Section: Microbiology
Topic: Microbiology

Comparison of enrichment methods for efficient nitrogen fixation on a biocathode

10.24072/pcjournal.365 - Peer Community Journal, Volume 4 (2024), article no. e12.

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The production of nitrogen fertilizers in modern agriculture is mostly based on the Haber-Bosch process, representing nearly 2% of the total energy consumed in the world. Low-energy bioelectrochemical fixation of N2 to microbial biomass was previously observed but the mechanisms of microbial interactions in N2-fixing electroactive biofilms are still poorly understood. The present study aims to develop a new method of enrichment of autotrophic and diazotrophic bacteria from soil samples with a better electron source availability than using H2 alone. The enrichment method was based on a multi-stage procedure. The first enrichment step was specifically designed for the selection of N2-fixing bacteria from soil samples with organic C as electron and carbon source. Then, a polarized cathode was used for the enrichment of autotrophic bacteria using H2 (hydrogenotrophic) or the cathode as electron source. This enrichment was compared with an enrichment culture of pure diazotrophic hydrogenotrophic bacteria without the use of a microbial electrochemical system. Interestingly, both methods showed comparable results for N2 fixation rates at day 340 of the enrichment with an estimated average of approximately 0.2 mgNfixed/L.d. Current densities up to -15 A/m² were observed in the polarized cathode enrichments and a significant increase of the microbial biomass on the cathode was shown between 132 and 214 days of enrichment.These results confirmed an enrichment in autotrophic and diazotrophic bacteria on the polarized cathode. It was hypothesied that autotrophic bacteria were able to use either the H2 produced at the cathode or directly the cathode through direct electron transfer (DET) as more biomass was produced than with H2 alone. Finally, the analysis of the enriched communities suggested that Desulforamulus ruminis mediated microbial interactions between autotrophic anaerobic and heterotrophic aerobic bacteria in polarized cathode enrichment. These interactions could play a key role in the development of biomass in these systems and on N2 fixation. Based on these findings, a conceptual model on the functioning of mixed cultures N2-fixing electroactive biofilms was proposed.

Published online:
DOI: 10.24072/pcjournal.365
Type: Research article
Keywords: Nitrogen fixation, Microbial electrochemical system, Biomass electrostimulation, Enrichment method
Rous, Axel 1; Santa-Catalina, Gaëlle 1; Desmond-Le Quémener, Elie 1; Trably, Eric 1; Bernet, Nicolas 1

1 INRAE, Univ Montpellier, LBE, 102 avenue des Étangs, 11100 Narbonne, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights
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Rous, Axel; Santa-Catalina, Gaëlle; Desmond-Le Quémener, Elie; Trably, Eric; Bernet, Nicolas. Comparison of enrichment methods for efficient nitrogen fixation on a biocathode. Peer Community Journal, Volume 4 (2024), article  no. e12. doi : 10.24072/pcjournal.365. https://peercommunityjournal.org/articles/10.24072/pcjournal.365/

Peer reviewed and recommended by PCI : 10.24072/pci.microbiol.100010

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

[1] Aullo, T.; Ranchou-Peyruse, A.; Ollivier, B.; Magot, M. Desulfotomaculum spp. And related gram-positive sulfate-reducing bacteria in deep subsurface environments, Frontiers in Microbiology, Volume 4 (2013) | DOI

[2] Bagali, S. Review: Nitrogen fixing microorganisms, Int. J. Microbiol. Res, Volume 3 (2012), pp. 46-52 | DOI

[3] Bergersen, F. The Quantitative Relationship between Nitrogen Fixation and the Acetylene-Reduction Assay, Australian Journal of Biological Sciences, Volume 23 (1970) no. 4, p. 4 | DOI

[4] Bowers, T.; Reid, N.; Lloyd-Jones, G. Composition of nifH in a wastewater treatment system reliant on N2 fixation, Applied Microbiology and Biotechnology, Volume 79 (2008) no. 5, pp. 811-818 | DOI

[5] Bueno Batista, M.; Dixon, R. Manipulating nitrogen regulation in diazotrophic bacteria for agronomic benefit, Biochemical Society Transactions, Volume 47 (2019) no. 2, pp. 603-614 | DOI

