Bioinformatics and metabolic flux analysis highlight a new mechanism involved in lactate oxidation in Clostridium tyrobutyricum

Predicting metabolic pathways and microbial interactions in dark fermentation systems treating real cheese whey effluents

Dark fermentation of agro-industrial effluents is a promising way for waste valorization. However, understanding the complex microbial dynamics and metabolic interactions within the microbial communities remains challenging. This study investigates the microbial communities involved in continuous hydrogen production from cheese whey and fermented cheese whey using functional profiling with PICRUSt2. The analysis reveals the primary roles of key microbial genera. Lactobacillus dominates carbohydrate consumption and lactate production, while Clostridium sensu stricto 12 and Caproiciproducens are engaged in a competitive dynamic for lactate utilization. Clostridium sensu stricto 12 drives hydrogen production via electron bifurcation reactions, whereas Caproiciproducens may utilize alternative energy conservation mechanisms. The interaction between these genera is influenced by substrate availability and process conditions. This study highlights the utility of functional profiling in elucidating microbial interactions and metabolic pathways in dark fermentation. The findings emphasize the importance of understanding microbial interactions to optimize biohydrogen production processes.

Feedstock variability impacts the bioconversion of sugar and lignin streams derived from corn stover by Clostridium tyrobutyricum and engineered Pseudomonas putida

Feedstock variability represents a challenge in lignocellulosic biorefineries, as it can influence both lignocellulose deconstruction and microbial conversion processes for biofuels and biochemicals production. The impact of feedstock variability on microbial performance remains underexplored, and predictive tools for microbial behaviour are needed to mitigate risks in biorefinery scale-up. Here, twelve batches of corn stover were deconstructed via deacetylation, mechanical refining, and enzymatic hydrolysis to generate lignin-rich and sugar streams. These batches and their derived streams were characterised to identify their chemical components, and the streams were used as substrates for producing muconate and butyrate by engineered Pseudomonas putida and wildtype Clostridium tyrobutyricum, respectively. Bacterial performance (growth, product titers, yields, and productivities) differed among the batches, but no strong correlations were identified between feedstock composition and performance. To provide metabolic insights into the origin of these differences, we evaluated the effect of twenty-three isolated chemical components on these microbes, including three components in relevant bioprocess settings in bioreactors, and we found that growth-inhibitory concentrations were outside the ranges observed in the streams. Overall, this study generates a foundational dataset on P. putida and C. tyrobutyricum performance to enable future predictive models and underscores their resilience in effectively converting fluctuating lignocellulose-derived streams into bioproducts.

Electron bifurcation and fluoride efflux systems implicated in defluorination of perfluorinated unsaturated carboxylic acids by Acetobacterium spp

Enzymatic cleavage of C─F bonds in per- and polyfluoroalkyl substances (PFAS) is largely unknown but avidly sought to promote systems biology for PFAS bioremediation. Here, we report the reductive defluorination of α, β-unsaturated per- and polyfluorocarboxylic acids by Acetobacterium spp. The microbial defluorination products were structurally confirmed and showed regiospecificity and stereospecificity, consistent with their formation by enzymatic reactions. A comparison of defluorination activities among several Acetobacterium species indicated that a functional fluoride exporter was required for the detoxification of the released fluoride. Results from both in vivo inhibition tests and in silico enzyme modeling suggested the involvement of enzymes of the flavin-based electron-bifurcating caffeate reduction pathway [caffeoyl-CoA reductase (CarABCDE)] in the reductive defluorination. This is a report on specific microorganisms carrying out enzymatic reductive defluorination of PFAS, which could be linked to electron-bifurcating reductases that are environmentally widespread.

Biohydrogen production by lactate-driven dark fermentation of real organic wastes derived from solid waste treatment plants

This study evaluated the hydrogen production potential through lactate-driven dark fermentation (LD-DF) of organic wastes from solid waste treatment plants, including the organic fraction of municipal solid waste (OFMSW), mixed sewage sludge, and two OFMSW leachates. In initial batch fermentations, only OFMSW supported a significant hydrogen yield (70.1 ± 7.7 NmL-H2/g-VS added) among the tested feedstocks. Lactate acted as an important hydrogen precursor, requiring the presence of carbohydrates for sequential two-step lactate-type fermentation. The impact of operational pH (5.5-6.5) and initial total solids (TS) concentration (5-12.5 % w/w) was also evaluated using OFMSW as substrate, obtaining hydrogen yields ranging from 6.6 to 55.9 NmL-H2/g-VSadded. The highest yield occurred at 6.5 pH and 7.5 % TS. The LD-DF pathway was indicated to be present under diverse pH and TS conditions, supported by employing a specialized microbial consortium capable of performing LD-DF, along with the observed changes in lactate levels during fermentation.

Electron-bifurcation and fluoride efflux systems in Acetobacterium spp. drive defluorination of perfluorinated unsaturated carboxylic acids

Enzymatic cleavage of C-F bonds in per- and polyfluoroalkyl substances (PFAS) is largely unknown but avidly sought to promote systems biology for PFAS bioremediation. Here, we report the reductive defluorination of α, β-unsaturated per- and polyfluorocarboxylic acids by Acetobacterium spp. Two critical molecular features in Acetobacterium species enabling reductive defluorination are (i) a functional fluoride efflux transporter (CrcB) and (ii) an electron-bifurcating caffeate reduction pathway (CarABCDE). The fluoride transporter was required for detoxification of released fluoride. Car enzymes were implicated in defluorination by the following evidence: (i) only Acetobacterium spp. with car genes catalyzed defluorination; (ii) caffeate and PFAS competed in vivo ; (iii) models from the X-ray structure of the electron-bifurcating reductase (CarC) positioned the PFAS substrate optimally for reductive defluorination; (iv) products identified by 19 F-NMR and high-resolution mass spectrometry were consistent with the model. Defluorination biomarkers identified here were found in wastewater treatment plant metagenomes on six continents.