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Cheng CY, Zhang MY, Niu YC, Zhang M, Geng YH, Deng H. Comparison of Fungal Genera Isolated from Cucumber Plants and Rhizosphere Soil by Using Various Cultural Media. J Fungi (Basel) 2023; 9:934. [PMID: 37755042 PMCID: PMC10532442 DOI: 10.3390/jof9090934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023] Open
Abstract
Plant endophytic fungi and rhizosphere soil fungi are often reported as biocontrol agents against plant pathogens or with plant growth promotion potential. Four treatments were performed in field and greenhouse experiments where cucumber plants were inoculated with Trichoderma harzianum and Fusarium oxysporum in 2022. The roots, stems and leaves of cucumber plants and their rhizosphere soil were collected twice individually from the field and greenhouse for isolation of cucumber endophytic and rhizosphere soil fungi. All fungal strains were identified through sequence similarity of the ITS1-5.8s-ITS2 rDNA region. The potato dextrose agar (PDA) media yielded the highest number of genera isolated from cucumber plants, rhizosphere soil and both compared to other media. There were no significant differences among the four media for the isolation of all cucumber endophytic fungi. However, in the roots, the number of endophytic fungi isolated by MRBA was significantly higher than that isolated on malt extract agar (MEA), while in the stems, the number of fungi isolated with PDA was significantly higher than that isolated with Martin's rose bengal agar medium (MRBA). PDA had significantly higher isolation efficiency for the rhizosphere soil fungi than MRBA. The 28 fungal genera had high isolation efficiency, and the endophytic Trichoderma strains were significantly more isolated by MEA than those of MRBA. It is suggested that PDA can be used as a basic medium, and different cultural media can be considered for specific fungal genera.
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Affiliation(s)
- Chong-Yang Cheng
- Plant Protection College, Henan Agricultural University, No. 95 Wen-Hua Road, Zhengzhou 450002, China; (C.-Y.C.); (M.Z.)
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, China; (M.-Y.Z.); (Y.-C.N.)
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, China
| | - Ming-Yuan Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, China; (M.-Y.Z.); (Y.-C.N.)
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, China
| | - Yong-Chun Niu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, China; (M.-Y.Z.); (Y.-C.N.)
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, China
| | - Meng Zhang
- Plant Protection College, Henan Agricultural University, No. 95 Wen-Hua Road, Zhengzhou 450002, China; (C.-Y.C.); (M.Z.)
| | - Yue-Hua Geng
- Plant Protection College, Henan Agricultural University, No. 95 Wen-Hua Road, Zhengzhou 450002, China; (C.-Y.C.); (M.Z.)
| | - Hui Deng
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, China; (M.-Y.Z.); (Y.-C.N.)
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, China
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Lv R, Yang X, Qiao M, Fang L, Li J, Yu Z. Exophialayunnanensis and Exophialayuxiensis (Chaetothyriales, Herpotrichiellaceae), two new species of soil-inhabiting Exophiala from Yunnan Province, China. MycoKeys 2022; 94:109-124. [PMID: 36760541 PMCID: PMC9836470 DOI: 10.3897/mycokeys.94.96782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
During a survey of soil fungi collected from Yunnan Province, China, two new species of Exophiala, E.yunnanensis and E.yuxiensis, were isolated from the soil of karst rocky desertification (KRD). The DNA sequences of these respective strains, including internal transcribed spacers (ITS), large subunit nuclear ribosomal RNA (LSU rRNA), partial small subunit (SSU) and β-tubulin (tub2) were sequenced and compared with those from species closely-related to Exophiala. Exophialayunnanensis differs from the phylogenetically closely related E.nagquensis and E.brunnea by its smaller aseptate conidia. Exophialayuxiensis is phylogenetically related to E.lecanii-corni, E.lavatrina and E.mali, but can be distinguished from them by its larger conidia. Full descriptions, illustrations and phylogenetic positions of E.yunnanensis and E.yuxiensis were provided.
