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Liu YJ, Gong S, Wang YB, Yang ZL, Hu WH, Feng B. Biogeography and community assembly of soil fungi from alpine meadows in southwestern China show the importance of climatic selection. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174477. [PMID: 38964412 DOI: 10.1016/j.scitotenv.2024.174477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 07/01/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Soil fungi are pivotal in alpine and arctic ecosystems that are vulnerable to climate changes. Previous studies have shown broad connections between soil fungi in the arctic and alpine regions, but most of these studies are mainly from Europe and North America, with more sporadic studies from East Asia. Currently, little is known about the biogeographic relationships between soil fungi in alpine meadows of southwestern China (AMSC) and other regions of the world. In addition, the regional-scale spatial patterns of fungal communities in the AMSC, as well as their driving factors and ecological processes, are also poorly understood. In this study, we collected roots and surrounding soils of two dominant ectomycorrhizal plants, Bistorta vivipara and B. macrophylla from the AMSC, and performed bioinformatic and statistical analyses based on high-throughput sequencing of ITS2 amplicons. We found that: (1) fungi from the AMSC were closely related with those from boreal forests and tundra, and saprotrophic fungi had higher dispersal potential than ectomycorrhizal fungi; (2) community compositions exhibited clear divergences among geographic regions and between root and soil samples; (3) climate was the predominant factor driving regional-scale spatial patterns but had less explanatory power for saprotrophic and total fungi from roots than those from soils; (4) homogeneous selection and drift were the key ecological processes governing community assembly, but in communities of saprotrophic and total fungi from soil samples, drift contributed less and its role was partially replaced by dispersal limitation. This study highlights the importance of climatic selection and stochastic processes on fungal community assembly in alpine regions, and emphasizes the significance of simultaneously investigating fungi with different trophic modes and from both roots and soils.
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Affiliation(s)
- Yong Jie Liu
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, China; School of Life Sciences, Yunnan University, China
| | - Sai Gong
- School of Horticulture, Anhui Agricultural University, China
| | - Yuan Bing Wang
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, China
| | - Zhu L Yang
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, China
| | - Wei Hong Hu
- School of Life Sciences, Yunnan University, China.
| | - Bang Feng
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, China.
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Romero F, Labouyrie M, Orgiazzi A, Ballabio C, Panagos P, Jones A, Tedersoo L, Bahram M, Guerra CA, Eisenhauer N, Tao D, Delgado-Baquerizo M, García-Palacios P, van der Heijden MGA. Soil health is associated with higher primary productivity across Europe. Nat Ecol Evol 2024; 8:1847-1855. [PMID: 39192006 DOI: 10.1038/s41559-024-02511-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 07/19/2024] [Indexed: 08/29/2024]
Abstract
Soil health is expected to be of key importance for plant growth and ecosystem functioning. However, whether soil health is linked to primary productivity across environmental gradients and land-use types remains poorly understood. To address this gap, we conducted a pan-European field study including 588 sites from 27 countries to investigate the link between soil health and primary productivity across three major land-use types: woodlands, grasslands and croplands. We found that mean soil health (a composite index based on soil properties, biodiversity and plant disease control) in woodlands was 31.4% higher than in grasslands and 76.1% higher than in croplands. Soil health was positively linked to cropland and grassland productivity at the continental scale, whereas climate best explained woodland productivity. Among microbial diversity indicators, we observed a positive association between the richness of Acidobacteria, Firmicutes and Proteobacteria and primary productivity. Among microbial functional groups, we found that primary productivity in croplands and grasslands was positively related to nitrogen-fixing bacteria and mycorrhizal fungi and negatively related to plant pathogens. Together, our results point to the importance of soil biodiversity and soil health for maintaining primary productivity across contrasting land-use types.
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Affiliation(s)
- Ferran Romero
- Plant-Soil Interactions group, Agroscope, Zurich, Switzerland.
| | - Maëva Labouyrie
- Plant-Soil Interactions group, Agroscope, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- European Commission, Joint Research Centre, Ispra, Italy
| | - Alberto Orgiazzi
- European Commission, Joint Research Centre, Ispra, Italy
- European Dynamics, Brussels, Belgium
| | | | - Panos Panagos
- European Commission, Joint Research Centre, Ispra, Italy
| | - Arwyn Jones
- European Commission, Joint Research Centre, Ispra, Italy
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Mohammad Bahram
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | - Carlos A Guerra
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
- Departamento de Geografía, Universidade de Coimbra, Coimbra, Portugal
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Dongxue Tao
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Seville, Spain
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Northeast Normal University, Changchun, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Seville, Spain
| | - Pablo García-Palacios
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Marcel G A van der Heijden
- Plant-Soil Interactions group, Agroscope, Zurich, Switzerland.
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.
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3
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Rao G, Song WL, Yan SZ, Chen SL. Unraveling the distribution pattern and driving forces of soil microorganisms under geographic barriers. Appl Environ Microbiol 2024; 90:e0135924. [PMID: 39171904 PMCID: PMC11409670 DOI: 10.1128/aem.01359-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 07/31/2024] [Indexed: 08/23/2024] Open
Abstract
The Altai Mountains (ALE) and the Greater Khingan Mountains (GKM) in northern China are forest regions dominated by coniferous trees. These geographically isolated regions provide an ideal setting for studying microbial biogeographic patterns. In this study, we employed high-throughput techniques to obtain DNA sequences of soil myxomycetes, bacteria, and fungi and explored the mechanisms underlying the assembly of both local and cross-regional microbial communities in relation to environmental factors. Our investigation revealed that the environmental heterogeneity in ALE and GKM significantly affected the succession and assembly of soil bacterial communities at cross-regional scales. Specifically, the optimal environmental factors affecting bacterial Bray-Curtis similarity were elevation and temperature seasonality. The spatial factors and climate change impact on bacterial communities under the geographical barriers surpassed that of local soil microenvironments. The assembly pattern of bacterial communities transitions from local drift to cross-regional heterogeneous selection. Environmental factors had a relatively weak influence on myxomycetes and fungi. Both soil myxomycetes and fungi faced considerable dispersal limitation at local and cross-regional scales, ultimately leading to weak geographical distribution patterns.IMPORTANCEThe impact of environmental selection and dispersal on the soil microbial spatial distribution is a key concern in microbial biogeography, particularly in large-scale geographical patterns. However, our current understanding remains limited. Our study found that soil bacteria displayed a distinct cross-regional geographical distribution pattern, primarily influenced by environmental selection. Conversely, the cross-regional geographical distribution patterns of soil myxomycetes and fungi were relatively weak. Their composition exhibited a weak association with the environment at local and cross-regional scales, with assembly primarily driven by dispersal limitation.
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Affiliation(s)
- Gu Rao
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wen-Long Song
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shu-Zhen Yan
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shuang-Lin Chen
- School of Life Sciences, Nanjing Normal University, Nanjing, China
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Quintero-Corrales CA, Vega M, Ramírez-Terrazo A, Águila B, Garibay-Orijel R. Downfall of an empire: Unmasking the hidden diversity and distribution of the Amanita rubescens species complex. Mycologia 2024; 116:642-649. [PMID: 38913569 DOI: 10.1080/00275514.2024.2355276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 05/10/2024] [Indexed: 06/26/2024]
Abstract
Amanita is one of the most salient mushroom genera due to its cultural, economic, and medical importance. Recently, many new Amanita species have been described worldwide, increasing the genus richness. However, several clades have cryptic diversity, and many species complexes have not yet been resolved. This is the case of the rubescent species in the Validae section, which have been widely cited under the name Amanita rubescens s.l. We used a four-locus matrix (nuc rDNA internal transcribed spacer [ITS] and 28S regions and genes for RNA polymerase II subunit 2 [rpb2], translation elongation factor 1-α [tef1-α], and β-tubulin [tub2]) to solve the phylogenetic relationships within the Amanita section Validae. To analyze the diversity and distribution patterns of species, we used an extensive ITS sequence sampling including environmental DNA databases. The phylogenetic analyses demonstrated that the Validae section is divided into three monophyletic and highly supported major clades: Mappae, Validae, and Rubescentes. At least 11 species-level clades within the Rubescentes clade were highly supported: A. cruentilemurum nom. prov. A. brunneolocularis, A. rubescens s.s. (European clade), A. rubescens s.s. (Asiatic clade), A. orsonii s.s. A. 'orsonii,' A. aureosubucula nom. prov., A. novinupta, A. flavorubens, and two undescribed North American species. We proved that A. rubescens s.s. has two segregated populations (European and Asiatic) and it is not naturally distributed in America. Furthermore, we found that America has more cryptic species within the Rubescentes clade than Eurasia.
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Affiliation(s)
- Christian A Quintero-Corrales
- Instituto de Biología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, 04510 México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, 04510 México
| | - Melania Vega
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, 04510 México
- Genética de la Conservación, Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México 04510 México
| | - Amaranta Ramírez-Terrazo
- Instituto de Biología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, 04510 México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, 04510 México
| | - Bernardo Águila
- Instituto de Biología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, 04510 México
| | - Roberto Garibay-Orijel
- Instituto de Biología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, 04510 México
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5
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Rao G, Song WL, Yan SZ, Chen SL. Community structure and assembly of myxomycetes in northern Chinese forests under geographic barriers. Mycologia 2024:1-12. [PMID: 39208238 DOI: 10.1080/00275514.2024.2386231] [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: 06/25/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024]
Abstract
The study of myxomycete biogeography has a long-standing history and has consistently drawn scholarly interest. Nevertheless, studies focusing specifically on the spatial and temporal distribution patterns of myxomycete diversity are relatively limited, with even fewer investigating the mechanisms driving the generation and maintenance of myxomycete diversity. Therefore, this study selected two geographically distant sampling sites within northern Chinese forests to investigate myxomycete species composition, community structure, environmental drivers, and assembly patterns under geographic barriers. We established plots in the Altai Mountains (ALE) and the Greater Khingan Mountains (GKM), gathered bark and litter, and conducted 80-day moist chamber cultures of myxomycetes. Additionally, myxomycete specimens were collected in the field simultaneously to supplement the data set. This study collected 541 myxomycete specimens belonging to 73 species from 28 genera, spanning 12 families and eight orders. The ALE and the GKM had 20 identical species, accounting for 27% of the total species. Myxomycetes from both regions exhibited abundant occurrence 18 days after cultivation, with the quantity on bark substrates notably higher than on litter. Arcyria pomiformis and Comatricha elegans were the most common species in moist chamber cultures. Mantel test outcomes revealed that environmental factors had no significant impact on myxomycete community similarity between the two areas, aligning with findings from the neutral community model analysis, indicating a predominant influence of stochastic processes on myxomycete community structure in moist chamber cultures. This study represents the first application of a quantitative framework to analyze myxomycete community assembly cultivated in moist chambers.
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Affiliation(s)
- Gu Rao
- School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Wen-Long Song
- School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Shu-Zhen Yan
- School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Shuang-Lin Chen
- School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
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6
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Douch JK, Vaughan LJ, Cooper JA, Holmes GD, Robinson R, Stefani F, Idnurm A, May TW. Taxonomic revision of fleshy species of Hydnellum, Neosarcodon, and Sarcodon (Thelephorales) from Australasia. Mycologia 2024:1-28. [PMID: 39208239 DOI: 10.1080/00275514.2024.2363211] [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: 12/13/2023] [Accepted: 05/30/2024] [Indexed: 09/04/2024]
Abstract
Stipitate Thelephorales are basidiomycetous, mostly hydnoid, ectomycorrhizal fungi. Some species have declined considerably, and some are threat-listed as vulnerable or endangered. These ecological concerns require a well-resolved taxonomy to understand diversity in this group of fungi and facilitate conservation. However, phylogenetic studies have mostly neglected Southern Hemisphere representatives. This study examines the fleshy species of stipitate Thelephorales from native forests in Australia and New Zealand, using morphological analyses and phylogenetic analyses of nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode) and D1-D2 domains at the 5' end of nuc 28S rDNA (28S) sequences amplified from DNA isolated from fungarium collections and environmental DNA (eDNA) sequences from the Australian Microbiome initiative. Five new species, Sarcodon austrofibulatus, Hydnellum gatesiae, H. nothofagacearum, H. pseudoioeides, and H. variisporum, are described, Sarcodon carbonarius is transferred to Neosarcodon, and a key is provided for the six named species in the region. Boletopsis and Neosarcodon are reported from Australia for the first time based on detections from eDNA in soil samples taken from native forests. The Australasian species of Hydnellum occupy a highly derived position with the phylogeny of the genus, the members of which are otherwise all from the Northern Hemisphere, suggestive of a long-distance dispersal origin for the Australasian species.
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Affiliation(s)
- James K Douch
- School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, Victoria 3004, Australia
| | - Luke J Vaughan
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, Victoria 3004, Australia
| | - Jerry A Cooper
- Landcare Research-Manaaki Whenua, PO Box 69040, Lincoln 7640, New Zealand
| | - Gareth D Holmes
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, Victoria 3004, Australia
| | - Richard Robinson
- Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Western Australia 6983, Australia
| | - Franck Stefani
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A OC6, Canada
| | - Alexander Idnurm
- School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tom W May
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, Victoria 3004, Australia
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7
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Tedersoo L, Magurno F, Alkahtani S, Mikryukov V. Phylogenetic classification of arbuscular mycorrhizal fungi: new species and higher-ranking taxa in Glomeromycota and Mucoromycota (class Endogonomycetes). MycoKeys 2024; 107:273-325. [PMID: 39169987 PMCID: PMC11336396 DOI: 10.3897/mycokeys.107.125549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 07/20/2024] [Indexed: 08/23/2024] Open
Abstract
Arbuscular mycorrhizal (AM) fungi - Glomeromycota and Endogonomycetes - comprise multiple species and higher-level taxa that have remained undescribed. We propose a mixed morphology- and DNA-based classification framework to promote taxonomic communication and shed light into the phylogenetic structure of these ecologically essential fungi. Based on eDNA samples and long reads as type materials, we describe 15 new species and corresponding genera (Pseudoentrophosporakesseensis, Hoforsarebekkae, Kahvenarebeccae, Kelottijaerviashannonae, Kungsaengenashadiae, Langduoadianae, Lehetuaindrekii, Lokrumastenii, Moosteastephanieae, Nikkaluoktamahdiehiae, Parniguacraigii, Riederbergasylviae, Ruuacoralieae, Tammsaareavivikae and Unemaeeanathalieae), the genus Parvocarpum as well as 19 families (Pseudoentrophosporaceae, Hoforsaceae, Kahvenaceae, Kelottijaerviaceae, Kungsaengenaceae, Langduoaceae, Lehetuaceae, Lokrumaceae, Moosteaceae, Nikkaluoktaceae, Parniguaceae, Riederbergaceae, Ruuaceae, Tammsaareaceae, Unemaeeaceae, Bifigurataceae, Planticonsortiaceae, Jimgerdemanniaceae and Vinositunicaceae) and 17 orders (Hoforsales, Kahvenales, Kelottijaerviales, Kungsaengenales, Langduoales, Lehetuales, Lokrumales, Moosteales, Nikkaluoktales, Parniguales, Riederbergales, Ruuales, Tammsaareales, Unemaeeales, Bifiguratales and Densosporales), and propose six combinations (Diversisporabareae, Diversisporanevadensis, Fuscutatacerradensis, Fuscutatareticulata, Viscosporadeserticola and Parvocarpumbadium) based on phylogenetic evidence. We highlight further knowledge gaps in the phylogenetic structure of AM fungi and propose an alphanumeric coding system for preliminary communication and reference-based eDNA quality-filtering of the remaining undescribed genus- and family-level groups. Using AM fungi as examples, we hope to offer a sound, mixed framework for classification to boost research in the alpha taxonomy of fungi, especially the "dark matter fungi".
