Genome sequencing of Cladophialophora exuberans, a novel candidate for bioremediation of hydrocarbon and heavy metal polluted habitats.

Nickolas Menezes da Silva, Guilherme Fonseca Reis, Flávia de Fátima Costa, Maria Eduarda Grisolia, Marlon Roger Geraldo, Bruno Paulo Rodrigues Lustosa, Bruna Jacomel Favoreto de Souza Lima, Vinicius Almir Weiss, Emanuel Maltempi de Souza, Ruoyu Li, Yinggai Song, Mariana Machado Fidelis Nascimento, Diogo Robl, Renata Rodrigues Gomes, G Sybren de Hoog, Vania Aparecida Vicente

Journal: Fungal biology 2023;127(5):1032-1042

PMID: 37142362

Full Text on Elsevier Science View on PubMed

Abstract

Cladophialophora exuberans is a filamentous fungus related to black yeasts in the order Chaetothyriales. These melanized fungi are known for their 'dual ecology', often occurring in toxic environments and also being frequently involved in human infection. Particularly Cladophialophora exuberans, C. immunda, C. psammophila, and Exophiala mesophila have been described with a pronounced ability to degrade aromatic compounds and xenobiotic volatiles, such as benzene, toluene, ethyl-benzene, and xylene, and are candidates for bioremediation applications. The objective of the present study is the sequencing, assembly, and description of the whole genome of C. exuberans focusing on genes and pathways related to carbon and toxin management, assessing the tolerance and bioremediation of lead and copper, and verifying the presence of genes for metal homeostasis. Genomic evaluations were carried out through a comparison with sibling species including clinical and environmental strains. Tolerance of metals was evaluated via a microdilution method establishing minimum inhibitory (MIC) and fungicidal concentrations (MFC), and agar diffusion assays. Heavy metal bioremediation was evaluated via graphite furnace atomic absorption spectroscopy (GFAAS). The final assembly of C. exuberans comprised 661 contigs, with genome size of 38.10 Mb, coverage of 89.9X and a GC content of 50.8%. In addition, inhibition of growth was shown at concentrations of 1250 ppm for copper and at 625 ppm for lead, using the MIC method. In the agar tests, the strain grew at 2500 ppm of copper and lead. In GFAAS tests, uptake capacities were observed of 89.2% and 95.7% for copper and lead, respectively, after 21 experimental days. This study enabled the annotation of genes involved in heavy metal homeostasis and also contributed to a better understanding of the mechanisms used in tolerance of and adaptation to extreme conditions.

Address: Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Paraná, Brazil; Center of Expertise in Mycology of Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, the Netherlands.; Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Paraná, Brazil.; Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil.; Center of Expertise in Mycology of Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, the Netherlands; Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil.; Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, Paraná, Brazil.; Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China; Research Center for Medical Mycology, Peking University, Beijing, China; National Clinical Research Center for Skin and Immune Diseases, Beijing, China.; Center of Expertise in Mycology of Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, the Netherlands; Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China; Research Center for Medical Mycology, Peking University, Beijing, China; National Clinical Research Center for Skin and Immune Diseases, Beijing, China.; Biotechnology Graduate Program, Federal University of Technology of Paraná, Ponta Grossa, Paraná, Brazil.; Microbiology, Immunology and Parasitology Department, Federal University of Santa Catarina, Florianopolis, Santa Catarina, Brazil.; Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Paraná, Brazil; Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil. Electronic address: [email protected].

DOI: 10.1016/j.funbio.2023.03.003

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MeSH Terms: Humans, Biodegradation, Environmental, Benzene, Copper, Agar, Ascomycota, Hydrocarbons, Metals, Heavy, Ecosystem