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Affiliation(s)
- Ruili Lv
- Laboratory for Conservation and Utilization of Bio-resources, Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, ChinaYunnan UniversityKunmingChina
| | - Xiaoqian Yang
- Laboratory for Conservation and Utilization of Bio-resources, Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, ChinaYunnan UniversityKunmingChina
| | - Min Qiao
- Laboratory for Conservation and Utilization of Bio-resources, Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, ChinaYunnan UniversityKunmingChina
| | - Linlin Fang
- Laboratory for Conservation and Utilization of Bio-resources, Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, ChinaYunnan UniversityKunmingChina
| | - Jianying Li
- Kunming Edible Fungi Institute of All China Federation of Supply and Marketing Cooperatives, Kunming 650221, ChinaKunming Edible Fungi Institute of All China Federation of Supply and Marketing CooperativesKunmingChina
| | - Zefen Yu
- Laboratory for Conservation and Utilization of Bio-resources, Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, ChinaYunnan UniversityKunmingChina
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Tagg AS, Sperlea T, Labrenz M, Harrison JP, Ojeda JJ, Sapp M. Year-Long Microbial Succession on Microplastics in Wastewater: Chaotic Dynamics Outweigh Preferential Growth. Microorganisms 2022; 10:microorganisms10091775. [PMID: 36144377 PMCID: PMC9506493 DOI: 10.3390/microorganisms10091775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Microplastics are a globally-ubiquitous aquatic pollutant and have been heavily studied over the last decade. Of particular interest are the interactions between microplastics and microorganisms, especially the pursuit to discover a plastic-specific biome, the so-called plastisphere. To follow this up, a year-long microcosm experimental setup was deployed to expose five different microplastic types (and silica beads control) to activated aerobic wastewater in controlled conditions, with microbial communities being measured four times over the course of the year using 16S rDNA (bacterial) and ITS (fungal) amplicon sequencing. The biofilm community shows no evidence of a specific plastisphere, even after a year of incubation. Indeed, the microbial communities (particularly bacterial) show a clear trend of increasing dissimilarity between plastic types as time increases. Despite little evidence for a plastic-specific community, there was a slight grouping observed for polyolefins (PE and PP) in 6–12-month biofilms. Additionally, an OTU assigned to the genus Devosia was identified on many plastics, increasing over time while showing no growth on silicate (natural particle) controls, suggesting this could be either a slow-growing plastic-specific taxon or a symbiont to such. Both substrate-associated findings were only possible to observe in samples incubated for 6–12 months, which highlights the importance of studying long-term microbial community dynamics on plastic surfaces.
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Affiliation(s)
- Alexander S. Tagg
- Leibniz-Institut für Ostseeforschung Warnemünde, Seestraße 15, 18119 Rostock, Germany
- Department of Chemical Engineering, Faculty of Science and Engineering, Swansea University, Swansea SA1 8EN, UK
- Correspondence:
| | - Theodor Sperlea
- Leibniz-Institut für Ostseeforschung Warnemünde, Seestraße 15, 18119 Rostock, Germany
| | - Matthias Labrenz
- Leibniz-Institut für Ostseeforschung Warnemünde, Seestraße 15, 18119 Rostock, Germany
| | - Jesse P. Harrison
- CSC—IT Center for Science Ltd., P.O. Box 405, FI-02101 Espoo, Finland
| | - Jesús J. Ojeda
- Department of Chemical Engineering, Faculty of Science and Engineering, Swansea University, Swansea SA1 8EN, UK
| | - Melanie Sapp
- Institute of Human Genetics, University Hospital Düsseldorf, Heinrich Heine University, Moorenstrasse 5, 40225 Düsseldorf, Germany
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Likar M, Grašič M, Stres B, Regvar M, Gaberščik A. Original Leaf Colonisers Shape Fungal Decomposer Communities of Phragmites australis in Intermittent Habitats. J Fungi (Basel) 2022; 8:jof8030284. [PMID: 35330286 PMCID: PMC8951327 DOI: 10.3390/jof8030284] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 01/29/2023] Open
Abstract
Common reed (Phragmites australis) has high biomass production and is primarily subjected to decomposition processes affected by multiple factors. To predict litter decomposition dynamics in intermittent lakes, it is critical to understand how communities of fungi, as the primary decomposers, form under different habitat conditions. This study reports the shotgun metagenomic sequencing of the initial fungal communities on common reed leaves decomposing under different environmental conditions. We demonstrate that a complex network of fungi forms already on the plant persists into the decomposition phase. Phragmites australis leaves contained at least five fungal phyla, with abundant Ascomycota (95.7%) and Basidiomycota (4.1%), identified as saprotrophs (48.6%), pathotrophs (22.5%), and symbiotrophs (12.6%). Most of the correlations between fungi in fresh and decomposing leaves were identified as co-occurrences (positive correlations). The geographic source of litter and leaf age did not affect the structure and diversity of fungal communities. Keystone taxa were mostly moisture-sensitive. Our results suggest that habitat has a strong effect on the formation of the fungal communities through keystone taxa. Nevertheless, it can also alter the proportions of individual fungal groups in the community through indirect effects on competition between the fungal taxa and their exploitation of favourable conditions.
