isolation-identification-bacterial-strains-from-skin-terrestrial

Isolation and Identification of Bacterial Strains from Skin of Terrestrial Amphibians

The microbiota is a vital element of higher organisms, with the cutaneous microbiota significantly contributing to the organism&#39;s defense against ...

UNIVERSITY OF L'AQUILA

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  and  microbial phytopathogens. Their antifungal activity was evaluated against  f. sp.  (FORL) and  (RHS). Antibacterial activity was evaluated against , ,  pv. , and  subsp. . 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  and . The  H12 and  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  and .

Biocontrol of Soil-Borne Pathogens of  L. and   L. by Plant Growth-Promoting Actinomycetes: In Vitro and In Planta Antagonistic Activity.

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 , , and . Among caves' actinomycetes,  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.

Actinomycetes from Caves: An Overview of Their Diversity, Biotechnological Properties, and Insights for Their Use in Soil Environments.

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 , , , and  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.

The "Infernaccio" Gorges: Microbial Diversity of Black Deposits and Isolation of Manganese-Solubilizing Bacteria.

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.

Exploring structure, microbiota, and metagenome functions of epigean and hypogean black deposits by microscopic, molecular and bioinformatic approaches.

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.

Solid-State Fermentation: Applications and Future Perspectives for Biostimulant and Biopesticides Production.

Monitoring the dynamics of the spore bank of arbuscular mycorrhizal fungi (AMF) is essential for the sustainable management and protection of agroecosystems. The most common method for extracting AMF spores from soil is the wet-sieving technique (WST). However, this method has many disadvantages. In this study, we modified the WST using new approaches: the ultrasound wet-sieving technique (UWST) and the ultrasound centrifuge technique (UCT). We enumerated and compared the numbers and quality of spores obtained from WST, UWST, and UCT to validate the new modified techniques. We extracted AMF spores from the rhizospheres of different plants, including wheat ( L.), bean ( L.), tomato ( L.), pepper ( L.), parsley ( Mill.), and turfgrass ( L.) collected from the Van Lake basin, Turkey. The highest and lowest AMF spore numbers were observed in wheat and turfgrass rhizospheres. The UCT allowed for the extraction of the highest number of spores from all rhizospheres, followed by the UWST and WST. The UWST and WST allowed for the extraction of similar spore numbers from wheat, pepper, parsley, and turfgrass rhizospheres. Beyond the high extracted spore number, UCT was shown to be a fast and low-material-consuming approach. These findings demonstrate that the UCT can be used to efficiently extract AMF spores in future research.

A New Technique for the Extraction of Arbuscular Mycorrhizae Fungal Spores from Rhizosphere.

Numerous microbial species participate in precipitation of carbonates in various natural environments, including soils, geological formations, freshwater biofilms and oceans. Despite the geochemical interest of such a biomineralization process, its molecular mechanisms and adaptive aspects remain poorly known. Many Gram-negative bacteria use cell-to-cell communication systems relying on N-acylhomoserine lactone (AHLs) signal molecules to express certain phenotypic traits in a density-dependent manner, a phenomenon referred as to quorum-sensing (QS). In this work, bacterial isolates collected from cave and rhizosphere soil were analyzed to study the occurrence of the AHL-mediated QS in bacterial calcium carbonate (CaCO) precipitation. To test the production of AHLs signal molecules, we cross-streaked Gram-negative calcifying strains, selected among the environmental strains studied, with the AHL-negative mutant  strain CV026. Only  LMG 11351 was able to restore violacein production in CV026 among the tested strains. The constructed AHL-negative mutant of  LMG 11351 could not precipitate CaCO on B-4 agar. Scanning Electron Microscopy (SEM) analysis on CaCO crystals obtained  shows crystals of different morphologies, calcified biofilms and bacteria in close contact with the precipitated crystals. In the inner layers of the bioliths deposited by  LMG 11351, a stream-like organization of the  imprints was not detected by SEM. Our data provide preliminary evidence that the activation of AHL-regulated genes may be a prerequisite for  bacterial carbonatogenesis, in some cases, confirming the specific role of bacteria as CaCO precipitating agents. We enhance the understanding of bacterial CaCO biomineralization and its potential biotechnology implications for QS-based strategies to enhance or decrease CaCO precipitation through specific bacterial processes. The AHL-negative mutant of  LMG 11351 (a well-known plant growth-promoting bacterium) could also be used to study plant-bacteria interactions. The adaptive role of bacterial CaCO biomineralization was also discussed.

Preliminary indication of the role of AHL-dependent quorum sensing systems in calcium carbonate precipitation in Gram-negative bacteria.

