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Pagani DM, Ventura SPR, Vu D, Mendes-Pereira T, Ribeiro Tomé LM, de Carvalho DS, Costa-Rezende DH, Kato RB, García GJY, Geml J, Robert V, They NH, Brenig B, Azevedo V, Scroferneker ML, Valente P, Góes-Neto A. Unveiling Fungal Community Structure along Different Levels of Anthropic Disturbance in a South American Subtropical Lagoon. J Fungi (Basel) 2023; 9:890. [PMID: 37754998 PMCID: PMC10532596 DOI: 10.3390/jof9090890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/19/2023] [Accepted: 08/29/2023] [Indexed: 09/28/2023] Open
Abstract
Studies of fungal communities through amplicon metagenomics in aquatic environments, particularly in freshwater ecosystems, are still relatively recent. Unfortunately, many of these water bodies are facing growing threats from human expansion, such as effluent discharge from various human activities. As a result, these effluents have the potential to significantly alter the characteristics of water bodies and, subsequently, impact the diversity of their resident microorganisms. In this context, our objective was to investigate whether the fungal community structure varies according to the presence of different anthropic disturbances. We expect (i) the diversity of fungi will be greater and (ii) more specific unique operational taxonomic units (OTUs) related to each ecotonal system will be found compared to other sites of a lagoon. The study was conducted in the Tramandaí Lagoon (subtropical southern Brazil) at four distinct sampling points (estuary, middle of the lagoon, crop field area, and near a residential area where the Tramandaí River flows into the lagoon). As expected, the estuary and residential zones, which are ecotones, exhibited greater fungal diversity and more specific OTUs compared to the middle of the lagoon and crop field area. Moreover, a substantial proportion of fungal taxa could not be identified at the genus level, with many only classified at the phylum level, indicating potential new lineages. These findings underscore our limited understanding of the subtropical freshwater mycobiota.
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Affiliation(s)
- Danielle Machado Pagani
- Programa de Pós-Graduação em Microbiologia Agrícola e do Ambiente, Universidade Federal do Rio Grande do Sul, Porto Alegre 90010-150, RS, Brazil; (D.M.P.); (P.V.)
| | - Stefânia P. R. Ventura
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (S.P.R.V.); (R.B.K.); (G.J.Y.G.); (V.A.)
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (D.V.); (V.R.)
| | - Thairine Mendes-Pereira
- Programa de Pós-Graduação em Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (T.M.-P.); (L.M.R.T.); (D.S.d.C.)
| | - Luiz Marcelo Ribeiro Tomé
- Programa de Pós-Graduação em Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (T.M.-P.); (L.M.R.T.); (D.S.d.C.)
| | - Daniel Santana de Carvalho
- Programa de Pós-Graduação em Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (T.M.-P.); (L.M.R.T.); (D.S.d.C.)
| | - Diogo Henrique Costa-Rezende
- Departamento de Ciências Biológicas, Programa de Pós-Graduação em Botânica, Universidade Estadual de Feira de Santana, Feira de Santana 44036-900, BA, Brazil;
| | - Rodrigo Bentes Kato
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (S.P.R.V.); (R.B.K.); (G.J.Y.G.); (V.A.)
| | - Glen Jasper Yupanqui García
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (S.P.R.V.); (R.B.K.); (G.J.Y.G.); (V.A.)
| | - József Geml
- ELKH-EKKE Lendület Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Leányka U. 6, 3300 Eger, Hungary;
| | - Vincent Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (D.V.); (V.R.)
| | - Ng Haig They
- Laboratório de Ecologia Aquática Microbiana, Programa de Pós-Graduação em Biologia de Ambientes Aquáticos Continentais, Departamento Interdisciplinar, Centro de Estudos Costeiros, Limnológicos e Marinhos, Universidade Federal do Rio Grande do Sul, Campus Litoral Norte, Tramandaí 95590-000, RS, Brazil;
| | - Bertram Brenig
- Institute of Veterinary Medicine, Georg-August-University Goettingen, 37073 Göttingen, Germany;
| | - Vasco Azevedo
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (S.P.R.V.); (R.B.K.); (G.J.Y.G.); (V.A.)
- Laboratory of Cellular and Molecular Genetics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Maria Lúcia Scroferneker
- Programa de Pós-Graduação em Ciências Médicas, Universidade Federal do Rio Grande do Sul, Porto Alegre 90010-150, RS, Brazil;
| | - Patricia Valente
- Programa de Pós-Graduação em Microbiologia Agrícola e do Ambiente, Universidade Federal do Rio Grande do Sul, Porto Alegre 90010-150, RS, Brazil; (D.M.P.); (P.V.)
| | - Aristóteles Góes-Neto
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (S.P.R.V.); (R.B.K.); (G.J.Y.G.); (V.A.)