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Affiliation(s)
- Matevž Likar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (M.G.); (M.R.); (A.G.)
- Correspondence: ; Tel.: +386-1-320-3-418
| | - Mateja Grašič
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (M.G.); (M.R.); (A.G.)
| | - Blaž Stres
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Marjana Regvar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (M.G.); (M.R.); (A.G.)
| | - Alenka Gaberščik
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (M.G.); (M.R.); (A.G.)
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Niu X, Xie W, Zhang J, Hu Q. Biodiversity of Entomopathogenic Fungi in the Soils of South China. Microorganisms 2019; 7:microorganisms7090311. [PMID: 31484332 PMCID: PMC6780753 DOI: 10.3390/microorganisms7090311] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/10/2019] [Accepted: 08/29/2019] [Indexed: 11/23/2022] Open
Abstract
The southern part of China, located in tropical and south subtropical areas has unique natural environments, but the distributions of entomopathogenic fungi (EFs) in the soil are not clear. In this research, 198 soil samples were collected from the four Provinces (Autonomous Region) of South China. The results indicated that a total of 292 fungal isolates were obtained from 176 soil samples. Then, based on the morphological and rDNA-ITS sequences analysis, 213 EFs isolates of 19 species in 12 genera were identified. Furthermore, Purpureocillium lilacinum with 75 isolates was recognized as the absolutely dominant EF species, while Isaria javanica, Metarhizium anisopliae, and Beauveria bassiana (respectively with 29, 26, and 26 isolates) were the richer species. The data also indicated that Guangxi Province has the best EFs diversity with the Shannon–Wiener index (SWI) of 2.29, the soils covered with grass had the best EFs diversity with the 2.14 SWI, while the orchard and fallow land had the lowest SWI of 1.52, which suggested that the diversity of plants and insects on ground, as well as the massive application of broad-spectrum fungicides, affect the EFs diversity in the soil. Finally, the rare species, Nectria mauritiicola and Scopulariopsis brumptii were first reported about their entomopathogenic activities against Bemisia tabaci. Our experiment will give new insights to the understanding of EFs distribution characteristics and their biodiversity conservation.
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Affiliation(s)
- Xiaoyan Niu
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Weiwen Xie
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Jing Zhang
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Qiongbo Hu
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
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Cheikh-Ali Z, Glynou K, Ali T, Ploch S, Kaiser M, Thines M, Bode HB, Maciá-Vicente JG. Diversity of exophillic acid derivatives in strains of an endophytic Exophiala sp. PHYTOCHEMISTRY 2015; 118:83-93. [PMID: 26296744 DOI: 10.1016/j.phytochem.2015.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 08/03/2015] [Accepted: 08/12/2015] [Indexed: 06/04/2023]
Abstract
Members of the fungal genus Exophiala are common saprobes in soil and water environments, opportunistic pathogens of animals, or endophytes in plant roots. Their ecological versatility could imply a capacity to produce diverse secondary metabolites, but only a few studies have aimed at characterizing their chemical profiles. Here, we assessed the secondary metabolites produced by five Exophiala sp. strains of a particular phylotype, isolated from roots of Microthlaspi perfoliatum growing in different European localities. Exophillic acid and two previously undescribed compounds were isolated from these strains, and their structures were elucidated by spectroscopic methods using MS, 1D and 2D NMR. Bioassays revealed a weak activity of these compounds against disease-causing protozoa and mammalian cells. In addition, 18 related structures were identified by UPLC/MS based on comparisons with the isolated structures. Three Exophiala strains produced derivatives containing a β-d-glucopyranoside moiety, and their colony morphology was distinct from the other two strains, which produced derivatives lacking β-d-glucopyranoside. Whether the chemical/morphological strain types represent variants of the same genotype or independent genetic populations within Exophiala remains to be evaluated.