Soilborne pathogens reduce 60% of the yield of onion crops. A common fungal pathogen causing wilt disease and severe losses is  basal rot (FBR). In this study, the combination of Arbuscular Mycorrhizal Fungi (AMF) with  was investigated against FBR. Onion samples were collected from the Ankara-Polatlı region. Among the isolates, isolate S6 was identified as  f. sp.  (FOC) using morphological and molecular methods and pathogenicity tests. Different combinations of AMF ( pure strain and the commercial AMF) and  were inoculated on susceptible onion cultivars (Seç, Gence, and Şampiyon). The effects of the treatments on FOC biocontrol were studied under growth chamber conditions. The results showed that Şampiyon was the most resistant, while Gence was the most susceptible to basal rot disease. Different colonization rates (8.91-24%), spore densities (16.4-50.4 spore/10 g soil), and the extent to which a plant needs mycorrhizal conditions to grow to its maximum potential (i.e., mycorrhizal dependencies-18.3-51.9%) were recorded by treatment. Both single and combined applications of AMF and  applications suppressed FOC. Suppressive effects were more pronounced when the  pure strain was used alone (when  was used, disease severity decreased from 90 to 68%,  < 0.05). The  pure strain also showed the best plant growth promotion and phosphorus content release. The results indicate an interesting potential use of  and the combination of AMF with  in the management of FOC in onions.

Onion  Basal Rot Disease Control by Arbuscular Mycorrhizal Fungi and .

Sustainable alternatives are essential to improving agriculture production to meet the growing world's critical demands. Cyanobacteria and microalgae are considered renewable resources with a wide range of potential uses in the agricultural sector. We aimed to isolate cyanobacteria and microalgae from the mud of a carbon dioxide-rich sulfur pond and to investigate their plant growth-promoting (PGP) and soil bio-consolidating ability. Mud samples were subjected to DNA extraction and 16S rRNA gene sequencing to characterize the prokaryotic community. Phototrophic culturable microbiota was isolated and evaluated for different PGP properties. The most relevant isolates were combined in a consortium and used for  bioconsolidation activity. In a greenhouse experiment, the isolates were evaluated for their ability to promote salinity stress tolerance in sunflower plants. Metabarcoding results showed that most Amplicon Sequence Variants (ASV) were associated with Actinobacteriota (35%), Proteobacteria (19%), and Acidobacteriota (11%) at the phylum level and  (32%) and uncultured (31%) lineages at the genus level. The culture-dependent method yielded eight isolates associated with cyanobacteria and microalgae genera. The isolates obtained showed interesting PGP activities. Isolates C1, C2, and M1 were selected based on phosphate solubilization (85.6 µg PO  mL on average), indoles (C1 and M1 0.54 µg mL IAA equivalents on average), and ACC deaminase activity (C2 and M1 6.00 µmol α-KB mg proteins h. The consortium efficiently consolidated sand particles in the presence of calcium carbonate by forming biomineralized aggregates.  results showed positive effects of the consortium on ., plant growth under normal conditions and salt stress. The positive effects on soil and plants indicated their effectiveness as bioconsolidants and biostimulant agents. Our findings highlight the interesting potential of cyanobacteria and microalgae applications in sustainable agriculture.

Isolation and characterization of cyanobacteria and microalgae from a sulfuric pond: Plant growth-promoting and soil bioconsolidation activities.

Arid ecosystems constitute a promising source of actinobacteria producing new bioactive molecules. This study aimed to explore different biological activities of actinomycetes isolated from the rhizosphere of  L. in the Ghardaia region, Algeria. A total of 18 actinobacteria were isolated and studied for their enzymatic and antimicrobial activities. All isolates shared cellulase and catalase activity; most of them produced amylase (94%), esterase (84%), lecithinase and lipoproteins (78%), caseinase (94%), and gelatinase (72%). The isolates could coagulate (56%) or peptonize (28%) skim milk. Overall, 72% of the isolates exhibited significant antibacterial activity against at least one test bacteria, while 56% demonstrated antifungal activity against at least one test fungi. Based on enzyme production and antimicrobial activity, isolate SGI16 was selected for secondary metabolite extraction by ethyl acetate. The crude extract of SGI16 was analyzed using DPPH and BSA denaturation inhibition tests, revealing significant antioxidant power (IC = 7.24 ± 0.21 μg mL) and protein denaturation inhibitory capacity (IC = 492.41 ± 0.47 μg mL). Molecular identification based on  analysis showed that SGI16 belonged to the genus . The findings highlight that date palms' rhizosphere actinobacteria are a valuable source of biomolecules of biotechnological interest.

Isolation of Actinobacteria from Date Palm Rhizosphere with Enzymatic, Antimicrobial, Antioxidant, and Protein Denaturation Inhibitory Activities.

