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Microbial patterns in rumen are associated with gain of weight in beef cattle. Antonie Van Leeuwenhoek 2020; 113:1299-1312. [PMID: 32577920 DOI: 10.1007/s10482-020-01440-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/15/2020] [Indexed: 10/24/2022]
Abstract
Ruminal microorganisms play a pivotal role in cattle nutrition. The discovery of the main microbes or of a microbial community responsible for enhancing the gain of weight in beef cattle might be used in therapeutic approaches to increase animal performance and cause less environmental damages. Here, we examined the differences in bacterial and fungal composition of rumen samples of Braford heifers raised in natural grassland of the Pampa Biome in Brazil. We aimed to detect microbial patterns in the rumen that could be correlated with the gain of weight. We hypothesized that microorganisms important to digestion process are increased in animals with a higher gain of weight. The gain of weight of seventeen healthy animals was monitored for 60 days. Ruminal samples were obtained and the 16S and ITS1 genes were amplified and sequenced to identify the closest microbial relatives within the microbial communities. A predictive model based on microbes responsible for the gain of weight was build and further tested using the entire dataset., The main differential abundant microbes between groups included the bacterial taxa RFN20, Prevotella, Anaeroplasma and RF16 and the fungal taxa Aureobasidium, Cryptococcus, Sarocladium, Pleosporales and Tremellales. The predictive model detected some of these taxa associated with animals with the high gain of weight group, most of them being organisms that have been correlated to the production of substances that improve the ruminal digestion process. These findings provide new insights about cattle nutrition and suggest the use of these microbes to improve beef cattle breeding.
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Han Y, Yang T, Xu G, Li L, Liu J. Characteristics and interactions of bioaerosol microorganisms from wastewater treatment plants. JOURNAL OF HAZARDOUS MATERIALS 2020; 391:122256. [PMID: 32062341 DOI: 10.1016/j.jhazmat.2020.122256] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 01/14/2020] [Accepted: 02/07/2020] [Indexed: 05/13/2023]
Abstract
Bacteria and fungi are abundant and ubiquitous in bioaerosols from wastewater treatment plants (WWTPs). However, the specificity and interactions of bioaerosol microorganism, particularly of potential pathogens, from WWTPs are still poorly understood. In this study, we investigated 9 full-scale WWTPs in different areas of China for 3 years, and found microbial variations in bioaerosols to be associated with regions, seasons, and processes. Relative humidity, total suspended particulates, wind speed, temperature, total organic carbon, NH4+, Cl- and Ca2+ were the major factors influencing this variation, and meteorological factors were more strongly associated with the variation than chemical composition. In total, 95 and 22 potential bacterial and fungal pathogens were detected in bioaerosols, respectively. The linear discriminant analysis effect size method suggested that Serratia, Yersinia, Klebsiella, and Bacillus were discriminative genera in bioaerosols on the whole, and were also hub niches in the interactions within potential bacterial pathogens, based on network analysis. Strong co-occurrences such as Serratia-Bacillus and Staphylococcus-Candida, and co-exclusions such as Rhodotorula-Cladosporium and Pseudomonas-Candida, were found within and between potential bacterial and fungal pathogens in bioaerosols from WWTPs. This study furthers understanding of the biology and ecology of bioaerosols from WWTPs, and offers a theoretical basis for determining bioaerosol control.
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Affiliation(s)
- Yunping Han
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, PR China.
| | - Tang Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, PR China.
| | - Guangsu Xu
- School of Resources and Environmental Engineering, Ludong University, Yantai 264025, PR China.
| | - Lin Li
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, PR China.
| | - Junxin Liu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, PR China.
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103
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Hujslová M, Gryndlerová H, Bystrianský L, Hršelová H, Gryndler M. Biofilm and planktonic microbial communities in highly acidic soil (pH < 3) in the Soos National Nature Reserve, Czech Republic. Extremophiles 2020; 24:577-591. [PMID: 32449144 DOI: 10.1007/s00792-020-01177-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/07/2020] [Indexed: 10/24/2022]
Abstract
Biofilm formation is a typical life strategy used by microorganisms populating acidic water systems. The same strategy might be used by microbes in highly acidic soils that are, however, neglected in this regard. In the present study, the microbial community in such highly acidic soil in the Soos National Nature Reserve (Czech Republic) has been investigated using high-throughput DNA sequencing and the organisms associated with biofilm life mode and those preferring planktonic life were distinguished using the biofilm trap technique. Our data show the differences between biofilm and planktonic microbiota fraction, although the majority of the organisms were capable of using both life modes. The by far most abundant prokaryotic genus was Acidiphilium and fungi were identified among the most abundant eukaryotic elements in biofilm formations. On the other hand, small flagellates from diverse taxonomical groups predominated in plankton. The application of cellulose amendment as well as the depth of sampling significantly influenced the composition of the detected microbial community.
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Affiliation(s)
- Martina Hujslová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic.
| | - Hana Gryndlerová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Lukáš Bystrianský
- Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, České mládeže 8, 40096, Ústí nad Labem, Czech Republic
| | - Hana Hršelová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Milan Gryndler
- Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, České mládeže 8, 40096, Ústí nad Labem, Czech Republic
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104
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Zeng W, Zhang B, Jiang L, Liu Y, Ding S, Chen G, Liang Z. Poly(malic acid) production from liquefied corn starch by simultaneous saccharification and fermentation with a novel isolated Aureobasidium pullulans GXL-1 strain and its techno-economic analysis. BIORESOURCE TECHNOLOGY 2020; 304:122990. [PMID: 32078901 DOI: 10.1016/j.biortech.2020.122990] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 06/10/2023]
Abstract
In this study, a novel Aureobasidium pullulans GXL-1 strain without melanin secretion was isolated for efficient polymalic acid (PMA) production. The PMA produced by GXL-1 was characterized, and its molecular mass was determined to be 1.621 kDa by gel permeation chromatography. Liquefied corn starch was shown to replace glucose for PMA production by GXL-1 through simultaneous saccharification and fermentation. The PMA titer obtained from batch fermentation was up to 49.0 ± 1.6 g/L in a 10 L fermentor, and the PMA yield and productivity obtained from repeated-batch fermentation were up to 0.50 g/g and 0.34 g/L·h, respectively. Furthermore, process design and techno-economic analysis were performed at an annual output level of 5000 metric tons by SuperPro Designer. Results showed that the production cost of $2.046/kg and payback period of 6.9 years were achieved by repeated-batch fermentation; this provides an economically feasible strategy for industrial-scale production of PMA.
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Affiliation(s)
- Wei Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
| | - Bin Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
| | - Li Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
| | - Yao Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
| | - Su Ding
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
| | - Guiguang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
| | - Zhiqun Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China.
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105
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A multidomain α-glucan synthetase 2 (AmAgs2) is the key enzyme for pullulan biosynthesis in Aureobasidium melanogenum P16. Int J Biol Macromol 2020; 150:1037-1045. [DOI: 10.1016/j.ijbiomac.2019.10.108] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/10/2019] [Accepted: 10/11/2019] [Indexed: 12/23/2022]
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Gebbie L, Dam TT, Ainscough R, Palfreyman R, Cao L, Harrison M, O'Hara I, Speight R. A snapshot of microbial diversity and function in an undisturbed sugarcane bagasse pile. BMC Biotechnol 2020; 20:12. [PMID: 32111201 PMCID: PMC7049217 DOI: 10.1186/s12896-020-00609-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/24/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Sugarcane bagasse is a major source of lignocellulosic biomass, yet its economic potential is not fully realised. To add value to bagasse, processing is needed to gain access to the embodied recalcitrant biomaterials. When bagasse is stored in piles in the open for long periods it is colonised by microbes originating from the sugarcane, the soil nearby or spores in the environment. For these microorganisms to proliferate they must digest the bagasse to access carbon for growth. The microbial community in bagasse piles is thus a potential resource for the discovery of useful and novel microbes and industrial enzymes. We used culturing and metabarcoding to understand the diversity of microorganisms found in a uniquely undisturbed bagasse storage pile and screened the cultured organisms for fibre-degrading enzymes. RESULTS Samples collected from 60 to 80 cm deep in the bagasse pile showed hemicellulose and partial lignin degradation. One hundred and four microbes were cultured from different layers and included a high proportion of oleaginous yeast and biomass-degrading fungi. Overall, 70, 67, 70 and 57% of the microbes showed carboxy-methyl cellulase, xylanase, laccase and peroxidase activity, respectively. These percentages were higher in microbes selectively cultured from deep layers, with all four activities found for 44% of these organisms. Culturing and amplicon sequencing showed that there was less diversity and therefore more selection in the deeper layers, which were dominated by thermophiles and acid tolerant organisms, compared with the top of pile. Amplicon sequencing indicated that novel fungi were present in the pile. CONCLUSIONS A combination of culture-dependent and independent methods was successful in exploring the diversity in the bagasse pile. The variety of species that was found and that are known for biomass degradation shows that the bagasse pile was a valuable selective environment for the identification of new microbes and enzymes with biotechnological potential. In particular, lignin-modifying activities have not been reported previously for many of the species that were identified, suggesting future studies are warranted.
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Affiliation(s)
- Leigh Gebbie
- Queensland University of Technology, 2 George St, Brisbane, QLD, 4000, Australia
| | - Tuan Tu Dam
- Queensland University of Technology, 2 George St, Brisbane, QLD, 4000, Australia
| | - Rebecca Ainscough
- Queensland University of Technology, 2 George St, Brisbane, QLD, 4000, Australia
| | - Robin Palfreyman
- Metabolomics Australia, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Li Cao
- Queensland University of Technology, 2 George St, Brisbane, QLD, 4000, Australia
| | - Mark Harrison
- Queensland University of Technology, 2 George St, Brisbane, QLD, 4000, Australia
| | - Ian O'Hara
- Queensland University of Technology, 2 George St, Brisbane, QLD, 4000, Australia
| | - Robert Speight
- Queensland University of Technology, 2 George St, Brisbane, QLD, 4000, Australia.
