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  • 1
    Online Resource
    Online Resource
    The “Infernaccio” Gorges: Microbial Diversity of Black Deposits and Isolation of Manganese-Solubilizing Bacteria
    MDPI AG ; 2022
    In:  Biology Vol. 11, No. 8 ( 2022-08-11), p. 1204-
    Details
    In: Biology, MDPI AG, Vol. 11, No. 8 ( 2022-08-11), p. 1204-
    Abstract: 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.
    Type of Medium: Online Resource
    ISSN: 2079-7737
    URL: Article
    DOI: 10.3390/biology11081204
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2661517-4
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  • 2
    Online Resource
    Online Resource
    Genetic Diversity of Trichoderma harzianum Isolates in Sunflower Rhizosphere: The Application of the URP Molecular Marker
    MDPI AG ; 2022
    In:  Sustainability Vol. 14, No. 22 ( 2022-11-15), p. 15111-
    Details
    In: Sustainability, MDPI AG, Vol. 14, No. 22 ( 2022-11-15), p. 15111-
    Abstract: The genetic diversity of 77 Trichoderma harzianum isolates collected from sunflower rhizosphere soils in Urmia, Khoy, and Salmas in West Azerbaijan province, Iran, was evaluated by using the Universal Rice Primer (URP) molecular marker. The DNA band pattern of the isolates was developed using seven primers of this marker. These primers produced 186 gene loci, out of which 182 loci were polymorphic. Accordingly, the genetic diversity of the isolates was calculated, and their kinship relations were determined by cluster analysis using the NTSYS software package. URP-6R had the highest marker index among the studied primers, followed by URP-1F, URP-4R, and URP-25F, implying their higher efficiency in discriminating between the isolates. The results showed that the URP marker could discriminate between isolates using macroscopic morphological characteristics, such as color and colony type, potential of pigment production in the culture medium, and colony growth rate. Furthermore, there was no significant relationship between the geographical distribution of the isolates and the band patterns generated by the primers except for a few cases. The results generally revealed that the URP marker was an efficient tool for determining the genetic diversity of T. harzianum.
    Type of Medium: Online Resource
    ISSN: 2071-1050
    URL: Article
    DOI: 10.3390/su142215111
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2518383-7
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  • 3
    Online Resource
    Online Resource
    Preliminary indication of the role of AHL-dependent quorum sensing systems in calcium carbonate precipitation in Gram-negative bacteria
    American Institute of Mathematical Sciences (AIMS) ; 2023
    In:  AIMS Microbiology Vol. 9, No. 4 ( 2023), p. 692-711
    Details
    In: AIMS Microbiology, American Institute of Mathematical Sciences (AIMS), Vol. 9, No. 4 ( 2023), p. 692-711
    Abstract: 〈abstract〉 〈p〉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〈sub〉3〈/sub〉) 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 〈italic〉Chromobacterium subtsugae〈/italic〉 strain CV026. Only 〈italic〉Burkholderia ambifaria〈/italic〉 LMG 11351 was able to restore violacein production in CV026 among the tested strains. The constructed AHL-negative mutant of 〈italic〉B. ambifaria〈/italic〉 LMG 11351 could not precipitate CaCO〈sub〉3〈/sub〉 on B-4 agar. Scanning Electron Microscopy (SEM) analysis on CaCO〈sub〉3〈/sub〉 crystals obtained 〈italic〉in vitro〈/italic〉 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 〈italic〉B. ambifaria〈/italic〉 LMG 11351, a stream-like organization of the 〈italic〉Burkholderia〈/italic〉 imprints was not detected by SEM. Our data provide preliminary evidence that the activation of AHL-regulated genes may be a prerequisite for 〈italic〉in vitro〈/italic〉 bacterial carbonatogenesis, in some cases, confirming the specific role of bacteria as CaCO〈sub〉3〈/sub〉 precipitating agents. We enhance the understanding of bacterial CaCO〈sub〉3〈/sub〉 biomineralization and its potential biotechnology implications for QS-based strategies to enhance or decrease CaCO〈sub〉3〈/sub〉 precipitation through specific bacterial processes. The AHL-negative mutant of 〈italic〉B. ambifaria〈/italic〉 LMG 11351 (a well-known plant growth-promoting bacterium) could also be used to study plant-bacteria interactions. The adaptive role of bacterial CaCO〈sub〉3〈/sub〉 biomineralization was also discussed.〈/p〉 〈/abstract〉
    Type of Medium: Online Resource
    ISSN: 2471-1888
    URL: Article
    DOI: 10.3934/microbiol.2023035
    Language: Unknown
    Publisher: American Institute of Mathematical Sciences (AIMS)
    Publication Date: 2023
    detail.hit.zdb_id: 2985106-3
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  • 4
    Online Resource
    Online Resource
    Arbuscular mycorrhizal symbiosis: plant growth improvement and induction of resistance under stressful conditions
    Informa UK Limited ; 2021
    In:  Journal of Plant Nutrition Vol. 44, No. 13 ( 2021-08-09), p. 1993-2028
    Details
    In: Journal of Plant Nutrition, Informa UK Limited, Vol. 44, No. 13 ( 2021-08-09), p. 1993-2028
    Type of Medium: Online Resource
    ISSN: 0190-4167 , 1532-4087
    URL: Article
    DOI: 10.1080/01904167.2021.1881552
    Language: English
    Publisher: Informa UK Limited
    Publication Date: 2021
    detail.hit.zdb_id: 2057445-9
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    Data_Sheet_1.docx
    Frontiers Media SA ; 2022
    In:  Frontiers in Microbiology Vol. 13 ( 2022-7-28)
    Details
    In: Frontiers in Microbiology, Frontiers Media SA, Vol. 13 ( 2022-7-28)
