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Bioresources for a sustainable agriculture: potentialities of Minimedusa polyspora and Chaetomium globosum as plant growth promoting fungi
Full text linkFeeding a constantly growing global population, while facing global change, without further impairing the environment is probably the greatest challenge our society is facing nowadays. Modern agriculture mostly depends on the use of agrochemicals, including chemical fertilizers, pesticides and herbicides, due to their determinant role in enhancing efficiently and economically crop production, to meet the constantly increasing food demand. However, modern agriculture pressures determine major detrimental impacts on the environment at different spatial and temporal scales, on all the natural matrices: air, soil, and water. Consequently, mitigating agriculture’s impacts on the environment represents an urgent need and a key strategy towards sustainability. Furthermore, this challenge is also concomitant with two other major challenges: increasing food production up to 60% by 2050 due to the world population growth, and adapting to a rapidly evolving climate change. In fact, due to climate change effects, plants are already more frequently subjected to severe abiotic (e.g. drought, flooding, extreme temperature) and biotic (e.g. pathogens and pest outbreaks) stresses, while future scenarios foresee these phenomena to become even more severe. In this context, plant growth promotion represents an interesting sustainable solution that may play a key role in increasing crop resilience and productivity in adverse environmental conditions, minimizing agrochemicals applications and tackling climate change effects. Indeed, in healthy ecosystems soil microorganisms, through the wide array of ecosystem services they provide, express a multifunctionality that support soil productivity and plant growth. In particular, microbial strains with high soil colonization potential and multiple plant growth promoting traits — such as the ability to stimulate the plant, increase nutrient availability, exert biocontrol activity against detrimental microorganisms, and biodegrade organic pollutant and detoxifying inorganic pollutants — present a higher efficacy due to their multipurpose applicability. In this context, fungi as multifunctional microorganisms, perfectly adapted to soil microhabitats, thanks to their functional traits, metabolic plasticity and highly potent and relatively non-specific enzymes, represent valuable and effective potential bioresources.
This thesis aimed to characterize Minimedusa polyspora (Hotson) Weresub & P. M. LeClair and Chaetomium globosum Kunze, two strains of soil saprotrophic fungi, for multiple activities — including biostimulation, biocontrol and bioremediation — that may contribute to plant growth promotion, to assess their potential as multifunctional bioresources for biotechnological application aimed at promoting a more sustainable agriculture. Therefore, following a general introduction and literature review on the topic, three chapters, each one addressing these species characterization for a specific activity that may contribute to plant growth promotion, are reported.
The first study presented in this thesis focused on assessing the efficacy of M. polyspora and C. globosum culture filtrates as biostimulant for the cultivation Cichorium intybus (L.), a plant of agricultural and medicinal interest. In a pot experiment set up in walk-in chambers, chicory plants, one month after the transfer of the seedlings in pots, were stimulated by soil drenching with 8 ml/pot (30 ml/kg of soil) of the culture filtrates obtained by a 14-days incubation of the fungal strains in Malt Extract Broth (MEB), or the same amount of uninoculated MEB in the control group. Fourteen days after the stimulation, plant biomasses were recovered to estimate several growth parameters and analyze the metabolomic variations occurred in roots and leaves through 1H-NMR 600 MHz.
We observed for the first time that M. polyspora culture filtrate promotes an increase of biomass, both in shoots and roots, and of the leaf area, while no increase was observed in plants treated with C. globosum culture filtrate. Based on 1H-NMR metabolomics data, differential metabolites and their related metabolic pathways were highlighted. A common response in C. intybus roots involving the synthesis of 3-OH-butyrate through the decrease of the synthesis of fatty acids and sterols, as a mechanism balancing the NADPH/NADP+ ratio, was observed in both the treatments with C. globosum and M. polyspora culture filtrates. The phenylpropanoid pathway was differently triggered by the fungal culture filtrates. C. globosum culture filtrate increased phenylalanine and chicoric acid in the roots. Chicoric acid, whose biosynthetic pathway in chicory plant is putative and still not well known, is a very promising natural compound playing an important role in plant defense. Instead, M. polyspora culture filtrate interestingly stimulated an increase of 4-OH benzoate, being benzoic acids precursors for a wide variety of essential compounds playing crucial roles in plant fitness and defense response activation. Therefore, both C. globosum and M. polyspora culture filtrates affected C. intybus metabolome and, based on the findings of this study, could be considered as promising fungal bioresources for further studies aimed the development of new biostimulants.
