BackgroundThree methods were developed for the application of stoichiometry-based network analysis approaches including elementary mode analysis to the study of mass and energy flows in microbial communities. Each has distinct advantages and disadvantages suitable for analyzing systems with different degrees of complexity and a priori knowledge. These approaches were tested and compared using data from the thermophilic, phototrophic mat communities from Octopus and Mushroom Springs in Yellowstone National Park (USA). The models were based on three distinct microbial guilds: oxygenic phototrophs, filamentous anoxygenic phototrophs, and sulfate-reducing bacteria. Two phases, day and night, were modeled to account for differences in the sources of mass and energy and the routes available for their exchange.ResultsThe in silico models were used to explore fundamental questions in ecology including the prediction of and explanation for measured relative abundances of primary producers in the mat, theoretical tradeoffs between overall productivity and the generation of toxic by-products, and the relative robustness of various guild interactions.ConclusionThe three modeling approaches represent a flexible toolbox for creating cellular metabolic networks to study microbial communities on scales ranging from cells to ecosystems. A comparison of the three methods highlights considerations for selecting the one most appropriate for a given microbial system. For instance, communities represented only by metagenomic data can be modeled using the pooled method which analyzes a community's total metabolic potential without attempting to partition enzymes to different organisms. Systems with extensive a priori information on microbial guilds can be represented using the compartmentalized technique, employing distinct control volumes to separate guild-appropriate enzymes and metabolites. If the complexity of a compartmentalized network creates an unacceptable computational burden, the nested analysis approach permits greater scalability at the cost of more user intervention through multiple rounds of pathway analysis.

The fungal endophyte, Ascocoryne sarcoides, produced aviation, gasoline and diesel-relevant hydrocarbons when grown on multiple substrates including cellulose as the sole carbon source. Substrate, growth stage, culturing pH, temperature and medium composition were statistically significant factors for the type and quantity of hydrocarbons produced. Gasoline range (C 5 -C 12 ), aviation range (C 8 -C 16 ) and diesel range (C 9 -C 36 ) organics were detected in all cultured media. Numerous non-oxygenated hydrocarbons were produced such as isopentane, 3,3-dimethyl hexane and d-limonene during exponential growth phase. Growth on cellulose at 23˚C and pH 5.8 produced the highest overall yield of fuel range organics (105 mg * g·biomass −1 ). A change in metabolism was seen in late stationary phase from catabolism of cellulose to potential oxidation of hydrocarbons resulting in the production of more oxygenated compounds with longer carbon chain length and fewer fuel-related compounds. The results outline rational strategies for controlling the composition of the fuel-like compounds by changing culturing parameters.

Volatile hydrocarbon production by Ascocoryne sacroides was studied over its growth cycle. Gas-phase compounds were measured continuously with a proton transfer reaction-mass spectrometry (PTR-MS) and at distinct time points with gas chromatography-mass spectrometry (GC-MS) using head space solid phase microextraction (SPME). The PTR-MS ion signal permitted temporal resolution of the volatile production while the SPME results revealed distinct compound identities. The quantitative PTR-MS results showed the volatile production was dominated by ethanol and acetaldehyde, while the concentration of the remainder of volatiles consistently reached 2,000 ppbv. The measurement of alcohols from the fungal culture by the two techniques correlated well. Notable compounds of fuel interest included nonanal, 1-octen-3-ol, 1-butanol, 3-methyl- and benzaldehyde. Abiotic comparison of the two techniques demonstrated SPME fiber bias toward higher molecular weight compounds, making quantitative efforts with SPME impractical. Together, PTR-MS and SPME GC-MS were shown as valuable tools for characterizing volatile fuel compound production from microbiological sources.

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Xuwen is currently a doctoral candidate in Chemical Engineering at Oregon State University. He currently has research focused on techno-economic analysis of glucosamine and lipid from algae.