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A Review of Microbial Molecular Profiling during Biomass Valorization

Abstract

The 21st century’s goal to reduce CO2 emission is the driving force to replace petroleum with biomass. Although biomass has the potential to provide about ∼25% of global energy demands, biomass valorization (conversion to value-added products [VAPs]) also contributes to CO2 emissions. The use of microbial consortia rather than a single species is more efficient for biomass valorization. Thus, several molecular methods have been developed to decipher the composition of these consortia. Understanding the composition and diversity of microbes in a fermentation-based biomass valorization will enable the synthesis of artificial consortia to produce desirable products. Most works have identified the dominant microbial species in different biomass valorization processes and highlighted the influence of variables such as nanoparticles and fermentation inhibitors on microbial diversity and dynamics. The prominent microbial species in the microbial consortium are also discussed. This review will guide future works on microbial molecular profiling during biomass valorization.

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References

  1. Jacquel, N., C.-W. Lo, Y.-H. Wei, H.-S. Wu, and S. S. Wang (2008) Isolation and purification of bacterial poly(3-hydroxyalkanoates). Biochem. Eng. J. 39: 15–27.

    CAS  Article  Google Scholar 

  2. Moscovici, M. (2015) Present and future medical applications of microbial exopolysaccharides. Front. Microbiol. 6: 1012.

    PubMed  Article  PubMed Central  Google Scholar 

  3. Rawoof, S. A. A., P. S. Kumar, D.-V. N. Vo, K. Devaraj, Y. Mani, T. Devaraj, and S. Subramanian (2021) Production of optically pure lactic acid by microbial fermentation: a review. Environ. Chem. Lett. 19: 539–556.

    CAS  Article  Google Scholar 

  4. Vaishnav, N., A. Singh, M. Adsul, P. Dixit, S. K. Sandhu, A. Mathur, S. K. Puri, and R. R. Singhania (2018) Penicillium: the next emerging champion for cellulase production. Bioresour. Technol. Rep. 2: 131–140.

    Article  Google Scholar 

  5. Verma, A., H. Singh, S. Anwar, A. Chattopadhyay, K. K. Tiwari, S. Kaur, and G. S. Dhilon (2017) Microbial keratinases: industrial enzymes with waste management potential. Crit. Rev. Biotechnol. 37: 476–491.

    CAS  PubMed  Article  Google Scholar 

  6. Mazzoli, R., F. Bosco, I. Mizrahi, E. A. Bayer, and E. Pessione (2014) Towards lactic acid bacteria-based biorefineries. Biotechnol. Adv. 32: 1216–1236.

    CAS  PubMed  Article  Google Scholar 

  7. Favaro, L., L. Alibardi, M. C. Lavagnolo, S. Casella, and M. Basaglia (2013) Effects of inoculum and indigenous microflora on hydrogen production from the organic fraction of municipal solid waste. Int. J. Hydrogen Energy. 38: 11774–11779.

    CAS  Article  Google Scholar 

  8. Xu, L. and U. Tschirner (2011) Improved ethanol production from various carbohydrates through anaerobic thermophilic co-culture. Bioresour. Technol. 102: 10065–10071.

    CAS  PubMed  Article  Google Scholar 

  9. Xiros, C. and M. H. Studer (2017) A multispecies fungal biofilm approach to enhance the celluloyltic efficiency of membrane reactors for consolidated bioprocessing of plant biomass. Front. Microbiol. 8: 1930.

    PubMed  Article  PubMed Central  Google Scholar 

  10. Minty, J. J., M. E. Singer, S. A. Scholz, C. H. Bae, J. H. Ahn, C. E. Foster, J. C. Liao, and X. N. Lin (2013) Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass. Proc. Natl. Acad. Sci. U. S. A. 110: 14592–14597.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  11. Kalyani, D., K.-M. Lee, T.-S. Kim, J. Li, S. S. Dhiman, Y. C. Kang, and J.-K. Lee (2013) Microbial consortia for saccharification of woody biomass and ethanol fermentation. Fuel (Lond.) 107: 815–822.

    CAS  Article  Google Scholar 

  12. Jawed, K., S. S. Yazdani, and M. A. Koffas (2019) Advances in the development and application of microbial consortia for metabolic engineering. Metab. Eng. Commun. 9: e00095. (Erratum published 2021, Metab. Eng. Commun. 13: e00186)

    PubMed  Article  PubMed Central  Google Scholar 

  13. Albergaria, H. and N. Arneborg (2016) Dominance of Saccharomyces cerevisiae in alcoholic fermentation processes: role of physiological fitness and microbial interactions. Appl. Microbiol. Biotechnol. 100: 2035–2046.

    CAS  PubMed  Article  Google Scholar 

  14. Aquilanti, L., S. Santarelli, G. Silvestri, A. Osimani, A. Petruzzelli, and F. Clementi (2007) The microbial ecology of a typical Italian salami during its natural fermentation. Int. J. Food Microbiol. 120: 136–145.

    CAS  PubMed  Article  Google Scholar 

  15. ben Omar, N. and F. Ampe (2000) Microbial community dynamics during production of the Mexican fermented maize dough pozol. Appl. Environ. Microbiol. 66: 3664–3673.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  16. Fontana, C., P. Sandro Cocconcelli, and G. Vignolo (2005) Monitoring the bacterial population dynamics during fermentation of artisanal Argentinean sausages. Int. J. Food Microbiol. 103: 131–142.

    CAS  PubMed  Article  Google Scholar 

  17. Mukisa, I. M., D. Porcellato, Y. B. Byaruhanga, C. M. B. K. Muyanja, K. Rudi, T. Langsrud, and J. A. Narvhus (2012) The dominant microbial community associated with fermentation of Obushera (sorghum and millet beverages) determined by culture-dependent and culture-independent methods. Int. J. Food Microbiol. 160: 1–10.

