Tracking biodiversity of plant-microbe interactions in urban environments

According to recent estimates, nearly 70% of the world’s population will live in urban environments by 2050. Urban green areas represent crucial components of modern cities as they provide many ecosystem services. Although plants are the undisputed protagonists of urban greenspaces, soil and, in particular its biota, are still overlooked. The aim of my PhD was to investigate the taxonomic and functional biodiversity of urban soils focusing on microbes (prokaryotes and fungi) while assessing their relationships with plant coverage and community composition and physico-chemical soil features. To reach these objectives a variety of approaches including ‘omics techniques, molecular, biochemical and bioinformatics analyses were applied on field samples collected in different sites across Italian cities. The first sampling campaign was carried out on a city-wide scale (Turin, autumn 2022) and a shotgun metagenomic approach was implemented with different aims. We first focused on monitoring the soil microbiota in an experimental site in Turin in which a nature-based solution, the use of a constructed urban technosol, was set-up three years before to support the establishment of a new urban green area. The taxonomic and functional microbial diversity of the technosol was profoundly different from that of the surrounding control soil, and the application of compost and microbial inoculum appears to have contributed significantly to the assembly of the microbiota. By expanding our study to a larger set of parks within the city of Turin, we revealed that the age of the park and the soil cover (grasslands or trees) had a significant impact on the fungal and prokaryotic communities in the soil. Interestingly, urbanisation altered the ecological functions of fungi, with an increase in pathogens and a decrease in symbionts which was particularly clear in recent parks. Also, the prokaryotic functions recovered from the metagenome-assembled genomes showed a pattern following the park age with an increased lipid and xenobiotic metabolisms and reduced secondary metabolic pathways. We expanded our analyses from a single-city to a national scale by considering urban lawns across five major Italian cities located along a latitudinal gradient (Milan, Turin, Florence, Rome, Naples). Data from soil microbiota were integrated with physiso-chemical parameters, plant community composition, soil arthropods and soil microbial enzymatic activities to define soil ecosystem functions and services. The multifunctionality (i.e. the average of the measured ecosystem services) of urban park lawns was lower than that of less disturbed areas. Furthermore, our data highlighted that, in the long term, park lawns tend to increase ecosystem services, with historical parks performing better than recent ones. The last experiment focused on the microbial communities associated with the roots of Celtis australis, a common endemic urban tree in Southern Europe combining culture-dependent and culture-independent (DNA meta-barcoding) approaches across an urban gradient in Turin's parks and avenues. Little impact on endophyte diversity was observed. However, the composition of microbial (prokaryotes and fungi) communities of the plant root endosphere was influenced by urbanisation. Furthermore, tree growth areas (park versus avenues) had a greater impact than the urban gradient on the predictive functionality of microbial communities. The isolation of root-associated bacteria allowed the identification of potential plant growth-promoting strains, possibly acting in synergy with AM fungi. Research perspectives will include additional trials under controlled conditions to analyse the ability of cultured bacteria, both as single inoculants and as consortia, to promote the growth of C. australis seedlings, focusing on the additive or synergistic effects that may arise from multiple plant-microbe and microbe-microbe interactions