• mycorrhizosphere
• root endosphere
• rhizosphere
• microbial communities
• arbuscular mycorrhizal fungi
• plant growth-promoting bacteria

As global population expands, there is an increasing pressure on the performance of the agricultural sector. Indeed, food has been repeatedly referenced as the “weak link” in the endeavour to secure the future of our civilization. In the meantime, concerns have been raised about the long-term effects of conventional agronomic practices allowing the abundant use of mineral fertilizers and other agro-chemicals. Therefore, in past decades, a distinct scientific attention was dedicated to the research of novel agricultural tools able to intensify crop production in a sustainable manner, many of which exploit the beneficial properties of root-associated microorganisms. Amongst them, arbuscular mycorrhizal fungi (AMF) represent an important group, as they establish mutualistic symbioses with the majority of crop plants, improving the mineral nutrition and stress resistance of their hosts. Moreover, AMF live closely associated with large and diverse microbial communities, enhancing and complementing the beneficial functions of mycorrhizal symbionts. Complex bacterial communities also appear in other compartments of the root-soil interface, such as the rhizosphere and the root endosphere. Many members of such microbiota possess plant growth-promoting (PGP) features, contributing to plant growth, nutrition and health, e.g. by N2-fixation, phosphate solubilization, plant hormones, siderophores and antibiotics production and systemic resistance induction. Although the importance of root-associated microbes seems indisputable, a better understanding of the dynamics of their communities would be crucial for advancing agricultural sustainability in the terms of facilitating the selection and development of future microbial inocula, monitoring the effects of conventional and novel agronomic practices and evaluating agro-ecosystem functions.
The aim of these studies was to gain a detailed insight into the interactions between beneficial microorganisms residing in the rhizosphere and root endosphere of plants, assessing the effects of different microbial inocula consisting of plant growth-promoting bacteria (PGPB) or AMF on the diversity and composition of root-associated microbial communities. In order to achieve the overall objective, an integrated set of tasks was executed, concentrating on different microbial groups and relations in the root-soil interface.
In the first two experiments, the effects of a commercial biostimulant (containing the PGPB strain Bacillus amyloliquefaciens IT-45) on the native rhizosphere bacterial communities and root-colonizing AMF assemblages of juvenile maize plants were investigated, considering interactions with mineral (NP) fertilization and maize genotype as well. The composition and diversity of the root-associated microbiota was assessed by PCR-DGGE analysis of the 16S and 18S rRNA genes and sequencing. In the first study, rhizosphere bacterial communities were mainly affected by the two maize genotypes differing for their early vigor. The predominant bacterial taxa affiliated with Flavobacterium, Limnobacter, Lysobacter, Massilia, Pedobacter, Polaromonas and Stenotrophomonas species, some reported for their PGP potentials, such as P solubilization, indole-3-acetic acid and antibiotics production. The biostimulant treatment with B. amyloliquefaciens IT-45 had a more pronounced effect on the rhizosphere bacterial community composition of the ordinary hybrid than on that of the high early vigor maize. In the second study, significant interactions were revealed between NP fertilization and the microbial biostimulant as affecting native AMF communities in maize plants. AMF assemblages were also strongly influenced by NP fertilization alone, which had negative impacts on root colonization rates and contrasting effects on AMF biodiversity in the two maize hybrids. Predominant native AMF were represented by Glomus, Funneliformis and Rhizoglomus species, all members of the family Glomeraceae, commonly described from agricultural and disturbed soils. Interestingly, Funneliformis mosseae appeared to be resilient across all treatments in both maize hybrids, while populations of the genus Rhizoglomus were more affected by the putative competition with the bacterial biostimulant for P-mobilizing in NP-enriched environments.
In the third experiment, the possible roles of AMF and their associated microbiota in the recruitment of root endophytic bacteria was investigated in a microcosm experiment, using crushed or intact spores of two AMF isolates of different taxonomic and geographic origins as inocula and micropropagated Prunus persica x Prunus amygdalus GF 677 as model plants. 16S rDNA metagenomic sequencing on the Illumina MiSeq platform allowed the identification of 275 bacterial genera, 183 families, 58 classes and 21 phyla in the root and spore samples. Root endophytic bacterial communities were dominated by Proteobacteria, Actinobacteriota, Bacteroidota and Myxococcota. Interestingly, a differential recruitment of root endophytes was observed in plant roots inoculated with crushed or intact AMF spores, possibly, as a consequence of the fungi representing “highways” for the transfer of their associated bacteria into plant roots. Mycorrhizal roots, inoculated with intact spores, hosted larger and more diverse bacterial communities and showed a relative enrichment of the genus Haliangium (Myxococcota) respect to those uninoculated or inoculated with crushed spores. Moreover, differential enrichments of the genera Actinoplanes, Hydrogenophaga, Niastella, Ohtaekwangia, Ramlibacter, Rhizobium/Agrobacterium, Saccharothrix, Steroidobacter and Variovorax were found among the different root treatments, while spore-associated communities were dominated by Bacillus, Haliangium, Lysobacter, Massilia, Nocardioides, Paenarthrobacter and Sphingomonas species. A high number of the identified bacterial taxa were previously reported to promote plant growth and/or improve mycorrhizal functions.
The results of these three studies, integrated with subsequent research works, may be useful to better understand the possible effects of microbial biostimulants on the native microbiota associated with plant roots. Such data will be crucial for the exploitation of beneficial microorganisms as novel biostimulants and biofertilizers aiming at increasing plant fitness and crop yield in more sustainable food production systems.