    CAS  PubMed  Article  Google Scholar 

  18. Cocolin, L., V. Alessandria, P. Dolci, R. Gorra, and K. Rantsiou (2013) Culture independent methods to assess the diversity and dynamics of microbiota during food fermentation. Int. J. Food Microbiol. 167: 29–43.

    CAS  PubMed  Article  Google Scholar 

  19. Botta, C. and L. Cocolin (2012) Microbial dynamics and biodiversity in table olive fermentation: culture-dependent and — independent approaches. Front. Microbiol. 3: 245.

    PubMed  Article  PubMed Central  Google Scholar 

  20. Rossen, L., K. Holmstrøm, J. E. Olsen, and O. F. Rasmussen (1991) A rapid polymerase chain reaction (PCR)-based assay for the identification of Listeria monocytogenes in food samples. Int. J. Food Microbiol. 14: 145–151.

    CAS  PubMed  Article  Google Scholar 

  21. Randazzo, C. L., S. Torriani, A. D. L. Akkermans, W. M. de Vos, and E. E. Vaughan (2002) Diversity, dynamics, and activity of bacterial communities during production of an artisanal Sicilian cheese as evaluated by 16S rRNA analysis. Appl. Environ. Microbiol. 68: 1882–1892.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  22. Alegría, A., P. Alvarez-Martín, N. Sacristán, E. Fernández, S. Delgado, and B. Mayo (2009) Diversity and evolution of the microbial populations during manufacture and ripening of Casín, a traditional Spanish, starter-free cheese made from cow’s milk. Int. J. Food Microbiol. 136: 44–51.

    PubMed  Article  CAS  Google Scholar 

  23. Wang, W., L. Yan, Z. Cui, Y. Gao, Y. Wang, and R. Jing (2011) Characterization of a microbial consortium capable of degrading lignocellulose. Bioresour. Technol. 102: 9321–9324.

    CAS  PubMed  Article  Google Scholar 

  24. Wang, X., H. Cui, J. Shi, X. Zhao, Y. Zhao, and Z. Wei (2015) Relationship between bacterial diversity and environmental parameters during composting of different raw materials. Bioresour. Technol. 198: 395–402.

    CAS  PubMed  Article  Google Scholar 

  25. Olsen, G. J., D. J. Lane, S. J. Giovannoni, N. R. Pace, and D. A. Stahl (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40: 337–365.

    CAS  PubMed  Article  Google Scholar 

  26. Venter, J. C., K. Remington, J. F. Heidelberg, A. L. Halpern, D. Rusch, J. A. Eisen, D. Wu, I. Paulsen, K. E. Nelson, W. Nelson, D. E. Fouts, S. Levy, A. H. Knap, M. W. Lomas, K. Nealson, O. White, J. Peterson, J. Hoffman, R. Parsons, H. Baden-Tillson, C. Pfannkoch, Y.-H. Rogers, and H. O. Smith (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science. 304: 66–74.

    CAS  PubMed  Article  Google Scholar 

  27. Thomas, T., J. Gilbert, and F. Meyer (2012) Metagenomics — a guide from sampling to data analysis. Microb. Inform. Exp. 2: 3.

    PubMed  Article  PubMed Central  Google Scholar 

  28. Ajayi-Banji, A. A., S. Rahman (2021) Efficacy of magnetite (Fe3O4) nanoparticles for enhancing solid-state anaerobic codigestion: Focus on reactor performance and retention time. Bioresour. Technol. 324: 124670.

    CAS  PubMed  Article  Google Scholar 

  29. Zerva, I., N. Remmas, and S. Ntougias (2019) Diversity and biotechnological potential of xylan-degrading microorganisms from orange juice processing waste. Water (Basel). 11: 274.

    CAS  Google Scholar 

  30. Portillo, M. and A. Mas (2016) Analysis of microbial diversity and dynamics during wine fermentation of Grenache grape variety by high-throughput barcoding sequencing. Lebensm. Wiss. Technol. 72: 317–321.

    CAS  Article  Google Scholar 

  31. Zapparoli, G., C. Reguant, A. Bordons, S. Torriani, and F. Dellaglio (2000) Genomic DNA fingerprinting of Oenococcus oeni strains by pulsed-field gel electrophoresis and randomly amplified polymorphic DNA-PCR. Curr. Microbiol. 40: 351–355.

    CAS  PubMed  Article  Google Scholar 

  32. Anyogu, A., B. Awamaria, J. P. Sutherland, and L. I. I. Ouoba (2014) Molecular characterisation and antimicrobial activity of bacteria associated with submerged lactic acid cassava fermentation. Food Control. 39: 119–127.

    CAS  Article  Google Scholar 

  33. Peng, X., S. Zhang, L. Li, X. Zhao, Y. Ma, and D. Shi (2018) Long-term high-solids anaerobic digestion of food waste: Effects of ammonia on process performance and microbial community. Bioresour. Technol. 262: 148–158.

    CAS  PubMed  Article  Google Scholar 

  34. David, V., S. Terrat, K. Herzine, O. Claisse, S. Rousseaux, R. Tourdot-Maréchal, I. Masneuf-Pomarede, L. Ranjard, and H. Alexandre (2014) High-throughput sequencing of amplicons for monitoring yeast biodiversity in must and during alcoholic fermentation. J. Ind. Microbiol. Biotechnol. 41: 811–821.

    CAS  PubMed  Article  Google Scholar 

  35. González, Á., N. Hierro, M. Poblet, A. Mas, and J. M. Guillamón (2005) Application of molecular methods to demonstrate species and strain evolution of acetic acid bacteria population during wine production. Int. J. Food Microbiol. 102: 295–304.

