Zhong Zhi-Ping, Solonenko Natalie E, Gazitúa Maria C, Kenny Donald V, Mosley-Thompson Ellen, Rich Virginia I, Van Etten James L, Thompson Lonnie G, Sullivan Matthew B
Byrd Polar and Climate Research Center, The Ohio State University, Columbus, OH, United States.
Department of Microbiology, The Ohio State University, Columbus, OH, United States.
Front Microbiol. 2018 May 25;9:1094. doi: 10.3389/fmicb.2018.01094. eCollection 2018.
Microorganisms in glacier ice provide tens to hundreds of thousands of years archive for a changing climate and microbial responses to it. Analyzing ancient ice is impeded by technical issues, including limited ice, low biomass, and contamination. While many approaches have been evaluated and advanced to remove contaminants on ice core surfaces, few studies leverage modern sequencing to establish decontamination protocols for glacier ice. Here we sought to apply such "clean" sampling techniques with decontamination approaches used elsewhere to investigate microorganisms archived in ice at ∼41 (D41, ∼20,000 years) and ∼49 m (D49, ∼30,000 years) depth in an ice core (GS3) from the summit of the Guliya ice cap in the northwestern Tibetan Plateau. Four "background" controls were established - a co-processed sterile water artificial ice core, two air samples collected from the ice processing laboratories, and a blank, sterile water sample - and used to assess contaminant microbial diversity and abundances. Amplicon sequencing revealed 29 microbial genera in these controls, but quantitative PCR showed that the controls contained about 50-100-times less 16S DNA than the glacial ice samples. As in prior work, we interpreted these low-abundance taxa in controls as "contaminants" and proportionally removed them from the GS3 ice amplicon data. Because of the low biomass in the controls, we also compared prokaryotic 16S DNA amplicons from pre-amplified (by re-conditioning PCR) and standard amplicon sequencing, and found the resulting microbial profiles to be repeatable and nearly identical. Ecologically, the contaminant-controlled ice microbial profiles revealed significantly different microorganisms across the two depths in the GS3 ice core, which is consistent with changing climate, as reported for other glacier ice samples. Many GS3 ice core genera, including , , , , , and , were also abundant in previously studied ice cores, which suggests wide distribution across glacier environments. Together these findings help further establish "clean" procedures for studying low-biomass ice microbial communities and contribute to a baseline understanding of microorganisms archived in glacier ice.
冰川冰中的微生物为气候变化以及微生物对气候变化的响应提供了数万年至数十万年前的记录。对古代冰的分析受到技术问题的阻碍，包括冰量有限、生物量低和污染。虽然已经评估并改进了许多方法来去除冰芯表面的污染物，但很少有研究利用现代测序技术来建立冰川冰的去污方案。在这里，我们试图应用这种“清洁”采样技术以及其他地方使用的去污方法，来研究藏西北古里雅冰帽顶部一个冰芯（GS3）中深度约41米（D41，约20000年）和约49米（D49，约30000年）处封存的微生物。建立了四个“背景”对照——一个共同处理的无菌水人工冰芯、从冰处理实验室采集的两个空气样本以及一个空白无菌水样本——并用于评估污染物微生物的多样性和丰度。扩增子测序在这些对照中揭示了29个微生物属，但定量PCR显示对照中含有的16S DNA比冰川冰样本少约50至100倍。与之前的工作一样，我们将对照中这些低丰度分类群解释为“污染物”，并按比例从GS3冰扩增子数据中去除它们。由于对照中的生物量较低，我们还比较了预扩增（通过重新条件PCR）和标准扩增子测序得到的原核16S DNA扩增子，发现得到的微生物图谱具有可重复性且几乎相同。从生态学角度来看，去除污染物后的冰微生物图谱显示，GS3冰芯两个深度的微生物存在显著差异，这与其他冰川冰样本所报道的气候变化一致。许多GS3冰芯属，包括 、 、 、 、 和 ，在之前研究的冰芯中也很丰富，这表明它们在冰川环境中分布广泛。这些发现共同有助于进一步建立研究低生物量冰微生物群落的“清洁”程序，并有助于对冰川冰中封存的微生物有一个基线了解。
