Measurement of Volatile Compounds for Real-Time Analysis of Soil Microbial Metabolic Response to Simulated Snowmelt

Abstract

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.

Analytical methods for the analysis of volatile natural products

“…As an excellent technique to measure a broad spectrum of volatile compounds, PTR-MS has been extensively used in many different elds of biogenic volatile organic compounds, ranging from laboratory experiments to eld studies. [333][334][335][336][337][338][339][340][341][342] The ability of PTR-MS to simultaneously monitor and quantify compounds from very diverse chemical groups with high sensitivity and non-invasively makes it an excellent method to monitor aroma, avor and fermentation related trace gases during growing, ripening or fruit storage. 190,[343][344][345] The applications of PTR-MS have enabled important advances in understanding sources of many VOCs, as well as their environmental effects in the atmosphere.…”

A Framework for the Systematic Selection of Biosensor Chassis for Environmental Synthetic Biology

“…Hydrating a dry soil stimulates metabolic activity in the rhizosphere, which releases volatiles that are highly transient and challenging to measure. 95 , 96 These volatiles play central roles in interspecies communication and community structuring, thereby meriting study using nondestructive, unbiased detection methods. 96 , 97 Additionally, volatile concentrations are impacted by the soil matrix, meaning that analytically detected concentrations can be significantly different from bioavailable concentrations.…”

“…As an example of how to use this framework, we can consider the case of sensing volatile organic compounds in response to drying–wetting cycles in the rhizosphere. Hydrating a dry soil stimulates metabolic activity in the rhizosphere, which releases volatiles that are highly transient and challenging to measure. , These volatiles play central roles in interspecies communication and community structuring, thereby meriting study using nondestructive, unbiased detection methods. , Additionally, volatile concentrations are impacted by the soil matrix, meaning that analytically detected concentrations can be significantly different from bioavailable concentrations . Biosensors offer a viable alternative to measuring such transient molecules in situ . , To thrive in the rhizosphere and measure transient signals, we need a chassis organism that is native to the rhizosphere.…”