Two distinct non-ribosomal peptide synthetase-independent siderophore synthetase gene clusters identified in Armillaria and other species in the Physalacriaceae

Siderophores are important for ferric iron solubilization, sequestration, transportation, and storage, especially under iron-limiting conditions such as aerobic conditions at high pH. Siderophores are mainly produced by non-ribosomal peptide synthetase-dependent siderophore pathway, non-ribosomal peptide synthetase-independent siderophore synthetase pathway, or the hybrid non-ribosomal peptide synthetases/non-ribosomal peptide synthetases-independent siderophore pathway. Outcompeting or inhibition of plant pathogens, alteration of host defense mechanisms, and alteration of plant-fungal interactions have been associated with fungal siderophores. To understand these mechanisms in fungi, studies have been conducted on siderophore biosynthesis by ascomycetes with limited focus on the basidiomycetes. Armillaria includes several species that are pathogens of woody plants and trees important to agriculture, horticulture, and forestry. The aim of this study was to investigate the presence of non-ribosomal peptide synthetases-independent siderophore synthetase gene cluster(s) in genomes of Armillaria species using a comparative genomics approach. Iron-dependent growth and siderophore biosynthesis in strains of selected Armillaria spp. were also evaluated in vitro. Two distinct non-ribosomal peptide synthetases-independent siderophore synthetase gene clusters were identified in all the genomes. All non-ribosomal peptide synthetases-independent siderophore synthetase genes identified putatively encode Type A' non-ribosomal peptide synthetases-independent siderophore synthetases, most of which have IucA_IucC and FhuF-like transporter domains at their N- and C-terminals, respectively. The effect of iron on culture growth varied among the strains studied. Bioassays using the CAS assay on selected Armillaria spp. revealed in vitro siderophore biosynthesis by all strains irrespective of added FeCl3 concentration. This study highlights some of the tools that Armillaria species allocate to iron homeostasis. The information generated from this study may in future aid in developing molecular based methods to control these phytopathogens.

Insight Into the Molecular Mechanisms Underpinning the Mycoremediation of Multiple Metals by Proteomic Technique

We investigated the fungus Aspergillus fumigatus PD-18 responses when subjected to the multimetal combination (Total Cr, Cd2+, Cu2+, Ni2+, Pb2+, and Zn2+) in synthetic composite media. To understand how multimetal stress impacts fungal cells at the molecular level, the cellular response of A. fumigatus PD-18 to 30 mg/L multimetal stress (5 mg/L of each heavy metal) was determined by proteomics. The comparative fungal proteomics displayed the remarkable inherent intracellular and extracellular mechanism of metal resistance and tolerance potential of A. fumigatus PD-18. This study reported 2,238 proteins of which 434 proteins were exclusively expressed in multimetal extracts. The most predominant functional class expressed was for cellular processing and signaling. The type of proteins and the number of proteins that were upregulated due to various stress tolerance mechanisms were post-translational modification, protein turnover, and chaperones (42); translation, ribosomal structure, and biogenesis (60); and intracellular trafficking, secretion, and vesicular transport (18). In addition, free radical scavenging antioxidant proteins, such as superoxide dismutase, were upregulated upto 3.45-fold and transporter systems, such as protein transport (SEC31), upto 3.31-fold to combat the oxidative stress caused by the multiple metals. Also, protein–protein interaction network analysis revealed that cytochrome c oxidase and 60S ribosomal protein played key roles to detoxify the multimetal. To the best of our knowledge, this study of A. fumigatus PD-18 provides valuable insights toward the growing research in comprehending the metal microbe interactions in the presence of multimetal. This will facilitate in development of novel molecular markers for contaminant bioremediation.

