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Frew A, Öpik M, Oja J, Vahter T, Hiiesalu I, Aguilar-Trigueros CA. Herbivory-driven shifts in arbuscular mycorrhizal fungal community assembly: increased fungal competition and plant phosphorus benefits. THE NEW PHYTOLOGIST 2024; 241:1891-1899. [PMID: 38084055 DOI: 10.1111/nph.19474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/26/2023] [Indexed: 01/05/2024]
Affiliation(s)
- Adam Frew
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, 2751, NSW, Australia
- Centre for Crop Health, University of Southern Queensland, Toowoomba, 4350, Qld, Australia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St 2, 504 09, Estonia
| | - Jane Oja
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St 2, 504 09, Estonia
| | - Tanel Vahter
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St 2, 504 09, Estonia
| | - Inga Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St 2, 504 09, Estonia
| | - Carlos A Aguilar-Trigueros
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, 2751, NSW, Australia
- Department of Biological and Environmental Sciences, University of Jyväskylä, 40014, Jyväskylän yliopisto, Finland
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2
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Wipulasena AYAP, Davison J, Helm A, Kasari L, Moora M, Prangel E, Reitalu T, Vahter T, Vasar M, Zobel M. Soil community composition in dynamic stages of semi-natural calcareous grassland. PLoS One 2023; 18:e0292425. [PMID: 37847721 PMCID: PMC10581465 DOI: 10.1371/journal.pone.0292425] [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: 07/06/2023] [Accepted: 09/20/2023] [Indexed: 10/19/2023] Open
Abstract
European dry thin-soil calcareous grasslands (alvars) are species-rich semi-natural habitats. Cessation of traditional management, such as mowing and grazing, leads to shrub and tree encroachment and the local extinction of characteristic alvar species. While soil microbes are known to play a critical role in driving vegetation and ecosystem dynamics, more information is needed about their composition and function in grasslands of different dynamic stages. Here we assess the composition of soil fungal, prokaryotic, and plant communities using soil environmental DNA from restored alvar grasslands in Estonia. The study areas included grasslands that had experienced different degrees of woody encroachment prior to restoration (woody plant removal and grazing), as well as unmanaged open grasslands. We found that, in general, different taxonomic groups exhibited correlated patterns of between-community variation. Previous forest sites, which had prior to restoration experienced a high degree of woody encroachment by ectomycorrhizal Scots pine, were compositionally most distinct from managed open grasslands, which had little woody vegetation even prior to restoration. The functional structure of plant and fungal communities varied in ways that were consistent with the representation of mycorrhizal types in the ecosystems prior to restoration. Compositional differences between managed and unmanaged open grasslands reflecting the implementation of grazing without further management interventions were clearer among fungal, and to an extent prokaryotic, communities than among plant communities. While previous studies have shown that during woody encroachment of alvar grassland, plant communities change first and fungal communities follow, our DNA-based results suggest that microbial communities reacted faster than plant communities during the restoration of grazing management in alvar grassland. We conclude that while the plant community responds faster to cessation of management, the fungal community responds faster to restoration of management. This may indicate hysteresis, where the eventual pathway back to the original state (grazed ecosystem) differs from the pathway taken towards the alternative state (abandoned semi-natural grassland ecosystem).