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, 2 Liivi, 50409 Tartu, Estonia
- Department of Zoology, College of Science, King Saud University, 12371 Riyadh, Saudi Arabia
| | - Franco Magurno
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland
| | - Saad Alkahtani
- Department of Zoology, College of Science, King Saud University, 12371 Riyadh, Saudi Arabia
| | - Vladimir Mikryukov
- Mycology and Microbiology Center, University of Tartu, 2 Liivi, 50409 Tartu, Estonia
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Quinteros-Urquieta C, Francois JP, Aguilar-Muñoz P, Orellana R, Villaseñor R, Moreira-Muñoz A, Molina V. Microbial Diversity of Soil in a Mediterranean Biodiversity Hotspot: Parque Nacional La Campana, Chile. Microorganisms 2024; 12:1569. [PMID: 39203411 PMCID: PMC11356564 DOI: 10.3390/microorganisms12081569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/22/2024] [Accepted: 07/25/2024] [Indexed: 09/03/2024] Open
Abstract
Parque Nacional La Campana (PNLC) is recognized worldwide for its flora and fauna, rather than for its microbial richness. Our goal was to characterize the structure and composition of microbial communities (bacteria, archaea and fungi) and their relationship with the plant communities typical of PNLC, such as sclerophyllous forest, xerophytic shrubland, hygrophilous forest and dry sclerophyllous forest, distributed along topoclimatic variables, namely, exposure, elevation and slope. The plant ecosystems, the physical and chemical properties of organic matter and the soil microbial composition were characterized by massive sequencing (iTag-16S rRNA, V4 and ITS1-5F) from the DNA extracted from the soil surface (5 cm, n = 16). A contribution of environmental variables, particularly related to each location, is observed. Proteobacteria (35.43%), Actinobacteria (32.86%), Acidobacteria (10.07%), Ascomycota (76.11%) and Basidiomycota (15.62%) were the dominant phyla. The beta diversity (~80% in its axes) indicates that bacteria and archaea are linked to their plant categories, where the xerophytic shrub stands out with the most particular microbial community. More specifically, Crenarchaeote, Humicola and Mortierella were dominant in the sclerophyllous forest; Chloroflexi, Cyanobacteria and Alternaria in the xerophytic shrubland; Solicoccozyma in the dry sclerophyllous forest; and Cladophialophora in the hygrophilous forest. In conclusion, the structure and composition of the microbial consortia is characteristic of PNLC's vegetation, related to its topoclimatic variables, which suggests a strong association within the soil microbiome.
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Affiliation(s)
- Carolina Quinteros-Urquieta
- Programa de Doctorado Interdisciplinario en Ciencias Ambientales, Universidad de Playa Ancha, Valparaíso 2340000, Chile;
| | - Jean-Pierre Francois
- Departamento de Ciencias y Geografía, Universidad de Playa Ancha, Valparaíso 2340000, Chile; (J.-P.F.); (P.A.-M.); (R.O.)
- HUB AMBIENTAL UPLA, Universidad de Playa Ancha, Valparaíso 2340000, Chile;
| | - Polette Aguilar-Muñoz
- Departamento de Ciencias y Geografía, Universidad de Playa Ancha, Valparaíso 2340000, Chile; (J.-P.F.); (P.A.-M.); (R.O.)
- HUB AMBIENTAL UPLA, Universidad de Playa Ancha, Valparaíso 2340000, Chile;
- Centro de Investigación Oceanográfica COPAS COASTAL, Universidad de Concepción, Concepción 4070386, Chile
| | - Roberto Orellana
- Departamento de Ciencias y Geografía, Universidad de Playa Ancha, Valparaíso 2340000, Chile; (J.-P.F.); (P.A.-M.); (R.O.)
- HUB AMBIENTAL UPLA, Universidad de Playa Ancha, Valparaíso 2340000, Chile;
| | - Rodrigo Villaseñor
- HUB AMBIENTAL UPLA, Universidad de Playa Ancha, Valparaíso 2340000, Chile;
| | - Andres Moreira-Muñoz
- Instituto de Geografía, Pontificia Universidad Católica de Valparaíso, Valparaíso 2362807, Chile;
| | - Verónica Molina
- Departamento de Ciencias y Geografía, Universidad de Playa Ancha, Valparaíso 2340000, Chile; (J.-P.F.); (P.A.-M.); (R.O.)
- HUB AMBIENTAL UPLA, Universidad de Playa Ancha, Valparaíso 2340000, Chile;
- Centro de Investigación Oceanográfica COPAS COASTAL, Universidad de Concepción, Concepción 4070386, Chile
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9
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Abrego N, Furneaux B, Hardwick B, Somervuo P, Palorinne I, Aguilar-Trigueros CA, Andrew NR, Babiy UV, Bao T, Bazzano G, Bondarchuk SN, Bonebrake TC, Brennan GL, Bret-Harte S, Bässler C, Cagnolo L, Cameron EK, Chapurlat E, Creer S, D'Acqui LP, de Vere N, Desprez-Loustau ML, Dongmo MAK, Jacobsen IBD, Fisher BL, Flores de Jesus M, Gilbert GS, Griffith GW, Gritsuk AA, Gross A, Grudd H, Halme P, Hanna R, Hansen J, Hansen LH, Hegbe ADMT, Hill S, Hogg ID, Hultman J, Hyde KD, Hynson NA, Ivanova N, Karisto P, Kerdraon D, Knorre A, Krisai-Greilhuber I, Kurhinen J, Kuzmina M, Lecomte N, Lecomte E, Loaiza V, Lundin E, Meire A, Mešić A, Miettinen O, Monkhouse N, Mortimer P, Müller J, Nilsson RH, Nonti PYC, Nordén J, Nordén B, Norros V, Paz C, Pellikka P, Pereira D, Petch G, Pitkänen JM, Popa F, Potter C, Purhonen J, Pätsi S, Rafiq A, Raharinjanahary D, Rakos N, Rathnayaka AR, Raundrup K, Rebriev YA, Rikkinen J, Rogers HMK, Rogovsky A, Rozhkov Y, Runnel K, Saarto A, Savchenko A, Schlegel M, Schmidt NM, Seibold S, Skjøth C, Stengel E, Sutyrina SV, Syvänperä I, Tedersoo L, Timm J, Tipton L, Toju H, Uscka-Perzanowska M, van der Bank M, van der Bank FH, Vandenbrink B, Ventura S, Vignisson SR, Wang X, Weisser WW, Wijesinghe SN, Wright SJ, Yang C, Yorou NS, Young A, Yu DW, Zakharov EV, Hebert PDN, Roslin T, Ovaskainen O. Airborne DNA reveals predictable spatial and seasonal dynamics of fungi. Nature 2024; 631:835-842. [PMID: 38987593 PMCID: PMC11269176 DOI: 10.1038/s41586-024-07658-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 06/04/2024] [Indexed: 07/12/2024]
Abstract
Fungi are among the most diverse and ecologically important kingdoms in life. However, the distributional ranges of fungi remain largely unknown as do the ecological mechanisms that shape their distributions1,2. To provide an integrated view of the spatial and seasonal dynamics of fungi, we implemented a globally distributed standardized aerial sampling of fungal spores3. The vast majority of operational taxonomic units were detected within only one climatic zone, and the spatiotemporal patterns of species richness and community composition were mostly explained by annual mean air temperature. Tropical regions hosted the highest fungal diversity except for lichenized, ericoid mycorrhizal and ectomycorrhizal fungi, which reached their peak diversity in temperate regions. The sensitivity in climatic responses was associated with phylogenetic relatedness, suggesting that large-scale distributions of some fungal groups are partially constrained by their ancestral niche. There was a strong phylogenetic signal in seasonal sensitivity, suggesting that some groups of fungi have retained their ancestral trait of sporulating for only a short period. Overall, our results show that the hyperdiverse kingdom of fungi follows globally highly predictable spatial and temporal dynamics, with seasonality in both species richness and community composition increasing with latitude. Our study reports patterns resembling those described for other major groups of organisms, thus making a major contribution to the long-standing debate on whether organisms with a microbial lifestyle follow the global biodiversity paradigms known for macroorganisms4,5.
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Affiliation(s)
- Nerea Abrego
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.
| | - Brendan Furneaux
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Bess Hardwick
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Panu Somervuo
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Isabella Palorinne
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | | | - Nigel R Andrew
- Natural History Museum, University of New England, Armidale, New South Wales, Australia
- Faculty of Science and Engineering, Southern Cross University, Northern Rivers, New South Wales, Australia
| | | | - Tan Bao
- Department of Biological Sciences, MacEwan University, Edmonton, Alberta, Canada
| | - Gisela Bazzano
- Centro de Zoología Aplicada, Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Svetlana N Bondarchuk
- Sikhote-Alin State Nature Biosphere Reserve named after K. G. Abramov, Terney, Russia
| | - Timothy C Bonebrake
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Georgina L Brennan
- Institute of Marine Sciences, Consejo Superior de Investigaciones Científicas (CSIC), Passeig Marítim de la Barceloneta, Barcelona, Spain
| | | | - Claus Bässler
- Department of Conservation Biology, Institute for Ecology, Evolution and Diversity, Faculty of Biological Sciences, Goethe-University Frankfurt, Frankfurt am Main, Germany
- Bavarian Forest National Park, Grafenau, Germany
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Luciano Cagnolo
- Instituto Multidisciplinario de Biología Vegetal, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Erin K Cameron
- Department of Environmental Science, Saint Mary's University, Halifax, Nova Scotia, Canada
| | - Elodie Chapurlat
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Simon Creer
- Molecular Ecology and Evolution at Bangor (MEEB), School of Biological Sciences, Bangor University, Bangor, Wales
| | - Luigi P D'Acqui
- Research Institute on Terrestrial Ecosystems - IRET, National Research Council - CNR and National Biodiversity Future Center, Palermo, Italy
| | - Natasha de Vere
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Michel A K Dongmo
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
- International Institute of Tropical Agriculture (IITA), Yaoundé, Cameroon
| | | | - Brian L Fisher
- Department of Entomology, California Academy of Sciences, San Francisco, CA, USA
- Madagascar Biodiversity Center, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo, Madagascar
| | | | - Gregory S Gilbert
- Department of Environmental Studies, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Gareth W Griffith
- Department of Life Sciences, Aberystwyth University, Aberystwyth, UK
| | - Anna A Gritsuk
- Sikhote-Alin State Nature Biosphere Reserve named after K. G. Abramov, Terney, Russia
| | - Andrin Gross
- Biodiversity and Conservation Biology Research Unit, SwissFungi Data Center, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Håkan Grudd
- Swedish Polar Research Secretariat, Abisko Scientific Research Station, Abisko, Sweden
| | - Panu Halme
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Rachid Hanna
- Center for Tropical Research, Congo Basin Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Jannik Hansen
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
| | | | - Apollon D M T Hegbe
- Research Unit in Tropical Mycology and Plant-Soil Fungi Interactions, Faculty of Agronomy, University of Parakou, Parakou, Republic of Benin
| | - Sarah Hill
- Natural History Museum, University of New England, Armidale, New South Wales, Australia
| | - Ian D Hogg
- Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, Nunavut, Canada
- Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, Ontario, Canada
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Jenni Hultman
- Department of Microbiology, University of Helsinki, Helsinki, Finland
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Kevin D Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand
| | - Nicole A Hynson
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Natalia Ivanova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- Nature Metrics North America Ltd., Guelph, Ontario, Canada
| | - Petteri Karisto
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Plant Health, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Deirdre Kerdraon
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Anastasia Knorre
- Science Department, National Park Krasnoyarsk Stolby, Krasnoyarsk, Russia
- Institute of Ecology and Geography, Siberian Federal University, Krasnoyarsk, Russia
| | | | - Juri Kurhinen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Masha Kuzmina
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Nicolas Lecomte
- Centre d'Études Nordiques and Canada Research Chair in Polar and Boreal Ecology, Department of Biology, Université de Moncton, Moncton, New Brunswick, Canada
| | - Erin Lecomte
- Centre d'Études Nordiques and Canada Research Chair in Polar and Boreal Ecology, Department of Biology, Université de Moncton, Moncton, New Brunswick, Canada
| | - Viviana Loaiza
- Department of Evolutionary Biology and Environmental Sciences, University of Zürich, Zurich, Switzerland
| | - Erik Lundin
- Swedish Polar Research Secretariat, Abisko Scientific Research Station, Abisko, Sweden
| | - Alexander Meire
- Swedish Polar Research Secretariat, Abisko Scientific Research Station, Abisko, Sweden
| | - Armin Mešić
- Laboratory for Biological Diversity, Rudjer Boskovic Institute, Zagreb, Croatia
| | - Otto Miettinen
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Norman Monkhouse
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Peter Mortimer
- Centre for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jörg Müller
- Bavarian Forest National Park, Grafenau, Germany
- Department of Conservation Biology and Forest Ecology, Julius Maximilians University Würzburg, Rauhenebrach, Germany
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Puani Yannick C Nonti
- Research Unit in Tropical Mycology and Plant-Soil Fungi Interactions, Faculty of Agronomy, University of Parakou, Parakou, Republic of Benin
| | - Jenni Nordén
- Norwegian Institute for Nature Research (NINA), Oslo, Norway
| | - Björn Nordén
- Norwegian Institute for Nature Research (NINA), Oslo, Norway
| | - Veera Norros
- Nature Solutions, Finnish Environment Institute (Syke), Helsinki, Finland
| | - Claudia Paz
- Department of Biodiversity, Institute of Biosciences, São Paulo State University, Rio Claro, Brazil
- Department of Entomology and Acarology, Laboratory of Pathology and Microbial Control, University of São Paulo, Piracicaba, Brazil
| | - Petri Pellikka
- Department of Geosciences and Geography, Faculty of Science, University of Helsinki, Helsinki, Finland
- State Key Laboratory for Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, Wuhan, China
- Wangari Maathai Institute for Environmental and Peace Studies, University of Nairobi, Kangemi, Kenya
| | - Danilo Pereira
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Laboratory of Biochemistry, Wageningen University, Wageningen, the Netherlands
| | - Geoff Petch
- School of Science and the Environment, University of Worcester, Worcester, UK
| | | | - Flavius Popa
- Department of Ecosystem Monitoring, Research & Conservation, Black Forest National Park, Bad Peterstal-Griesbach, Germany
| | - Caitlin Potter
- Department of Life Sciences, Aberystwyth University, Aberystwyth, UK
| | - Jenna Purhonen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- School of Resource Wisdom, University of Jyväskylä, Jyväskylä, Finland
| | - Sanna Pätsi
- Biodiversity Unit, University of Turku, Turku, Finland
| | - Abdullah Rafiq
- Molecular Ecology and Evolution at Bangor (MEEB), School of Biological Sciences, Bangor University, Bangor, Wales
