A Genomic and Transcriptomic Study on the DDT-Resistant Trichoderma hamatum FBL 587: First Genetic Data into Mycoremediation Strategies for DDT-Polluted Sites.

Trichoderma hamatum FBL 587 isolated from DDT-contaminated agricultural soils stands out as a remarkable strain with DDT-resistance and the ability to enhance DDT degradation process in soil. Here, whole genome sequencing and RNA-Seq studies for T. hamatum FBL 587 under exposure to DDT were performed. In the 38.9 Mb-genome of T. hamatum FBL 587, 10,944 protein-coding genes were predicted and annotated, including those of relevance to mycoremediation such as production of secondary metabolites and siderophores. The genome-scale transcriptional responses of T. hamatum FBL 587 to DDT exposure showed 1706 upregulated genes, some of which were putatively involved in the cellular translocation and degradation of DDT. With regards to DDT removal capacity, it was found upregulation of metabolizing enzymes such as P450s, and potentially of downstream DDT-transforming enzymes such as epoxide hydrolases, FAD-dependent monooxygenases, glycosyl- and glutathione-transferases. Based on transcriptional responses, the DDT degradation pathway could include transmembrane transporters of DDT, antioxidant enzymes for oxidative stress due to DDT exposure, as well as lipases and biosurfactants for the enhanced solubility of DDT. Our study provides the first genomic and transcriptomic data on T. hamatum FBL 587 under exposure to DDT, which are a base for a better understanding of mycoremediation strategies for DDT-polluted sites.

Bioremediation of Dichlorodiphenyltrichloroethane (DDT)-Contaminated Agricultural Soils: Potential of Two Autochthonous Saprotrophic Fungal Strains.

DDT (dichlorodiphenyltrichloroethane) was used worldwide as an organochlorine insecticide to control agricultural pests and vectors of several insect-borne human diseases. It was banned in most industrialized countries; however, due to its persistence in the environment, DDT residues remain in environmental compartments, becoming long-term sources of exposure. To identify and select fungal species suitable for bioremediation of DDT-contaminated sites, soil samples were collected from DDT-contaminated agricultural soils in Poland, and 38 fungal taxa among 18 genera were isolated. Two of them, Trichoderma hamatum FBL 587 and Rhizopus arrhizus FBL 578, were tested for tolerance in the presence of 1-mg liter-1 DDT concentration by using two indices based on fungal growth rate and biomass production (the tolerance indices Rt:Rc and TI), showing a clear tolerance to DDT. The two selected strains were studied to evaluate catabolic versatility on 95 carbon sources with or without DDT by using the Phenotype MicroArray system and to investigate the induced oxidative stress responses. The two strains were able to use most of the substrates provided, resulting in both high metabolic versatility and ecological functionality in the use of carbon sources, despite the presence of DDT. The activation of specific metabolic responses with species-dependent antioxidant enzymes to cope with the induced chemical stress has been hypothesized, since the presence of DDT promoted a higher formation of reactive oxygen species in fungal cells than the controls. The tested fungi represent attractive potential candidates for bioremediation of DDT-contaminated soil and are worthy of further investigations.IMPORTANCE The spread and environmental accumulation of DDT over the years represent not only a threat to human health and ecological security but also a major challenge because of the complex chemical processes and technologies required for remediation. Saprotrophic fungi, isolated from contaminated sites, hold promise for their bioremediation potential toward toxic organic compounds, since they might provide an environment-friendly solution to contamination. Once we verified the high tolerance of autochthonous fungal strains to high concentrations of DDT, we showed how fungi from different phyla demonstrate a high metabolic versatility in the presence of DDT. The isolates showed the singular ability to keep their functionality, despite the DDT-induced production of reactive oxygen species.

Understanding fungal potential in the mitigation of contaminated areas in the Czech Republic: tolerance, biotransformation of hexachlorocyclohexane (HCH) and oxidative stress analysis.

The study of the soil microbial community represents an important step in better understanding the environmental context. Therefore, biological characterisation and physicochemical integration are keys when defining contaminated sites. Fungi play a fundamental role in the soil, by providing and supporting ecological services for ecosystems and human wellbeing. In this research, 52 soil fungal taxa were isolated from in situ pilot reactors installed to a contaminated site in Czech Republic with a high concentration of hexachlorocyclohexane (HCH). Among the identified isolates, 12 strains were selected to evaluate their tolerance to different isomers of HCH by using specific indices (Rt:Rc; T.I.) and to test their potential in xenobiotic biotransformation. Most of the selected taxa was not significantly affected by exposure to HCH, underlining the elevated tolerance of all the tested fungal taxa, and different metabolic intermediates of HCH dechlorination were observed. The oxidative stress responses to HCH for two selected species, Penicillium simplicissimum and Trichoderma harzianum, were investigated in order to explore their toxic responses and to evaluate their potential functioning in bioremediation of contaminated environments. This research suggests that the isolated fungal species may provide opportunities for new eco-friendly, integrated and cost-effective solutions for environmental management and remediation, considering their efficient adaptation to stressful conditions.