- Programa de Pós-Graduação em Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (T.M.-P.); (L.M.R.T.); (D.S.d.C.)
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2
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Čačković A, Kajan K, Selak L, Marković T, Brozičević A, Pjevac P, Orlić S. Hydrochemical and Seasonally Conditioned Changes of Microbial Communities in the Tufa-Forming Freshwater Network Ecosystem. mSphere 2023:e0060222. [PMID: 37097185 DOI: 10.1128/msphere.00602-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Freshwater network ecosystems consist of interconnected lotic and lentic environments within the same catchment area. Using Plitvice Lakes as an example, we studied the changes in environmental conditions and microbial communities (bacteria and fungi) that occur with downstream flow. Water samples from tributaries, interlake streams, connections of the cascading lakes, and the Korana River, the main outflow of the system, were characterized using amplicon sequencing of bacterial 16S rRNA and fungal ITS2 genes. Our results show that different environmental conditions and bacterial and fungal communities prevail among the three stream types within the freshwater network ecosystem during multiple sampling seasons. Microbial community differences were also confirmed along the longitudinal gradient between the most distant sampling sites. The higher impact of "mass effect" was evident during spring and winter, while "species sorting" and "environmental selection" was more pronounced during summer. Prokaryotic community assembly was majorly influenced by deterministic processes, while fungal community assembly was highly dominated by stochastic processes, more precisely by the undominated fraction, which is not dominated by any process. Despite the differences between stream types, the microbial community of Plitvice Lakes is shown to be very stable by the core microbiome that makes up the majority of stream communities. Our results suggest microbial community succession along the river-lake continuum of microbial communities in small freshwater network ecosystems with developed tufa barriers. IMPORTANCE Plitvice Lakes represent a rare freshwater ecosystem consisting of a complex network of lakes and waterfalls connecting them, as well as rivers and streams supplying water to the lake basin. The unique geomorphological, hydrological, biogeochemical, and biological phenomenon of Plitvice Lakes lies in the biodynamic process of forming tufa barriers. In addition to microbial communities, abiotic water factors also have a major influence on the formation of tufa. Therefore, it is important to understand how changes in environmental conditions and microbial community assembly affect the functioning of the ecosystem of a freshwater network with developed tufa barriers.
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Affiliation(s)
- Andrea Čačković
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Katarina Kajan
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Zagreb, Croatia
| | - Lorena Selak
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | | | - Andrijana Brozičević
- Scientific Research Center "Dr. Ivo Pevalek," Plitvice Lakes National Park, Plitvička Jezera, Croatia
| | - Petra Pjevac
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna, Vienna, Austria
| | - Sandi Orlić
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Zagreb, Croatia
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3
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Masumoto S, Kitagawa R, Kaneko R, Nishizawa K, Matsuoka S, Uchida M, Mori AS. Discrepancies of fungi and plants in the pattern of beta-diversity with environmental gradient imply a comprehensive community assembly rule. FEMS Microbiol Ecol 2023; 99:6965348. [PMID: 36581318 DOI: 10.1093/femsec/fiac157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/24/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
Beta-diversity partitioning has shown that the nestedness component is developed with environmental stress in a variety of taxa. However, soil fungal community may maintain its turnover components in contrast to the development of plants' nestedness component, and the potential causes remain unclear. To investigate the process of species turnover of soil fungi along a stress gradient in the Arctic, we divided species turnover component into sub-components: βsim_hete and βsim_homo representing species turnover with and without a change in the guilds, respectively. The results indicate that fungal communities maintain their turnover components, unlike plant communities; however, their βsim_hete increased under stressful conditions. Additionally, GDM analysis showed that βsim_hete was mainly explained by stress gradient and plant nestedness, suggesting that the functionality of soil fungi was ecologically filtered by environmental stress and plant community structure. The discordant trend of beta-diversity values between plant and fungi (i.e. development of plant nestedness and maintenance of fungal turnover) is possibly not caused by different assembly rules working in parallel on the two taxa, but according to an ecological rule that reflects plant-fungal interaction.