Moving on, in the second study presented in this thesis, M. polyspora and C. globosum biocontrol potential against the phytopathogenic fungi Alternaria alternata (Fr.) Keissl., Berkeleyomyces basicola (Berk. & Broome) W.J. Nel, Z.W. de Beer, T.A. Duong & M.J. Wingf. and Botrytis cinerea Pers. was investigated.
Plant diseases, resulting in an annual estimated loss of 10–15% of world's major crops, represent a major threat to global crops production and social and political stability of nations. 70–80% of these diseases are caused by pathogenic fungi, numbers that are expected to increase in future years due to the effect of climate change on plant-pathogens interactions. In the effort to transition to a more sustainable and resilient agriculture, the application of biological control agents and their secondary metabolites represent a promising option to support the achievement of food security, without further compromise ecosystems’ health. Therefore, it is important deepening the potential of known fungal biocontrol agents against the existing fungal pathogens, shedding further light on their action mechanisms and discovering new efficient fungal strains suitable for biotechnological applications. In vitro screenings, despite presenting several limitations, constitute valuable methods for the identification of potential biocontrol agents. Therefore, through an array of in vitro plate assays M. polyspora and C. globosum were assessed for their ability to inhibit A. alternata, B. basicola and B. cinerea growth, aiming also to gain insight on possible antimicriobial mechanism/s involved in their biological control action. More specifically, a dual culture assay, a dual culture for volatile antimicrobial compounds (performed in two different conditions), and a culture filtrate antifungal activity assay were designed to try to discriminate the impact of direct and indirect biological control mechanisms. This study results show that both M. polyspora and C. globosum were able to inhibit, to a different extent, all the pathogens’ growth in the dual culture assay, suggesting a mechanism of biocontrol involving competition for nutrients and space. M. polyspora, based on the culture filtrate antifungal activity assay, was found to exert its inhibition on all the pathogens thanks also to an antibiosis mechanism through the release of diffusible compounds. Moreover, M. polyspora culture filtrate resulted to be particularly effective especially against B. basicola whose growth was completely inhibited; furthermore, its high inhibition effect against this species was also observed in the dual culture for volatile antimicrobial compounds assay, suggesting that M. polyspora antagonism against B. basicola occurs through multiple or mixed mechanisms. Therefore, based on this preliminary study’s results M. polyspora and C. globosum are promising biocontrol agents of three fungal phytopathogens of economical and agronomical relevance, and consequently species of interest for further studies in this area aimed at validating their potential as antagonists in in vivo conditions.
Finally, the last study focused on evaluating M. polyspora and C. globosum bioremediation potentialities towards glyphosate. Addressing, in particular, their ability to tolerate and utilize glyphosate as a nutritional source and eventually degrade it. Indeed, glyphosate is the most commonly used herbicide worldwide. Its improper use during recent decades has resulted in glyphosate contamination of soils and waters. Fungal bioremediation is an environmentally friendly, cost effective, and feasible solution to glyphosate contamination in soils. In this study, M. polyspora and C. globosum together with other 16 saprotrophic fungal strains were screened in vitro for their ability to tolerate and eventually utilize Roundup at two different concentrations (1 mM and 10 mM) in different cultural conditions as a nutritional source. M. polyspora and C. globosum were found to be tolerant to RoundUp, a glyphosate-based herbicide, only at the concentration of 1 mM, while a concentration of 10 mM completely inhibited their growth. Moreover, Purpureocillium lilacinum was further screened to evaluate the ability to break down and utilize glyphosate as a P source in a liquid medium. The dose-response effect for Roundup, and the difference in toxicity between pure glyphosate and Roundup were also studied. This study’s results highlight the ability of several strains to tolerate 1 mM and 10 mM Roundup and to utilize it as a nutritional source. P. lilacinum was reported for the first time for its ability to degrade glyphosate to a considerable extent (80%) and to utilize it as a P source, without showing dose-dependent negative effects on growth. Pure glyphosate was found to be more toxic than Roundup for P. lilacinum. Our results showed that pure glyphosate toxicity can be only partially addressed by the pH decrease determined in the culture medium. In conclusion, despite the strains studied in this thesis were not able to degrade glyphosate, experimental results emphasized the in vitro noteworthy potential in glyphosate degradation of P. lilacinum, another fungal strain of biotechnological interest.
