Improving bio-inoculation for sustainable agriculture
Authors:   , Hashmi Isha Ihtsham 
Published: January 2024

Global environmental pollution is one of the greatest threats to the inhabitants of planet Earth. Among the different types of environmental problems, the present study discusses issues related to the extensive utilization of agrochemicals in conventional agriculture by focusing on plant health and soil microbes as integral parts of terrestrial ecosystems. In conventional agriculture, inappropriate management practices and the use of agrochemicals have led to a negative impact on both soil and water. As a result, the search for sustainable alternatives in agriculture has become a priority. In the mycorrhizosphere, microbes are involved in many beneficial activities supporting the whole soil ecosystem and thus are considered as crucial actors of soil functioning. With such a perspective, an in vitro screening was carried out to evaluate the plant growth promoting (PGP) activities of different endospore forming bacteria (EFB), as well as of fungi with different ecological niches. We found that most of the screened EFB possessed one or more PGP traits. The fungal species that were screened were also positive for PGP traits. Moreover, confrontation of these bacteria and fungi resulted in many different interactions (antagonistic, neutral or positive). Interestingly, these findings did not only depend on the competing microbes, but also on the medium used, pointing at the importance of the nutritional context in microbial interactions. After the in vitro screening, the PGP effect of three different Bacillus strains was assessed in planta. Different bacterial inoculation schemes were compared: each strain alone or the three as a consortium and both life forms, vegetative cells and endospores, were compared. Then, the effect of the bio-inoculants was measured at different levels of complexity, from in vitro conditions to a field trial. This step-wise approach allowed deciphering whether more complex bio-inoculants (as compared to single strains) were more effective in promoting plant growth and whether this had any impact on the autochthonous microbial communities. The results obtained demonstrated that bacterial consortia were more consistent in promoting plant growth than single strains, even when in contact with the autochthonous soil microbes. Importantly, the bio-inoculated bacteria did not affect the structure of the native microbial communities, as demonstrated by using targeted metagenomics on both fungal and bacterial communities. This thesis also highlighted microbial interactions between members belonging to two kingdoms, i.e. bacteria and fungi. Both of them play crucial roles in terrestrial ecosystem functioning and are known for their diversified nutritional capabilities. This can lead to all type of interactions, from positive to negative ones. In this thesis, one antagonistic interaction, the mycophageous life-style of bacteria was investigated in detail. In mycophagy, bacteria obtain nutrients from living fungi and exert a negative impact on the fungal partner. The findings of this work suggest that the bacterium Lysinibacillus sphaericus 1003 has a preferential mycophagous lifestyle towards the phytopathogenic fungus Rhizoctonia solani, while it does not harm the saprophytic Trichoderma rossicum. The bacterium can grow at the expense of the living mycelium of R. solani and, more importantly, has a negative impact on fungal biomass. In contrast, and even though L. sphaericus 1003 grew at the expense of T. rossicum, the bacterium has a positive effect on T. rossicum biomass. Therefore, this differential behavior towards a plant pathogen and a plant beneficial fungus could constitute an interesting model to better understand the role of mycophagy in soil carbon cycling. Overall, this study brings novel insights in the frame of a sustainable exploitation of agricultural ecosystems by combining different types of bio-inoculation methods. Moreover, aspects related to future developments required in the field of plant growth promotion and biocontrol are discussed at the end of this study.