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Black Yeast Genomes Assembled from Plastic Fabric Metagenomes Reveal an Abundance of Hydrocarbon Degradation Genes. Microbiol Resour Announc 2021; 10:10/14/e01459-20. [PMID: 33833030 PMCID: PMC8032472 DOI: 10.1128/mra.01459-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the assembly and annotation of 10 different black yeast genomes from microbiome metagenomic data derived from biofouled plastic fabrics. The draft genomes are estimated to be 9 to 33.2 Mb, with 357 to 5,108 contigs and G+C contents of 43.9% to 57.4%, and they harbor multiple genes for hydrocarbon adaptation and degradation.
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Serra I, Capusoni C, Molinari F, Musso L, Pellegrino L, Compagno C. Marine Microorganisms for Biocatalysis: Selective Hydrolysis of Nitriles with a Salt-Resistant Strain of Meyerozyma guilliermondii. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:229-239. [PMID: 30684102 DOI: 10.1007/s10126-019-09875-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 01/07/2019] [Indexed: 06/09/2023]
Abstract
A screening among marine yeasts was carried out for nitrile hydrolyzing activity. Meyerozyma guilliermondii LM2 (UBOCC-A-214008) was able to efficiently grow on benzonitrile and cyclohexanecarbonitrile (CECN) as sole nitrogen sources. A two-step one-pot method for obtaining cells of M. guilliermondii LM2 (UBOCC-A-214008) endowed with high nitrilase activity was established; the resulting whole cells converted different nitriles with high molar conversions and showed interesting enantioselectivity toward racemic substrates. Nitrilase from M. guilliermondii LM2 (UBOCC-A-214008) displayed high activity on aromatic substrates, but also arylaliphatic and aliphatic substrates were accepted. Salt-resistant M. guilliermondii LM2 (UBOCC-A-214008) was used in media with different salinity, being highly active up to 1.5 M NaCl concentration. Finally, hydrolysis of nitriles was efficiently performed using a bioprocess (yeast growth and biotransformation with resting cells) entirely carried out in seawater.
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Affiliation(s)
- Immacolata Serra
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Via L. Mangiagalli 25, Milan, Italy.
| | - Claudia Capusoni
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Via L. Mangiagalli 25, Milan, Italy
| | - Francesco Molinari
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Via L. Mangiagalli 25, Milan, Italy
| | - Loana Musso
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Via L. Mangiagalli 25, Milan, Italy
| | - Luisa Pellegrino
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Via L. Mangiagalli 25, Milan, Italy
| | - Concetta Compagno
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Via L. Mangiagalli 25, Milan, Italy
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Martínková L. Nitrile metabolism in fungi: A review of its key enzymes nitrilases with focus on their biotechnological impact. FUNGAL BIOL REV 2019. [DOI: 10.1016/j.fbr.2018.11.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Zhang C, Sirijovski N, Adler L, Ferrari BC. Exophiala macquariensis sp. nov., a cold adapted black yeast species recovered from a hydrocarbon contaminated sub-Antarctic soil. Fungal Biol 2019; 123:151-158. [DOI: 10.1016/j.funbio.2018.11.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/22/2018] [Accepted: 11/26/2018] [Indexed: 11/29/2022]
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Attili-Angelis D, Duarte APM, Pagnocca FC, Nagamoto NS, de Vries M, Stielow JB, de Hoog GS. Novel Phialophora species from leaf-cutting ants (tribe Attini). FUNGAL DIVERS 2014. [DOI: 10.1007/s13225-013-0275-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Cladophialophora abundans, a novel species of Chaetothyriales isolated from the natural environment. Mycol Prog 2013. [DOI: 10.1007/s11557-013-0924-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Gong JS, Lu ZM, Li H, Zhou ZM, Shi JS, Xu ZH. Metagenomic technology and genome mining: emerging areas for exploring novel nitrilases. Appl Microbiol Biotechnol 2013; 97:6603-11. [PMID: 23801047 DOI: 10.1007/s00253-013-4932-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 04/15/2013] [Accepted: 04/15/2013] [Indexed: 11/28/2022]
Abstract