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107
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A. Whitehead K, M. Liauw C, S. T. Wilson-Nieuwenhuis J, J. Slate A, Deisenroth T, Preuss A, Verran J. The effect of the surface properties of poly(methyl methacrylate) on the attachment, adhesion and retention of fungal conidia. AIMS BIOENGINEERING 2020. [DOI: 10.3934/bioeng.2020015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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108
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Cao W, Cao W, Shen F, Luo J, Yin J, Qiao C, Wan Y. Membrane-assisted β-poly(L-malic acid) production from bagasse hydrolysates by Aureobasidium pullulans ipe-1. BIORESOURCE TECHNOLOGY 2020; 295:122260. [PMID: 31654946 DOI: 10.1016/j.biortech.2019.122260] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
Membrane-assisted β-poly(L-malic acid) (PMLA) production from bagasse hydrolysates was developed. For the first time, it was found that mixing the acid and enzyme hydrolysates was unfavorable for PMLA production because too high hexose: pentose ratio and glucose concentration in the mixed sugar could inhibit the assimilation of pentose. 120 g/L sugar concentrations in the acid hydrolysate was suitable for PMLA production with 23.2 g/L PMLA and 34.7 g/L biomass. Moreover, an integrated membrane process consisting of ultrafiltration, nanofiltration and reverse osmosis membranes could concentrate sugars and adjust acetic acid concentration prior to fermentation of lignocellulosic sugars. Meanwhile, it was found that 1.46 g/L acetic acid was preferred for PMLA production from enzyme hydrolysate or sole glucose which respectively increased PMLA production and cell growth by 25.4% and 5.9% from sole glucose, while it showed no significant enhancement in PMLA production with a higher cell growth and productivity from acid hydrolysate.
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Affiliation(s)
- Weifeng Cao
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Weilei Cao
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Shen
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Jianquan Luo
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Junxiang Yin
- China National Center for Biotechnology Development, Beijing 100036, China
| | - Changsheng Qiao
- College of Bioengineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yinhua Wan
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China.
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109
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Jia SL, Ma Y, Chi Z, Liu GL, Hu Z, Chi ZM. Genome sequencing of a yeast-like fungal strain P6, a novel species of Aureobasidium spp.: insights into its taxonomy, evolution, and biotechnological potentials. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01531-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Abstract
Purpose
This study aimed to look insights into taxonomy, evolution, and biotechnological potentials of a yeast-like fungal strain P6 isolated from a mangrove ecosystem.
Methods
The genome sequencing for the yeast-like fungal strain P6 was conducted on a Hiseq sequencing platform, and the genomic characteristics and annotations were analyzed. The central metabolism and gluconate biosynthesis pathway were studied through the genome sequence data by using the GO, KOG, and KEGG databases. The secondary metabolite potentials were also evaluated.
Results
The whole genome size of the P6 strain was 25.41Mb and the G + C content of its genome was 50.69%. Totally, 6098 protein-coding genes and 264 non-coding RNA genes were predicted. The annotation results showed that the yeast-like fungal strain P6 had complete metabolic pathways of TCA cycle, EMP pathway, pentose phosphate pathway, glyoxylic acid cycle, and other central metabolic pathways. Furthermore, the inulinase activity associated with β-fructofuranosidase and high glucose oxidase activity in this strain have been demonstrated. It was found that this yeast-like fungal strain was located at root of most species of Aureobasidium spp. and at a separate cluster of all the phylogenetic trees. The P6 strain was predicted to contain three NRPS gene clusters, five type-I PKS gene clusters, and one type-I NRPS/PKS gene cluster via analysis at the antiSMASH Website. It may synthesize epichloenin A, fusaric acid, elsinochromes, and fusaridione A.
Conclusions
Based on its unique DNA sequence, taxonomic position in the phylogenetic tree and evolutional position, the yeast-like fungal strain P6 was identified as a novel species Aureobasidium hainanensis sp. nov. P6 isolate and had highly potential applications.
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110
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Ramírez-Castrillón M, Usman LM, Silva-Bedoya LM, Osorio-Cadavid E. Dominant yeasts associated to mango (Mangifera indica) and rose apple (Syzygium malaccense) fruit pulps investigated by culture-based methods. AN ACAD BRAS CIENC 2019; 91:e20190052. [PMID: 31800704 DOI: 10.1590/0001-3765201920190052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 07/02/2019] [Indexed: 05/30/2023] Open
Abstract
The biotechnological potential of yeasts associated to different habitats in Colombia has been poorly studied, especially the yeasts associated with different plant structures. Fruit pulps are interesting substrates mainly for the growth of yeast species, that can positively affect the productivity and quality of some bioeconomic species. Therefore, the objective of this study was to identify the dominant yeast species associated with mango and rose apple fruit pulps in Cali, Colombia. A total of 90 isolates were obtained, which were grouped considering their colony morphology. The D1/D2 domain of the large ribosomal RNA gene (LSU rRNA gene) or internal transcribed spacer (ITS) 1, ribosomal gene 5.8S and ITS 2 (ITS) regions of one to several representative isolates from each group was sequenced and compared with type strains for identification. The species Hanseniaspora thailandica, H. opuntiae and Clavispora lusitaniae were reported as shared by both fruits, specific for rose apple (H. uvarum, Pichia terricola, Rhodosporidiobolus ruineniae and Candida albicans), or for Mango (Meyerozyma caribbica, M. guilliermondii, C. natalensis, Aureobasidium pullulans, Pichia sp., Saturnispora diversa and C. jaroonii). Two morphotypes were not identified at the taxonomic level of species and were reported as candidates for new species, belonging to the genera Wickerhamomyces and Pichia.
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Affiliation(s)
| | - Luisa M Usman
- Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad del Valle, Calle 13, 100-00 Cali, Valle del Cauca, Colombia
| | - Lina M Silva-Bedoya
- Maestría en Ciencias Biotecnología, Universidad Nacional de Colombia, sede Medellín, Carrera 65, 59A-110 Medellín, Antioquia, Colombia
| | - Esteban Osorio-Cadavid
- Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad del Valle, Calle 13, 100-00 Cali, Valle del Cauca, Colombia
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111
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Wang X, Glawe DA, Weller DM, Okubara PA. Real-time PCR assays for the quantification of native yeast DNA in grape berry and fermentation extracts. J Microbiol Methods 2019; 168:105794. [PMID: 31783049 DOI: 10.1016/j.mimet.2019.105794] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/23/2019] [Accepted: 11/23/2019] [Indexed: 12/11/2022]
Abstract
Native yeasts comprise part of the microbial community in grape vineyards and play roles in alcoholic fermentation and wine quality. Monitoring populations of native yeast in vineyards, during fermentation and after bottling will provide viticulturalists and oenologists with information needed to help control spoilage and to enhance desirable wine properties. This is especially crucial for low-intervention winemaking, in which fermentation is driven by native rather than starter microbes. In this study, we report real-time polymerase chain reaction (qPCR) assays for rapid quantification of seven grape yeast species or species combinations that occur in vineyards of Washington State and throughout the world. The assays targeted Candida californica, Curvibasidium pallidicorallinum, Metschnikowia spp., Meyerozyma caribbica/Me. guilliermondii, and Saccharomyces cerevisiae/S. bayanus. We also developed assays for the spoilage yeast Brettanomyces bruxellensis, and the yeast-like fungus Aureobasidium pullulans. Primers were designed for sequences in the internal transcribed spacer (ITS) and large ribosome subunit (LSU) gene. Known populations of yeast cells, added to fermentation extract, were significantly correlated to amounts of purified DNA in picograms (pg) for most of the yeasts; exceptions were A. pullulans and Cu. pallidicorallinum. The utility of the Metschnikowia, Meyerozyma and Saccharomyces assays was further validated by good correlations (R2 = 0.75-0.83) between the number of target sequences and pg of DNA from qPCR for selected vineyard and fermentation samples. Overall, the assays will aid in species identification and monitoring of specific yeasts from cultures, vineyards and fermentation samples. Topics: Food Microbiology, Microbiological Method.
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Affiliation(s)
- Xuefei Wang
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dean A Glawe
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
| | - David M Weller
- USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, Washington 99164-6430, USA.
| | - Patricia A Okubara
- USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, Washington 99164-6430, USA.
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112
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Perini L, Mogrovejo DC, Tomazin R, Gostinčar C, Brill FHH, Gunde-Cimerman N. Phenotypes Associated with Pathogenicity: Their Expression in Arctic Fungal Isolates. Microorganisms 2019; 7:microorganisms7120600. [PMID: 31766661 PMCID: PMC6955883 DOI: 10.3390/microorganisms7120600] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 01/01/2023] Open
Abstract
Around 85% of the environments on Earth are permanently or seasonally colder than 5 °C. Among those, the poles constitute unique biomes, which harbor a broad variety of microbial life, including an abundance of fungi. Many fungi have an outstanding ability to withstand extreme conditions and play vital ecosystem roles of decomposers as well as obligate or facultative symbionts of many other organisms. Due to their dispersal capabilities, microorganisms from cryosphere samples can be distributed around the world. Such dispersal involves both species with undefined pathogenicity and potentially pathogenic strains. Here we describe the isolation of fungal species from pristine Arctic locations in Greenland and Svalbard and the testing of the expression of characteristics usually associated with pathogenic species, such as growth at 37 °C, hemolytic ability, and susceptibility to antifungal agents. A total of 320 fungal isolates were obtained, and 24 of the most abundant and representative species were further analyzed. Species known as emerging pathogens, like Aureobasidium melanogenum, Naganishia albida, and Rhodotorula mucilaginosa, were able to grow at 37 °C, showed beta-hemolytic activity, and were intrinsically resistant to commonly used antifungals such as azoles and echinocandins. Antifungal resistance screening revealed a low susceptibility to voriconazole in N. albida and Penicillium spp. and to fluconazole in Glaciozyma watsonii and Glaciozyma-related taxon.
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Affiliation(s)
- Laura Perini
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia; (C.G.); (N.G.-C.)
- Correspondence:
| | - Diana C. Mogrovejo
- MicroArctic Research Group, Dr. Brill + Partner GmbH Institut für Hygiene und Mikrobiologie, Stiegstück 34, 22339 Hamburg, Germany; (D.C.M.); (F.H.H.B.)
| | - Rok Tomazin
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, SI-1000 Ljubljana, Slovenia;
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia; (C.G.); (N.G.-C.)
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Florian H. H. Brill
- MicroArctic Research Group, Dr. Brill + Partner GmbH Institut für Hygiene und Mikrobiologie, Stiegstück 34, 22339 Hamburg, Germany; (D.C.M.); (F.H.H.B.)
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia; (C.G.); (N.G.-C.)
