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Senthil Kumar CM, D'Silva S, Praveena R, Kaprakkaden A, Athira Krishnan LR, Balaji Rajkumar M, Srinivasan V, Dinesh R. Zinc solubilization and organic acid production by the entomopathogenic fungus, Metarhizium pingshaense sheds light on its key ecological role in the environment. Sci Total Environ 2024; 923:171348. [PMID: 38438046 DOI: 10.1016/j.scitotenv.2024.171348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/19/2024] [Accepted: 02/27/2024] [Indexed: 03/06/2024]
Abstract
We report for the first-time higher zinc (Zn) solubilization efficiency and plant growth promotion by an entomopathogenic fungus (EPF), Metarhizium pingshaense IISR-EPF-14, which was earlier isolated from Conogethes punctiferalis, a pest of global importance. The Zn solubilizing efficiency of the fungus varied depending on the type of insoluble source of Zn used, which was observed to be 1.6 times higher in Zn3(PO4)2-amended media compared to ZnO media. In liquid media, there was a 6.2-fold increase in available Zn in ZnO-amended media, whereas a 20.2-fold increase in available Zn was recorded in Zn3(PO4)2 medium. We ascribe the production of various organic acids such as gluconic, keto-gluconic, oxalic, tartaric, malonic, succinic and formic acids, which in general, interact with insoluble Zn sources and make them soluble by forming metal cations and displacing anions as the major mechanism for Zn solubilization by M. pingshaense. However, the type and amount of organic acid produced in the media varied depending on the source of Zn used and the incubation period. Application of the fungus alone and in combination with insoluble Zn sources enhanced various plant growth parameters in rice and cardamom plants. Moreover, the uptake of Zn in rice plants was enhanced up to ~2.5-fold by fungal application. The fungus also exhibited various other plant growth-promoting traits, such as production of Indole-3-acetic acid, ammonia, siderophores, solubilization of mineral phosphate, and production of hydrolytic enzymes such as α-amylase, protease, and pectinase. Hence, apart from its use as a biological control agent, M. pingshaense has the potential to be used as a bio-fortifier to enhance the solubilization and uptake of Zn from nutrient poor soils under field conditions. Our findings shed light on the broader ecological role played by this fungus and widen its scope for utilization in sustainable agriculture.
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Affiliation(s)
- C M Senthil Kumar
- Division of Crop Protection, ICAR - Indian Institute of Spices Research, Marikunnu P.O., Kozhikode 673 012, Kerala, India.
| | - Sharon D'Silva
- Division of Crop Protection, ICAR - Indian Institute of Spices Research, Marikunnu P.O., Kozhikode 673 012, Kerala, India
| | - R Praveena
- Division of Crop Protection, ICAR - Indian Institute of Spices Research, Marikunnu P.O., Kozhikode 673 012, Kerala, India
| | - Anees Kaprakkaden
- Division of Crop Production and Post-Harvest Technology, ICAR - Indian Institute of Spices Research, Marikunnu P.O., Kozhikode 673 012, Kerala, India
| | - L R Athira Krishnan
- Division of Crop Protection, ICAR - Indian Institute of Spices Research, Marikunnu P.O., Kozhikode 673 012, Kerala, India
| | - M Balaji Rajkumar
- ICAR - Indian Institute of Spices Research, Regional Station, Appangala, Madikeri - 571 201, Karnataka, India
| | - V Srinivasan
- Division of Crop Production and Post-Harvest Technology, ICAR - Indian Institute of Spices Research, Marikunnu P.O., Kozhikode 673 012, Kerala, India
| | - R Dinesh
- Division of Crop Production and Post-Harvest Technology, ICAR - Indian Institute of Spices Research, Marikunnu P.O., Kozhikode 673 012, Kerala, India
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Djotan AKG, Matsushita N, Fukuda K. Paired Root-Soil Samples and Metabarcoding Reveal Taxon-Based Colonization Strategies in Arbuscular Mycorrhizal Fungi Communities in Japanese Cedar and Cypress Stands. Microb Ecol 2023; 86:2133-2146. [PMID: 37115261 PMCID: PMC10497666 DOI: 10.1007/s00248-023-02223-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/17/2023] [Indexed: 05/25/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) in the roots and soil surrounding their hosts are typically independently investigated and little is known of the relationships between the communities of the two compartments. We simultaneously collected root and surrounding soil samples from Cryptomeria japonica (Cj) and Chamaecyparis obtusa (Co) at three environmentally different sites. Based on molecular and morphological analyses, we characterized their associated AMF communities. Cj was more densely colonized than Co and that root colonization intensity was significantly correlated with soil AMF diversity. The communities comprised 15 AMF genera dominated by Glomus and Paraglomus and 1443 operational taxonomic units (OTUs) of which 1067 and 1170 were in roots and soil, respectively. AMF communities were significantly different among sites, and the root AMF communities were significantly different from those of soil at each site. The root and soil AMF communities responded differently to soil pH. At the genus level, Glomus and Acaulospora were abundant in roots while Paraglomus and Redeckera were abundant in soil. Our findings suggest that AMF colonizing roots are protected from environmental stresses in soil. However, the root-soil-abundant taxa have adapted to both environments and represent a model AMF symbiont. This evidence of strategic exploitation of the rhizosphere by AMF supports prior hypotheses and provides insights into community ecology.
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Affiliation(s)
- Akotchiffor Kevin Geoffroy Djotan
- Graduate School of Agricultural and Life Sciences (Laboratory of Forest Botany), University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Norihisa Matsushita
- Graduate School of Agricultural and Life Sciences (Laboratory of Forest Botany), University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kenji Fukuda
- Graduate School of Agricultural and Life Sciences (Laboratory of Forest Botany), University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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Tayyab M, Fallah N, Zhang C, Pang Z, Islam W, Lin S, Lin W, Zhang H. Sugarcane cultivar-dependent changes in assemblage of soil rhizosphere fungal communities in subtropical ecosystem. Environ Sci Pollut Res Int 2022; 29:20795-20807. [PMID: 34741271 DOI: 10.1007/s11356-021-17229-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Sugarcane cultivars (Saccharum officinarum L.) are widely cultivated for both sugar and renewable energy in China. The response of rhizosphere fungal composition and diversity to different emerging sugarcane cultivars is limited. Therefore, utilizing high-throughput sequencing, we explored fungal communities' structure in soils adhering to six sugarcane cultivars' roots (Guitang 08-120, Regan14-62, Guitang 08-1180, Haizhe 22, Liucheng 05-136, Taitang 22) in Guangxi Province, China. Our results suggested that sugarcane varieties significantly altered rhizosphere soil attributes, with Haizhe 22 having substantially lower soil pH, organic matter (OM), available phosphorus (AP), and soil water contents (SWC) than others cultivars. Different sugarcane varieties did not substantially affected the Shannon fungal diversity index, but the apparent effect on fungal richness was significant. Beta diversity analysis revealed that "Haizhe 22" distinguished the fungal community from the other five cultivars. Soil pH, OM, cultivars, and soil moisture were crucial determinants in shaping soil fungal composition. The Haizhe 22 rhizosphere significantly enriched the operational taxonomic units (OTUs) assigned to two fungal genera (Cephalotheca and Sagenomella), while rhizosphere of other verities significantly enriched the OTUs assigned to four fungal genera (Chaetomium, Chaetosphaeria, Mortierella, and Talaromyces), suggesting their essential role in plant development, disease tolerance, and bioremediation. These findings may help in selecting or breeding innovative genotypes capable of supporting abundant rhizosphere fungi beneficial to plants that would likely improve crops' agronomic potential and maintain soil ecosystem sustainability.