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Affiliation(s)
- Zakaria Cheikh-Ali
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, 60438 Frankfurt am Main, Germany
| | - Kyriaki Glynou
- Institute of Ecology, Evolution and Diversity, Goethe Universität Frankfurt, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany
| | - Tahir Ali
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Sebastian Ploch
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute, Parasite Chemotherapy, Socinstrasse 57, P.O. Box, 4002 Basel, Switzerland
| | - Marco Thines
- Institute of Ecology, Evolution and Diversity, Goethe Universität Frankfurt, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany; Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Helge B Bode
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, 60438 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt, 60438 Frankfurt am Main, Germany.
| | - Jose G Maciá-Vicente
- Institute of Ecology, Evolution and Diversity, Goethe Universität Frankfurt, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany.
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Haňáčková Z, Koukol O, Štursová M, Kolařík M, Baldrian P. Fungal succession in the needle litter of a montane Picea abies forest investigated through strain isolation and molecular fingerprinting. FUNGAL ECOL 2015. [DOI: 10.1016/j.funeco.2014.09.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Fredriksson NJ, Hermansson M, Wilén BM. Impact of T-RFLP data analysis choices on assessments of microbial community structure and dynamics. BMC Bioinformatics 2014; 15:360. [PMID: 25381552 PMCID: PMC4232699 DOI: 10.1186/s12859-014-0360-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 10/23/2014] [Indexed: 12/25/2022] Open
Abstract
Background Terminal restriction fragment length polymorphism (T-RFLP) analysis is a common DNA-fingerprinting technique used for comparisons of complex microbial communities. Although the technique is well established there is no consensus on how to treat T-RFLP data to achieve the highest possible accuracy and reproducibility. This study focused on two critical steps in the T-RFLP data treatment: the alignment of the terminal restriction fragments (T-RFs), which enables comparisons of samples, and the normalization of T-RF profiles, which adjusts for differences in signal strength, total fluorescence, between samples. Results Variations in the estimation of T-RF sizes were observed and these variations were found to affect the alignment of the T-RFs. A novel method was developed which improved the alignment by adjusting for systematic shifts in the T-RF size estimations between the T-RF profiles. Differences in total fluorescence were shown to be caused by differences in sample concentration and by the gel loading. Five normalization methods were evaluated and the total fluorescence normalization procedure based on peak height data was found to increase the similarity between replicate profiles the most. A high peak detection threshold, alignment correction, normalization and the use of consensus profiles instead of single profiles increased the similarity of replicate T-RF profiles, i.e. lead to an increased reproducibility. The impact of different treatment methods on the outcome of subsequent analyses of T-RFLP data was evaluated using a dataset from a longitudinal study of the bacterial community in an activated sludge wastewater treatment plant. Whether the alignment was corrected or not and if and how the T-RF profiles were normalized had a substantial impact on ordination analyses, assessments of bacterial dynamics and analyses of correlations with environmental parameters. Conclusions A novel method for the evaluation and correction of the alignment of T-RF profiles was shown to reduce the uncertainty and ambiguity in alignments of T-RF profiles. Large differences in the outcome of assessments of bacterial community structure and dynamics were observed between different alignment and normalization methods. The results of this study can therefore be of value when considering what methods to use in the analysis of T-RFLP data. Electronic supplementary material The online version of this article (doi:10.1186/s12859-014-0360-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nils Johan Fredriksson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
| | - Malte Hermansson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
| | - Britt-Marie Wilén
- Department of Civil and Environmental Engineering, Water Environment Technology, Chalmers University of Technology, Gothenburg, Sweden.
