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Anthropogenic disturbance on natural ecosystems is growing in frequency and magnitude affecting all ecosystems components. Understanding the response of different types of biocoenosis to human disturbance is urgently needed and it can be achieved by adopting a metacommunity framework. With the aid of advanced molecular techniques, we investigated sediment communities of Fungi, Bacteria and Archaea in four Italian show caves, aiming to disentangle the effects induced by tourism on their diversity and to highlight changes in the driving forces that shape their community composition. We modelled diversity measures against proxies of tourism pressure. With this approach we demonstrate that the cave tourism has a direct effect on the community of Bacteria and an indirect influence on Fungi and Archaea. By analysing the main driving forces influencing the community composition of the three microbial groups, we highlighted that stochastic factors override dispersal-related processes and environmental selection in show caves compared to undisturbed areas. Thanks to this approach, we provide new perspectives on the dynamics of microbial communities under human disturbance suggesting that a proper understanding of the underlying selective mechanisms requires a comprehensive and multi-taxonomic approach.
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Microbiota , Turismo , Humanos , Cuevas/microbiología , Bacterias , Archaea , HongosRESUMEN
To date, the highly adapted cave microbial communities are challenged by the expanding anthropization of these subterranean habitats. Although recent advances in characterizing show-caves microbiome composition and functionality, the anthropic effect on promoting the establishment, or reducing the presence of specific microbial guilds has never been studied in detail. This work aims to investigate the whole microbiome (Fungi, Algae, Bacteria and Archaea) of four Italian show-caves, displaying different environmental and geo-morphological conditions and one recently discovered natural cave to highlight potential human-induced microbial traits alterations. Results indicate how show-caves share common microbial traits in contrast to the natural one; the first are characterized by microorganisms related to outdoor environment and/or capable of exploiting extra inputs of organic matter eventually supplied by tourist flows (i.e. Chaetomium and Phoma for fungi and Pseudomonas for bacteria). Yet, variation in microalgae assemblage composition was reported in show-caves, probably related to the effect of the artificial lighting. This study provides insights into the potential microbiome cave contamination by human-related bacteria (e.g. Lactobacillus and Staphylococcus) and commensal/opportunistic human associated fungi (e.g. Candida) and dermatophytes. This work is critical to untangle caves microbiome towards management and conservation of these fragile ecosystems.
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Cuevas , Microbiota , Humanos , Cuevas/microbiología , Efectos Antropogénicos , Bacterias , Archaea , HongosRESUMEN
Six strains of black meristematic fungi were isolated from Antarctic soils, gasoline car tanks and from the marine alga Flabellia petiolata. These fungi were characterized by morphological, physiological and phylogenetic analyses. According to the maximum-likelihood analysis reconstructed with ITS and LSU sequences, these strains belonged to the genus Knufia. Knufia obscura sp. nov. (holotype CBS 148926) and Knufia victoriae sp. nov. (holotype CBS 149015) are proposed as two novel species and descriptions of their morphological, physiological and phylogenetic features are presented. Based on the maximum-likelihood analyses, K. obscura was closely related to Knufia hypolithi (99â% bootstrap support), while K. victoriae clustered in the clade of Knufia cryptophialidica and Knufia perfecta (93â% bootstrap support). Knufia victoriae, recorded in Antarctic soil samples, had a psychrophilic behaviour, with optimal growth between 10 and 15 °C and no growth recorded at 20 °C. Knufia obscura, from a gasoline car tank and algae, displayed optimal growth between 20 and 25 °C and was more tolerant to salinity than K. victoriae.
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Ácidos Grasos , Gasolina , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Ambientes Extremos , Ácidos Grasos/química , Filogenia , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , SueloRESUMEN
Fungi are an essential component of marine ecosystems, although little is known about their global distribution and underwater diversity, especially in sediments. Microplastics (MPs) are widespread contaminants worldwide and threaten the organisms present in the oceans. In this study, we investigated the fungal abundance and diversity in sediments, as well as the MPs, of three sites with different anthropogenic impacts in the Mediterranean Sea: the harbor of Livorno, the marine protected area "Secche della Meloria"; and an intermediate point, respectively. A total of 1526 isolates were cultured and identified using a polyphasic approach. For many of the fungal species this is the first record in a marine environment. A comparison with the mycobiota associated with the sediments and MPs underlined a "substrate specificity", highlighting the complexity of MP-associated fungal assemblages, potentially leading to altered microbial activities and hence changes in ecosystem functions. A further driving force that acts on the fungal communities associated with sediments and MPs is sampling sites with different anthropogenic impacts.
