Sustainable agriculture: leveraging microorganisms for a circular economy

Abstract

Microorganisms serve as linchpins in agricultural systems. Classic examples include microbial composting for nutrient recovery, using microorganisms in biogas technology for agricultural waste utilization, and employing biofilters to reduce emissions from stables or improve water quality in aquaculture. This mini-review highlights the importance of microbiome analysis in understanding microbial diversity, dynamics, and functions, fostering innovations for a more sustainable agriculture. In this regard, customized microorganisms for soil improvement, replacements for harmful agrochemicals or antibiotics in animal husbandry, and (probiotic) additives in animal nutrition are already in or even beyond the testing phase for a large-scale conventional agriculture. Additionally, as climate change reduces arable land, new strategies based on closed-loop systems and controlled environment agriculture, emphasizing microbial techniques, are being developed for regional food production. These strategies aim to secure the future food supply and pave the way for a sustainable, resilient, and circular agricultural economy. KEY POINTS: • Microbial strategies facilitate the integration of multiple trophic levels, essential for cycling carbon, nitrogen, phosphorus, and micronutrients. • Exploring microorganisms in integrated biological systems is essential for developing practical agricultural solutions. • Technological progress makes sustainable closed-entity re-circulation systems possible, securing resilient future food production.

Keywords: Indoor farming; Microbiome; Omics; Probiotics; Sequencing.

Fig. 1

Strategies for utilizing microorganisms in the interaction between animal- and plant-based agriculture include minimizing harmful gaseous emissions through probiotic feed and modifications to the gut microbiome of animals. These emissions can be utilized in plant cultivation via microbial biofiltration, while solid or liquid emissions can be processed through microbial bioconversion. Plant growth is further enhanced by employing plant growth–promoting microorganisms (PGPM) and modifying microbial communities in the rhizosphere and soil to improve plant health and biomass yields. Note that microbial protein is used both as feed and as prebiotics

Fig. 2

Strategies for using microorganisms in aquaculture include optimizing sustainable feed through microbially produced alternatives, manipulating the gut microbiome to enhance animal health and biomass yields, and extensively employing microbial biofiltration methods to purify recirculating water and minimize resource consumption. This purification process can also be integrated with plant cultivation in systems like aquaponics (Chapter “Towards circular processes—coupling of animal and plant agriculture”)

Fig. 3

Closed-loop system for coupled animal and plant-based agriculture in a controlled environment. The solid, liquid, and gaseous emissions from livestock are upgraded by microalgae and insects to higher value biomass in order to produce feed, e.g., for aquaculture. This is combined with vegetable farming according to the principle of aquaponics to produce food for humans and at the same time residual materials for animal feed. The recirculation system is powered by renewable energy and enables an optimal reuse of nitrogen, phosphorus, micronutrients (turquois), and, above all, water (blue), while minimizing environmentally harmful emissions. The microorganisms essential for the operation and coupling of the trophic levels play a key role in this system