    PubMed  Article  CAS  Google Scholar 

  36. de Melo Pereira, G. V., D. P. de Carvalho Neto, B. L. Maske, J. De Dea Lindner, A. S. Vale, G. R. Favero, J. Viesser, J. C. de Carvalho, A. Góes-Neto, and C. R. Soccol (2022) An updated review on bacterial community composition of traditional fermented milk products: what next-generation sequencing has revealed so far? Crit. Rev. Food Sci. Nutr. 62: 1870–1889.

    CAS  PubMed  Article  Google Scholar 

  37. Neefs, J.-M., Y. Van de Peer, P. De Rijk, S. Chapelle, and R. De Wachter (1993) Compilation of small ribosomal subunit RNA structures. Nucleic Acids Res. 21: 3025–3049.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  38. Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, and K. G. Field (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature. 345: 60–63.

    CAS  PubMed  Article  Google Scholar 

  39. Ros, M., J. de Souza Oliveira Filho, M. D. Perez Murcia, M. A. Bustamante, R. Moral, M. D. Coll, A. B. Lopez Santisima-Trinidad, and J. A. Pascual (2017) Mesophilic anaerobic digestion of pig slurry and fruit and vegetable waste: dissection of the microbial community structure. J. Clean. Prod. 156: 757–765.

    CAS  Article  Google Scholar 

  40. Sahoo, R. K., E. Subudhi, and M. Kumar (2014) Quantitative approach to track lipase producing Pseudomonas sp. S1 in nonsterilized solid state fermentation. Lett. Appl. Microbiol. 58: 610–616.

    CAS  PubMed  Article  Google Scholar 

  41. Caporaso, J. G., J. Kuczynski, J. Stombaugh, K. Bittinger, F. D. Bushman, E. K. Costello, N. Fierer, A. G. Peña, J. K. Goodrich, J. I. Gordon, G. A. Huttley, S. T. Kelley, D. Knights, J. E. Koenig, R. E. Ley, C. A. Lozupone, D. McDonald, B. D. Muegge, M. Pirrung, J. Reeder, J. R. Sevinsky, P. J. Turnbaugh, W. A. Walters, J. Widmann, T. Yatsunenko, J. Zaneveld, and R. Knight (2010) QIIME allows analysis of high-throughput community sequencing data. Nat. Methods. 7: 335–336.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  42. Edgar, R. C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 26: 2460–2461.

    CAS  PubMed  Article  Google Scholar 

  43. Schloss, P. D., S. L. Westcott, T. Ryabin, J. R. Hall, M. Hartmann, E. B. Hollister, R. A. Lesniewski, B. B. Oakley, D. H. Parks, C. J. Robinson, J. W. Sahl, B. Stres, G. G. Thallinger, D. J. Van Horn, and C. F. Weber (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75: 7537–7541.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  44. Claesson, M. J., Q. Wang, O. O’Sullivan, R. Greene-Diniz, J. R. Cole, R. P. Ross, and P. W. O’Toole (2010) Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res. 38: e200.

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  45. Hugon, P., J.-C. Lagier, C. Robert, C. Lepolard, L. Papazian, D. Musso, B. Vialettes, and D. Raoult (2013) Molecular studies neglect apparently gram-negative populations in the human gut microbiota. J. Clin. Microbiol. 51: 3286–3293.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  46. Liu, Z., C. Lozupone, M. Hamady, F. D. Bushman, and R. Knight (2007) Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res. 35: e120.

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  47. Kostinek, M., I. Specht, V. A. Edward, C. Pinto, M. Egounlety, C. Sossa, S. Mbugua, C. Dortu, P. Thonart, L. Taljaard, M. Mengu, C. M. Franz, and W. H. Holzapfel (2007) Characterisation and biochemical properties of predominant lactic acid bacteria from fermenting cassava for selection as starter cultures. Int. J. Food Microbiol. 114: 342–351.

    CAS  PubMed  Article  Google Scholar 

  48. Plengvidhya, V., F. BreidtJr., Z. Lu, and H. P. Fleming (2007) DNA fingerprinting of lactic acid bacteria in sauerkraut fermentations. Appl. Environ. Microbiol. 73: 7697–7702.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  49. Vouidibio Mbozo, A. B., S. C. Kobawila, A. Anyogu, B. Awamaria, D. Louembe, J. P. Sutherland, and L. I. Ouoba (2017) Investigation of the diversity and safety of the predominant Bacillus pumilus sensu lato and other Bacillus species involved in the alkaline fermentation of cassava leaves for the production of Ntoba Mbodi. Food Control. 82: 154–162.

    CAS  Article  Google Scholar 

  50. Ampe, F., N. ben Omar, C. Moizan, C. Wacher, and J. P. Guyot (1999) Polyphasic study of the spatial distribution of microorganisms in Mexican pozol, a fermented maize dough, demonstrates the need for cultivation-independent methods to investigate traditional fermentations. Appl. Environ. Microbiol. 65: 5464–5473.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  51. Hamad, S. H., M. C. Dieng, M. A. Ehrmann, and R. F. Vogel (1997) Characterization of the bacterial flora of Sudanese sorghum flour and sorghum sourdough. J. Appl. Microbiol. 83: 764–770.

    CAS  PubMed  Article  Google Scholar 

  52. Quast, C., E. Pruesse, P. Yilmaz, J. Gerken, T. Schweer, P. Yarza, J. Peplies, and F. O. Glöckner (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41: D590–D596.

    CAS  PubMed  Article  Google Scholar 

  53. Compeau, P. E. C., P. A. Pevzner, and G. Tesler (2011) How to apply de Bruijn graphs to genome assembly. Nat. Biotechnol. 29: 987–991.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  54. Chen, Y., J. Sheng, T. Jiang, J. Stevens, X. Feng, and N. Wei (2016) Transcriptional profiling reveals molecular basis and novel genetic targets for improved resistance to multiple fermentation inhibitors in Saccharomyces cerevisiae. Biotechnol. Biofuels. 9: 9.

