Low-temperature caproate production, microbial diversity, and metabolic pathway in xylose anaerobic fermentation

Abstract

● Converting xylose to caproate under a low temperature of 20 °C by MCF was verified.

● Final concentration of caproate from xylose in a batch reactor reached 1.6 g/L.

● Changing the substrate to ethanol did not notably increase the caproate production.

● Four genera, including Bifidobacterium , were revealed as caproate producers.

● The FAB pathway and incomplete RBO pathway were revealed via metagenomic analysis.

Mixed culture fermentation (MCF) is challenged by the unqualified activity of enriched bacteria and unwanted methane dissolution under low temperatures. In this work, caproate production from xylose was investigated by MCF at a low temperature (20 °C). The results showed that a 9 d long hydraulic retention time (HRT) in a continuously stirred tank reactor was necessary for caproate production (~0.3 g/L, equal to 0.6 g COD/L) from xylose (10 g/L). The caproate concentration in the batch mode was further increased to 1.6 g/L. However, changing the substrate to ethanol did not promote caproate production, resulting in ~1.0 g/L after 45 d of operation. Four genera, Bifidobacterium, Caproiciproducens, Actinomyces, and Clostridium_sensu_stricto_12, were identified as the enriched caproate-producing bacteria. The enzymes in the fatty acid biosynthesis (FAB) pathway for caproate production were identified via metagenomic analysis. The enzymes for the conversion of (C_n+2)-2,3-Dehydroxyacyl-CoA to (C_n+2)-Acyl-CoA (i.e., EC 1.3.1.8 and EC 1.3.1.38) in the reverse β-oxidation (RBO) pathway were not identified. These results could extend the understanding of low-temperature caproate production.

Graphical abstract

Keywords

Xylose fermentation / Caproate / Low temperature / Bifidobacterium / FAB pathway / RBO pathway

References

[1] Alessandri G, van Sinderen D, Ventura M. (2021). The genus bifidobacterium: from genomics to functionality of an important component of the mammalian gut microbiota running title: Bifidobacterial adaptation to and interaction with the host. Computational and Structural Biotechnology Journal, 19: 1472–1487

[2] Alvarado-Cuevas Z D, López-Hidalgo A M, Ordoñez L G, Oceguera-Contreras E, Ornelas-Salas J T, De León-Rodríguez A. (2015). Biohydrogen production using psychrophilic bacteria isolated from Antarctica. International Journal of Hydrogen Energy, 40(24): 7586–7592

[3] Alvarez-Guzmán C L, Oceguera-Contreras E, Ornelas-Salas J T, Balderas-Hernández V E, De León-Rodríguez A. (2016). Biohydrogen production by the psychrophilic G088 strain using single carbohydrates as substrate. International Journal of Hydrogen Energy, 41(19): 8092–8100

[4] Beale D J, Karpe A V, McLeod J D, Gondalia S V, Muster T H, Othman M Z, Palombo E A, Joshi D. (2016). An ‘omics’ approach towards the characterisation of laboratory scale anaerobic digesters treating municipal sewage sludge. Water Research, 88: 346–357

[5] Crognale S, Braguglia C M, Gallipoli A, Gianico A, Rossetti S, Montecchio D. (2021). Direct conversion of food waste extract into caproate: metagenomics assessment of chain elongation process. Microorganisms, 9(2): 327

[6] Dai K, Wen J L, Wang Y L, Wu Z G, Zhao P J, Zhang H H, Wang J J, Zeng R J, Zhang F. (2019). Impacts of medium composition and applied current on recovery of volatile fatty acids during coupling of electrodialysis with an anaerobic digester. Journal of Cleaner Production, 207: 483–489

[7] Dai K, Zhang W, Zeng R J, Zhang F. (2020). Production of chemicals in thermophilic mixed culture fermentation: mechanism and strategy. Critical Reviews in Environmental Science and Technology, 50(1): 1–30

[8] Dang C, Wu Z, Zhang M, Li X, Sun Y, Wu R A, Zheng Y, Xia Y. (2022). Microorganisms as bio-filters to mitigate greenhouse gas emissions from high-altitude permafrost revealed by nanopore-based metagenomics. iMeta, 1(2): 24

[9] Dessì P, Lakaniemi A M, Lens P N L. (2017). Biohydrogen production from xylose by fresh and digested activated sludge at 37, 55 and 70 °C. Water Research, 115: 120–129

