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Song JY, Wu HX, Li JC, Ding WF, Gong CL, Zeng XY, Wijayawardene NN, Yang DX. Taxonomy and evolution history of two new litter-decomposing Ciliochorella (Amphisphaeriales, Sporocadaceae). MycoKeys 2023; 100:95-121. [PMID: 38025587 PMCID: PMC10660159 DOI: 10.3897/mycokeys.100.108863] [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: 07/01/2023] [Accepted: 10/21/2023] [Indexed: 12/01/2023] Open
Abstract
The genus Ciliochorella is a group of pestalotioid fungi, which typically occurs in subtropical and tropical areas. Species from the Ciliochorella genus play important roles in the decomposition of litter. In this study, we introduce two new species (Ciliochorellachinensissp. nov. and C.savannicasp. nov.) that were found on leaf litter collected from savanna-like vegetation in hot dry valleys of southwestern China. Phylogenetic analyses of combined LSU, ITS and tub2 sequence datasets indicated that C.chinensis and C.savannica respectively form a distinct clade within the Ciliochorella genus. The comparison of the morphological characteristics indicated that the two new species are well differentiated within this genus species. Analysis of the evolutionary history suggests that Ciliochorella originated from the Eurasian continent during the Paleogene (38 Mya). Further, we find that both new species can produce cellulase and laccase, playing a decomposer role.
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Affiliation(s)
- Jia-Yu Song
- International Fungal Research and Development Centre, Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, ChinaInternational Fungal Research and Development Centre, Institute of Highland Forest Science, Chinese Academy of ForestryKunmingChina
| | - Hai-Xia Wu
- International Fungal Research and Development Centre, Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, ChinaInternational Fungal Research and Development Centre, Institute of Highland Forest Science, Chinese Academy of ForestryKunmingChina
- Key Laboratory of Breeding and Utilization of Resource Insects, National Forestry and Grassland Administration, Kunming 650224, ChinaKey Laboratory of Breeding and Utilization of Resource Insects, National Forestry and Grassland AdministrationKunmingChina
| | - Jin-Chen Li
- International Fungal Research and Development Centre, Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, ChinaInternational Fungal Research and Development Centre, Institute of Highland Forest Science, Chinese Academy of ForestryKunmingChina
| | - Wei-Feng Ding
- International Fungal Research and Development Centre, Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, ChinaInternational Fungal Research and Development Centre, Institute of Highland Forest Science, Chinese Academy of ForestryKunmingChina
- Key Laboratory of Breeding and Utilization of Resource Insects, National Forestry and Grassland Administration, Kunming 650224, ChinaKey Laboratory of Breeding and Utilization of Resource Insects, National Forestry and Grassland AdministrationKunmingChina
| | - Cui-Ling Gong
- International Fungal Research and Development Centre, Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, ChinaInternational Fungal Research and Development Centre, Institute of Highland Forest Science, Chinese Academy of ForestryKunmingChina
| | - Xiang-Yu Zeng
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, ChinaGuizhou UniversityGuiyangChina
| | - Nalin N. Wijayawardene
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan 655011, ChinaQujing Normal UniversityQujingChina
| | - Da-Xin Yang
- Kunming Branch (KMB), Chinese Academy of Sciences (CAS), Kunming, Yunnan 650204, ChinaKunming Branch (KMB), Chinese Academy of Sciences (CAS)KunmingChina
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Samaradiwakara NP, de Farias ARG, Tennakoon DS, Aluthmuhandiram JVS, Bhunjun CS, Chethana KWT, Kumla J, Lumyong S. Appendage-Bearing Sordariomycetes from Dipterocarpus alatus Leaf Litter in Thailand. J Fungi (Basel) 2023; 9:625. [PMID: 37367561 DOI: 10.3390/jof9060625] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023] Open
Abstract
Leaf litter is an essential functional aspect of forest ecosystems, acting as a source of organic matter, a protective layer in forest soils, and a nurturing habitat for micro- and macro-organisms. Through their successional occurrence, litter-inhabiting microfungi play a key role in litter decomposition and nutrient recycling. Despite their importance in terrestrial ecosystems and their abundance and diversity, information on the taxonomy, diversity, and host preference of these decomposer taxa is scarce. This study aims to clarify the taxonomy and phylogeny of four saprobic fungal taxa inhabiting Dipterocarpus alatus leaf litter. Leaf litter samples were collected from Doi Inthanon National Park in Chiang Mai, northern Thailand. Fungal isolates were characterized based on morphology and molecular phylogeny of the nuclear ribosomal DNA (ITS, LSU) and protein-coding genes (tub2, tef1-α, rpb2). One novel saprobic species, Ciliochorella dipterocarpi, and two new host records, Pestalotiopsis dracontomelon and Robillarda australiana, are introduced. The newly described taxa are compared with similar species, and comprehensive descriptions, micrographs, and phylogenetic trees are provided.
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Affiliation(s)
- Nethmini P Samaradiwakara
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | | | - Danushka S Tennakoon
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Janith V S Aluthmuhandiram
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Chitrabhanu S Bhunjun
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - K W Thilini Chethana
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Jaturong Kumla
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Saisamorn Lumyong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok 10300, Thailand
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Figueiredo MA, da Silva TH, Pinto OHB, Leite MGP, de Oliveira FS, Messias MCTB, Rosa LH, Câmara PEAS, Lopes FAC, Kozovits AR. Metabarcoding of Soil Fungal Communities in Rupestrian Grassland Areas Preserved and Degraded by Mining: Implications for Restoration. MICROBIAL ECOLOGY 2023; 85:1045-1055. [PMID: 36708392 DOI: 10.1007/s00248-023-02177-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 01/17/2023] [Indexed: 05/04/2023]
Abstract
Rupestrian grasslands are vegetation complexes of the Cerrado biome (Brazilian savanna), exhibiting simultaneously great biodiversity and important open-pit mining areas. There is a strong demand for the conservation of remaining areas and restoration of degraded. This study evaluated, using next-generation sequencing, the diversity and ecological aspects of soil fungal communities in ferruginous rupestrian grassland areas preserved and degraded by bauxite mining in Brazil. In the preserved and degraded area, respectively, 565 and 478 amplicon sequence variants (ASVs) were detected. Basidiomycota and Ascomycota comprised nearly 72% of the DNA, but Ascomycota showed greater abundance than Basidiomycota in the degraded area (64% and 10%, respectively). In the preserved area, taxa of different hierarchical levels (Agaromycetes, Agaricales, Mortierelaceae, and Mortierella) associated with symbiosis and decomposition were predominant. However, taxa that colonize environments under extreme conditions and pathogens (Dothideomycetes, Pleoporales, Pleosporaceae, and Curvularia) prevailed in the degraded area. The degradation reduced the diversity, and modified the composition of taxa and predominant ecological functions in the community. The lack of fungi that facilitate plant establishment and development in the degraded area suggests the importance of seeking the restoration of this community to ensure the success of the ecological restoration of the environment. The topsoil of preserved area can be a source of inocula of several groups of fungi important for the restoration process but which occur in low abundance or are absent in the degraded area.