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  55. Verce, M., J. Schoonejans, C. Hernandez Aguirre, R. Molina-Bravo, L. De Vuyst, and S. Weckx (2021) A combined metagenomics and metatranscriptomics approach to unravel Costa Rican cocoa box fermentation processes reveals yet unreported microbial species and functionalities. Front. Microbiol. 12: 641185.

    PubMed  Article  PubMed Central  Google Scholar 

  56. Ercolini, D. (2013) High-throughput sequencing and metagenomics: moving forward in the culture-independent analysis of food microbial ecology. Appl. Environ. Microbiol. 79: 3148–3155.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  57. Erkus, O., V. C. L. de Jager, R. T. C. M. Geene, I. van Alen-Boerrigter, L. Hazelwood, S. A. F. T. van Hijum, M. Kleerebezem, and E. J. Smid (2016) Use of propidium monoazide for selective profiling of viable microbial cells during Gouda cheese ripening. Int. J. Food Microbiol. 228: 1–9.

    CAS  PubMed  Article  Google Scholar 

  58. Simmons, C. W., A. P. Reddy, P. D’haeseleer, J. Khudyakov, K. Billis, A. Pati, B. A. Simmons, S. W. Singer, M. P. Thelen, and J. S. VanderGheynst (2014) Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw. Biotechnol. Biofuels. 7: 495.

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  59. Alessi, A. M., S. M. Bird, N. C. Oates, Y. Li, A. A. Dowle, E. H. Novotny, E. R. deAzevedo, J. P. Bennett, I. Polikarpov, J. Young, S. J. McQueen-Mason, and N. C. Bruce (2018) Defining functional diversity for lignocellulose degradation in a microbial community using multi-omics studies. Biotechnol. Biofuels. 11: 166.

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  60. He, B., S. Jin, J. Cao, L. Mi, and J. Wang (2019) Metatranscriptomics of the Hu sheep rumen microbiome reveals novel cellulases. Biotechnol. Biofuels. 12: 153.

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  61. Muyzer, G., E. C. de Waal, and A. G. Uitterlinden (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59: 695–700.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  62. Cocolin, L., M. Manzano, C. Cantoni, and G. Comi (2001) Denaturing gradient gel electrophoresis analysis of the 16S rRNA gene V1 region to monitor dynamic changes in the bacterial population during fermentation of Italian sausages. Appl. Environ. Microbiol. 67: 5113–5121.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  63. Masoud, W., L. B. Cesar, L. Jespersen, and M. Jakobsen (2004) Yeast involved in fermentation of Coffea arabica in East Africa determined by genotyping and by direct denaturating gradient gel electrophoresis. Yeast. 21: 549–556.

    CAS  PubMed  Article  Google Scholar 

  64. Wei, Q., H. Wang, Z. Chen, Z. Lv, Y. Xie, and F. Lu (2013) Profiling of dynamic changes in the microbial community during the soy sauce fermentation process. Appl. Microbiol. Biotechnol. 97: 9111–9119.

    CAS  PubMed  Article  Google Scholar 

  65. Cocolin, L., L. F. Bisson, and D. A. Mills (2000) Direct profiling of the yeast dynamics in wine fermentations. FEMS Microbiol. Lett. 189: 81–87.

    CAS  PubMed  Article  Google Scholar 

  66. El Sheikha, A. F. (2019) Molecular detection of mycotoxigenic fungi in foods: the case for using PCR-DGGE. Food Biotechnol. 33: 54–108.

    CAS  Article  Google Scholar 

  67. Zhang, W., Y. Mo, J. Yang, J. Zhou, Y. Lin, A. Isabwe, J. Zhang, X. Gao, and Z. Yu (2018) Genetic diversity pattern of microeukaryotic communities and its relationship with the environment based on PCR-DGGE and T-RFLP techniques in Dongshan Bay, southeast China. Cont. Shelf Res. 164: 1–9.

    Article  Google Scholar 

  68. Han, R., Y. Yuan, Q. Cao, Q. Li, L. Chen, D. Zhu, and D. Liu (2018) PCR-DGGE analysis on microbial community structure of rural household biogas digesters in Qinghai Plateau. Curr. Microbiol. 75: 541–549.

    CAS  PubMed  Article  Google Scholar 

  69. Salvachúa, D., A. Z. Werner, I. Pardo, M. Michalska, B. A. Black, B. S. Donohoe, S. J. Haugen, R. Katahira, S. Notonier, K. J. Ramirez, A. Amore, S. O. Purvine, E. M. Zink, P. E. Abraham, R. J. Giannone, S. Poudel, P. D. Laible, R. L. Hettich, and G. T. Beckham (2020) Outer membrane vesicles catabolize lignin-derived aromatic compounds in Pseudomonas putida KT2440. Proc. Natl. Acad. Sci. U. S. A. 117: 9302–9310.

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  70. Cleary, D. F. R., K. Smalla, L. C. S. Mendonça-Hagler, and N. C. M. Gomes (2012) Assessment of variation in bacterial composition among microhabitats in a mangrove environment using DGGE fingerprints and barcoded pyrosequencing. PLoS One. 7: e29380.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  71. Heid, C. A., J. Stevens, K. J. Livak, and P. M. Williams (1996) Real time quantitative PCR. Genome Res. 6: 986–994.

    CAS  PubMed  Article  Google Scholar 

  72. De Vuyst, L., N. Camu, T. De Winter, K. Vandemeulebroecke, V. Van de Perre, M. Vancanneyt, P. De Vos, and I. Cleenwerck (2008) Validation of the (GTG)(5)-rep-PCR fingerprinting technique for rapid classification and identification of acetic acid bacteria, with a focus on isolates from Ghanaian fermented cocoa beans. Int. J. Food Microbiol. 125: 79–90.

