Shen Liang, Liu Yongqin, Allen Michelle A, Xu Baiqing, Wang Ninglian, Williams Timothy J, Wang Feng, Zhou Yuguang, Liu Qing, Cavicchioli Ricardo
State Key Laboratory of Tibetan Plateau Earth System and Resources Environment, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.
College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
Microbiome. 2021 Jun 12;9(1):136. doi: 10.1186/s40168-021-01084-z.
Microorganisms drive critical global biogeochemical cycles and dominate the biomass in Earth's expansive cold biosphere. Determining the genomic traits that enable psychrophiles to grow in cold environments informs about their physiology and adaptive responses. However, defining important genomic traits of psychrophiles has proven difficult, with the ability to extrapolate genomic knowledge to environmental relevance proving even more difficult.
Here we examined the bacterial genus Arthrobacter and, assisted by genome sequences of new Tibetan Plateau isolates, defined a new clade, Group C, that represents isolates from polar and alpine environments. Group C had a superior ability to grow at -1°C and possessed genome G+C content, amino acid composition, predicted protein stability, and functional capacities (e.g., sulfur metabolism and mycothiol biosynthesis) that distinguished it from non-polar or alpine Group A Arthrobacter. Interrogation of nearly 1000 metagenomes identified an over-representation of Group C in Canadian permafrost communities from a simulated spring-thaw experiment, indicative of niche adaptation, and an under-representation of Group A in all polar and alpine samples, indicative of a general response to environmental temperature.
The findings illustrate a capacity to define genomic markers of specific taxa that potentially have value for environmental monitoring of cold environments, including environmental change arising from anthropogenic impact. More broadly, the study illustrates the challenges involved in extrapolating from genomic and physiological data to an environmental setting. Video Abstract.
微生物驱动着全球关键的生物地球化学循环，并在地球广袤的寒冷生物圈中占据着生物量的主导地位。确定使嗜冷菌能够在寒冷环境中生长的基因组特征，有助于了解它们的生理机能和适应性反应。然而，事实证明，定义嗜冷菌的重要基因组特征颇具难度，而将基因组知识外推至与环境的相关性则更是难上加难。
在此，我们研究了节杆菌属，并在新的青藏高原分离株的基因组序列的辅助下，定义了一个新的分支，即C组，该组代表来自极地和高山环境的分离株。C组在-1°C下具有更强的生长能力，其基因组的G+C含量、氨基酸组成、预测的蛋白质稳定性以及功能能力（例如硫代谢和肌醇硫醇生物合成）使其有别于非极地或高山的A组节杆菌。对近1000个宏基因组的分析表明，在模拟春融实验的加拿大永久冻土群落中，C组的含量过高，这表明其具有生态位适应性；而在所有极地和高山样本中，A组的含量过低，这表明其对环境温度有普遍反应。
这些发现表明，有能力定义特定分类群的基因组标记，这些标记可能对寒冷环境的环境监测具有价值，包括人为影响引起的环境变化。更广泛地说，该研究说明了从基因组和生理数据外推至环境背景所涉及的挑战。视频摘要。
