Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence
Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence
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DOI：
10.1128/aem.02646-18
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发表时间：
2019-04-01
影响因子：
4.4
通讯作者：
Mackelprang, Rachel
中科院分区：
文献类型：
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作者：
Burkert, Alexander;Douglas, Thomas A.;Mackelprang, Rachel
永久冻土承载着一个微生物群落，尽管极端的环境条件下，如水压力，零度以下的温度，高盐度和低养分可用性，这些微生物仍然生存和繁殖了数千年。多年冻土微生物群落组成的研究多采用基于DNA的方法，如宏基因组学和16 S rRNA基因测序。然而，这些方法不能区分活跃、死亡和休眠细胞。这在古冻土中尤其令人担忧，在那里，恒定的零度以下温度可以保护DNA免受死亡生物的伤害，休眠可能是一种常见的生存策略。为了解决这个问题，我们应用了（i）活/死差异染色结合显微镜，（ii）内生孢子富集，以及（iii）选择性耗尽死细胞中的DNA，以跨越更新世永久冻土年代序列（19，000年、27，000年和33，000年）的永久冻土微生物群落。细胞计数和16 S rRNA基因扩增子从活的，死的，和休眠细胞的分析揭示了这些池之间的社区如何不同，它们是如何受到土壤理化性质的影响，以及它们是否随着地质时代的变化。我们发现的证据表明，能够形成内生孢子的细胞不一定是休眠的，芽孢杆菌类的成员更有可能形成内生孢子，以应对长期的压力与冻土环境条件比梭菌属的成员，这是更有可能坚持作为营养细胞在我们的老样品。我们还发现，去除保存在永久冻土中的外源性“遗迹”DNA并没有显着改变微生物群落组成。这些结果将活的、死的和休眠的微生物群落与物理化学特征联系起来，并为古冻土中微生物群落的生存提供了见解。重要意义尽管覆盖了15%的土地面积（C. Tarnocai等人，Global Biogeochem Cycles 23：GB2023，2009，https：//doi.org/10.1029/2008G8003327）。这种永久冻土碳在解冻后迅速降解（E。A. G. Schuur等人，Nature 520：171-179，2015，https：//doi.org/10.1038/nature14338）。了解微生物群落在永冻层将有助于了解的速率和形式的永冻层C和N循环解冻后的知识基础。永久冻土也是冰冻的外星环境的一种模拟，在古代永久冻土中存在可行生物的证据对于那些在遥远世界寻找潜在生命的人来说是很有意义的。如果我们能够确定微生物群落在永冻层中生存的策略，它可能会让我们深入了解生命（如果存在的话）如何在地球以外的冰冻环境中生存。我们的工作意义重大，因为它有助于了解微生物如何在永久冻土地带的极端环境条件下适应和生存。
Permafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions, such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods, such as metagenomics and 16S rRNA gene sequencing. However, these methods do not distinguish among active, dead, and dormant cells. This is of particular concern in ancient permafrost, where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this, we applied (i) LIVE/DEAD differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19,000, 27,000, and 33,000 years old). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of the class Bacilli were more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of the Clostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous "relic" DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provide insights into the survival of microbial communities in ancient permafrost.IMPORTANCE Permafrost soils store more than half of Earth's soil carbon despite covering similar to 15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23: GB2023, 2009, https://doi.org/10.1029/2008G8003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171-179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.