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113
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Ametrano CG, Grewe F, Crous PW, Goodwin SB, Liang C, Selbmann L, Lumbsch HT, Leavitt SD, Muggia L. Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota). IMA Fungus 2019; 10:19. [PMID: 32647623 PMCID: PMC7325674 DOI: 10.1186/s43008-019-0018-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022] Open
Abstract
Dothideomycetes is the most diverse fungal class in Ascomycota and includes species with a wide range of lifestyles. Previous multilocus studies have investigated the taxonomic and evolutionary relationships of these taxa but often failed to resolve early diverging nodes and frequently generated inconsistent placements of some clades. Here, we use a phylogenomic approach to resolve relationships in Dothideomycetes, focusing on two genera of melanized, extremotolerant rock-inhabiting fungi, Lichenothelia and Saxomyces, that have been suggested to be early diverging lineages. We assembled phylogenomic datasets from newly sequenced (4) and previously available genomes (238) of 242 taxa. We explored the influence of tree inference methods, supermatrix vs. coalescent-based species tree, and the impact of varying amounts of genomic data. Overall, our phylogenetic reconstructions provide consistent and well-supported topologies for Dothideomycetes, recovering Lichenothelia and Saxomyces among the earliest diverging lineages in the class. In addition, many of the major lineages within Dothideomycetes are recovered as monophyletic, and the phylogenomic approach implemented strongly supports their relationships. Ancestral character state reconstruction suggest that the rock-inhabiting lifestyle is ancestral within the class.
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Affiliation(s)
- Claudio G Ametrano
- Department of Life Sciences, University of Trieste, via Giorgieri 10, 34127 Trieste, Italy
| | - Felix Grewe
- Grainger Bioinformatics Center and Integrative Research Center, Science and Education, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605 USA
| | - Pedro W Crous
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85176, 3508 AD Utrecht, The Netherlands
| | - Stephen B Goodwin
- USDA-ARS, Crop Production and Pest Control Research Unit and Department of Botany and Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 USA
| | - Chen Liang
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109 China
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell' Università, 01100 Viterbo, Italy.,Italian National Antarctic Museum (MNA), Mycological Section, Genoa, Italy
| | - H Thorsten Lumbsch
- Grainger Bioinformatics Center and Integrative Research Center, Science and Education, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605 USA
| | - Steven D Leavitt
- Department of Biology and M.L. Bean Life Science Museum, Brigham Young University, 4102 Life Science Building, Provo, UT 84602 USA
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, via Giorgieri 10, 34127 Trieste, Italy
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114
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Mitchison-Field LMY, Vargas-Muñiz JM, Stormo BM, Vogt EJD, Van Dierdonck S, Pelletier JF, Ehrlich C, Lew DJ, Field CM, Gladfelter AS. Unconventional Cell Division Cycles from Marine-Derived Yeasts. Curr Biol 2019; 29:3439-3456.e5. [PMID: 31607535 PMCID: PMC7076734 DOI: 10.1016/j.cub.2019.08.050] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/07/2019] [Accepted: 08/20/2019] [Indexed: 12/13/2022]
Abstract
Fungi have been found in every marine habitat that has been explored; however, the diversity and functions of fungi in the ocean are poorly understood. In this study, fungi were cultured from the marine environment in the vicinity of Woods Hole, MA, USA, including from plankton, sponge, and coral. Our sampling resulted in 35 unique species across 20 genera. We observed many isolates by time-lapse, differential interference contrast (DIC) microscopy and analyzed modes of growth and division. Several black yeasts displayed highly unconventional cell division cycles compared to those of traditional model yeast systems. Black yeasts have been found in habitats inhospitable to other life and are known for halotolerance, virulence, and stress resistance. We find that this group of yeasts also shows remarkable plasticity in terms of cell size control, modes of cell division, and cell polarity. Unexpected behaviors include division through a combination of fission and budding, production of multiple simultaneous buds, and cell division by sequential orthogonal septations. These marine-derived yeasts reveal alternative mechanisms for cell division cycles that seem likely to expand the repertoire of rules established from classic model system yeasts.
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Affiliation(s)
- Lorna M Y Mitchison-Field
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Marine Biological Laboratory, Woods Hole, MA 02354, USA
| | - José M Vargas-Muñiz
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Benjamin M Stormo
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ellysa J D Vogt
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sarah Van Dierdonck
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27708, USA
| | - James F Pelletier
- Marine Biological Laboratory, Woods Hole, MA 02354, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Christoph Ehrlich
- Marine Biological Laboratory, Woods Hole, MA 02354, USA; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Daniel J Lew
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27708, USA
| | - Christine M Field
- Marine Biological Laboratory, Woods Hole, MA 02354, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
| | - Amy S Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Marine Biological Laboratory, Woods Hole, MA 02354, USA.
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115
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Gostinčar C, Turk M, Zajc J, Gunde‐Cimerman N. Fifty Aureobasidium pullulans genomes reveal a recombining polyextremotolerant generalist. Environ Microbiol 2019; 21:3638-3652. [PMID: 31112354 PMCID: PMC6852026 DOI: 10.1111/1462-2920.14693] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 04/17/2019] [Accepted: 05/20/2019] [Indexed: 01/31/2023]
Abstract
The black yeast Aureobasidium pullulans is a textbook example of a generalistic and ubiquitous fungus thriving in a wide variety of environments. To investigate whether A. pullulans is a true generalist, or alternatively, whether part of its versatility can be attributed to intraspecific specialization masked by cryptic diversification undetectable by traditional phylogenetic analyses, we sequenced and analysed the genomes of 50 strains of A. pullulans from different habitats and geographic locations. No population structure was observed in the sequenced strains. Decay of linkage disequilibrium over shorter physical distances (<100 bp) than in many sexually reproducing fungi indicates a high level of recombination in the species. A homothallic mating locus was found in all of the sequenced genomes. Aureobasidium pullulans appears to have a homogeneous population genetics structure, which is best explained by good dispersal and high levels of recombination. This means that A. pullulans is a true generalist that can inhabit different habitats without substantial specialization to any of these habitats at the genomic level. Furthermore, in the future, the high level of A. pullulans recombination can be exploited for the identification of genomic loci that are involved in the many biotechnologically useful traits of this black yeast.
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Affiliation(s)
- Cene Gostinčar
- Department of Biology, Biotechnical FacultyUniversity of Ljubljana, Jamnikarjeva 101, SI‐1000LjubljanaSlovenia
- Lars Bolund Institute of Regenerative Medicine, BGI‐QingdaoQingdao 266555China
| | - Martina Turk
- Department of Biology, Biotechnical FacultyUniversity of Ljubljana, Jamnikarjeva 101, SI‐1000LjubljanaSlovenia
| | - Janja Zajc
- Department of Biology, Biotechnical FacultyUniversity of Ljubljana, Jamnikarjeva 101, SI‐1000LjubljanaSlovenia
- National Institute of BiologyVečna pot 111, SI‐1000LjubljanaSlovenia
| | - Nina Gunde‐Cimerman
- Department of Biology, Biotechnical FacultyUniversity of Ljubljana, Jamnikarjeva 101, SI‐1000LjubljanaSlovenia
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116
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Genome editing of different strains of Aureobasidium melanogenum using an efficient Cre/loxp site-specific recombination system. Fungal Biol 2019; 123:723-731. [DOI: 10.1016/j.funbio.2019.06.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/31/2019] [Accepted: 06/03/2019] [Indexed: 01/19/2023]
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117
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Zhang LL, Li J, Wang YL, Liu S, Wang ZP, Yu XJ. Integrated Approaches to Reveal Genes Crucial for Tannin Degradation in Aureobasidium melanogenum T9. Biomolecules 2019; 9:E439. [PMID: 31480670 PMCID: PMC6769594 DOI: 10.3390/biom9090439] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/27/2019] [Accepted: 08/27/2019] [Indexed: 11/26/2022] Open
Abstract
Tannins biodegradation by a microorganism is one of the most efficient ways to produce bioproducts of high value. However, the mechanism of tannins biodegradation by yeast has been little explored. In this study, Aureobasidium melanogenum T9 isolated from red wine starter showed the ability for tannins degradation and had its highest biomass when the initial tannic acid concentration was 20 g/L. Furthermore, the genes involved in the tannin degradation process were analyzed. Genes tan A, tan B and tan C encoding three different tannases respectively were identified in the A. melanogenum T9. Among these genes, tan A and tan B can be induced by tannin acid simultaneously at both gene transcription and protein expression levels. Our assay result showed that the deletion of tanA and tanB resulted in tannase activity decline with 51.3 ± 4.1 and 64.1 ± 1.9 U/mL, respectively, which is much lower than that of A. melanogenum T9 with 91.3 ± 5.8 U/mL. In addition, another gene coding gallic acid decarboxylase (gad) was knocked out to better clarify its function. Mutant Δgad completely lost gallic acid decarboxylase activity and no pyrogallic acid was seen during the entire cultivation process, confirming that there was a sole gene encoding decarboxylase in the A. melanogenum T9. These results demonstrated that tanA, tanB and gad were crucial for tannin degradation and provided new insights for the mechanism of tannins biodegradation by yeast. This finding showed that A. melanogenum has potential in the production of tannase and metabolites, such as gall acid and pyrogallol.
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Affiliation(s)
- Lin-Lin Zhang
- College of Chemistry & Environmental Engineering, Shandong University of Science & Technology, Qingdao 266510, China
| | - Jie Li
- Laboratory for Marine Fisheries and Aquaculture-Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Yi-Lin Wang
- College of Science, China University of Petroleum, Qingdao 266580, China
| | - Song Liu
- Development & Reform Bureau, West Coast New Area, Qingdao 266000, China
| | - Zhi-Peng Wang
- Key Laboratory of Sustainable Development of Polar Fishery, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China.