[6] Burris, R.; Roberts, G. Biological Nitrogen Fixation, Annual Review of Nutrition, Volume 13 (1993) no. 1 | DOI

[7] Carmona-Martínez, A.; Trably, E.; Milferstedt, K.; Lacroix, R.; Etcheverry, L.; Bernet, N. Long-term continuous production of H2 in a microbial electrolysis cell (MEC) treating saline wastewater, Water Research, Volume 81 (2015), pp. 149-156 | DOI

[8] Cassan, F.; Salamone, I. Azospirillum: Cell physiology, plant response, agronomic and environmental research in Argentina, 2008

[9] Chakraborty, T.; Akhtar, N. Biofertilizers: Prospects and Challenges for Future, Biofertilizers, John Wiley Sons, Ltd, 2021, pp. 575-590 | DOI

[10] Chen, S.; Jing, X.; Yan, Y.; Huang, S.; Liu, X.; Chen, P.; Zhou, S. Bioelectrochemical nitrogen fixation to extracellular ammonium by Pseudomonas stutzeri, Applied and Environmental Microbiology, Volume 87 (2020) no. 5 | DOI

[11] Cherkasov, N.; Ibhadon, A.; Fitzpatrick, P. A review of the existing and alternative methods for greener nitrogen fixation, Chemical Engineering and Processing: Process Intensification, Volume 90 (2015), pp. 24-33 | DOI

[12] De Vrieze, J. Toward a low-energy bioelectrochemical fixation of N2 via mixed cultures electroactive biofilms, Peer Community in Microbiology (2023) | DOI

[13] Deng, J.; Iñiguez, J.; Liu, C. Electrocatalytic Nitrogen Reduction at Low Temperature, Joule, Volume 2 (2018) no. 5, pp. 846-856 | DOI

[14] Dos Santos, P.; Fang, Z.; Mason, S.; Setubal, J.; Dixon, R. Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes, BMC Genomics, Volume 13 (2012) no. 1, p. 162 | DOI

[15] Franche, C.; Lindström, K.; Elmerich, C. Nitrogen-fixing bacteria associated with leguminous and non-leguminous plants, Plant and Soil, Volume 321 (2009) no. 1, pp. 35-59 | DOI

[16] Gaby, J.; Buckley, D. A Comprehensive Evaluation of PCR Primers to Amplify the nifH Gene of Nitrogenase, PLoS ONE, Volume 7 (2012) no. 7, p. 42149 | DOI

[17] Ghodhbane-Gtari, F.; Nouioui, I.; Hezbri, K.; Lundstedt, E.; D’Angelo, T.; McNutt, Z.; Laplaze, L.; Gherbi, H.; Vaissayre, V.; Svistoonoff, S.; Ahmed, H.; Boudabous, A.; Tisa, L. The plant-growth-promoting actinobacteria of the genus Nocardia induces root nodule formation in Casuarina glauca, Antonie van Leeuwenhoek, Volume 112 (2019) no. 1, pp. 75-90 | DOI

[18] Hafeez, F.; yasmin, S.; Ariani, D.; Renseigné, N.; Zafar, y.; Malik, A.; K. Plant growth-promoting bacteria as biofertilizer, Agronomy for Sustainable Development, Volume 26 (2006) no. 2, pp. 143-150 | DOI

[19] Hardy, R.; Burns, R.; Holsten, R. Applications of the acetylene-ethylene assay for measurement of nitrogen fixation, Soil Biology and Biochemistry, Volume 5 (1973) no. 1, pp. 47-81 | DOI

[20] Heldal, M.; Norland, S.; Tumyr, O. X-ray microanalytic method for measurement of dry matter and elemental content of individual bacteria, Applied and Environmental Microbiology, Volume 50 (1985) no. 5, pp. 1251-1257 | DOI

[21] Hu, J.; Tang, H.; Wang, Y.; Yang, C.; Gao, M.; Tsang, Y.; Li, J. Effect of dissolved solids released from biochar on soil microbial metabolism, Environmental Science: Processes Impacts, Volume 24 (2022) no. 4, pp. 598-608 | DOI