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Affiliation(s)
- Maurílio Assis Figueiredo
- Programa de Pós-Graduação em Evolução Crustal e Recursos Naturais, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil.
| | - Thamar Holanda da Silva
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | | | | | | | - Luiz Henrique Rosa
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | | | - Alessandra Rodrigues Kozovits
- Departamento de Biodiversidade, Evolução e Meio Ambiente, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
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Bhunjun CS, Phukhamsakda C, Hyde KD, McKenzie EHC, Saxena RK, Li Q. Do all fungi have ancestors with endophytic lifestyles? FUNGAL DIVERS 2023. [DOI: 10.1007/s13225-023-00516-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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5
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Ghobad-Nejhad M, Antonín V, Moghaddam M, Langer E. Resources of Iranian agarics (Basidiomycota) with an outlook on their antioxidant potential. Front Microbiol 2022; 13:1015440. [DOI: 10.3389/fmicb.2022.1015440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Agaric fungi are an important group of macromycetes with diverse ecological and functional properties, yet are poorly studied in many parts of the world. Here, we comprehensively analyzed 558 agaric species in Iran to reveal their resources of edible and poisonous species as well as their ecological guilds and luminescence potential. We also made a thorough survey of the antioxidant activity of the species. Phylogenetic relationships were reconstructed based on nuclear ribosomal LSU and ITS sequences. Our results reveal that agarics of Iran comprise about 189 edible, 128 poisonous, 254 soil saprotrophic, 172 ectomycorrhizal, 146 wood-inhabiting, 18 leaf/litter-inhabiting, 9 parasitic, and 19 luminescent species. Twenty percent of the Iranian agaric species possess antioxidant activity, phylogenetically distributed in four orders and 21 agaric families. About 5% of the antioxidant species can be considered strong antioxidants, many of which are also edible and could be utilized to develop functional foods. This is the first study combining phylogeny and antioxidant potential of agaric mushrooms in a large scale, and the obtained results would guide the selection of agaric taxa to be examined in the future for taxonomic revisions, biotechnological applications, and applied phylogeny studies.
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Fungal community succession on decomposing leaf litter across five phylogenetically related tree species in a subtropical forest. FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00508-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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7
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Phukhamsakda C, Nilsson RH, Bhunjun CS, de Farias ARG, Sun YR, Wijesinghe SN, Raza M, Bao DF, Lu L, Tibpromma S, Dong W, Tennakoon DS, Tian XG, Xiong YR, Karunarathna SC, Cai L, Luo ZL, Wang Y, Manawasinghe IS, Camporesi E, Kirk PM, Promputtha I, Kuo CH, Su HY, Doilom M, Li Y, Fu YP, Hyde KD. The numbers of fungi: contributions from traditional taxonomic studies and challenges of metabarcoding. FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00502-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
AbstractThe global diversity of fungi has been estimated using several different approaches. There is somewhere between 2–11 million estimated species, but the number of formally described taxa is around 150,000, a tiny fraction of the total. In this paper, we examine 12 ascomycete genera as case studies to establish trends in fungal species descriptions, and introduce new species in each genus. To highlight the importance of traditional morpho-molecular methods in publishing new species, we introduce novel taxa in 12 genera that are considered to have low species discovery. We discuss whether the species are likely to be rare or due to a lack of extensive sampling and classification. The genera are Apiospora, Bambusicola, Beltrania, Capronia, Distoseptispora, Endocalyx, Neocatenulostroma, Neodeightonia, Paraconiothyrium, Peroneutypa, Phaeoacremonium and Vanakripa. We discuss host-specificity in selected genera and compare the number of species epithets in each genus with the number of ITS (barcode) sequences deposited in GenBank and UNITE. We furthermore discuss the relationship between the divergence times of these genera with those of their hosts. We hypothesize whether there might be more species in these genera and discuss hosts and habitats that should be investigated for novel species discovery.
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9
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Osono T, Hirose D, Matsuoka S. Variability of decomposing ability among fungi associated with the bleaching of subtropical leaf litter. Mycologia 2021; 113:703-714. [PMID: 33989137 DOI: 10.1080/00275514.2021.1908009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
A diverse array of fungi take part in decomposition, but the variability of their decomposing ability is not fully understood. A total of 49 isolates of Ascomycota and Basidiomycota were obtained from bleached areas of leaf litter in a subtropical forest in southern Japan, and their ability to decompose leaves and recalcitrant compounds was quantified in pure culture. Mass loss of leaves of Castanopsis sieboldii (Fagaceae) and Schima wallichii (Theaceae) was evaluated at 20 C for 12 wk in vitro. Fungi caused a loss of -0.4% to 34.3% of the original leaf mass. The greatest mass loss was caused by four isolates of Mycena (Tricholomataceae). Isolates of Lachnocladiaceae caused greater mass loss of recalcitrant compounds, registered as acid-unhydrolyzable residue (AUR), which includes lignin, relative to Xylariaceae. Isolates of Rhytismataceae, Lachnocladiaceae, Marasmiaceae, and Omphalotaceae exhibited selective decomposition of AUR, Mycena exhibited simultaneous decomposition of AUR and components other than AUR, and Xylariaceae exhibited selective decomposition of components other than AUR. Mass losses of leaves and AUR caused by each fungal isolate were similar for C. sieboldii and S. wallichii. The Mycena isolates obtained from C. sieboldii caused greater mass losses of leaves and AUR than those obtained from the other tree species, suggesting a "home-field advantage" of decomposing potentialities, with implications for natural interactions beyond the in vitro system evaluated here.
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Affiliation(s)
- Takashi Osono
- Faculty of Science and Engineering, Doshisha University, Kyoto 610-0394, Japan
| | - Dai Hirose
- School of Pharmacy, Nihon University, Japan
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10
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Fungi in Remediation of Hazardous Wastes: Current Status and Future Outlook. Fungal Biol 2021. [DOI: 10.1007/978-3-030-68260-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Osono T. Decomposition of Organic Chemical Components in Wood by Tropical Xylaria Species. J Fungi (Basel) 2020; 6:jof6040186. [PMID: 32977379 PMCID: PMC7712814 DOI: 10.3390/jof6040186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/20/2020] [Accepted: 09/22/2020] [Indexed: 11/24/2022] Open
Abstract
The ability of Xylaria species obtained from tropical wood and leaf litter to cause a mass loss of lignin and carbohydrates in wood was examined in vitro with pure culture decomposition tests. The mass loss of wood of four tree species caused by nine Xylaria isolates ranged from 4.5% to 28.4% of the original wood mass. These Xylaria isolates have a potential ability to decompose lignin and other recalcitrant compounds, collectively registered as acid unhydrolyzable residues or Klason lignin in wood. The origin of isolates (i.e., isolates from wood versus leaf litter) did not affect the mass loss of acid unhydrolyzable residue in wood. The Xylaria isolates tested generally caused a selective decomposition of polymer carbohydrates in wood in preference to acid unhydrolyzable residue. The mass loss of acid unhydrolyzable residue caused by Xylaria isolates varied with the tree species of the wood and was negatively related to the initial content of acid unhydrolyzable residue in wood, implying the limiting effect of lignin and recalcitrant compounds on wood decomposition by Xylaria isolates.