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The order Lulworthiales, with its sole family Lulworthiaceae, consists of strictly marine genera found on a wide range of substrates such as seagrasses, seaweeds, and seafoam. Twenty-one unidentified Lulworthiales were isolated in previous surveys aimed at broadening our understanding of the biodiversity hosted in the Mediterranean Sea. Here, these organisms, mostly found in association with Posidonia oceanica and with submerged woods, were examined using thorough multi-locus phylogenetic analyses and morphological observations. Maximum-likelihood and Bayesian phylogeny based on nrITS, nrSSU, nrLSU, and four protein-coding genes led to the introduction of three novel species of the genus Paralulworthia: P. candida, P. elbensis, and P. mediterranea. Once again, the marine environment is a confirmed huge reservoir of novel fungal lineages with an under-investigated biotechnological potential waiting to be explored.
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Polyethylene (PE) is the most abundant non-degradable plastic waste, posing a constant and serious threat to the whole ecosystem. In the present study, the fungal community of plastic wastes contaminating a landfill soil has been studied. After 6 months of enrichment, 95 fungi were isolated, mostly belonging to the Ascomycota phylum. They were screened under in vitro condition: most of fungi (97%) were capable of growing in the presence of PE powder (5-10 g L-1) as sole carbon source. Fusarium strains better tolerated high concentration of PE. Up to 13 strains were chosen for further degradation trails, where the process was monitored by respirometry tests and by observing changes in PE chemical and physical structure by FTIR analysis and SEM images. Major results were observed for Fusarium oxysporum, Fusarium falciforme and Purpureocillum lilacinum, as they caused strong oxidation phenomena and changes in the PE film morphology. Results suggested that the initial oxidation mechanisms targeted first the methyl terminal groups. Changes in the infrared spectra were strongly strain-dependent, denoting the activation of different degradation pathways. Through the SEM analysis, the actual damages provoked by fungi were observed, including swellings, pits and furrows, bumps and partial exfoliations. Considering the rising concern about plastic disposal worldwide, the ability of these fungi to colonize PE and utilize it as carbon source is of great interest, as no pretreatments and pro-oxidant stimulants were needed.
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Ecosistema , Polietileno , Biodegradación Ambiental , Hongos , FusariumRESUMEN
The polyphyletic group of black fungi within the Ascomycota (Arthoniomycetes, Dothideomycetes, and Eurotiomycetes) is ubiquitous in natural and anthropogenic habitats. Partly because of their dark, melanin-based pigmentation, black fungi are resistant to stresses including UV- and ionizing-radiation, heat and desiccation, toxic metals, and organic pollutants. Consequently, they are amongst the most stunning extremophiles and poly-extreme-tolerant organisms on Earth. Even though ca. 60 black fungal genomes have been sequenced to date, [mostly in the family Herpotrichiellaceae (Eurotiomycetes)], the class Dothideomycetes that hosts the largest majority of extremophiles has only been sparsely sampled. By sequencing up to 92 species that will become reference genomes, the "Shed light in The daRk lineagES of the fungal tree of life" (STRES) project will cover a broad collection of black fungal diversity spread throughout the Fungal Tree of Life. Interestingly, the STRES project will focus on mostly unsampled genera that display different ecologies and life-styles (e.g., ant- and lichen-associated fungi, rock-inhabiting fungi, etc.). With a resequencing strategy of 10- to 15-fold depth coverage of up to ~550 strains, numerous new reference genomes will be established. To identify metabolites and functional processes, these new genomic resources will be enriched with metabolomics analyses coupled with transcriptomics experiments on selected species under various stress conditions (salinity, dryness, UV radiation, oligotrophy). The data acquired will serve as a reference and foundation for establishing an encyclopedic database for fungal metagenomics as well as the biology, evolution, and ecology of the fungi in extreme environments.