Biochemical and Metabolomic Responses of Antarctic Bacterium Planococcus sp. O5 Induced by Copper Ion

Heavy metal pollution in the Antarctic has gone beyond our imagination. Copper toxicity is a selective pressure on Planococcus sp. O5. We observed relatively broad tolerance in the polar bacterium. The heavy metal resistance pattern is Pb2+ > Cu2+ > Cd2+ > Hg2+ > Zn2+. In the study, we combined biochemical and metabolomics approaches to investigate the Cu2+ adaptation mechanisms of the Antarctic bacterium. Biochemical analysis revealed that copper treatment elevated the activity of antioxidants and enzymes, maintaining the bacterial redox state balance and normal cell division and growth. Metabolomics analysis demonstrated that fatty acids, amino acids, and carbohydrates played dominant roles in copper stress adaptation. The findings suggested that the adaptive mechanisms of strain O5 to copper stress included protein synthesis and repair, accumulation of organic permeable substances, up-regulation of energy metabolism, and the formation of fatty acids.

Biosorption of Copper in Swine Manure Using Aspergillus and Yeast: Characterization and Its Microbial Diversity Study

Dietary copper supplementation in the feed of piglets generally exceeds 250-800 mg/kg, where a higher quantity (>250 mg/kg) can promote growth and improve feed conversion. Despite the reported positive effects, 90% of copper is excreted and can accumulate and pollute the soil. Data indicate that fungi have a biosorptive capacity for copper. Thus, the objectives of the present experiment were to study the effects of adding different strains of fungi on the biosorptive capacity for copper in swine manure and to evaluate potential effects on microbiota profiles. Aspergillus niger (AN), Aspergillus oryzae (AO), and Saccharomyces cerevisiae (SC) were selected, and each added 0.4% into swine manure, which contain 250 mg/kg of copper. The incubations lasted for 29 days, and biosorption parameters were analyzed on the 8th (D8), 15th (D15), 22nd (D22), and 29th (D29) day. Results showed that after biosorption, temperature was 18.47-18.77°C; pH was 6.33-6.91; and content of aflatoxin B1, ochratoxin A, and deoxynivalenol were low. In addition, residual copper concentration with AN was the lowest on D15, D22, and D29. The copper biosorption rate was also highest with AN, averaging 84.85% on D29. Biosorption values for AO reached 81.12% and for SC were lower than 80%. Illumina sequencing of 16S and ITS rRNA gene revealed that fungal treatments reduced the diversity and richness of fungal abundance, but had no effect on bacterial abundance. Unknown_Marinilabiliaceae, Proteiniphilum, Tissierella, and Curvibacter were the dominant bacteria, while Aspergillus and Trichoderma were the dominant fungi. However, the added strain of S. cerevisiae was observed to be lower than the dominant fungi, which contained less than 0.05%. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment predicted via PICRUSt2 that there were bacterial genes potentially related to various aspects of metabolism and environmental information processing. Overall, data indicated that Aspergillus can provide microbial materials for adsorption of copper.

Insights into nanomycoremediation: Secretomics and mycogenic biopolymer nanocomposites for heavy metal detoxification

Our environment thrives on the subtle balance achieved by the forever cyclical nature of building and rebuilding life through natural processes. Fungi, being the evident armor of bioremediation, is the indispensable element of the soil food web, contribute to be the nature's most dynamic arsenal with non-specific enzymes like peroxidase (POX), glutathione peroxidase (GPx), catalase (CAT), superoxide dismutase (SOD), non-enzymatic compounds like thiol (-SH) groups and non-protein compounds such as glutathione (GSH) and metallothionein (MT). Recently, the area of nanomycoremediation has been gaining momentum as a powerful tool for environmental clean-up strategies with its ability to detoxify heavy metals with its unique characteristics to adapt mechanisms such as biosorption, bioconversion, and biodegradation to harmless end products. The insight into the elaborate secretomic processes provides us with huge opportunities for creating a magnificent living bioremediation apparatus. This review discusses the scope and recent advances in the lesser understood area, nanomycoremediation, the state-of-the-art, innovative, cost-effective and promising tool for detoxification of heavy metal pollutants and focuses on the metabolic capabilities and secretomics with nanobiotechnological interventions.