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Affiliation(s)
- Takashi Osono
- Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0394, Japan
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12
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Tennakoon DS, Thambugala KM, Wanasinghe DN, Gentekaki E, Promputtha I, Kuo CH, Hyde KD. Additions to Phaeosphaeriaceae (Pleosporales): Elongaticollum gen. nov., Ophiosphaerella taiwanensis sp. nov., Phaeosphaeriopsis beaucarneae sp. nov. and a new host record of Neosetophoma poaceicola from Musaceae. MycoKeys 2020; 70:59-88. [PMID: 32821215 PMCID: PMC7398961 DOI: 10.3897/mycokeys.70.53674] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 06/03/2020] [Indexed: 11/12/2022] Open
Abstract
A novel ascomycetous genus, Elongaticollum, occurring on leaf litter of Hedychium coronarium (Zingiberaceae) in Taiwan, is described and illustrated. Elongaticollum is characterized by dark brown to black, superficial, obpyriform, pycnidial conidiomata with a distinct elongate neck, and oval to oblong, hyaline, aseptate conidia. Phylogenetic analyses (maximum likelihood, maximum parsimony and Bayesian) of combined ITS, LSU, SSU and tef1-α sequence data revealed Elongaticollum as a distinct genus within the family Phaeosphaeriaceae with high statistical support. In addition, Ophiosphaerella taiwanensis and Phaeosphaeriopsis beaucarneae are described as new species from dead leaves of Agave tequilana and Beaucarnea recurvata (Asparagaceae), respectively. Neosetophoma poaceicola is reported as a new host record from dead leaves of Musa acuminata (Musaceae). Newly described taxa are compared with other similar species and comprehensive descriptions and micrographs are provided.
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Affiliation(s)
- Danushka S Tennakoon
- Department of Plant Medicine, National Chiayi University, 300 Syuefu Road, Chiayi City 60004, Taiwan.,School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand.,Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Kasun M Thambugala
- Genetics and Molecular Biology Unit, Faculty of Applied Sciences, University of Sri Jayewardenepura, Gangodawila, Nugegoda, Sri Lanka
| | - Dhanushka N Wanasinghe
- CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia (KLPB), Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunnan, China
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand.,Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Itthayakorn Promputtha
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.,Environmental Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Chang-Hsin Kuo
- Department of Plant Medicine, National Chiayi University, 300 Syuefu Road, Chiayi City 60004, Taiwan
| | - Kevin D Hyde
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand.,Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand.,CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia (KLPB), Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunnan, China.,Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.,Institute of Plant Health, Zhongkai University of Agriculture and Engineering, Haizhu District, Guangzhou 510225, China
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Bharati SL, Sarma C, Hazarika PJ, Chaurasia PK, Anand N, Yadava S. Novel Mn(III) Porphyrins and Prospects of Their Application in Catalysis. RUSS J INORG CHEM+ 2019. [DOI: 10.1134/s0036023619030045] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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16
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Irfan M, Mehmood S, Irshad M, Anwar Z. Optimized production, purification and molecular characterization of fungal laccase through Alternaria alternata. TURKISH JOURNAL OF BIOCHEMISTRY 2018. [DOI: 10.1515/tjb-2017-0239] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Objective
Industrial effluents and agriculture biomass are main environmental hazards which are facing by developing country like Pakistan. Along with various other industrial applications, laccases are also involved in the oxidation of various industrial hazardous compounds to detoxify them. This study was designed to produce and purify laccase from ascomyceteous fungi, i.e. Alternaria alternata through solid stat fermentation.
Materials and methods
Abundantly available Sarkanda grass “Saccharum spontaneum” was used as agro-waste substrate for laccase production from fungus A. alternata. Previously only white rot fungi are familiar for laccase production and almost no work has been done on laccase production by A. alternata. In this research work, different physical and chemical parameters were optimized for maximum laccase production through solid state fermentation (SSF).
Results
Enzyme was purified and its molecular weight was determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Maximum laccase activity (21.87±0.0115 unit/mL) was detected on 7th day of incubation having pH 5 of the medium at 35°C. None of the added metal ions increased laccase production. Galactose and “yeast extract” used as optimum carbon and nitrogen source for highest laccase production.
Conclusion
A monomeric protein (laccase) having approximately 51 kDa molecular weight obtained after SDS-PAGE.
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Affiliation(s)
- Muhammad Irfan
- Department of Biochemistry and Molecular Biology , University of Gujrat , Gujrat , Pakistan
| | - Sajid Mehmood
- Department of Biochemistry and Molecular Biology , University of Gujrat , Gujrat , Pakistan
| | - Muhammad Irshad
- Department of Biochemistry and Molecular Biology , University of Gujrat , Gujrat , Pakistan
| | - Zahid Anwar
- Department of Biochemistry and Molecular Biology , University of Gujrat , Gujrat , Pakistan
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Hyde KD, Norphanphoun C, Chen J, Dissanayake AJ, Doilom M, Hongsanan S, Jayawardena RS, Jeewon R, Perera RH, Thongbai B, Wanasinghe DN, Wisitrassameewong K, Tibpromma S, Stadler M. Thailand’s amazing diversity: up to 96% of fungi in northern Thailand may be novel. FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0415-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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18
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Zhao RL, Li GJ, Sánchez-Ramírez S, Stata M, Yang ZL, Wu G, Dai YC, He SH, Cui BK, Zhou JL, Wu F, He MQ, Moncalvo JM, Hyde KD. A six-gene phylogenetic overview of Basidiomycota and allied phyla with estimated divergence times of higher taxa and a phyloproteomics perspective. FUNGAL DIVERS 2017. [DOI: 10.1007/s13225-017-0381-5] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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19
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Martínková L, Kotik M, Marková E, Homolka L. Biodegradation of phenolic compounds by Basidiomycota and its phenol oxidases: A review. CHEMOSPHERE 2016; 149:373-382. [PMID: 26874626 DOI: 10.1016/j.chemosphere.2016.01.022] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 12/09/2015] [Accepted: 01/06/2016] [Indexed: 06/05/2023]
Abstract
The phylum Basidiomycota include organisms with enormous bioremediation potential. A variety of processes were proposed at the lab scale for using these fungi and their phenol oxidases in the degradation of phenolics. Here we present a survey of this topic using literature published mostly over the last 10 years. First, the sources of the enzymes are summarized. The laccase and tyrosinase were mainly from Trametes versicolor and Agaricus bisporus, respectively. Recently, however, new promising wild-type producers of the enzymes have emerged and a number of recombinant strains were also constructed, based mainly on yeasts or Aspergillus strains as hosts. The next part of the study summarizes the enzyme and whole-cell applications for the degradation of phenols, polyphenols, cresols, alkylphenols, naphthols, bisphenols and halogenated (bis)phenols in model mixtures or real wastewaters from the food, paper and coal industries, or municipal and hospital sewage. The enzymes were applied as free (crude or purified) enzymes or as enzymes immobilized in various supports or CLEAs, and optionally recycled or used in continuous mode. Alternatively, growing cultures or harvested mycelia were used instead. The products, which were characterized as quinones and their polymers in some cases, could be eliminated by filtration, flocculation or adsorption onto chitosan. The purity of a treated wastewater was monitored using a sensitive aquatic organism. It is concluded that low-cost sources of these enzymes should be searched for and the benefits of enzymatic, biological and physico-chemical methods could be combined to make the processes fit for industrial use.