| | - Dimby Raharinjanahary
- Madagascar Biodiversity Center, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo, Madagascar
| | - Niklas Rakos
- Swedish Polar Research Secretariat, Abisko Scientific Research Station, Abisko, Sweden
| | - Achala R Rathnayaka
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, Thailand
| | | | - Yury A Rebriev
- Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don, Russia
| | - Jouko Rikkinen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Hanna M K Rogers
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Andrey Rogovsky
- Science Department, National Park Krasnoyarsk Stolby, Krasnoyarsk, Russia
| | - Yuri Rozhkov
- State Nature Reserve Olekminsky, Olekminsk, Russia
| | - Kadri Runnel
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Annika Saarto
- Biodiversity Unit, University of Turku, Turku, Finland
| | - Anton Savchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Markus Schlegel
- Biodiversity and Conservation Biology Research Unit, SwissFungi Data Center, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Niels Martin Schmidt
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
- Arctic Research Center, Aarhus University, Roskilde, Denmark
| | - Sebastian Seibold
- Forest Zoology, TUD Dresden University of Technology, Berchtesgaden, Germany
- Terrestrial Ecology Research Group, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Carsten Skjøth
- School of Science and the Environment, University of Worcester, Worcester, UK
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Elisa Stengel
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology (Zoology III), Julius Maximilians University Würzburg, Rauhenebrach, Germany
| | - Svetlana V Sutyrina
- Sikhote-Alin State Nature Biosphere Reserve named after K. G. Abramov, Terney, Russia
| | - Ilkka Syvänperä
- Kevo Subarctic Research Institute, Biodiversity Unit, University of Turku, Utsjoki, Finland
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
- College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Jebidiah Timm
- Institute of Arctic Biology, University of Alaska, Fairbanks, AK, USA
| | - Laura Tipton
- School of Natural Science and Mathematics, Chaminade University of Honolulu, Honolulu, HI, USA
| | - Hirokazu Toju
- Laboratory of Ecosystems and Coevolution, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Center for Living Systems Information Science (CeLiSIS), Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | | | - Michelle van der Bank
- African Centre for DNA Barcoding (ACDB), University of Johannesburg, Auckland Park, South Africa
| | - F Herman van der Bank
- African Centre for DNA Barcoding (ACDB), University of Johannesburg, Auckland Park, South Africa
| | - Bryan Vandenbrink
- Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, Nunavut, Canada
| | - Stefano Ventura
- Research Institute on Terrestrial Ecosystems - IRET, National Research Council - CNR and National Biodiversity Future Center, Palermo, Italy
| | | | - Xiaoyang Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wolfgang W Weisser
- Terrestrial Ecology Research Group, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Subodini N Wijesinghe
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, Thailand
| | | | - Chunyan Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Nourou S Yorou
- Research Unit in Tropical Mycology and Plant-Soil Fungi Interactions, Faculty of Agronomy, University of Parakou, Parakou, Republic of Benin
| | - Amanda Young
- Institute of Arctic Biology, University of Alaska, Fairbanks, AK, USA
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- School of Biological Sciences, University of East Anglia, Norwich, UK
- Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Center of Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Evgeny V Zakharov
- Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, Ontario, Canada
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Paul D N Hebert
- Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, Ontario, Canada
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Tomas Roslin
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Otso Ovaskainen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
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10
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Ullah S, Huyop F, Wahab RA, Huda N, Oyewusi HA, Sujana IGA, Saloko S, Andriani AASPR, Mohamad MAN, Abdul Hamid AA, Mohd Nasir MH, Antara NS, Gunam IBW. The first ITS1 profiling of honey samples from the Southeast Asian region Lombok, Bali and Banggi Island. Sci Rep 2024; 14:14122. [PMID: 38898099 PMCID: PMC11187073 DOI: 10.1038/s41598-024-64838-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/13/2024] [Indexed: 06/21/2024] Open
Abstract
Southern Asian flowers offer honeybees a diversity of nectar. Based on its geographical origin, honey quality varies. Traditional methods are less authentic than DNA-based identification. The origin of honey is determined by pollen, polyphenolic, and macro-microorganisms. In this study, amplicon sequencing targets macro-microorganisms in eDNA using the ITS1 region to explore honey's geographical location and authentication. The variety of honey samples was investigated using ITS1 with Illumina sequencing. For all four honey samples, raw sequence reads showed 979,380 raw ITS1 amplicon reads and 375 ASVs up to the phylum level. The highest total number of 202 ASVs up to phylum level identified Bali honey with 211,189 reads, followed by Banggi honey with 309,207 a total number of 111 ASVs, and Lombok represents only 63 ASVs up to phylum level with several read 458,984. Based on Shannon and Chao1, honey samples from Bali (B2) and (B3) exhibited higher diversity than honey from Lombok (B1) and green honey from Sabah (B4), while the Simpson index showed that Banggi honey (B4) had higher diversity. Honey samples had significant variance in mycobiome taxonomic composition and abundance. Zygosaccharomyces and Aspergillus were the main genera found in Lombok honey, with percentages of 68.81% and 29.76% respectively. Bali honey samples (B2 and B3) were identified as having a significant amount of the genus Aureobasidium, accounting for 40.81% and 25% of the readings, respectively. The microbiome composition of Banggi honey (B4) showed a high presence of Zygosaccharomyces 45.17% and Aureobasidium 35.24%. The ITS1 analysis effectively distinguishes between honey samples of different origins and its potential as a discriminatory tool for honey origin and authentication purposes.
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Affiliation(s)
- Saeed Ullah
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Malaysia
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Malaysia.
- Bioindustry Laboratory, Department of Agro-Industrial Technology, Udayana University, Denpasar, Indonesia.
| | - Roswanira Ab Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Malaysia
| | - Nurul Huda
- Faculty of Sustainable Agriculture, Universiti Malaysia Sabah, 90509, Sandakan, Sabah, Malaysia
| | - Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Malaysia
- Biochemistry Unit, Department of Science Technology, The Federal Polytechnic, P. M. B 5351, Ado Ekiti, Ekiti State, Nigeria
| | - I Gede Arya Sujana
- Bioindustry Laboratory, Department of Agro-Industrial Technology, Udayana University, Denpasar, Indonesia
| | - Satrijo Saloko
- Faculty of Food Technology and Agro Industry, University of Mataram, Mataram, Nusa Tenggara Barat, 83126, Indonesia
| | | | - Mohd Azrul Naim Mohamad
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia
| | - Mohd Hamzah Mohd Nasir
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia
| | - Nyoman Semadi Antara
- Bioindustry Laboratory, Department of Agro-Industrial Technology, Udayana University, Denpasar, Indonesia
| | - Ida Bagus Wayan Gunam
- Bioindustry Laboratory, Department of Agro-Industrial Technology, Udayana University, Denpasar, Indonesia.
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11
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Tedersoo L, Hosseyni Moghaddam MS, Mikryukov V, Hakimzadeh A, Bahram M, Nilsson RH, Yatsiuk I, Geisen S, Schwelm A, Piwosz K, Prous M, Sildever S, Chmolowska D, Rueckert S, Skaloud P, Laas P, Tines M, Jung JH, Choi JH, Alkahtani S, Anslan S. EUKARYOME: the rRNA gene reference database for identification of all eukaryotes. Database (Oxford) 2024; 2024:baae043. [PMID: 38865431 PMCID: PMC11168333 DOI: 10.1093/database/baae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/14/2024] [Accepted: 05/23/2024] [Indexed: 06/14/2024]
Abstract
Molecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants. It is particularly useful for the identification of arbuscular mycorrhizal fungi as it bridges the four commonly used molecular markers-ITS1, ITS2, 18S V4-V5 and 28S D1-D2 subregions. The key benefits of this database over other annotated reference sequence databases are that it is not restricted to certain taxonomic groups and it includes all rRNA markers. EUKARYOME also offers a number of reference long-read sequences that are derived from (meta)genomic and (meta)barcoding-a unique feature that can be used for taxonomic identification and chimera control of third-generation, long-read, high-throughput sequencing data. Taxonomic assignments of rRNA genes in the database are verified based on phylogenetic approaches. The reference datasets are available in multiple formats from the project homepage, http://www.eukaryome.org.
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Liivi 2, Tartu 50400, Estonia
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, Tartu 50400, Estonia
- Department of Zoology, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | | | - Vladimir Mikryukov
- Mycology and Microbiology Center, University of Tartu, Liivi 2, Tartu 50400, Estonia
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, Tartu 50400, Estonia
| | - Ali Hakimzadeh
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, Tartu 50400, Estonia
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, Tartu 50400, Estonia
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, Uppsala 75651, Sweden
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 461, Göteborg 40530, Sweden
| | - Iryna Yatsiuk
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, Tartu 50400, Estonia
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Arne Schwelm
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
- Department of Environment, Soils and Land-Use, Teagasc, Oak Park House, Wexford R93 XE12, Ireland
| | - Kasia Piwosz
- National Marine Fisheries Research Institute, Kołłątaja 1, Gdynia 81332, Poland
| | - Marko Prous
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, Tartu 50400, Estonia
- Ecology and Genetics Research Unit, University of Oulu, Box 8000, Oulu 90014, Finland
| | - Sirje Sildever
- Department of Marine Systems, Tallinn University of Technology, Mäealuse 14a, Tallinn 12618, Estonia
| | - Dominika Chmolowska
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, Kraków 31016, Poland
| | - Sonja Rueckert
- Eukaryotic Microbiology, Faculty of Biology, University of Duisburg-Essen, Universitätsstraße 1, Essen, Nordrhein-Westfalen 45141, Germany
| | - Pavel Skaloud
- Department of Botany, Faculty of Science, Charles University, Benatska 2, Praha 12800, Czech Republic
| | - Peeter Laas
- Department of Marine Systems, Tallinn University of Technology, Mäealuse 14a, Tallinn 12618, Estonia
- Institute of Technology, University of Tartu, Nooruse 1, Tartu 50400, Estonia
| | - Marco Tines
- Department for Biological Sciences, Institute for Ecology, Evolution, and Diversity, Goethe University Frankfurt am Main, Max-von-Laue-Str. 13, Frankfurt am Main 60438, Germany
- Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Straße 14-16, Frankfurt am Main 60325, Germany
| | - Jae-Ho Jung
- Department of Biology, Gangneung-Wonju National University, Jukheon-gil 7, Gangneung 25457, South Korea
| | - Ji Hye Choi
- Department of Biology, Gangneung-Wonju National University, Jukheon-gil 7, Gangneung 25457, South Korea
| | - Saad Alkahtani
- Department of Zoology, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, Tartu 50400, Estonia
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12
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Ovaskainen O, Abrego N, Furneaux B, Hardwick B, Somervuo P, Palorinne I, Andrew NR, Babiy UV, Bao T, Bazzano G, Bondarchuk SN, Bonebrake TC, Brennan GL, Bret-Harte S, Bässler C, Cagnolo L, Cameron EK, Chapurlat E, Creer S, D'Acqui LP, de Vere N, Desprez-Loustau ML, Dongmo MAK, Dyrholm Jacobsen IB, Fisher BL, Flores de Jesus M, Gilbert GS, Griffith GW, Gritsuk AA, Gross A, Grudd H, Halme P, Hanna R, Hansen J, Hansen LH, Hegbe ADMT, Hill S, Hogg ID, Hultman J, Hyde KD, Hynson NA, Ivanova N, Karisto P, Kerdraon D, Knorre A, Krisai-Greilhuber I, Kurhinen J, Kuzmina M, Lecomte N, Lecomte E, Loaiza V, Lundin E, Meire A, Mešić A, Miettinen O, Monkhause N, Mortimer P, Müller J, Nilsson RH, Nonti PYC, Nordén J, Nordén B, Paz C, Pellikka P, Pereira D, Petch G, Pitkänen JM, Popa F, Potter C, Purhonen J, Pätsi S, Rafiq A, Raharinjanahary D, Rakos N, Rathnayaka AR, Raundrup K, Rebriev YA, Rikkinen J, Rogers HMK, Rogovsky A, Rozhkov Y, Runnel K, Saarto A, Savchenko A, Schlegel M, Schmidt NM, Seibold S, Skjøth C, Stengel E, Sutyrina SV, Syvänperä I, Tedersoo L, Timm J, Tipton L, Toju H, Uscka-Perzanowska M, van der Bank M, Herman van der Bank F, Vandenbrink B, Ventura S, Vignisson SR, Wang X, Weisser WW, Wijesinghe SN, Joseph Wright S, Yang C, Yorou NS, Young A, Yu DW, Zakharov EV, Hebert PDN, Roslin T. Global Spore Sampling Project: A global, standardized dataset of airborne fungal DNA. Sci Data 2024; 11:561. [PMID: 38816458 PMCID: PMC11139991 DOI: 10.1038/s41597-024-03410-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 05/21/2024] [Indexed: 06/01/2024] Open
Abstract
Novel methods for sampling and characterizing biodiversity hold great promise for re-evaluating patterns of life across the planet. The sampling of airborne spores with a cyclone sampler, and the sequencing of their DNA, have been suggested as an efficient and well-calibrated tool for surveying fungal diversity across various environments. Here we present data originating from the Global Spore Sampling Project, comprising 2,768 samples collected during two years at 47 outdoor locations across the world. Each sample represents fungal DNA extracted from 24 m3 of air. We applied a conservative bioinformatics pipeline that filtered out sequences that did not show strong evidence of representing a fungal species. The pipeline yielded 27,954 species-level operational taxonomic units (OTUs). Each OTU is accompanied by a probabilistic taxonomic classification, validated through comparison with expert evaluations. To examine the potential of the data for ecological analyses, we partitioned the variation in species distributions into spatial and seasonal components, showing a strong effect of the annual mean temperature on community composition.
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Affiliation(s)
- Otso Ovaskainen
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland.
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P. O. Box 65, 00014, Helsinki, Finland.