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Affiliation(s)
- Muhammad Tayyab
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Nyumah Fallah
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Caifang Zhang
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, China
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Ziqin Pang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Waqar Islam
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sheng Lin
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, China
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Wenxiong Lin
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, China.
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China.
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, 35002, China.
| | - Hua Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Dutra-Silva L, Pereira GE, Batista LR, Matteoli FP. Fungal diversity and occurrence of mycotoxin producing fungi in tropical vineyards. World J Microbiol Biotechnol 2021; 37:112. [PMID: 34081209 DOI: 10.1007/s11274-021-03081-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 05/29/2021] [Indexed: 11/28/2022]
Abstract
Grapevine cultivars are distributed worldwide, nevertheless the fermentation of its grape berries renders distinct wine products that are highly associated to the local fungal community. Despite the symbiotic association between wine and the fungal metabolism, impacting both the terroir and mycotoxin production, few studies have explored the vineyard ecosystem fungal community using both molecular marker sequencing and mycotoxin production assessment. In this study, we investigated the fungal community of three grapevine cultivars (Vitis vinifera L.) in two tropical vineyards. Illumina MiSeq sequencing was performed on two biocompartments: grape berries (GB) and grapevine soil (GS); yielding a total of 578,495 fungal internal transcribed spacer 1 reads, which were used for taxonomic classification. GB and GS fungal communities were mainly constituted by Ascomycota phylum. GS harbors a significant richer and more diverse fungal community than GB. Among GB samples, Syrah grape berries exclusively shared fungal community included wine-associated yeasts (e.g. Saccharomycopsis vini) that may play key roles in wine terroir. Mycotoxin production assessment revealed the high potential of Aspergillus section Flavi and Penicillium section Citrina isolates to produce aflatoxin B1-B2 and citrinin, respectively. This is the first study to employ next-generation sequencing to investigate vineyard associated fungal community in Brazil. Our findings provide valuable insights on the available tools for fungal ecology assessment applied to food products emphasizing the coexistence between classical and molecular tools.
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Affiliation(s)
- Lorena Dutra-Silva
- Department of Food Sciences, Federal University of Lavras, Lavras, MG, Brazil
| | - Giuliano E Pereira
- Brazilian Agricultural Research Corporation/Embrapa Grape & Wine, Bento Gonçalves, RS, Brazil
| | | | - Filipe P Matteoli
- Department of Soil Science, Luiz de Queiroz College of Agriculture, Piracicaba, SP, Brazil.
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Albornoz FE, Orchard S, Standish RJ, Dickie IA, Bending GD, Hilton S, Lardner T, Foster KJ, Gleeson DB, Bougoure J, Barbetti MJ, You MP, Ryan MH. Evidence for Niche Differentiation in the Environmental Responses of Co-occurring Mucoromycotinian Fine Root Endophytes and Glomeromycotinian Arbuscular Mycorrhizal Fungi. Microb Ecol 2021; 81:864-873. [PMID: 33145650 DOI: 10.1007/s00248-020-01628-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/15/2020] [Indexed: 05/21/2023]
Abstract
Fine root endophytes (FRE) were traditionally considered a morphotype of arbuscular mycorrhizal fungi (AMF), but recent genetic studies demonstrate that FRE belong within the subphylum Mucoromycotina, rather than in the subphylum Glomeromycotina with the AMF. These findings prompt enquiry into the fundamental ecology of FRE and AMF. We sampled FRE and AMF in roots of Trifolium subterraneum from 58 sites across temperate southern Australia. We investigated the environmental drivers of composition, richness, and root colonization of FRE and AMF by using structural equation modelling and canonical correspondence analyses. Root colonization by FRE increased with increasing temperature and rainfall but decreased with increasing phosphorus (P). Root colonization by AMF increased with increasing soil organic carbon but decreased with increasing P. Richness of FRE decreased with increasing temperature and soil pH. Richness of AMF increased with increasing temperature and rainfall but decreased with increasing soil aluminium (Al) and pH. Aluminium, soil pH, and rainfall were, in decreasing order, the strongest drivers of community composition of FRE; they were also important drivers of community composition of AMF, along with temperature, in decreasing order: rainfall, Al, temperature, and soil pH. Thus, FRE and AMF showed the same responses to some (e.g. soil P, soil pH) and different responses to other (e.g. temperature) key environmental factors. Overall, our data are evidence for niche differentiation among these co-occurring mycorrhizal associates.
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Affiliation(s)
- Felipe E Albornoz
- UWA School of Agriculture and Environment, and the UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Hwy, Crawley (Perth), WA, 6009, Australia.
| | - Suzanne Orchard
- UWA School of Agriculture and Environment, and the UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Hwy, Crawley (Perth), WA, 6009, Australia
| | - Rachel J Standish
- Environmental and Conservation Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Ian A Dickie
- School of Biological Science, University of Canterbury, Christchurch, New Zealand
| | - Gary D Bending
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Sally Hilton
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Tim Lardner
- UWA School of Agriculture and Environment, and the UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Hwy, Crawley (Perth), WA, 6009, Australia
| | - Kevin J Foster
- UWA School of Agriculture and Environment, and the UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Hwy, Crawley (Perth), WA, 6009, Australia
| | - Deirdre B Gleeson
- UWA School of Agriculture and Environment, and the UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Hwy, Crawley (Perth), WA, 6009, Australia
| | - Jeremy Bougoure
- UWA School of Agriculture and Environment, and the UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Hwy, Crawley (Perth), WA, 6009, Australia
| | - Martin J Barbetti
- UWA School of Agriculture and Environment, and the UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Hwy, Crawley (Perth), WA, 6009, Australia
| | - Ming Pei You
- UWA School of Agriculture and Environment, and the UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Hwy, Crawley (Perth), WA, 6009, Australia
| | - Megan H Ryan
- UWA School of Agriculture and Environment, and the UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Hwy, Crawley (Perth), WA, 6009, Australia
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Pereira APDA, Santana MC, Zagatto MRG, Brandani CB, Wang JT, Verma JP, Singh BK, Cardoso EJBN. Nitrogen-fixing trees in mixed forest systems regulate the ecology of fungal community and phosphorus cycling. Sci Total Environ 2021; 758:143711. [PMID: 33223162 DOI: 10.1016/j.scitotenv.2020.143711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 06/11/2023]
Abstract
The fungal community plays an important role in forest ecosystems via the provision of resources to plant nutrition and productivity. However, the ecology of the fungal network and its relationship with phosphorus (P) dynamics remain poorly understood in mixed forest plantations. Here, we analyzed the fungal community using the amplicon sequencing in plantations of pure Eucalyptus grandis, with (E + N) and without N fertilization (E), besides pure Acacia mangium (A), and in a consortium of E. grandis and A. mangium (E + A), at 27 and 39 months after planting. We analyzed chemical, physical and biochemical soil and litter attributes related to P cycling, and the fungal community structure to find out if mixed plantations can increase fungal connections and to identify their role in the P dynamics in the soil-litter system. Soil organic fraction (OF), phosphorus in OF, total-P and acid phosphatase activity were significantly higher in E + A and A treatments regardless of the sampling period. Total N and P, richness, and Shannon diversity of the fungi in the litter was significantly higher in the treatments E + A and A. The fungal community structure in litter differed between treatments and sampling periods, and E + A showed an intermediate structure between the two pure treatments (E) and (A). E + A correlated highly with P dynamics when evaluated by both Pearson and redundancy analyses, particularly in the litter layer. Co-occurrence networks of fungal taxa became simpler in pure E. grandis plantations, whereas mixed system (E + A) showed a more connected and complex network. Our findings provide novel evidence that mixed forest plantations promote positive responses in the fungal community connections, which are closely related to P availability in the system, prominently in the litter layer. This indicates that the litter layer represents a specific niche to improve nutrient cycling by fungi in mixed forest ecosystems.
