The environmental conditions of caves shape microbiota. Within caves’ microbial communities, actinomycetes are among the most abundant bacteria. Cave actinomycetes have gained increasing attention during the last decades due to novel bioactive compounds with antibacterial, antioxidant and anticancer activities. However, their potential role in soil environments is still unknown. This review summarises the literature dealing with actinomycetes from caves, underlining for the first time their potential roles in soil environments. We provide an overview of their diversity and biotechnological properties, underling their potential role in soil environments applications. The contribution of caves’ actinomycetes in soil fertility and bioremediation and crops biostimulation and biocontrol are discussed. The survey on the literature show that several actinomycetes genera are present in cave ecosystems, mainly Streptomyces, Micromonospora, and Nocardiopsis. Among caves’ actinomycetes, Streptomyces is the most studied genus due to its ubiquity, survival capabilities, and metabolic versatility. Despite actinomycetes’ outstanding capabilities and versatility, we still have inadequate information regarding cave actinomycetes distribution, population dynamics, biogeochemical processes, and metabolisms. Research on cave actinomycetes needs to be encouraged, especially concerning environmental soil applications to improve soil fertility and health and to antagonise phytopathogens.

Biotic stress caused by pathogenic microorganisms leads to damage in crops. Tomato and carrot are among the most important vegetables cultivated worldwide. These plants are attacked by several pathogens, affecting their growth and productivity. Fourteen plant growth-promoting actinomycetes (PGPA) were screened for their in vitro biocontrol activity against Solanum lycopersicum and Daucus carota microbial phytopathogens. Their antifungal activity was evaluated against Fusarium oxysporum f. sp. radicis-lycopersici (FORL) and Rhizoctonia solani (RHS). Antibacterial activity was evaluated against Pseudomonas syringae, Pseudomonas corrugata, Pseudomonas syringae pv. actinidiae, and Pectobacterium carotovorum subsp. carotovorum. Strains that showed good in vitro results were further investigated in vitro (cell-free supernatants activity, scanning electron microscope observations of fungal inhibition). The consortium of the most active PGPA was then utilized as biocontrol agents in planta experiments on S. lycopersicum and D. carota. The Streptomyces albidoflavus H12 and Nocardiopsis aegyptica H14 strains showed the best in vitro biocontrol activities. The diffusible and volatile compounds and cell-free supernatants of these strains showed both antifungal (in vitro inhibition up to 85%, hyphal desegregation and fungicidal properties) and antibacterial activity (in vitro inhibition >25 mm and bactericidal properties). Their consortium was also able to counteract the infection symptoms of microbial phytopathogens during in planta experiments, improving plant status. The results obtained highlight the efficacy of the selected actinomycetes strains as biocontrol agents of S. lycopersicum and D. carota.

With the expansion of the green products market and the worldwide policies and strategies directed toward a green revolution and ecological transition, the demand for innovative approaches is always on the rise. Among the sustainable agricultural approaches, microbial-based products are emerging over time as effective and feasible alternatives to agrochemicals. However, the production, formulation, and commercialization of some products can be challenging. Among the main challenges are the industrial production processes that ensure the quality of the product and its cost on the market. In the context of a circular economy, solid-state fermentation (SSF) might represent a smart approach to obtaining valuable products from waste and by-products. SSF enables the growth of various microorganisms on solid surfaces in the absence or near absence of free-flowing water. It is a valuable and practical method and is used in the food, pharmaceutical, energy, and chemical industries. Nevertheless, the application of this technology in the production of formulations useful in agriculture is still limited. This review summarizes the literature dealing with SSF agricultural applications and the future perspective of its use in sustainable agriculture. The survey showed good potential for SSF to produce biostimulants and biopesticides useful in agriculture.

The present study explored the microbial diversity of black deposits found in the “Infernaccio” gorge. X-ray Powdered Diffraction (XRPD) was used to investigate the crystallinity of the samples and to identify the minerals. Scanning electron microscope and energy-dispersive X-ray spectroscopy (SEM-EDS) were used to detect the bacterial imprints, analyze microbe–mineral interactions, and highlight the chemical element distribution in the black deposits. 16S rRNA gene metabarcoding allowed the study of Archaea and Bacteria communities. Mn-oxide-solubilizing isolates were also obtained and characterized by culturable and molecular approaches. The multidisciplinary approach showed the occurrence of deposits composed of birnessite, diopside, halloysite, and leucite. Numerous bacterial imprints confirmed the role of microorganisms in forming these deposits. The Bacteria and Archaea communities associated with these deposits and runoff waters are dynamic and shaped by seasonal changes. The uncultured and unknown taxa are the most common and abundant. These amplicon sequence variants (ASVs) were mainly assigned to Proteobacteria and Bacteroidetes phyla. Six isolates showed interesting Mn solubilization abilities under microaerophilic conditions. Molecular characterization associated isolates to Brevibacterium, Bacillus, Neobacillus, and Rhodococcus genera. The findings enriched our knowledge of geomicrobiological aspects of one of the Earth’s hidden habitats. The study also unveiled the potential of this environment as an isolation source of biotechnologically relevant bacteria.