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, N-7491, Norway.
| | - Nerea Abrego
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland
- Department of Agricultural Sciences, University of Helsinki, P.O. Box 27, FI-00014, Helsinki, Finland
| | - Brendan Furneaux
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland
| | - Bess Hardwick
- Department of Agricultural Sciences, University of Helsinki, P.O. Box 27, FI-00014, Helsinki, Finland
| | - Panu Somervuo
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P. O. Box 65, 00014, Helsinki, Finland
| | - Isabella Palorinne
- Department of Agricultural Sciences, University of Helsinki, P.O. Box 27, FI-00014, Helsinki, Finland
| | - Nigel R Andrew
- Natural History Museum, Zoology, University of New England, Armidale, NSW, 2351, Australia
- Faculty of Science and Engineering, Southern Cross University, Northern Rivers, NSW, 2480, Australia
| | | | - Tan Bao
- Department of Biological Sciences, MacEwan University, 10, 700 - 104 Avenue, Edmonton, AB, T5J 2P2, Canada
| | - Gisela Bazzano
- Universidad Nacional de Còrdoba, Facultad de Ciencias Exactas Físicas y Naturales, Centro de Zoología Aplicada, Córdoba, Argentina
| | - Svetlana N Bondarchuk
- Sikhote-Alin State Nature Biosphere Reserve named after K. G. Abramov, 44 Partizanskaya Str., Terney, Primorsky krai, 692150, Russia
| | - Timothy C Bonebrake
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Georgina L Brennan
- CSIC, Institute of Marine Sciences, Passeig Marítim de la Barceloneta, 37-49ES08003, Barcelona, Spain
| | | | - Claus Bässler
- Goethe-University Frankfurt, Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Conservation Biology, D- 60438, Frankfurt am Main, Germany
- Bavarian Forest National Park, Freyunger Str. 2, D-94481, Grafenau, Germany
- Ecology of Fungi, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Universitätsstraße 30, 95440, Bayreuth, Germany
| | - Luciano Cagnolo
- Consejo de Investigaciones Científicas y Técnicas (CONICET), Instituto Multidisciplinario de Biología Vegetal, Córdoba, Argentina
| | - Erin K Cameron
- Department of Environmental Science, Saint Mary's University, 923 Robie St., Halifax, NS, B3H 3C3, Canada
| | - Elodie Chapurlat
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Simon Creer
- Molecular Ecology and Evolution at Bangor (MEEB), School of Environmental and Natural Sciences, Bangor University, Environment Centre Wales, Deiniol Road, Bangor, Gwynedd, Wales, LL57 2UW, UK
| | - Luigi P D'Acqui
- Research Institute on Terrestrial Ecosystems - IRET, National Research Council - CNR, Via Madonna del Piano n° 10, 50019, Sesto Fiorentino, Firenze, Italy
- National Biodiversity Future Center, Palermo, Italy
| | - Natasha de Vere
- Natural History Museum of Denmark, University of Copenhagen, Gothersgade 130, 1123, København K, Denmark
| | | | - Michel A K Dongmo
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
- International Institute of Tropical Agriculture (IITA), P.O. Box 2008 (Messa), Yaoundé, Cameroon
| | | | - Brian L Fisher
- Entomology, 55 Music Concourse Drive, California Academy of Sciences, San Francisco, CA, 94118, USA
- Madagascar Biodiversity Center, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo, 101, Madagascar
| | | | - Gregory S Gilbert
- Environmental Studies Department, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA, 95065, USA
| | - Gareth W Griffith
- Department of Life Sciences, Aberystwyth University, Aberystwyth, Ceredigion, WALES SY23 3DD, UK
| | - Anna A Gritsuk
- Sikhote-Alin State Nature Biosphere Reserve named after K. G. Abramov, 44 Partizanskaya Str., Terney, Primorsky krai, 692150, Russia
| | - Andrin Gross
- Research Unit Biodiversity and Conservation Biology, SwissFungi, Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Håkan Grudd
- Swedish Polar Research Secretariat, Abisko Scientific Research Station, Vetenskapens väg 38, SE-981 07, Abisko, Sweden
| | - Panu Halme
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland
| | - Rachid Hanna
- Center for Tropical Research, Congo Basin Institute, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA
| | - Jannik Hansen
- Department of Ecoscience, Aarhus University, Dk-4000, Roskilde, Denmark
| | - Lars Holst Hansen
- Department of Ecoscience, Aarhus University, Dk-4000, Roskilde, Denmark
| | - Apollon D M T Hegbe
- Research Unit in Tropical Mycology and Plant-Soil Fungi Interactions, Faculty of Agronomy, University of Parakou, BP 123, Parakou, Republic of Benin
| | - Sarah Hill
- Natural History Museum, Zoology, University of New England, Armidale, NSW, 2351, Australia
| | - Ian D Hogg
- Canadian High Arctic Research Station, Polar Knowledge Canada, PO Box 2150, 1 Uvajuq Road, Cambridge Bay, Nunavut, X0B 0C0, Canada
- Department of Integrative Biology, College of Biological Science, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
- School of Science, University of Waikato, Private Bag 3105, Hamilton, 3240, New Zealand
| | - Jenni Hultman
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014, Helsinki, Finland
- Natural Resources Institute Finland, Latokartanonkaari 9, 00790, Helsinki, Finland
| | - Kevin D Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Nicole A Hynson
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Natalia Ivanova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Nature Metrics North America Ltd., 590 Hanlon Creek Boulevard, Unit 11, Guelph, ON, N1C 0A1, Canada
| | - Petteri Karisto
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Plant Health, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Deirdre Kerdraon
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Anastasia Knorre
- Science Department, National Park Krasnoyarsk Stolby, 26a Kariernaya str., 660006, Krasnoyarsk, Russia
- Institute of Ecology and Geography, Siberian Federal University, 79 Svobodny pr., 660041, Krasnoyarsk, Russia
| | - Irmgard Krisai-Greilhuber
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Wien, Austria
| | - Juri Kurhinen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P. O. Box 65, 00014, Helsinki, Finland
| | - Masha Kuzmina
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Nicolas Lecomte
- Centre d'études nordiques and Canada Research Chair in Polar and Boreal Ecology, Department of Biology, Pavillon Rémi-Rossignol, 18, Antonine-Maillet, Université de Moncton, Moncton, NB, E1A 3E9, Canada
| | - Erin Lecomte
- Centre d'études nordiques and Canada Research Chair in Polar and Boreal Ecology, Department of Biology, Pavillon Rémi-Rossignol, 18, Antonine-Maillet, Université de Moncton, Moncton, NB, E1A 3E9, Canada
| | - Viviana Loaiza
- Department of Evolutionary Biology and Environmental Sciences, University of Zürich, Zürich, Switzerland
| | - Erik Lundin
- Swedish Polar Research Secretariat, Abisko Scientific Research Station, Vetenskapens väg 38, SE-981 07, Abisko, Sweden
| | - Alexander Meire
- Swedish Polar Research Secretariat, Abisko Scientific Research Station, Vetenskapens väg 38, SE-981 07, Abisko, Sweden
| | - Armin Mešić
- Laboratory for Biological Diversity, Rudjer Boskovic Institute, Bijenicka cesta 54, HR-10000, Zagreb, Croatia
| | - Otto Miettinen
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, 00014, Helsinki, Finland
| | - Norman Monkhause
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Peter Mortimer
- Centre for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jörg Müller
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology (Zoology III), Julius Maximilians University Würzburg, Rauhenebrach, Germany
- Bavarian Forest National Park, Grafenau, Germany
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 461, 405 30, Göteborg, Sweden
| | - Puani Yannick C Nonti
- Research Unit in Tropical Mycology and Plant-Soil Fungi Interactions, Faculty of Agronomy, University of Parakou, BP 123, Parakou, Republic of Benin
| | - Jenni Nordén
- Norwegian Institute for Nature Research (NINA), Sognsveien 68, N-0855, Oslo, Norway
| | - Björn Nordén
- Norwegian Institute for Nature Research (NINA), Sognsveien 68, N-0855, Oslo, Norway
| | - Claudia Paz
- Department of Biodiversity, Institute of Biosciences, São Paulo State University, Av 24A 1515, Rio Claro, SP, 13506-900, Brazil
- Department of Entomology and Acarology, Laboratory of Pathology and Microbial Control, University of São Paulo, CEP 13418-900, Piracicaba, SP, Brazil
| | - Petri Pellikka
- Department of Geosciences and Geography, Faculty of Science, University of Helsinki, P.O. Box 64, 00014, Helsinki, Finland
- State Key Laboratory for Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, Wuhan, 430079, China
- Wangari Maathai Institute for Environmental and Peace Studies, University of Nairobi, P.O. Box 29053, 00625, Kangemi, Kenya
| | - Danilo Pereira
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
| | - Geoff Petch
- School of Science and the Environment, University of Worcester, Henwick Grove, Worcester, WR2 6AJ, UK
| | - Juha-Matti Pitkänen
- Natural Resources Institute Finland, Latokartanonkaari 9, 00790, Helsinki, Finland
| | - Flavius Popa
- Department of Ecosystem Monitoring, Research & Conservation, Black Forest National Park, Kniebisstraße 67, 77740, Bad Peterstal-Griesbach, Germany
| | - Caitlin Potter
- Department of Life Sciences, Aberystwyth University, Aberystwyth, Ceredigion, WALES SY23 3DD, UK
| | - Jenna Purhonen
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland
- School of Resource Wisdom, University of Jyväskylä, P.O. Box 35, FIN-40014, Jyväskylä, Finland
| | - Sanna Pätsi
- The Biodiversity Unit of the University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Abdullah Rafiq
- Molecular Ecology and Evolution at Bangor (MEEB), School of Environmental and Natural Sciences, Bangor University, Environment Centre Wales, Deiniol Road, Bangor, Gwynedd, Wales, LL57 2UW, UK
| | - Dimby Raharinjanahary
- Madagascar Biodiversity Center, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo, 101, Madagascar
| | - Niklas Rakos
- Swedish Polar Research Secretariat, Abisko Scientific Research Station, Vetenskapens väg 38, SE-981 07, Abisko, Sweden
| | - Achala R Rathnayaka
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Katrine Raundrup
- Greenland Institute of Natural Resources, Kivioq 2, P.O. Box 570, 3900, Nuuk, Greenland
| | - Yury A Rebriev
- Southern Scientific Center of the Russian Academy of Sciences, 41 Chekhov ave., Rostov-on-Don, 344006, Russia
| | - Jouko Rikkinen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P. O. Box 65, 00014, Helsinki, Finland
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, 00014, Helsinki, Finland
| | - Hanna M K Rogers
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Andrey Rogovsky
- Science Department, National Park Krasnoyarsk Stolby, 26a Kariernaya str., 660006, Krasnoyarsk, Russia
| | - Yuri Rozhkov
- State Nature Reserve Olekminsky, Olekminsk, Russian Federation, Russia
| | - Kadri Runnel
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, 50409, Tartu, Estonia
| | - Annika Saarto
- The Biodiversity Unit of the University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Anton Savchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, 50409, Tartu, Estonia
| | - Markus Schlegel
- Research Unit Biodiversity and Conservation Biology, SwissFungi, Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Niels Martin Schmidt
- Department of Ecoscience, Aarhus University, Dk-4000, Roskilde, Denmark
- Arctic Research Center, Aarhus University, Dk-4000, Roskilde, Denmark
| | - Sebastian Seibold
- TUD Dresden University of Technology, Forest Zoology, Pienner Str. 7, 01737, Tharandt, Germany
- Technical University of Munich, Terrestrial Ecology Research Group, Department of Life Science Systems, School of Life Sciences, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany
| | - Carsten Skjøth
- School of Science and the Environment, University of Worcester, Henwick Grove, Worcester, WR2 6AJ, UK
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, DK-4000, Roskilde, Denmark
| | - Elisa Stengel
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology (Zoology III), Julius Maximilians University Würzburg, Rauhenebrach, Germany
| | - Svetlana V Sutyrina
- Sikhote-Alin State Nature Biosphere Reserve named after K. G. Abramov, 44 Partizanskaya Str., Terney, Primorsky krai, 692150, Russia
| | - Ilkka Syvänperä
- The Biodiversity Unit of the University of Turku, Kevontie 470, 99980, Utsjoki, Finland
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
- College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Jebidiah Timm
- Institute of Arctic Biology, University of Alaska, Fairbanks, AK, USA
| | - Laura Tipton
- School of Natural Science and Mathematics, Chaminade University of Honolulu, Honolulu, HI, USA
| | - Hirokazu Toju
- Laboratory of Ecosystems and Coevolution, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
- Center for Living Systems Information Science (CeLiSIS), Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | | | - Michelle van der Bank
- African Centre for DNA Barcoding (ACDB), University of Johannesburg, PO BOX 524, Auckland Park, 2006, South Africa
| | - F Herman van der Bank
- African Centre for DNA Barcoding (ACDB), University of Johannesburg, PO BOX 524, Auckland Park, 2006, South Africa
| | - Bryan Vandenbrink
- Canadian High Arctic Research Station, Polar Knowledge Canada, PO Box 2150, 1 Uvajuq Road, Cambridge Bay, Nunavut, X0B 0C0, Canada
| | - Stefano Ventura
- Research Institute on Terrestrial Ecosystems - IRET, National Research Council - CNR, Via Madonna del Piano n° 10, 50019, Sesto Fiorentino, Firenze, Italy
- National Biodiversity Future Center, Palermo, Italy
| | - Solvi R Vignisson
- Sudurnes Science and Learning Center, Garðvegi 1, 245, Sandgerði, Iceland
| | - Xiaoyang Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wolfgang W Weisser
- Technical University of Munich, Terrestrial Ecology Research Group, Department of Life Science Systems, School of Life Sciences, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany
| | - Subodini N Wijesinghe
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - S Joseph Wright
- Smithsonian Tropical Research Institute, Apartado, 0843-03092, Balboa, Panama
| | - Chunyan Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Nourou S Yorou
- Research Unit in Tropical Mycology and Plant-Soil Fungi Interactions, Faculty of Agronomy, University of Parakou, BP 123, Parakou, Republic of Benin
| | - Amanda Young
- Institute of Arctic Biology, University of Alaska, Fairbanks, AK, USA
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
- Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Evgeny V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Paul D N Hebert
- Canadian High Arctic Research Station, Polar Knowledge Canada, PO Box 2150, 1 Uvajuq Road, Cambridge Bay, Nunavut, X0B 0C0, Canada
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Tomas Roslin
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P. O. Box 65, 00014, Helsinki, Finland
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
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Tedersoo L, Drenkhan R, Abarenkov K, Anslan S, Bahram M, Bitenieks K, Buegger F, Gohar D, Hagh‐Doust N, Klavina D, Makovskis K, Zusevica A, Pritsch K, Padari A, Põlme S, Rahimlou S, Rungis D, Mikryukov V. The influence of tree genus, phylogeny, and richness on the specificity, rarity, and diversity of ectomycorrhizal fungi. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13253. [PMID: 38575147 PMCID: PMC10994715 DOI: 10.1111/1758-2229.13253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 03/13/2024] [Indexed: 04/06/2024]
Abstract
Partner specificity is a well-documented phenomenon in biotic interactions, yet the factors that determine specificity in plant-fungal associations remain largely unknown. By utilizing composite soil samples, we identified the predictors that drive partner specificity in both plants and fungi, with a particular focus on ectomycorrhizal associations. Fungal guilds exhibited significant differences in overall partner preference and avoidance, richness, and specificity to specific tree genera. The highest level of specificity was observed in root endophytic and ectomycorrhizal associations, while the lowest was found in arbuscular mycorrhizal associations. The majority of ectomycorrhizal fungal species showed a preference for one of their partner trees, primarily at the plant genus level. Specialist ectomycorrhizal fungi were dominant in belowground communities in terms of species richness and relative abundance. Moreover, all tree genera (and occasionally species) demonstrated a preference for certain fungal groups. Partner specificity was not related to the rarity of fungi or plants or environmental conditions, except for soil pH. Depending on the partner tree genus, specific fungi became more prevalent and relatively more abundant with increasing stand age, tree dominance, and soil pH conditions optimal for the partner tree genus. The richness of partner tree species and increased evenness of ectomycorrhizal fungi in multi-host communities enhanced the species richness of ectomycorrhizal fungi. However, it was primarily the partner-generalist fungi that contributed to the high diversity of ectomycorrhizal fungi in mixed forests.