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Affiliation(s)
- L Martínková
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic.
| | - M Kotik
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic
| | - E Marková
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic; Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technická 3, CZ-166 28 Prague, Czech Republic
| | - L Homolka
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic
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Gacura MD, Sprockett DD, Heidenreich B, Blackwood CB. Comparison of pectin-degrading fungal communities in temperate forests using glycosyl hydrolase family 28 pectinase primers targeting Ascomycete fungi. J Microbiol Methods 2016; 123:108-13. [PMID: 26899925 DOI: 10.1016/j.mimet.2016.02.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 02/15/2016] [Accepted: 02/16/2016] [Indexed: 01/22/2023]
Abstract
Fungi have developed a wide assortment of enzymes to break down pectin, a prevalent polymer in plant cell walls that is important in plant defense and structure. One enzyme family used to degrade pectin is the glycosyl hydrolase family 28 (GH28). In this study we developed primers for the amplification of GH28 coding genes from a database of 293 GH28 sequences from 40 fungal genomes. The primers were used to successfully amplify GH28 pectinases from all Ascomycota cultures tested, but only three out of seven Basidiomycota cultures. In addition, we further tested the primers in PCRs on metagenomic DNA extracted from senesced tree leaves from different forest ecosystems, followed by cloning and sequencing. Taxonomic specificity for Ascomycota GH28 genes was tested by comparing GH28 composition in leaves to internal transcribed spacer (ITS) amplicon composition using pyrosequencing. All sequences obtained from GH28 primers were classified as Ascomycota; in contrast, ITS sequences indicated that fungal communities were up to 39% Basidiomycetes. Analysis of leaf samples indicated that both forest stand and ecosystem type were important in structuring fungal communities. However, site played the prominent role in explaining GH28 composition, whereas ecosystem type was more important for ITS composition, indicating possible genetic drift between populations of fungi. Overall, these primers will have utility in understanding relationships between fungal community composition and ecosystem processes, as well as detection of potentially pathogenic Ascomycetes.
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Affiliation(s)
- Matthew D Gacura
- Department of Biological Sciences, Kent State University, Kent, OH 44242, United States.
| | - Daniel D Sprockett
- Department of Biological Sciences, Kent State University, Kent, OH 44242, United States
| | - Bess Heidenreich
- Department of Biological Sciences, Kent State University, Kent, OH 44242, United States
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Hyde KD, Fryar S, Tian Q, Bahkali AH, Xu J. Lignicolous freshwater fungi along a north–south latitudinal gradient in the Asian/Australian region; can we predict the impact of global warming on biodiversity and function? FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2015.07.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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22
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Park JW, Kang HW, Ha BS, Kim SI, Kim S, Ro HS. Strain-dependent response to Cu2+ in the expression of laccase in Pycnoporus coccineus. Arch Microbiol 2015; 197:589-96. [DOI: 10.1007/s00203-015-1090-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Revised: 01/30/2015] [Accepted: 02/05/2015] [Indexed: 10/24/2022]
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23
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Levasseur A, Lomascolo A, Chabrol O, Ruiz-Dueñas FJ, Boukhris-Uzan E, Piumi F, Kües U, Ram AFJ, Murat C, Haon M, Benoit I, Arfi Y, Chevret D, Drula E, Kwon MJ, Gouret P, Lesage-Meessen L, Lombard V, Mariette J, Noirot C, Park J, Patyshakuliyeva A, Sigoillot JC, Wiebenga A, Wösten HAB, Martin F, Coutinho PM, de Vries RP, Martínez AT, Klopp C, Pontarotti P, Henrissat B, Record E. The genome of the white-rot fungus Pycnoporus cinnabarinus: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown. BMC Genomics 2014; 15:486. [PMID: 24942338 PMCID: PMC4101180 DOI: 10.1186/1471-2164-15-486] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 05/19/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Saprophytic filamentous fungi are ubiquitous micro-organisms that play an essential role in photosynthetic carbon recycling. The wood-decayer Pycnoporus cinnabarinus is a model fungus for the study of plant cell wall decomposition and is used for a number of applications in green and white biotechnology. RESULTS The 33.6 megabase genome of P. cinnabarinus was sequenced and assembled, and the 10,442 predicted genes were functionally annotated using a phylogenomic procedure. In-depth analyses were carried out for the numerous enzyme families involved in lignocellulosic biomass breakdown, for protein secretion and glycosylation pathways, and for mating type. The P. cinnabarinus genome sequence revealed a consistent repertoire of genes shared with wood-decaying basidiomycetes. P. cinnabarinus is thus fully equipped with the classical families involved in cellulose and hemicellulose degradation, whereas its pectinolytic repertoire appears relatively limited. In addition, P. cinnabarinus possesses a complete versatile enzymatic arsenal for lignin breakdown. We identified several genes encoding members of the three ligninolytic peroxidase types, namely lignin peroxidase, manganese peroxidase and versatile peroxidase. Comparative genome analyses were performed in fungi displaying different nutritional strategies (white-rot and brown-rot modes of decay). P. cinnabarinus presents a typical distribution of all the specific families found in the white-rot life style. Growth profiling of P. cinnabarinus was performed on 35 carbon sources including simple and complex substrates to study substrate utilization and preferences. P. cinnabarinus grew faster on crude plant substrates than on pure, mono- or polysaccharide substrates. Finally, proteomic analyses were conducted from liquid and solid-state fermentation to analyze the composition of the secretomes corresponding to growth on different substrates. The distribution of lignocellulolytic enzymes in the secretomes was strongly dependent on growth conditions, especially for lytic polysaccharide mono-oxygenases. CONCLUSIONS With its available genome sequence, P. cinnabarinus is now an outstanding model system for the study of the enzyme machinery involved in the degradation or transformation of lignocellulosic biomass.
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Affiliation(s)
- Anthony Levasseur
- INRA, UMR1163 Biotechnologie des Champignons Filamenteux, Aix-Marseille Université, Polytech Marseille, 163 avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France.
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Tun HM, Mauroo NF, Yuen CS, Ho JCW, Wong MT, Leung FCC. Microbial diversity and evidence of novel homoacetogens in the gut of both geriatric and adult giant pandas (Ailuropoda melanoleuca). PLoS One 2014; 9:e79902. [PMID: 24475017 PMCID: PMC3901650 DOI: 10.1371/journal.pone.0079902] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 09/25/2013] [Indexed: 12/20/2022] Open
Abstract
Recent studies have described the bacterial community residing in the guts of giant pandas, together with the presence of lignocellulolytic enzymes. However, a more comprehensive understanding of the intestinal microbial composition and its functional capacity in giant pandas remains a major goal. Here, we conducted a comparison of bacterial, fungal and homoacetogenic microbial communities from fecal samples taken from two geriatric and two adult captive giant pandas. 16S rDNA amplicon pyrosequencing revealed that Firmicutes and Proteobacteria are the most abundant microbiota in both geriatric and adult giant pandas. However, members of phylum Actinobacteria found in adult giant pandas were absent in their geriatric counterparts. Similarly, ITS1 amplicon pyrosequencing identified developmental changes in the most abundant fungal classes from Sordariomycetes in adult pandas to Saccharomycetes in geriatric pandas. Geriatric pandas exhibited significantly higher abundance of a potential probiotic fungus (Candida tropicalis) as compared to adult pandas, indicating their importance in the normal digestive physiology of aged pandas. Our study also reported the presence of a lignocellulolytic white-rot fungus, Perenniporia medulla-panis, and the evidence of novel homoacetogens residing in the guts of giant pandas.