    CAS  PubMed  Article  Google Scholar 

  73. Kumar, M., A. Joshi, R. Kashyap, and S. Khanna (2011) Production of xylanase by Promicromonospora sp MARS with rice straw under non sterile conditions. Process Biochem. 46: 1614–1618.

    CAS  Article  Google Scholar 

  74. Paludan-Müller, C., R. Valyasevi, H. H. Huss, and L. Gram (2002) Genotypic and phenotypic characterization of garlic-fermenting lactic acid bacteria isolated from som-fak, a Thai low-salt fermented fish product. J. Appl. Microbiol. 92: 307–314.

    PubMed  Article  Google Scholar 

  75. Wu, Y. R. and J. He (2013) Characterization of anaerobic consortia coupled lignin depolymerization with biomethane generation. Bioresour. Technol. 139: 5–12.

    CAS  PubMed  Article  Google Scholar 

  76. de Oliveira, C. T., L. Pellenz, J. Q. Pereira, A. Brandelli, and D. J. Daroit (2016) Screening of bacteria for protease production and feather degradation. Waste Biomass Valorization. 7: 447–453.

    Article  CAS  Google Scholar 

  77. Joblin, K. N., G. E. Naylor, and A. G. Williams (1990) Effect of Methanobrevibacter smithii on xylanolytic activity of anaerobic ruminal fungi. Appl. Environ. Microbiol. 56: 2287–2295.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  78. Bader, J., E. Mast-Gerlach, M. K. Popović, R. Bajpai, and U. Stahl (2010) Relevance of microbial coculture fermentations in biotechnology. J. Appl. Microbiol. 109: 371–387.

    CAS  PubMed  Article  Google Scholar 

  79. Pandhal, J. and J. Noirel (2014) Synthetic microbial ecosystems for biotechnology. Biotechnol. Lett. 36: 1141–1151.

    CAS  PubMed  Article  Google Scholar 

  80. Joblin, K. N., H. Matsui, G. E. Naylor, and K. Ushida (2002) Degradation of fresh ryegrass by methanogenic co-cultures of ruminal fungi grown in the presence or absence of Fibrobacter succinogenes. Curr. Microbiol. 45: 46–53.

    CAS  PubMed  Article  Google Scholar 

  81. Cheng, X.-Y. and C.-Z. Liu (2012) Fungal pretreatment enhances hydrogen production via thermophilic fermentation of cornstalk. Appl. Energy. 91: 1–6.

    CAS  Article  Google Scholar 

  82. Pessiot, J., R. Nouaille, M. Jobard, R. R. Singhania, A. Bournilhas, G. Christophe, P. Fontanille, P. Peyret, G. Fonty, and C. Larroche (2012) Fed-batch anaerobic valorization of slaughterhouse by-products with mesophilic microbial consortia without methane production. Appl. Biochem. Biotechnol. 167: 1728–1743.

    CAS  PubMed  Article  Google Scholar 

  83. Zhang, J., J. Liu, Z. Shi, L. Liu, and J. Chen (2010) Manipulation of B. megaterium growth for efficient 2-KLG production by K. vulgare. Process Biochem. 45: 602–606.

    CAS  Article  Google Scholar 

  84. Liu, Y., M. Ding, W. Ling, Y. Yang, X. Zhou, B.-Z. Li, T. Chen, Y. Nie, M. Wang, B. Zeng, X. Li, H. Liu, B. Sun, H. Xu, J. Zhang, Y. Jiao, Y. Hou, H. Yang, S. Xiao, Q. Lin, X. He, W. Liao, Z. Jin, Y. Xie, B. Zhang, T. Li, X. Lu, J. Li, F. Zhang, X.-L. Wu, H. Song, and Y.-J. Yuan (2017) A three-species microbial consortium for power generation. Energy Environ. Sci. 10: 1600–1609.

    CAS  Article  Google Scholar 

  85. Shahab, R. L., S. Brethauer, M. P. Davey, A. G. Smith, S. Vignolini, J. S. Luterbacher, and M. H. Studer (2020) A heterogeneous microbial consortium producing short-chain fatty acids from lignocellulose. Science. 369: eabb1214.

    CAS  PubMed  Article  Google Scholar 

  86. Poszytek, K., M. Ciezkowska, A. Sklodowska, and L. Drewniak (2016) Microbial Consortium with High Cellulolytic Activity (MCHCA) for enhanced biogas production. Front. Microbiol. 7: 324.

    PubMed  Article  PubMed Central  Google Scholar 

  87. Sun, Y., Z. Xu, Y. Zheng, J. Zhou, and Z. Xiu (2019) Efficient production of lactic acid from sugarcane molasses by a newly microbial consortium CEE-DL15. Process Biochem. 81: 132–138.

    CAS  Article  Google Scholar 

  88. Schwalm, N. D., III, W. Mojadedi, E. S. Gerlach, M. Benyamin, M. A. Perisin, and K. L. Akingbade (2019) Developing a microbial consortium for enhanced metabolite production from simulated food waste. Fermentation (Basel) 5: 98.

    CAS  Article  Google Scholar 

  89. Zhou, K., K. Qiao, S. Edgar, and G. Stephanopoulos (2015) Distributing a metabolic pathway among a microbial consortium enhances production of natural products. Nat. Biotechnol. 33: 377–383.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  90. Zhao, C., J. P. Sinumvayo, Y. Zhang, and Y. Li (2019) Design and development of a “Y-shaped” microbial consortium capable of simultaneously utilizing biomass sugars for efficient production of butanol. Metab. Eng. 55: 111–119.

    CAS  PubMed  Article  Google Scholar 

  91. Chen, Y., Z. Yang, Y. Zhang, Y. Xiang, R. Xu, M. Jia, J. Cao, and W. Xiong (2020) Effects of different conductive nanomaterials on anaerobic digestion process and microbial community of sludge. Bioresour. Technol. 304: 123016.