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Mono- and polycyclic aromatic hydrocarbons (PAHs) are widespread and recalcitrant pollutants that threaten both environmental and human health. By exploiting the powerful enzymatic machinery of fungi, mycoremediation in contaminated sites aims at removing a wide range of pollutants in a cost-efficient and environmentally friendly manner. Next-generation sequencing (NGS) techniques are powerful tools for understanding the molecular basis of biotransformation of PAHs by selected fungal strains, allowing genome mining to identify genetic features of biotechnological value. Trichoderma lixii MUT3171, isolated from a historically PAH-contaminated soil in Italy, can grow on phenanthrene, as a sole carbon source. Here, we report the draft genome sequence of T. lixii MUT3171 obtained with high-throughput sequencing method. The genome of T. lixii MUT3171 was compared with other 14 Trichoderma genomes, highlighting both shared and unique features that can shed a light on the biotransformation of PAHs. Moreover, the genes potentially involved in the production of important biosurfactants and bioactive molecules have been investigated. The gene repertoire of T. lixii MUT3171 indicates a high degrading potential and provides hints on putative survival strategies in a polluted environment.
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Fungi are widely distributed in the Oceans, interact with other organisms and play roles that range from pathogenic to mutualistic. The present work focuses on the characterization of the cultivable mycobiota associated with the seagrass Posidonia oceanica (L.) Delile collected off the Elba Island (Italy). We identified 102 taxa (mainly Ascomycota) by the mean of a polyphasic approach. Leaves, rhizomes, roots and matte were characterized by unique mycobiota revealing a "plant-part-specificity." The comparison with the mycobiota associated with the green alga Flabellia petiolata and the brown alga Padina pavonica underlined a "substrate specificity." Indeed, despite being part of the same phytocoenosis, these photosynthetic organisms recruit different fungal communities. The mycobiota seems to be necessary for the host's defense and protection, playing, in this way, remarkable ecological roles. Among the 61 species detected in association with P. oceanica (including two species belonging to the newly introduced genus Paralulworthia), 37 were reported for the first time from the Mediterranean Sea.
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Elbamycellarosea sp. nov., introduced in the new genus Elbamycella, was collected in the Mediterranean Sea in association with the seagrass Posidoniaoceanica and with the brown alga Padinapavonica. The affiliation of the new taxon to the family Juncigenaceae is supported by both morphology and phylogenetic inference based on a combined nrSSU and nrLSU sequence dataset. Maximum-likelihood and Bayesian phylogeny proved Elbamycella gen. nov. as a distinct genus within Juncigenaceae. The new genus has been compared with closely related genera and is characterised by a unique suite of characters, such as ascospores with polar appendages and peculiar shape and dimension of ascomata and asci.