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Affiliation(s)
| | - Maiele C Santana
- 'Luiz de Queiroz' College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Maurício R G Zagatto
- 'Luiz de Queiroz' College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Carolina B Brandani
- New Mexico State University, College of Agricultural, Consumer and Environmental Sciences, Clayton Livestock Research Center, NM, United States
| | - Jun-Tao Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia
| | - Jay P Verma
- Institute of Environment and Sustainable Development, Banaras Hindu University, Uttar Pradesh, India
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia; Global Centre for Land-Based Innovation, Western Sydney University, Sydney, Australia
| | - Elke J B N Cardoso
- 'Luiz de Queiroz' College of Agriculture, University of São Paulo, Piracicaba, Brazil
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Lourenço KS, Suleiman AKA, Pijl A, Cantarella H, Kuramae EE. Dynamics and resilience of soil mycobiome under multiple organic and inorganic pulse disturbances. Sci Total Environ 2020; 733:139173. [PMID: 32454291 DOI: 10.1016/j.scitotenv.2020.139173] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/30/2020] [Accepted: 04/30/2020] [Indexed: 06/11/2023]
Abstract
Disturbances in soil can cause short-term soil changes, consequently changes in microbial community what may result in long-lasting ecological effects. Here, we evaluate how multiple pulse disturbances effect the dynamics and resilience of fungal community, and the co-occurrence of fungal and bacterial communities in a 389 days field experiment. We used soil under sugarcane cultivation as soil ecosystem model, and organic residue (vinasse - by-product of sugarcane ethanol production) combined or not with inorganic (organic residue applied 30 days before or together with mineral N fertilizer) amendments as disturbances. Application of organic residue alone as a single disturbance or 30 days prior to a second disturbance with mineral N resulted in similar changes in the fungal community. The simultaneous application of organic and mineral N as a single pulse disturbance had the greatest impact on the fungal community. Organic amendment increased the abundance of saprotrophs, fungal species capable of denitrification, and fungi described to have copiotrophic and oligotrophic lifestyles. Furthermore, the changes in the fungal community were not correlated with the changes in the bacterial community. The fungal community was neither resistant nor resilient to organic and inorganic disturbances over the one-year sampling period. Our findings provide insights on the immediate and delayed responses of the fungal community over one year to disturbance by organic and inorganic amendments.
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Affiliation(s)
- Késia Silva Lourenço
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708, PB, Wageningen, the Netherlands; Soils and Environmental Resources Center, Agronomic Institute of Campinas (IAC), Av. Barão de Itapura 1481, 13020-902 Campinas, SP, Brazil
| | - Afnan Khalil Ahmad Suleiman
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708, PB, Wageningen, the Netherlands; KWR Watercycle Research Institute, Groningenhaven 7, 3433, PE, Nieuwegein, The Netherlands
| | - Agata Pijl
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708, PB, Wageningen, the Netherlands
| | - Heitor Cantarella
- Soils and Environmental Resources Center, Agronomic Institute of Campinas (IAC), Av. Barão de Itapura 1481, 13020-902 Campinas, SP, Brazil
| | - Eiko Eurya Kuramae
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708, PB, Wageningen, the Netherlands; Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands.
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Piepenbring M, Maciá-Vicente JG, Codjia JEI, Glatthorn C, Kirk P, Meswaet Y, Minter D, Olou BA, Reschke K, Schmidt M, Yorou NS. Mapping mycological ignorance - checklists and diversity patterns of fungi known for West Africa. IMA Fungus 2020; 11:13. [PMID: 32699745 PMCID: PMC7341642 DOI: 10.1186/s43008-020-00034-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Scientific information about biodiversity distribution is indispensable for nature conservation and sustainable management of natural resources. For several groups of animals and plants, such data are available, but for fungi, especially in tropical regions like West Africa, they are mostly missing. Here, information for West African countries about species diversity of fungi and fungus-like organisms (other organisms traditionally studied by mycologists) is compiled from literature and analysed in its historical context for the first time. More than 16,000 records of fungi representing 4843 species and infraspecific taxa were found in 860 publications relating to West Africa. Records from the Global Biodiversity Information Facility (GBIF) database (2395 species), and that of the former International Mycological Institute fungal reference collection (IMI) (2526 species) were also considered. The compilation based on literature is more comprehensive than the GBIF and IMI data, although they include 914 and 679 species names, respectively, which are not present in the checklist based on literature. According to data available in literature, knowledge on fungal richness ranges from 19 species (Guinea Bissau) to 1595 (Sierra Leone). In estimating existing species diversity, richness estimators and the Hawksworth 6:1 fungus to plant species ratio were used. Based on the Hawksworth ratio, known fungal diversity in West Africa represents 11.4% of the expected diversity. For six West African countries, however, known fungal species diversity is less than 2%. Incomplete knowledge of fungal diversity is also evident by species accumulation curves not reaching saturation, by 45.3% of the fungal species in the checklist being cited only once for West Africa, and by 66.5% of the fungal species in the checklist reported only for a single country. The documentation of different systematic groups of fungi is very heterogeneous because historically investigations have been sporadic. Recent opportunistic sampling activities in Benin showed that it is not difficult to find specimens representing new country records. Investigation of fungi in West Africa started just over two centuries ago and it is still in an early pioneer phase. To promote proper exploration, the present checklist is provided as a tool to facilitate fungal identification in this region and to aid conceptualisation and justification of future research projects. Documentation of fungal diversity is urgently needed because natural habitats are being lost on a large scale through altered land use and climate change.