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Affiliation(s)
- A. Y. Ayesh Piyara Wipulasena
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - John Davison
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Aveliina Helm
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Liis Kasari
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Mari Moora
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Elisabeth Prangel
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Triin Reitalu
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Tanel Vahter
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Martti Vasar
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
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3
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Touré GPT, Koné AW, Nandjui J, Ebou AET, Otinga AN, Maïga AA, Kouadjo CGZ, Tiho S, Zézé A. Changes in arbuscular mycorrhizal fungal communities, mycorrhizal soil infectivity, and phosphorus availability under Chromolaena odorata (Asteraceae) invasions in a West-African forest-savanna ecotone. MYCORRHIZA 2023; 33:257-275. [PMID: 37289330 DOI: 10.1007/s00572-023-01113-9] [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: 02/01/2023] [Accepted: 05/17/2023] [Indexed: 06/09/2023]
Abstract
Substantial areas of agricultural lands in Sub-Saharan Africa have been invaded by Chromolaena odorata (Asteraceae), but the consequences for arbuscular mycorrhiza fungi (AMF) remains poorly understood. This study explores changes in diverse AMF community attributes and soil available phosphorus following C. odorata invasion in forest and savanna fragments in Côte d'Ivoire (West Africa). Invaded-forest (COF) and savanna (COS) sites were compared to adjacent natural forest (FOR) and savanna (SAV) fragments, respectively. Physico-chemical variables and AMF spore density parameters were determined for soil samples from 0-20 cm depth. An 18S ribosomal RNA metabarcoding analysis of AMF communities was conducted. In addition, cowpea (Vigna unguiculata) was grown on soils collected from these sites under greenhouse conditions for determination of soil mycorrhizal infectivity. Noticeable changes in the composition of AMF communities in C. odorata relative to nearby forest and savanna non-invaded sites were observed. AMF-specific richness in COS (47 species) was lower than that in SAV (57 species) while it was higher in COF (68 species) than in FOR (63 species). COF and COS differed in AMF specific composition (Dissimilarity index = 50.6%). Chromolaena odorata invasions resulted in increased relative abundances of the genera Claroideoglomus and Glomus in COF, a decreased relative abundance of Paraglomus in COS and decreased relative abundances of Ambispora in both COF and COS. Total and healthy spore densities, cowpea root colonization intensity and soil available P were all higher in invaded sites than in natural ecosystems. Remarkably, although these values were different in FOR and SAV, they turned out to be similar in COF and COS (4.6 and 4.2 total spores g-1 soil, 2.3 and 2.0 healthy spores g-1 soil, and 52.6 and 51.6% root colonization, respectively) suggesting a C. odorata-specific effect. These findings indicate that soil mycorrhizal potential and phosphorus availability have improved following C. odorata invasion.
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Affiliation(s)
- Guy-Pacome T Touré
- UR Gestion Durable des Sols, Laboratoire Géosciences, UFR Sciences de la Nature, Université Nangui Abrogoua, 02 BP 801, Abidjan 02, Côte d'Ivoire.
- Laboratoire de Biotechnologie Végétale et Microbienne, UMRI 28 Sciences Agronomique et Génie Rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, BP 1093, Côte d'Ivoire.
| | - Armand W Koné
- UR Gestion Durable des Sols, Laboratoire Géosciences, UFR Sciences de la Nature, Université Nangui Abrogoua, 02 BP 801, Abidjan 02, Côte d'Ivoire
| | - Jacob Nandjui
- Laboratoire de Biotechnologie Végétale et Microbienne, UMRI 28 Sciences Agronomique et Génie Rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, BP 1093, Côte d'Ivoire
| | - Anicet E T Ebou
- Laboratoire de Biotechnologie Végétale et Microbienne, UMRI 28 Sciences Agronomique et Génie Rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, BP 1093, Côte d'Ivoire
- Laboratoire de Bioinformatique et de Biostatistique, UMRI 28 Sciences Agronomique et Génie Rural, Institut National Polytechnique Félix Houphouët-Boigny, BP 1093, Yamoussoukro, Côte d'Ivoire
| | - Abigael N Otinga
- Department of Soil Science, School of Agriculture and Biotechnology, University of Eldoret, P.O. Box 1125-30100, Eldoret, Kenya
| | - Assoumane A Maïga
- DER Sciences Sociales & Economiques, Institut Polytechnique Rural de Formation et de Recherche Appliquée (IPR/IFRA), Katibougou, Bamako, Mali
| | - Claude G Z Kouadjo
