The occurrence and ecology of microbial chain elongation of carboxylates in soils

Chain elongation is a growth-dependent anaerobic metabolism that combines acetate and ethanol into butyrate, hexanoate, and octanoate. While the model microorganism for chain elongation, Clostridium kluyveri, was isolated from a saturated soil sample in the 1940s, chain elongation has remained unexplored in soil environments. During soil fermentative events, simple carboxylates and alcohols can transiently accumulate up to low mM concentrations, suggesting in situ possibility of microbial chain elongation. Here, we examined the occurrence and microbial ecology of chain elongation in four soil types in microcosms and enrichments amended with chain elongation substrates. All soils showed evidence of chain elongation activity with several days of incubation at high (100 mM) and environmentally relevant (2.5 mM) concentrations of acetate and ethanol. Three soils showed substantial activity in soil microcosms with high substrate concentrations, converting 58% or more of the added carbon as acetate and ethanol to butyrate, butanol, and hexanoate. Semi-batch enrichment yielded hexanoate and octanoate as the most elongated products and microbial communities predominated by C. kluyveri and other Firmicutes genera not known to undergo chain elongation. Collectively, these results strongly suggest a niche for chain elongation in anaerobic soils that should not be overlooked in soil microbial ecology studies.

Evolving the core microbial community in pit mud based on bioturbation of fortified Daqu

Directional stress is an effective measure to evolve community structure and improve bioactivity of pit mud (PM). In this study, adding fortified Daqu in artificial PM (APM) was to disturb the microbial community and affect the metabolites furthermore. To evaluate the effect of fortified Daqu on culturing APM, microbial communities of APMs with/without adding fortified Daqu were investigated by fluorescence in situ hybridization and Illumina Miseq. These results indicated that microbes (Clostridium sp., Clostridium kluyveri, hydrogenotrophic methanogens, and acetotrophic methanogens) related to the production of key aroma compounds increased notably when fortified Daqu was added. Especially the hydrogenotrophic and acetotrophic methanogens increased by 5.19- and 4.63-fold after 30-days’ culture. Then metabolites (organic acids, volatile compounds) were also analyzed by HPLC and HS-SPME-GC-MS. Results showed that the content of butyric acid and hexanoic acid was significantly higher when adding fortified Daqu. What’s more, the proportion of esters and phenols were higher compared with the APM without adding fortified Daqu as well. The microbial compositions of APMs with/without adding fortified Daqu were observed in this study, which indicated the microbial community evolving in functional community in favor of liquor-brewing and suggested a novelty process was developed by disturbing the community diversity.

Modeling a co-culture of Clostridium autoethanogenum and Clostridium kluyveri to increase syngas conversion to medium-chain fatty-acids

Microbial fermentation of synthesis gas (syngas) is becoming more attractive for sustainable production of commodity chemicals. To date, syngas fermentation focuses mainly on the use of Clostridium species for the production of small organic molecules such as ethanol and acetate. The cocultivation of syngas-fermenting microorganisms with chain-elongating bacteria can expand the range of possible products, allowing, for instance, the production of medium-chain fatty acids (MCFA) and alcohols from syngas. To explore these possibilities, we report herein a genome-scale, constraint-based metabolic model to describe growth of a co-culture of Clostridium autoethanogenum and Clostridium kluyveri on syngas for the production of valuable compounds. Community flux balance analysis was used to gain insight into the metabolism of the two strains and their interactions, and to reveal potential strategies enabling production of butyrate and hexanoate. The model suggests that addition of succinate is one strategy to optimize the production of medium-chain fatty-acids from syngas with this co-culture. According to the predictions, addition of succinate increases the pool of crotonyl-CoA and the ethanol/acetate uptake ratio in C. kluyveri, resulting in the flux of up to 60% of electrons into hexanoate. Other potential way to optimize butyrate and hexanoate is to increase ethanol production by C. autoethanogenum. Deletion of either formate transport, acetaldehyde dehydrogenase or formate dehydrogenase (ferredoxin) from the metabolic model of C. autoethanogenum leads to a (potential) increase in ethanol production up to 150%, which is clearly very attractive.