16S rRNA/rRNA Gene Ratios and Cell Activity Staining Reveal Consistent Patterns of Microbial Activity in Plant-Associated Soil
16S rRNA/rRNA Gene Ratios and Cell Activity Staining Reveal Consistent Patterns of Microbial Activity in Plant-Associated Soil
复制标题
DOI：
10.1128/msystems.00003-19
复制
发表时间：
2019-03-01
期刊：
影响因子：
6.4
通讯作者：
Shade, Ashley
中科院分区：
文献类型：
--
作者：
Bowsher, Alan W.;Kearns, Patrick J.;Shade, Ashley
在任何给定的时间，只有一部分微生物群落成员在其环境中活跃。其他的则处于休眠状态，代谢率大大降低。区分活跃和不活跃的微生物细胞和分类群，以了解它们对生态系统过程的功能贡献，并了解微生物活动对变化的反应，这是很有意义的。在用于评估微生物活性-休眠动力学的方法中，16 S rRNA/rRNA基因扩增子（16 S比率）和用5-氰基-2，3-二甲苯基四唑氯化物（CTC）进行的活性细胞染色是两种最常见的方法，但每种方法都有局限性。鉴于在原地活动休眠动态代理只有通过实验室的方法，需要进一步的研究，以评估这些方法的协议和潜在的互补性的水平。我们进行了两个实验，调查植物相关土壤中的微生物活性。首先，我们用植物激素处理玉米田土壤来模拟植物土壤胁迫信号，其次，我们使用了暴露于干旱或营养富集的普通菜豆植物的根际土壤。总的来说，当处理效果较大时，16 S比率和CTC方法在处理之间表现出相似的相对活性模式，并且它们不同的情况可以归因于群落大小的变化（例如，细胞死亡或生长）。因此，无论用于评估活动的方法，我们建议量化群落规模，以告知生态解释。我们的研究结果表明，16 S比和CTC方法报告可比的活动模式，可以应用于观察生态动态随时间，空间，或实验treatment.IMPORTANCE虽然大多数的微生物在自然生态系统中是休眠的，相对知之甚少的动态的活性和休眠的微生物池通过空间和时间。有限的知识微生物活性休眠动力学的部分原因是目前用于量化活性类群的方法的不确定性。在这里，我们直接比较了两种最常见的方法（16 S比值和活性细胞染色），用于估计植物相关土壤中的微生物活性，发现它们在总体模式上基本一致。我们的研究结果表明，16 S比值和活性细胞染色提供了测量和解释土壤中的微生物活性休眠动态的补充信息。他们还支持16 S rRNA/rRNA基因比率具有比较价值的观点，并提供了一种高通量的基于测序的选择，用于了解微生物组活性的相对变化，只要这种方法与群落大小的定量相结合。
At any given time, only a subset of microbial community members are active in their environment. The others are in a state of dormancy, with strongly reduced metabolic rates. It is of interest to distinguish active and inactive microbial cells and taxa to understand their functional contributions to ecosystem processes and to understand shifts in microbial activity in response to change. Of the methods used to assess microbial activity-dormancy dynamics, 16S rRNA/rRNA gene amplicons (16S ratios) and active cell staining with 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) are two of the most common, yet each method has limitations. Given that in situ activity-dormancy dynamics are proxied only by laboratory methods, further study is needed to assess the level of agreement and potential complementarity of these methods. We conducted two experiments investigating microbial activity in plant-associated soils. First, we treated corn field soil with phytohormones to simulate plant soil stress signaling, and second, we used rhizosphere soil from common bean plants exposed to drought or nutrient enrichment. Overall, the 16S ratio and CTC methods exhibited similar patterns of relative activity across treatments when treatment effects were large, and the instances in which they differed could be attributed to changes in community size (e.g., cell death or growth). Therefore, regardless of the method used to assess activity, we recommend quantifying community size to inform ecological interpretation. Our results suggest that the 16S ratio and CTC methods report comparable patterns of activity that can be applied to observe ecological dynamics over time, space, or experimental treatment.IMPORTANCE Although the majority of microorganisms in natural ecosystems are dormant, relatively little is known about the dynamics of the active and dormant microbial pools through both space and time. The limited knowledge of microbial activity-dormancy dynamics is in part due to uncertainty in the methods currently used to quantify active taxa. Here, we directly compared two of the most common methods (16S ratios and active cell staining) for estimating microbial activity in plant-associated soil and found that they were largely in agreement in the overarching patterns. Our results suggest that 16S ratios and active cell staining provide complementary information for measuring and interpreting microbial activity-dormancy dynamics in soils. They also support the idea that 16S rRNA/rRNA gene ratios have comparative value and offer a high-throughput, sequencing-based option for understanding relative changes in microbiome activity, as long as this method is coupled with quantification of community size.