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Hubka V, Nováková A, Kolařík M, Jurjević Ž, Peterson SW. Revision of Aspergillus section Flavipedes: seven new species and proposal of section Jani sect. nov. Mycologia 2014; 107:169-208. [PMID: 25344259 DOI: 10.3852/14-059] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Aspergillus section Flavipedes contains species found worldwide in soils and rhizospheres, indoor and cave environments, as endophytes, food contaminants and occasionally as human pathogens. They produce many extensively studied bioactive secondary metabolites and biotechnologically relevant enzymes. The taxa were revised based on phylogenetic analysis of sequences from four loci (β-tubulin, calmodulin, RPB2, ITS rDNA), two PCR fingerprinting methods, micro- and macromorphology and physiology. Section Flavipedes includes three known and seven new species: A. ardalensis, A. frequens, A. luppii, A. mangaliensis, A. movilensis, A. polyporicola and A. spelaeus. The name A. neoflavipes was proposed for Fennellia flavipes a distinct species from its supposed asexual state A. flavipes. Aspergillus iizukae, A. frequens and A. mangaliensis are the most common and widely distributed species, whereas A. flavipes s. str. is rare. A dichotomous key based on the combination of morphology and physiology is provided for all recognized species. Aspergillus section Jani is established to contain A. janus and A. brevijanus, species previously classified as members of sect. Versicolores, Terrei or Flavipedes. This new section is strongly supported by phylogenetic data and morphology. Section Jani species produce three types of conidiophores and conidia, and colonies have green and white sectors making them distinctive. Accessory conidia found in pathogenic A. terreus were found in all members of sects. Flavipedes and Jani. Our data indicated that A. frequens is a clinically relevant and produces accessory conidia during infection.
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Affiliation(s)
- Vit Hubka
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague 2, Czech RepublicInstitute of Microbiology AS CR, v.v.i, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Alena Nováková
- Institute of Microbiology AS CR, v.v.i, Vídeňská 1083, 142 20 Prague 4, Czech Republic, and Institute of Soil Biology, Biology Centre AS CR, v.v.i., Na Sádkách 7, 370 05 České Budějovice, Czech Republic
| | - Miroslav Kolařík
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague 2, Czech Republic, and Institute of Microbiology AS CR, v.v.i, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Željko Jurjević
- EMSL Analytical Inc., 200 Route 130 North, Cinnaminson, New Jersey 08077
| | - Stephen W Peterson
- Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, 1815 N. University Street, Peoria, Illinois 61604
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Humily F, Farrant GK, Marie D, Partensky F, Mazard S, Perennou M, Labadie K, Aury JM, Wincker P, Segui AN, Scanlan DJ, Garczarek L. Development of a targeted metagenomic approach to study a genomic region involved in light harvesting in marine Synechococcus. FEMS Microbiol Ecol 2014; 88:231-49. [PMID: 24862161 DOI: 10.1111/1574-6941.12285] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 11/14/2013] [Accepted: 01/12/2014] [Indexed: 12/01/2022] Open
Abstract
Synechococcus, one of the most abundant cyanobacteria in marine ecosystems, displays a broad pigment diversity. However, the in situ distribution of pigment types remains largely unknown. In this study, we combined flow cytometry cell sorting, whole-genome amplification, and fosmid library construction to target a genomic region involved in light-harvesting complex (phycobilisome) biosynthesis and regulation. Synechococcus community composition and relative contamination by heterotrophic bacteria were assessed at each step of the pipeline using terminal restriction fragment length polymorphism targeting the petB and 16S rRNA genes, respectively. This approach allowed us to control biases inherent to each method and select reliable WGA products to construct a fosmid library from a natural sample collected off Roscoff (France). Sequencing of 25 fosmids containing the targeted region led to the assembly of whole or partial phycobilisome regions. Most contigs were assigned to clades I and IV consistent with the known dominance of these clades in temperate coastal waters. However, one of the fosmids contained genes distantly related to their orthologs in reference genomes, suggesting that it belonged to a novel phylogenetic clade. Altogether, this study provides novel insights into Synechococcus community structure and pigment type diversity at a representative coastal station of the English Channel.