Victoriomyces antarcticus gen. nov., sp. nov., a distinct evolutionary lineage of the Cephalothecaceae (Ascomycota) based on sequence-based phylogeny and morphology.

In this study, we propose a new genus, Victoriomyces, with a new species, Victoriomyces antarcticus, isolated from soil samples collected in Victoria Land, Antarctica. To determine its taxonomic status and evolutionary relationships, phylogenetic analysis was performed on DNA sequences from the nuclear 18S rRNA, 28S rRNA and the second largest subunit of RNA polymerase II (RPB2) genes. Victoriomyces antarcticus constitutes one well-supported distinct lineage within the Cephalothecaceae (family incertae sedis in Sordariomycetes), in which the only recognised asexual morphs belong to the genus Phialemonium and to Acremonium thermophilum. Victoriomyces antarcticus can be clearly distinguished from these taxa by means of DNA sequence analysis and its morphological traits that consist in having a Metarhizium-like asexual morph, dark red-coloured disk-like structures, immature bodies and the production of an intense red pigment in the growth media. Finally, we inferred the divergence time of V. antarcticus and the Cephalothecaceae using Bayesian analysis and secondary calibration. The holotype of V. antarcticus is FBL 165. The ex-type strain has been deposited as MUT 3686T and CCF 6158T. An additional strain of the species is FBL 577. The MycoBank number is MB 823713 for the genus and MB 823714 for the species.

Metabolic synergies in the biotransformation of organic and metallic toxic compounds by a saprotrophic soil fungus.

The saprotrophic fungus Penicillium griseofulvum was chosen as model organism to study responses to a mixture of hexachlorocyclohexane (HCH) isomers (α-HCH, ß-HCH, γ-HCH, δ-HCH) and potentially toxic metals (vanadium, lead) in solid and liquid media. The P. griseofulvum FBL 500 strain was isolated from polluted soil containing high concentrations of HCH isomers and potentially toxic elements (Pb, V). Experiments were performed in order to analyse the tolerance/resistance of this fungus to xenobiotics and to shed further light on fungal potential in inorganic and organic biotransformations. The aim was to examine the ecological and bioremedial potential of this fungus verifying the presence of mechanisms that allow it to transform HCH isomers and metals under different extreme test conditions. To our knowledge, this work is the first to provide evidence on the biotransformation of HCH mixtures, in combination with toxic metals, by a saprotrophic non-white-rot fungus and on the metabolic synergies involved.

Saprotrophic soil fungi to improve phosphorus solubilisation and release: In vitro abilities of several species.

Modern agriculture is dependent on phosphate rock (PR), which is a nonrenewable resource. Improvement of phosphorus (P) availability for crops in agricultural soils represents a key strategy to slow down the depletion of PR. The aim of this study was to identify potential P biofertilisers among saprotrophic fungal species. We tested 30 fungal strains belonging to 28 taxa (4 Zygomycota and 24 Ascomycota) and with different life strategies. The study showed that many saprotrophic fungi have the ability to mobilise P from insoluble forms according to a variety of mechanisms. Our results expand the pool of P solubilising fungal species, also suggesting a new solubilisation index and shedding light on parameters that could be basic in the selection of efficient soil P-biofertilisers fungi. Rhizopus stolonifer var. stolonifer, Aspergillus niger and Alternaria alternata were found to be the best performing strains in terms of amounts of TCP solubilisation.

Phenotype MicroArray™ system in the study of fungal functional diversity and catabolic versatility.

Fungi cover a range of important ecological functions associated with nutrient and carbon cycling in leaf litter and soil. As a result, research on existing relationships between fungal functional diversity, decomposition rates and competition is of key interest. Indeed, availability of nutrients in soil is largely the consequence of organic matter degradation dynamics. The Biolog® Phenotype MicroArrays™ (PM) system allows for the testing of fungi against many different carbon sources at any one time. The use and potential of the PM system as a tool for studying niche overlap and catabolic versatility of saprotrophic fungi is discussed here, and examples of its application are provided.

