Comparative analysis of microbial diversity in batch reactor with direct interspecies electron transfer system using an effective and inexpensive method mgDNA extraction

  • L. Alzate-Gaviria
  • D. Valero
  • E. España-Gamboa
  • M. González-Muñoz
  • A. Cortés-Velázquez
  • J. Dominguez-Maldonado
  • D. Pérez-Brito
  • R. Tapia-Tussell Centro de Investigación Científica de Yucatán A.C
Keywords: Metagenomic DNA extraction, carbon biofilm, sludge sample, PCR based 16S rRNA analysis

Abstract

Recently, metagenomic DNA based analysis gained importance in fields such as environmental sciences and bioenergy, where mixed microbial communities embedded in complex matrixes, play a crucial role. Therefore, financially economical, and high quality metagenomic DNA extraction protocols are needed. In this work, a rapid and inexpensive method for high quality DNA extraction from a variety of complex samples was performed; the average DNA yield was 71.65 ng µL−1, with an average purity of 1.68 (A260/A280). The cost of extraction per sample was about 76 % less in comparison with commercial kits and the time needed to obtain the DNA pellets was about 4 hours. The DNA was suitable for 16S rRNA gene amplification by PCR and for next generation sequencing analysis, employing a MiSeq Ilumina platform. A high microbial diversity was detected in this study, and three main groups of bacteria were observed, which were developed according to the effect of the activated carbon had on them. The analysis performed showed a great difference between the samples, highlighting the differences between the microbial communities developed in the activated carbon biofilm and the bacteria detected in the reactor without activated carbon.

References

Arunasri, K., Annie Modestra, J., Yeruva, D. K., Vamshi Krishna, K., & Venkata Mohan, S. (2016). Polarized potential and electrode materials implication on electro-fermentative di-hydrogen production: Microbial assemblages and hydrogenase gene copy variation. Bioresource Technology, 200, 691–698. https://doi.org/10.1016/j.biortech.2015.10.091

Baishya, R., Chatterjee, R., Banerjee, S., & Hasnain, S. (2020). Application of FESEM and FTIR for evaluation of Staphylococcus aureus biofilms grown on chitin and polycarbonate membrane. Revista Mexicana de Ingeniería Química, 20(1), 493–508. https://doi.org/10.24275/rmiq/Mat2175

Barua, S., & Dhar, B. R. (2017). Advances towards understanding and engineering direct interspecies electron transfer in anaerobic digestion. Bioresource Technology, 244, 698–707. https://doi.org/10.1016/j.biortech.2017.08.023

Bertin, L., Berselli, S., Fava, F., Petrangeli-Papini, M., & Marchetti, L. (2004). Anaerobic digestion of olive mill wastewaters in biofilm reactors packed with granular activated carbon and “Manville” silica beads. Water Research, 38(14–15), 3167–3178. https://doi.org/10.1016/j.watres.2004.05.004

Canto-Canché, B., Tzec-Simá, M., Vázquez-Loría, J. I., Espadas-Álvarez, H., Chí-Manzanero, B. H., Rojas-Herrera, R., Valdez-Ojeda, R., & Alzate-Gaviria, L. (2013). Methodology Simple and inexpensive DNA extraction protocol for studying the bacterial composition of sludges used in microbial fuel cells. Genetics and Molecular Research, 12(1), 282–292. https://doi.org/10.4238/2013.February.4.2

Dang, Y., Sun, D., Woodard, T. L., Wang, L.-Y., Nevin, K. P., & Holmes, D. E. (2017). Stimulation of the anaerobic digestion of the dry organic fraction of municipal solid waste (OFMSW) with carbon-based conductive materials. Bioresource Technology, 238, 30–38. https://doi.org/10.1016/j.biortech.2017.04.021

Erable, B., Duţeanu, N. M., Ghangrekar, M. M., Dumas, C., & Scott, K. (2010). Application of electro-active biofilms. Biofouling, 26(1), 57–71. https://doi.org/10.1080/08927010903161281

Fagbohungbe, M. O., Herbert, B. M. J., Hurst, L., Li, H., Usmani, S. Q., & Semple, K. T. (2016). Impact of biochar on the anaerobic digestion of citrus peel waste. Bioresource Technology, 216, 142–149. https://doi.org/10.1016/j.biortech.2016.04.106

Flemming, H.-C., & Wingender, J. (2010). The biofilm matrix. Nature Reviews Microbiology, 8(9), 623–633. https://doi.org/10.1038/nrmicro2415

García, R., Hernández, S., Ortiz, I., & Cercado, B. (2019). Use of hydrolysate from agave bagasse for Bio-hydrogen production in microbial electrolysis cells. Revista Mexicana de Ingeniería Química, 18(3), 865–874. https://doi.org/10.24275/uam/izt/dcbi/revmexingquim/2019v18n3/Garcia

