Mulay Sayali A, Vishnivetskaya Tatiana A, Hochanadel Leah H, Klingeman Dawn M, Lloyd Karen G, Pelletier Dale A, Podar Mircea
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN, USA.
bioRxiv. 2025 May 14:2025.05.14.654084. doi: 10.1101/2025.05.14.654084.
In diverse environments, microbes drive a myriad of processes, from geochemical and nutrient cycling to interspecies interactions, including in association with plants and animals. Their physiological state is dynamic and impacted by abiotic and biotic conditions, responding to environmental fluctuations by changes in cellular metabolism, according to their genetic potential. Molecular, cellular and genomic approaches can identify and measure microbial responses and adaptation to environmental changes in native communities. However, isolating the individual microbes that respond to specific changes has been difficult. To address that, we implemented BONCAT-Live, by integrating bio-orthogonal non-canonical amino acid tagging (BONCAT) in diverse native communities, with isolation and cultivation of cells responding to specific stimuli, at different time scales. In frozen Arctic permafrost samples, we identified and isolated dormant bacteria that become active after thawing under native or nutrient enriched conditions. From a tree rhizosphere, we isolated strains that thrive under high concentrations of root exudates that act as defense compounds and nutrients. In the human oral microbiome, we identified and isolated bacteria that rapidly proliferated when exposed to metabolites provided by the host or other co-occurring microbes. Further characterization of isolated bacterial strains will provide opportunities for in depth determination of how these microbes adapt to changes in their environments, individually and as part of model communities.
在多样的环境中，微生物驱动着无数的过程，从地球化学和养分循环到种间相互作用，包括与动植物的共生关系。它们的生理状态是动态的，受非生物和生物条件的影响，根据其遗传潜力，通过细胞代谢的变化对环境波动做出反应。分子、细胞和基因组方法可以识别和测量微生物对自然群落中环境变化的反应和适应情况。然而，分离出对特定变化做出反应的单个微生物一直很困难。为了解决这个问题，我们实施了“活细胞生物正交非天然氨基酸标记技术（BONCAT）”，即在不同的自然群落中整合生物正交非天然氨基酸标记（BONCAT），并在不同时间尺度上分离和培养对特定刺激做出反应的细胞。在冰冻的北极永久冻土样本中，我们识别并分离出了在自然条件或营养丰富条件下解冻后变得活跃的休眠细菌。从树木根际，我们分离出了在高浓度作为防御化合物和养分的根系分泌物下茁壮成长的菌株。在人类口腔微生物群中，我们识别并分离出了在接触宿主或其他共生微生物提供的代谢产物时迅速增殖的细菌。对分离出的细菌菌株进行进一步表征，将为深入确定这些微生物如何单独以及作为模型群落的一部分适应其环境变化提供机会。