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Two ascomycete strains were isolated from creosote-contaminated railway sleeper wood. By using a polyphasic approach combining morpho-physiological observations of colonies with molecular tools, the strains were identified as Fusarium oxysporum Schltdl. (IBPPM 543, MUT 4558; GenBank accession no. MG593980) and Lecanicillium aphanocladii Zare & W. Gams (IBPPM 542, MUT 242; GenBank accession no. MG593981). Both strains degraded hazardous pollutants, including polycyclic aromatic hydrocarbons, anthraquinone-type dyes, and oil. Oil was better degraded by F. oxysporum, but the aromatic compounds were better degraded by L. aphanocladii. With both strains, the degradation products of anthracene, phenanthrene, and fluorene were 9,10-anthraquinone, 9,10-phenanthrenequinone, and 9-fluorenone, respectively. During pollutant degradation, F. oxysporum and L. aphanocladii produced an emulsifying compound(s). Both fungi produced extracellular Mn-peroxidases, enzymes possibly involved in the fungal degradation of the pollutants. This is the first report on the ability of L. aphanocladii to degrade four-ring PAHs, anthraquinone-type dyes, and oil, with the simultaneous production of an extracellular Mn-peroxidase
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Asunto(s)
Ascomicetos/aislamiento & purificación , Contaminantes Ambientales/metabolismo , Hypocreales/aislamiento & purificación , Aceites/metabolismo , Madera/microbiología , Microbiología Ambiental , Hypocreales/metabolismo , Hidrocarburos Policíclicos Aromáticos/metabolismo , Biotransformación , Enzimas/análisis , Hypocreales/clasificaciónRESUMEN
Two ascomycete strains were isolated from creosote-contaminated railway sleeper wood. By using a polyphasic approach combining morpho-physiological observations of colonies with molecular tools, the strains were identified as Fusarium oxysporum Schltdl. (IBPPM 543, MUT 4558; GenBank accession no. MG593980) and Lecanicillium aphanocladii Zare & W. Gams (IBPPM 542, MUT 242; GenBank accession no. MG593981). Both strains degraded hazardous pollutants, including polycyclic aromatic hydrocarbons, anthraquinone-type dyes, and oil. Oil was better degraded by F. oxysporum, but the aromatic compounds were better degraded by L. aphanocladii. With both strains, the degradation products of anthracene, phenanthrene, and fluorene were 9,10-anthraquinone, 9,10-phenanthrenequinone, and 9-fluorenone, respectively. During pollutant degradation, F. oxysporum and L. aphanocladii produced an emulsifying compound(s). Both fungi produced extracellular Mn-peroxidases, enzymes possibly involved in the fungal degradation of the pollutants. This is the first report on the ability of L. aphanocladii to degrade four-ring PAHs, anthraquinone-type dyes, and oil, with the simultaneous production of an extracellular Mn-peroxidase.
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Contaminantes Ambientales/metabolismo , Hypocreales/aislamiento & purificación , Hypocreales/metabolismo , Aceites/metabolismo , Hidrocarburos Policíclicos Aromáticos/metabolismo , Biotransformación , Microbiología Ambiental , Enzimas/análisis , Hypocreales/clasificación , Hypocreales/enzimología , Madera/microbiologíaRESUMEN
Viable and metabolically active fungi in toxic mixed liquors, treating landfill leachates and municipal wastewaters, were identified by culture depending methods. A selective culture medium consisting of wastewater and agar (WA) restrained fungi that could be randomly present (94% of the 51 taxa retrieved on WA were sample-specific), overcoming the problem of fast growing fungi or mycoparasite fungi. Moreover, WA allowed the isolation of fungi with a possible role in the degradation of pollutants typically present in the two wastewaters. Phoma medicaginis var. medicaginis, Chaetomium globosum, and Geotrichum candidum were mainly found in municipal wastewater, whereas Pseudallescheria boydii, Scedosporium apiospermum, Aspergillus pseudodeflectus, and Scopulariopsis brevicaulis were typical of landfill leachate.
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Hongos/aislamiento & purificación , Aguas Residuales/microbiología , Contaminantes Químicos del Agua/análisis , Agar/química , Ascomicetos/aislamiento & purificación , Aspergillus/aislamiento & purificación , Chaetomium/aislamiento & purificación , Recuento de Colonia Microbiana , Monitoreo del Ambiente , Hongos/clasificación , Geotrichum/aislamiento & purificación , Concentración de Iones de Hidrógeno , Pseudallescheria/aislamiento & purificación , Scedosporium/aislamiento & purificación , Scopulariopsis/aislamiento & purificaciónRESUMEN
Marine fungi are part of the huge and understudied biodiversity hosted in the sea. To broaden the knowledge on fungi inhabiting the Mediterranean Sea and their role in sponge holobiont, three sponges namely Aplysina cavernicola, Crambe crambe and Phorbas tenacior were collected in Villefranche sur Mer, (France) at about 25 m depth. The fungal communities associated with the sponges were isolated using different techniques to increase the numbers of fungi isolated. All fungi were identified to species level giving rise to 19, 13 and 3 species for P. tenacior, A. cavernicola and C. crambe, respectively. Of note, 35.7% and 50.0% of the species detected were either reported for the first time in the marine environment or in association with sponges. The mini-satellite analysis confirmed the uniqueness of the mycobiota of each sponge, leading to think that the sponge, with its metabolome, may shape the microbial community.