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
- College of ScienceKing Saud UniversityRiyadhSaudi Arabia
| | - Rein Drenkhan
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | | | - Sten Anslan
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Mohammad Bahram
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - Kriss Bitenieks
- Latvian State Forest Research Institute ‘Silava’ (LSFRI Silava)SalaspilsLatvia
| | - Franz Buegger
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH), Research Unit Environmental SimulationNeuherbergGermany
| | - Daniyal Gohar
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Niloufar Hagh‐Doust
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Darta Klavina
- Latvian State Forest Research Institute ‘Silava’ (LSFRI Silava)SalaspilsLatvia
| | - Kristaps Makovskis
- Latvian State Forest Research Institute ‘Silava’ (LSFRI Silava)SalaspilsLatvia
| | - Austra Zusevica
- Latvian State Forest Research Institute ‘Silava’ (LSFRI Silava)SalaspilsLatvia
| | - Karin Pritsch
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH), Research Unit Environmental SimulationNeuherbergGermany
| | - Allar Padari
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | - Sergei Põlme
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
- Natural History MuseumUniversity of TartuTartuEstonia
| | - Saleh Rahimlou
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Dainis Rungis
- Latvian State Forest Research Institute ‘Silava’ (LSFRI Silava)SalaspilsLatvia
| | - Vladimir Mikryukov
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
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ullah S, Huda N, Wahab RA, Hamid AAA, Nasir MHM, Mohamad MAN, Ahmad HF, Oyewusi HA, Huyop F. Baseline amplicon sequencing data for the ITS2 region in the green honey of Banggi Island, Sabah. Data Brief 2024; 52:110044. [PMID: 38328502 PMCID: PMC10847015 DOI: 10.1016/j.dib.2024.110044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 02/09/2024] Open
Abstract
Green honey, was discovered on Banggi Island, Sabah, showing high in essential amino acids and chlorophyll derivatives. Despite its lucrative market potential owing to its distinctive color, uncertainties persist regarding its nature. This study leverages amplicon sequencing by targeting micro- and macro-organisms present in honey environmental DNA (eDNA) using Internal Transcribed Spacer 2 (ITS2) region, enabling the identification of floral and microorganism sources that represent the honey's composition. The investigation into green honey from Banggi Island concerns the prevalence of honey adulteration and authenticity for economic gain. Adulteration methods, such as the addition of sugar syrups, compromise honey purity. Using a sequencing approach would help in determining the geographic origin and verifying the authenticity of the honey. The study aims to identify plant species or microorganisms in honey's eDNA. To authenticate honey, we utilized ITS2 with Illumina sequencing, exploring the diversity of green honey samples. Raw sequence reads obtained for the green honey sample revealed 1,438,627 raw reads, with a GC average of 49.22 %. A total of 44 amplicon sequence variances (ASVs) were identified, including three genera: Zygosaccharomyces with two species, Fraxinus with three species, and the genus Ficaria with only one species. Their respective relative abundances were 98.55%, 0.94%, and 0.51%. Zygosaccharomyces rouxii and Zygosaccharomyces mellis were identified as the pre-dominant yeast species in honey, while the Fraxinus and Ficaria genus represent common plant species in Sabah, particularly in Banggi Island. The dominance of Zygosaccharomyces species aligns with their known prevalence in honey, affirming the reliability of our findings. The presence of Fraxinus and Ficaria in the honey sample correlates with its abundance in the local environment. This amplicon sequencing approach not only contributes to our understanding of green honey composition but also serves as a valuable resource for authenticating honey origin in Malaysia, particularly for green honey from Banggi Island, Sabah. Our study pioneers the application of ITS2 amplicon sequencing for green honey amplicon sequencing, providing valuable insights into its composition and origin. This methodology, with a focus on eDNA, contributes to the authentication and quality determination of honey in Malaysia, addressing the pressing concerns of adulteration and variability in production practices.
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Affiliation(s)
- Saeed ullah
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
| | - Nurul Huda
- Faculty of Sustainable Agriculture, Universiti Malaysia Sabah, 90509 Sandakan, Sabah, Malaysia
| | - Roswanira Ab. Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota, 25200 Kuantan, Pahang, Malaysia
| | - Mohd Hamzah Mohd Nasir
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota, 25200 Kuantan, Pahang, Malaysia
| | - Mohd Azrul Naim Mohamad
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota, 25200 Kuantan, Pahang, Malaysia
| | - Hajar Fauzan Ahmad
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al Sultan Abdullah, 26300 Gambang, Pahang, Malaysia
| | - Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
- Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, Ado Ekiti PMB 5351, Ekiti State, Nigeria
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
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Abarenkov K, Nilsson RH, Larsson KH, Taylor AS, May T, Frøslev TG, Pawlowska J, Lindahl B, Põldmaa K, Truong C, Vu D, Hosoya T, Niskanen T, Piirmann T, Ivanov F, Zirk A, Peterson M, Cheeke T, Ishigami Y, Jansson A, Jeppesen T, Kristiansson E, Mikryukov V, Miller J, Oono R, Ossandon F, Paupério J, Saar I, Schigel D, Suija A, Tedersoo L, Kõljalg U. The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered. Nucleic Acids Res 2024; 52:D791-D797. [PMID: 37953409 PMCID: PMC10767974 DOI: 10.1093/nar/gkad1039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/14/2023] Open
Abstract
UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region and offers nearly 10 million such sequences for reference. These are clustered into ∼2.4M species hypotheses (SHs), each assigned a unique digital object identifier (DOI) to promote unambiguous referencing across studies. UNITE users have contributed over 600 000 third-party sequence annotations, which are shared with a range of databases and other community resources. Recent improvements facilitate the detection of cross-kingdom biological associations and the integration of undescribed groups of organisms into everyday biological pursuits. Serving as a digital twin for eukaryotic biodiversity and communities worldwide, the latest release of UNITE offers improved avenues for biodiversity discovery, precise taxonomic communication and integration of biological knowledge across platforms.
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Affiliation(s)
- Kessy Abarenkov
- Natural History Museum, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 453, 405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 453, 405 30 Göteborg, Sweden
| | - Karl-Henrik Larsson
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 453, 405 30 Göteborg, Sweden
- Natural History Museum, University of Oslo, Box 1172 Blindern, 0318 Oslo, Norway
| | - Andy F S Taylor
- The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, UK
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen AB24 3UU, UK
| | - Tom W May
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, VIC 3004, Australia
| | - Tobias Guldberg Frøslev
- Global Biodiversity Information Facility (GBIF), Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Julia Pawlowska
- Institute of Evolutionary Biology, Faculty of Biology, University of Warsaw, ul. Zwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Björn Lindahl
- Swedish University of Agricultural Sciences, Department of Soil and Environment, Box 7014, SE-750 07 Uppsala, Sweden
| | - Kadri Põldmaa
- Natural History Museum, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Camille Truong
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, VIC 3004, Australia
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, The Netherlands
| | | | - Tuula Niskanen
- Botany Unit, Finnish Museum of Natural History, P.O.Box 7, 00014 University of Helsinki, Finland
| | - Timo Piirmann
- Natural History Museum, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Filipp Ivanov
- Natural History Museum, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Allan Zirk
- Natural History Museum, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Marko Peterson
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Tanya E Cheeke
- School of Biological Sciences, Washington State University, 2710 Crimson Way, Richland, WA 9935, USA
| | - Yui Ishigami
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Arnold Tobias Jansson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 453, 405 30 Göteborg, Sweden
| | - Thomas Stjernegaard Jeppesen
- Global Biodiversity Information Facility (GBIF), Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Vladimir Mikryukov
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Joseph T Miller
- Global Biodiversity Information Facility (GBIF), Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Ryoko Oono
- Department of Ecology, Evolution, and Marine Biology, University of California at Santa Barbara, USA
| | | | - Joana Paupério
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Irja Saar
- Natural History Museum, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Dmitry Schigel
- Global Biodiversity Information Facility (GBIF), Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Ave Suija
- Natural History Museum, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Urmas Kõljalg
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
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16
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Yurkov AP, Kryukov AA, Gorbunova AO, Kudriashova TR, Kovalchuk AI, Gorenkova AI, Bogdanova EM, Laktionov YV, Zhurbenko PM, Mikhaylova YV, Puzanskiy RK, Bagrova TN, Yakhin OI, Rodionov AV, Shishova MF. Diversity of Arbuscular Mycorrhizal Fungi in Distinct Ecosystems of the North Caucasus, a Temperate Biodiversity Hotspot. J Fungi (Basel) 2023; 10:11. [PMID: 38248921 PMCID: PMC10817546 DOI: 10.3390/jof10010011] [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: 11/13/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Abstract
BACKGROUND Investigations that are focused on arbuscular mycorrhizal fungus (AMF) biodiversity is still limited. The analysis of the AMF taxa in the North Caucasus, a temperate biodiversity hotspot, used to be limited to the genus level. This study aimed to define the AMF biodiversity at the species level in the North Caucasus biotopes. METHODS The molecular genetic identification of fungi was carried out with ITS1 and ITS2 regions as barcodes via sequencing using Illumina MiSeq, the analysis of phylogenetic trees for individual genera, and searches for operational taxonomic units (OTUs) with identification at the species level. Sequences from MaarjAM and NCBI GenBank were used as references. RESULTS We analyzed >10 million reads in soil samples for three biotopes to estimate fungal biodiversity. Briefly, 50 AMF species belonging to 20 genera were registered. The total number of the AM fungus OTUs for the "Subalpine Meadow" biotope was 171/131, that for "Forest" was 117/60, and that for "River Valley" was 296/221 based on ITS1/ITS2 data. The total number of the AM fungus species (except for virtual taxa) for the "Subalpine Meadow" biotope was 24/19, that for "Forest" was 22/13, and that for "River Valley" was 28/24 based on ITS1/ITS2 data. Greater AMF diversity, as well as number of OTUs and species, in comparison with that of forest biotopes, characterized valley biotopes (disturbed ecosystems; grasslands). The correlation coefficient between "Percentage of annual plants" and "Glomeromycota total reads" r = 0.76 and 0.81 for ITS1 and ITS2, respectively, and the correlation coefficient between "Percentage of annual plants" and "OTUs number (for total species)" was r = 0.67 and 0.77 for ITS1 and ITS2, respectively. CONCLUSION High AMF biodiversity for the river valley can be associated with a higher percentage of annual plants in these biotopes and the active development of restorative successional processes.
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Affiliation(s)
- Andrey P. Yurkov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
| | - Alexey A. Kryukov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
| | - Anastasiia O. Gorbunova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
| | - Tatyana R. Kudriashova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
- Graduate School of Biotechnology and Food Science, Peter the Great St. Petersburg Polytechnic University, 194064 St. Petersburg, Russia
| | - Anastasia I. Kovalchuk
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
- Graduate School of Biotechnology and Food Science, Peter the Great St. Petersburg Polytechnic University, 194064 St. Petersburg, Russia
| | - Anastasia I. Gorenkova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Ekaterina M. Bogdanova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Yuri V. Laktionov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
| | - Peter M. Zhurbenko
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197022 St. Petersburg, Russia; (P.M.Z.); (Y.V.M.); (A.V.R.)
| | - Yulia V. Mikhaylova
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197022 St. Petersburg, Russia; (P.M.Z.); (Y.V.M.); (A.V.R.)
| | - Roman K. Puzanskiy
- Laboratory of Analytical Phytochemistry, Komarov Botanical Institute of the Russian Academy of Sciences, 197022 St. Petersburg, Russia;
- Faculty of Ecology, Russian State Hydrometeorological University, 192007 St. Petersburg, Russia;
| | - Tatyana N. Bagrova
- Faculty of Ecology, Russian State Hydrometeorological University, 192007 St. Petersburg, Russia;
| | - Oleg I. Yakhin
- Institute of Biochemistry and Genetics, The Ufa Federal Research Center of the Russian Academy of Sciences, 450054 Ufa, Russia;
| | - Alexander V. Rodionov
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197022 St. Petersburg, Russia; (P.M.Z.); (Y.V.M.); (A.V.R.)
| | - Maria F. Shishova
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
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17
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Awad A, Pena R. An improved method for extraction of soil fungal mycelium. MethodsX 2023; 11:102477. [PMID: 38023315 PMCID: PMC10679939 DOI: 10.1016/j.mex.2023.102477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023] Open
Abstract
Fungal mycelium is a major component of the soil microbiome. The soil hyphosphere represents a complex and dynamic niche for specific microorganisms, where multitrophic interactions occur, affecting ecosystem processes. However, extracting fungal mycelium from the soil to enable its taxonomical, chemical, and structural characterisation is challenging in the absence of a fast, efficient, and low-cost procedure. In this study, an old method (Bingle and Paul 1985), based on successive soil wet filtrations and density gradient centrifugation, was improved and tested in three different soil types (silty clay, silty clay loam, and loamy sand). The improved method reduced the number of filtrations by about five times and the centrifugation time from 40 min to 1 min. It avoided using any chemical substance which may impair further chemical analyses or DNA isolation and amplification. The method efficiency was about 50 % in the clay and 23 % in the sandy soils. However, a pre-step consisting of removing the fine-root fragments and other debris under the stereomicroscope may increase the method efficiency to more than 65 %, independent of the soil type.•A simple, efficient, and low-cost method suitable for extracting soil mycelium from a large number of samples.•The protocol includes successive soil wet filtrations and sucrose gradient centrifugation.•The method efficiency increases if the fine-root fragments and other debris are previously removed from the soil.
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Větrovský T, Kolaříková Z, Lepinay C, Awokunle Hollá S, Davison J, Fleyberková A, Gromyko A, Jelínková B, Kolařík M, Krüger M, Lejsková R, Michalčíková L, Michalová T, Moora M, Moravcová A, Moulíková Š, Odriozola I, Öpik M, Pappová M, Piché-Choquette S, Skřivánek J, Vlk L, Zobel M, Baldrian P, Kohout P. GlobalAMFungi: a global database of arbuscular mycorrhizal fungal occurrences from high-throughput sequencing metabarcoding studies. THE NEW PHYTOLOGIST 2023; 240:2151-2163. [PMID: 37781910 DOI: 10.1111/nph.19283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 09/04/2023] [Indexed: 10/03/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi are crucial mutualistic symbionts of the majority of plant species, with essential roles in plant nutrient uptake and stress mitigation. The importance of AM fungi in ecosystems contrasts with our limited understanding of the patterns of AM fungal biogeography and the environmental factors that drive those patterns. This article presents a release of a newly developed global AM fungal dataset (GlobalAMFungi database, https://globalamfungi.com) that aims to reduce this knowledge gap. It contains almost 50 million observations of Glomeromycotinian AM fungal amplicon DNA sequences across almost 8500 samples with geographical locations and additional metadata obtained from 100 original studies. The GlobalAMFungi database is built on sequencing data originating from AM fungal taxon barcoding regions in: i) the small subunit rRNA (SSU) gene; ii) the internal transcribed spacer 2 (ITS2) region; and iii) the large subunit rRNA (LSU) gene. The GlobalAMFungi database is an open source and open access initiative that compiles the most comprehensive atlas of AM fungal distribution. It is designed as a permanent effort that will be continuously updated by its creators and through the collaboration of the scientific community. This study also documented applicability of the dataset to better understand ecology of AM fungal taxa.
