustering of globally occurring acidophilic members of TMEG that collectively belong to a distinct order within Thermoplasmata with yet unclear functional roles in the ecosystem.