[10] Geng Z Q, Qian D K, Hu Z Y, Wang S, Yan Y, van Loosdrecht M C M, Zeng R J, Zhang F. (2021). Identification of extracellular key enzyme and intracellular metabolic pathway in alginate-degrading consortia via an integrated metaproteomic/metagenomic analysis. Environmental Science & Technology, 55(24): 16636–16645

[11] Grootscholten T I M, Steinbusch K J J, Hamelers H V M, Buisman C J N. (2013). Chain elongation of acetate and ethanol in an upflow anaerobic filter for high rate MCFA production. Bioresource Technology, 135: 440–445

[12] He J, Shi Z, Luo T, Zhang S, Liu Y, Luo G. (2021). Phenol promoted caproate production via two-stage batch anaerobic fermentation of organic substance with ethanol as electron donor for chain elongation. Water Research, 204: 117601

[13] Herrmann G, Jayamani E, Mai G, Buckel W. (2008). Energy conservation via electron-transferring flavoprotein in anaerobic bacteria. Journal of Bacteriology, 190(3): 784–791

[14] Jeon B S, Kim B C, Um Y, Sang B I. (2010). Production of hexanoic acid from D-galactitol by a newly isolated Clostridium sp. BS-1. Applied Microbiology and Biotechnology, 88(5): 1161–1167

[15] Kougias P G, Angelidaki I. (2018). Biogas and its opportunities: a review. Frontiers of Environmental Science & Engineering, 12(3): 14

[16] Lambrecht J, Cichocki N, Schattenberg F, Kleinsteuber S, Harms H, Müller S, Sträuber H. (2019). Key sub-community dynamics of medium-chain carboxylate production. Microbial Cell Factories, 18(1): 92

[17] Leng L, Nobu M K, Narihiro T, Yang P, Amy Tan G Y, Lee P H. (2019). Shaping microbial consortia in coupling glycerol fermentation and carboxylate chain elongation for Co-production of 1,3-propanediol and caproate: Pathways and mechanisms. Water Research, 148: 281–291

[18] Liu Y, He P, Shao L, Zhang H, Lü F. (2017). Significant enhancement by biochar of caproate production via chain elongation. Water Research, 119: 150–159

[19] Luo J, Fang S, Huang W, Wang F, Zhang L, Fang F, Cao J, Wu Y, Wang D. (2022). New insights into different surfactants’ impacts on sludge fermentation: focusing on the particular metabolic processes and microbial genetic traits. Frontiers of Environmental Science & Engineering, 16(8): 106

[20] Mahato P, Rajagopal R, Goyette B, Adhikary S. (2022). Low-temperature anaerobic digestion of chicken manure at high organic and nitrogen loads-strategies for controlling short chain fatty acids. Bioresource Technology, 351: 127049

[21] McKeown R M, Hughes D, Collins G, Mahony T, O’Flaherty V. (2012). Low-temperature anaerobic digestion for wastewater treatment. Current Opinion in Biotechnology, 23(3): 444–451

[22] Min B, Román Ó B, Angelidaki I. (2008). Importance of temperature and anodic medium composition on microbial fuel cell (MFC) performance. Biotechnology Letters, 30(7): 1213–1218

[23] Nzeteu C O, Trego A C, Abram F, O’Flaherty V. (2018). Reproducible, high-yielding, biological caproate production from food waste using a single-phase anaerobic reactor system. Biotechnology for Biofuels, 11(1): 108

[24] Piwowarek K, Lipińska E, Hać-Szymańczuk E, Kieliszek M, Ścibisz I. (2018). Propionibacterium spp.-source of propionic acid, vitamin B12, and other metabolites important for the industry. Applied Microbiology and Biotechnology, 102(2): 515–538

[25] Qian D K, Geng Z Q, Sun T, Dai K, Zhang W, Jianxiong Zeng R, Zhang F. (2020). Caproate production from xylose by mesophilic mixed culture fermentation. Bioresource Technology, 308: 123318

[26] Quispe-Cardenas E, Rogers S. (2021). Microbial adaptation and response to high ammonia concentrations and precipitates during anaerobic digestion under psychrophilic and mesophilic conditions. Water Research, 204: 117596