- Laboratoire Central de Biotechnologies (LCB), Centre National de Recherche Agronomique (CNRA), Abidjan, Côte d'Ivoire
| | - Seydou Tiho
- Laboratoire d'Ecologie et de Développement Durable (LEDD), UFR Sciences de la Nature, Université Nangui Abrogoua, 02 BP 801, Abidjan 02, Côte d'Ivoire
| | - Adolphe Zézé
- Laboratoire de Biotechnologie Végétale et Microbienne, UMRI 28 Sciences Agronomique et Génie Rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, BP 1093, Côte d'Ivoire
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Vahter T, Lillipuu EM, Oja J, Öpik M, Vasar M, Hiiesalu I. Do commercial arbuscular mycorrhizal inoculants contain the species that they claim? MYCORRHIZA 2023; 33:211-220. [PMID: 36786883 DOI: 10.1007/s00572-023-01105-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 02/08/2023] [Indexed: 06/08/2023]
Abstract
The use of arbuscular mycorrhizal (AM) fungal inoculants as a means to promote plant growth is gaining momentum worldwide. Although there is an increasing number of commercial products available for various applications, the quality of these remains uncertain. We determined the AM fungal species composition in eleven inoculants from four producers by using DNA metabarcoding and compared them to the AM fungal species declared on the product labels. Our DNA metabarcoding of the inoculants revealed a concerning discrepancy between the declared and detected AM fungal species compositions of the products. While nine products contained at least one declared species, two did not contain any matching species and all inoculants but one contained additional species not declared on the product label. These findings highlight the need for better guidelines and industry standards to ensure consumer protection in the AM fungal inoculum market. Additionally, we call for caution when using commercial AM fungal inoculants in scientific experiments without confirmatory information about their species composition.
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Affiliation(s)
- Tanel Vahter
- Institute of Ecology and Earth Sciences, University of Tartu, 2 J. Liivi Street, 50409, Tartu, Estonia.
| | - Epp Maria Lillipuu
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czech Republic
| | - Jane Oja
- Institute of Ecology and Earth Sciences, University of Tartu, 2 J. Liivi Street, 50409, Tartu, Estonia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, 2 J. Liivi Street, 50409, Tartu, Estonia
| | - Martti Vasar
- Institute of Ecology and Earth Sciences, University of Tartu, 2 J. Liivi Street, 50409, Tartu, Estonia
| | - Inga Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, 2 J. Liivi Street, 50409, Tartu, Estonia
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5
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Liu S, Vasar M, Öpik M, Koorem K. Disturbance induces similar shifts in arbuscular mycorrhizal fungal communities from grassland and arable field soils. MYCORRHIZA 2023; 33:153-164. [PMID: 36930376 DOI: 10.1007/s00572-023-01108-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/23/2023] [Indexed: 06/08/2023]
Abstract
Anthropogenic disturbances play an increasingly important role in structuring the diversity and functioning of soil organisms such as arbuscular mycorrhizal (AM) fungi. Frequently, multiple land-use practices, which may represent disturbances for AM fungal communities, operate simultaneously in different habitats. It is not known, however, how previous land-use history and specific habitat type influence AM fungal community response to disturbances. We applied mechanical (cutting to stimulate tillage) and chemical (herbicide addition) disturbances to AM fungal communities from meadow and arable field soils. Our results indicated that AM fungal communities from meadows, which previously had experienced mowing, were more species rich than communities from fields that had experienced intensive land-use practices. There were no significant differences, however, in the responses to disturbance of the AM fungal communities from field and meadow soils. We expected mechanical disturbance to promote taxa from the family Glomeraceae which are expected to exhibit a ruderal life-history strategy; instead, the abundance of this family increased in response to chemical disturbance. Simultaneous application of mechanical disturbance and herbicide decreased only the abundance of Diversisporaceae. No AM fungal families increased in abundance when both mechanical and chemical disturbances were applied simultaneously, but all disturbances increased the abundance of culturable AM fungi. Our study demonstrates that although chemical and mechanical forms of disturbance favor different AM fungal families, existing information about family-level characteristics may not adequately characterize the life history strategies of AM fungus species.