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Affiliation(s)
- Tomáš Větrovský
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Zuzana Kolaříková
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czechia
| | - Clémentine Lepinay
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Sandra Awokunle Hollá
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St 2, 504 09, Tartu, Estonia
| | - Anna Fleyberková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Anastasiia Gromyko
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Barbora Jelínková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Miroslav Kolařík
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Manuela Krüger
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czechia
| | - Renata Lejsková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Lenka Michalčíková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Tereza Michalová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St 2, 504 09, Tartu, Estonia
| | - Andrea Moravcová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
- Faculty of Science, Charles University, Albertov 6, 128 43, Prague, Czechia
| | - Štěpánka Moulíková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Iñaki Odriozola
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St 2, 504 09, Tartu, Estonia
| | - Monika Pappová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Sarah Piché-Choquette
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Jakub Skřivánek
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
- Faculty of Science, Charles University, Albertov 6, 128 43, Prague, Czechia
| | - Lukáš Vlk
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St 2, 504 09, Tartu, Estonia
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Petr Kohout
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
- Faculty of Science, Charles University, Albertov 6, 128 43, Prague, Czechia
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19
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Mikryukov V, Dulya O, Zizka A, Bahram M, Hagh-Doust N, Anslan S, Prylutskyi O, Delgado-Baquerizo M, Maestre FT, Nilsson H, Pärn J, Öpik M, Moora M, Zobel M, Espenberg M, Mander Ü, Khalid AN, Corrales A, Agan A, Vasco-Palacios AM, Saitta A, Rinaldi A, Verbeken A, Sulistyo B, Tamgnoue B, Furneaux B, Duarte Ritter C, Nyamukondiwa C, Sharp C, Marín C, Gohar D, Klavina D, Sharmah D, Dai DQ, Nouhra E, Biersma EM, Rähn E, Cameron E, De Crop E, Otsing E, Davydov E, Albornoz F, Brearley F, Buegger F, Zahn G, Bonito G, Hiiesalu I, Barrio I, Heilmann-Clausen J, Ankuda J, Doležal J, Kupagme J, Maciá-Vicente J, Djeugap Fovo J, Geml J, Alatalo J, Alvarez-Manjarrez J, Põldmaa K, Runnel K, Adamson K, Bråthen KA, Pritsch K, Tchan Issifou K, Armolaitis K, Hyde K, Newsham KK, Panksep K, Lateef AA, Hansson L, Lamit L, Saba M, Tuomi M, Gryzenhout M, Bauters M, Piepenbring M, Wijayawardene NN, Yorou N, Kurina O, Mortimer P, Meidl P, Kohout P, Puusepp R, Drenkhan R, Garibay-Orijel R, Godoy R, Alkahtani S, Rahimlou S, Dudov S, Põlme S, Ghosh S, Mundra S, Ahmed T, Netherway T, Henkel T, Roslin T, Nteziryayo V, Fedosov V, Onipchenko V, Yasanthika WAE, Lim Y, Van Nuland M, Soudzilovskaia N, Antonelli A, Kõljalg U, Abarenkov K, Tedersoo L. Connecting the multiple dimensions of global soil fungal diversity. SCIENCE ADVANCES 2023; 9:eadj8016. [PMID: 38019923 PMCID: PMC10686567 DOI: 10.1126/sciadv.adj8016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023]
Abstract
How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different levels of taxonomic and phylogenetic diversity of fungi and their ecological groups. We show the impact of precipitation and temperature interactions on local fungal species richness (alpha diversity) across different climates. Our findings reveal how temperature drives fungal compositional turnover (beta diversity) and phylogenetic diversity, linking them with regional species richness (gamma diversity). We integrate fungi into the principles of global biodiversity distribution and present detailed maps for biodiversity conservation and modeling of global ecological processes.
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Affiliation(s)
- Vladimir Mikryukov
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
| | - Olesya Dulya
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
| | - Alexander Zizka
- Department of Biology, Philipps-University, Marburg 35032, Germany
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden
| | - Niloufar Hagh-Doust
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
| | - Oleh Prylutskyi
- Department of Mycology and Plant Resistance, School of Biology, V.N. Karazin Kharkiv National University, Kharkiv 61022, Ukraine
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistemico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), Consejo Superior de Investigaciones Científicas, Sevilla 41012, Spain
| | - Fernando T. Maestre
- Instituto Multidisciplinar para el Estudio del Medio ‘Ramón Margalef’ and Departamento de Ecología, Universidad de Alicante, Alicante 03690, Spain
| | - Henrik Nilsson
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg 40530, Sweden
| | - Jaan Pärn
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
| | - Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
| | - Mikk Espenberg
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
| | - Ülo Mander
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
| | | | - Adriana Corrales
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Universidad del Rosario, Bogotá 111221, Colombia
| | - Ahto Agan
- Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu 51006, Estonia
| | - Aída-M. Vasco-Palacios
- Grupo de BioMicro y Microbiología Ambiental, Escuela de Microbiologia, Universidad de Antioquia UdeA, Medellin 050010, Colombia
| | - Alessandro Saitta
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Palermo 90128, Italy
| | - Andrea Rinaldi
- Department of Biomedical Sciences, University of Cagliari, Cagliari 09124, Italy
| | | | - Bobby Sulistyo
- Department Biology, Ghent University, Ghent 9000, Belgium
| | - Boris Tamgnoue
- Department of Crop Science, University of Dschang, Dschang, Cameroon
| | - Brendan Furneaux
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
| | | | - Casper Nyamukondiwa
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye 10071, Botswana
| | - Cathy Sharp
- Natural History Museum of Zimbabwe, Bulawayo, Zimbabwe
| | - César Marín
- Centro de Investigación e Innovación para el Cambio Climático (CiiCC), Universidad SantoTomás, Valdivia, Chile
| | - Daniyal Gohar
- Center of Mycology and Microbiology, University of Tartu, Tartu 50409, Estonia
| | - Darta Klavina
- Latvian State Forest Research Institute Silava, Salaspils 2169, Latvia
| | - Dipon Sharmah
- Department of Botany, Jawaharlal Nehru Rajkeeya Mahavidyalaya, Pondicherry University, Port Blair 744101, India
| | - Dong-Qin Dai
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan 655011, China
| | - Eduardo Nouhra
- Instituto Multidisciplinario de Biología Vegetal (CONICET), Universidad Nacional de Córdoba, Cordoba 5000, Argentina
| | - Elisabeth Machteld Biersma
- Natural History Museum of Denmark, Copenhagen 1123, Denmark
- British Antarctic Survey, NERC, High Cross, Cambridge CB3 0ET, UK
| | - Elisabeth Rähn
- Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu 51006, Estonia
| | - Erin Cameron
- Department of Environmental Science, Saint Mary's University, Halifax B3H 3C3, Canada
| | - Eske De Crop
- Department Biology, Ghent University, Ghent 9000, Belgium
| | - Eveli Otsing
- Center of Mycology and Microbiology, University of Tartu, Tartu 50409, Estonia
| | | | - Felipe Albornoz
- Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Wembley 6014, Australia
| | - Francis Brearley
- Department of Natural Sciences, Manchester Metropolitan University, Manchester M1 5GD, UK
| | - Franz Buegger
- Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Geoffrey Zahn
- Biology Department, Utah Valley University, Orem, UT 84058, USA
| | - Gregory Bonito
- Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824-6254, USA
| | - Inga Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
| | - Isabel Barrio
- Faculty of Natural and Environmental Sciences, Agricultural University of Iceland, Reykjavík 112, Iceland
| | - Jacob Heilmann-Clausen
- Center for Macroecology, Evolution and Climate, University of Copenhagen, Copenhagen 1350, Denmark
| | - Jelena Ankuda
- Vokė branch, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry (LAMMC), Vilnius LT-02232, Lithuania
| | - Jiri Doležal
- Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice 37005, Czech Republic
| | - John Kupagme
- Center of Mycology and Microbiology, University of Tartu, Tartu 50409, Estonia
| | - Jose Maciá-Vicente
- Department of Environmental Sciences, Plant Ecology and Nature Conservation, Wageningen University and Research, Wageningen 6708, Netherlands
| | | | - József Geml
- ELKH-EKKE Lendület Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger 3300, Hungary
| | - Juha Alatalo
- Environmental Science Center, Qatar University, Doha, Qatar
| | | | - Kadri Põldmaa
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
- Natural History Museum, University of Tartu, Tartu 51003, Estonia
| | - Kadri Runnel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
| | - Kalev Adamson
- Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu 51006, Estonia
| | - Kari-Anne Bråthen
- Department of Arctic and Marine Biology, The Arctic University of Norway, Tromsø 9019, Norway
| | - Karin Pritsch
- Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Kassim Tchan Issifou
- Research Unit Tropical Mycology and Plants-Soil Fungi Interactions, University of Parakou, Parakou 00229, Benin
| | - Kęstutis Armolaitis
- Department of Silviculture and Ecology, Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry (LAMMC), Girionys 53101, Lithuania
| | - Kevin Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Kevin K. Newsham
- British Antarctic Survey, NERC, High Cross, Cambridge CB3 0ET, UK
| | - Kristel Panksep
- Chair of Hydrobiology and Fishery, Estonian University of Life Sciences, Tartu 51006, Estonia
| | - Adebola Azeez Lateef
- Department of Plant Biology, Faculty of Life Science, University of Ilorin, Ilorin 240102, Nigeria
- Department of Forest Sciences, University of Helsinki, Helsinki 00014, Finland
| | - Linda Hansson
- Gothenburg Centre for Sustainable Development, Gothenburg 41133, Sweden
| | - Louis Lamit
- Department of Biology, Syracuse University, Syracuse 13244, USA
| | - Malka Saba
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Maria Tuomi
- Department of Arctic and Marine Biology, The Arctic University of Norway, Tromsø 9019, Norway
| | - Marieka Gryzenhout
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Marijn Bauters
- Department of Environment, Faculty of Bioscience Engineering, Ghent University, Ghent 9000, Belgium
| | - Meike Piepenbring
- Mycology Working Group, Goethe University Frankfurt am Main, Frankfurt am Main 60438, Germany
| | - Nalin N. Wijayawardene
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, China
| | - Nourou Yorou
- Research Unit Tropical Mycology and Plants-Soil Fungi Interactions, University of Parakou, Parakou 00229, Benin
| | - Olavi Kurina
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu 51006, Estonia
| | - Peter Mortimer
- Center For Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Peter Meidl
- Freie Universität Berlin, Institut für Biologie, Berlin 14195, Germany
| | - Petr Kohout
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Rasmus Puusepp
- Center of Mycology and Microbiology, University of Tartu, Tartu 50409, Estonia
| | - Rein Drenkhan
- Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu 51006, Estonia
| | - Roberto Garibay-Orijel
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Roberto Godoy
- Instituto Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Saad Alkahtani
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Saleh Rahimlou
- Center of Mycology and Microbiology, University of Tartu, Tartu 50409, Estonia
| | - Sergey Dudov
- Department of Ecology and Plant Geography, Moscow Lomonosov State University, Moscow 119234, Russia
| | - Sergei Põlme
- Center of Mycology and Microbiology, University of Tartu, Tartu 50409, Estonia
- Natural History Museum, University of Tartu, Tartu 51003, Estonia
| | - Soumya Ghosh
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Sunil Mundra
- Department of Biology, College of Science, United Arab Emirates University (UAEU), Al Ain, UAE
| | - Talaat Ahmed
- Environmental Science Center, Qatar University, Doha, Qatar
| | - Tarquin Netherway
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden
| | - Terry Henkel
- Department of Biological Sciences, California State Polytechnic University, Arcata, CA 95521, USA
| | - Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden
| | - Vincent Nteziryayo
- Department of Food Science and Technology, University of Burundi, Bujumbura Burundi
| | - Vladimir Fedosov
- Department of Ecology and Plant Geography, Moscow Lomonosov State University, Moscow 119234, Russia
| | - Vladimir Onipchenko
- Department of Ecology and Plant Geography, Moscow Lomonosov State University, Moscow 119234, Russia
| | | | - Young Lim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, Korea
| | - Michael Van Nuland
- Society for the Protection of Underground Networks (SPUN), Dover, DE 19901, USA
| | | | | | - Urmas Kõljalg
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
- Natural History Museum, University of Tartu, Tartu 51003, Estonia
| | - Kessy Abarenkov
- Natural History Museum, University of Tartu, Tartu 51003, Estonia
| | - Leho Tedersoo
- Center of Mycology and Microbiology, University of Tartu, Tartu 50409, Estonia
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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20
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Li P, Tedersoo L, Crowther TW, Wang B, Shi Y, Kuang L, Li T, Wu M, Liu M, Luan L, Liu J, Li D, Li Y, Wang S, Saleem M, Dumbrell AJ, Li Z, Jiang J. Global diversity and biogeography of potential phytopathogenic fungi in a changing world. Nat Commun 2023; 14:6482. [PMID: 37838711 PMCID: PMC10576792 DOI: 10.1038/s41467-023-42142-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 10/02/2023] [Indexed: 10/16/2023] Open
Abstract
Phytopathogenic fungi threaten global food security but the ecological drivers of their global diversity and biogeography remain unknown. Here, we construct and analyse a global atlas of potential phytopathogenic fungi from 20,312 samples across all continents and major oceanic island regions, eleven land cover types, and twelve habitat types. We show a peak in the diversity of phytopathogenic fungi in mid-latitude regions, in contrast to the latitudinal diversity gradients observed in aboveground organisms. Our study identifies climate as an important driver of the global distribution of phytopathogenic fungi, and our models suggest that their diversity and invasion potential will increase globally by 2100. Importantly, phytopathogen diversity will increase largely in forest (37.27-79.12%) and cropland (34.93-82.51%) ecosystems, and this becomes more pronounced under fossil-fuelled industry dependent future scenarios. Thus, we recommend improved biomonitoring in forests and croplands, and optimised sustainable development approaches to reduce potential threats from phytopathogenic fungi.
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Affiliation(s)
- Pengfa Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, 210095, Nanjing, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Thomas W Crowther
- Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Baozhan Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, 210095, Nanjing, China.
| | - Yu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Lu Kuang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, 210095, Nanjing, China
| | - Ting Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, 210095, Nanjing, China
| | - Meng Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Ming Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Lu Luan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Jia Liu
- Soil and Fertilizer & Resources and Environment Institute, Jiangxi Academy of Agricultural Sciences, 330200, Nanchang, China
| | - Dongzhen Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, 100091, Beijing, China
| | - Yongxia Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, 100091, Beijing, China
| | - Songhan Wang
- College of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Muhammad Saleem
- Department of Biological Sciences, Alabama State University, Montgomery, AL, 36104, USA
| | - Alex J Dumbrell
- School of Life Sciences, University of Essex, Colchester, Essex, UK.
| | - Zhongpei Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, 210095, Nanjing, China.