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Affiliation(s)
- Meike Piepenbring
- Department of Mycology, Goethe University Frankfurt am Main, Biologicum, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany
| | - Jose G Maciá-Vicente
- Department of Mycology, Goethe University Frankfurt am Main, Biologicum, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany
| | - Jean Evans I Codjia
- Research Unit Tropical Mycology and Plant-Soil Fungi Interactions, Faculty of Agronomy, University of Parakou, BP 123 Parakou, Benin.,Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
| | - Carola Glatthorn
- Department of Mycology, Goethe University Frankfurt am Main, Biologicum, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany
| | - Paul Kirk
- Royal Botanic Garden, Kew, Richmond, Surrey UK
| | - Yalemwork Meswaet
- Department of Mycology, Goethe University Frankfurt am Main, Biologicum, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany
| | - David Minter
- CABI International, Bakeham Lane, Egham, Surrey TW20 9TY UK
| | - Boris Armel Olou
- Research Unit Tropical Mycology and Plant-Soil Fungi Interactions, Faculty of Agronomy, University of Parakou, BP 123 Parakou, Benin.,Department of Ecology, University of Kassel, Heinrich-Plett-Str. 40, Kassel, Germany
| | - Kai Reschke
- Department of Mycology, Goethe University Frankfurt am Main, Biologicum, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany
| | - Marco Schmidt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany.,Palmengarten der Stadt Frankfurt am Main, Siesmayerstr. 61, 60323 Frankfurt am Main, Germany
| | - Nourou Soulemane Yorou
- Research Unit Tropical Mycology and Plant-Soil Fungi Interactions, Faculty of Agronomy, University of Parakou, BP 123 Parakou, Benin
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Montesinos-Navarro A, Díaz G, Torres P, Caravaca F, Roldán A. Phylogenetic rewiring in mycorrhizal-plant interaction networks increases community stability in naturally fragmented landscapes. Commun Biol 2019; 2:452. [PMID: 31840098 PMCID: PMC6895200 DOI: 10.1038/s42003-019-0700-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 11/14/2019] [Indexed: 11/26/2022] Open
Abstract
Although ecological networks are usually considered a static representation of species' interactions, the interactions can change when the preferred partners are absent (rewiring). In mutualistic networks, rewiring with non-preferred partners can palliate extinction cascades, contributing to communities' stability. In spite of its significance, whether general patterns can shape the rewiring of ecological interactions remains poorly understood. Here, we show a phylogenetic constraint in the rewiring of mycorrhizal networks, so that rewired interactions (i.e., with non-preferred hosts) tend to involve close relatives of preferred hosts. Despite this constraint, rewiring increases the robustness of the fungal community to the simulated loss of their host species. We identify preferred and non-preferred hosts based on the probability that, when the two partners co-occur, they actually interact. Understanding general patterns in the rewiring of interactions can improve our predictions of community responses to interactions' loss, which influences how global changes will affect ecosystem stability.
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Affiliation(s)
- Alicia Montesinos-Navarro
- Centro de Investigaciones Sobre Desertificación (CIDE, CSIC-UV-GV), Carretera de Moncada-Náquera Km 4.5, 46113 Moncada, Valencia Spain
| | - Gisela Díaz
- Departamento de Biología Aplicada, Área de Botánica, Universidad Miguel Hernández, Elche, Alicante Spain
| | - Pilar Torres
- Departamento de Biología Aplicada, Área de Botánica, Universidad Miguel Hernández, Elche, Alicante Spain
| | - Fuensanta Caravaca
- CSIC—Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation, Campus de Espinardo, Murcia, Spain
| | - Antonio Roldán
- CSIC—Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation, Campus de Espinardo, Murcia, Spain
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10
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Araújo CAS, Ferreira PC, Pupin B, Dias LP, Avalos J, Edwards J, Hallsworth JE, Rangel DEN. Osmotolerance as a determinant of microbial ecology: A study of phylogenetically diverse fungi. Fungal Biol 2020; 124:273-88. [PMID: 32389289 DOI: 10.1016/j.funbio.2019.09.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 08/23/2019] [Accepted: 09/03/2019] [Indexed: 12/11/2022]
Abstract
Osmotic stress induced by high solute concentration can prevent fungal metabolism and growth due to alterations in properties of the cytosol, changes in turgor, and the energy required to synthesize and retain compatible solutes. We used germination to quantify tolerance/sensitivity to the osmolyte KCl (0.1-4.5 M, in 0.1 M increments) for 71 strains (40 species) of ecologically diverse fungi. These include 11 saprotrophic species (17 strains, including two xerophilic species), five mycoparasitic species (five strains), six plant-pathogenic species (13 strains), and 19 entomopathogenic species (36 strains). A dendrogram obtained from cluster analyses, based on KCl inhibitory concentrations 50 % and 90 % calculated by Probit Analysis, revealed three groups of fungal isolates accordingly to their osmotolerance. The most-osmotolerant group (Group 3) contained the majority of saprotrophic fungi, and Aspergillus niger (F19) was the most tolerant. The highly xerophilic Aspergillus montevidense and Aspergillus pseudoglaucus were the second- and third-most tolerant species, respectively. All Aspergillus and Cladosporium species belonged to Group 3, followed by the entomopathogens Colletotrichum fioriniae, Simplicillium lanosoniveum, and Trichothecium roseum. Group 2 exhibited a moderate osmotolerance, and included plant-pathogens such as Colletotrichum and Fusarium, mycoparasites such as Clonostachys spp, some saprotrophs such as Mucor and Penicillium spp., and some entomopathogens such as Isaria, Lecanicillium, Mariannaea, Simplicillium, and Torrubiella. Group 1 contained the osmo-sensitive strains: the rest of the entomopathogens and the mycoparasitic Gliocladium and Trichoderma. Although stress tolerance did not correlate with their primary ecological niche, classification of these 71 fungal strains was more closely aligned with their ecology than with their phylogenetic relatedness. We discuss the implications for both microbial ecology and fungal taxonomy.
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11
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Büntgen U, Jäggi M, Egli S, Heule M, Peter M, Zagyva I, Krusic PJ, Zimermann S, Bagi I. No radioactive contamination from the Chernobyl disaster in Hungarian white truffles (Tuber magnatum). Environ Pollut 2019; 252:1643-1647. [PMID: 31284206 DOI: 10.1016/j.envpol.2019.06.108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/18/2019] [Accepted: 06/26/2019] [Indexed: 06/09/2023]
Abstract
Despite being one of the most expensive gourmet foods, it remains unclear if the iconic White Truffle (Tuber magnatum Pico; hereinafter WT) accumulates radioactivity at harmful levels comparable to other fungal species. Here, we measure the active radiocaesium-137 concentration (137Cs) in ten hypogeous WT fruitbodies from southern Hungary, and the soils in which they were growing. All WTs reveal non-significant 137Cs values, thus providing an 'all clear' for WT hunters in the species' northernmost habitats, where corresponding soil samples occasionally exhibit slight 137Cs concentrations. Our results are particularly relevant in the light of a rapidly increasing global demand for WTs and their subsequent trading extent and price inflation, because up to 600 kg of fresh fruitbodies are harvested each year in southern Hungary. Moreover, some of Europe's forest ecosystems, in which mushroom picking is common practise, are still contaminated with 137Cs from the Chernobyl fallout more than 30 years ago, posing a serious threat to human health.
