Joint ventures in plant performance: integrating plant traits, arbuscular mycorrhizal fungi, and microbial partnerships to boost productivity

Abstract

Agricultural efficiency, including in floriculture, requires sustainable methods to increase productivity while reducing the environmental impact of chemical fertilizers and pesticides. Overuse of fertilizers leads to soil degradation, water pollution, and biodiversity loss. One promising alternative is the use of plant-beneficial microorganisms as biofertilizers. However, optimizing the use of these microbial inoculants—either as single strains or complex microbial communities—remains challenging, especially in balancing nutrient inputs and maximizing plant-microbe interactions in commercial flower production. In this thesis, chrysanthemum (Chrysanthemum indicum L.) was used as a model plant for vegetative propagation to investigate the interactions between plant genetics, microbial inoculation, and nutrient availability during early root development. The study aims to understand how genotype-microbiome-environment interactions shape plant growth and nutrient use efficiency in chrysanthemum cultivation. In Chapter 2, the genetic variability among chrysanthemum cultivars and its influence on rhizosphere bacterial and fungal communities were investigated. Results showed that different cultivars select distinct rhizosphere microbiomes while maintaining a shared core of microbial species. Genetic differences among cultivars influenced the composition of these microbial communities. In Chapter 3, microbial inoculations with bacterial isolates and arbuscular mycorrhizal fungi (AMF), along with AMF-accompanying microbiomes (AMFc), were tested on chrysanthemum growth and rhizosphere microbiome composition. AMFc had a stronger effect on microbiome assembly and plant growth compared to single bacterial strains, highlighting the potential of complex microbial inoculations. In Chapter 4, AMF propagation was examined over 11 cycles of millet cultivation using trap propagation methods. The study evaluated traits such as indole-3-acetic acid (IAA) production and phosphate solubilization. AMFc consistently increased IAA production, particularly under low microbial activity, underscoring the importance of AMF in maintaining beneficial soil microbiomes and improving nutrient cycling. In Chapter 5, co-inoculation with AMFc and two bacterial strains (SMF006 and SMF018) was tested for its effects on chrysanthemum growth and root architecture. Co-inoculation with AMFc and SMF006 enhanced root dry biomass and enriched beneficial microbial taxa, including Sphingomonas, Taibaiella, Trichoderma, and Penicillium. In Chapter 6, the effects of nutrient availability on the interaction between AMFc and bacterial isolate SMF006 were explored. Genomic analysis of SMF006 revealed plant growth-promoting traits like nitrogen fixation, siderophore production, and IAA production. Increased nutrient input reduced microbial recruitment in the endophytic and epiphytic communities, indicating that nutrient limitation enhances microbial recruitment and plant growth promotion. Overall, this thesis highlights the potential of combining AMFc with beneficial bacterial strains to enhance plant growth, and reduce the need for chemical inputs. By optimizing microbial inoculation strategies and understanding plant-microbe interactions, this research provides a framework for more sustainable and efficient flower production systems.