| | - Xin-Jun Yu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
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118
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Ademakinwa AN, Agboola FK. Kinetic and thermodynamic investigations of cell-wall degrading enzymes produced by Aureobasidium pullulans via induction with orange peels: application in lycopene extraction. Prep Biochem Biotechnol 2019; 49:949-960. [DOI: 10.1080/10826068.2019.1650375] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Adedeji Nelson Ademakinwa
- Department of Physical and Chemical Sciences, Elizade University, Ilara-Mokin, Nigeria
- Department of Biochemistry and Molecular Biology, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Femi Kayode Agboola
- Department of Biochemistry and Molecular Biology, Obafemi Awolowo University, Ile-Ife, Nigeria
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119
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Jiang H, Chen TJ, Chi Z, Hu Z, Liu GL, Sun Y, Zhang SH, Chi ZM. Macromolecular pullulan produced by Aureobasidium melanogenum 13-2 isolated from the Taklimakan desert and its crucial roles in resistance to the stress treatments. Int J Biol Macromol 2019; 135:429-436. [DOI: 10.1016/j.ijbiomac.2019.05.190] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/15/2019] [Accepted: 05/26/2019] [Indexed: 11/29/2022]
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120
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Feng J, Li T, Zhang X, Chen J, Zhao T, Zou X. Efficient production of polymalic acid from xylose mother liquor, an environmental waste from the xylitol industry, by a T-DNA-based mutant of Aureobasidium pullulans. Appl Microbiol Biotechnol 2019; 103:6519-6527. [DOI: 10.1007/s00253-019-09974-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 06/01/2019] [Accepted: 06/10/2019] [Indexed: 10/26/2022]
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121
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Nerva L, Turina M, Zanzotto A, Gardiman M, Gaiotti F, Gambino G, Chitarra W. Isolation, molecular characterization and virome analysis of culturable wood fungal endophytes in esca symptomatic and asymptomatic grapevine plants. Environ Microbiol 2019; 21:2886-2904. [DOI: 10.1111/1462-2920.14651] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Luca Nerva
- Council for Agricultural Research and Economics – Research Centre for Viticulture and Enology CREA‐VE Via XXVIII Aprile 26, 31015 Conegliano (TV) Italy
- Institute for Sustainable Plant Protection CNR, Strada delle Cacce 73, 10135 Torino Italy
| | - Massimo Turina
- Institute for Sustainable Plant Protection CNR, Strada delle Cacce 73, 10135 Torino Italy
| | - Alessandro Zanzotto
- Council for Agricultural Research and Economics – Research Centre for Viticulture and Enology CREA‐VE Via XXVIII Aprile 26, 31015 Conegliano (TV) Italy
| | - Massimo Gardiman
- Council for Agricultural Research and Economics – Research Centre for Viticulture and Enology CREA‐VE Via XXVIII Aprile 26, 31015 Conegliano (TV) Italy
| | - Federica Gaiotti
- Council for Agricultural Research and Economics – Research Centre for Viticulture and Enology CREA‐VE Via XXVIII Aprile 26, 31015 Conegliano (TV) Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection CNR, Strada delle Cacce 73, 10135 Torino Italy
| | - Walter Chitarra
- Council for Agricultural Research and Economics – Research Centre for Viticulture and Enology CREA‐VE Via XXVIII Aprile 26, 31015 Conegliano (TV) Italy
- Institute for Sustainable Plant Protection CNR, Strada delle Cacce 73, 10135 Torino Italy
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122
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Gnat S, Nowakiewicz A, Zięba P. TAXONOMY OF DERMATOPHYTES – THE CLASSIFICATION SYSTEMS MAY CHANGE BUT THE IDENTIFICATION PROBLEMS REMAIN THE SAME. ADVANCEMENTS OF MICROBIOLOGY 2019. [DOI: 10.21307/pm-2019.58.1.049] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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123
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Zhang Y, Feng J, Wang P, Xia J, Li X, Zou X. CRISPR/Cas9-mediated efficient genome editing via protoplast-based transformation in yeast-like fungus Aureobasidium pullulans. Gene 2019; 709:8-16. [PMID: 31132514 DOI: 10.1016/j.gene.2019.04.079] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/05/2019] [Accepted: 04/27/2019] [Indexed: 01/30/2023]
Abstract
Aureobasidium pullulans, a yeast-like fungus with strong environmental adaptability, remains a potential host for bio-production of different valuable metabolites. However, its potential application is limited by low-efficient genetic manipulation. In this study, CRISPR/Cas9-mediated genome editing via protoplast-based transformation system was developed. To test CRISPR/Cas9 mediated genomic mutagenesis, the orotidine 5-phosphate decarboxylase (umps) gene was used as a counter-selectable selection marker. By co-transforming of two plasmids harboring cas9 gene and a guide RNA targeting umps, respectively, the CRISPR/Cas9 system could significantly increase frequency of mutation in the targeting site of guide RNA. To further validate that CRISPR/Cas9 stimulated homologous recombination with donor DNA, a color reporter system of beta-glucuronidase (gus) gene was developed for calculating positive mutation rate. The results showed that positive mutation rate with CRISPR/Cas9 system was ~40% significantly higher than only with the donor DNA (~4%). Furthermore, the different posttranscriptional RNA processing schemes were analyzed by compared the effects of flanking gRNA with self-cleaving ribozymes or tRNA. The result demonstrated that gRNA processed by self-cleaving ribozymes achieves higher positive mutant rate. This study provided foundation for a simple and powerful genome editing tool for A. pullulans. Moreover, a counter-selectable selection marker (umps) and a color reporter system (gus) were being developed as genetic parts for strain engineering.
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Affiliation(s)
- Yuan Zhang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China
| | - Jun Feng
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China
| | - Pan Wang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China
| | - Jun Xia
- College of Chemistry and Chemical Engineering, Huaiyin Normal University, Huai'an 223300, PR China
| | - Xiaorong Li
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China.
| | - Xiang Zou
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China.
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124
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Wang M, Danesi P, James TY, Al-Hatmi AMS, Najafzadeh MJ, Dolatabadi S, Ming C, Liou GY, Kang Y, de Hoog S. Comparative pathogenicity of opportunistic black yeasts in Aureobasidium. Mycoses 2019; 62:803-811. [PMID: 31107996 DOI: 10.1111/myc.12931] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 12/01/2022]
Abstract
Aureobasidium pullulans and A. melanogenum are black-yeast-like surface colonisers and are commonly encountered as contaminants in the hospital. The species are able to produce melanin which play a role in protection against environmental stress and irradiation. Aureobasidium melanogenum shows higher frequency in opportunistic infections compared to A. pullulans. Comparative pathogenicity of opportunistic black yeasts between Aureobasidium pullulans and A. melanogenum to explain the observed differences in frequency in infection. Degrees of melanisation and thermotolerance were measured, and virulence of strains from different sources was examined in Galleria mellonela and murine infection models. Aureobasidium melanogenum responds with increased melanisation to temperature stress and generally survives at 37°C, A. pullulans on average scored less on these parameters. In the murine model, differences between species were not significant, but the melanised A. melanogenum group showed the highest virulence. This result was not reproducible in Galleria mellonella larvae at 25°C. The A. melanogenum black group showed higher pathogenicity in murine model, indicating that the combination of melanisation and thermotolerance rather than species affiliation is instrumental. Galleria larvae did not survive very well at 37°C, and hence, this model is judged insufficient to detect the small virulence differences observed in Aureobasidium.
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Affiliation(s)
- Meizhu Wang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education of Guizhou & Guizhou Talent Base for Microbiology and Human Health, Key Laboratory of Medical Microbiology and Parasitology of Education Department of Guizhou, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China.,Center of Expertise in Mycology, Radboud University Medical Center/CWZ, Nijmegen, The Netherlands.,Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Patrizia Danesi
- Laboratorio di Parassitologia, Istituto Zooprofilattico Sperimentale delle Venezie, Venice, Italy
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - Abdullah M S Al-Hatmi
- Center of Expertise in Mycology, Radboud University Medical Center/CWZ, Nijmegen, The Netherlands.,Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Ministry of Health, Directorate General of Health Services, Ibri, Oman
| | - Mohammad Javad Najafzadeh
- Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Somayeh Dolatabadi
- Faculty of Engineering, Sabzevar University of New Technology, Sabzevar, Iran
| | - Chunyan Ming
- Department of Clinical Laboratory Center, Nanchong Central Hospital, Nanchong, China
| | - Guey-Yuh Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Yingqian Kang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education of Guizhou & Guizhou Talent Base for Microbiology and Human Health, Key Laboratory of Medical Microbiology and Parasitology of Education Department of Guizhou, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China.,Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Sybren de Hoog
- Center of Expertise in Mycology, Radboud University Medical Center/CWZ, Nijmegen, The Netherlands.,Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
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125
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Faiza M, Huang S, Lan D, Wang Y. New insights on unspecific peroxygenases: superfamily reclassification and evolution. BMC Evol Biol 2019; 19:76. [PMID: 30866798 PMCID: PMC6417270 DOI: 10.1186/s12862-019-1394-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 02/20/2019] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Unspecific peroxygenases (UPO) (EC 1.11.2.1) represent an intriguing oxidoreductase sub-subclass of heme proteins with peroxygenase and peroxidase activity. With over 300 identified substrates, UPOs catalyze numerous oxidations including 1- or 2- electron oxygenation, selective oxyfunctionalizations, which make them most significant in organic syntheses and potentially attractive as industrial biocatalysts. There are very few UPOs available with distinct properties, notably, MroUPO which shows behavior ranging between UPO and another heme-thiolate peroxidase, called Chloroperoxidase (CPO). It prompted us to search for more UPOs in fungal kingdom which led us to studying their relationship with CPO. RESULTS In this study, we searched for novel UPOs in more than 800 fungal genomes and found 113 putative UPO-encoding sequences distributed in 35 different fungal species (or strains), amongst which single sequence per species were subjected to phylogeny study along with CPOs. Our phylogenetic study show that the UPOs are distributed in Basidiomycota and Ascomycota phyla of fungi. The sequence analysis helped to classify the UPOs into five distinct subfamilies: classic AaeUPO and four new subfamilies with potential new traits. We have also shown that each of these five subfamilies (supported by) have their own signature motifs. Surprisingly, some of the CPOs appeared to be a type of UPOs indicating that they were previously identified incorrectly. Selection pressure was observed on important motifs in UPOs which could have driven their functional divergence. Furthermore, the sites having different evolutionary rates caused by the functional divergence were also identified on some motifs along with the other relevant amino acid residues. Finally, we predicted critical amino acids responsible for the functional divergence in the UPOs and identified some sequence differences among UPOs, CPOs, and MroUPO to predict it's ranging behavior. CONCLUSION This study discovers new UPOs, provides a glimpse of their evolution from CPOs, and presents new insight on their functional divergence. We present a new classification of UPOs and shed new light on its phylogenetics. These different UPOs may exhibit a wide range of characteristics and specificities which may help in various fields of synthetic chemistry and industrial biocatalysts, and may as well lead to an advancement towards the understanding of physiological role of UPOs in fungi.
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Affiliation(s)
- Muniba Faiza
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640 China
| | - Shengfeng Huang
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Dongming Lan
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640 China
| | - Yonghua Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640 China
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126
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Kitiyanant V, Lotrakul P, Kanchanabanca C, Padungros P, Punnapayak H, Prasongsuk S, Chanvorachote P. Fusigen Reduces Intracellular Reactive Oxygen Species and Nitric Oxide Levels. In Vivo 2019; 33:425-432. [PMID: 30804121 DOI: 10.21873/invivo.11490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 01/15/2019] [Accepted: 01/16/2019] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM Oxidative stress caused by the production of excessive cellular reactive oxygen species (ROS) and high levels of nitric oxide contribute to several human pathologies. This study aimed to examine the anti-oxidant effects of fusigen, a compound produced from Aureobasidium melanogenum. MATERIALS AND METHODS Extracts of A. melanogenum were selected as a source for the isolation of fusigen. The anti-oxidant, nitric oxide suppression, as well as the free radical scavenging activities of fusigen were tested in BEAS-2B human bronchial epithelial cell line (BEAS-2B cells) and human dermal papilla cells (DP cells) using specific fluorescence dyes and flow cytometry analysis. Cell viability was determined by the MTT assay. RESULTS Fusigen did not exert cytotoxicity in the human normal BEAS-2B and DP cells at concentrations up to 100 μM. Fusigen decreased basal levels of cellular ROS, as well as the levels of ROS induced by hydrogen peroxide and ferrous ion enrichment. ROS decreasing effect was confirmed in DP cells. In addition, fusigen treatment suppressed intracellular NO levels in both BEAS-2B and DP cells. CONCLUSION The optimal process of production of purified fusigen from A. melanogenum was determined. Fusigen exhibited a low cytotoxic effect and the potential to suppress ROS and NO. These results demonstrated that fusigen may be used for the treatment or prevention of human diseases.