Glass, E. M., & Meyer, F. (2011). The Metagenomics RAST Server: A Public Resource for the Automatic Phylogenetic and Functional Analysis of Metagenomes. In Handbook of Molecular Microbial Ecology I (Vol. 9, Issue 1, pp. 325–331). John Wiley & Sons, Inc. https://doi.org/10.1002/9781118010518.ch37

González-Gamboa, N., Domínguez-Benetton, X., Pacheco-Catalán, D., Kumar-Kamaraj, S., Valdés-Lozano, D., Domínguez-Maldonado, J., & Alzate-Gaviria, L. (2018). Effect of Operating Parameters on the Performance Evaluation of Benthic Microbial Fuel Cells Using Sediments from the Bay of Campeche, Mexico. Sustainability, 10(7), 2446. https://doi.org/10.3390/su10072446

González-Muñoz, M., Dominguez-Benetton, X., Domínguez-Maldonado, J., Valdés-Lozano, D., Pacheco-Catalán, D., Ortega-Morales, O., & Alzate-Gaviria, L. (2018). Polarization Potential Has No Effect on Maximum Current Density Produced by Halotolerant Bioanodes. Energies, 11(3), 529. https://doi.org/10.3390/en11030529

González-Paz, J. R., Ordaz, A., Jan-Roblero, J., Fernández-Linares, L. C., & Guerrero-Barajas, C. (2020). Sulfate reduction in a sludge gradually acclimated to acetate as the sole electron donor and its potential application as inoculum in a microbial fuel cell. Revista Mexicana de Ingeniería Química, 19(3), 1053–1069. https://doi.org/https://doi.org/10.24275/rmiq/IA805

Goswami, R., Chattopadhyay, P., Shome, A., Banerjee, S. N., Chakraborty, A. K., Mathew, A. K., & Chaudhury, S. (2016). An overview of physico-chemical mechanisms of biogas production by microbial communities: a step towards sustainable waste management. 3 Biotech, 6(1), 72. https://doi.org/10.1007/s13205-016-0395-9

Guermazi-Toumi, S., Chouari, R., & Sghir, A. (2019). Molecular analysis of methanogen populations and their interactions within anaerobic sludge digesters. Environmental Technology, 40(22), 2864–2879. https://doi.org/10.1080/09593330.2018.1455747

Guerrero Barajas, C., Alanís-Sánchez, B. M., Flores-Ortiz, C. M., Cruz-Maya, J. A., & Jan-Roblero, J. (2019). Enhanced removal of Methyl Tert-Butyl Eter by yeast extract supplementation to a bacterial consortium. Revista Mexicana de Ingeniería Química, 18(2), 589–604. https://doi.org/10.24275/uam/izt/dcbi/revmexingquim/2019v18n2/Guerrero

Guo, K., Freguia, S., Dennis, P. G., Chen, X., Donose, B. C., Keller, J., Gooding, J. J., & Rabaey, K. (2013). Effects of Surface Charge and Hydrophobicity on Anodic Biofilm Formation, Community Composition, and Current Generation in Bioelectrochemical Systems. Environmental Science & Technology, 47(13), 7563–7570. https://doi.org/10.1021/es400901u

Holmes, D. E., Nevin, K. P., Woodard, T. L., Peacock, A. D., & Lovley, D. R. (2007). Prolixibacter bellariivorans gen. nov., sp. nov., a sugar-fermenting, psychrotolerant anaerobe of the phylum Bacteroidetes, isolated from a marine-sediment fuel cell. International Journal of Systematic and Evolutionary Microbiology, 57(4), 701–707. https://doi.org/10.1099/ijs.0.64296-0

Kiseleva, L., Garushyants, S. K., Ma, H., Simpson, D. J. W., Fedorovich, V., Cohen, M. F., & Goryanin, I. (2015). Taxonomic and functional metagenomic analysis of anodic communities in two pilot-scale microbial fuel cells treating different industrial wastewaters. Journal of Integrative Bioinformatics, 12(3), 1–15. https://doi.org/10.2390/biecoll-jib-2015-273

Liu, F., Rotaru, A.-E., Shrestha, P. M., Malvankar, N. S., Nevin, K. P., & Lovley, D. R. (2012). Promoting direct interspecies electron transfer with activated carbon. Energy & Environmental Science, 5(10), 8982–8989. https://doi.org/10.1039/C2EE22459C

Park, J.-H., Kang, H.-J., Park, K.-H., & Park, H.-D. (2018). Direct interspecies electron transfer via conductive materials: A perspective for anaerobic digestion applications. Bioresource Technology, 254, 300–311. https://doi.org/10.1016/j.biortech.2018.01.095