[27] Ren Y, Yu G, Shi C, Liu L, Guo Q, Han C, Zhang D, Zhang L, Liu B, Gao H. . (2022). Majorbio cloud: a one-stop, comprehensive bioinformatic platform for multiomics analyses. iMeta, 1(2): e12

[28] Roghair M, Hoogstad T, Strik D P B T B, Plugge C M, Timmers P H A, Weusthuis R A, Bruins M E, Buisman C J N. (2018). Controlling ethanol use in chain elongation by CO₂ loading rate. Environmental Science & Technology, 52(3): 1496–1505

[29] Saady N M C, Massé D I. (2015). High rate psychrophilic anaerobic digestion of high solids (35 %) dairy manure in sequence batch reactor. Bioresource Technology, 186(0): 74–80

[30] Saha S, Basak B, Hwang J H, Salama E S, Chatterjee P K, Jeon B H. (2020). Microbial symbiosis: a network towards biomethanation. Trends in Microbiology, 28(12): 968–984

[31] Shrestha S, Xue S, Kitt D, Song H, Truyers C, Muermans M, Smets I, Raskin L. (2022). Anaerobic dynamic membrane bioreactor development to facilitate organic waste conversion to medium-chain carboxylic acids and their downstream recovery. ACS ES&T Engineering, 2(2): 169–180

[32] Tang J, Dai K, Wang Q T, Zheng S J, Hong S D, Jianxiong Zeng R, Zhang F. (2022). Caproate production from xylose via the fatty acid biosynthesis pathway by genus Caproiciproducens dominated mixed culture fermentation. Bioresource Technology, 351: 126978

[33] Temudo M F, Muyzer G, Kleerebezem R, van Loosdrecht M C M. (2008). Diversity of microbial communities in open mixed culture fermentations: impact of the pH and carbon source. Applied Microbiology and Biotechnology, 80(6): 1121–1130

[34] Wang J, Yin Y. (2022). Biological production of medium-chain carboxylates through chain elongation: an overview. Biotechnology Advances, 55: 107882

[35] Wang Y, Wei W, Wu S L, Ni B J. (2020). Zerovalent iron effectively enhances medium-chain fatty acids production from waste activated sludge through improving sludge biodegradability and electron transfer efficiency. Environmental Science & Technology, 54(17): 10904–10915

[36] Weimer P J, Nerdahl M, Brandl D J. (2015). Production of medium-chain volatile fatty acids by mixed ruminal microorganisms is enhanced by ethanol in co-culture with Clostridium kluyveri. Bioresource Technology, 175(0): 97–101

[37] Wu Q, Bao X, Guo W, Wang B, Li Y, Luo H, Wang H, Ren N. (2019). Medium chain carboxylic acids production from waste biomass: Current advances and perspectives. Biotechnology Advances, 37(5): 599–615

[38] Wu Y, Ma H, Zheng M, Wang K. (2015). Lactic acid production from acidogenic fermentation of fruit and vegetable wastes. Bioresource Technology, 191: 53–58

[39] Xu X, Sun Y, Sun Y, Li Y. (2022). Bioaugmentation improves batch psychrophilic anaerobic co-digestion of cattle manure and corn straw. Bioresource Technology, 343: 126118

[40] Zhang F, Zhang W, Qian D K, Dai K, van Loosdrecht M C M, Zeng R J. (2019a). Synergetic alginate conversion by a microbial consortium of hydrolytic bacteria and methanogens. Water Research, 163: 114892

[41] Zhang W, Zhang F, Li Y X, Jiang Y, Zeng R J. (2019b). No difference in inhibition among free acids of acetate, propionate and butyrate on hydrogenotrophic methanogen of Methanobacterium formicicum. Bioresource Technology, 294: 122237

[42] ZhangX, Gu J, MengS, LiuY (2022a). Dissolved methane in anaerobic effluent: emission or recovery? Frontiers of Environmental Science & Engineering, 16(4): 54

[43] Zhang Z, Ni B J, Zhang L, Liu Z, Fu W, Dai X, Sun J. (2022b). Medium-chain fatty acids production from carbohydrates-rich wastewater through two-stage yeast biofilm processes without external electron donor addition: Biofilm development and pH impact. Science of the Total Environment, 828: 154428

RIGHTS & PERMISSIONS

Higher Education Press