Nitrilase is one of the most important members in the nitrilase superfamily and it is widely used for bioproduction of commodity chemicals and pharmaceutical intermediates as well as bioremediation of nitrile-contaminated wastes. However, its application was hindered by several limitations. Searching for new nitrilases and improving their application performances are the driving force for researchers. Genetic data resources in various databases are quite rich in post-genomic era. Besides, more than 99 % of microbes in the environment are unculturable. Metagenomic technology and genome mining are thus becoming burgeoning areas and provide unprecedented opportunities for searching more useful novel nitrilases due to the abundance of already existing but unexplored gene resources, namely uncharacterized genome information in the database and unculturable microbes in the natural environment. These techniques seem to be innovative and highly efficient. This study reviews the current status and future directions of metagenomics and genome mining in nitrilase exploration. Moreover, it discussed their utilization in coping with the challenges for nitrilase application. In the next several years, with the rapid development of nitrile biocatalysis, these two techniques would be bound to attract increasing attentions and even become a dominant trend for finding more novel nitrilases. Also, this review would provide guidance for exploitation of other commercially important enzymes.
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Affiliation(s)
- Jin-Song Gong
- School of Pharmaceutical Science, Jiangnan University, Wuxi, 214122, People's Republic of China
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Isola D, Selbmann L, de Hoog GS, Fenice M, Onofri S, Prenafeta-Boldú FX, Zucconi L. Isolation and screening of black fungi as degraders of volatile aromatic hydrocarbons. Mycopathologia 2013; 175:369-79. [PMID: 23475324 DOI: 10.1007/s11046-013-9635-2] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 01/25/2013] [Indexed: 11/26/2022]
Abstract
Black fungi reported as degraders of volatile aromatic compounds were isolated from hydrocarbon-polluted sites and indoor environments. Several of the species encountered are known opportunistic pathogens or are closely related to pathogenic species causing severe mycoses, among which are neurological infections in immunocompetent individuals. Given the scale of the problem of environmental pollution and the phylogenetic relation of aromate-degrading black fungi with pathogenic siblings, it is of great interest to select strains able to mineralize these substrates efficiently without any risk for public health. Fifty-six black strains were obtained from human-made environments rich in hydrocarbons (gasoline car tanks, washing machine soap dispensers) after enrichment with some phenolic intermediates of toluene and styrene fungal metabolism. Based on ITS sequencing identification, the majority of the obtained isolates were members of the genus Exophiala. Exophiala xenobiotica was found to be the dominant black yeast present in the car gasoline tanks. A higher biodiversity, with three Exophiala species, was found in soap dispensers of washing machines. Strains obtained were screened using a 2,6-dichlorophenol-indophenol (DCPIP) assay, optimized for black fungi, to assess their potential ability to degrade toluene. Seven out of twenty strains tested were able to use toluene as carbon source.
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Affiliation(s)
- Daniela Isola
- Università degli Studi della Tuscia, Largo dell'Università s.n.c., 01100, Viterbo, Italy.
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de Oliveira JR, Mizuno CM, Seleghim MHR, Javaroti DCD, Rezende MOO, Landgraf MD, Sette LD, Porto ALM. Biotransformation of phenylacetonitrile to 2-hydroxyphenylacetic acid by marine fungi. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2013; 15:97-103. [PMID: 22790719 DOI: 10.1007/s10126-012-9464-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2011] [Accepted: 05/11/2012] [Indexed: 06/01/2023]
Abstract
Marine fungi belonging to the genera Aspergillus, Penicillium, Cladosporium, and Bionectria catalyzed the biotransformation of phenylacetonitrile to 2-hydroxyphenylacetic acid. Eight marine fungi, selected and cultured with phenylacetonitrile in liquid mineral medium, catalyzed it quantitative biotransformation to 2-hydroxyphenylacetic acid. In this study, the nitrile group was firstly hydrolysed, and then, the aromatic ring was hydroxylated, producing 2-hydroxyphenylacetic acid with 51 % yield isolated. In addition, the 4-fluorophenylacetonitrile was exclusively biotransformed to 4-fluorophenylacetic acid by Aspergillus sydowii Ce19 (yield = 51 %). The enzymatic biotransformation of nitriles is not trivial, and here, we describe an efficient method for production of phenylacetic acids in mild conditions.