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Affiliation(s)
- Shota Masumoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Ryo Kitagawa
- Kansai Research Center, Forestry and Forest Products Research Institute, Fushimi, Kyoto 612-0855, Japan
| | - Ryo Kaneko
- National Institute of Polar Research, Tachikawa, Tokyo 190-8518, Japan
| | - Keita Nishizawa
- Research Center for Advanced Science and Technology, the University of Tokyo, Meguro, Tokyo 153-8904, Japan
| | - Shunsuke Matsuoka
- Field Science Education and Research Center, Kyoto University, Nantan, Kyoto 601-0703, Japan
| | - Masaki Uchida
- National Institute of Polar Research, Tachikawa, Tokyo 190-8518, Japan.,School of Multidisciplinary Sciences, The Graduate University for Advanced Studies, Tachikawa, Tokyo 190-8518, Japan
| | - Akira S Mori
- Research Center for Advanced Science and Technology, the University of Tokyo, Meguro, Tokyo 153-8904, Japan
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4
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Biderre‐Petit C, Charvy J, Bronner G, Chauvet M, Debroas D, Gardon H, Hennequin C, Jouan‐Dufournel I, Moné A, Monjot A, Ravet V, Vellet A, Lepère C. FreshOmics
: a manually curated and standardized –omics database for investigating freshwater microbiomes. Mol Ecol Resour 2022; 23:222-232. [DOI: 10.1111/1755-0998.13692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Corinne Biderre‐Petit
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Jean‐Christophe Charvy
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Gisèle Bronner
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Marina Chauvet
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Didier Debroas
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Hélène Gardon
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Claire Hennequin
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Isabelle Jouan‐Dufournel
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Anne Moné
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Arthur Monjot
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Viviane Ravet
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Agnès Vellet
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Cécile Lepère
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
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5
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Matsuoka S, Sugiyama Y, Nagano M, Doi H. Influence of DNA extraction kits on freshwater fungal DNA metabarcoding. PeerJ 2022; 10:e13477. [PMID: 35651749 PMCID: PMC9150701 DOI: 10.7717/peerj.13477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 05/01/2022] [Indexed: 01/17/2023] Open
Abstract
Background Environmental DNA (eDNA) metabarcoding is a common technique for efficient biodiversity monitoring, especially of microbes. Recently, the usefulness of aquatic eDNA in monitoring the diversity of both terrestrial and aquatic fungi has been suggested. In eDNA studies, different experimental factors, such as DNA extraction kits or methods, can affect the subsequent analyses and the results of DNA metabarcoding. However, few methodological studies have been carried out on eDNA of fungi, and little is known about how experimental procedures can affect the results of biodiversity analysis. In this study, we focused on the effect of DNA extraction method on fungal DNA metabarcoding using freshwater samples obtained from rivers and lakes. Methods DNA was extracted from freshwater samples using the DNeasy PowerSoil kit, which is mainly used to extractmicrobial DNA from soil, and the DNeasy Blood & Tissue kit, which is commonly used for eDNA studies on animals. We then compared PCR inhibition and fungal DNA metabarcoding results; i.e., operational taxonomic unit (OTU) number and composition of the extracted samples. Results No PCR inhibition was detected in any of the samples, and no significant differences in the number of OTUs and OTU compositions were detected between the samples processed using different kits. These results indicate that both DNA extraction kits may provide similar diversity results for the river and lake samples evaluated in this study. Therefore, it may be possible to evaluate the diversity of fungi using a unified experimental method, even with samples obtained for diversity studies on other taxa such as those of animals.
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Affiliation(s)
- Shunsuke Matsuoka
- Field Science Education and Research Center, Kyoto University, Kyoto, Japan
| | - Yoriko Sugiyama
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Mariko Nagano
- Department of Bioenvironmental Design, Kyoto University of Advanced Science, Kameoka, Japan
| | - Hideyuki Doi
- Graduate School of Information Science, University of Hyogo, Kobe, Japan
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6
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Tedersoo L, Bahram M, Zinger L, Nilsson RH, Kennedy PG, Yang T, Anslan S, Mikryukov V. Best practices in metabarcoding of fungi: From experimental design to results. Mol Ecol 2022; 31:2769-2795. [PMID: 35395127 DOI: 10.1111/mec.16460] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 02/07/2022] [Accepted: 03/30/2022] [Indexed: 02/06/2023]
Abstract
The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems. Here we provide an overview of current best practices in metabarcoding analysis of fungal communities, from experimental design through molecular and computational analyses. By reanalysing published data sets, we demonstrate that operational taxonomic units (OTUs) outperform amplified sequence variants (ASVs) in recovering fungal diversity, a finding that is particularly evident for long markers. Additionally, analysis of the full-length ITS region allows more accurate taxonomic placement of fungi and other eukaryotes compared to the ITS2 subregion. Finally, we show that specific methods for compositional data analyses provide more reliable estimates of shifts in community structure. We conclude that metabarcoding analyses of fungi are especially promising for integrating fungi into the full microbiome and broader ecosystem functioning context, recovery of novel fungal lineages and ancient organisms as well as barcoding of old specimens including type material.