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Affiliation(s)
- Florian Humily
- UPMC-Université Paris VI, Station Biologique, Roscoff Cedex, France; CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Oceanic Plankton Group, Marine Phototrophic Prokaryotes Team, Roscoff Cedex, France
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Higginbotham S, Wong WR, Linington RG, Spadafora C, Iturrado L, Arnold AE. Sloth hair as a novel source of fungi with potent anti-parasitic, anti-cancer and anti-bacterial bioactivity. PLoS One 2014; 9:e84549. [PMID: 24454729 PMCID: PMC3893167 DOI: 10.1371/journal.pone.0084549] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/15/2013] [Indexed: 01/30/2023] Open
Abstract
The extraordinary biological diversity of tropical forests harbors a rich chemical diversity with enormous potential as a source of novel bioactive compounds. Of particular interest are new environments for microbial discovery. Sloths – arboreal mammals commonly found in the lowland forests of Panama – carry a wide variety of micro- and macro-organisms on their coarse outer hair. Here we report for the first time the isolation of diverse and bioactive strains of fungi from sloth hair, and their taxonomic placement. Eighty-four isolates of fungi were obtained in culture from the surface of hair that was collected from living three-toed sloths (Bradypus variegatus, Bradypodidae) in Soberanía National Park, Republic of Panama. Phylogenetic analyses revealed a diverse group of Ascomycota belonging to 28 distinct operational taxonomic units (OTUs), several of which are divergent from previously known taxa. Seventy-four isolates were cultivated in liquid broth and crude extracts were tested for bioactivity in vitro. We found a broad range of activities against strains of the parasites that cause malaria (Plasmodium falciparum) and Chagas disease (Trypanosoma cruzi), and against the human breast cancer cell line MCF-7. Fifty fungal extracts were tested for antibacterial activity in a new antibiotic profile screen called BioMAP; of these, 20 were active against at least one bacterial strain, and one had an unusual pattern of bioactivity against Gram-negative bacteria that suggests a potentially new mode of action. Together our results reveal the importance of exploring novel environments for bioactive fungi, and demonstrate for the first time the taxonomic composition and bioactivity of fungi from sloth hair.
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Affiliation(s)
- Sarah Higginbotham
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
- * E-mail:
| | - Weng Ruh Wong
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Roger G. Linington
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Carmenza Spadafora
- Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Panama, Republic of Panama
| | - Liliana Iturrado
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
| | - A. Elizabeth Arnold
- School of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America
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Weissbrodt DG, Schneiter GS, Fürbringer JM, Holliger C. Identification of trigger factors selecting for polyphosphate- and glycogen-accumulating organisms in aerobic granular sludge sequencing batch reactors. WATER RESEARCH 2013; 47:7006-18. [PMID: 24200006 DOI: 10.1016/j.watres.2013.08.043] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 08/12/2013] [Accepted: 08/27/2013] [Indexed: 05/06/2023]
Abstract
Nutrient removal performances of sequencing batch reactors using granular sludge for intensified biological wastewater treatment rely on optimal underlying microbial selection. Trigger factors of bacterial selection and nutrient removal were investigated in these novel biofilm systems with specific emphasis on polyphosphate- (PAO) and glycogen-accumulating organisms (GAO) mainly affiliated with Accumulibacter and Competibacter, respectively. In a first dynamic reactor operated with stepwise changes in concentration and ratio of acetate and propionate (Ac/Pr) under anaerobic feeding and aerobic starvation conditions and without wasting sludge periodically, propionate favorably selected for Accumulibacter (35% relative abundance) and stable production of granular biomass. A Plackett-Burman multifactorial experimental design was then used to screen in eight runs of 50 days at stable sludge retention time of 15 days for the main effects of COD concentration, Ac/Pr ratio, COD/P ratio, pH, temperature, and redox conditions during starvation. At 95% confidence level, pH was mainly triggering direct Accumulibacter selection and nutrient removal. The overall PAO/GAO competition in granular sludge was statistically equally impacted by pH, temperature, and redox factors. High Accumulibacter abundances (30-47%), PAO/GAO ratios (2.8-8.4), and phosphorus removal (80-100%) were selected by slightly alkaline (pH > 7.3) and lower mesophilic (<20 °C) conditions, and under full aeration during fixed 2-h starvation. Nitrogen removal by nitrification and denitrification (84-97%) was positively correlated to pH and temperature. In addition to alkalinity, non-limited organic conditions, 3-carbon propionate substrate, sludge age control, and phase length adaptation under alternating aerobic-anoxic conditions during starvation can lead to efficient nutrient-removing granular sludge biofilm systems.
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Affiliation(s)
- David G Weissbrodt
- Ecole Polytechnique Fédérale de Lausanne, School of Architecture, Civil and Environmental Engineering, Institute of Environmental Engineering, Laboratory for Environmental Biotechnology, Lausanne, Switzerland.