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Affiliation(s)
- Siqiao Liu
- Institute of Ecology and Earth Sciences, University of Tartu, 2 J. Liivi Street, 50409, Tartu, Estonia.
| | - Martti Vasar
- Institute of Ecology and Earth Sciences, University of Tartu, 2 J. Liivi Street, 50409, Tartu, Estonia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, 2 J. Liivi Street, 50409, Tartu, Estonia
| | - Kadri Koorem
- Institute of Ecology and Earth Sciences, University of Tartu, 2 J. Liivi Street, 50409, Tartu, Estonia
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6
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Venbrux M, Crauwels S, Rediers H. Current and emerging trends in techniques for plant pathogen detection. FRONTIERS IN PLANT SCIENCE 2023; 14:1120968. [PMID: 37223788 PMCID: PMC10200959 DOI: 10.3389/fpls.2023.1120968] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 03/21/2023] [Indexed: 05/25/2023]
Abstract
Plant pathogenic microorganisms cause substantial yield losses in several economically important crops, resulting in economic and social adversity. The spread of such plant pathogens and the emergence of new diseases is facilitated by human practices such as monoculture farming and global trade. Therefore, the early detection and identification of pathogens is of utmost importance to reduce the associated agricultural losses. In this review, techniques that are currently available to detect plant pathogens are discussed, including culture-based, PCR-based, sequencing-based, and immunology-based techniques. Their working principles are explained, followed by an overview of the main advantages and disadvantages, and examples of their use in plant pathogen detection. In addition to the more conventional and commonly used techniques, we also point to some recent evolutions in the field of plant pathogen detection. The potential use of point-of-care devices, including biosensors, have gained in popularity. These devices can provide fast analysis, are easy to use, and most importantly can be used for on-site diagnosis, allowing the farmers to take rapid disease management decisions.
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Affiliation(s)
- Marc Venbrux
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
| | - Sam Crauwels
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
| | - Hans Rediers
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
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7
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Zuev AG, Krivosheina MG, Leonov VD, Öpik M, Vasar M, Saraeva AK, Tiunov AV, Goncharov AA. Mycorrhiza-feeding soil invertebrates in two coniferous forests traced with 13C labelling. MYCORRHIZA 2023; 33:59-68. [PMID: 36662299 DOI: 10.1007/s00572-023-01102-y] [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: 08/31/2022] [Accepted: 01/10/2023] [Indexed: 06/17/2023]
Abstract
Mycorrhizal fungi represent a potentially abundant carbon resource for soil animals, but their role in soil food webs remains poorly understood. To detect taxa that are trophically linked to the extraradical mycelium of mycorrhizal fungi, we used stable isotope (13C) labelling of whole trees in combination with the in-growth mesh bag technique in two coniferous forests. This allowed us to detect the flux of carbon in the mycelium of mycorrhizal fungi, and consequently in the tissues of soil invertebrates. The mycorrhizal fungal genera constituted 93.5% of reads in mycelium samples from the in-growth mesh bags. All mycelium from in-growth mesh bags and about 32% of the invertebrates sampled (in total 11 taxa) received the 13C label after 45 days of exposure. The extent of feeding of soil invertebrates on the mycelium of mycorrhizal fungi depended on the taxonomic affinity of the animals. The strongest trophic link to the mycorrhiza-derived carbon was detected in Isotomidae (Collembola) and Oppiidae (Oribatida). The label was also observed in the generalist predators, indicating the propagation of mycorrhiza-derived carbon into the higher trophic levels of the soil food web. Higher 13C labelling in the tissues of euedaphic Collembola and Oribatida compared to atmobiotic and hemiedaphic families indicates the importance of mycorrhizal fungi as a food resource for invertebrates in deeper soil horizons.
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Affiliation(s)
- Andrey G Zuev
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky Prospect 33, Moscow, 119071, Russia.