[22] Hu, X.; Kerckhof, F.-M.; Ghesquière, J.; Bernaerts, K.; Boeckx, P.; Clauwaert, P.; Boon, N. Microbial Protein out of Thin Air: Fixation of Nitrogen Gas by an Autotrophic Hydrogen-Oxidizing Bacterial Enrichment, Environmental Science Technology, Volume 54 (2020) no. 6, p. 6 | DOI

[23] Huda, N.; Tanvir, R.; Badar, J.; Ali, I.; Rehman, Y. Arsenic-Resistant Plant Growth Promoting Pseudoxanthomonas mexicana S254 and Stenotrophomonas maltophilia S255 Isolated from Agriculture Soil Contaminated by Industrial Effluent, Sustainability, Volume 14 (2022) no. 17, p. 17 | DOI

[24] Kandemir, T.; Schuster, M.; Senyshyn, A.; Behrens, M.; Schlögl, R. The Haber–Bosch Process Revisited: On the Real Structure and Stability of “Ammonia Iron” under Working Conditions, Angewandte Chemie International Edition, Volume 52 (2013) no. 48, p. 48 | DOI

[25] Khan, K.; Mack, R.; Castillo, X.; Kaiser, M.; Joergensen, R. Microbial biomass, fungal and bacterial residues, and their relationships to the soil organic matter C/N/P/S ratios, Geoderma, Volume 271 (2016), pp. 115-123 | DOI

[26] Kifle, M.; Laing, M. Isolation and Screening of Bacteria for Their Diazotrophic Potential and Their Influence on Growth Promotion of Maize Seedlings in Greenhouses, Frontiers in Plant Science, Volume 6 (2016) | DOI

[27] Kim, J.; Rees, D. Nitrogenase and biological nitrogen fixation, Biochemistry, Volume 33 (1994) no. 2, p. 2 | DOI

[28] Klemps, R.; Cypionka, H.; Widdel, F.; Pfennig, N. Growth with hydrogen, and further physiological characteristics of Desulfotomaculum species, Archives of Microbiology, Volume 143 (1985) no. 2, pp. 203-208 | DOI

[29] Li, F.; Li, F.; Lin, Y.; Guo, L.; Zhang, L.; Li, R.; Tian, Q.; Wang, Y.; Wang, Y.; Zhang, X.; Liu, J.; Fan, C. Investigating the performance and mechanism of nitrogen gas fixation and conversion to ammonia based on biocathode bioelectrochemistry system, Journal of Chemical Technology Biotechnology, Volume 97 (2022) no. 8, pp. 2163-2170 | DOI

[30] Liu, A.; Yang, Y.; Ren, X.; Zhao, Q.; Gao, M.; Guan, W.; Meng, F.; Gao, L.; Yang, Q.; Liang, X.; Ma, T. Current Progress of Electrocatalysts for Ammonia Synthesis Through Electrochemical Nitrogen Reduction Under Ambient Conditions, ChemSusChem, Volume 13 (2020) no. 15, pp. 3766-3788 | DOI

[31] Liu, C.; Sakimoto, K.; Colón, B.; Silver, P.; Nocera, D. Ambient nitrogen reduction cycle using a hybrid inorganic–biological system, Proceedings of the National Academy of Sciences, Volume 114 (2017) no. 25 | DOI

[32] Liu, F.; Zhao, C.; Xia, L.; Yang, F.; Chang, X.; Wang, Y. Biofouling characteristics and identification of preponderant bacteria at different nutrient levels in batch tests of a recirculating cooling water system, Environmental Technology, Volume 32 (2011) no. 8, pp. 901-910 | DOI

[33] Loferer-Krößbacher, M.; Klima, J.; Psenner, R. Determination of Bacterial Cell Dry Mass by Transmission Electron Microscopy and Densitometric Image Analysis, Applied and Environmental Microbiology, Volume 64 (1998) no. 2, pp. 688-694 | DOI

[34] Logan, B.; Rossi, R.; Ragab, A.; Saikaly, P. Electroactive microorganisms in bioelectrochemical systems, Nature Reviews Microbiology, Volume 17 (2019) no. 5, p. 5 | DOI