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Affiliation(s)
- Hein Min Tun
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Nathalie France Mauroo
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong SAR
- Hong Kong Wildlife Health Foundation, Hong Kong, Hong Kong SAR
| | - Chan San Yuen
- Clinical Laboratory, Veterinary Center, Ocean Park Corporation, Hong Kong, Hong Kong SAR
| | - John Chi Wang Ho
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Mabel Ting Wong
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Frederick Chi-Ching Leung
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
- Bioinformatics Center, Nanjing Agricultural University, Nanjing, China
- * E-mail:
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Fedorova TV, Shakhova NV, Klein OI, Glazunova OA, Maloshenok LG, Kulikova NA, Psurtseva NV, Koroleva OV. Comparative analysis of the ligninolytic potential of basidiomycetes belonging to different taxonomic and ecological groups. APPL BIOCHEM MICRO+ 2013; 49:570-9. [DOI: 10.1134/s0003683813060082] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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26
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Syringyl-rich lignin renders poplars more resistant to degradation by wood decay fungi. Appl Environ Microbiol 2013; 79:2560-71. [PMID: 23396333 DOI: 10.1128/aem.03182-12] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In order to elucidate the effects of lignin composition on the resistance of wood to degradation by decay fungi, wood specimens from two transgenic poplar lines expressing an Arabidopsis gene encoding ferulate 5-hydroxylase (F5H) driven by the cinnimate-4-hydroxylase promoter (C4H::F5H) that increased syringyl/guaiacyl (S/G) monolignol ratios relative to those in the untransformed control wood were incubated with six different wood decay fungi. Alterations in wood weight and chemical composition were monitored over the incubation period. The results showed that transgenic poplar lines extremely rich in syringyl lignin exhibited a drastically improved resistance to degradation by all decay fungi evaluated. Lignin monomer composition and its distribution among cell types and within different cell layers were the sole wood chemistry parameters determining wood durability. Since transgenic poplars with exceedingly high syringyl contents were recalcitrant to degradation, where wood durability is a critical factor, these genotypes may offer improved performance.
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Lomascolo A, Uzan-Boukhris E, Herpoël-Gimbert I, Sigoillot JC, Lesage-Meessen L. Peculiarities of Pycnoporus species for applications in biotechnology. Appl Microbiol Biotechnol 2011; 92:1129-49. [PMID: 22038244 DOI: 10.1007/s00253-011-3596-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 09/02/2011] [Accepted: 09/18/2011] [Indexed: 11/24/2022]
Abstract
The genus Pycnoporus forms a cosmopolitan group of four species belonging to the polyporoid white-rot fungi, the most representative group of homobasidiomycetes causing wood decay. Pycnoporus fungi are listed as food- and cosmetic-grade microorganisms and emerged in the early 1990s as a genus whose biochemistry, biodegradation and biotechnological properties have since been progressively detailed. First highlighted for their original metabolic pathways involved in the functionalization of plant cell wall aromatic compounds to yield high-value molecules, e.g. aromas and antioxidants, the Pycnoporus species were later explored for their potential to produce various enzymes of industrial interest, such as hydrolases and oxidases. However, the most noteworthy feature of the genus Pycnoporus is its ability to overproduce high redox potential laccase-a multi-copper extracellular phenoloxidase-as the predominant ligninolytic enzyme. A major potential use of the Pycnoporus fungi is thus to harness their laccases for various applications such as the bioconversion of agricultural by-products and raw plant materials into valuable products, the biopulping and biobleaching of paper pulp and the biodegradation of organopollutants, xenobiotics and industrial contaminants. All the studies performed in the last decade show the genus Pycnoporus to be a strong contender for white biotechnology. In this review, we describe the properties of Pycnoporus fungi in relation to their biotechnological applications and potential.
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Affiliation(s)
- Anne Lomascolo
- UMR INRA de Biotechnologie des Champignons Filamenteux, ESIL, Marseille, France.
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28
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Kulikova NA, Klein OI, Stepanova EV, Koroleva OV. Use of basidiomycetes in industrial waste processing and utilization technologies: Fundamental and applied aspects (review). APPL BIOCHEM MICRO+ 2011. [DOI: 10.1134/s000368381106007x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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29
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Edwards IP, Zak DR, Kellner H, Eisenlord SD, Pregitzer KS. Simulated atmospheric N deposition alters fungal community composition and suppresses ligninolytic gene expression in a northern hardwood forest. PLoS One 2011; 6:e20421. [PMID: 21701691 PMCID: PMC3119081 DOI: 10.1371/journal.pone.0020421] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 04/29/2011] [Indexed: 11/19/2022] Open
Abstract
High levels of atmospheric nitrogen (N) deposition may result in greater terrestrial carbon (C) storage. In a northern hardwood ecosystem, exposure to over a decade of simulated N deposition increased C storage in soil by slowing litter decay rates, rather than increasing detrital inputs. To understand the mechanisms underlying this response, we focused on the saprotrophic fungal community residing in the forest floor and employed molecular genetic approaches to determine if the slower decomposition rates resulted from down-regulation of the transcription of key lignocellulolytic genes, by a change in fungal community composition, or by a combination of the two mechanisms. Our results indicate that across four Acer-dominated forest stands spanning a 500-km transect, community-scale expression of the cellulolytic gene cbhI under elevated N deposition did not differ significantly from that under ambient levels of N deposition. In contrast, expression of the ligninolytic gene lcc was significantly down-regulated by a factor of 2-4 fold relative to its expression under ambient N deposition. Fungal community composition was examined at the most southerly of the four sites, in which consistently lower levels of cbhI and lcc gene expression were observed over a two-year period. We recovered 19 basidiomycete and 28 ascomycete rDNA 28S operational taxonomic units; Athelia, Sistotrema, Ceratobasidium and Ceratosebacina taxa dominated the basidiomycete assemblage, and Leotiomycetes dominated the ascomycetes. Simulated N deposition increased the proportion of basidiomycete sequences recovered from forest floor, whereas the proportion of ascomycetes in the community was significantly lower under elevated N deposition. Our results suggest that chronic atmospheric N deposition may lower decomposition rates through a combination of reduced expression of ligninolytic genes such as lcc, and compositional changes in the fungal community.
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Affiliation(s)
- Ivan P Edwards
- School of Natural Resources and Environment, University of Michigan, Ann Arbor, Michigan, United States of America.