    CAS  PubMed  Article  Google Scholar 

  92. Ajay, C. M., S. Mohan, P. Dinesha, and M. A. Rosen (2020) Review of impact of nanoparticle additives on anaerobic digestion and methane generation. Fuel (Lond.) 277: 118234.

    CAS  Article  Google Scholar 

  93. Huangfu, X., Y. Xu, C. Liu, Q. He, J. Ma, C. Ma, and R. Huang (2019) A review on the interactions between engineered nanoparticles with extracellular and intracellular polymeric substances from wastewater treatment aggregates. Chemosphere. 219: 766–783.

    CAS  PubMed  Article  Google Scholar 

  94. Zhang, J., Z. Wang, T. Lu, J. Liu, Y. Wang, P. Shen, and Y. Wei (2019) Response and mechanisms of the performance and fate of antibiotic resistance genes to nano-magnetite during anaerobic digestion of swine manure. J. Hazard. Mater. 366: 192–201.

    CAS  PubMed  Article  Google Scholar 

  95. Jing, Y., J. Wan, I. Angelidaki, S. Zhang, and G. Luo (2017) iTRAQ quantitative proteomic analysis reveals the pathways for methanation of propionate facilitated by magnetite. Water Res. 108: 212–221.

    CAS  PubMed  Article  Google Scholar 

  96. Baek, G., J. Kim, K. Cho, H. Bae, and C. Lee (2015) The biostimulation of anaerobic digestion with (semi)conductive ferric oxides: their potential for enhanced biomethanation. Appl. Microbiol. Biotechnol. 99: 10355–10366.

    CAS  PubMed  Article  Google Scholar 

  97. Yin, Q., J. Miao, B. Li, and G. Wu (2017) Enhancing electron transfer by ferroferric oxide during the anaerobic treatment of synthetic wastewater with mixed organic carbon. Int. Biodeterior. Biodegradation. 119: 104–110.

    CAS  Article  Google Scholar 

  98. Abdelsalam, E., M. Samer, Y. A. Attia, M. A. Abdel-Hadi, H. E. Hassan, and Y. Badr (2017) Influence of zero valent iron nanoparticles and magnetic iron oxide nanoparticles on biogas and methane production from anaerobic digestion of manure. Energy (Oxf.) 120: 842–853.

    CAS  Article  Google Scholar 

  99. Kökdemir Ünşar, E. and N. A. Perendeci (2018) What kind of effects do Fe2O3 and Al2O3 nanoparticles have on anaerobic digestion, inhibition or enhancement? Chemosphere. 211: 726–735.

    PubMed  Article  CAS  Google Scholar 

  100. Zhao, Z., Y. Zhang, Y. Li, X. Quan, and Z. Zhao (2018) Comparing the mechanisms of ZVI and Fe3O4 for promoting waste-activated sludge digestion. Water Res. 144: 126–133.

    CAS  PubMed  Article  Google Scholar 

  101. Baral, N. R. and A. Shah (2014) Microbial inhibitors: formation and effects on acetone-butanol-ethanol fermentation of lignocellulosic biomass. Appl. Microbiol. Biotechnol. 98: 9151–9172.

    CAS  PubMed  Article  Google Scholar 

  102. Tian, H., I. A. Fotidis, E. Mancini, L. Treu, A. Mahdy, M. Ballesteros, C. González-Fernández, and I. Angelidaki (2018) Acclimation to extremely high ammonia levels in continuous biomethanation process and the associated microbial community dynamics. Bioresour. Technol. 247: 616–623.

    CAS  PubMed  Article  Google Scholar 

  103. Wang, F. Q., H. Xie, W. Chen, E. T. Wang, F. G. Du, and A. D. Song (2013) Biological pretreatment of corn stover with ligninolytic enzyme for high efficient enzymatic hydrolysis. Bioresour. Technol. 144: 572–578.

    CAS  PubMed  Article  Google Scholar 

  104. Sasano, Y., D. Watanabe, K. Ukibe, T. Inai, I. Ohtsu, H. Shimoi, and H. Takagi (2012) Overexpression of the yeast transcription activator Msn2 confers furfural resistance and increases the initial fermentation rate in ethanol production. J. Biosci. Bioeng. 113: 451–455.

    CAS  PubMed  Article  Google Scholar 

  105. Kim, D. and J.-S. Hahn (2013) Roles of the Yap1 transcription factor and antioxidants in Saccharomyces cerevisiae’s tolerance to furfural and 5-hydroxymethylfurfural, which function as thiol-reactive electrophiles generating oxidative stress. Appl. Environ. Microbiol. 79: 5069–5077.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  106. Conway, J. M., B. S. McKinley, N. L. Seals, D. Hernandez, P. A. Khatibi, S. Poudel, R. J. Giannone, R. L. Hettich, A. M. Williams-Rhaesa, G. L. Lipscomb, M. Adams, and R. M. Kelly (2017) Functional analysis of the glucan degradation locus in Caldicellulosiruptor bescii reveals essential roles of component glycoside hydrolases in plant biomass deconstruction. Appl. Environ. Microbiol. 83: e01828–17.

    PubMed  Article  PubMed Central  Google Scholar 

  107. Peng, X., W. Qiao, S. Mi, X. Jia, H. Su, and Y. Han (2015) Characterization of hemicellulase and cellulase from the extremely thermophilic bacterium Caldicellulosiruptor owensensis and their potential application for bioconversion of lignocellulosic biomass without pretreatment. Biotechnol. Biofuels. 8: 131.