[35] Martín, A.; Shinagawa, T.; Pérez-Ramírez, J. Electrocatalytic Reduction of Nitrogen: From Haber-Bosch to Ammonia Artificial Leaf, Chem, Volume 5 (2019) no. 2, p. 2 | DOI

[36] Masclaux-Daubresse, C.; Daniel-Vedele, F.; Dechorgnat, J.; Chardon, F.; Gaufichon, L.; Suzuki, A. Nitrogen uptake, assimilation and remobilization in plants: Challenges for sustainable and productive agriculture, Annals of Botany, Volume 105 (2010) no. 7, pp. 1141-1157 | DOI

[37] McMurdie, P. https://github.com/joey711/phyloseq, 2023 (Phyloseq [R].)

[38] Moscoviz, R.; Desmond-Le Quéméner, E.; Trably, E.; Bernet, N. Bioelectrochemical Systems for the Valorization of Organic Residues, Biorefinery: Integrated Sustainable Processes for Biomass Conversion to Biomaterials, Biofuels, and Fertilizers, Springer International Publishing, 2019, pp. 511-534 | DOI

[39] Paul, D.; Noori, M.; Rajesh, P.; Ghangrekar, M.; Mitra, A. Modification of carbon felt anode with graphene oxide-zeolite composite for enhancing the performance of microbial fuel cell, Sustainable Energy Technologies and Assessments, Volume 26 (2018), pp. 77-82 | DOI

[40] Peoples, M.; Craswell, E. Biological nitrogen fixation: Investments, expectations and actual contributions to agriculture, Plant and Soil, Volume 141 (1992) no. 1, pp. 13-39 | DOI

[41] Pogoreutz, C.; Rädecker, N.; Cárdenas, A.; Gärdes, A.; Wild, C.; Voolstra, C. Nitrogen Fixation Aligns with nifH Abundance and Expression in Two Coral Trophic Functional Groups, Frontiers in Microbiology, Volume 8 (2017) | DOI

[42] Poly, F.; Ranjard, L.; Nazaret, S.; Gourbière, F.; Monrozier, L. Comparison of nifH Gene Pools in Soils and Soil Microenvironments with Contrasting Properties, Applied and Environmental Microbiology, Volume 67 (2001) no. 5, pp. 2255-2262 | DOI

[43] Postgate, J. Nitrogen Fixation by Sporulating Sulphate-reducing Bacteria Including Rumen Strains, Microbiology, Volume 63 (1970) no. 1, pp. 137-139 | DOI

[44] Rago, L.; Zecchin, S.; Villa, F.; Goglio, A.; Corsini, A.; Cavalca, L.; Schievano, A. Bioelectrochemical Nitrogen fixation (e-BNF): Electro-stimulation of enriched biofilm communities drives autotrophic nitrogen and carbon fixation, Bioelectrochemistry, Volume 125 (2019), pp. 105-115 | DOI

[45] Rojas-Tapias, D.; Moreno-Galván, A.; Pardo-Díaz, S.; Obando, M.; Rivera, D.; Bonilla, R. Effect of inoculation with plant growth-promoting bacteria (PGPB) on amelioration of saline stress in maize (Zea mays, Applied Soil Ecology, Volume 61 (2012), pp. 264-272 | DOI

[46] Rous, A. Script and data used for the article “Comparison of enrichment methods for efficient nitrogen fixation on a biocathode”, Recherche Data Gouv, V1, 2023 | DOI

[47] Rozendal, R.; Leone, E.; Keller, J.; Rabaey, K. Efficient hydrogen peroxide generation from organic matter in a bioelectrochemical system, Electrochemistry Communications, Volume 11 (2009) no. 9, pp. 1752-1755 | DOI

[48] Ryan, R.; Monchy, S.; Cardinale, M.; Taghavi, S.; Crossman, L.; Avison, M.; Berg, G.; Lelie, D.; Dow, J. The versatility and adaptation of bacteria from the genus Stenotrophomonas, Nature Reviews Microbiology, Volume 7 (2009) no. 7 | DOI