Plugge, C. M., Balk, M., & Stams, A. J. M. (2002). Desulfotomaculum thermobenzoicum subsp. thermosyntrophicum subsp. nov., a thermophilic, syntrophic, propionate-oxidizing, spore-forming bacterium. International Journal of Systematic and Evolutionary Microbiology, 52(2), 391–399. https://doi.org/10.1099/00207713-52-2-391

Poggi-Varaldo, H. M., Valdés, L., Esparza-García, F., & Fernández-Villagómez, G. (1997). Solid substrate anaerobic co-digestion of paper mill sludge, biosolids, and municipal solid waste. Water Science and Technology, 35(2–3), 197–204. https://doi.org/10.2166/wst.1997.0517

Rohlf, J. (2004). NTSYS-PC Version 2.11 T. Numerical Taxonomy and Multivariate Analysis System. Applied Bioestastistics. Inc.

Rotaru, A.-E., Shrestha, P. M., Liu, F., Shrestha, M., Shrestha, D., Embree, M., Zengler, K., Wardman, C., Nevin, K. P., & Lovley, D. R. (2014). A new model for electron flow during anaerobic digestion: direct interspecies electron transfer to Methanosaeta for the reduction of carbon dioxide to methane. Energy & Environmental Science, 7(1), 408–415. https://doi.org/10.1039/C3EE42189A

Rousseau, R., Santaella, C., Bonnafous, A., Achouak, W., Godon, J.-J., Delia, M.-L., & Bergel, A. (2016). Halotolerant bioanodes: The applied potential modulates the electrochemical characteristics, the biofilm structure and the ratio of the two dominant genera. Bioelectrochemistry, 112, 24–32. https://doi.org/10.1016/j.bioelechem.2016.06.006

Santoro, C., Arbizzani, C., Erable, B., & Ieropoulos, I. (2017). Microbial fuel cells: From fundamentals to applications. A review. Journal of Power Sources, 356, 225–244. https://doi.org/10.1016/j.jpowsour.2017.03.109

Saratale, R. G., Saratale, G. D., Pugazhendhi, A., Zhen, G., Kumar, G., Kadier, A., & Sivagurunathan, P. (2017). Microbiome involved in microbial electrochemical systems (MESs): A review. Chemosphere, 177, 176–188. https://doi.org/10.1016/j.chemosphere.2017.02.143

Venkata Mohan, S., Raghavulu, S. V., Goud, R. K., Srikanth, S., Babu, V. L., & Sarma, P. N. (2010). Microbial diversity analysis of long term operated biofilm configured anaerobic reactor producing biohydrogen from wastewater under diverse conditions. International Journal of Hydrogen Energy, 35(22), 12208–12215. https://doi.org/10.1016/j.ijhydene.2010.08.008

Wannapokin, A., Ramaraj, R., Whangchai, K., & Unpaprom, Y. (2018). Potential improvement of biogas production from fallen teak leaves with co-digestion of microalgae. 3 Biotech, 8(2), 123. https://doi.org/10.1007/s13205-018-1084-7

Xu, S., He, C., Luo, L., Lü, F., He, P., & Cui, L. (2015). Comparing activated carbon of different particle sizes on enhancing methane generation in upflow anaerobic digester. Bioresource Technology, 196, 606–612. https://doi.org/10.1016/j.biortech.2015.08.018

Yang, Y., Zhang, Y., Li, Z., Zhao, Z., Quan, X., & Zhao, Z. (2017). Adding granular activated carbon into anaerobic sludge digestion to promote methane production and sludge decomposition. Journal of Cleaner Production, 149(Supplement C), 1101–1108. https://doi.org/https://doi.org/10.1016/j.jclepro.2017.02.156

Zhang, J., Zhao, W., Zhang, H., Wang, Z., Fan, C., & Zang, L. (2018). Recent achievements in enhancing anaerobic digestion with carbon- based functional materials. Bioresource Technology, 266, 555–567. https://doi.org/10.1016/j.biortech.2018.07.076

Zhao, Z., Zhang, Y., Yu, Q., Dang, Y., Li, Y., & Quan, X. (2016). Communities stimulated with ethanol to perform direct interspecies electron transfer for syntrophic metabolism of propionate and butyrate. Water Research, 102, 475–484. https://doi.org/10.1016/j.watres.2016.07.005

Published
2021-07-26
How to Cite
Alzate-Gaviria, L., Valero, D., España-Gamboa, E., González-Muñoz, M., Cortés-Velázquez, A., Dominguez-Maldonado, J., Pérez-Brito, D., & Tapia-Tussell, R. (2021). Comparative analysis of microbial diversity in batch reactor with direct interspecies electron transfer system using an effective and inexpensive method mgDNA extraction. Revista Mexicana De Ingeniería Química, 20(3), Bio2401. Retrieved from http://www.rmiq.org/ojs311/index.php/rmiq/article/view/2401

Most read articles by the same author(s)