Designing a Waste-Based Culture Medium for the Production of Plant Growth Promoting Microorganisms Based on Cladodes Juice from Opuntia ficus-indica Pruning

Genome Insights into Beneficial Microbial Strains Composing SIMBA Microbial Consortia Applied as Biofertilizers for Maize, Wheat and Tomato

For the safe use of microbiome-based solutions in agriculture, the genome sequencing of strains composing the inoculum is mandatory to avoid the spread of virulence and multidrug resistance genes carried by them through horizontal gene transfer to other bacteria in the environment. Moreover, the annotated genomes can enable the design of specific primers to trace the inoculum into the soil and provide insights into the molecular and genetic mechanisms of plant growth promotion and biocontrol activity. In the present work, the genome sequences of some members of beneficial microbial consortia that have previously been tested in greenhouse and field trials as promising biofertilizers for maize, tomato and wheat crops have been determined. Strains belong to well-known plant-growth-promoting bacterial genera such as Bacillus, Burkholderia, Pseudomonas and Rahnella. The genome size of strains ranged from 4.5 to 7.5 Mbp, carrying many genes spanning from 4402 to 6697, and a GC content of 0.04% to 3.3%. The annotation of the genomes revealed the presence of genes that are implicated in functions related to antagonism, pathogenesis and other secondary metabolites possibly involved in plant growth promotion and gene clusters for protection against oxidative damage, confirming the plant-growth-promoting (PGP) activity of selected strains. All the target genomes were found to possess at least 3000 different PGP traits, belonging to the categories of nitrogen acquisition, colonization for plant-derived substrate usage, quorum sensing response for biofilm formation and, to a lesser extent, bacterial fitness and root colonization. No genes putatively involved in pathogenesis were identified. Overall, our study suggests the safe application of selected strains as "plant probiotics" for sustainable agriculture.

Opuntia ficus indica cladode as fermentation feedstock for lactic acid production by Lactobacillus acidophilus LA 5

Opuntia ficus-indica cladodes are by-products which contain high amounts of fibres, bioactive and functional compounds. Given their high annual productivity per hectare, cladodes represent a cheap and suitable substrate, usable for fermentation processes. We investigated their potential as a substrate for the growth and production of lactic acid from Lactobacillus acidophilus LA-5. A separate hydrolysis and fermentation was performed. The concentration of reducing sugars obtained after the dilute acid and enzymatic hydrolysis was 28.45 g/L. The lactobacillus count ranged from 6.03 to 8.1 log CFU/mL, whereas lactic acid yield and productivity were 0.63 g/g and 0.73 g/L h, respectively. The maximum lactic acid concentration was found to be 17.5 g/L. This study reports the possibility of using the O. ficus indica cladode for lactic acid production by LA-5 aiming to reduce costs for sustainable industrial production.

Culturomics- and metagenomics-based insights into the soil microbiome preservation and application for sustainable agriculture

Soil health is crucial for global food production in the context of an ever-growing global population. Microbiomes, a combination of microorganisms and their activities, play a pivotal role by biodegrading contaminants, maintaining soil structure, controlling nutrients' cycles, and regulating the plant responses to biotic and abiotic stresses. Microbiome-based solutions along the soil-plant continuum, and their scaling up from laboratory experiments to field applications, hold promise for enhancing agricultural sustainability by harnessing the power of microbial consortia. Synthetic microbial communities, i.e., selected microbial consortia, are designed to perform specific functions. In contrast, natural communities leverage indigenous microbial populations that are adapted to local soil conditions, promoting ecosystem resilience, and reducing reliance on external inputs. The identification of microbial indicators requires a holistic approach. It is fundamental for current understanding the soil health status and for providing a comprehensive assessment of sustainable land management practices and conservation efforts. Recent advancements in molecular technologies, such as high-throughput sequencing, revealed the incredible diversity of soil microbiomes. On one hand, metagenomic sequencing allows the characterization of the entire genetic composition of soil microbiomes, and the examination of their functional potential and ecological roles; on the other hand, culturomics-based approaches and metabolic fingerprinting offer complementary information by providing snapshots of microbial diversity and metabolic activities both in and ex-situ. Long-term storage and cryopreservation of mixed culture and whole microbiome are crucial to maintain the originality of the sample in microbiome biobanking and for the development and application of microbiome-based innovation. This review aims to elucidate the available approaches to characterize diversity, function, and resilience of soil microbial communities and to develop microbiome-based solutions that can pave the way for harnessing nature's untapped resources to cultivate crops in healthy soils, to enhance plant resilience to abiotic and biotic stresses, and to shape thriving ecosystems unlocking the potential of soil microbiomes is key to sustainable agriculture. Improving management practices by incorporating beneficial microbial consortia, and promoting resilience to climate change by facilitating adaptive strategies with respect to environmental conditions are the global challenges of the future to address the issues of climate change, land degradation and food security.

