Unveiling genomic features linked to traits of plant-growth-promoting bacterial communities from sugarcane.

Microorganisms are ubiquitous, and those inhabiting plants have been the subject of several studies. Plant-associated bacteria exhibit various biological mechanisms that enable them to colonize host plants and, in some cases, enhance their fitness. In this study, we describe the genomic features predicted to be associated with plant growth-promoting traits in six bacterial communities isolated from sugarcane. The use of highly accurate single-molecule real-time sequencing technology for metagenomic samples from these bacterial communities allowed us to recover 17 genomes. The taxonomic assignments for the binned genomes were performed, revealing taxa distributed across three main phyla: Bacillota, Bacteroidota, and Pseudomonadota, with the latter being the most representative. Subsequently, we functionally annotated the metagenome-assembled genomes (MAGs) to characterize their metabolic pathways related to plant growth-promoting traits. Our study successfully identified the enrichment of important functions related to phosphate and potassium acquisition, modulation of phytohormones, and mechanisms for coping with abiotic stress. These findings could be linked to the robust colonization of these sugarcane endophytes.

Sugarcane cultivation practices modulate rhizosphere microbial community composition and structure.

Sugarcane (Saccharum spp.) represents a crop of great economic importance, remarkably relevant in the food industry and energy supply chains from renewable sources. However, its conventional cultivation involves the intensive use of fertilizers, pesticides, and other agrochemical agents whose detrimental effects on the environment are notorious. Alternative systems, such as organic farming, have been presented as an environmentally friendly way of production. Still, the outcomes of different cropping systems on the microbiota associated with sugarcane-whose role in its health and growth is crucial-remain underexplored. Thus, we studied the rhizospheric microbiota of two adjacent sugarcane fields, which differ in terms of the type of farming system. For this, we used the sequencing of taxonomic markers of prokaryotes (gene 16S rRNA, subregions V3-V4) and fungi (Internal transcribed spacer 2) and evaluated the changes caused by the systems. Our results show a well-conserved microbiota composition among farming systems in the highest taxonomic ranks, such as phylum, class, and order. Also, both systems showed very similar alpha diversity indices and shared core taxa with growth-promoting capacities, such as bacteria from the Bacillus and Bradyrhizobium genera and the fungal genus Trichoderma. However, the composition at more specific levels denotes differences, such as the separation of the samples concerning beta diversity and the identification of 74 differentially abundant taxa between the systems. Of these, 60 were fungal taxa, indicating that this microbiota quota is more susceptible to changes caused by farming systems. The analysis of co-occurrence networks also showed the formation of peripheral sub-networks associated with the treatments-especially in fungi-and the presence of keystone taxa in terms of their ability to mediate relationships between other members of microbial communities. Considering that both crop fields used the same cultivar and had almost identical soil properties, we conclude that the observed findings are effects of the activities intrinsic to each system and can contribute to a better understanding of the effects of farming practices on the plant microbiome.

Farming systems influence the compositional, structural, and functional characteristics of the sugarcane-associated microbiome.

Sugarcane (Saccharum spp.) has been produced worldwide as a relevant source of food and sustainable energy. However, the constant need to increase crop yield has led to excessive use of synthetic agrochemical inputs such as inorganic fertilizers, herbicides, and pesticides in plant cultures. It is known that these conventional practices can lead to deleterious effects on health and the environment. Organic farming emerges as a sustainable alternative to conventional systems; however, farm management influences in plant-associated microbiomes remain unclear. Here, the aim is to identify the effects of farming systems on the sugarcane microbiota. To address this issue, we sampled the microbiota from soils and plants under organic and conventional farming from two crop fields in Brazil. Then, we evaluated their compositional, structural, and functional traits through amplification and sequencing of phylogenetic markers of bacteria (16S rRNA gene, V3-V4 region) and fungi (Internal Transcribed Spacer - ITS2). The data processing and analyses by the DADA2 pipeline revealed 12,839 bacterial and 3,222 fungal sequence variants. Moreover, differences between analogous niches were detected considering the contrasting farming systems, with samples from the conventional system showing a slightly greater richness and diversity of microorganisms. The composition is also different between the farming systems, with 389 and 401 differentially abundant taxa for bacteria and fungi, respectively, including taxa capable of promoting plant growth. The microbial co-occurrence networks showed structural changes in microbial communities, where organic networks were more cohesive since they had closer taxa and less modularity by niches. Finally, the functional prediction revealed enriched metabolic pathways, including the increased presence of antimicrobial resistance in the conventional farming system. Taken together, our findings reveal functional, structural, and compositional adaptations of the microbial communities associated with sugarcane plants in the field, according to farming management. With this, we point out the need to unravel the mechanisms driving these adaptations.

Bacterial communities associated with sugarcane under different agricultural management exhibit a diversity of plant growth-promoting traits and evidence of synergistic effect.

Plant-associated microbiomes have been a target of interest for the prospection of microorganisms, which may be acting as effectors to increase agricultural productivity. For years, the search for beneficial microorganisms has been carried out from the characterization of functional traits of growth-promotion using tests with a few isolates. However, eventually, the expectations with positive results may not be realized when the evaluation is performed in association with plants. In our study, we accessed the cultivable sugarcane microbiome under two conditions of agronomic management: organic and conventional. From the use of a new customized culture medium, we recovered 944 endophytic and epiphytic bacterial communities derived from plant roots, stalks, leaves, and rhizospheric soil. This could be accomplished by using a large-scale approach, initially performing an in planta (Cynodon dactylon) screening process of inoculation to avoid early incompatibility. The inoculation was performed using the bacterial communities, considering that in this way, they could act synergistically. This process resulted in 38 candidate communities, 17 of which had higher Indole-3-acetic acid (IAA) production and phosphate solubilization activity and, were submitted to a new in planta test using Brachiaria ruziziensis and quantification of functional traits for growth-promotion and physiological tests. Enrichment analysis of selected communities has shown that they derived mainly from epiphytic populations of sugarcane stalks under conventional management. The sequencing of the V3-V4 region of the 16S rRNA gene revealed 34 genera and 24 species distributed among the phylum Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. We also observed a network of genera in these communities where the genus Chryseobacterium stands out with a greater degree of interaction, indicating a possible direct or indirect role as a keystone taxon in communities with plant-growth promotion capacities. From the results achieved, we can conclude that the approach is useful in the recovery of a set of sugarcane bacterial communities and that there is, evidence of synergistic action providing benefits to plants, and that they are compatible with plants of the same family (Poaceae). Thus, we are reporting the beneficial bacterial communities identified as suitable candidates with rated potential to be exploited as bioinoculants for crops.