Summary: Fertilizers are costly inputs into crop systems. To compensate for inefficiencies and losses from soil, farmers apply on average double the amount of nitrogen (N) fertilizer acquired by crops. We explored if N efficiency improves with biofertilizers formulated with organic waste, mineral N or plant growth‐promoting rhizobacteria (PGPR). We compared treatments receiving mineral N fertilizer or biofertilizers at industry‐recommended (100%) or lower (60%) N rates at two commercial sugarcane farms. Biofertilizer at the 60% N‐rate generated promising results at one farm with significantly higher biomass and sugar yield than the no‐N control, which matched the 100% mineral N treatment. This yield difference was accompanied by a shift in microbial diversity and composition. Correlation analysis confirmed that shifts in microbial communities were strongly linked to soil mineral N levels, as well as crop productivity and yield. Microbial co‐occurrence networks further revealed that biofertilizer, including treatments with an added PGPR, can enhance bacterial associations, especially in the context of complex fungal networks. Collectively, the results confirm that biofertilizers have quantifiable effects on soil microbial communities in a crop system setting, which underscores the opportunities for biofertilizers to promote N use efficiency and the circular N economy.

Paraburkholderia sp. SOS3 is a plant growth-promoting bacterium (PGPB) that displays pleiotropic effects and has the potential to be applied at a large scale across several agronomically important crops. The use of SOS3 is a suitable option to reduce the use of chemical fertilisers. While the benefits of SOS3 have been demonstrated in vitro, its potential applications at large scale are limited due to low biomass yield in current batch culture systems. Here, we developed a strategy for high-cell density cultivation of SOS3 in instrumented bioreactors, moving from low-biomass yield in a complex medium to high-biomass yield in a semi-defined medium. We achieved a 40-fold increase in biomass production, achieving cell densities of up to 11 g/L (OD₆₀₀ = 40). This result was achieved when SOS3 was cultivated using a fed-batch strategy. Biomass productivity, initially 0.02 g/L/h in batch cultures, was improved 12-fold, reaching 0.24 g/L/h during fed-batch cultures. The biomass yield was also improved 10-fold from 0.07 to 0.71 g_biomass/g_solids. Analysis of the fermentation profile of SOS3 indicated minimal production of by-products and accumulation of polyhydroxybutyrate (PHB) during the exponential growth phase associated with nitrogen limitation in the medium. By implementing proteomics analysis in fed-batch cultures, we identified the expression of four metabolic pathways associated with growth-promoting effects, which may be used as a qualitative parameter to guarantee the efficacy of SOS3 when used as a bioinoculant. Ultimately, we confirmed that the high-cell density cultures maintained their plant growth-promoting capacity when tested in sorghum and maize under glasshouse conditions.

Phosphorus (P) fertilisers are under scrutiny due to resource constraints and environmental impacts. Simple rock phosphate (RP) modifications with acids and co-applied with microbial inoculum could offer sustainable alternative P fertiliser products. We evaluated the effects of acid-treated rock phosphate (RP) in combination with fungal inoculum on plant establishment, environmental impacts (nutrient leaching) and soil quality in a 5-month pot trial. The treatments were evaluated in a clayey Vertisol and a silty Acrisol using cotton (Gossypium hirsutum) as a model plant. The RP treatments - apart from the unmodified and HCl products - were effective in promoting plant establishment with two of the microbial formulations superior to conventional P fertilisers by an average factor of 2 in both soil types (p < 0.05). All RP products restricted P leaching compared with conventional P fertilisers (p < 0.05), by an average factor of 5 for diammonium phosphate (DAP) in both soil types and 3 for the triple superphosphate TSP (only in Acrisol). Nitrate leaching from all treatments was high although much lower from the RP treatments compared with the conventional fertilisers towards the end of the establishment trial, by an average factor of 1.5 (p < 0.05). Ranking analysis revealed that some RP treatments showed evidence for improved ongoing soil quality, including decreased P leaching and soil acidification risks. Microbial analysis showed complex interactions between treatment and soil type. Nonetheless, inoculum persistence at the end of the plant establishment phase was observed for all pots analysed. Our results demonstrate that relatively simple modifications to RP could pave the way for developing sustainable P fertilisers.

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