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Affiliation(s)
- Ulf Büntgen
- Department of Geography, University of Cambridge, Downing Place, CB2 3EN, UK; Swiss Federal Research Institute WSL, Zürcherstr 111, 8903 Birmensdorf, Switzerland; Global Change Research Centre (CzechGlobe), Bělidla 986/4a, Brno 603 00 Brno, Czech Republic; Department of Geography, Faculty of Science, Masaryk University, Kotlářská 2, 613 00 Brno, Czech Republic.
| | - Maya Jäggi
- Paul Scherer Institute PSI, Forschungsstr 111, 5232 Villigen, Switzerland.
| | - Simon Egli
- Swiss Federal Research Institute WSL, Zürcherstr 111, 8903 Birmensdorf, Switzerland
| | - Martin Heule
- Paul Scherer Institute PSI, Forschungsstr 111, 5232 Villigen, Switzerland
| | - Martina Peter
- Swiss Federal Research Institute WSL, Zürcherstr 111, 8903 Birmensdorf, Switzerland
| | - Imre Zagyva
- NEFAG Zrt., Kaán Károly u. 71, 7000 Szolnok, Hungary
| | - Paul J Krusic
- Department of Geography, University of Cambridge, Downing Place, CB2 3EN, UK; Department of Physical Geography, Stockholm University, SE-10691, Stockholm, Sweden
| | - Stephan Zimermann
- Swiss Federal Research Institute WSL, Zürcherstr 111, 8903 Birmensdorf, Switzerland
| | - Istvan Bagi
- NEFAG Zrt., Kaán Károly u. 71, 7000 Szolnok, Hungary
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12
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Thomas P, Büntgen U. A risk assessment of Europe's black truffle sector under predicted climate change. Sci Total Environ 2019; 655:27-34. [PMID: 30469066 DOI: 10.1016/j.scitotenv.2018.11.252] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/16/2018] [Accepted: 11/17/2018] [Indexed: 06/09/2023]
Abstract
The black truffle (Tuber melanosporum) is a highly revered culinary icon species that grows symbiotically with its host trees across several parts of southern Europe. Where harvested under natural or cultivated conditions, truffles can have a significant socioeconomic impact and may even form a key component of cultural identity. Although some aspects of truffle biology and ecology have been elucidated recently, the role of abiotic, environmental and climatic factors in the production and maturation of their fruitbodies is still largely unknown. Based on 36-year-long, continuous records of Mediterranean truffle yield, we demonstrate that decreased summer precipitation together with increased summer temperatures significantly reduce the fungus' subsequent winter harvest. Using state-of-the-art climate model projections, we predict that a significant decline of 78-100% in southern European truffle production is likely to occur between 2071 and 2100. The additional threats of forecasted heatwaves, forest fires, pest and disease outbreaks are discussed along with socioeconomic and ecological consequences of a warmer and dryer future climate. Our results emphasize the need for unravelling the direct and indirect effects of climate change on Europe's truffle sector and underline the importance of conservation initiatives at local to international scales.
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Affiliation(s)
- Paul Thomas
- University of Stirling, Stirling FK9 4LA, UK; Mycorrhizal Systems Ltd, Lancashire PR25 2SD, UK.
| | - Ulf Büntgen
- Department of Geography, University of Cambridge, Cambridge CB2 3EN, UK; Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland; Global Change Research Centre (CzechGlobe), 603 00 Brno, Czech Republic; Department of Geography, Faculty of Science, Masaryk University, 613 00 Brno, Czech Republic
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Kearns PJ, Bulseco-McKim AN, Hoyt H, Angell JH, Bowen JL. Nutrient Enrichment Alters Salt Marsh Fungal Communities and Promotes Putative Fungal Denitrifiers. Microb Ecol 2019; 77:358-369. [PMID: 29978357 DOI: 10.1007/s00248-018-1223-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 06/24/2018] [Indexed: 06/08/2023]
Abstract
Enrichment of ecosystems with excess nutrients is occurring at an alarming rate and has fundamentally altered ecosystems worldwide. Salt marshes, which lie at the land-sea interface, are highly effective at removing anthropogenic nutrients through the action of macrophytes and through microbial processes in coastal sediments. The response of salt marsh bacteria to excess nitrogen has been documented; however, the role of fungi and their response to excess nitrogen in salt marsh sediments is not fully understood. Here, we document the response of salt marsh fungal communities to long-term excess nitrate in four distinct marsh habitats within a northern temperate marsh complex. We show that salt marsh fungal communities varied as a function of salt marsh habitat, with both fungal abundance and diversity increasing with carbon quantity. Nutrient enrichment altered fungal communities in all habitats through an increase in fungal abundance and the proliferation of putative fungal denitrifiers. Nutrient enrichment also altered marsh carbon quality in low marsh surface sediments where fungal response to nutrient enrichment was most dramatic, suggesting nutrient enrichment can alter organic matter quality in coastal sediments. Our results indicate that fungi, in addition to bacteria, likely play an important role in anaerobic decomposition of salt marsh sediment organic matter.
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Affiliation(s)
- Patrick J Kearns
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, 430 Nahant Rd., Nahant, MA, 01908, USA
- Biology Department, Tufts University, Medford, MA, 02155, USA
| | - Ashley N Bulseco-McKim
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, 430 Nahant Rd., Nahant, MA, 01908, USA
| | - Helen Hoyt
- Department of Biology, Carleton College, Northfield, MN, 55057, USA
| | - John H Angell
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA
- Biology Department, Boston University, Boston, MA, 02215, USA
| | - Jennifer L Bowen
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, 430 Nahant Rd., Nahant, MA, 01908, USA.
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Ahumada-Rudolph R, Novoa V, Becerra J. Morphological response to salinity, temperature, and pH changes by marine fungus Epicoccum nigrum. Environ Monit Assess 2018; 191:35. [PMID: 30593600 DOI: 10.1007/s10661-018-7166-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 12/17/2018] [Indexed: 06/09/2023]
Abstract
Epicoccum nigrum (strain LQRA39-P) was isolated from sediments collected in Chilean Patagonian fjords using microscopy and molecular techniques. We analyzed adaptive responses of cell wall morphology to salinity, temperature, and pH in order to explain the ability of E. nigrum to co-inhabit both marine and freshwater environments. For this purpose, E. nigrum was cultured in a series of media with variations in salinity (freshwater and seawater), pH (acidic, neutral, and basic), and temperature (5 to 25 °C). Changes were observed through transmission electron microscopy. A direct correlation between increased salinity and cell wall thickening (> 0.2 μm) was observed, along with a significant relationship between pH and the presence of extracellular polymeric substances (EPS) on the outside of the cell wall. The observed morphological changes could confirm that an ubiquitous fungus such as E. nigrum requires adaptive responses to co-inhabit freshwater, marine, and terrestrial substrates.