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Bahram
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Lucie Zinger
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, France.,Naturalis Biodiversity Center, Leiden, The Netherlands
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Peter G Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, USA
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Vladimir Mikryukov
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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7
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Senanayake IC, Pem D, Rathnayaka AR, Wijesinghe SN, Tibpromma S, Wanasinghe DN, Phookamsak R, Kularathnage ND, Gomdola D, Harishchandra D, Dissanayake LS, Xiang MM, Ekanayaka AH, McKenzie EHC, Hyde KD, Zhang HX, Xie N. Predicting global numbers of teleomorphic ascomycetes. FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00498-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
AbstractSexual reproduction is the basic way to form high genetic diversity and it is beneficial in evolution and speciation of fungi. The global diversity of teleomorphic species in Ascomycota has not been estimated. This paper estimates the species number for sexual ascomycetes based on five different estimation approaches, viz. by numbers of described fungi, by fungus:substrate ratio, by ecological distribution, by meta-DNA barcoding or culture-independent studies and by previous estimates of species in Ascomycota. The assumptions were made with the currently most accepted, “2.2–3.8 million” species estimate and results of previous studies concluding that 90% of the described ascomycetes reproduce sexually. The Catalogue of Life, Species Fungorum and published research were used for data procurement. The average value of teleomorphic species in Ascomycota from all methods is 1.86 million, ranging from 1.37 to 2.56 million. However, only around 83,000 teleomorphic species have been described in Ascomycota and deposited in data repositories. The ratio between described teleomorphic ascomycetes to predicted teleomorphic ascomycetes is 1:22. Therefore, where are the undiscovered teleomorphic ascomycetes? The undescribed species are no doubt to be found in biodiversity hot spots, poorly-studied areas and species complexes. Other poorly studied niches include extremophiles, lichenicolous fungi, human pathogens, marine fungi, and fungicolous fungi. Undescribed species are present in unexamined collections in specimen repositories or incompletely described earlier species. Nomenclatural issues, such as the use of separate names for teleomorph and anamorphs, synonyms, conspecific names, illegitimate and invalid names also affect the number of described species. Interspecies introgression results in new species, while species numbers are reduced by extinctions.
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8
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Effectiveness assessment of using riverine water eDNA to simultaneously monitor the riverine and riparian biodiversity information. Sci Rep 2021; 11:24241. [PMID: 34930992 PMCID: PMC8688430 DOI: 10.1038/s41598-021-03733-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/09/2021] [Indexed: 11/09/2022] Open
Abstract
Both aquatic and terrestrial biodiversity information can be detected in riverine water environmental DNA (eDNA). However, the effectiveness of using riverine water eDNA to simultaneously monitor the riverine and terrestrial biodiversity information remains unidentified. Here, we proposed that the monitoring effectiveness could be approximated by the transportation effectiveness of land-to-river and upstream-to-downstream biodiversity information flows and described by three new indicators. Subsequently, we conducted a case study in a watershed on the Qinghai-Tibet Plateau. The results demonstrated that there was higher monitoring effectiveness on summer or autumn rainy days than in other seasons and weather conditions. The monitoring of the bacterial biodiversity information was more efficient than the monitoring of the eukaryotic biodiversity information. On summer rainy days, 43-76% of species information in riparian sites could be detected in adjacent riverine water eDNA samples, 92-99% of species information in riverine sites could be detected in a 1-km downstream eDNA sample, and half of dead bioinformation (the bioinformation labeling the biological material that lacked life activity and fertility) could be monitored 4-6 km downstream for eukaryotes and 13-19 km downstream for bacteria. The current study provided reference method and data for future monitoring projects design and for future monitoring results evaluation.
