Engineering Nitrogen-Fixing Microbiomes with Waste-Derived Carbon Sources: Toward Circular and Resilient Biofertilizer Solution

Nicolás Rodríguez-Romero^1,2Juan Carlos Clavijo-Salinas²Julien Wist^2,3Carlos Gutierrez²Daniel Uribe-Velez¹Elaine Holmes^3,4,5Janeth Sanabria^3*

• ¹Universidad Nacional de Colombia Instituto de Biotecnologia, Bogotá, Colombia
• ²Universidad del Valle, Cali, Colombia
• ³Murdoch University Australian National Phenome Centre, Murdoch, Australia
• ⁴Imperial College London Faculty of Medicine, London, United Kingdom
• ⁵Imperial College London Institute of Global Health Innovation, London, United Kingdom

Microbiome engineering has emerged as a promising strategy to drive biotechnological developments across diverse fields. Microbiome-based fertilizers could significantly contribute to the gradual replacement of synthetic chemical fertilizers, potentially leading to substantial environmental and economic impacts. This study employed microbiome engineering to develop a self-assembled nitrogen-fixing microbial community utilizing carbon compounds from animal waste. This was achieved by enriching soil samples in bioreactors supplied with nitrogen via air pumping and fed with volatile fatty acids (VFAs) as the only carbon source. VFAs are the most common by-products of anaerobic waste fermentation. Results show a self-assembled community, dominated by Sinirhodobacter spp. (44.4%), Aureimonas spp. (17.7%), and Taibaiella spp. (12.4%), capable of fixing 2.7 times more nitrogen than the initial microbiome. During cultivation, inorganic nitrogen forms were detected in the supernatant at concentrations of up to 12.7 mg·L⁻¹. Once the self-assembled community was inoculated in tomato plants, Pseudomonas spp. and Exiguobacterium spp. became the most abundant and significantly enhanced tomato plant growth in both hydroponic and soil-based systems. Plant height and yield were comparable to those achieved with conventional synthetic nitrogen fertilizers. This study shows the potential of this methodology for developing effective biofertilizers while promoting a circular economy strategy that transforms waste into high-value bioproducts. This approach, combined with the simplicity of the bioreactor system, offers a viable and sustainable solution for developing countries with limited technological resources, and materializes the One Health vision while simultaneously protecting the health of people, crops, and animals.