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Daebeler A, Gansen M, Frenzel P. Methyl fluoride affects methanogenesis rather than community composition of methanogenic archaea in a rice field soil. PLoS One 2013; 8:e53656. [PMID: 23341965 PMCID: PMC3544908 DOI: 10.1371/journal.pone.0053656] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 12/04/2012] [Indexed: 11/19/2022] Open
Abstract
The metabolic pathways of methane formation vary with environmental conditions, but whether this can also be linked to changes in the active archaeal community structure remains uncertain. Here, we show that the suppression of aceticlastic methanogenesis by methyl fluoride (CH3F) caused surprisingly little differences in community composition of active methanogenic archaea from a rice field soil. By measuring the natural abundances of carbon isotopes we found that the effective dose for a 90% inhibition of aceticlastic methanogenesis in anoxic paddy soil incubations was <0.75% CH3F (v/v). The construction of clone libraries as well as t-RFLP analysis revealed that the active community, as indicated by mcrA transcripts (encoding the α subunit of methyl-coenzyme M reductase, a key enzyme for methanogenesis), remained stable over a wide range of CH3F concentrations and represented only a subset of the methanogenic community. More precisely, Methanocellaceae were of minor importance, but Methanosarcinaceae dominated the active population, even when CH3F inhibition only allowed for aceticlastic methanogenesis. In addition, we detected mcrA gene fragments of a so far unrecognised phylogenetic cluster. Transcription of this phylotype at methyl fluoride concentrations suppressing aceticlastic methanogenesis suggests that the respective organisms perform hydrogenotrophic methanogenesis. Hence, the application of CH3F combined with transcript analysis is not only a useful tool to measure and assign in situ acetate usage, but also to explore substrate usage by as yet uncultivated methanogens.
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Affiliation(s)
- Anne Daebeler
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Martina Gansen
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Peter Frenzel
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- * E-mail:
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Weissbrodt DG, Shani N, Sinclair L, Lefebvre G, Rossi P, Maillard J, Rougemont J, Holliger C. PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data. BMC Microbiol 2012; 12:306. [PMID: 23270314 PMCID: PMC3566925 DOI: 10.1186/1471-2180-12-306] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 12/18/2012] [Indexed: 12/23/2022] Open
Abstract
Background In molecular microbial ecology, massive sequencing is gradually replacing classical fingerprinting techniques such as terminal-restriction fragment length polymorphism (T-RFLP) combined with cloning-sequencing for the characterization of microbiomes. Here, a bioinformatics methodology for pyrosequencing-based T-RF identification (PyroTRF-ID) was developed to combine pyrosequencing and T-RFLP approaches for the description of microbial communities. The strength of this methodology relies on the identification of T-RFs by comparison of experimental and digital T-RFLP profiles obtained from the same samples. DNA extracts were subjected to amplification of the 16S rRNA gene pool, T-RFLP with the HaeIII restriction enzyme, 454 tag encoded FLX amplicon pyrosequencing, and PyroTRF-ID analysis. Digital T-RFLP profiles were generated from the denoised full pyrosequencing datasets, and the sequences contributing to each digital T-RF were classified to taxonomic bins using the Greengenes reference database. The method was tested both on bacterial communities found in chloroethene-contaminated groundwater samples and in aerobic granular sludge biofilms originating from wastewater treatment systems. Results PyroTRF-ID was efficient for high-throughput mapping and digital T-RFLP profiling of pyrosequencing datasets. After denoising, a dataset comprising ca. 10′000 reads of 300 to 500 bp was typically processed within ca. 20 minutes on a high-performance computing cluster, running on a Linux-related CentOS 5.5 operating system, enabling parallel processing of multiple samples. Both digital and experimental T-RFLP profiles were aligned with maximum cross-correlation coefficients of 0.71 and 0.92 for high- and low-complexity environments, respectively. On average, 63±18% of all experimental T-RFs (30 to 93 peaks per sample) were affiliated to phylotypes. Conclusions PyroTRF-ID profits from complementary advantages of pyrosequencing and T-RFLP and is particularly adapted for optimizing laboratory and computational efforts to describe microbial communities and their dynamics in any biological system. The high resolution of the microbial community composition is provided by pyrosequencing, which can be performed on a restricted set of selected samples, whereas T-RFLP enables simultaneous fingerprinting of numerous samples at relatively low cost and is especially adapted for routine analysis and follow-up of microbial communities on the long run.