[49] Sim, J.; An, J.; Elbeshbishy, E.; Ryu, H.; Lee, H.-S. Characterization and optimization of cathodic conditions for H2O2 synthesis in microbial electrochemical cells, Bioresource Technology, Volume 195 (2015), pp. 31-36 | DOI

[50] Singh, R.; Singh, P.; Li, H.-B.; Guo, D.-J.; Song, Q.-Q.; Yang, T.; Malviya, M.; Song, X.-P.; Li, Y.-R. Plant-PGPR interaction study of plant growth-promoting diazotrophs Kosakonia radicincitans BA1 and Stenotrophomonas maltophilia COA2 to enhance growth and stress-related gene expression in Saccharum spp, Journal of Plant Interactions, Volume 15,427-445 (2020) | DOI

[51] Soundararajan, M.; Ledbetter, R.; Kusuma, P.; Zhen, S.; Ludden, P.; Bugbee, B.; Ensign, S.; Seefeldt, L. Phototrophic N2 and CO2 Fixation Using a Rhodopseudomonas palustris-H2 Mediated Electrochemical System With Infrared Photons, Frontiers in Microbiology, Volume 10 (2019), p. 1817 | DOI

[52] Stoddard, S.; Smith, B.; Hein, R.; Roller, B.; Schmidt, T. rrnDB: Improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development, Nucleic Acids Research, Volume 43 (2015) no. D1, p. 593 | DOI

[53] Temple, S.; Vance, C.; Stephen Gantt, J. Glutamate synthase and nitrogen assimilation, Trends in Plant Science, Volume 3 (1998) no. 2, pp. 51-56 | DOI

[54] Tilak, K.; Schneider, K.; Schlegel, H. Autotrophic growth of nitrogen-fixingAzospirillum species and partial characterization of hydrogenase from strain CC, Current Microbiology, Volume 13 (1986) no. 6, pp. 291-297 | DOI

[55] Wickham, H.; Averick, M.; Bryan, J.; Chang, W.; McGowan, L.; François, R.; Grolemund, G.; Hayes, A.; Henry, L.; Hester, J.; Kuhn, M.; Pedersen, T.; Miller, E.; Bache, S.; Müller, K.; Ooms, J.; Robinson, D.; Seidel, D.; Spinu, V.; Takahashi, K.; Vaughan, D.; Wilke, C.; Woo, K.; Yutani, H. Welcome to the Tidyverse, Journal of Open Source Software, Volume 4 (2019) no. 43 | DOI

[56] Wiegel, J. K. Xanthobacter, Bergey's Manual of Systematics of Archaea and Bacteria, 2015, pp. 1-22 | DOI

[57] Wresta, A.; Widyarani, R.; Boopathy, R.; Setiadi, T. Thermodynamic approach to estimating reactions and stoichiometric coefficients of anaerobic glucose and hydrogen utilization, Engineering Reports, Volume 3 (2021) no. 6, p. 12347 | DOI

[58] Wu, Y.; Zaiden, N.; Cao, B. The Core- and Pan-Genomic Analyses of the Genus Comamonas: From Environmental Adaptation to Potential Virulence, Frontiers in Microbiology, Volume 9 (2018), p. 3096 | DOI

[59] Yadav, R.; Chiranjeevi, P.; Yadav, S.; Singh, R.; Patil, S. Electricity-driven bioproduction from CO2 and N2 feedstocks using enriched mixed microbial culture, Journal of CO2 Utilization, Volume 60 (2022), p. 101997 | DOI

[60] Zaybak, Z.; Pisciotta, J.; Tokash, J.; Logan, B. Enhanced start-up of anaerobic facultatively autotrophic biocathodes in bioelectrochemical systems, Journal of Biotechnology, Volume 168 (2013) no. 4, pp. 478-485 | DOI

[61] Zhang, L.; Tian, C.; Wang, H.; Gu, W.; Zheng, D.; Cui, M.; Wang, X.; He, X.; Zhan, G.; Li, D. Improving electroautotrophic ammonium production from nitrogen gas by simultaneous carbon dioxide fixation in a dual-chamber microbial electrolysis cell, Bioelectrochemistry (Amsterdam, Netherlands, Volume 144 (2022), p. 108044 | DOI

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