In conclusion, based on this thesis’ results M. polyspora and C. globosum showed promising potentialities as plant growth promoting fungi and should be further studied as bioresources for eventual biotechnological applications towards a sustainable agriculture.
This thesis, in addition to the studies addressing its aim, includes also an additional section composed of three published papers dealing with topics regarding fungal species conservation applying IUCN red-listing criteria and the biotechnological potentialities of strains preserved in the culture collection of the Fungal Biodiversity Laboratory of the Department of Environmental Biology, Sapienza University of Rome
Fungi as bioresources for remediation of HCH-contaminated soils: from microbial community-level physiological profile to selective isolation in enrichment
No full textThe interaction between human activities and global change (including persistent chemicals
pollution) poses severe threats for the soil microbiota thus reducing the provision of ecosystem
services1. In this context -, -, and -hexachlorocyclohexane (HCH) are highly persistent organic
pollutants ofglobal concern, and a severe risk for human health and ecosystem functioning.
Soil fungi, thanksto the ability to tolerate, bioaccumulate and biodegrade HCH, are important
bioresources as biobased solutions for HCH-contaminated soil remediation. The study area
was selected within the National Priority Site “Bacino del Fiume Sacco” in the Metropolitan
City of Rome (Italy). Soil cores, up to 1 m of depth, were collected from 2 plots and later
divided in topsoil (TS: 0-10 cm) and subsoil (SS: 10-100 cm) samples. The first goal was to
characterize the microbial community level physiological profile, so the soil samples were
analysed by the Biolog EcoPlateTM Technique2 to compare metabolic activities of the
communities at different depths (TS and SS). Moving on, the project focused on the fungal
fraction of the microbial community, evaluating the fungal loaddifferences between TS and
SS, through the count of the colony forming units (CFUs/dry soil weight). The CFUs results
show a higher fungal load in topsoil than that in subsoil by one order of magnitude. To isolate
fungal bioresources suitable for HCH degradation, a selective enrichment procedure with a high
concentration HCH mixture as the only carbon source, was carried out. At the end of the
procedure several species, mainly belonging to Fusarium and Alternaria genera,were isolated
and are currently preserved in the Culture Collection of the Fungal Biodiversity Laboratory
(FBL) of the Department of Environmental Biology of Sapienza University of Rome. The
isolated fungi represent useful bioresources for further studies aimed at the development of
mycoremediation application for HCH contaminated soil remediation
Fungi in action against hexachlorocyclohexane: a focus on biosurfactants from fungal biodiversity
No full textHexachlorocyclohexane (HCH) is a highly persistent organic pollutant of global concern, involving severe
risks for human health and ecosystem functioning. Mycoremediation represents a feasible nature-based
solution for the restoration of soils polluted by HCH thanks to the ability of fungi to tolerate, bioaccumulate
and degrade it. Known for its insecticidal properties of one of its isomers (γ-HCH), it has been used for a long
time in European soils and despite the ban in the Stockholm Convention, high concentrations exceeding the
threshold values have been found in many areas. One of this is the National Priority Site “Bacino del Fiume
Sacco” within the Metropolitan City of Rome that has been selected as study area. Soil cores up to 1m of depth,
divided in topsoil and subsoil samples, were collected from 2 plots. To isolate fungi able to utilize HCH as the
sole C-source, an isolation in enrichment conditions was carried out providing an high concentration of
isomers’ mixture (α-, β-, γ- and δ-HCH). A total of 49 fungal strains was isolated, mostly belonging to
Fusarium and Alternaria genera. To evaluate the ability of these fungi to produce biosurfactants, metabolites
that enhance HCH biodegradability, three tests were carried out: oil emulsification activity test, oil
displacement test and drop collapse assay. The results of the assays showed the ability of some strains to
produce biosurfactants, making them suitable candidates for further investigation
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Study of tricalcium phosphate solubilization by some soil microfungi and evaluation of their potential as efficient plant growth-promoting organisms for Glycine max