A New Method for Selective Extraction of Torularhodin from Red Yeast Using CO2-SFE Technique

Torularhodin is a dark pink colored carotenoid belonging to the xanthophylls group that can be biologically synthesized by red yeasts, especially by Rhodotorula and Sporobolomyces genera. The growing interest in this molecule is due to its biological activities such as antioxidant, anticholesterolemic, anti-inflammatory, antimicrobial, and anticancer. To satisfy potential commercial markets, numerous methods have been proposed to develop a cost-effective and environmentally friendly downstream process for the purification of torularhodin. However, obtaining high purity products without resorting to the use of toxic solvents, which can leave residues in the final preparations, remains a major challenge. In this context, the present study aimed to develop a new efficient method for the isolation of torularhodin from the red yeast Rhodotorula strain ELP2022 by applying the extraction technique with supercritical CO2 (CO2-SFE) in two sequential steps. In particular, in the first step, the dried lysed biomass of yeast was subjected to the action of CO2 in supercritical conditions (CO2SC) as sole solvent for extraction of apolar carotenoids. In the second step, the residual biomass was subjected to the action of CO2SC using ethanol as a polar co-solvent for the extraction of torularhodin. Both steps were carried out at different operating parameters of temperature (40 and 60 °C) and pressure (from 300 to 500 bar) with a constant CO2 flow of 6 L min-1. Regardless of the operating conditions used, this method allowed to obtain an orange-colored oily extract and a red-colored extract after the first and second step, respectively. In all trials, torularhodin represented no less than 95.2% ± 0.70 of the total carotenoids in the red extracts obtained from the second step. In particular, the best results were obtained by performing both steps at 40 °C and 300 bar, and the maximum percentage of torularhodin achieved was 97.9% ± 0.88. Since there are no data on the selective recovery of torularhodin from red yeast using the SFE technique, this study may be a good starting point to optimize and support the development of industrial production of torularhodin by microbial synthesis. This new method can significantly reduce the environmental impact of torularhodin recovery and can be considered an innovation for which an Italian patent application has been filed. In a circular bioeconomy approach, this method will be validated up to a pilot scale, culturing the strain Rhodotorula spp. ELP2022 on low-cost media derived from agri-food wastes.

Cross Cultivation on Homologous/Heterologous Plant-Based Culture Media Empowers Host-Specific and Real Time In Vitro Signature of Plant Microbiota

Alliances of microbiota with plants are masked by the inability of in vitro cultivation of their bulk. Pure cultures piled in international centers originated from dissimilar environments/hosts. Reporting that plant root/leaf-based culture media support the organ-specific growth of microbiota, it was of interest to further investigate if a plant-based medium prepared from homologous (maize) supports specific/adapted microbiota compared to another prepared from heterologous plants (sunflower). The culture-independent community of maize phyllosphere was compared to communities cross-cultivated on plant broth-based media: CFU counts and taxa prevalence (PCR-DGGE; Illumina MiSeq amplicon sequencing). Similar to total maize phyllospheric microbiota, culture-dependent communities were overwhelmed by Proteobacteria (>94.3–98.3%); followed by Firmicutes (>1.3–3.7%), Bacteroidetes (>0.01–1.58%) and Actinobacteria (>0.06–0.34%). Differential in vitro growth on homologous versus heterologous plant-media enriched/restricted various taxa. In contrast, homologous cultivation over represented members of Proteobacteria (ca. > 98.0%), mainly Pseudomonadaceae and Moraxellaceae; heterologous cultivation and R2A enriched Firmicutes (ca. > 3.0%). The present strategy simulates/fingerprints the chemical composition of host plants to expand the culturomics of plant microbiota, advance real-time in vitro cultivation and lab-keeping of compatible plant microbiota, and identify preferential pairing of plant-microbe partners toward future synthetic community (SynComs) research and use in agriculture.