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Affiliation(s)
- Vorawat Kitiyanant
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Pongtharin Lotrakul
- Plant Biomass Utilization Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | | | - Panuwat Padungros
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Hunsa Punnapayak
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia
| | - Sehanat Prasongsuk
- Plant Biomass Utilization Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Pithi Chanvorachote
- Department of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand .,Cell-based Drug and Health Product Development Research Unit, Chulalongkorn University, Bangkok, Thailand
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127
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Bewick AJ, Hofmeister BT, Powers RA, Mondo SJ, Grigoriev IV, James TY, Stajich JE, Schmitz RJ. Diversity of cytosine methylation across the fungal tree of life. Nat Ecol Evol 2019; 3:479-490. [PMID: 30778188 PMCID: PMC6533610 DOI: 10.1038/s41559-019-0810-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 01/13/2019] [Indexed: 12/22/2022]
Abstract
The generation of thousands of fungal genomes is leading to a better understanding of genes and genomic organization within the kingdom. However, the epigenome, which includes DNA and chromatin modifications, remains poorly investigated in fungi. Large comparative studies in animals and plants have deepened our understanding of epigenomic variation, particularly of the modified base 5-methylcytosine (5mC), but taxonomic sampling of disparate groups is needed to develop unifying explanations for 5mC variation. Here we utilize the largest phylogenetic resolution of 5mC methyltransferases (5mC MTases) and genome evolution to better understand levels and patterns of 5mC across fungi. We show that extant 5mC MTase genotypes are descendent from ancestral maintenance and de novo genotypes, whereas the 5mC MTases DIM-2 and RID are more recently derived, and that 5mC levels are correlated with 5mC MTase genotype and transposon content. Our survey also revealed that fungi lack canonical gene body methylation, which distinguishes fungal epigenomes from certain insect and plant species. However, some fungal species possess independently derived clusters of contiguous 5mC encompassing many genes. In some cases, DNA repair pathways and the N6-methyladenine (6mA) DNA modification negatively coevolved with 5mC pathways, which additionally contributed to interspecific epigenomic variation across fungi.
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Affiliation(s)
- Adam J Bewick
- Department of Genetics, University of Georgia, Athens, GA, USA.
| | | | - Rob A Powers
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Stephen J Mondo
- US Department of Energy Joint Genome Institute, Walnut Creek, Berkeley, CA, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, USA
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128
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Zou X, Cheng C, Feng J, Song X, Lin M, Yang ST. Biosynthesis of polymalic acid in fermentation: advances and prospects for industrial application. Crit Rev Biotechnol 2019; 39:408-421. [DOI: 10.1080/07388551.2019.1571008] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Xiang Zou
- College of Pharmaceutical Sciences, Chongqing Engineering Research Center for Pharmaceutical Process and Quality Control, Southwest University, Chongqing, PR China
| | - Chi Cheng
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, USA
| | - Jun Feng
- College of Pharmaceutical Sciences, Chongqing Engineering Research Center for Pharmaceutical Process and Quality Control, Southwest University, Chongqing, PR China
| | - Xiaodan Song
- College of Pharmaceutical Sciences, Chongqing Engineering Research Center for Pharmaceutical Process and Quality Control, Southwest University, Chongqing, PR China
| | - Meng Lin
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, USA
| | - Shang-Tian Yang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, USA
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129
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Zeng W, Zhang B, Li M, Ding S, Chen G, Liang Z. Development and benefit evaluation of fermentation strategies for poly(malic acid) production from malt syrup by Aureobasidium melanogenum GXZ-6. BIORESOURCE TECHNOLOGY 2019; 274:479-487. [PMID: 30553959 DOI: 10.1016/j.biortech.2018.12.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 12/07/2018] [Accepted: 12/08/2018] [Indexed: 06/09/2023]
Abstract
Malt syrup, as a low-cost substrate without any pretreatment, was proved to be able to replace maltose for ploymalic acid (PMA) production by Aureobasidium melanogenum GXZ-6. The PMA titer of 55.53 ± 1.72 g/L was obtained by batch fermentation in a 10-L fermentor with addition of malate, citrate and sodium malonate. Then, a higher PMA titer of 124.07 ± 2.28 g/L was obtained in fed-batch fermentation, which increased by 123.43% than that from batch fermentation. Moreover, repeated-batch fermentation with three batches gave a PMA titer of 64.06 g/L on average with a higher yield of 0.81 g/g and productivity of 0.56 g/L·h. Fermentation process and economics analysis were performed by SuperPro Designer for a 2000 metric tons plant. Results showed that PMA production cost was as low as $ 1.716/kg by fed-batch fermentation, which provides an economical strategy for large-scale PMA production.
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Affiliation(s)
- Wei Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, Guangxi, China; College of Life Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Bin Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, Guangxi, China; College of Life Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Mengxuan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, Guangxi, China; College of Life Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Su Ding
- College of Life Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Guiguang Chen
- College of Life Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Zhiqun Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, Guangxi, China; College of Life Science and Technology, Guangxi University, Nanning 530004, Guangxi, China.
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130
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Aung T, Jiang H, Chen CC, Liu GL, Hu Z, Chi ZM, Chi Z. Production, Gene Cloning, and Overexpression of a Laccase in the Marine-Derived Yeast Aureobasidium melanogenum Strain 11-1 and Characterization of the Recombinant Laccase. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:76-87. [PMID: 30456695 DOI: 10.1007/s10126-018-9860-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/07/2018] [Indexed: 06/09/2023]
Abstract
Aureobasidium melanogenum strain 11-1 with a high laccase activity was isolated from a mangrove ecosystem. Under the optimal conditions, the 11-1 strain yielded the highest laccase activity up to 3120.0 ± 170 mU/ml (1.2 U/mg protein) within 5 days. A laccase gene (LAC1) of the yeast strain 11-1 contained two introns and encoded a protein with 570 amino acids and four conserved copper-binding domains typical of the fungal laccase. Expression of the LAC1 gene in the yeast strain 11-1 made a recombinant yeast strain produce the laccase activity of 6005 ± 140 mU/ml. The molecular weight of the recombinant laccase after removing the sugar was about 62.5 kDa. The optimal temperature and pH of the recombinant laccase were 40 °C and 3.2, respectively, and it was stable at a temperature less than 25 °C. The laccase was inhibited in the presence of sodium dodecyl sulfate (SDS), ethylenediaminetetraacetic acid (EDTA), phenylmethanesulfonyl fluoride (PMSF), and DL-dithiothreitol (DTT). The Km and Vmax values of the laccase for 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) was 6.3 × 10-2 mM and 177.4 M/min, respectively. Many synthetic dyes were greatly decolored by the laccase.
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Affiliation(s)
- Thu Aung
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Yushan Road, No. 5, Qingdao, China
| | - Hong Jiang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Yushan Road, No. 5, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Shi, 266003, Shandong Sheng, Qingdao, China
| | - Cheng-Cheng Chen
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Yushan Road, No. 5, Qingdao, China
| | - Guang-Lei Liu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Yushan Road, No. 5, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Shi, 266003, Shandong Sheng, Qingdao, China
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou, China
| | - Zhen-Ming Chi
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Yushan Road, No. 5, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Shi, 266003, Shandong Sheng, Qingdao, China.
| | - Zhe Chi
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Yushan Road, No. 5, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Shi, 266003, Shandong Sheng, Qingdao, China.
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131
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Zajc J, Gostinčar C, Černoša A, Gunde-Cimerman N. Stress-Tolerant Yeasts: Opportunistic Pathogenicity Versus Biocontrol Potential. Genes (Basel) 2019; 10:genes10010042. [PMID: 30646593 PMCID: PMC6357073 DOI: 10.3390/genes10010042] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/03/2019] [Accepted: 01/09/2019] [Indexed: 01/26/2023] Open
Abstract
Stress-tolerant fungi that can thrive under various environmental extremes are highly desirable for their application to biological control, as an alternative to chemicals for pest management. However, in fungi, the mechanisms of stress tolerance might also have roles in mammal opportunism. We tested five species with high biocontrol potential in agriculture (Aureobasidium pullulans, Debayomyces hansenii, Meyerozyma guilliermondii, Metschnikowia fructicola, Rhodotorula mucilaginosa) and two species recognized as emerging opportunistic human pathogens (Exophiala dermatitidis, Aureobasidium melanogenum) for growth under oligotrophic conditions and at 37 °C, and for tolerance to oxidative stress, formation of biofilms, production of hydrolytic enzymes and siderophores, and use of hydrocarbons as sole carbon source. The results show large overlap between traits desirable for biocontrol and traits linked to opportunism (growth under oligotrophic conditions, production of siderophores, high oxidative stress tolerance, and specific enzyme activities). Based on existing knowledge and these data, we suggest that oligotrophism and thermotolerance together with siderophore production at 37 °C, urease activity, melanization, and biofilm production are the main traits that increase the potential for fungi to cause opportunistic infections in mammals. These traits should be carefully considered when assessing safety of potential biocontrol agents.
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Affiliation(s)
- Janja Zajc
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia.
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.
- Institut 'Jožef Stefan', Jamova cesta 39, SI-1000 Ljubljana, Slovenia.
| | - Anja Černoša
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia.
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.