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Affiliation(s)
- Ramón Ahumada-Rudolph
- Laboratorio de Bioprocesos y Biotratamientos, Departamento de Ingeniería en Maderas, Universidad del Bío-Bío, Collao 1202, PO Box 5-C, Concepción, Chile
| | - Vanessa Novoa
- Department of Geography, School of Architecture, Urbanism and Geography, Universidad de Concepción, Víctor Lamas 1290, PO Box 160-C, Concepción, Chile.
| | - José Becerra
- Laboratorio de Química de Productos Naturales, Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Víctor Lamas 1290, PO Box 160-C, Concepción, Chile
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15
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Mota-Gutierrez J, Ferrocino I, Rantsiou K, Cocolin L. Metataxonomic comparison between internal transcribed spacer and 26S ribosomal large subunit (LSU) rDNA gene. Int J Food Microbiol 2019; 290:132-40. [PMID: 30340111 DOI: 10.1016/j.ijfoodmicro.2018.10.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/04/2018] [Accepted: 10/08/2018] [Indexed: 12/12/2022]
Abstract
Next-generation sequencing has been used to strengthen knowledge about taxonomic diversity and ecology of fungi within food ecosystems. However, primer amplification and identification bias could edge our understanding into the fungal ecology. The aim of this study is to compare the performance of two primer pairs over two nuclear ribosomal RNA (rRNA) regions of the fungal kingdom, namely the ITS2 and 26S regions. Fermented cocoa beans were employed as biological material and the fungal ecology during fermentation was studied using amplicon-based sequencing tools, making use of a manually curated 26S database constructed in this study, and validated with SILVA's database. To explore potential biases introduced by PCR amplification of fungal communities, a mock community of known composition was prepared and tested. The relative abundances observed for ITS2 suggest that species with longer amplification fragments are underestimated and concurrently species that render shorter amplification fragments are overestimated. However, this correlation between amplicon length and estimation is not valid for all the species analysed. Variability in the amplification lengths contributed to the preferential amplification phenomenon. DNA extracted from twenty fermented cocoa bean samples were used to assess the performance of the two target regions. Overall, the metataxonomic data set recovered similar taxonomic composition and provided consistent results in OTU richness among biological samples. However, 26S region provided higher alpha diversity index and greater fungal rRNA taxonomic depth and robustness results compared with ITS2. Based on the results of this study we suggest the use of the 26S region for targeting fungi. Furthermore, this study showed the efficacy of the manually curated reference database optimized for annotation of mycobiota by using the 26S as a gene target.
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Barbosa RN, Bezerra JDP, Souza-Motta CM, Frisvad JC, Samson RA, Oliveira NT, Houbraken J. New Penicillium and Talaromyces species from honey, pollen and nests of stingless bees. Antonie Van Leeuwenhoek 2018; 111:1883-1912. [PMID: 29654567 PMCID: PMC6153986 DOI: 10.1007/s10482-018-1081-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/31/2018] [Indexed: 01/05/2023]
Abstract
Penicillium and Talaromyces species have a worldwide distribution and are isolated from various materials and hosts, including insects and their substrates. The aim of this study was to characterize the Penicillium and Talaromyces species obtained during a survey of honey, pollen and the inside of nests of Melipona scutellaris. A total of 100 isolates were obtained during the survey and 82% of those strains belonged to Penicillium and 18% to Talaromyces. Identification of these isolates was performed based on phenotypic characters and β-tubulin and ITS sequencing. Twenty-one species were identified in Penicillium and six in Talaromyces, including seven new species. These new species were studied in detail using a polyphasic approach combining phenotypic, molecular and extrolite data. The four new Penicillium species belong to sections Sclerotiora (Penicillium fernandesiae sp. nov., Penicillium mellis sp. nov., Penicillium meliponae sp. nov.) and Gracilenta (Penicillium apimei sp. nov.) and the three new Talaromyces species to sections Helici (Talaromyces pigmentosus sp. nov.), Talaromyces (Talaromyces mycothecae sp. nov.) and Trachyspermi (Talaromyces brasiliensis sp. nov.). The invalidly described species Penicillium echinulonalgiovense sp. nov. was also isolated during the survey and this species is validated here.
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Affiliation(s)
- Renan N Barbosa
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- Departamento de Micologia Prof. Chaves Batista, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, s/n, Centro de Biociências, Cidade Universitária, CEP: 50670-901, Recife, PE, Brazil
| | - Jadson D P Bezerra
- Departamento de Micologia Prof. Chaves Batista, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, s/n, Centro de Biociências, Cidade Universitária, CEP: 50670-901, Recife, PE, Brazil
| | - Cristina M Souza-Motta
- Departamento de Micologia Prof. Chaves Batista, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, s/n, Centro de Biociências, Cidade Universitária, CEP: 50670-901, Recife, PE, Brazil
| | - Jens C Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Robert A Samson
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Neiva T Oliveira
- Departamento de Micologia Prof. Chaves Batista, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, s/n, Centro de Biociências, Cidade Universitária, CEP: 50670-901, Recife, PE, Brazil
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.
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Argüelles-Moyao A, Garibay-Orijel R. Ectomycorrhizal fungal communities in high mountain conifer forests in central Mexico and their potential use in the assisted migration of Abies religiosa. Mycorrhiza 2018; 28:509-521. [PMID: 29948411 DOI: 10.1007/s00572-018-0841-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 05/29/2018] [Indexed: 06/08/2023]
Abstract
Abies religiosa forests in central Mexico are the only overwinter refuge of the monarch butterfly and provide important ecosystem services. These forests have lost 55% of their original area and as a consequence, diversity and biotic interactions in these ecosystems are in risk. The aim of this study was to compare the soil fungal diversity and community structure in the Abies religiosa forests and surrounding Pinus montezumae, Pinus hartwegii, and coniferous mixed forest plant communities to provide data on ecology of mycorrhizal interactions for the assisted migration of A. religiosa. We sampled soil from five coniferous forests, extracted total soil DNA, and sequenced the ITS2 region by Illumina MiSeq. The soil fungi community was integrated by 1746 taxa with a species turnover ranging from 0.280 to 0.461 between sampling sites. In the whole community, the more abundant and frequent species were Russula sp. (aff. olivobrunnea), Mortierella sp.1, and Piloderma sp. (aff. olivacearum). The ectomycorrhizal fungi were the more frequent and abundant functional group. A total of 298 species (84 ectomycorrhizal) was shared in the five conifer forests; these widely distributed species were dominated by Russulaceae and Clavulinaceae. The fungal community composition was significantly influenced by altitude and the lowest species turnover happened between the two A. religiosa forests even though they have different soil types. As Pinus montezumae forests have a higher altitudinal distribution adjacent to A. religiosa and share the largest number of ectomycorrhizal fungi with it, we suggest these forests as a potential habitat for new A. religiosa populations.
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Affiliation(s)
- Andrés Argüelles-Moyao
- Laboratorio de Sistemática, Ecología y Aprovechamiento de Hongos Ectomicorrízicos, Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria. Del. Coyoacán, C.P. 04510, Mexico City, CDMX, Mexico
- Posgrado en Ciencias Biológicas, Edificio B, 1° Piso, Unidad de Posgrado, Circuito de Posgrados, Universidad Nacional Autónoma de México, Ciudad Universitaria, Del. Coyoacán, C.P. 04510, Mexico City, CDMX, Mexico
| | - Roberto Garibay-Orijel
- Laboratorio de Sistemática, Ecología y Aprovechamiento de Hongos Ectomicorrízicos, Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria. Del. Coyoacán, C.P. 04510, Mexico City, CDMX, Mexico.