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21
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Hiiesalu I, Schweichhart J, Angel R, Davison J, Doležal J, Kopecký M, Macek M, Řehakova K. Plant-symbiotic fungal diversity tracks variation in vegetation and the abiotic environment along an extended elevational gradient in the Himalayas. FEMS Microbiol Ecol 2023; 99:fiad092. [PMID: 37562924 DOI: 10.1093/femsec/fiad092] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/30/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023] Open
Abstract
Arbuscular mycorrhizal (AM) fungi can benefit plants under environmental stress, and influence plant adaptation to warmer climates. However, very little is known about the ecology of these fungi in alpine environments. We sampled plant roots along a large fraction (1941-6150 m asl (above sea level)) of the longest terrestrial elevational gradient on Earth and used DNA metabarcoding to identify AM fungi. We hypothesized that AM fungal alpha and beta diversity decreases with increasing elevation, and that different vegetation types comprise dissimilar communities, with cultured (putatively ruderal) taxa increasingly represented at high elevations. We found that the alpha diversity of AM fungal communities declined linearly with elevation, whereas within-site taxon turnover (beta diversity) was unimodally related to elevation. The composition of AM fungal communities differed between vegetation types and was influenced by elevation, mean annual temperature, and precipitation. In general, Glomeraceae taxa dominated at all elevations and vegetation types; however, higher elevations were associated with increased presence of Acaulosporaceae, Ambisporaceae, and Claroideoglomeraceae. Contrary to our expectation, the proportion of cultured AM fungal taxa in communities decreased with elevation. These results suggest that, in this system, climate-induced shifts in habitat conditions may facilitate more diverse AM fungal communities at higher elevations but could also favour ruderal taxa.
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Affiliation(s)
- Inga Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50 409 Tartu, Estonia
| | - Johannes Schweichhart
- Biology Centre of the CAS, Institute of Soil Biology and Biochemistry, Na Sádkách 702/7 , 370 05 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic
| | - Roey Angel
- Biology Centre of the CAS, Institute of Soil Biology and Biochemistry, Na Sádkách 702/7 , 370 05 České Budějovice, Czech Republic
| | - John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50 409 Tartu, Estonia
| | - Jiři Doležal
- Institute of Botany of the CAS, Dukelská 135, 379 01 Třeboň, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic
| | - Martin Kopecký
- Institute of Botany of the CAS, Zámek 1, 252 43 Průhonice, Czech Republic
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 21, Praha 6, Czech Republic
| | - Martin Macek
- Institute of Botany of the CAS, Zámek 1, 252 43 Průhonice, Czech Republic
| | - Klára Řehakova
- Biology Centre of the CAS, Institute of Hydrobiology, Na Sádkách 702/7, 370 05 České Budějovice, Czech Republic
- Institute of Botany of the CAS, Dukelská 135, 379 01 Třeboň, Czech Republic
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22
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Labouyrie M, Ballabio C, Romero F, Panagos P, Jones A, Schmid MW, Mikryukov V, Dulya O, Tedersoo L, Bahram M, Lugato E, van der Heijden MGA, Orgiazzi A. Patterns in soil microbial diversity across Europe. Nat Commun 2023; 14:3311. [PMID: 37291086 PMCID: PMC10250377 DOI: 10.1038/s41467-023-37937-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 04/06/2023] [Indexed: 06/10/2023] Open
Abstract
Factors driving microbial community composition and diversity are well established but the relationship with microbial functioning is poorly understood, especially at large scales. We analysed microbial biodiversity metrics and distribution of potential functional groups along a gradient of increasing land-use perturbation, detecting over 79,000 bacterial and 25,000 fungal OTUs in 715 sites across 24 European countries. We found the lowest bacterial and fungal diversity in less-disturbed environments (woodlands) compared to grasslands and highly-disturbed environments (croplands). Highly-disturbed environments contain significantly more bacterial chemoheterotrophs, harbour a higher proportion of fungal plant pathogens and saprotrophs, and have less beneficial fungal plant symbionts compared to woodlands and extensively-managed grasslands. Spatial patterns of microbial communities and predicted functions are best explained when interactions among the major determinants (vegetation cover, climate, soil properties) are considered. We propose guidelines for environmental policy actions and argue that taxonomical and functional diversity should be considered simultaneously for monitoring purposes.
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Affiliation(s)
- Maëva Labouyrie
- Department of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy
- Plant-Soil-Interactions, Research Division Agroecology and Environment, Agroscope, Zürich, Switzerland
| | | | - Ferran Romero
- Plant-Soil-Interactions, Research Division Agroecology and Environment, Agroscope, Zürich, Switzerland
| | - Panos Panagos
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy
| | - Arwyn Jones
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy
| | | | - Vladimir Mikryukov
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Olesya Dulya
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Mohammad Bahram
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Emanuele Lugato
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy
| | - Marcel G A van der Heijden
- Department of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland.
- Plant-Soil-Interactions, Research Division Agroecology and Environment, Agroscope, Zürich, Switzerland.
| | - Alberto Orgiazzi
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy.
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23
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Wang B, McCormack ML, Ricciuto DM, Yang X, Iversen CM. Embracing fine-root system complexity in terrestrial ecosystem modeling. GLOBAL CHANGE BIOLOGY 2023; 29:2871-2885. [PMID: 36861355 DOI: 10.1111/gcb.16659] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/15/2023] [Indexed: 05/03/2023]
Abstract
Projecting the dynamics and functioning of the biosphere requires a holistic consideration of whole-ecosystem processes. However, biases toward leaf, canopy, and soil modeling since the 1970s have constantly left fine-root systems being rudimentarily treated. As accelerated empirical advances in the last two decades establish clearly functional differentiation conferred by the hierarchical structure of fine-root orders and associations with mycorrhizal fungi, a need emerges to embrace this complexity to bridge the data-model gap in still extremely uncertain models. Here, we propose a three-pool structure comprising transport and absorptive fine roots with mycorrhizal fungi (TAM) to model vertically resolved fine-root systems across organizational and spatial-temporal scales. Emerging from a conceptual shift away from arbitrary homogenization, TAM builds upon theoretical and empirical foundations as an effective and efficient approximation that balances realism and simplicity. A proof-of-concept demonstration of TAM in a big-leaf model both conservatively and radically shows robust impacts of differentiation within fine-root systems on simulating carbon cycling in temperate forests. Theoretical and quantitative support warrants exploiting its rich potentials across ecosystems and models to confront uncertainties and challenges for a predictive understanding of the biosphere. Echoing a broad trend of embracing ecological complexity in integrative ecosystem modeling, TAM may offer a consistent framework where modelers and empiricists can work together toward this grand goal.
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Affiliation(s)
- Bin Wang
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Daniel M Ricciuto
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Xiaojuan Yang
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Colleen M Iversen
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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24
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van Galen LG, Orlovich DA, Lord JM, Nilsen AR, Dutoit L, Larcombe MJ. Correlated evolution in an ectomycorrhizal host-symbiont system. THE NEW PHYTOLOGIST 2023; 238:1215-1229. [PMID: 36751898 DOI: 10.1111/nph.18802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Mechanisms of diversification in fungi are relatively poorly known. Many ectomycorrhizal symbionts show preference for particular host genera or families, so host-symbiont selection may be an important driver of fungal diversification in ectomycorrhizal systems. However, whether ectomycorrhizal hosts and symbionts show correlated evolutionary patterns remains untested, and it is unknown whether fungal specialisation also occurs in systems dominated by hosts from the same genus. We use metabarcoding of ectomycorrhizal fungi collected with hyphal ingrowth bags from Nothofagus forests across southern New Zealand to investigate host-symbiont specialisation and correlated evolution. We examine how ectomycorrhizal communities differ between host species and look for patterns of host-symbiont cophylogeny. We found substantial differences in ectomycorrhizal communities associated with different host taxa, particularly between hosts from different subgenera (Lophozonia and Fuscospora), but also between more closely related hosts. Twenty-four per cent of fungal taxa tested showed affiliations to particular hosts, and tests for cophylogeny revealed significant correlations between host relatedness and the fungal phylogeny that extended to substantial evolutionary depth. These results provide new evidence of correlated evolution in ectomycorrhizal systems, indicating that preferences among closely related host species may represent an important evolutionary driver for local lineage diversification in ectomycorrhizal fungi.
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Affiliation(s)
- Laura G van Galen
- Department of Botany, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - David A Orlovich
- Department of Botany, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Janice M Lord
- Department of Botany, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Andy R Nilsen
- Department of Botany, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Matthew J Larcombe
- Department of Botany, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
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25
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Nilsson RH, Ryberg M, Wurzbacher C, Tedersoo L, Anslan S, Põlme S, Spirin V, Mikryukov V, Svantesson S, Hartmann M, Lennartsdotter C, Belford P, Khomich M, Retter A, Corcoll N, Gómez Martinez D, Jansson T, Ghobad-Nejhad M, Vu D, Sanchez-Garcia M, Kristiansson E, Abarenkov K. How, not if, is the question mycologists should be asking about DNA-based typification. MycoKeys 2023; 96:143-157. [PMID: 37214179 PMCID: PMC10194844 DOI: 10.3897/mycokeys.96.102669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 03/28/2023] [Indexed: 05/24/2023] Open
Abstract
Fungal metabarcoding of substrates such as soil, wood, and water is uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside the scope of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings challenge the present stance of some in the mycological community - that the current situation is satisfactory and that no change is needed to "the code" - and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. The present authors hope for a revitalized and deepened discussion on DNA-based typification, because to us it seems harmful and counter-productive to intentionally deny the overwhelming majority of extant fungi a formal standing under the International Code of Nomenclature for algae, fungi, and plants.
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Affiliation(s)
- R. Henrik Nilsson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
| | - Martin Ryberg
- Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, 85748 Garching, Germany
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Liivi 2, 50409 Tartu, Estonia
- College of Science, King Saud University, 1145 Riyadh, Saudi Arabia
| | - Sten Anslan
- Mycology and Microbiology Center, University of Tartu, Liivi 2, 50409 Tartu, Estonia
| | - Sergei Põlme
- Mycology and Microbiology Center, University of Tartu, Liivi 2, 50409 Tartu, Estonia
| | - Viacheslav Spirin
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, 50409 Tartu, Estonia
| | - Vladimir Mikryukov
- Mycology and Microbiology Center, University of Tartu, Liivi 2, 50409 Tartu, Estonia
| | - Sten Svantesson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
- Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Martin Hartmann
- Botany Unit (Mycology), Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014, Helsinki, Finland
| | - Charlotte Lennartsdotter
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
| | - Pauline Belford
- Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Maryia Khomich
- Interaction Design and Software Engineering, Chalmers University of Technology, Lindholmsplatsen 1, 417 56 Göteborg, Sweden
| | - Alice Retter
- Department of Clinical Science, University of Bergen, Box 7804, 5020 Bergen, Norway
| | - Natàlia Corcoll
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
| | - Daniela Gómez Martinez
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
| | - Tobias Jansson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
| | - Masoomeh Ghobad-Nejhad
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
| | - Duong Vu
- Department of Biotechnology, Iranian Research Organization for Science and Technology, PO Box 3353-5111, Tehran 3353136846, Iran
| | | | - Erik Kristiansson
- Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Kessy Abarenkov
- Mycology and Microbiology Center, University of Tartu, Liivi 2, 50409 Tartu, Estonia
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Bhunjun CS, Phukhamsakda C, Hyde KD, McKenzie EHC, Saxena RK, Li Q. Do all fungi have ancestors with endophytic lifestyles? FUNGAL DIVERS 2023. [DOI: 10.1007/s13225-023-00516-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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27
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DNA metabarcoding reveals compositional and functional differences in fungal communities among Amazonian canga formations. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2022.101209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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28
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Peng Z, Wei S, Hu Y, Qi B, Yuan C, Wang Q, Li Y. Assessment of Fungal Diversity in Minqin County, a Typical Arid Region in Northwestern China. Curr Microbiol 2023; 80:62. [PMID: 36593374 DOI: 10.1007/s00284-022-03167-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 12/23/2022] [Indexed: 01/03/2023]
Abstract
Minqin County is located in the Shiyang River Basin. As a typical arid area, it is eroded by the Badain Jaran and Tengger Desert all year round, and knowledge of the fungal diversity in this area is limited. Therefore, fungal community structure and distribution in the soil of the artificial forest, desert transition zone, farmland, and desert were investigated using amplicon sequencing of the fungal ITS gene. Ten fungal phyla and 23 classes were identified, including 1131 fungi OTUs, Sordariomycetes, Dothideomycetes, Pezizomycetes, and Agaricomycetes were the most abundant classes. Although most OTUs are shared among habitats, fungal community composition among samples was highly variable, which may influence the design of restoration practices in this area.
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Affiliation(s)
- Zhanwu Peng
- Information Center, Jilin Agricultural University, Changchun, China
| | - Shuwei Wei
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Yaping Hu
- Nanjing Institute of Environmental Science, Nanjing, China
| | - Bao Qi
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Chaofeng Yuan
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Qi Wang
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.
| | - Yu Li
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
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29
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Tedersoo L, Mikryukov V, Zizka A, Bahram M, Hagh‐Doust N, Anslan S, Prylutskyi O, Delgado‐Baquerizo M, Maestre FT, Pärn J, Öpik M, Moora M, Zobel M, Espenberg M, Mander Ü, Khalid AN, Corrales A, Agan A, Vasco‐Palacios A, Saitta A, Rinaldi AC, Verbeken A, Sulistyo BP, Tamgnoue B, Furneaux B, Ritter CD, Nyamukondiwa C, Sharp C, Marín C, Gohar D, Klavina D, Sharmah D, Dai DQ, Nouhra E, Biersma EM, Rähn E, Cameron E, De Crop E, Otsing E, Davydov EA, Albornoz F, Brearley FQ, Buegger F, Zahn G, Bonito G, Hiiesalu I, Barrio IC, Heilmann‐Clausen J, Ankuda J, Kupagme JY, Maciá‐Vicente JG, Fovo JD, Geml J, Alatalo JM, Alvarez‐Manjarrez J, Põldmaa K, Runnel K, Adamson K, Bråthen KA, Pritsch K, Tchan KI, Armolaitis K, Hyde KD, Newsham K, Panksep K, Lateef AA, Tiirmann L, Hansson L, Lamit LJ, Saba M, Tuomi M, Gryzenhout M, Bauters M, Piepenbring M, Wijayawardene N, Yorou NS, Kurina O, Mortimer PE, Meidl P, Kohout P, Nilsson RH, Puusepp R, Drenkhan R, Garibay‐Orijel R, Godoy R, Alkahtani S, Rahimlou S, Dudov SV, Põlme S, Ghosh S, Mundra S, Ahmed T, Netherway T, Henkel TW, Roslin T, Nteziryayo V, Fedosov VE, Onipchenko V, Yasanthika WAE, Lim YW, Soudzilovskaia NA, Antonelli A, Kõljalg U, Abarenkov K. Global patterns in endemicity and vulnerability of soil fungi. GLOBAL CHANGE BIOLOGY 2022; 28:6696-6710. [PMID: 36056462 PMCID: PMC9826061 DOI: 10.1111/gcb.16398] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/09/2022] [Indexed: 05/29/2023]
Abstract
Fungi are highly diverse organisms, which provide multiple ecosystem services. However, compared with charismatic animals and plants, the distribution patterns and conservation needs of fungi have been little explored. Here, we examined endemicity patterns, global change vulnerability and conservation priority areas for functional groups of soil fungi based on six global surveys using a high-resolution, long-read metabarcoding approach. We found that the endemicity of all fungi and most functional groups peaks in tropical habitats, including Amazonia, Yucatan, West-Central Africa, Sri Lanka, and New Caledonia, with a negligible island effect compared with plants and animals. We also found that fungi are predominantly vulnerable to drought, heat and land-cover change, particularly in dry tropical regions with high human population density. Fungal conservation areas of highest priority include herbaceous wetlands, tropical forests, and woodlands. We stress that more attention should be focused on the conservation of fungi, especially root symbiotic arbuscular mycorrhizal and ectomycorrhizal fungi in tropical regions as well as unicellular early-diverging groups and macrofungi in general. Given the low overlap between the endemicity of fungi and macroorganisms, but high conservation needs in both groups, detailed analyses on distribution and conservation requirements are warranted for other microorganisms and soil organisms.