Soil salinization, extreme climate conditions, and phytopathogens are abiotic and biotic stressors that remarkably reduce agricultural productivity. Recently, nanomaterials have gained attention as effective agents for agricultural applications to mitigate such stresses. This review aims to critically appraise the available literature on interactions involving nanomaterials, plants, and microorganisms. This review explores the role of nanomaterials in enhancing plant growth and mitigating biotic and abiotic stresses. These materials can be synthesized by microbes, plants, and algae, and they can be applied as fertilizers and stress amelioration agents. Nanomaterials facilitate nutrient uptake, improve water retention, and enhance the efficiency of active ingredient delivery. Nanomaterials strengthen plant antioxidant systems, regulate photosynthesis, and stabilize hormonal pathways. Concurrently, their antimicrobial and protective properties provide resilience against biotic stressors, including pathogens and pests, by promoting plant immune responses and optimizing microbial-plant symbiosis. The synergistic interactions of nanomaterials with beneficial microorganisms optimize plant growth under stress conditions. These materials also serve as carriers of nutrients, growth regulators, and pesticides, thus acting like "smart fertilizers. While nanotechnology offers great promise, addressing potential environmental and ecotoxicological risks associated with their use is necessary. This review outlines pathways for leveraging nanotechnology to achieve resilient, sustainable, and climate-smart agricultural systems by integrating molecular insights and practical applications.

Nanomaterials-plants-microbes interaction: plant growth promotion and stress mitigation.

The present study investigated the contribution of microbial communities in producing "living stones" and the suitability of these clasts as sources of microorganisms with biomineralisation abilities. The calcareous samples were analysed for their microbial community (16S rRNA gene metabarcoding and culturable approach) and in vitro regeneration tests. Scanning electron microscopy and Energy Dispersive Spectroscopy (SEM-EDX) were applied to investigate microbial aggregation structures and footprints in natural and in vitro samples. The metabarcoding unveiled amplicon sequence variants (ASVs) assigned to lineages with biomineralisation abilities (e.g., Proteobacteria and Actinobacteriota). The culturable approach resulted in nineteen calcifying isolates with diverse morphological, metabolic, and mineral precipitation properties. Based on mineralising properties, Stenotrophomonas maltophilia, Lysinbacillus fusiformis, and Microbacterium ginsengiterrae were identified at the molecular level. In vitro regeneration tests and SEM-EDX analyses confirmed the active role of the endogenous microorganisms in forming these "living stones". These findings allow us to hypothesise an essential role of microbial precipitation in forming these "living stones", previously described as of abiotic origin. The current study findings provide a solid scientific foundation for future investigations. The obtained bacterial isolates and their potential applications in bioremediation, construction, and cultural heritage restoration demonstrate the direct applicability of our study in sectors involving biomaterials application. STATEMENT OF SIGNIFICANCE: We studied some "living stones" that can be found worldwide and whose origin is still not completely understood. Geologists have not yet fully explained the origin of these inorganic structures that grow in size over time. The results obtained from our microbiological investigations allowed us to discover that microorganisms play a crucial role in forming these masses. In the investigations of the structures and microbial communities within the stones, we identified specific bacteria that actively contribute to forming minerals and isolated bacteria that can form biominerals. These findings deepen our understanding of natural processes involved in the formation of these structures and show their potential for several applications (e.g., building materials or cultural heritage preservation).

Article	Year
Biocontrol of Soil-Borne Pathogens of L. and L. by Plant Growth-Promoting Actinomycetes: In Vitro and In Planta Antagonistic Activity. Pathogens (Basel, Switzerland)\| PubMed ID: 34684253	2021
Actinomycetes from Caves: An Overview of Their Diversity, Biotechnological Properties, and Insights for Their Use in Soil Environments. Microorganisms\| PubMed ID: 35208907	2022
The "Infernaccio" Gorges: Microbial Diversity of Black Deposits and Isolation of Manganese-Solubilizing Bacteria. Biology\| PubMed ID: 36009831	2022
Exploring structure, microbiota, and metagenome functions of epigean and hypogean black deposits by microscopic, molecular and bioinformatic approaches. Scientific reports\| PubMed ID: 36371463	2022
Solid-State Fermentation: Applications and Future Perspectives for Biostimulant and Biopesticides Production. Microorganisms\| PubMed ID: 37374910	2023
A New Technique for the Extraction of Arbuscular Mycorrhizae Fungal Spores from Rhizosphere. Journal of fungi (Basel, Switzerland)\| PubMed ID: 37623616	2023
Preliminary indication of the role of AHL-dependent quorum sensing systems in calcium carbonate precipitation in Gram-negative bacteria. AIMS microbiology\| PubMed ID: 38173968	2023
Onion Basal Rot Disease Control by Arbuscular Mycorrhizal Fungi and . Plants (Basel, Switzerland)\| PubMed ID: 38337919	2024
Isolation and characterization of cyanobacteria and microalgae from a sulfuric pond: Plant growth-promoting and soil bioconsolidation activities. AIMS microbiology\| PubMed ID: 39628714	2024
Isolation of Actinobacteria from Date Palm Rhizosphere with Enzymatic, Antimicrobial, Antioxidant, and Protein Denaturation Inhibitory Activities. Biomolecules\| PubMed ID: 39858459	2025
Nanomaterials-plants-microbes interaction: plant growth promotion and stress mitigation. Frontiers in microbiology\| PubMed ID: 39881995	2024
Erratic calcareous deposits: Biotic formation insights and biomineralising bacterial strain isolation. Acta biomaterialia\| PubMed ID: 39954754	2025

Beatrice Farda

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