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9
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Masumoto S, Kitagawa R, Nishizawa K, Kaneko R, Osono T, Hasegawa M, Matsuoka S, Uchida M, Mori AS. Functionally explicit partitioning of plant β-diversity reveal soil fungal assembly in the subarctic tundra. FEMS Microbiol Ecol 2021; 97:6366230. [PMID: 34494103 DOI: 10.1093/femsec/fiab129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 09/02/2021] [Indexed: 11/14/2022] Open
Abstract
Metabarcoding technologies for soil fungal DNA pools have enabled to capture the diversity of fungal community and the agreement of their β-diversity with plant β-diversity. However, processes underlying the synchrony of the aboveground-belowground biodiversity is still unclear. By using partitioning methods for plant β-diversity, this study explored the process driving synchrony in tundra ecosystems, in which drastic vegetation shifts are observed with climate warming. Our methods based on Baselga's partitioning enabled the division of plant β-diversity into two phenomena and three functional components. Correlation of fungal β-diversity with the components of plant β-diversity showed that the spatial replacement of fungi was promoted by plant species turnover, in particular, plant species turnover with functional exchange. In addition, spatial variety of graminoid or forbs species, rather than shrubs, enhanced fungal β-diversity. These results suggest the importance of small-scale factors such as plant-fungal interactions or local environments modified by plants for the fungal community assemblage. The process-based understanding of community dynamics of plants and fungi allows us to predict the ongoing shrub encroachment in the Arctic region, which could weaken the aboveground-belowground synchrony.
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Affiliation(s)
- Shota Masumoto
- Graduate School of Environment and Information Sciences, Yokohama National University, Kanagawa 240-8501, Japan
| | - Ryo Kitagawa
- Kansai Research Center, Forestry and Forest Products Research Institute, Kyoto 612-0855, Japan
| | - Keita Nishizawa
- Graduate School of Environment and Information Sciences, Yokohama National University, Kanagawa 240-8501, Japan
| | - Ryo Kaneko
- National Institute of Polar Research, Tokyo 190-8518, Japan
| | - Takashi Osono
- Faculty of Science and Engineering, Doshisha University, Kyoto 610-0394, Japan
| | - Motohiro Hasegawa
- Faculty of Science and Engineering, Doshisha University, Kyoto 610-0394, Japan
| | - Shunsuke Matsuoka
- Graduate School of Simulation Studies, University of Hyogo, Hyogo, 650-0047, Japan
| | - Masaki Uchida
- National Institute of Polar Research, Tokyo 190-8518, Japan.,School of Multidisciplinary Sciences, The Graduate University for Advanced Studies, Tokyo 190-8518, Japan
| | - Akira S Mori
- Graduate School of Environment and Information Sciences, Yokohama National University, Kanagawa 240-8501, Japan
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10
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Matsuoka S, Sugiyama Y, Shimono Y, Ushio M, Doi H. Evaluation of seasonal dynamics of fungal DNA assemblages in a flow-regulated stream in a restored forest using eDNA metabarcoding. Environ Microbiol 2021; 23:4797-4806. [PMID: 34258854 DOI: 10.1111/1462-2920.15669] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 11/27/2022]
Abstract
Investigation of seasonal variation in fungal communities is essential for understanding biodiversity and ecosystem functions. However, the conventional sampling method, with substrate removal and high spatial heterogeneity of community composition, makes surveying the seasonality of fungal communities challenging. Recently, water environmental DNA (eDNA) analysis has been explored for its utility in biodiversity surveys. In this study, we assessed whether the seasonality of fungal communities can be detected by monitoring eDNA in a forest stream. We conducted monthly water sampling in a forest stream over 2 years and used DNA metabarcoding to identify fungal eDNA. The stream water contained DNA from functionally diverse aquatic and terrestrial fungi, such as plant decomposers, parasites and mutualists. The variation in the fungal assemblage showed a regular annual periodicity, meaning that the assemblages in a given season were similar, irrespective of the year or sampling. Furthermore, the strength of the annual periodicity varied among functional groups. Our results suggest that forest streams may act as a 'trap' for terrestrial fungal DNA derived from different habitats, allowing the analysis of fungal DNA in stream water to provide information about the temporal variation in fungal communities in both the aquatic and the surrounding terrestrial ecosystems.