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Crambe (Esponja)/microbiología , Microbiota , Animales , Biodiversidad , Hongos/aislamiento & purificación , Mar Mediterráneo , Filogenia , Poríferos/microbiología , Agua de Mar/microbiologíaRESUMEN
Tannins are secondary metabolites that are widely distributed in the plant kingdom. They act as growth inhibitors for many microorganisms: they are released upon microbial attack, helping to fight infection in plant tissues. Extraction of tannins from plants is an active industrial sector with several applications, including oenology, animal feeding, mining, the chemical industry, and, in particular, the tanning industry. However, tannins are also considered very recalcitrant pollutants in wastewater of diverse origin. The ability to grow on plant substrates rich in tannins and on industrial tannin preparations is usually considered typical of some species of fungi. These organisms are able to tolerate the toxicity of tannins thanks to the production of enzymes that transform or degrade these substrates, mainly through hydrolysis and oxidation. Filamentous fungi capable of degrading tannins could have a strong environmental impact as bioremediation agents, in particular in the treatment of tanning wastewaters.
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Hongos/efectos de los fármacos , Hongos/metabolismo , Taninos/química , Taninos/metabolismo , Eliminación de Residuos Líquidos/métodos , Biotransformación , Proteínas Fúngicas/metabolismo , Lacasa/metabolismo , Taninos/farmacologíaRESUMEN
Tannins are a complex family of polyphenolic compounds, widely distributed in the plant kingdom where they act as growth inhibitors towards many microorganisms including bacteria, yeasts, and fungi. Tannins are one of the major components of tannery wastewaters and may cause serious environmental pollution. In the present study, four different tannins (the hydrolysable chestnut ellagitannin and tara gallotannin and the condensed quebracho and wattle tannins) were characterized from a mycological point of view with the aim of selecting fungal strains capable of growing in the presence of high tannin concentration and thus potentially useful in industrial biotransformations of these compounds or in the bioremediation of tannery wastewaters. A total of 125 isolates of filamentous fungi belonging to 10 species and four genera (Aspergillus, Paecilomyces, Penicillium, and Talaromyces) were isolated from the tannin industrial preparations. Miniaturized biotransformation tests were set up with 10 fungal strains and the high-performance liquid chromatography (HPLC) analysis pointed out a strong activity of all the tested fungi on both chestnut and tara tannins. Two strains (Aspergillus tubingensis MUT 990 and Paecilomyces variotii MUT 1125), tested against a real tannery wastewater, were particularly efficient in chemical oxygen demand (COD) and tannin removal (> 60%), with a detoxification above 74%. These results indicate that these fungi are potentially exploitable in the treatment of tannery wastewaters.
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Hongos/metabolismo , Microbiología Industrial/métodos , Taninos/metabolismo , Aguas Residuales/microbiología , Purificación del Agua/métodos , Biodegradación Ambiental , Biotransformación , Taninos/análisis , Aguas Residuales/químicaRESUMEN
Fungi are known to be present in the activated sludge of wastewater treatment plants (WWTP). Their study should be at the base of an overall vision of the plant effectiveness and of effluents sanitary impact. Moreover, it could be fundamental for the implementation of successful bioaugmentation strategies aimed at the removal of recalcitrant or toxic compounds. This is one of the first studies on the cultivable autochthonous mycoflora present in the mixed liquors of two WWTP treating either vegetable or chromium tannery effluents. All samples showed a risk associated with potential pathogens or toxigenic species and high ecotoxicity (Lepidium sativum and Raphidocelis subcapitata were the most sensitive organisms). Diverse fungal populations developed, depending on the origin of the samples (63% of the 102 identified taxa were sample-specific). The use of a fungistatic was determinant for the isolation and, thus, for the identification of sample-specific species with a lower growth rate. The incubation temperature also affected the mycoflora composition, even though at lower extent. A selective medium, consisting of agarised wastewater, allowed isolating fungi with a biodegradation potential. Pseudallescheria boydii/Scedosporium apiospermum species complex was ubiquitously dominant, indicating a possible role in the degradation of pollutants in both WWTP. Other species, i.e. Trichoderma spp., Trematosphaeria grisea, Geotrichum candidum, Lichtheimia corymbifera, Acremonium furcatum, Penicillium simplicissimum, Penicillium dangeardii, Fusarium solani, Scopulariopsis brevicaulis potentially could be involved in the degradation of specific pollutants of vegetable or chromium tannery wastewaters. However, several of these fungi are potential pathogens and their application, for an in situ treatment, must be carefully evaluated.