Manganese (Mn) is essential for plant growth, as it serves as a cofactor for enzymes involved in photosynthesis, antioxidant synthesis, and defense against pathogens. It also plays a role in nutrient uptake, root growth, and soil microbial communities. However, the availability of Mn in the soil can be limited due to factors like soil pH, redox potential, organic matter content, and mineralogy. The excessive use of chemical fertilizers containing Mn can lead to negative consequences for soil and environmental health, such as soil and water pollution. Recent research highlights the significance of microbial interactions in enhancing Mn uptake in plants, offering a more environmentally friendly approach to address Mn deficiencies. Microbes employ various strategies, including pH reduction, organic acid production, and the promotion of root growth, to increase Mn bioavailability. They also produce siderophores, anti-pathogenic compounds, and form symbiotic relationships with plants, thereby facilitating Mn uptake, transport, and stimulating plant growth, while minimizing negative environmental impacts. This review explores the factors impacting the mobility of Mn in soil and plants, and highlights the problems caused by the scarcity of Mn in the soil and the use of chemical fertilizers, including the consequences. Furthermore, it investigates the potential of different soil microbes in addressing these challenges using environmentally friendly methods. This review suggests that microbial interactions could be a promising strategy for improving Mn uptake in plants, resulting in enhanced agricultural productivity and environmental sustainability. However, further research is needed to fully understand these interactions’ mechanisms and optimize their use in agricultural practices.

This study revealed how Bacteria and Archaea communities and their metabolic functions differed between two groups of black deposits identified in gorge and cave environments. Scanning electron microscopy coupled with energy dispersive spectroscopy was used to analyse the presence of microbial biosignatures and the elemental composition of samples. Metabarcoding of the V3–V4 regions of 16S rRNA was used to investigate Bacteria and Archaea communities. Based on 16S rRNA sequencing results, PICRUSt software was used to predict metagenome functions. Micrographs showed that samples presented microbial biosignatures and microanalyses highlighted Mn concretions and layers on Al-Si surfaces. The 16S rRNA metabarcoding alpha-diversity metrics showed similar Simpson's and Shannon indices and different values of the Chao-1 index. The amplicon sequence variants (ASVs) analysis at the different taxonomic levels showed a diverse genera composition. However, the communities of all samples shared the presence of uncultured ASVs belonging to the Gemmatales family (Phylogenesis: Gemmataceae; Planctomycetes; Planctomycetota; Bacteria). The predicted metagenome functions analysis revealed diverse metabolic profiles of the Cave and Gorge groups. Genes coding for essential Mn metabolism were present in all samples. Overall, the findings on structure, microbiota, and predicted metagenome functions showed a similar microbial contribution to epigean and hypogean black deposits Mn metabolism.

Intensive agricultural practices have led to intense soil degradation and soil fertility losses. Many soil-borne diseases affect these intensive agricultural soils, worsening the physical-chemical and fertility imbalances. Among the numerous pathogens, the genus Fusarium includes members that destroy many crops, including Crocus sativus L., which also impairs the composition and functions of the microbial communities. This work aimed to investigate, for the first time, the bacterial communities of the rhizosphere of saffron in the presence and absence of fusariosis. The rhizosphere of the saffron fields in the territory of L’Aquila (Italy) with and without fusariosis was sampled and subjected to a microbiological analysis. Culture-dependent methods characterized the fusariosis. The dehydrogenase activity assay was estimated. The metabarcoding of the 16S rRNA gene, a metagenome functioning prediction, and a network analysis were also carried out. The results showed that fusariosis, when it is linked to intensive agricultural practices, causes alterations in the microbial communities of the rhizosphere. The culture-dependent and independent approaches have shown changes in the bacterial community in the presence of fusariosis, with functional and enzymatic imbalances. The samples showed a prevalence of uncultured and unknown taxa. Most of the known Amplicon Sequence Variants (ASVs) were associated with the Pseudomonadoa (syn. Proteobacteria) lineage. The composition and richness of this phylum were significantly altered by the presence of Fusarium. Moreover, pathogenesis appeared to improve the ASVs interconnections. The metagenome functions were also modified in the presence of fusariosis.

This study examines culturable diazotrophs and non-culturable bacteria found in the rhizospheres and root pseudonodules of wild blackberry plants (Rubus ulmifolius) that dwell on an unmanaged calcareous nitrogen-deficient soil. The DNA was extracted from the nodules and rhizospheres, and 16S rRNA gene metabarcoding was carried out. The metagenome functions were predicted with bioinformatic approaches. The soil samples were analyzed for the physico-chemical properties. The culturable diazotrophs were isolated and evaluated for the biochemical and plant growth-promoting properties. The soil was classified as nutrient-depleted calcareous soil. The microbial communities of the nodules and rhizospheres showed marked differences. The Pseudomonadota was the nodules’ dominant phyla (90%), while the Actinobacteriota was the most abundant (63%) in the rhizospheres. Stenotrophomonas was the dominant genus (55%) in the nodules, while the Streptomyces genus was widely present (39%) in the rhizospheres. The differences among the nodule and rhizosphere microbial communities were also highlighted by the metagenome function predictions. The gene copies (KOs) revealed the most interesting findings. Similar KOs involved in the nitrogen fixation were found to be similar in terms of the nodules and rhizospheres. However, the nitrate reduction was higher in the rhizosphere, while the denitrification was more prominent in the nodules. Nine diazotrophs were isolated from the nodules and rhizospheres. The plant growth promoting traits’ characterization has shown the interesting potential of the isolates in improving the acquisition of nutrients in plants, promoting their growth, and tolerating stress. Based on interesting biochemical and plant growth-promoting traits, the isolate N2A was further characterized and identified as Pantoea agglomerans.