Bioremediation mechanism and potential of copper by actively growing fungus Trichoderma lixii CR700 isolated from electroplating wastewater

Present study investigated the Cu²⁺ removal potential of Trichoderma lixii CR700, isolated from enormously heavy metal polluted electroplating wastewater. In the batch study, actively growing CR700 was able to remove 84.6% of Cu²⁺ at the concentration 10 mg/L of Cu²⁺ within 120 h after incubation and the accumulated and surface adsorbed amount of Cu was 0.51 and 0.47 mg/g of dry biomass respectively. T. lixii CR700 also showed efficient Cu²⁺ removal potential in the pH ranges from 5.0 to 8.0, in the presence of other co-occurring contaminant such as heavy metal, anions and metabolic inhibitor as well from real tannery wastewater. Alteration on cell surface of Cu²⁺ treated mycelia of T. lixii CR700 was analyzed using scanning electron microscope. Fourier transform infrared spectroscopic analysis was performed to identify the role of surface functional group in Cu²⁺ adsorption which revealed that COO^─ functional group lead Cu²⁺ adsorption onto the surface of T. lixii CR700. Thus, T. lixii CR700 uses simultaneous surface sorption and accumulation mechanism in Cu²⁺ removal and can be potentially applied for bioremediation of Cu²⁺ contaminated wastewater in ecofriendly, safe and sustainable way.

Metabolomic and secretomic approach to the resistance features of the fungus Aspergillus niger IOC 4687 to copper stress

Metabolomic and secretomic analyses of Aspergillus niger IOC 4687 indicated the features of resistance of this strain to copper stress. To investigate the metabolites produced under oxidative stress conditions, gas chromatography-mass spectrometry analysis was performed. The secretome principal component analysis results showed that mannitol could be the main metabolite responsible for conferring resistance to the fungus, and gluconic acid is the possible cause of copper desorption because of its chelating ability. The meta-analysis of the metabolome of A. niger IOC 4687 indicated that a low concentration of sorbitol and ribonolactone during growth may be an indicator of oxidative stress.

Dynamic proteomic analysis of Phanerochaete chrysosporium under copper stress

The model white rot fungus Phanerochaete chrysosporium is frequently preferred for heavy metal accumulation studies due to its high resistance to heavy metals, including copper (Cu). Here, the response of P. chrysosporium under Cu stress at different time points was investigated for the first time by a detailed proteomic analysis using 2DE MALDI-TOF/MS and nanoLC-MS/MS techniques. A total of 123 Cu-responsive protein spots were determined using 2DE approach, and 104 of them were corresponded to 73 distinct open reading frames (ORFs). Of identified ones, 88 spots were over-, and 16 spots were underrepresented. The majority of these proteins showed to the strongest response at 8th h of Cu exposure. Using nanoLC-MS/MS analysis, a total of 167 differentially produced proteins were identified from Cu-exposed cultures after enrichment of the membrane proteins followed by SILAC. Seventy four, 66, and 69 overrepresented, and 56, 71, and 64 underrepresented proteins were identified at 2 h, 4 h, and 8 h of Cu exposure, respectively. The bioinformatic analysis of these proteins revealed that intracellular trafficking proteins such as Ran GTPase and a p24 family protein, and certain proteins involved in posttranslational modification, protein turnover and folding were Cu-responsive. Three important transcription factors (TFs), NAC, BTF3, and homeobox TFs, 40S and 60S ribosomal proteins, chaperones such as Hsp26/Hsp42 and mortalin, as well as 20S proteasome, 14-3-3 proteins and Hsp90 involve in Cu-stress response of P. chrysosporium. Moreover, certain elements of translation machinery, the proteins related with aspartate, methionine, and pyruvate metabolisms, transketolase, and trehalase related with carbohydrate metabolism, citrate synthase, fumarase, V-ATPase, and F0F1-type ATPase playing role in energy production and conversion, transport proteins such as multidrug resistance and p24 family proteins as well as actin-related proteins involved in cytoskeleton remodeling were determined to be Cu-responsive. The present proteome analysis revealed that P. chrysosporium mainly regulates translational and posttranslational processes, certain transport processes, many metabolic pathways and cytoskeleton to overcome the Cu-induced oxidative stress.