Frank Yulia A, Kadnikov Vitaly V, Gavrilov Sergey N, Banks David, Gerasimchuk Anna L, Podosokorskaya Olga A, Merkel Alexander Y, Chernyh Nikolai A, Mardanov Andrey V, Ravin Nikolai V, Karnachuk Olga V, Bonch-Osmolovskaya Elizaveta A
Department of Plant Physiology and Biotechnology, Tomsk State University Tomsk, Russia.
Federal Research Centre (FRC) Biotechnology, Institute of Bioengineering Moscow, Russia.
Front Microbiol. 2016 Dec 27;7:2101. doi: 10.3389/fmicb.2016.02101. eCollection 2016.
The goal of this work was to study the diversity of microorganisms inhabiting a deep subsurface aquifer system in order to understand their functional roles and interspecies relations formed in the course of buried organic matter degradation. A microbial community of a deep subsurface thermal aquifer in the Tomsk Region, Western Siberia was monitored over the course of 5 years via a 2.7 km deep borehole 3P, drilled down to a Palaeozoic basement. The borehole water discharges with a temperature of ca. 50°C. Its chemical composition varies, but it steadily contains acetate, propionate, and traces of hydrocarbons and gives rise to microbial mats along the surface flow. Community analysis by PCR-DGGE 16S rRNA genes profiling, repeatedly performed within 5 years, revealed several dominating phylotypes consistently found in the borehole water, and highly variable diversity of prokaryotes, brought to the surface with the borehole outflow. The major planktonic components of the microbial community were and spp. The composition of the minor part of the community was unstable, and molecular analysis did not reveal any regularity in its variations, except some predominance of uncultured s. Batch cultures with complex organic substrates inoculated with water samples were set in order to enrich prokaryotes from the variable part of the community. PCR-DGGE analysis of these enrichments yielded uncultured , and . A continuous-flow microaerophilic enrichment culture with a water sample amended with acetate contained , which was previously detected in the microbial mat developing at the outflow of the borehole. Cultivation results allowed us to assume that variable components of the 3P well community are hydrolytic organotrophs, degrading buried biopolymers, while the constant planktonic components of the community degrade dissolved fermentation products to methane and CO, possibly via interspecies hydrogen transfer. Occasional washout of minor community components capable of oxygen respiration leads to the development of microbial mats at the outflow of the borehole where residual dissolved fermentation products are aerobically oxidized. Long-term community analysis with the combination of molecular and cultivation techniques allowed us to characterize stable and variable parts of the community and propose their environmental roles.
这项工作的目标是研究栖息于深层地下含水层系统中的微生物多样性，以便了解它们在埋藏有机物降解过程中形成的功能作用和种间关系。通过钻入古生代基底的2.7千米深的3P钻孔，对西西伯利亚托木斯克地区深层地下热水含水层的微生物群落进行了为期5年的监测。钻孔水的温度约为50°C。其化学成分各不相同，但始终含有乙酸盐、丙酸盐和微量碳氢化合物，并在地表水流沿线形成微生物垫。通过PCR-DGGE 16S rRNA基因图谱分析在5年内反复进行群落分析，结果显示在钻孔水中始终发现有几种优势系统型，并且随着钻孔流出物带到地表的原核生物具有高度可变的多样性。微生物群落的主要浮游成分是 和 属。群落次要部分的组成不稳定，分子分析未发现其变化有任何规律，除了未培养的 属有一定优势。为了从群落的可变部分富集原核生物，用采集的水样接种复杂有机底物进行分批培养。对这些富集培养物进行PCR-DGGE分析，得到了未培养的 、 和 。用乙酸盐改良的水样进行连续流微需氧富集培养，得到了 ，该菌先前在钻孔流出物处形成的微生物垫中被检测到。培养结果使我们推测，3P井群落的可变成分是水解有机营养菌，降解埋藏的生物聚合物，而群落中恒定的浮游成分可能通过种间氢转移将溶解的发酵产物降解为甲烷和二氧化碳。偶尔冲刷掉能够进行有氧呼吸的次要群落成分，导致钻孔流出物处形成微生物垫，在那里残留的溶解发酵产物被有氧氧化。结合分子和培养技术进行的长期群落分析，使我们能够表征群落的稳定和可变部分，并提出它们的环境作用。