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Biodegradación Ambiental , Residuos Industriales/análisis , Curtiembre , Eliminación de Residuos Líquidos/métodos , Cromo , Ecotoxicología , Hongos/metabolismo , Aguas del Alcantarillado , Aguas ResidualesRESUMEN
Algae-inhabiting marine fungi represent a taxonomically and ecologically interesting group of microorganisms still largely neglected, especially in temperate regions. The aim of this study was to isolate and to identify the culturable mycobiota associated with Flabellia petiolata, a green alga frequently retrieved in the Mediterranean basin. Twenty algal thalli were collected from two different sampling sites in the Mediterranean Sea (Elba Island, Italy). A polyphasic approach showed the presence of a relevant alga-associated mycobiota with 64 taxa identified. The fungal isolates belonged mainly to Ascomycota (61 taxa), while only three Basidiomycota were detected. The phylogenetic position of sterile mycelia and cryptic taxa, inferred on the basis of LSU partial region, highlighted the presence of putative new phylogenetic lineages within Dothideomycetes and Sordariomycetes. This work represents the first quali-quantitative analysis of the culturable mycobiota associated to a green alga in the Mediterranean Sea.
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Chlorophyta/microbiología , Hongos/aislamiento & purificación , Teorema de Bayes , Hongos/clasificación , Mar Mediterráneo , FilogeniaRESUMEN
Bioremediation of marine environment could be the response to oil spills threats. In the present study the fungal community from a Mediterranean marine site chronically interested by oil spills was investigated. Sixty-seven taxa were isolated from water sample and 17 from sediments; for many of the identified species is the first report in seawater and sediments, respectively. The growth of 25% of the fungal isolates was stimulated by crude oil as sole carbon source. Four strains were selected to screen hydrocarbons degradation using the 2,6-dichlorophenol indophenol (DCPIP) colorimetric assay. A. terreus MUT 271, T. harzianum MUT 290 and P. citreonigrum MUT 267 displayed a high decolorization percentage (DP≥68%). A. terreus displayed also the highest decreases of hydrocarbons compounds (up to 40%) quantified by gas-chromatography analysis. These results suggest that the selected fungi could represent potential bioremediation agents with strong crude oil degradative capabilities.
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Hongos/clasificación , Contaminación por Petróleo , Agua de Mar/microbiología , Biodegradación Ambiental , Hongos/aislamiento & purificación , Hidrocarburos/metabolismo , Región Mediterránea , Petróleo/metabolismoRESUMEN
Rhizosphere and root-associated microbiota are crucial in determining plant health and in increasing productivity of agricultural crops. To date, research has mainly focused on the bacterial dimension of the microbiota. However, interest in the mycobiota is increasing, since fungi play a key role in soil ecosystems. We examined the effect of plant genotype, soil, and of Fusarium oxysporum f. sp. lycopersici (Fol) on the cultivable component of rhizosphere and root-associated mycobiota of tomato. Resistant and susceptible varieties were cultivated on two different soils (A and B), under glasshouse conditions. Isolated fungi were identified by morphological and molecular approaches. Differences were found between the rhizosphere and the roots, which in general displayed a lower number of species. The structure of the mycobiota was significantly affected by the soil type in the rhizosphere as well as by the plant genotype within the roots (NPERMANOVA, p < 0.05). The addition of Fol changed the community structure, particularly in soil A, where Penicillium spp. and Fusarium spp. were the dominant responding fungi. Overall, the results indicated that i) soil type and plant genotype affect the fungal communities; ii) plant roots select few species from the rhizosphere; and iii) the fungal community structure is influenced by Fol.