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Affiliation(s)
- Shunsuke Matsuoka
- Graduate School of Information Science, University of Hyogo, Kobe, Japan
| | - Yoriko Sugiyama
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Yoshito Shimono
- Graduate School of Bioresources, Mie University, Tsu, Japan.,Osaka Museum of Nature History, Osaka, Japan
| | - Masayuki Ushio
- Hakubi Center, Kyoto University, Kyoto, Japan.,Center for Ecological Research, Kyoto University, Kyoto, Japan
| | - Hideyuki Doi
- Graduate School of Information Science, University of Hyogo, Kobe, Japan
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11
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Uchida N, Kubota K, Aita S, Kazama S. Aquatic insect community structure revealed by eDNA metabarcoding derives indices for environmental assessment. PeerJ 2020; 8:e9176. [PMID: 32566391 PMCID: PMC7293852 DOI: 10.7717/peerj.9176] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 04/21/2020] [Indexed: 12/25/2022] Open
Abstract
Environmental DNA (eDNA) analysis provides an efficient and objective approach for monitoring and assessing ecological status; however, studies on the eDNA of aquatic insects, such as Ephemeroptera, Plecoptera, and Trichoptera (EPT), are limited despite its potential as a useful indicator of river health. Here, we investigated the community structures of aquatic insects using eDNA and evaluated the applicability of eDNA data for calculating assessment indices. Field surveys were conducted to sample river water for eDNA at six locations from upstream to downstream of two rivers in Japan in July and November 2016. Simultaneously, aquatic insects were collected using the traditional Surber net survey method. The communities of aquatic insects were revealed using eDNA by targeting the cytochrome oxidase subunit I gene in mitochondrial DNA via metabarcoding analyses. As a result, the eDNA revealed 63 families and 75 genera of aquatic insects, which was double than that detected by the Surber net survey (especially for families in Diptera and Hemiptera). The seasonal differences of communities were distinguished by both the eDNA and Surber net survey data. Furthermore, the total nitrogen concentration, a surrogate of organic pollution, showed positive correlations with biotic environmental assessment indices (i.e., EPT index and Chironomidae index) calculated using eDNA at the genus-level resolution but the indices calculated using the Surber net survey data. Our results demonstrated that eDNA analysis with higher taxonomic resolution can provide as a more sensitive environmental assessment index than the traditional method that requires biotic samples.
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Affiliation(s)
- Noriko Uchida
- International Research Institute of Disaster Science, Tohoku University, Sendai, Miyagi, Japan.,Department of Civil and Environmental Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Kengo Kubota
- Department of Civil and Environmental Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Shunsuke Aita
- School of Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - So Kazama
- Department of Civil and Environmental Engineering, Tohoku University, Sendai, Miyagi, Japan
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12
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Shirouzu T, Matsuoka S, Doi H, Nagata N, Ushio M, Hosaka K. Complementary molecular methods reveal comprehensive phylogenetic diversity integrating inconspicuous lineages of early-diverged wood-decaying mushrooms. Sci Rep 2020; 10:3057. [PMID: 32080243 PMCID: PMC7033186 DOI: 10.1038/s41598-020-59620-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/03/2020] [Indexed: 11/28/2022] Open
Abstract
Among terrestrial microorganisms, mushroom-forming fungi have been relatively well investigated, however the inconspicuous strains may be overlooked by conventional visual investigations causing underestimation of their phylogenetic diversity. Herein, we sought to obtain a comprehensive phylogenetic diversity profile for the early-diverging wood-decaying mushrooms Dacrymycetes, using an approach that combines fruiting-body collection, culture isolation, and environmental DNA (eDNA) metabarcoding of decaying branches. Among the 28 operational taxonomic units (OTUs) detected during a three-year investigation, 10 each were from fruiting bodies and cultured mycelia and 27 were detected as eDNA sequences. eDNA metabarcoding revealed various lineages across the Dacrymycetes phylogeny. Alternatively, fruiting-body and culture surveys uncovered only ~50% of the OTUs detected through eDNA metabarcoding, suggesting that several inconspicuous or difficult-to-isolate strains are latent in the environment. Further, eDNA and culture surveys revealed early-diverging clades that were not identified in the fruiting-body survey. Thus, eDNA and culture-based techniques can uncover inconspicuous yet phylogenetically important mushroom lineages that may otherwise be overlooked via typical visual investigations.
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Affiliation(s)
- Takashi Shirouzu
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie, 514-8507, Japan.
| | - Shunsuke Matsuoka
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Hideyuki Doi
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Nobuaki Nagata
- Collection Center, National Museum of Nature and Science, 4-1-1 Amakubo, Ibaraki, 305-0005, Japan
| | - Masayuki Ushio
- Hakubi Center, Kyoto University, Kyoto, 606-8501, Japan
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga, 520-2113, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, 332-0012, Japan
| | - Kentaro Hosaka
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, 305-0005, Japan
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