Data_Sheet_1_Measurement of Volatile Compounds for Real-Time Analysis of Soil Microbial Metabolic Response to Simulated Snowmelt.ZIP

Snowmelt dynamics are a significant determinant of microbial metabolism in soil and regulate global biogeochemical cycles of carbon and nutrients by creating seasonal variations in soil redox and nutrient pools. With an increasing concern that climate change accelerates both snowmelt timing and rate, obtaining an accurate characterization of microbial response to snowmelt is important for understanding biogeochemical cycles intertwined with soil. However, observing microbial metabolism and its dynamics non-destructively remains a major challenge for systems such as soil. Microbial volatile compounds (mVCs) emitted from soil represent information-dense signatures and when assayed non-destructively using state-of-the-art instrumentation such as Proton Transfer Reaction-Time of Flight-Mass Spectrometry (PTR-TOF-MS) provide time resolved insights into the metabolism of active microbiomes. In this study, we used PTR-TOF-MS to investigate the metabolic trajectory of microbiomes from a subalpine forest soil, and their response to a simulated wet-up event akin to snowmelt. Using an information theory approach based on the partitioning of mutual information, we identified mVC metabolite pairs with robust interactions, including those that were non-linear and with time lags. The biological context for these mVC interactions was evaluated by projecting the connections onto the Kyoto Encyclopedia of Genes and Genomes (KEGG) network of known metabolic pathways. Simulated snowmelt resulted in a rapid increase in the production of trimethylamine (TMA) suggesting that anaerobic degradation of quaternary amine osmo/cryoprotectants, such as glycine betaine, may be important contributors to this resource pulse. Unique and synergistic connections between intermediates of methylotrophic pathways such as dimethylamine, formaldehyde and methanol were observed upon wet-up and indicate that the initial pulse of TMA was likely transformed into these intermediates by methylotrophs. Increases in ammonia oxidation signatures (transformation of hydroxylamine to nitrite) were observed in parallel, and while the relative role of nitrifiers or methylotrophs cannot be confirmed, the inferred connection to TMA oxidation suggests either a direct or indirect coupling between these processes. Overall, it appears that such mVC time-series from PTR-TOF-MS combined with causal inference represents an attractive approach to non-destructively observe soil microbial metabolism and its response to environmental perturbation.

雪融动态是土壤微生物代谢的关键决定因素，并通过塑造土壤氧化还原状态与养分库的季节变化，调控全球碳与养分生物地球化学循环。当前学界愈发担忧气候变化会同时加快融雪的时间与速率，因此精准表征微生物对融雪的响应，对于理解与土壤紧密耦合的生物地球化学循环至关重要。然而，对土壤等生态系统开展微生物代谢及其动态的无损观测，仍是一项重大挑战。土壤释放的微生物挥发性化合物（microbial volatile compounds, mVCs）是信息密度极高的特征信号；借助质子转移反应-飞行时间-质谱（Proton Transfer Reaction-Time of Flight-Mass Spectrometry, PTR-TOF-MS）这类尖端仪器开展无损检测时，可实现对活性微生物群落代谢的时序解析。本研究采用PTR-TOF-MS，探究亚高山森林土壤微生物群落的代谢轨迹，以及其对模拟融雪式补水事件的响应。本研究基于互信息划分的信息论方法，筛选出具有强相互作用的mVC代谢物对，其中包含非线性与时滞相互作用的代谢物对。通过将这些相互作用映射至京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）已知代谢通路网络，本研究解析了mVC相互作用的生物学背景。模拟融雪事件导致三甲胺（trimethylamine, TMA）的产生量快速上升，这表明季铵类渗透/冷冻保护剂（如甘氨酸甜菜碱）的厌氧降解，可能是该资源脉冲的重要来源。补水事件后，我们观测到甲基营养通路中间体（如二甲胺、甲醛与甲醇）间存在独特且协同的相互作用，这表明初始产生的TMA很可能被甲基营养菌转化为上述中间体。同时观测到氨氧化特征（羟胺转化为亚硝酸盐）的增强；尽管无法明确硝化菌与甲基营养菌的相对贡献，但推断其与TMA氧化存在关联，提示两类过程存在直接或间接的耦合关系。综上，将PTR-TOF-MS获取的mVC时序数据与因果推断方法相结合，似乎是一种极具应用前景的无损观测土壤微生物代谢及其对环境扰动响应的手段。