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Affiliation(s)
- Julieta Rangel de Oliveira
- Instituto de Química de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense 400, CEP 13560-970, CP 780, São Carlos, SP, Brazil
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Gong JS, Lu ZM, Li H, Shi JS, Zhou ZM, Xu ZH. Nitrilases in nitrile biocatalysis: recent progress and forthcoming research. Microb Cell Fact 2012; 11:142. [PMID: 23106943 PMCID: PMC3537687 DOI: 10.1186/1475-2859-11-142] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 10/23/2012] [Indexed: 12/27/2022] Open
Abstract
Over the past decades, nitrilases have drawn considerable attention because of their application in nitrile degradation as prominent biocatalysts. Nitrilases are derived from bacteria, filamentous fungi, yeasts, and plants. In-depth investigations on their natural sources function mechanisms, enzyme structure, screening pathways, and biocatalytic properties have been conducted. Moreover, the immobilization, purification, gene cloning and modifications of nitrilase have been dwelt upon. Some nitrilases are used commercially as biofactories for carboxylic acids production, waste treatment, and surface modification. This critical review summarizes the current status of nitrilase research, and discusses a number of challenges and significant attempts in its further development. Nitrilase is a significant and promising biocatalyst for catalytic applications.
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Affiliation(s)
- Jin-Song Gong
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, People's Republic of China
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He YC, Zhou Q, Ma CL, Cai ZQ, Wang LQ, Zhao XY, Chen Q, Gao DZ, Zheng M, Wang XD, Sun Q. Biosynthesis of benzoylformic acid from benzoyl cyanide by a newly isolated Rhodococcus sp. CCZU10-1 in toluene-water biphasic system. BIORESOURCE TECHNOLOGY 2012; 115:88-95. [PMID: 22033370 DOI: 10.1016/j.biortech.2011.09.084] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2011] [Revised: 09/17/2011] [Accepted: 09/20/2011] [Indexed: 05/31/2023]
Abstract
Benzoylformic acid was synthesized from the hydrolysis of benzoyl cyanide by a newly isolated Rhodococcus sp. CCZU10-1. In this study, an aqueous-toluene biphasic system was developed for highly efficient production of benzoylformic acid from the hydrolysis of benzoyl cyanide. In the aqueous-toluene biphasic system, the phase volume ratio, buffer pH and reaction temperature were optimized. Using fed-batch method, a total of 932 mM benzoylformic acid accumulated in the reaction mixture after the 10th feed. Moreover, enzymatic hydrolysis of benzoyl cyanide using calcium alginate entrapped resting cells was carried out in the aqueous-toluene biphasic system, and efficient biocatalyst recycling was achieved as a result of cell immobilization in calcium alginate, with a product-to-biocatalyst ratio of 14.26g benzoylformic acid g(-1) dry cell weight (DCW) cell after 20 cycles of repeated use.
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Affiliation(s)
- Yu-Cai He
- Laboratory of Biochemical Engineering, College of Pharmaceutical and Life Sciences, Changzhou University, Changzhou 213164, China.