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  108. Lochner, A., R. J. Giannone, M. RodriguezJr., M. B. Shah, J. R. Mielenz, M. Keller, G. Antranikian, D. E. Graham, and R. L. Hettich (2011) Use of label-free quantitative proteomics to distinguish the secreted cellulolytic systems of Caldicellulosiruptor bescii and Caldicellulosiruptor obsidiansis. Appl. Environ. Microbiol. 77: 4042–4054.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  109. Brunecky, R., M. Alahuhta, Q. Xu, B. S. Donohoe, M. F. Crowley, I. A. Kataeva, S. J. Yang, M. G. Resch, M. W. Adams, V. V. Lunin, M. E. Himmel, and Y. J. Bomble (2013) Revealing nature’s cellulase diversity: the digestion mechanism of Caldicellulosiruptor bescii CelA. Science. 342: 1513–1516.

    CAS  PubMed  Article  Google Scholar 

  110. Bing, R. G., C. T. Straub, D. B. Sulis, J. P. Wang, M. W. W. Adams, and R. M. Kelly (2022) Plant biomass fermentation by the extreme thermophile Caldicellulosiruptor bescii for coproduction of green hydrogen and acetone: technoeconomic analysis. Bioresour. Technol. 348: 126780.

    CAS  PubMed  Article  Google Scholar 

  111. Ali, N., H. I. Hamouda, H. Su, J. Feng, Z.-Y. Liu, M. Lu, and F.-L. Li (2020) A two-stage anaerobic bioconversion of corn stover: impact of pure bacterial pretreatment on methane production. Environ. Technol. Innov. 20: 101141.

    CAS  Article  Google Scholar 

  112. Hamilton-Brehm, S. D., J. J. Mosher, T. Vishnivetskaya, M. Podar, S. Carroll, S. Allman, T. J. Phelps, M. Keller, and J. G. Elkins (2010) Caldicellulosiruptor obsidiansis sp. nov., an anaerobic, extremely thermophilic, cellulolytic bacterium isolated from Obsidian Pool, Yellowstone National Park. Appl. Environ. Microbiol. 76: 1014–1020.

    CAS  PubMed  Article  Google Scholar 

  113. Kataeva, I., M. B. Foston, S.-J. Yang, S. Pattathil, A. K. Biswal, F. L. PooleII, M. Basen, A. M. Rhaesa, T. P. Thomas, P. Azadi, V. Olman, T. D. Saffold, K. E. Mohler, D. L. Lewis, C. Doeppke, Y. Zeng, T. J. Tschaplinski, W. S. York, M. Davis, D. Mohnen, Y. Xu, A. J. Ragauskas, S.-Y. Ding, R. M. Kelly, M. G. Hahn, and M. W. W. Adams (2013) Carbohydrate and lignin are simultaneously solubilized from unpretreated switchgrass by microbial action at high temperature. Energy Environ. Sci. 6: 2186–2195.

    CAS  Article  Google Scholar 

  114. del Cerro, C., E. Erickson, T. Dong, A. R. Wong, E. K. Eder, S. O. Purvine, H. D. Mitchell, K. K. Weitz, L. M. Markillie, M. C. Burnet, D. W. Hoyt, R. K. Chu, J. F. Cheng, K. J. Ramirez, R. Katahira, W. Xiong, M. E. Himmel, V. Subramanian, J. G. Linger, and D. Salvachúa (2021) Intracellular pathways for lignin catabolism in white-rot fungi. Proc. Natl. Acad. Sci. U. S. A. 118: e2017381118.

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  115. Coelho-Moreira, J. D. S., G. M. Maciel, R. Castoldi, S. D. S. Mariano, F. D. Inácio, A. Bracht, and R. M. Peralta (2013) Involvement of lignin-modifying enzymes in the degradation of herbicides. pp. 165–187. In: A. J. Price and J. A. Kelton (eds.). Herbicides — Advances in Research. IntechOpen, London, UK.

    Google Scholar 

  116. Vasco-Correa, J. and Y. Li (2015) Solid-state anaerobic digestion of fungal pretreated Miscanthus sinensis harvested in two different seasons. Bioresour. Technol. 185: 211–217.

    CAS  PubMed  Article  Google Scholar 

  117. Zhao, J., X. Ge, J. Vasco-Correa, and Y. Li (2014) Fungal pretreatment of unsterilized yard trimmings for enhanced methane production by solid-state anaerobic digestion. Bioresour. Technol. 158: 248–252.

    CAS  PubMed  Article  Google Scholar 

  118. Akyol, Ç., O. Ince, M. Bozan, E. G. Ozbayram, and B. Ince (2019) Biological pretreatment with Trametes versicolor to enhance methane production from lignocellulosic biomass: a metagenomic approach. Ind. Crops Prod. 140: 111659.

    CAS  Article  Google Scholar 

  119. Mustafa, A. M., T. G. Poulsen, and K. Sheng (2016) Fungal pretreatment of rice straw with Pleurotus ostreatus and Trichoderma reesei to enhance methane production under solidstate anaerobic digestion. Appl. Energy. 180: 661–671.

    CAS  Article  Google Scholar 

  120. Yadav, M., K. Paritosh, N. Pareek, and V. Vivekanand (2019) Coupled treatment of lignocellulosic agricultural residues for augmented biomethanation. J. Clean. Prod. 213: 75–88.

    CAS  Article  Google Scholar 

  121. González, C., Y. Wu, A. Zuleta-Correa, G. Jaramillo, and J. Vasco-Correa (2021) Biomass to value-added products using microbial consortia with white-rot fungi. Bioresour. Technol. Rep. 16: 100831.

    Article  CAS  Google Scholar 

  122. Wang, W., T. Yuan, and B. Cui (2014) Biological pretreatment with white rot fungi and their co-culture to overcome lignocellulosic recalcitrance for improved enzymatic digestion. Bioresources. 9: 3968–3976.

    Google Scholar 

  123. Wang, R., T. You, G. Yang, and F. Xu (2017) Efficient short time white rot—brown rot fungal pretreatments for the enhancement of enzymatic saccharification of corn cobs. ACS Sustain. Chem. Eng. 5: 10849–10857.