Wood-inhabiting fungi in southern Italy forest stands: morphogroups, vegetation types and decay classes.

The authors conducted an ecological study of forests subjected to varying management. The aim of the study was to extend and integrate, within a multivariate context, knowledge of how saproxylic fungal communities behave along altitudinal/vegetational gradients in response to the varying features and quality of coarse woody debris (CWD). The intra-annual seasonal monitoring of saproxylic fungi, based on sporocarp inventories, was used to investigate saproxylic fungi in relation to vegetation types and management categories. We analyzed fungal species occurrence, recorded according to the presence/absence and frequency of sporocarps, on the basis of the harvest season, of coarse woody debris decay classes as well as other environmental and ecological variables. Two-way cluster analysis, DCA and Spearman's rank correlations, for indirect gradient analysis, were performed to identify any patterns of seasonality and decay. Most of the species were found on CWD in an intermediate decay stage. The first DCA axis revealed the vegetational/microclimate gradient as the main driver of fungal community composition, while the second axis corresponded to a strong gradient of CWD decay classes.

Biotransformation of ß-hexachlorocyclohexane by the saprotrophic soil fungus Penicillium griseofulvum.

ß-Hexachlorocyclohexane (ß-HCH) is a persistent organic pollutant (POP) of global concern with potentially toxic effects on humans and ecosystems. Fungal tolerance and biotransformation of toxic substances hold considerable promise in environmental remediation technologies as many fungi can tolerate extreme environmental conditions and possess efficient extracellular degradative enzymes with relatively non-specific activities. In this research, we have investigated the potential of a saprotrophic soil fungus, Penicillium griseofulvum Dierckx, isolated from soils with high concentrations of isomers of hexachlorocyclohexane, to biotransform ß-HCH, the most recalcitrant isomer to microbial activity. The growth kinetics of the fungus were characterized after growth in stirred liquid Czapek-Dox medium. It was found that P. griseofulvum was able to grow in the presence of 1 mg L(-1) ß-HCH and in stressful nutritional conditions at different concentrations of sucrose in the medium (0 and 5 g L(-1)). The effects of ß-HCH and the toluene, used as a solvent for ß-HCH addition, on P. griseofulvum were investigated by means of a Phenotype MicroArray™ technique, which suggested the activation of certain metabolic pathways as a response to oxidative stress due to the presence of the xenobiotics. Gas chromatographic analysis of ß-HCH concentration confirmed biodegradation of the isomer with a minimum value of ß-HCH residual concentration of 18.6%. The formation of benzoic acid derivatives as dead-end products of ß-HCH biotransformation was observed and this could arise from a possible biodegradation pathway for ß-HCH with important connections to fungal secondary metabolism.

Microbiological Analysis of Surfaces of Leonardo Da Vinci's Atlantic Codex: Biodeterioration Risk.

Following the discovery of discoloration on some pages of the Atlantic Codex (AC) of Leonardo da Vinci kept in the Biblioteca Ambrosiana in Milan, some investigations have been carried out to verify the presence of microorganisms, such as bacteria and fungi. To verify the presence of microorganisms a noninvasive method of sampling has been used that was efficient and allowed us to highlight the microbial facies of the material that was examined using conventional microbiological techniques. The microclimatic conditions in the storage room as well as the water content of the volume were also assessed. The combined observations allowed the conclusion that the discoloration of suspected biological origin on some pages of AC is not related to the presence or current attack of microbial agents.

Species-abundance distribution patterns of soil fungi: contribution to the ecological understanding of their response to experimental fire in Mediterranean maquis (southern Italy).

Experimental fires, of both low and high intensity, were lit during summer 2000 and the following 2 y in the Castel Volturno Nature Reserve, southern Italy. Soil samples were collected Jul 2000-Jul 2002 to analyze the soil fungal community dynamics. Species abundance distribution patterns (geometric, logarithmic, log normal, broken-stick) were compared. We plotted datasets with information both on species richness and abundance for total, xerotolerant and heat-stimulated soil microfungi. The xerotolerant fungi conformed to a broken-stick model for both the low- and high intensity fires at 7 and 84 d after the fire; their distribution subsequently followed logarithmic models in the 2 y following the fire. The distribution of the heat-stimulated fungi changed from broken-stick to logarithmic models and eventually to a log-normal model during the post-fire recovery. Xerotolerant and, to a far greater extent, heat-stimulated soil fungi acquire an important functional role following soil water stress and/or fire disturbance; these disturbances let them occupy unsaturated habitats and become increasingly abundant over time.