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132
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Pinto C, Custódio V, Nunes M, Songy A, Rabenoelina F, Courteaux B, Clément C, Gomes AC, Fontaine F. Understand the Potential Role of Aureobasidium pullulans, a Resident Microorganism From Grapevine, to Prevent the Infection Caused by Diplodia seriata. Front Microbiol 2018; 9:3047. [PMID: 30619138 PMCID: PMC6297368 DOI: 10.3389/fmicb.2018.03047] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/27/2018] [Indexed: 12/12/2022] Open
Abstract
Grapevine trunk diseases (GTDs) are one of the major concern amongst grapevine diseases, responsible for the decline of vineyards and for several economical losses. Since grapevine is naturally colonized by resident microorganisms such as Aureobasidium pullulans, the present challenge is to understand their biocontrol potential and how such microorganisms can be successfully integrated in the control of GTDs. In this context, the first priority consists to exploit the plant-beneficial-phytopathogen interactions in plant model systems, to identify the most prevalent equilibrium limiting expression of GTDs. In the current study, we deep characterized the interaction of a resident and abundant microorganism from grapevine - Aureobasidium pullulans strain Fito_F278 - against D. seriata F98.1, a Botryosphaeria dieback agent, and with plant (cv Chardonnay). Results revealed that A. pullulans strain Fito_F278 was able to reduce significantly the mycelium growth of D. seriata F98.1 at 33.41 ± 0.55%, under in vitro conditions, though this reduction is possibly dependent on a direct interaction between strain Fito_F278 and pathogen. Furthermore, strain Fito_F278 was able to promote an induction of some plant defense responses in cutting plants, 1 week after the D. seriata F98.1 infection. Results evidenced that strain Fito_F278 colonized efficiently grapevine at both epiphyte and endophyte level, could persist on plant roots for long-periods (up to 2 months after its inoculation) and grow at different pH and high salinity conditions. Moreover, a significant decrease of the microbial load from soil and rhizosphere was observed in plants treated with the strain Fito_F278, suggesting its competitivity potential in a microbial ecosystem. Altogether, the present study gives the first insights about the interaction of A. pullulans strain Fito_F278, a resident microorganism, with grapevine, its potential role against a Botryosphaeria dieback agent, and highlights its importance to toward more resilient grapevine.
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Affiliation(s)
- Cátia Pinto
- SFR Condorcet – FR CNRS 3417, Unité Résistance Induite et Bioprotection des Plantes (RIBP), Université de Reims Champagne-Ardenne, Reims, France
- Genomics Unit, Biocant – Biotechnology Innovation Center, Cantanhede, Portugal
| | - Valéria Custódio
- Genomics Unit, Biocant – Biotechnology Innovation Center, Cantanhede, Portugal
| | - Mariana Nunes
- Genomics Unit, Biocant – Biotechnology Innovation Center, Cantanhede, Portugal
| | - Aurélie Songy
- SFR Condorcet – FR CNRS 3417, Unité Résistance Induite et Bioprotection des Plantes (RIBP), Université de Reims Champagne-Ardenne, Reims, France
| | - Fanja Rabenoelina
- SFR Condorcet – FR CNRS 3417, Unité Résistance Induite et Bioprotection des Plantes (RIBP), Université de Reims Champagne-Ardenne, Reims, France
| | - Barbara Courteaux
- SFR Condorcet – FR CNRS 3417, Unité Résistance Induite et Bioprotection des Plantes (RIBP), Université de Reims Champagne-Ardenne, Reims, France
| | - Christophe Clément
- SFR Condorcet – FR CNRS 3417, Unité Résistance Induite et Bioprotection des Plantes (RIBP), Université de Reims Champagne-Ardenne, Reims, France
| | - Ana Catarina Gomes
- Genomics Unit, Biocant – Biotechnology Innovation Center, Cantanhede, Portugal
- Center for Neurosciences and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Florence Fontaine
- SFR Condorcet – FR CNRS 3417, Unité Résistance Induite et Bioprotection des Plantes (RIBP), Université de Reims Champagne-Ardenne, Reims, France
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133
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van Nieuwenhuijzen EJ, Sailer MF, van den Heuvel ER, Rensink S, Adan OCG, Samson RA. Vegetable oils as carbon and energy source for Aureobasidium melanogenum in batch cultivation. Microbiologyopen 2018; 8:e00764. [PMID: 30515994 PMCID: PMC6562153 DOI: 10.1002/mbo3.764] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/10/2018] [Accepted: 10/12/2018] [Indexed: 11/22/2022] Open
Abstract
Dark homogenous fungal‐based layers called biofinishes and vegetable oils are key ingredients of an innovative wood protecting system. The aim of this study was to determine which of the vegetable oils that have been used to generate biofinishes on wood will provide carbon and energy for the biofinish‐inhabiting fungus Aureobasidium melanogenum, and to determine the effect of the oil type and the amount of oil on the cell yield. Aureobasidium melanogenum was cultivated in shake flasks with different types and amounts of carbon‐based nutrients. Oil‐related total cell and colony‐forming unit growth were demonstrated in suspensions with initially 1% raw linseed, stand linseed, and olive oil. Oil‐related cell growth was also demonstrated with raw linseed oil, using an initial amount of 0.02% and an oil addition during cultivation. Nile red staining showed the accumulation of fatty acids inside cells grown in the presence of oil. In conclusion, each tested vegetable oil was used as carbon and energy source by A. melanogenum. The results indicated that stand linseed oil provides less carbon and energy than olive and raw linseed oil. This research is a fundamental step in unraveling the effects of vegetable oils on biofinish formation.
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Affiliation(s)
| | - Michael F Sailer
- Saxion University of Applied Sciences, Enschede, The Netherlands.,Xylotrade BV, Goor, The Netherlands
| | - Edwin R van den Heuvel
- Department of Mathematics and Computer Science, University of Technology Eindhoven, Eindhoven, The Netherlands
| | | | - Olaf C G Adan
- Department of Applied Physics, University of Technology Eindhoven, Eindhoven, The Netherlands
| | - Robert A Samson
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
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134
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Snyder AB, Biango-Daniels MN, Hodge KT, Worobo RW. Nature Abhors a Vacuum: Highly Diverse Mechanisms Enable Spoilage Fungi to Disperse, Survive, and Propagate in Commercially Processed and Preserved Foods. Compr Rev Food Sci Food Saf 2018; 18:286-304. [DOI: 10.1111/1541-4337.12403] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/30/2018] [Accepted: 10/02/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Abigail B. Snyder
- the Dept. of Extension; The Ohio State Univ.; 1680 Madison Ave. Wooster OH 44691 USA
| | - Megan N. Biango-Daniels
- the Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science; Cornell Univ.; Ithaca NY 14850 USA
| | - Kathie T. Hodge
- the Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science; Cornell Univ.; Ithaca NY 14850 USA
| | - Randy W. Worobo
- the Dept. of Food Science; Cornell Univ.; 411 Tower Rd. Ithaca NY 14850 USA
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135
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Palla M, Digiacomo M, Cristani C, Bertini S, Giovannetti M, Macchia M, Manera C, Agnolucci M. Composition of health-promoting phenolic compounds in two extra virgin olive oils and diversity of associated yeasts. J Food Compost Anal 2018. [DOI: 10.1016/j.jfca.2018.08.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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136
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Tabasum S, Noreen A, Maqsood MF, Umar H, Akram N, Nazli ZIH, Chatha SAS, Zia KM. A review on versatile applications of blends and composites of pullulan with natural and synthetic polymers. Int J Biol Macromol 2018; 120:603-632. [DOI: 10.1016/j.ijbiomac.2018.07.154] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 07/17/2018] [Accepted: 07/24/2018] [Indexed: 02/07/2023]
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137
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Diguță CF, Proca IG, Jurcoane Ș, Matei F. Molecular characterization by PCR-RFLP of indigenous fungal isolates from hypersaline stream water in România. Folia Microbiol (Praha) 2018; 64:407-414. [PMID: 30426303 DOI: 10.1007/s12223-018-0664-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 11/09/2018] [Indexed: 11/27/2022]
Abstract
This is the first exhaustive report on the fungal community biodiversity in hypersaline water in România. A total of 27 fungal strains (19 molds and eight yeast) have been isolated from Lopătari hypersaline water, Buzau County. Based on classical investigation, these strains have been identified as belonging to the genera Aureobasidium, Alternaria, Aspergillus, Penicillium, and Fusarium. The molecular characterization of fungal isolates at species level was performed using PCR-RFLP analysis of the 5.8S-ITS region. PCR products were digested with different combinations of endonucleases. The most frequently isolated species were Aspergillus niger (14.81% of all isolates), A. versicolor, (14.81%) and Penicillium crustosum (14.81%). In addition, ribosomal restriction patterns which exhibited profiles specific to Aureobasidium pullulans were derived, and to discriminate between Aureobasidium isolates, the elongase-encoding gene (ELO) was chosen as a genetic marker followed by digestion with endonuclease HhaI. Five yeast isolates displayed restriction patterns corresponding to Aureobasidium melanogenum (18.52%) and three isolates to Aureobasidium pullulans (11.11%). In addition, the RFLP types of Aureobasidium pullulans varieties with HhaI are clearly distinguished and could be applied to assess the intraspecific variability.
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Affiliation(s)
- Camelia Filofteia Diguță
- Faculty of Biotechnology, University of Agronomic Sciences and Veterinary Medicine, 59, Mărăşti Blv., Bucharest, Romania.
| | - Irinel Gabriel Proca
- Faculty of Biotechnology, University of Agronomic Sciences and Veterinary Medicine, 59, Mărăşti Blv., Bucharest, Romania
| | - Ștefana Jurcoane
- Faculty of Biotechnology, University of Agronomic Sciences and Veterinary Medicine, 59, Mărăşti Blv., Bucharest, Romania
| | - Florentina Matei
- Faculty of Biotechnology, University of Agronomic Sciences and Veterinary Medicine, 59, Mărăşti Blv., Bucharest, Romania
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138
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Zhao SF, Jiang H, Chi Z, Liu GL, Chi ZM, Chen TJ, Yang G, Hu Z. Genome sequencing of Aureobasidium pullulans P25 and overexpression of a glucose oxidase gene for hyper-production of Ca2+-gluconic acid. Antonie Van Leeuwenhoek 2018; 112:669-678. [DOI: 10.1007/s10482-018-1197-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/02/2018] [Indexed: 11/30/2022]
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139
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140
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Abstract
The saprophytic yeast-like fungus Aureobasidium pullulans has been well documented for over 60 years in the microbiological literature. It is ubiquitous in distribution, being found in a variety of environments (plant surfaces, soil, water, rock surfaces and manmade surfaces), and with a worldwide distribution from cold to warm climates and wet/humid regions to arid ones. Isolates and strains of A. pullulans produce a wide range of natural products well documented in the international literature and which have been regarded as safe for biotechnological and environmental applications. Showing antagonistic activity against plant pathogens (especially post-harvest pathogens) is one of the major applications currently in agriculture of the fungus, with nutrient and space competition, production of volatile organic compounds, and production of hydrolytic enzymes and antimicrobial compounds (antibacterial and antifungal). The fungus also shows a positive role on mycotoxin biocontrol through various modes, with the most striking being that of binding and/or absorption. A. pullulans strains have been reported to produce very useful industrial enzymes, such as β-glucosidase, amylases, cellulases, lipases, proteases, xylanases and mannanases. Pullulan (poly-α-1,6-maltotriose biopolymer) is an A. pullulans trademark product with significant properties and biotechnological applications in the food, cosmetic and pharmaceutical industries. Poly (β-l-malic acid), or PMA, which is a natural biopolyester, and liamocins, a group of produced heavy oils and siderophores, are among other valuable compounds detected that are of possible biotechnological use. The fungus also shows a potential single-cell protein source capacity with high levels of nucleic acid components and essential amino acids, but this remains to be further explored. Last but not least, the fungus has shown very good biocontrol against aerial plant pathogens. All these properties are of major interest in the vitivinicultural sector and are thoroughly reviewed under this prism, concluding on the importance that A. pullulans may have if used at both vineyard and winery levels. This extensive array of properties provides excellent tools for the viticulturist/farmer as well as for the oenologist to combat problems in the field and create a high-quality wine.