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30
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Osono T, To-Anun C, Hagiwara Y, Hirose D. Decomposition of wood, petiole and leaf litter by Xylaria species from northern Thailand. FUNGAL ECOL 2011. [DOI: 10.1016/j.funeco.2010.11.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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31
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Laccase activity and putative laccase genes in marine-derived basidiomycetes. Fungal Biol 2010; 114:863-72. [DOI: 10.1016/j.funbio.2010.08.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Revised: 07/27/2010] [Accepted: 08/03/2010] [Indexed: 11/18/2022]
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32
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Brijwani K, Rigdon A, Vadlani PV. Fungal laccases: production, function, and applications in food processing. Enzyme Res 2010; 2010:149748. [PMID: 21048859 PMCID: PMC2962899 DOI: 10.4061/2010/149748] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 08/22/2010] [Indexed: 12/05/2022] Open
Abstract
Laccases are increasingly being used in food industry for production of cost-effective and healthy foods. To sustain this trend widespread availability of laccase and efficient production systems have to be developed. The present paper delineate the recent developments that have taken place in understanding the role of laccase action, efforts in overexpression of laccase in heterologous systems, and various cultivation techniques that have been developed to efficiently produce laccase at the industrial scale. The role of laccase in different food industries, particularly the recent developments in laccase application for food processing, is discussed.
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Affiliation(s)
- Khushal Brijwani
- Bioprocessing Laboratory, Department of Grain Science and Industry, Kansas State University, Manhattan, KS 66506, USA
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33
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Yadav M, Yadav P, Yadav KDS. Purification, characterization, and coal depolymerizing activity of lignin peroxidase from Gloeophyllum sepiarium MTCC-1170. BIOCHEMISTRY (MOSCOW) 2009; 74:1125-31. [DOI: 10.1134/s0006297909100083] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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34
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Pangallo D, Chovanová K, Šimonovičová A, Ferianc P. Investigation of microbial community isolated from indoor artworks and air environment: identification, biodegradative abilities, and DNA typing. Can J Microbiol 2009; 55:277-87. [DOI: 10.1139/w08-136] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This study deals with establishing the characteristics of a microbial community isolated from indoor artworks and the surrounding air environment. It is one of the few studies on microbial degradation of indoor artworks. It shows the potential biodegradative risk that can occur if artworks are not exhibited and conserved in an appropriate environment. The microbial community isolated from the indoor artworks and air environment was examined by cultural and molecular methods. Different plate assays were used to screen the biodegradative activity of the isolated microflora: Remazol Brilliant Blue R, phenol red, and Azure B for the ligninolytic properties; Ostazin brilliant red H-3B for cellulose degradation; CaCO3glucose agar for solubilization activity; and B4 agar for biomineralization. To type the bacterial and fungal isolates, 2 PCR methods, repetitive extragenic palindromes (REP) and random amplified microsatellite polymorphisms (RAMP) were used. The art objects were principally colonized by fungi. The most commonly isolated strains were represented by hyphomycetes of the genera Penicillium , Aspergillus , Cladosporium , and Chaetomium . Members of these genera showed intensive biodegradation activity, both on wood and on stone. Bacteria were predominant in the air, exhibiting complex communities, both in the air and on the artworks. The most frequently isolated genera were Bacillus and Staphylococcus with extensive biodegradation abilities. REP-PCR revealed high variability within strains belonging to the same genus. RAMP is a new PCR-based method, used in this research for the first time to cluster the microfilamentous fungi and to characterize and select especially Penicillium and Aspergillus strains, which were isolated in a large number.
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Affiliation(s)
- Domenico Pangallo
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia
- Caravella s.r.o, Tupolevova 2, 851 01 Bratislava, Slovakia
- Department of Soil Science, Faculty of Natural Sciences, Comenius University, Mlynska dolina B-2, 84215 Bratislava 4, Slovakia
| | - Katarina Chovanová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia
- Caravella s.r.o, Tupolevova 2, 851 01 Bratislava, Slovakia
- Department of Soil Science, Faculty of Natural Sciences, Comenius University, Mlynska dolina B-2, 84215 Bratislava 4, Slovakia
| | - Alexandra Šimonovičová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia
- Caravella s.r.o, Tupolevova 2, 851 01 Bratislava, Slovakia
- Department of Soil Science, Faculty of Natural Sciences, Comenius University, Mlynska dolina B-2, 84215 Bratislava 4, Slovakia
| | - Peter Ferianc
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia
- Caravella s.r.o, Tupolevova 2, 851 01 Bratislava, Slovakia
- Department of Soil Science, Faculty of Natural Sciences, Comenius University, Mlynska dolina B-2, 84215 Bratislava 4, Slovakia
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Artz RRE, Reid E, Anderson IC, Campbell CD, Cairney JWG. Long term repeated prescribed burning increases evenness in the basidiomycete laccase gene pool in forest soils. FEMS Microbiol Ecol 2009; 67:397-410. [PMID: 19187216 DOI: 10.1111/j.1574-6941.2009.00650.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Repeated prescribed burning alters the biologically labile fraction of nutrients and carbon of soil organic matter (SOM). Using a long-term (30 years) repeated burning experiment where burning has been carried out at a 2- or 4-year frequency, we analysed the effect of prescribed burning on gross potential C turnover rates and phenol oxidase activity in relation to shifts in SOM composition as observed using Fourier-transform infrared spectroscopy. In tandem, we assessed the genetic diversity of basidiomycete laccases. While the overall effect of burning was a decline in phenol oxidase activity, Shannon diversity and evenness of laccases was significantly higher in burned sites. Co-correspondence analysis of SOM composition and laccase operational taxonomic unit frequency data also suggested a strong correlation. While this correlation could indicate that the observed increase in laccase genetic diversity due to burning is due to increased resource diversity, a temporal replacement of the most abundant members of the assembly by an otherwise dormant pool of fungi cannot be excluded. As such, our results fit the intermediate disturbance hypothesis. Effects were stronger in plots burned in 2-year rotations, suggesting that the 4-year burn frequency may be a more sustainable practice to ensure the long-term stability of C cycling in such ecosystems.
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Affiliation(s)
- Rebekka R E Artz
- The Macaulay Institute, Soils Group, Craigiebuckler, Aberdeen, Scotland, UK.
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Morgenstern I, Klopman S, Hibbett DS. Molecular evolution and diversity of lignin degrading heme peroxidases in the Agaricomycetes. J Mol Evol 2008; 66:243-57. [PMID: 18292958 DOI: 10.1007/s00239-008-9079-3] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The plant and microbial peroxidase superfamily encompasses three classes of related protein families. Class I includes intracellular peroxidases of prokaryotic origin, class II includes secretory fungal peroxidases, including the lignin degrading enzymes manganese peroxidase (MnP), lignin peroxidase (LiP), and versatile peroxidase (VP), and class III includes the secretory plant peroxidases. Here, we present phylogenetic analyses using maximum parsimony and Bayesian methods that address the origin and diversification of class II peroxidases. Higher-level analyses used published full-length sequences from all members of the plant and microbial peroxidase superfamily, while lower-level analyses used class II sequences only, including 43 new sequences generated from Agaricomycetes (mushroom-forming fungi and relatives). The distribution of confirmed and proposed catalytic sites for manganese and aromatic compounds in class II peroxidases, including residues supposedly involved in three different long range electron transfer pathways, was interpreted in the context of phylogenies from the lower-level analyses. The higher-level analyses suggest that class II sequences constitute a monophyletic gene family within the plant and microbial peroxidase superfamily, and that they have diversified extensively in the basidiomycetes. Peroxidases of unknown function from the ascomycete Magnaporthe grisea were found to be the closest relatives of class II sequences and were selected to root class II sequences in the lower-level analyses. LiPs evidently arose only once in the Polyporales, which harbors many white-rot taxa, whereas MnPs and VPs are more widespread and may have multiple origins. Our study includes the first reports of partial sequences for MnPs in the Hymenochaetales and Corticiales.