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Veach AM, Stokes CE, Knoepp J, Jumpponen A, Baird R. Fungal Communities and Functional Guilds Shift Along an Elevational Gradient in the Southern Appalachian Mountains. Microb Ecol 2018; 76:156-168. [PMID: 29204781 DOI: 10.1007/s00248-017-1116-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/20/2017] [Indexed: 05/03/2023]
Abstract
Nitrogen deposition alters forest ecosystems particularly in high elevation, montane habitats where nitrogen deposition is greatest and continues to increase. We collected soils across an elevational (788-1940 m) gradient, encompassing both abiotic (soil chemistry) and biotic (vegetation community) gradients, at eight locations in the southern Appalachian Mountains of southwestern North Carolina and eastern Tennessee. We measured soil chemistry (total N, C, extractable PO4, soil pH, cation exchange capacity [ECEC], percent base saturation [% BS]) and dissected soil fungal communities using ITS2 metabarcode Illumina MiSeq sequencing. Total soil N, C, PO4, % BS, and pH increased with elevation and plateaued at approximately 1400 m, whereas ECEC linearly increased and C/N decreased with elevation. Fungal communities differed among locations and were correlated with all chemical variables, except PO4, whereas OTU richness increased with total N. Several ecological guilds (i.e., ectomycorrhizae, saprotrophs, plant pathogens) differed in abundance among locations; specifically, saprotroph abundance, primarily attributable to genus Mortierella, was positively correlated with elevation. Ectomycorrhizae declined with total N and soil pH and increased with total C and PO4 where plant pathogens increased with total N and decreased with total C. Our results demonstrate significant turnover in taxonomic and functional fungal groups across elevational gradients which facilitate future predictions on forest ecosystem change in the southern Appalachians as nitrogen deposition rates increase and regional temperature and precipitation regimes shift.
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Affiliation(s)
- Allison M Veach
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA.
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, 37831, USA.
| | - C Elizabeth Stokes
- Department of Forest Products, Mississippi State University, Starkville, MS, 39762, USA
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS, 39762, USA
| | - Jennifer Knoepp
- USDA, Forest Service, Southern Research Station, Center for Forest Watershed Research, Coweeta Hydrologic Laboratory, Otto, NC, 28763, USA
| | - Ari Jumpponen
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Richard Baird
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS, 39762, USA
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Veresoglou SD, Wang D, Andrade-Linares DR, Hempel S, Rillig MC. Fungal Decision to Exploit or Explore Depends on Growth Rate. Microb Ecol 2018; 75:289-292. [PMID: 28791465 DOI: 10.1007/s00248-017-1053-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/31/2017] [Indexed: 05/28/2023]
Affiliation(s)
- Stavros D Veresoglou
- Institut für Biologie, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany.
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany.
| | - Dongwei Wang
- Institut für Biologie, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany
| | - Diana R Andrade-Linares
- Institut für Biologie, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany
| | - Stefan Hempel
- Institut für Biologie, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany
| | - Matthias C Rillig
- Institut für Biologie, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany
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20
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Kohout P, Tedersoo L. Effect of soil moisture on root-associated fungal communities of Erica dominans in Drakensberg mountains in South Africa. Mycorrhiza 2017; 27:397-406. [PMID: 28083703 DOI: 10.1007/s00572-017-0760-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/03/2017] [Indexed: 06/06/2023]
Abstract
Ericoid mycorrhiza represents a key adaptation of the Ericaceae plants to facilitate their establishment in harsh conditions. The Ericaceae are a large family of flowering plants, with global distribution. However, our current knowledge about the ericoid mycorrhizal fungal diversity and ecology largely relates to the Northern Hemisphere. Our study focused on the assembly of root-associated fungal (RAF) communities of Erica dominans in two types of microhabitats of contrasting moisture along an elevation gradient in Drakensberg mountains in South Africa. RAF communities were determined by 454-sequencing of the internal transcribed spacer (ITS) region of ribosomal DNA. The majority of RAF showed affinity to the orders Helotiales, Pezizales, and Pleosporales. Microhabitat type as well as elevation had significant but weak effect on RAF community composition. We identified two putative ericoid mycorrhizal fungi, the ecological niches of which were differentiated between the studied microhabitats. Our study also provides one of the first comprehensive data about RAF communities of Ericaceae on African continent and shows the occurrence of the most studied ericoid mycorrhizal fungus Pezoloma ericae (belonging to P. ericae aggregate) in roots of Ericaceae host plant in Africa.
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Affiliation(s)
- Petr Kohout
- Institute of Ecology and Earth Sciences, University of Tartu, 50411, Tartu, Estonia.
- Institute of Botany, Academy of Sciences of the Czech Republic, 252 43, Průhonice, Czech Republic.
- Department of Experimental Plant Biology, Faculty of Science, Charles University, 128 01, Prague 2, Czech Republic.
| | - Leho Tedersoo
- Natural History Museum, University of Tartu, 50411, Tartu, Estonia
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Barbosa RN, Leong SL, Vinnere-Pettersson O, Chen AJ, Souza-Motta CM, Frisvad JC, Samson RA, Oliveira NT, Houbraken J. Phylogenetic analysis of Monascus and new species from honey, pollen and nests of stingless bees. Stud Mycol 2017; 86:29-51. [PMID: 28539687 DOI: 10.1016/j.simyco.2017.04.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The genus Monascus was described by van Tieghem (1884) to accommodate M. ruber and M. mucoroides, two species with non-ostiolate ascomata. Species delimitation in the genus is still mainly based on phenotypic characters, and taxonomic studies that include sequence data are limited. The genus is of economic importance. Species are used in fermented Asian foods as food colourants (e.g. ‘red rice’ (ang-kak, angka)) and found as spoilage organisms, and recently Monascus was found to be essential in the lifecycle of stingless bees. In this study, a polyphasic approach was applied combining morphological characters, ITS, LSU, β-tubulin, calmodulin and RNA polymerase II second largest subunit sequences and extrolite data, to delimit species and to study phylogenetic relationships in Monascus. Furthermore, 30 Monascus isolates from honey, pollen and nests of stingless bees in Brazil were included. Based on this polyphasic approach, the genus Monascus is resolved in nine species, including three new species associated with stingless bees (M. flavipigmentosus sp. nov., M. mellicola sp. nov., M. recifensis sp. nov., M. argentinensis, M. floridanus, M. lunisporas, M. pallens, M. purpureus, M. ruber), and split in two new sections (section Floridani sect. nov., section Rubri sect. nov.). Phylogenetic analysis showed that the xerophile Monascus eremophilus does not belong in Monascus and monophyly in Monascus is restored with the transfer of M. eremophilus to Penicillium (P. eremophilum comb. nov.). A list of accepted and excluded Monascus and Basipetospora species is given, together with information on (ex-)types cultures and barcode sequence data.
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Luo J, Walsh E, Miller S, Blystone D, Dighton J, Zhang N. Root endophytic fungal communities associated with pitch pine, switchgrass, and rosette grass in the pine barrens ecosystem. Fungal Biol 2017; 121:478-487. [PMID: 28390505 DOI: 10.1016/j.funbio.2017.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 01/26/2017] [Accepted: 01/28/2017] [Indexed: 11/27/2022]
Abstract
Almost all plants in nature harbour fungi in their roots but the knowledge on distribution and the underlying principles of assemblage is still poorly developed for the root-associated fungi. In this study we analysed the root endophytic fungal communities associated with switchgrass, rosette grass, and pitch pine in the acidic, oligotrophic pine barrens ecosystem. A total of 434 fungal isolates were obtained from 600 root segments of 60 plant samples. DNA barcoding and morphological analyses identified 92 fungal species, which belong to 39 genera in six classes. Compared to other ecosystems, the pine barrens has a higher proportion of Leotiomycetes. The fungal community associated with pitch pine was significantly different from those associated with the grasses, while less difference was found between those associated with the two grasses. Our results suggest that edaphic factors and host specificity play a role in shaping root endophytic fungal community. This study also corroborates our previous finding that plant roots in the pine barrens are a rich reservoir of novel fungi.