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141
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Liu NN, Chi Z, Liu GL, Chen TJ, Jiang H, Hu Z, Chi ZM. α-Amylase, glucoamylase and isopullulanase determine molecular weight of pullulan produced by Aureobasidium melanogenum P16. Int J Biol Macromol 2018; 117:727-734. [DOI: 10.1016/j.ijbiomac.2018.05.235] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 05/29/2018] [Accepted: 05/31/2018] [Indexed: 11/25/2022]
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142
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Kurek J, Kwaśniewska-Sip P, Myszkowski K, Cofta G, Murias M, Barczyński P, Jasiewicz B, Kurczab R. 7-Deacetyl-10-alkylthiocolchicine derivatives - new compounds with potent anticancer and fungicidal activity. MEDCHEMCOMM 2018; 9:1708-1714. [PMID: 30429975 PMCID: PMC6195099 DOI: 10.1039/c8md00352a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 08/14/2018] [Indexed: 11/21/2022]
Abstract
A series of new semi-synthetic 7-deacetyl-10-alkylthiocolchicne derivatives with ethyl, n-propyl, i-propyl and n-butyl substituents were synthesised and characterised by spectroscopic methods, elemental analysis, DFT calculations and molecular docking simulations. All the synthesized compounds have been tested for fungicidal and anticancer activities against SKOV-3, LoVo, MCF-7, MDA-MB-231 and the lung-derived fibroblast CCD39Lu. All the new colchicine derivatives exhibit significantly higher cytotoxicity towards the SKOV-3 tumour cell line than the natural product - colchicine. The most effective cytotoxic agents were 7-deacetyl-10-n-buthylthiocolchicine and 7-deacetyl-10-i-propylthiocolchicine. Among all the compounds tested, 7-deacetyl-10-n-buthylthiocolchicine exhibited the highest fungicidal activity. Molecular modeling indicated that several mutations found in the β-tubulin unit of the tested fungal strains are crucial for antifungal activity and selectivity of 7-deacetyl-10-n-buthylthiocolchicine. The obtained results may be useful for the development of selective colchicine derivatives as effective fungicidal and/or anticancer drugs.
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Affiliation(s)
- Joanna Kurek
- Faculty of Chemistry , Adam Mickiewicz University , Umultowska 89b , 61-614 Poznań , Poland . ; ;
| | - Patrycja Kwaśniewska-Sip
- Wood Technology Institute , Environmental Protection and Wood Chemistry Department , Winiarska 1 , 60-654 Poznan , Poland .
| | - Krzysztof Myszkowski
- Department of Toxicology , Poznan University of Medical Sciences , Dojazd 30 , 60-631 Poznań , Poland . ;
| | - Grzegorz Cofta
- Institute of Chemical Wood Technology , University of Life Science , Wojska Polskiego 38/42 , 60-037 Poznań , Poland .
| | - Marek Murias
- Department of Toxicology , Poznan University of Medical Sciences , Dojazd 30 , 60-631 Poznań , Poland . ;
| | - Piotr Barczyński
- Faculty of Chemistry , Adam Mickiewicz University , Umultowska 89b , 61-614 Poznań , Poland . ; ;
| | - Beata Jasiewicz
- Faculty of Chemistry , Adam Mickiewicz University , Umultowska 89b , 61-614 Poznań , Poland . ; ;
| | - Rafał Kurczab
- Department of Medicinal Chemistry , Institute of Pharmacology , Polish Academy of Sciences , Smętna 12 , 31-343 Kraków , Poland .
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Lu Y, Liu G, Jiang H, Chi Z, Chi Z. An insight into the iron acquisition and homeostasis in Aureobasidium melanogenum HN6.2 strain through genome mining and transcriptome analysis. Funct Integr Genomics 2018; 19:137-150. [PMID: 30251029 DOI: 10.1007/s10142-018-0633-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 08/07/2018] [Accepted: 08/23/2018] [Indexed: 11/26/2022]
Abstract
Aureobasidium melanogenum HN6.2 is a unique yeast strain who can produce the siderophore of fusigen under iron starvation to guarantee its survival. However, a comprehensive understanding of mechanisms involved in iron acquisition and homeostasis for it is still vacant. In this study, genome sequencing and mining revealed that A. melanogenum HN6.2 strain was the first yeast species that exclusively possessed all the four known mechanisms for the iron acquisition: (i) the siderophore-mediated iron uptake; (ii) reductive iron assimilation; (iii) low-affinity ferrous uptake; and (iv) heme utilization, which suggested its stronger adaptability than Aspergillus fumigatus and Saccharomyces cerevisiae. This HN6.2 strain also employed the vacuolar iron storage for immobilizing the excessive iron to avoid its cellular toxicity. Specially, genome mining indicated that A. melanogenum HN6.2 strain could also synthesize ferricrocin siderophore. Further HPLC and Q-Tof-MS analysis confirmed that the siderophores synthesized by this strain consisted of cyclic fusigen, linear fusigen, ferricrocin, and hydroxyferricrocin and they played parallel roles as both intracellular and extracellular siderophores. Also, the heme utilization for this strain was experimentally verified by the knock-out of heme oxygenase gene. For iron homeostasis, the transcriptome analysis revealed that this strain mainly employed two central regulators of SreA/HapX to tune iron uptake and storage at the transcriptional level. It was also noted that mitogen-activated protein kinase C gene (MpkC) exhibited a transcriptional up-regulation under iron sufficiency, suggesting that it may serve as another factor involved in the repression of siderophore biosynthesis. This is the first genetic blueprint of iron acquisition and homeostasis for A. melanogenum.
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Affiliation(s)
- Yi Lu
- College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Guanglei Liu
- College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Hong Jiang
- College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Zhenming Chi
- College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Zhe Chi
- College of Marine Life Science, Ocean University of China, Qingdao, 266003, China.
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145
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You S, Tu T, Ma R, Huang HQ, Wang Y, Bai YG, Su XY, Cai HY, Yao B, Luo HY. Functional Analysis of a Highly Active β-Glucanase from Bispora sp. MEY-1 Using Its C-terminally Truncated Mutant. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:9728-9737. [PMID: 30043608 DOI: 10.1021/acs.jafc.8b01928] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A β-1,3-1,4-glucanase-encoding gene, Bisglu16B, was identified in Bispora sp. MEY-1. The deduced BisGlu16B consists of an N-terminal signal peptide, a catalytic module of glycoside hydrolase family 16 (GH16), and a C-terminal serine/proline-rich module. After expression in Pichia pastoris GS115, the purified recombinant BisGlu16B showed maximal activity at pH 4.0 and 55 °C and had broad substrate specificity (β-1,3-/β-1,4-mixed, β-1,3-, β-1,4-, and β-1,6-linked glucan, and β-1,4-mannan). The enzyme possessed high specific activities toward barley β-glucan (34 700 U·mg-1), lichenan (23 900 U·mg-1), and laminarin (9 000 U·mg-1). After removing the C-terminal module, the truncated mutant, BisGlu16B-ΔC, retained similar enzymatic properties to the wild type but displayed significantly enhanced activities (up to 2.5-fold). Functional and structural analyses indicated that the C-terminal module plays a key role in the substrate binding of BisGlu16B. This study provided an excellent candidate glucanase for industrial purposes and revealed the functions of a C-terminal serine/proline-rich region.
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Affiliation(s)
- Shuai You
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture , Feed Research Institute, Chinese Academy of Agricultural Sciences , Beijing 100081 , People's Republic of China
| | - Tao Tu
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture , Feed Research Institute, Chinese Academy of Agricultural Sciences , Beijing 100081 , People's Republic of China
| | - Rui Ma
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture , Feed Research Institute, Chinese Academy of Agricultural Sciences , Beijing 100081 , People's Republic of China
| | - Huo-Qing Huang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture , Feed Research Institute, Chinese Academy of Agricultural Sciences , Beijing 100081 , People's Republic of China
| | - Yuan Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture , Feed Research Institute, Chinese Academy of Agricultural Sciences , Beijing 100081 , People's Republic of China
| | - Ying-Guo Bai
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture , Feed Research Institute, Chinese Academy of Agricultural Sciences , Beijing 100081 , People's Republic of China
| | - Xiao-Yun Su
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture , Feed Research Institute, Chinese Academy of Agricultural Sciences , Beijing 100081 , People's Republic of China
| | - Hui-Yi Cai
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture , Feed Research Institute, Chinese Academy of Agricultural Sciences , Beijing 100081 , People's Republic of China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture , Feed Research Institute, Chinese Academy of Agricultural Sciences , Beijing 100081 , People's Republic of China
| | - Hui-Ying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture , Feed Research Institute, Chinese Academy of Agricultural Sciences , Beijing 100081 , People's Republic of China
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Efficient Production of Polymalic Acid by a Novel Isolated Aureobasidium pullulans Using Metabolic Intermediates and Inhibitors. Appl Biochem Biotechnol 2018; 187:612-627. [PMID: 30014335 DOI: 10.1007/s12010-018-2825-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 06/19/2018] [Indexed: 10/28/2022]
Abstract
Polymalic acid (PMA) is a linear anionic polyester composed of L-malic acid monomers, which have potential applications as drug carriers, surgical suture, and biodegradable plastics. In this study, a novel strain of Aureobasidium pullulans var. melanogenum GXZ-6 was isolated and identified according to the morphological observation and deoxyribonucleic acid internal-transcribed spacer sequence analysis, and the product of PMA was characterized by FT-IR, 13C-NMR, and 1H-NMR spectra. The PMA titer of GXZ-6 reached 62.56 ± 1.18 g L-1 with productivity of 0.35 g L-1 h-1 using optimized medium with addition of metabolic intermediates (citrate and malate) and inhibitor (malonate) by batch fermentation in a 10-L fermentor. Besides that the malate for PMA synthesis in GXZ-6 might mainly come from the glyoxylate cycle, based on results, citrate, malate, malonate, and maleate increased while succinate and fumarate inhibited the production of PMA, which was different from that of other A. pullulans. This study provided a potential strain and a simple metabolic control strategy for high-titer production of PMA and shared novel information on the biosynthesis pathway of PMA in A. pullulans.