| | - Marina G Krivosheina
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky Prospect 33, Moscow, 119071, Russia
| | - Vladislav D Leonov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky Prospect 33, Moscow, 119071, Russia
| | - Maarja Öpik
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 J. Liivi St, Tartu, 50409, Estonia
| | - Martti Vasar
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 J. Liivi St, Tartu, 50409, Estonia
| | - Anna K Saraeva
- Forest Research Institute, Karelian Research Center, Russian Academy of Sciences, Petrozavodsk, 185910, Russia
| | - Alexei V Tiunov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky Prospect 33, Moscow, 119071, Russia
| | - Anton A Goncharov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky Prospect 33, Moscow, 119071, Russia
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8
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Tosi M, Ogilvie CM, Spagnoletti FN, Fournier S, Martin RC, Dunfield KE. Cover Crops Modulate the Response of Arbuscular Mycorrhizal Fungi to Water Supply: A Field Study in Corn. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12051015. [PMID: 36903877 PMCID: PMC10005079 DOI: 10.3390/plants12051015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 05/14/2023]
Abstract
Cover crops (CCs) were found to improve soil health by increasing plant diversity and ground cover. They may also improve water supply for cash crops by reducing evaporation and increasing soil water storage capacity. However, their influence on plant-associated microbial communities, including symbiotic arbuscular mycorrhizal fungi (AMF), is less well understood. In a corn field trial, we studied the response of AMF to a four-species winter CC, relative to a no-CC control, as well as to two contrasting water supply levels (i.e., drought and irrigated). We measured AMF colonization of corn roots and used Illumina MiSeq sequencing to study the composition and diversity of soil AMF communities at two depths (i.e., 0-10 and 10-20 cm). In this trial, AMF colonization was high (61-97%), and soil AMF communities were represented by 249 amplicon sequence variants (ASVs) belonging to 5 genera and 33 virtual taxa. Glomus, followed by Claroideoglomus and Diversispora (class Glomeromycetes), were the dominant genera. Our results showed interacting effects between CC treatments and water supply levels for most of the measured variables. The percentage of AMF colonization, arbuscules, and vesicles tended to be lower in irrigated than drought sites, with significant differences detected only under no-CC. Similarly, soil AMF phylogenetic composition was affected by water supply only in the no-CC treatment. Changes in the abundance of individual virtual taxa also showed strong interacting effects between CCs, irrigation, and sometimes soil depth, although CC effects were clearer than irrigation effects. An exception to these interactions was soil AMF evenness, which was higher in CC than no-CC, and higher under drought than irrigation. Soil AMF richness was not affected by the applied treatments. Our results suggest that CCs can affect the structure of soil AMF communities and modulate their response to water availability levels, although soil heterogeneity could influence the final outcome.
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Affiliation(s)
- Micaela Tosi
- School of Environmental Sciences, University of Guelph, 50 Stone Rd. E, Guelph, ON N1G 2W1, Canada
| | - Cameron M. Ogilvie
- Department of Plant Agriculture, University of Guelph, 50 Stone Rd. E, Guelph, ON N1G 2W1, Canada
| | - Federico N. Spagnoletti
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), Consejo Nacional de Investigaciones Científicas (CONICET), Avda. San Martín 4453, Buenos Aires C1417DSE, Argentina
- Cátedra de Microbiología, Facultad de Agronomía, Universidad de Buenos Aires, Avda. San Martín 4453, Buenos Aires C1417DSE, Argentina
| | - Sarah Fournier
- School of Environmental Sciences, University of Guelph, 50 Stone Rd. E, Guelph, ON N1G 2W1, Canada
| | - Ralph C. Martin
- Department of Plant Agriculture, University of Guelph, 50 Stone Rd. E, Guelph, ON N1G 2W1, Canada
| | - Kari E. Dunfield
- School of Environmental Sciences, University of Guelph, 50 Stone Rd. E, Guelph, ON N1G 2W1, Canada
- Correspondence:
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Sepp SK, Vasar M, Davison J, Oja J, Anslan S, Al-Quraishy S, Bahram M, Bueno CG, Cantero JJ, Fabiano EC, Decocq G, Drenkhan R, Fraser L, Garibay Oriel R, Hiiesalu I, Koorem K, Kõljalg U, Moora M, Mucina L, Öpik M, Põlme S, Pärtel M, Phosri C, Semchenko M, Vahter T, Vasco Palacios AM, Tedersoo L, Zobel M. Global diversity and distribution of nitrogen-fixing bacteria in the soil. FRONTIERS IN PLANT SCIENCE 2023; 14:1100235. [PMID: 36743494 PMCID: PMC9895822 DOI: 10.3389/fpls.2023.1100235] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Our knowledge of microbial biogeography has advanced in recent years, yet we lack knowledge of the global diversity of some important functional groups. Here, we used environmental DNA from 327 globally collected soil samples to investigate the biodiversity patterns of nitrogen-fixing bacteria by focusing on the nifH gene but also amplifying the general prokaryotic 16S SSU region. Globally, N-fixing prokaryotic communities are driven mainly by climatic conditions, with most groups being positively correlated with stable hot or seasonally humid climates. Among soil parameters, pH, but also soil N content were most often shown to correlate with the diversity of N-fixer groups. However, specific groups of N-fixing prokaryotes show contrasting responses to the same variables, notably in Cyanobacteria that were negatively correlated with stable hot climates, and showed a U-shaped correlation with soil pH, contrary to other N-fixers. Also, the non-N-fixing prokaryotic community composition was differentially correlated with the diversity and abundance of N-fixer groups, showing the often-neglected impact of biotic interactions among bacteria.