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Affiliation(s)
- Jing Luo
- Department of Plant Biology, 201 Foran Hall, 59 Dudley Road, Rutgers University, New Brunswick, NJ 08901, USA
| | - Emily Walsh
- Department of Plant Biology, 201 Foran Hall, 59 Dudley Road, Rutgers University, New Brunswick, NJ 08901, USA
| | - Stephen Miller
- Department of Plant Biology, 201 Foran Hall, 59 Dudley Road, Rutgers University, New Brunswick, NJ 08901, USA
| | - David Blystone
- Department of Plant Biology, 201 Foran Hall, 59 Dudley Road, Rutgers University, New Brunswick, NJ 08901, USA
| | - John Dighton
- Rutgers Pinelands Field Station, DEENR, SEBS and Biology, Camden, PO Box 206, 501 Four Mile Road, New Lisbon, NJ 08064, USA
| | - Ning Zhang
- Department of Plant Biology, 201 Foran Hall, 59 Dudley Road, Rutgers University, New Brunswick, NJ 08901, USA; Department of Biochemistry and Microbiology, 76 Lipman Drive, Rutgers University, New Brunswick, NJ 08901, USA.
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Pinzari F, Ceci A, Abu-Samra N, Canfora L, Maggi O, Persiani A. Phenotype MicroArray™ system in the study of fungal functional diversity and catabolic versatility. Res Microbiol 2016; 167:710-722. [PMID: 27283363 DOI: 10.1016/j.resmic.2016.05.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 05/18/2016] [Accepted: 05/26/2016] [Indexed: 11/30/2022]
Abstract
Fungi cover a range of important ecological functions associated with nutrient and carbon cycling in leaf litter and soil. As a result, research on existing relationships between fungal functional diversity, decomposition rates and competition is of key interest. Indeed, availability of nutrients in soil is largely the consequence of organic matter degradation dynamics. The Biolog® Phenotype MicroArrays™ (PM) system allows for the testing of fungi against many different carbon sources at any one time. The use and potential of the PM system as a tool for studying niche overlap and catabolic versatility of saprotrophic fungi is discussed here, and examples of its application are provided.
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Affiliation(s)
- Flavia Pinzari
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia agraria, Centro di Ricerca per lo Studio delle Relazioni tra Pianta e Suolo (CREA-RPS), Via della Navicella 2-4, 00184 Rome, Italy; Natural History Museum, Life Sciences Department, Cromwell Road, London SW7 5BD, UK.
| | - Andrea Ceci
- Dipartimento di Biologia ambientale, Sapienza Università di Roma, P.le Aldo Moro, 00185 Rome, Italy.
| | - Nadir Abu-Samra
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia agraria, Centro di Ricerca per lo Studio delle Relazioni tra Pianta e Suolo (CREA-RPS), Via della Navicella 2-4, 00184 Rome, Italy.
| | - Loredana Canfora
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia agraria, Centro di Ricerca per lo Studio delle Relazioni tra Pianta e Suolo (CREA-RPS), Via della Navicella 2-4, 00184 Rome, Italy.
| | - Oriana Maggi
- Dipartimento di Biologia ambientale, Sapienza Università di Roma, P.le Aldo Moro, 00185 Rome, Italy.
| | - Annamaria Persiani
- Dipartimento di Biologia ambientale, Sapienza Università di Roma, P.le Aldo Moro, 00185 Rome, Italy.
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Ma X, Baron JL, Vikram A, Stout JE, Bibby K. Fungal diversity and presence of potentially pathogenic fungi in a hospital hot water system treated with on-site monochloramine. Water Res 2015; 71:197-206. [PMID: 25618520 DOI: 10.1016/j.watres.2014.12.052] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/09/2014] [Accepted: 12/30/2014] [Indexed: 06/04/2023]
Abstract
Currently, our knowledge of fungal ecology in engineered drinking water systems is limited, despite the potential for these systems to serve as a reservoir for opportunistic pathogens. In this study, hot water samples were collected both prior to and following the addition of monochloramine as an on-site disinfectant in a hospital hot water system. Fungal ecology was then analyzed by high throughput sequencing of the fungal ITS1 region. The results demonstrate that the genera Penicillium, Aspergillus, Peniophora, Cladosporium and Rhodosporidium comprised the core fungal biome of the hospital hot water system. Penicillium dominated the fungal community with an average relative abundance of 88.89% (±6.37%). ITS1 sequences of fungal genera containing potential pathogens such as Aspergillus, Candida, and Fusarium were also detected in this study. No significant change in fungal community structure was observed before and after the initiation of on-site monochloramine water treatment. This work represents the first report of the effects of on-site secondary water disinfection on fungal ecology in premise plumbing system, and demonstrates the necessity of considering opportunistic fungal pathogens during the evaluation of secondary premise plumbing disinfection systems.
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Affiliation(s)
- Xiao Ma
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Julianne L Baron
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA 15261, USA; Special Pathogens Laboratory, Pittsburgh, PA 15219, USA
| | - Amit Vikram
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Janet E Stout
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA; Special Pathogens Laboratory, Pittsburgh, PA 15219, USA
| | - Kyle Bibby
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Computational and Systems Biology, University of Pittsburgh Medical School, Pittsburgh, PA 15261, USA.
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25
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Dannemiller KC, Reeves D, Bibby K, Yamamoto N, Peccia J. Fungal high-throughput taxonomic identification tool for use with next-generation sequencing (FHiTINGS). J Basic Microbiol 2013; 54:315-21. [PMID: 23765392 DOI: 10.1002/jobm.201200507] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 11/13/2012] [Indexed: 01/21/2023]
Abstract
Improvements in DNA sequencing technology provide unprecedented opportunities to explore fungal diversity, but also present challenges in data analysis due to the large number of sequences generated. Here, we describe an open source software program "FHiTINGS" that utilizes the output of a BLASTn (blastall) search to rapidly identify, classify, and parse internal transcribed spacer (ITS) DNA sequences produced in fungal ecology studies that utilize next-generation DNA sequencing. This tool was designed for use with 454 pyrosequencing and is also appropriate for use with any sequencing platform that allows for BLAST searches against the indicated ITS database. For each sequence, FHiTINGS uses the lowest common ancestor method (LCA) to produce a single identification from BLAST output results, and then assigns taxonomic ranks from species through kingdom when possible for each sequence based on the Index Fungorum database. The program then sums and sorts this data into tabular form to enable rapid analysis of the sample, including α-diversity measures or richness. In silico testing demonstrates the time required to analyze and classify 1000 sequences is reduced from over 2 h by manual sorting to <1 min of computational time when using FHiTINGS, and that the classification output from the software is consistent with that derived from manual sorting of the data.
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Affiliation(s)
- Karen C Dannemiller
- Department of Chemical and Environmental Engineering, Yale University, 9 Hillhouse Ave, PO Box 208286, New Haven, CT, 06520, USA
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