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147
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Wajda Ł, Wyderka M, Polak Z, Duda-Chodak A, Makarewicz M. Examination of novel Aureobasidium pullulans isolates dominating apple microflora and assessing their potential for apple juice spoilage. World J Microbiol Biotechnol 2018; 34:115. [PMID: 29998388 PMCID: PMC6096541 DOI: 10.1007/s11274-018-2497-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 07/07/2018] [Indexed: 11/26/2022]
Abstract
There is very little up to date information regarding apple microflora so in the current study we decided to address that issue and assess whether dominant fungi which reside in fruit might spoil apple juice. Microorganisms were isolated from apples of Koksa Górska harvested in the middle of October in 2016 and 2017. Identification of isolates was based on the sequencing of ribosomal DNA. Some isolates were characteristic for a particular year but in both years apple microflora was dominated by Aureobasidium pullulans. Based on phylogenetic analysis it was stated that only one isolate (LW81) was closely related to strains which are already described in available databases. All other isolates collected in the current study differed significantly from sequences stored in databases, tending to form a common cluster. It was possible to predict secondary structure of ITS2 region only for the isolate LW81, while we managed to establish the length and location of 5.8S gene in Rfam database for all sequences. A. pullulans is known exopolysaccharide producer so obtained microorganisms were tested for their ability to synthesise those substances on Czapek-Dox agar. The strain which proved to be the most significant exopolysaccharide producer (isolate LW14) was inoculated in the sterilised apple juice at three different initial cell number (100, 1000 and 10,000 cfu/ml) and subjected to pasteurisation. In all cases pasteurisation eliminated fungal growth effectively, therefore A. pullulans strains should not pose any risk to the quality of pasteurised apple juices.
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Affiliation(s)
- Łukasz Wajda
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A str, 30-387 Krakow, Poland
| | - Magdalena Wyderka
- Department of Fermentation Technology and Technical Microbiology, Faculty of Food Technology, University of Agriculture in Krakow, ul. Balicka 122, 30-149 Krakow, Poland
| | - Zuzanna Polak
- Department of Fermentation Technology and Technical Microbiology, Faculty of Food Technology, University of Agriculture in Krakow, ul. Balicka 122, 30-149 Krakow, Poland
| | - Aleksandra Duda-Chodak
- Department of Fermentation Technology and Technical Microbiology, Faculty of Food Technology, University of Agriculture in Krakow, ul. Balicka 122, 30-149 Krakow, Poland
| | - Małgorzata Makarewicz
- Department of Fermentation Technology and Technical Microbiology, Faculty of Food Technology, University of Agriculture in Krakow, ul. Balicka 122, 30-149 Krakow, Poland
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Kalyana Chakravarthy S, Jayasudha R, Ranjith K, Dutta A, Pinna NK, Mande SS, Sharma S, Garg P, Murthy SI, Shivaji S. Alterations in the gut bacterial microbiome in fungal Keratitis patients. PLoS One 2018; 13:e0199640. [PMID: 29933394 PMCID: PMC6014669 DOI: 10.1371/journal.pone.0199640] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 06/11/2018] [Indexed: 12/12/2022] Open
Abstract
Dysbiosis in the gut microbiome has been implicated in several diseases including auto-immune diseases, inflammatory diseases, cancers and mental disorders. Keratitis is an inflammatory disease of the eye significantly contributing to corneal blindness in the developing world. It would be worthwhile to investigate the possibility of dysbiosis in the gut microbiome being associated with Keratitis. Here, we have analyzed fungal and bacterial populations in stool samples through high-throughput sequencing of the ITS2 region for fungi and V3-V4 region of 16S rRNA gene for bacteria in healthy controls (HC, n = 31) and patients with fungal keratitis (FK, n = 32). Candida albicans (2 OTUs), Aspergillus (1 OTU) and 3 other denovo-OTUs were enriched in FK samples and an unclassified denovo-OTU was enriched in HC samples. However, the overall abundances of these ‘discriminatory’ OTUs were very low (< 0.001%) and not indicative of significant dysbiosis in the fungal community inhabiting the gut of FK patients. In contrast, the gut bacterial richness and diversity in FK patients was significantly decreased when compared to HC. 52 OTUs were significantly enriched in HC samples whereas only 5 OTUs in FK. The OTUs prominently enriched in HC were identified as Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Lachnospira, Mitsuokella multacida, Bacteroides plebeius, Megasphaera and Lachnospiraceae. In FK samples, 5 OTUs affiliated to Bacteroides fragilis, Dorea, Treponema, Fusobacteriaceae, and Acidimicrobiales were significantly higher in abundance. The functional implications are that Faecalibacterium prausnitzii, an anti-inflammatory bacterium and Megasphaera, Mitsuokella multacida and Lachnospira are butyrate producers, which were enriched in HC patients, whereas Treponema and Bacteroides fragilis, which are pathogenic were abundant in FK patients, playing a potential pro-inflammatory role. Heatmap, PCoA plots and functional profiles further confirm the distinct patterns of gut bacterial composition in FK and HC samples. Our study demonstrates dysbiosis in the gut bacterial microbiomes of FK patients compared to HC. Further, based on inferred functions, it appears that dysbiosis in the gut of FK subjects is strongly associated with the disease phenotype with decrease in abundance of beneficial bacteria and increase in abundance of pro-inflammatory and pathogenic bacteria.
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Affiliation(s)
- Sama Kalyana Chakravarthy
- Jhaveri Microbiology Centre, Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy campus, Hyderabad, India
| | - Rajagopalaboopathi Jayasudha
- Jhaveri Microbiology Centre, Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy campus, Hyderabad, India
| | - Konduri Ranjith
- Jhaveri Microbiology Centre, Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy campus, Hyderabad, India
| | - Anirban Dutta
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, India
| | - Nishal Kumar Pinna
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, India
| | - Sharmila S. Mande
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, India
| | - Savitri Sharma
- Jhaveri Microbiology Centre, Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy campus, Hyderabad, India
| | - Prashant Garg
- Tej Kohli Cornea Institute, L. V. Prasad Eye Institute, Kallam Anji Reddy campus, Hyderabad, India
| | - Somasheila I. Murthy
- Tej Kohli Cornea Institute, L. V. Prasad Eye Institute, Kallam Anji Reddy campus, Hyderabad, India
| | - Sisinthy Shivaji
- Jhaveri Microbiology Centre, Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy campus, Hyderabad, India
- * E-mail:
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Monrad RN, Eklöf J, Krogh KBRM, Biely P. Glucuronoyl esterases: diversity, properties and biotechnological potential. A review. Crit Rev Biotechnol 2018; 38:1121-1136. [PMID: 29739247 DOI: 10.1080/07388551.2018.1468316] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Glucuronoyl esterases (GEs) belonging to the carbohydrate esterase family 15 (CE15) are involved in microbial degradation of lignocellulosic plant materials. GEs are capable of degrading complex polymers of lignin and hemicellulose cleaving ester bonds between glucuronic acid residues in xylan and lignin alcohols. GEs promote separation of lignin, hemicellulose and cellulose which is crucial for efficient utilization of biomass as an energy source and feedstock for further processing into products or chemicals. Genes encoding GEs are found in both fungi and bacteria, but, so far, bacterial GEs are essentially unexplored, and despite being discovered >10 years ago, only a limited number of GEs have been characterized. The first laboratory scale example of improved xylose and glucuronic acid release by the synergistic action of GE with cellulolytic enzymes was only reported recently (improved C5 sugar and glucuronic acid yields) and, until now, not much is known about their biotechnology potential. In this review, we discuss the diversity, structure and properties of microbial GEs and consider the status of their action on natural substrates and in biological systems in relation to their future industrial use.
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Affiliation(s)
| | | | | | - Peter Biely
- b Institute of Chemistry, Slovak Academy of Sciences , Bratislava , Slovak Republic
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150
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Guo J, Huang S, Chen Y, Guo X, Xiao D. Heterologous expression of Spathaspora passalidarum xylose reductase and xylitol dehydrogenase genes improved xylose fermentation ability of Aureobasidium pullulans. Microb Cell Fact 2018; 17:64. [PMID: 29712559 PMCID: PMC5925849 DOI: 10.1186/s12934-018-0911-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 04/24/2018] [Indexed: 11/16/2022] Open
Abstract
Background Aureobasidium pullulans is a yeast-like fungus that can ferment xylose to generate high-value-added products, such as pullulan, heavy oil, and melanin. The combinatorial expression of two xylose reductase (XR) genes and two xylitol dehydrogenase (XDH) genes from Spathaspora passalidarum and the heterologous expression of the Piromyces sp. xylose isomerase (XI) gene were induced in A. pullulans to increase the consumption capability of A. pullulans on xylose. Results The overexpression of XYL1.2 (encoding XR) and XYL2.2 (encoding XDH) was the most beneficial for xylose utilization, resulting in a 17.76% increase in consumed xylose compared with the parent strain, whereas the introduction of the Piromyces sp. XI pathway failed to enhance xylose utilization efficiency. Mutants with superior xylose fermentation performance exhibited increased intracellular reducing equivalents. The fermentation performance of all recombinant strains was not affected when glucose or sucrose was utilized as the carbon source. The strain with overexpression of XYL1.2 and XYL2.2 exhibited excellent fermentation performance with mimicked hydrolysate, and pullulan production increased by 97.72% compared with that of the parent strain. Conclusions The present work indicates that the P4 mutant (using the XR/XDH pathway) with overexpressed XYL1.2 and XYL2.2 exhibited the best xylose fermentation performance. The P4 strain showed the highest intracellular reducing equivalents and XR and XDH activity, with consequently improved pullulan productivity and reduced melanin production. This valuable development in aerobic fermentation by the P4 strain may provide guidance for the biotransformation of xylose to high-value products by A. pullulans through genetic approach. Electronic supplementary material The online version of this article (10.1186/s12934-018-0911-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jian Guo
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Siyao Huang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Yefu Chen
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
| | - Xuewu Guo
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Dongguang Xiao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
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