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Affiliation(s)
- David G Weissbrodt
- Ecole Polytechnique Fédérale de Lausanne, School of Architecture, Civil and Environmental Engineering, Laboratory for Environmental Biotechnology, Station 6, Lausanne 1015, Switzerland
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Roberts DM, Schofield PG, Donn S, Daniell TJ. Directed terminal restriction analysis tool (DRAT): an aid to enzyme selection for directed terminal-restriction fragment length polymorphisms. Methods Ecol Evol 2011. [DOI: 10.1111/j.2041-210x.2011.00139.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Identification and characterization of potential performance-related gut microbiotas in broiler chickens across various feeding trials. Appl Environ Microbiol 2011; 77:5868-78. [PMID: 21742925 DOI: 10.1128/aem.00165-11] [Citation(s) in RCA: 212] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Three broiler feeding trials were investigated in order to identify gut bacteria consistently linked with improvements in bird performance as measured by feed efficiency. Trials were done in various geographic locations and varied in diet composition, broiler breed, and bird age. Gut microbial communities were investigated using microbial profiling. Eight common performance-linked operational taxonomic units (OTUs) were identified within both the ilea (180, 492, and 564-566) and ceca (140-142, 218-220, 284-286, 312, and 482) across trials. OTU 564-566 was associated with lower performance, while OTUs 140-142, 482, and 492 were associated with improved performance. Targeted cloning and sequencing of these eight OTUs revealed that they represented 26 bacterial species or phylotypes which clustered phylogenetically into seven groups related to Lactobacillus spp., Ruminococcaceae, Clostridiales, Gammaproteobacteria, Bacteroidales, Clostridiales/Lachnospiraceae, and unclassified bacteria/clostridia. Where bacteria were identifiable to the phylum level, they belonged predominantly to the Firmicutes, with Bacteroidetes and Proteobacteria also identified. Some of the potential performance-related phylotypes showed high sequence identity with classified bacteria (Lactobacillus salivarius, Lactobacillus aviarius, Lactobacillus crispatus, Faecalibacterium prausnitzii, Escherichia coli, Gallibacterium anatis, Clostridium lactatifermentans, Ruminococcus torques, Bacteroides vulgatus, and Alistipes finegoldii). The 16S rRNA gene sequence information generated will allow quantitative assays to be developed which will enable elucidations of which of these phylotypes are truly performance related. This information could be used to monitor strategies to improve feed efficiency and feed formulation for optimal gut health.
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Iskandar NL, Zainudin NAIM, Tan SG. Tolerance and biosorption of copper (Cu) and lead (Pb) by filamentous fungi isolated from a freshwater ecosystem. J Environ Sci (China) 2011; 23:824-30. [PMID: 21790056 DOI: 10.1016/s1001-0742(10)60475-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Filamentous fungi are able to accumulate significant amount of metals from their environment. The potential of fungal biomass as agents for biosorption of heavy metals from contaminated sediments is currently receiving attention. In the present study, a total of 41 isolates of filamentous fungi obtained from the sediment of the Langat River, Selangor, Malaysia were screened for their tolerance and uptake capability of copper (Cu) and lead (Pb). The isolates were identified as Aspergillus niger, A. fumigatus, Trichoderma asperellum, Penicillium simplicissimum and P. janthinellum. A. niger and P. simplicissimum, were able to survive at 1000 mg/L of Cu(II) concentration on Potato Dextrose Agar (PDA) while for Pb, only A. niger survived at 5000 mg/L concentration. The results showed that A. niger, P. simplicissimum and T. asperellum have a better uptake capacity for Pb compared to Cu and the findings indicated promising biosorption of Cu and Pb by these filamentous fungi from aqueous solution. The present study was also determined the maximum removal of Cu(II) and Pb(II) that was performed by A. niger. The metal removal which occurred at Cu(II) 200 mg/L was (20.910 +/- 0.581) mg/g and at 250 mg/L of Pb(II) was (54.046 +/- 0.328) mg/g.
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Affiliation(s)
- Nur Liyana Iskandar
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
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