Aspergillus affinis sp. nov., a novel ochratoxin A-producing Aspergillus species (section Circumdati) isolated from decomposing leaves.

Two ochratoxin A (OTA)-producing Aspergillus isolates, recently collected from submerged riparian decomposing leaves in Italy, were found to have a similar morphology to Aspergillus cretensis (subgenus Circumdati, section Circumdati). However, marked differences emerged between these two novel isolates and A. cretensis as the former displayed different colony features and had larger vesicles, metulae, phialides and conidia, as well as a distinct sclerotial form and size. In order to determine the taxonomic status and to infer the evolutionary relationships of these two morphologically identical isolates, a molecular phylogenetic analysis was performed on all the officially recognized lineages in the section Circumdati. The DNA sequences and the deduced amino acid residues from the nuclear loci were analysed. Both rRNA and protein coding genes were assessed, which are widely used to differentiate taxa belonging to genus Aspergillus at various evolutionary levels. The 5.8S rDNA gene and internal transcribed spacers (ITS), the D1/D2 domains of the 28S rDNA gene, a region of the tubulin beta chain gene (benA) and part of the calmodulin gene (cmd) were amplified by PCR and then sequenced. The analysis of the rRNA regions and of the benA and cmd sequence data indicated that the two isogenic isolates belonged to a genetically distinct OTA-producing species of the genus Aspergillus. The isolates are proposed as representing a novel species, Aspergillus affinis sp. nov., with the type strain ATCC MYA-4773T=CBS 129190=417). Phylogenetically, A. affinis sp. nov. appeared to be very closely related to A. cretensis, from which it could be distinguished by means of a morphological trait analysis.

Penicillium simile sp. nov. revealed by morphological and phylogenetic analysis.

The morphology of three phenetically identical Penicillium isolates, collected from the bioaerosol in a restoration laboratory in Italy, displayed macro- and microscopic characteristics that were similar though not completely ascribable to Penicillium raistrickii. For this reason, a phylogenetic approach based on DNA sequencing analysis was performed to establish both the taxonomic status and the evolutionary relationships of these three peculiar isolates in relation to previously described species of the genus Penicillium. We used four nuclear loci (both rRNA and protein coding genes) that have previously proved useful for the molecular investigation of taxa belonging to the genus Penicillium at various evolutionary levels. The internal transcribed spacer region (ITS1-5.8S-ITS2), domains D1 and D2 of the 28S rDNA, a region of the tubulin beta chain gene (benA) and part of the calmodulin gene (cmd) were amplified by PCR and sequenced. Analysis of the rRNA genes and of the benA and cmd sequence data indicates the presence of three isogenic isolates belonging to a genetically distinct species of the genus Penicillium, here described and named Penicillium simile sp. nov. (ATCC MYA-4591(T)  = CBS 129191(T)). This novel species is phylogenetically different from P. raistrickii and other related species of the genus Penicillium (e.g. Penicillium scabrosum), from which it can be distinguished on the basis of morphological trait analysis.

Effects of elevation, slope position and livestock exclusion on microfungi isolated from soils of Mediterranean grasslands.

The fungal communities of grassland soils in Spain from four sites at different elevations were studied. Each site contained grazed and fenced ungrazed plots. These plots were situated in two slope positions (upper and lower zones). The ungrazed plots, fenced off 6 y before the sampling, were part of a study of global change that simulates conditions of rural abandonment, which is widespread in Iberian countries, since Spain joined the European Union. We analyzed the structure of the soil fungi communities and its relationship with herbaceous vegetation. The distribution of 207 taxa of fungi revealed that the elevation was the main factor of fungal variability; the effect of grazing and slope position were associated with less variability. Although a halt in grazing resulted in the accumulation of standing plants and plant litter in these ecosystems, it had relatively little effect on soil microfungi and appeared to be related mainly to growing conditions affected by that accumulation.

[Effectiveness of the maintenance operations on the air conditioning systems of a university building in relation to the microbiological quality of the air indoor]. / Efficacia degli interventi di manutenzione sugli impianti di condizionamento di un edificio universitario in relazione alla qualità microbiologica dell'aria indoor.

The microbiological quality of the air indoor is influenced from various factors and one of the most important is represented from the maintenance of the conditioning systems. In this study it has been estimated the effectiveness of an intervention of cleaning and maintenance on the systems of conditioning of an university building executing sampling before and after such intervention. The two results were confronted and it is observed as the maintenance of the air conditioners has influenced on the quality of the air indoor.