    Article  CAS  Google Scholar 

  124. Ma, K. and Z. Ruan (2015) Production of a lignocellulolytic enzyme system for simultaneous bio-delignification and saccharification of corn stover employing co-culture of fungi. Bioresour. Technol. 175: 586–593.

    CAS  PubMed  Article  Google Scholar 

  125. Hermosilla, E., O. Rubilar, H. Schalchli, A. S. da Silva, V. Ferreira-Leitao, and M. C. Diez (2018) Sequential white-rot and brown-rot fungal pretreatment of wheat straw as a promising alternative for complementary mild treatments. Waste Manag. 79: 240–250.

    CAS  PubMed  Article  Google Scholar 

  126. Xie, P., L. Fan, L. Huang, and C. Zhang (2020) An innovative co-fungal treatment to poplar bark sawdust for delignification and polyphenol enrichment. Ind. Crops Prod. 157: 112896.

    CAS  Article  Google Scholar 

  127. Yoon, L. W., G. C. Ngoh, A. S. M. Chua, M. F. Abdul Patah, and W. H. Teoh (2019) Process intensification of cellulase and bioethanol production from sugarcane bagasse via an integrated saccharification and fermentation process. Chem. Eng. Process. 142: 107528.

    CAS  Article  Google Scholar 

  128. Horisawa, S., A. Inoue, and Y. Yamanaka (2019) Direct ethanol production from lignocellulosic materials by mixed culture of wood rot fungi Schizophyllum commune, Bjerkandera adusta, and Fomitopsis palustris. Fermentation (Basel). 5: 21.

    CAS  Article  Google Scholar 

  129. Horisawa, S., H. Ando, O. Ariga, and Y. Sakuma (2015) Direct ethanol production from cellulosic materials by consolidated biological processing using the wood rot fungus Schizophyllum commune. Bioresour. Technol. 197: 37–41.

    CAS  PubMed  Article  Google Scholar 

  130. Tri, C. L. and I. Kamei (2020) Butanol production from cellulosic material by anaerobic co-culture of white-rot fungus Phlebia and bacterium Clostridium in consolidated bioprocessing. Bioresour. Technol. 305: 123065.

    CAS  PubMed  Article  Google Scholar 

  131. Biderre-Petit, C., D. Jézéquel, E. Dugat-Bony, F. Lopes, J. Kuever, G. Borrel, E. Viollier, G. Fonty, and P. Peyret (2011) Identification of microbial communities involved in the methane cycle of a freshwater meromictic lake. FEMS Microbiol. Ecol. 77: 533–545.

    CAS  PubMed  Article  Google Scholar 

  132. Kumar, M., S. You, J. Beiyuan, G. Luo, J. Gupta, S. Kumar, L. Singh, S. Zhang, and D. C. W. Tsang (2021) Lignin valorization by bacterial genus Pseudomonas: state-of-the-art review and prospects. Bioresour. Technol. 320: 124412.

    CAS  PubMed  Article  Google Scholar 

  133. Elmore, J. R., G. N. Dexter, D. Salvachúa, M. O’Brien, D. M. Klingeman, K. Gorday, J. K. Michener, D. J. Peterson, G. T. Beckham, and A. M. Guss (2020) Engineered Pseudomonas putida simultaneously catabolizes five major components of corn stover lignocellulose: glucose, xylose, arabinose, p-coumaric acid, and acetic acid. Metab. Eng. 62: 62–71.

    CAS  PubMed  Article  Google Scholar 

  134. Lee, S., J.-H. Sohn, J.-H. Bae, S. C. Kim, and B. H. Sung (2020) Current status of Pseudomonas putida engineering for lignin valorization. Biotechnol. Bioprocess Eng. 25: 862–871.

    CAS  Article  Google Scholar 

  135. Yang, C., F. Yue, Y. Cui, Y. Xu, Y. Shan, B. Liu, Y. Zhou, and X. Lü (2018) Biodegradation of lignin by Pseudomonas sp. Q18 and the characterization of a novel bacterial DyP-type peroxidase. J. Ind. Microbiol. Biotechnol. 45: 913–927.

    CAS  PubMed  Article  Google Scholar 

  136. Ghosh, T., T.-D. Ngo, A. Kumar, C. Ayranci, and T. Tang (2019) Cleaning carbohydrate impurities from lignin using Pseudomonas fluorescens. Green Chem. 21: 1648–1659.

    CAS  Article  Google Scholar 

  137. Wang, X., L. Lin, J. Dong, W. Wang, H. Wang, Z. Zhang, and X. Yu (2018) Simultaneous improvements of Pseudomonas cell growth and polyhydroxyalkanoate production from a lignin derivative for lignin-consolidated bioprocessing. Appl. Environ. Microbiol. 84: e01469–18.

    CAS  PubMed  PubMed Central  Google Scholar 

  138. Nikel, P. I. and V. de Lorenzo (2018) Pseudomonas putida as a functional chassis for industrial biocatalysis: from native biochemistry to trans-metabolism. Metab. Eng. 50: 142–155.

    CAS  PubMed  Article  Google Scholar 

  139. Zerva, I., N. Remmas, P. Melidis, G. Sylaios, P. Stathopoulou, G. Tsiamis, and S. Ntougias (2022) Biotreatment, microbial community structure and valorization potential of pepper processing wastewater in an immobilized cell bioreactor. Waste and Biomass Valor. 13: 1431–1447.

    CAS  Article  Google Scholar 

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Adeniyi, A., Bello, I., Mukaila, T. et al. A Review of Microbial Molecular Profiling during Biomass Valorization. Biotechnol Bioproc E 27, 515–532 (2022). https://doi.org/10.1007/s12257-022-0026-8

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Keywords

  • biomass valorization
  • microbial diversity
  • culture-independent techniques
  • nanoparticles