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Waterborne Exophiala species causing disease in cold-blooded animals. Persoonia - Molecular Phylogeny and Evolution of Fungi 2011; 27:46-72. [PMID: 22403476 PMCID: PMC3251318 DOI: 10.3767/003158511x614258] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Accepted: 10/16/2011] [Indexed: 11/25/2022]
Abstract
The majority of mesophilic waterborne species of the black yeast genus Exophiala (Chaetothyriales) belong to a single clade judging from SSU rDNA data. Most taxa are also found to cause cutaneous or disseminated infections in cold-blooded, water animals, occasionally reaching epidemic proportions. Hosts are mainly fish, frogs, toads, turtles or crabs, all sharing smooth, moist or mucous skins and waterborne or amphibian lifestyles; occasionally superficial infections in humans are noted. Cold-blooded animals with strictly terrestrial life styles, such as reptiles and birds are missing. It is concluded that animals with moist skins, i.e. those being waterborne and those possessing sweat glands, are more susceptible to black yeast infection. Melanin and the ability to assimilate alkylbenzenes are purported general virulence factors. Thermotolerance influences the choice of host. Exophiala species in ocean water mostly have maximum growth temperatures below 30 °C, whereas those able to grow until 33(−36) °C are found in shallow waters and occasionally on humans. Tissue responses vary with the phylogenetic position of the host, the lower animals showing poor granulome formation. Species circumscriptions have been determined by multilocus analyses involving partial ITS, TEF1, BT2 and ACT1.
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Zhang Z, Gao L, Zhao C, Qiu J. Nitrile- and amide-hydrolysing activity of acrylic acid-tolerant yeast Trichosporon asahii ZZB-1. ANN MICROBIOL 2011. [DOI: 10.1007/s13213-011-0298-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Seyedmousavi S, Badali H, Chlebicki A, Zhao J, Prenafeta-Boldú FX, De Hoog GS. Exophiala sideris, a novel black yeast isolated from environments polluted with toxic alkyl benzenes and arsenic. Fungal Biol 2011; 115:1030-7. [PMID: 21944215 DOI: 10.1016/j.funbio.2011.06.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 05/13/2011] [Accepted: 06/06/2011] [Indexed: 11/19/2022]
Abstract
A novel species of the black yeast genus Exophiala (order Chaetothyriales) is described. Strains were repeatedly obtained by enriching samples of wild berries from different plants, guano-rich soil and from oak railway ties treated with arsenic creosote under a toluene-rich atmosphere. An identical strain was encountered in a closed arsenic mine polluted by alkyl benzenes. Its potential use for purposes of bioremediation is discussed.
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Affiliation(s)
- Seyedmojtaba Seyedmousavi
- Department of Medical Mycology and Parasitology, Faculty of Medicine and Medical Sciences, Islamic Azad University, Ardabil Branch Ardabil, Iran
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Isolation, Identification, and Culture Optimization of a Novel Glycinonitrile-Hydrolyzing Fungus—Fusarium oxysporum H3. Appl Biochem Biotechnol 2011; 165:963-77. [DOI: 10.1007/s12010-011-9312-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 06/19/2011] [Indexed: 10/18/2022]
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Abstract
The biota of black fungi in humid indoor environments was established using a protocol that consisted of non-selective and selective isolation procedures. In total, 113 samples were taken from bathrooms of residences in The Netherlands, Germany and Austria. Samples were processed either (i) directly by culturing on agar media, or (ii) by pre-incubating samples for enrichment in mineral solutions with perlite granules under constant toluene atmosphere for three months. Dilutions from the latter were then cultured and incubated as were those directly plated to agar media. Black colonies were selected and identified by sequencing the rDNA Internal Transcribed Spacer (ITS) region. Twenty-eight strains of black fungi were found in 26 positive samples without enrichment, and 42 strains were isolated from 38 positive samples after enrichment in toluene. The great majority of black fungal species were members of the order Chaetothyriales, which is the main order of melanized human opportunistic pathogens. Cladosporium species (Capnodiales) were the most frequent isolates when no enrichment was applied, as opposed to Exophiala species (Chaetothyriales) with enrichment. The enrichment method provides insight into a fungal biota commonly occurring in homes which has previously been overlooked. Several species have been previously known only from cutaneous infections and could suggest that bathrooms are a likely reservoir of these fungi.
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Affiliation(s)
- X Lian
- Centraalbureau voor Schimmelcultures Fungal Biodiversity Centre, Utrecht, The Netherlands
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