No full textThe potential of use of fungi and bacteria as biological fertilizers is widely recognized and represents a key strategy to improve the phosphorous (P) availability for crops. P is both mobilized and sequestered in soil by the interaction of biological and geochemical processes. Exchangeable P represents a short-term storage pool that can replenish the soil solution. The aims of this research were to study P solubilisation mechanisms of some selected fungal strains with different life strategies and to evaluate their potential to promote efficiently soy growth. Saprotrophic fungi play very important geoactive roles in P biogeochemical cycle, for instance by leaching minerals and solubilizing insoluble P with different mechanisms in soils. The soybean is one of the most important plant for food production worldwide. P depletion is one of the most relevant abiotic constraints that threaten soybean production. Chemical analyses with SEM/EDXA, colorimetric quantification and ICP-MS were performed to quantify TCP solubilised by fungi in liquid medium and P concentration in fungal biomass (1–6). Tested fungi were able to solubilise tricalcium phosphate (TCP) in different extents, increasing P concentration in liquid medium and in biomass. Evaluation of soy growth promotion ability and fungal-plant interactions were studied by microscopy and histological evaluation of seedlings
From biodiversity to bioresources: evaluation of potentialities in mycoremediation of fungal bioresources isolated from an Italian decommissioned military site
No full textMilitary sites, both active and decommissioned, are rarely studied and may represent a source of fungal bioresources with potential applications for the remediation of co-contaminated soils. The aims of this study were both deepening the knowledge on fungal communities of a decommissioned military site and identifying indigenous bioresources showing potentialities for downstream mycoremediation applications. The culturable fractions of soil fungal communities of an Italian decommissioned military site were isolated from six representative sampling plots. In addition, the fungal community of the rhizosphere of Plantago lanceolata was also isolated. α and β diversity indices were used to analyze biodiversity data of the isolated fungal communities. A polycyclic aromatic hydrocarbons (PAHs) enrichment microplate experiment in the presence of Zn, Pb, and Zn-Pb co-contamination was conducted, followed by in vitro functional traits screenings, to select the isolates with the best potential for future mycoremediation applications. Globally 101 taxa, accounting for a total of 546 strains, were isolated from the samples. The enrichment results highlighted several fungal species showing the ability to use PAHs as nutritional source, even in the co-presence of potentially toxic elements. Finally, the analysis of their functional traits revealed their potential for biotechnological applications in soil detoxification
Draft genome sequence of the biosurfactant producing Minimedusa polyspora FBL 503 (basidiomycota; agaricomycotina)
No full textThe soil microfungi that release biosurfactants and tolerate recalcitrant organic pollutants such as polycyclic aromatic hydrocarbons (PAHs) may be of outstanding importance for mycoremediation of polluted sites, in a cost-efficient and environmentally friendly manner. Minimedusa polyspora FBL 503 (Agaricomycetes, Cantharellales) showed characteristics with a high biotech potential. The strain FBL 503 tolerated naphthalene, phenanthrene, pyrene, each PAH at 20 mg/L, and a mix of them (1:1:1) at 60 mg/L as well as exhibited biosurfactant activity. In particular, the production of biosurfactants was carried out in yeast extract broth (10g/L) with the addition of 40g/L of olive oil. Fourteen days after inoculation, the culture medium was recovered and the production of biosurfactants was evaluated by means of the oil dispersion test. The activity of the biosurfactants found in the culture filtrate was evaluated on olive oil, diesel oil, and exhausted motor oils from a scooter and a freeze-dryer vacuum pump. The biosurfactants from FBL 503 resulted efficient, to different extent, in displacing all the tested oils.
In this context, we obtained the draft genome sequence of the strain FBL 503 with Illumina platform. The genome was assembled denovo and was used to functionally annotate M. polyspora FBL 503. We calculated the predicted genes, including genes encoding secreted CAZymes, proteases, and lipases present in the genome. Moreover, mining the genome for genes involved in secondary metabolism biosynthesis resulted in the identification of biosynthetic gene clusters. The genes encoding enzymes for the enhanced solubility of PAHs such as biosurfactants and lipases, which could be included in the PAH degradation pathway, were found in the M. polyspora FBL 503 genome. Our genomic data on FBL 503 are a basis for transcriptomic approaches under exposure to organic pollutants.
The INAIL-DIT (PAR 2019-2021) financially supported the genome sequencing of M. polyspora FBL 503
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