Research Network Chemistry meets Microbiology, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria.
Department of Biology, University of Konstanz, Konstanz, Germany.
mBio. 2019 Feb 12;10(1):e02189-18. doi: 10.1128/mBio.02189-18.
Microbial diversity in the environment is mainly concealed within the rare biosphere (all species with <0.1% relative abundance). While dormancy explains a low-abundance state very well, the mechanisms leading to rare but active microorganisms remain elusive. We used environmental systems biology to genomically and transcriptionally characterize " Desulfosporosinus infrequens," a low-abundance sulfate-reducing microorganism cosmopolitan to freshwater wetlands, where it contributes to cryptic sulfur cycling. We obtained its near-complete genome by metagenomics of acidic peat soil. In addition, we analyzed anoxic peat soil incubated under -like conditions for 50 days by -targeted qPCR and metatranscriptomics. The population stayed at a constant low abundance under all incubation conditions, averaging 1.2 × 10 16S rRNA gene copies per cm³ soil. In contrast, transcriptional activity of " Desulfosporosinus infrequens" increased at day 36 by 56- to 188-fold when minor amendments of acetate, propionate, lactate, or butyrate were provided with sulfate, compared to the no-substrate-control. Overall transcriptional activity was driven by expression of genes encoding ribosomal proteins, energy metabolism, and stress response but not by expression of genes encoding cell growth-associated processes. Since our results did not support growth of these highly active microorganisms in terms of biomass increase or cell division, they had to invest their sole energy for maintenance, most likely counterbalancing acidic pH conditions. This finding explains how a rare biosphere member can contribute to a biogeochemically relevant process while remaining in a zero-growth state over a period of 50 days. The microbial rare biosphere represents the largest pool of biodiversity on Earth and constitutes, in sum of all its members, a considerable part of a habitat's biomass. Dormancy or starvation is typically used to explain the persistence of low-abundance microorganisms in the environment. We show that a low-abundance microorganism can be highly transcriptionally active while remaining in a zero-growth state for at least 7 weeks. Our results provide evidence that this zero growth at a high cellular activity state is driven by maintenance requirements. We show that this is true for a microbial keystone species, in particular a cosmopolitan but permanently low-abundance sulfate-reducing microorganism in wetlands that is involved in counterbalancing greenhouse gas emissions. In summary, our results provide an important step forward in understanding time-resolved activities of rare biosphere members relevant for ecosystem functions.
环境中的微生物多样性主要隐藏在稀有生物界(相对丰度<0.1%的所有物种)中。虽然休眠很好地解释了低丰度状态,但导致稀有但活跃的微生物的机制仍然难以捉摸。我们使用环境系统生物学对普遍存在于淡水湿地的低丰度硫酸盐还原微生物“脱硫贫养菌”进行了基因组学和转录组学研究,它有助于隐蔽的硫循环。我们通过酸性泥炭土的宏基因组学获得了它的近完整基因组。此外,我们通过对在类似条件下培养 50 天的缺氧泥炭土进行靶向 qPCR 和宏转录组学分析。在所有培养条件下,该种群的丰度一直保持在较低的恒定水平,平均每立方厘米土壤中有 1.2×10 16S rRNA 基因拷贝。相比之下,当用硫酸盐提供少量乙酸盐、丙酸盐、乳酸盐或丁酸盐作为补充时,“脱硫贫养菌”的转录活性在第 36 天增加了 56-188 倍,与无底物对照相比。总的转录活性是由核糖体蛋白、能量代谢和应激反应相关基因的表达驱动的,但不是由与细胞生长相关过程的基因表达驱动的。由于我们的结果不支持这些高度活跃的微生物在生物量增加或细胞分裂方面的生长,它们必须将其唯一的能量用于维持,这很可能抵消了酸性 pH 条件。这一发现解释了为什么一个稀有生物界成员可以在 50 天的时间内保持零生长状态的情况下,仍然对生物地球化学相关过程做出贡献。微生物稀有生物界代表了地球上最大的生物多样性库,并且在其所有成员的总和中,构成了栖息地生物量的相当一部分。休眠或饥饿通常被用来解释低丰度微生物在环境中的持久性。我们表明,一种低丰度的微生物可以在保持零生长状态至少 7 周的情况下保持高度转录活性。我们的结果提供了证据表明,这种在高细胞活性状态下的零生长是由维持需求驱动的。我们表明,这对于一种微生物关键种是正确的,特别是在湿地中普遍存在但始终处于低丰度的硫酸盐还原微生物,它有助于抵消温室气体排放。总之,我们的结果为理解与生态系统功能相关的稀有生物界成员的时间分辨活性提供了重要的一步。