    Abstract: This study aimed to estimate the green formation lampenflora of “Stiffe” caves in order to evaluate their suitability as an isolation source of cyanobacteria useful for the production of polyhydroxyalkanoates (PHAs). The cave system was chosen as the sampling site due to its touristic use and the presence of high-impact illuminations. The biofilms and the mats of the illuminated walls were sampled. Samples were investigated by 16S rRNA gene analysis and culturable cyanobacteria isolation. The isolated strains were then screened for the production of PHAs under typical culturing and nutritional starvation. Cultures were checked for PHA accumulation, poly-β-hydroxybutyrate (PHB) presence (infrared spectroscopy), and pigment production. The 16S rRNA gene metabarcoding. Highlighted a considerable extent of the pressure exerted by anthropogenic activities. However, the isolation yielded eleven cyanobacteria isolates with good PHA (mainly PHB)-producing abilities and interesting pigment production rates (chlorophyll a and carotenoids). Under normal conditions (BG11 0 ), the accumulation abilities ranged from 266 to 1,152 ng mg dry biomass –1 . The optimization of bioprocesses through nutritional starvation resulted in a 2.5-fold increase. Fourier transform infrared (FTIR) studies established the occurrence of PHB within PHAs extracted by cyanobacteria isolates. The comparison of results with standard strains underlined good production rates. For C2 and C8 strains, PHA accumulation rates under starvation were higher than Azospirillum brasilense and similar to Synechocystis cf. salina 192. This study broadened the knowledge of the microbial communities of mats and biofilms on the lightened walls of the caves. These findings suggested that these structures, which are common in tourist caves, could be used to isolate valuable strains before remediation measures are adopted.
    Type of Medium: Online Resource
    ISSN: 1664-302X
    URL: Article
    URL: Article
    DOI: 10.3389/fmicb.2022.933398
    DOI: 10.3389/fmicb.2022.933398.s001
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2587354-4
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  • 6
    Online Resource
    Online Resource
    Bacterial Microbiota and Soil Fertility of Crocus sativus L. Rhizosphere in the Presence and Absence of Fusarium spp.
    MDPI AG ; 2022
    In:  Land Vol. 11, No. 11 ( 2022-11-15), p. 2048-
    Details
    In: Land, MDPI AG, Vol. 11, No. 11 ( 2022-11-15), p. 2048-
    Abstract: 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.
    Type of Medium: Online Resource
    ISSN: 2073-445X
    URL: Article
    DOI: 10.3390/land11112048
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2682955-1
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  • 7
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    Online Resource
    Actinomycetes from Caves: An Overview of Their Diversity, Biotechnological Properties, and Insights for Their Use in Soil Environments
    MDPI AG ; 2022
    In:  Microorganisms Vol. 10, No. 2 ( 2022-02-16), p. 453-
    Details
    In: Microorganisms, MDPI AG, Vol. 10, No. 2 ( 2022-02-16), p. 453-
    Abstract: 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.
    Type of Medium: Online Resource
    ISSN: 2076-2607
    URL: Article
    DOI: 10.3390/microorganisms10020453
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2720891-6
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  • 8
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    Online Resource
    Enhancing Manganese Availability for Plants through Microbial Potential: A Sustainable Approach for Improving Soil Health and Food Security
    MDPI AG ; 2023
    In:  Bacteria Vol. 2, No. 3 ( 2023-08-06), p. 129-141
    Details
    In: Bacteria, MDPI AG, Vol. 2, No. 3 ( 2023-08-06), p. 129-141
    Abstract: 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.
    Type of Medium: Online Resource
    ISSN: 2674-1334
    URL: Article
    DOI: 10.3390/bacteria2030010
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 3136481-0
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  • 9
    Online Resource
    Online Resource
    Microbial Community Investigation of Wild Brambles with Root Nodulation from a Calcareous Nitrogen-Deficient Soil
    MDPI AG ; 2022
    In:  Soil Systems Vol. 6, No. 4 ( 2022-12-09), p. 96-
    Details
    In: Soil Systems, MDPI AG, Vol. 6, No. 4 ( 2022-12-09), p. 96-
    Abstract: 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.
    Type of Medium: Online Resource
    ISSN: 2571-8789
    URL: Article
    DOI: 10.3390/soilsystems6040096
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2932897-4
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  • 10
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    Online Resource
    A New Technique for the Extraction of Arbuscular Mycorrhizae Fungal Spores from Rhizosphere
    MDPI AG ; 2023
    In:  Journal of Fungi Vol. 9, No. 8 ( 2023-08-14), p. 845-
    Details
    In: Journal of Fungi, MDPI AG, Vol. 9, No. 8 ( 2023-08-14), p. 845-
    Abstract: 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 (Triticum aestivum L.), bean (Phaseolus vulgaris L.), tomato (Solanum lycopersicum L.), pepper (Piper nigrum L.), parsley (Petroselinum crispum Mill.), and turfgrass (Lolium perenne 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.
    Type of Medium: Online Resource
    ISSN: 2309-608X
    URL: Article
    DOI: 10.3390/jof9080845
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2784229-0
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