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | | | | | - Mohammad Bahram
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | | | - Sten Anslan
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Oleh Prylutskyi
- Department of Mycology and Plant Resistance, School of BiologyV.N. Karazin Kharkiv National UniversityKharkivUkraine
| | - Manuel Delgado‐Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, and Unidad Asociada CSIC‐UPO (BioFun)Universidad Pablo de OlavideSevillaSpain
| | - Fernando T. Maestre
- Departamento de Ecología, Instituto Multidisciplinar para el Estudio del Medio ‘Ramón Margalef’Universidad de AlicanteAlicanteSpain
| | - Jaan Pärn
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Maarja Öpik
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Mari Moora
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Martin Zobel
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Mikk Espenberg
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Ülo Mander
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | | | - Adriana Corrales
- Centro de Investigaciones en Microbiología y Biotecnología‐UR (CIMBIUR)Universidad del RosarioBogotáColombia
| | - Ahto Agan
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | - Aída‐M. Vasco‐Palacios
- BioMicro, Escuela de MicrobiologíaUniversidad de Antioquia UdeAMedellinAntioquiaColombia
| | - Alessandro Saitta
- Department of Agricultural, Food and Forest SciencesUniversity of PalermoPalermoItaly
| | - Andrea C. Rinaldi
- Department of Biomedical SciencesUniversity of CagliariCagliariItaly
| | | | - Bobby P. Sulistyo
- Department of BiomedicineIndonesia International Institute for Life SciencesJakartaIndonesia
| | - Boris Tamgnoue
- Department of Crop ScienceUniversity of DschangDschangCameroon
| | - Brendan Furneaux
- Department of Ecology and GeneticsUppsala UniversityUppsalaSweden
| | | | - Casper Nyamukondiwa
- Department of Biological Sciences and BiotechnologyBotswana International University of Science and TechnologyPalapyeBotswana
| | - Cathy Sharp
- Natural History Museum of ZimbabweBulawayoZimbabwe
| | - César Marín
- Centro de Investigación e Innovación para el Cambio Climático (CiiCC)Universidad SantoTomásSantiagoChile
| | - Daniyal Gohar
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Darta Klavina
- Latvian State Forest Research Insitute SilavaSalaspilsLatvia
| | - Dipon Sharmah
- Department of Botany, Jawaharlal Nehru Rajkeeya MahavidyalayaPondicherry UniversityPort BlairIndia
| | - Dong Qin Dai
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingChina
| | - Eduardo Nouhra
- Instituto Multidisciplinario de Biología Vegetal (CONICET)Universidad Nacional de CórdobaCordobaArgentina
| | | | - Elisabeth Rähn
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | - Erin K. Cameron
- Department of Environmental ScienceSaint Mary's UniversityHalifaxCanada
| | | | - Eveli Otsing
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | | | | | - Francis Q. Brearley
- Department of Natural SciencesManchester Metropolitan UniversityManchesterUK
| | | | | | - Gregory Bonito
- Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Inga Hiiesalu
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Isabel C. Barrio
- Faculty of Natural and Environmental SciencesAgricultural University of IcelandHvanneyriIceland
| | | | - Jelena Ankuda
- Department of Silviculture and EcologyInstitute of Forestry of Lithuanian Research Centre for Agriculture and Forestry (LAMMC)GirionysLithuania
| | - John Y. Kupagme
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Jose G. Maciá‐Vicente
- Plant Ecology and Nature ConservationWageningen University & ResearchWageningenThe Netherlands
| | | | - József Geml
- ELKH‐EKKE Lendület Environmental Microbiome Research GroupEszterházy Károly Catholic UniversityEgerHungary
| | | | | | - Kadri Põldmaa
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Kadri Runnel
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Kalev Adamson
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | - Kari Anne Bråthen
- Department of Arctic and Marine BiologyThe Arctic University of NorwayTromsøNorway
| | | | - Kassim I. Tchan
- Research Unit Tropical Mycology and Plants‐Soil Fungi InteractionsUniversity of ParakouParakouBenin
| | - Kęstutis Armolaitis
- Department of Silviculture and EcologyInstitute of Forestry of Lithuanian Research Centre for Agriculture and Forestry (LAMMC)GirionysLithuania
| | - Kevin D. Hyde
- Center of Excellence in Fungal ResearchMae Fah Luang UniversityChiang RaiThailand
| | | | - Kristel Panksep
- Chair of Hydrobiology and FisheryEstonian University of Life SciencesTartuEstonia
| | | | - Liis Tiirmann
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Linda Hansson
- Gothenburg Centre for Sustainable DevelopmentGothenburgSweden
| | - Louis J. Lamit
- Department of BiologySyracuse UniversitySyracuseNew YorkUSA
- Department of Environmental and Forest BiologyState University of New York College of Environmental Science and ForestrySyracuseNew YorkUSA
| | - Malka Saba
- Department of Plant SciencesQuaid‐i‐Azam UniversityIslamabadPakistan
| | - Maria Tuomi
- Department of Arctic and Marine BiologyThe Arctic University of NorwayTromsøNorway
| | - Marieka Gryzenhout
- Department of GeneticsUniversity of the Free StateBloemfonteinSouth Africa
| | | | - Meike Piepenbring
- Mycology Working GroupGoethe University Frankfurt am MainFrankfurt am MainGermany
| | - Nalin Wijayawardene
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingChina
| | - Nourou S. Yorou
- Research Unit Tropical Mycology and Plants‐Soil Fungi InteractionsUniversity of ParakouParakouBenin
| | - Olavi Kurina
- Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartuEstonia
| | - Peter E. Mortimer
- Center For Mountain Futures, Kunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Peter Meidl
- Institut für BiologieFreie Universität BerlinBerlinGermany
| | - Petr Kohout
- Institute of MicrobiologyCzech Academy of SciencesPragueCzech Republic
| | - Rolf Henrik Nilsson
- Gothenburg Global Biodiversity CentreUniversity of GothenburgGothenburgSweden
| | - Rasmus Puusepp
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Rein Drenkhan
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | | | - Roberto Godoy
- Instituto Ciencias Ambientales y EvolutivasUniversidad Austral de ChileValdiviaChile
| | - Saad Alkahtani
- College of ScienceKing Saud UniversityRiyadhSaudi Arabia
| | - Saleh Rahimlou
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Sergey V. Dudov
- Department of Ecology and Plant GeographyMoscow Lomonosov State UniversityMoscowRussia
| | - Sergei Põlme
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Soumya Ghosh
- Department of GeneticsUniversity of the Free StateBloemfonteinSouth Africa
| | - Sunil Mundra
- Department of Biology, College of ScienceUnited Arab Emirates UniversityAbu DhabiUAE
| | - Talaat Ahmed
- Environmental Science CenterQatar UniversityDohaQatar
| | - Tarquin Netherway
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - Terry W. Henkel
- Department of Biological SciencesCalifornia State Polytechnic UniversityArcataCaliforniaUSA
| | - Tomas Roslin
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - Vincent Nteziryayo
- Department of Food Science and TechnologyUniversity of BurundiBujumburaBurundi
| | - Vladimir E. Fedosov
- Department of Ecology and Plant GeographyMoscow Lomonosov State UniversityMoscowRussia
| | | | | | - Young Woon Lim
- School of Biological Sciences and Institute of MicrobiologySeoul National UniversitySeoulSouth Korea
| | | | | | - Urmas Kõljalg
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
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30
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New-Generation Sequencing Technology in Diagnosis of Fungal Plant Pathogens: A Dream Comes True? J Fungi (Basel) 2022; 8:jof8070737. [PMID: 35887492 PMCID: PMC9320658 DOI: 10.3390/jof8070737] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/01/2022] [Accepted: 07/11/2022] [Indexed: 02/01/2023] Open
Abstract
The fast and continued progress of high-throughput sequencing (HTS) and the drastic reduction of its costs have boosted new and unpredictable developments in the field of plant pathology. The cost of whole-genome sequencing, which, until few years ago, was prohibitive for many projects, is now so affordable that a new branch, phylogenomics, is being developed. Fungal taxonomy is being deeply influenced by genome comparison, too. It is now easier to discover new genes as potential targets for an accurate diagnosis of new or emerging pathogens, notably those of quarantine concern. Similarly, with the development of metabarcoding and metagenomics techniques, it is now possible to unravel complex diseases or answer crucial questions, such as "What's in my soil?", to a good approximation, including fungi, bacteria, nematodes, etc. The new technologies allow to redraw the approach for disease control strategies considering the pathogens within their environment and deciphering the complex interactions between microorganisms and the cultivated crops. This kind of analysis usually generates big data that need sophisticated bioinformatic tools (machine learning, artificial intelligence) for their management. Herein, examples of the use of new technologies for research in fungal diversity and diagnosis of some fungal pathogens are reported.
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31
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Eberhardt U, Kong A, Montoya A, Schütz N, Bartlett P, Beker HJ. Not (only) poison pies - Hebeloma (Agaricales, Hymenogastraceae) in Mexico. MycoKeys 2022; 90:163-202. [PMID: 36760422 PMCID: PMC9849069 DOI: 10.3897/mycokeys.90.85267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/07/2022] [Indexed: 11/12/2022] Open
Abstract
The species of Hebeloma have been little studied in Mexico, but have received attention as edibles and in trials to enhance production of edible fungi and tree growth through inoculation of seedlings with ectomycorrhizal fungi. Here we describe three new species of Hebeloma that are currently known only from Mexico. These species belong to separate sections of the genus: H.ambustiterranum is a member of H.sect.Hebeloma, H.cohaerens belongs to H.sect.Theobromina, while H.magnicystidiatum belongs to H.sect.Denudata. All three species were collected from subtropical pine-oak woodland; all records of H.cohaerens came from altitudes above 2500 m. Hebelomaambustiterranum is commonly sold in the local markets of Tlaxcala as a prized edible mushroom. An additional nine species are reported from Mexico, of which eight are new records for the country: H.aanenii, H.eburneum, H.excedens, H.ingratum, H.neurophyllum, H.sordidulum, H.subaustrale and H.velutipes. First modern descriptions of H.neurophyllum and H.subaustrale, originally described from the USA, are given here.
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Affiliation(s)
- Ursula Eberhardt
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - Alejandro Kong
- Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Km 10.5 carretera San Martín Texmelucan-Tlaxcala, San Felipe Ixtacuixtla, Tlaxcala, 90120, Mexico
| | - Adriana Montoya
- Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Km 10.5 carretera San Martín Texmelucan-Tlaxcala, San Felipe Ixtacuixtla, Tlaxcala, 90120, Mexico
| | - Nicole Schütz
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - Peter Bartlett
- La Baraka, Gorse Hill Road, Virginia Water, Surrey GU25 4AP, United Kingdom
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32
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Saar I, Thorn RG, Nagasawa E, Henkel TW, Cooper JA. A phylogenetic overview of Squamanita, with descriptions of nine new species and four new combinations. Mycologia 2022; 114:769-797. [PMID: 35695889 DOI: 10.1080/00275514.2022.2059639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode) sequence data from eight type specimens of previously described Squamanita species were obtained. Phylogenetic analysis of ITS and partial nuc 28S rDNA data revealed Squamanita as paraphyletic splitting into two monophyletic groups, which we recognize as the genera Squamanita and Dissoderma. We accept 14 Squamanita and nine Dissoderma species, provide the first sequences of 13 of these, and describe six new species of Squamanita and three new species of Dissoderma. We transfer three species of Squamanita into Dissoderma, one into Cystoderma, and treat S. basii and S. umbilicata as synonyms of D. paradoxum. Squamanita can be distinguished from Dissoderma by the generally larger fleshier basidiomata with a tricholomatoid or amanitoid stature and yellowish to tawny brown pileus and often similarly colored stipe. Most species have cheilo- and pleurocystidia. Species of Dissoderma are small, collybioid or mycenoid, lack cystidia, and the pileus and often upper stipe are purplish gray. Both genera parasitize basidiomata of other agarics.
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Affiliation(s)
- Irja Saar
- Institute of Ecology and Earth Sciences, University of Tartu, 2 J. Liivi St., 50409 Tartu, Estonia
| | - R Greg Thorn
- Department of Biology, University of Western Ontario, 1151 Richmond St. N., London, Ontario, N6A 5B7, Canada
| | - Eiji Nagasawa
- Tottori Mycological Institute, 211, Kokoge, Tottori 689-1125, Japan
| | - Terry W Henkel
- Department of Biological Sciences, California State Polytechnic University, Humboldt, 1 Harpst St., Arcata, California 95521 , USA
| | - Jerry A Cooper
- Manaaki Whenua-Landcare Research, 54 Gerald Street, Lincoln 7608, New Zealand
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33
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Phukhamsakda C, Nilsson RH, Bhunjun CS, de Farias ARG, Sun YR, Wijesinghe SN, Raza M, Bao DF, Lu L, Tibpromma S, Dong W, Tennakoon DS, Tian XG, Xiong YR, Karunarathna SC, Cai L, Luo ZL, Wang Y, Manawasinghe IS, Camporesi E, Kirk PM, Promputtha I, Kuo CH, Su HY, Doilom M, Li Y, Fu YP, Hyde KD. The numbers of fungi: contributions from traditional taxonomic studies and challenges of metabarcoding. FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00502-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
AbstractThe global diversity of fungi has been estimated using several different approaches. There is somewhere between 2–11 million estimated species, but the number of formally described taxa is around 150,000, a tiny fraction of the total. In this paper, we examine 12 ascomycete genera as case studies to establish trends in fungal species descriptions, and introduce new species in each genus. To highlight the importance of traditional morpho-molecular methods in publishing new species, we introduce novel taxa in 12 genera that are considered to have low species discovery. We discuss whether the species are likely to be rare or due to a lack of extensive sampling and classification. The genera are Apiospora, Bambusicola, Beltrania, Capronia, Distoseptispora, Endocalyx, Neocatenulostroma, Neodeightonia, Paraconiothyrium, Peroneutypa, Phaeoacremonium and Vanakripa. We discuss host-specificity in selected genera and compare the number of species epithets in each genus with the number of ITS (barcode) sequences deposited in GenBank and UNITE. We furthermore discuss the relationship between the divergence times of these genera with those of their hosts. We hypothesize whether there might be more species in these genera and discuss hosts and habitats that should be investigated for novel species discovery.
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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: 60] [Impact Index Per Article: 30.0] [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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Fernández N, Fontenla S, Fioroni F, Soto-Mancilla M, Carron A, Moguilevsky D, Marchelli P, Marín C, Mestre MC. Mycorrhizas in Nothofagus From South America: What Do We Know From Nursery and Field Experiences? Fungal Biol 2022. [DOI: 10.1007/978-3-031-12994-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Marín C, Godoy R, Rubio J. Gaps in South American Mycorrhizal Biodiversity and Ecosystem Function Research. Fungal Biol 2022. [DOI: 10.1007/978-3-031-12994-0_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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