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Affiliation(s)
- Ingo Morgenstern
- Department of Biology, Clark University, 950 Main Street, Worcester, MA 01610, USA.
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37
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Chapter 4 Ecophysiology: Impact of environment on growth, synthesis of compatible solutes and enzyme production. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/s0275-0287(08)80006-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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38
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Does Atmospheric NO 3 − Deposition Alter the Abundance and Activity of Ligninolytic Fungi in Forest Soils? Ecosystems 2007. [DOI: 10.1007/s10021-007-9096-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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39
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Pangallo D, Simonovicová A, Chovanová K, Ferianc P. Wooden art objects and the museum environment: identification and biodegradative characteristics of isolated microflora. Lett Appl Microbiol 2007; 45:87-94. [PMID: 17594466 DOI: 10.1111/j.1472-765x.2007.02138.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS The identification of culturable microbial communities on wooden art objects and from indoor air, and the analysis of their biodegradative properties. METHODS AND RESULTS Common and newly-developed agar media were used for the isolation of fungal and bacterial microflora. The identification was carried out by traditional methods and by the sequencing of 16S or 18S rDNA PCR products. Different plate assays were employed to screen the lignolytic and cellulolytic activities of the isolated microflora. Interesting bacteria were isolated from art objects even though the fungi were the principal contaminants of art works. Various fungal and bacterial species exhibited their lignolytic and cellulolytic activity by the decolorization of Remazol Brilliant Blue R, Phenol Red, Azure B and Ostazin Brilliant Red H-3B. CONCLUSIONS The microbial communities on wooden art objects exposed in an indoor environment were identified. The study showed the biodegradative power of many microorganisms, and new data were added to this field barely investigated. SIGNIFICANCE AND IMPACT OF THE STUDY By the development of new culture media and the evaluation of different biodegradative plate assays, a strategy for the analysis of microflora in wooden art objects was established. Several aspects of the study could be also exploited for biotechnology applications.
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MESH Headings
- Agar
- Air Microbiology
- Air Pollution, Indoor
- Art
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Bacteria/metabolism
- Biodegradation, Environmental
- Cellulose/metabolism
- Culture Media
- DNA, Bacterial/analysis
- DNA, Bacterial/isolation & purification
- DNA, Fungal/analysis
- DNA, Fungal/isolation & purification
- DNA, Ribosomal/analysis
- Fungi/classification
- Fungi/genetics
- Fungi/isolation & purification
- Fungi/metabolism
- Lignin/metabolism
- Museums
- Polymerase Chain Reaction
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 18S/genetics
- Sequence Analysis, DNA
- Slovakia
- Wood/microbiology
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Affiliation(s)
- D Pangallo
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovak Republic.
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Kellner H, Luis P, Buscot F. Diversity of laccase-like multicopper oxidase genes in Morchellaceae: identification of genes potentially involved in extracellular activities related to plant litter decay. FEMS Microbiol Ecol 2007; 61:153-63. [PMID: 17466024 DOI: 10.1111/j.1574-6941.2007.00322.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Despite the important role played by soil-inhabiting ascomycetes in plant litter decay processes, studies on the diversity and function of their laccase-like multicopper oxidase (LMCO) genes are scarce. In the present work, the LMCO gene diversity in 15 strains representing nine Morchellaceae and one Discinaceae species was evaluated by PCR. One to six different genes were found within the species, representing 26 different sequence types. Cluster analysis revealed LMCO genes belonging to four main gene families encoding different protein classes (Class I-IV). To identify the genes related to extracellular activities and potentially involved in litter decay processes, liquid cultures were induced by different aromatic compounds. Morchella conica and Verpa conica showed the strongest LMCO activity enhancement in the presence of the naturally occurring phenolic compound guaiacol, and their expressed LMCO genes were identified by sequencing. Only genes belonging to the gene families encoding the Class II and III proteins were expressed. Both genes (Class II and III) of the mycorrhizal-like strain M. conica were exclusively expressed in the presence of guaiacol. In contrast to the saprotrophic strain V. conica, the gene encoding the Class III protein was constitutively expressed as it was also found in control cultures without guaiacol.
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Affiliation(s)
- Harald Kellner
- Department of Soil Ecology, Helmholtz--Centre for Environmental Research Ltd., UFZ Leipzig-Halle, Germany
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41
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Hoegger PJ, Kilaru S, James TY, Thacker JR, Kües U. Phylogenetic comparison and classification of laccase and related multicopper oxidase protein sequences. FEBS J 2006; 273:2308-26. [PMID: 16650005 DOI: 10.1111/j.1742-4658.2006.05247.x] [Citation(s) in RCA: 281] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A phylogenetic analysis of more than 350 multicopper oxidases (MCOs) from fungi, insects, plants, and bacteria provided the basis for a refined classification of this enzyme family into laccases sensu stricto (basidiomycetous and ascomycetous), insect laccases, fungal pigment MCOs, fungal ferroxidases, ascorbate oxidases, plant laccase-like MCOs, and bilirubin oxidases. Within the largest group of enzymes, formed by the 125 basidiomycetous laccases, the gene phylogeny does not strictly follow the species phylogeny. The enzymes seem to group at least partially according to the lifestyle of the corresponding species. Analyses of the completely sequenced fungal genomes showed that the composition of MCOs in the different species can be very variable. Some species seem to encode only ferroxidases, whereas others have proteins which are distributed over up to four different functional clusters in the phylogenetic tree.
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Affiliation(s)
- Patrik J Hoegger
- Georg-August-University Göttingen, Institute of Forest Botany, Göttingen, Germany.
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42
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Laufer Z, Beckett RP, Minibayeva FV, Lüthje S, Böttger M. Occurrence of laccases in lichenized ascomycetes of the Peltigerineae. ACTA ACUST UNITED AC 2006; 110:846-53. [PMID: 16797954 DOI: 10.1016/j.mycres.2006.03.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2005] [Revised: 02/01/2006] [Accepted: 03/10/2006] [Indexed: 11/29/2022]
Abstract
Following our previous findings of high extracellular redox activity in lichens, the results of the work presented here identify the enzymes involved as laccases. Despite numerous data on laccases in fungi and flowering plants, this is the first report of the occurrence of laccases in lichenized ascomycetes. Extracellular laccase activity was measured in 40 species of lichens from different taxonomic groupings and contrasting habitats. Out of 20 species tested from suborder Peltigerineae, 18 displayed laccase activity, while activity was absent in species tested from other lichen groups. Identification of the enzymes as laccases was confirmed by the ability of lichen leachates to readily metabolize substrates such as 2,2'-azino(bis-3-ethylbenzthiazoline-6-sulfonate) (ABTS), syringaldazine and o-tolidine in the absence of hydrogen peroxide, sensitivity of the enzymes to cyanide and azide, the enzymes having typical laccase pH and temperature optima, and an absorption spectrum with a peak at 614nm. Desiccation and wounding stimulated laccase activity. Laccase activity was not increased after treatment with normal inducers of laccase synthesis, suggesting that they are constitutively expressed. Electrophoresis showed that the active form of laccase from Peltigera malacea was a tetramer with an unusually high molecular mass of 340kDa and an isoelectric point (pI) of 4.7. The finding of abundant extracellular redox enzymes known to actively produce reactive oxygen species suggest that their roles may include increasing nutrient supply to lichens by delignification, and deterring pathogens by contributing to the oxidative burst. Furthermore, once released into the environment, they may participate in the carbon cycle by facilitating the breakdown or formation of humic substances.
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Affiliation(s)
- Zsanett Laufer
- School of Biological and Conservation Sciences, University of KwaZulu-Natal, Private Bag X01, Pietermaritzburg, Scottsville 3209, Republic of South Africa
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Zak DR, Blackwood CB, Waldrop MP. A molecular dawn for biogeochemistry. Trends Ecol Evol 2006; 21:288-95. [PMID: 16769427 DOI: 10.1016/j.tree.2006.04.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2005] [Revised: 03/13/2006] [Accepted: 04/03/2006] [Indexed: 10/24/2022]
Abstract
Biogeochemistry is at the dawn of an era in which molecular advances enable the discovery of novel microorganisms having unforeseen metabolic capabilities, revealing new insight into the underlying processes regulating elemental cycles at local to global scales. Traditionally, biogeochemical inquiry began by studying a process of interest, and then focusing downward to uncover the microorganisms and metabolic pathways mediating that process. With the ability to sequence functional genes from the environment, molecular approaches now enable the flow of inquiry in the opposite direction. Here, we argue that a focus on functional genes, the microorganisms in which they reside, and the interaction of those organisms with the broader microbial community could transform our understanding of many globally important biogeochemical processes.
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Affiliation(s)
- Donald R Zak
- School of Natural Resources & Environment, University of Michigan, Ann Arbor, MI 48109-1115, USA.
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Abstract
Laccases of fungi attract considerable attention due to their possible involvement in the transformation of a wide variety of phenolic compounds including the polymeric lignin and humic substances. So far, more than a 100 enzymes have been purified from fungal cultures and characterized in terms of their biochemical and catalytic properties. Most ligninolytic fungal species produce constitutively at least one laccase isoenzyme and laccases are also dominant among ligninolytic enzymes in the soil environment. The fact that they only require molecular oxygen for catalysis makes them suitable for biotechnological applications for the transformation or immobilization of xenobiotic compounds.
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Affiliation(s)
- Petr Baldrian
- Laboratory of Biochemistry of Wood-Rotting Fungi, Institute of Microbiology ASCR, Prague, Czech Republic.
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Dhouib A, Hamza M, Zouari H, Mechichi T, Hmidi R, Labat M, Martinez MJ, Sayadi S. Screening for Ligninolytic Enzyme Production by Diverse Fungi from Tunisia. World J Microbiol Biotechnol 2005. [DOI: 10.1007/s11274-005-5774-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Luis P, Kellner H, Zimdars B, Langer U, Martin F, Buscot F. Patchiness and spatial distribution of laccase genes of ectomycorrhizal, saprotrophic, and unknown basidiomycetes in the upper horizons of a mixed forest cambisol. MICROBIAL ECOLOGY 2005; 50:570-9. [PMID: 16341831 DOI: 10.1007/s00248-005-5047-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2005] [Accepted: 06/13/2005] [Indexed: 05/05/2023]
Abstract
Decomposition of plant litter by the soil microbial community is an important process of controlling nutrient cycling and soil humus formation. Fungal laccases are key players in litter-associated polyphenol degradation, but little is known about the diversity and spatial distribution of fungal species with laccase genes in soils. Diversity of basidiomycete laccase genes was assessed in a cambisolic forest soil, and the spatial distribution of the sequences was mapped in a 100-m(2) plot by using polymerase chain reaction (PCR) on soil DNA extracts. Diversity of laccase sequences was higher in the organic horizon and decreased with the depth. A total of 167 different sequences sharing 44-96% oligonucleotide similarity was found in 13 soil cores harvested in the 100-m(2) plot. Dissimilarity in laccase sequence content was 67% between adjacent cores; 45.5%, 35.5% and 19% of laccase sequences were attributed to ectomycorrhizal, unknown and saprotrophic basidiomycetes, respectively. Most dominant sequences were attributed to the extramatrical hyphae of known ectomycorrhizal taxa (e.g., Russulaceae) and restricted to small patches (<0.77 m(2)) in a specific soil horizon. Soil fungi with laccase genes occupied different niches and showed strikingly variable distribution patterns. The distribution of laccase sequences, and corresponding fungi, likely reflected a part of the oxidative potential in soils.
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Affiliation(s)
- Patricia Luis
- Institute of Biology I, Department of Terrestrial Ecology, University of Leipzig, Johannisallee 21, D-04103, Leipzig, Germany.
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Wang Z, Binder M, Hibbett DS. Life history and systematics of the aquatic discomycete Mitrula (Helotiales, Ascomycota) based on cultural, morphological, and molecular studies. AMERICAN JOURNAL OF BOTANY 2005; 92:1565-1574. [PMID: 21646174 DOI: 10.3732/ajb.92.9.1565] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Mitrula species represent a group of aquatic discomycetes with uncertain position in the Helotiales and an unknown life history. Mitrula species were studied using a combination of cultural, morphological, and molecular techniques. Pure colonies were isolated from Mitrula elegans, and conidia were induced in vitro. Herbarium materials from Europe, Asia, and North America were studied. Sequences of rDNA, including partial small subunit rDNA, large subunit DNA and ITS, were used to infer phylogenetic relationships both within Mitrula and between Mitrula and other inoperculate discomycetes, with special attention to fungi that resemble Mitrula in morphology or ecology. Equally weighted parsimony analyses, likelihood analyses, constrained parsimony analyses, and Bayesian analyses were performed. Results suggest that (1) the anamorph of M. elegans produces brown bicellular conidia, (2) a new subalpine species M. brevispora is distinct, (3) more than six lineages and clades can be recognized in Mitrula, (4) the morphological species M. elegans is not monophyletic, (5) a close relationship between Mitrula and either Geoglossaceae or Sclerotiniaceae is not supported, (6) the Helotiaceae is paraphyletic, and (7) Mitrula belongs to a clade within the Helotiales that also includes other aero-aquatic genera, Cudoniella, Hydrocina, Vibrissea, Ombrophila, and Hymenoscyphus.
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Affiliation(s)
- Zheng Wang
- Department of Biology, Clark University, 950 Main Street, Worcester, Massachusetts 01610 USA
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