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Affiliation(s)
- Siim-Kaarel Sepp
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Martti Vasar
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Jane Oja
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Saleh Al-Quraishy
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - C. Guillermo Bueno
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Juan José Cantero
- Universidad Nacional de Córdoba, Instituto Multidisciplinario de Biología Vegetal, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
- Universidad Nacional de Río Cuarto, Departamento de Biología Agrícola, Facultad de Agronomía y Veterinaria, Córdoba, Argentina
| | | | - Guillaume Decocq
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR CNRS 7058), Jules Verne University of Picardie, Amiens, France
| | - Rein Drenkhan
- Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Lauchlan Fraser
- Department of Natural Resource Sciences, Thompson Rivers University, Kamloops, BC, Canada
| | - Roberto Garibay Oriel
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Inga Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Kadri Koorem
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Urmas Kõljalg
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Ladislav Mucina
- Iluka Chair in Vegetation Science and Biogeography, Harry Butler Institute, Murdoch University, Perth, Australia
- Department of Geography & Environmental Studies, Stellenbosch University, Stellenbosch, South Africa
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Sergei Põlme
- Center of Mycology and Microbiology, University of Tartu, Tartu, Estonia
| | - Meelis Pärtel
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Cherdchai Phosri
- Department of Biology, Nakhon Phanom University, Nakhon Phanom, Thailand
| | - Marina Semchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Tanel Vahter
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Aida M. Vasco Palacios
- Grupo de Microbiología Ambiental y Grupo BioMicro, Escuela de Microbiología, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Leho Tedersoo
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Center of Mycology and Microbiology, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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10
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Vasar M, Davison J, Moora M, Sepp SK, Anslan S, Al-Quraishy S, Bahram M, Bueno CG, Cantero JJ, Fabiano EC, Decocq G, Drenkhan R, Fraser L, Oja J, Garibay-Orijel R, Hiiesalu I, Koorem K, Mucina L, Öpik M, Põlme S, Pärtel M, Phosri C, Semchenko M, Vahter T, Doležal J, Palacios AMV, Tedersoo L, Zobel M. Metabarcoding of soil environmental DNA to estimate plant diversity globally. FRONTIERS IN PLANT SCIENCE 2023; 14:1106617. [PMID: 37143888 PMCID: PMC10151745 DOI: 10.3389/fpls.2023.1106617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/03/2023] [Indexed: 05/06/2023]
Abstract
Introduction Traditional approaches to collecting large-scale biodiversity data pose huge logistical and technical challenges. We aimed to assess how a comparatively simple method based on sequencing environmental DNA (eDNA) characterises global variation in plant diversity and community composition compared with data derived from traditional plant inventory methods. Methods We sequenced a short fragment (P6 loop) of the chloroplast trnL intron from from 325 globally distributed soil samples and compared estimates of diversity and composition with those derived from traditional sources based on empirical (GBIF) or extrapolated plant distribution and diversity data. Results Large-scale plant diversity and community composition patterns revealed by sequencing eDNA were broadly in accordance with those derived from traditional sources. The success of the eDNA taxonomy assignment, and the overlap of taxon lists between eDNA and GBIF, was greatest at moderate to high latitudes of the northern hemisphere. On average, around half (mean: 51.5% SD 17.6) of local GBIF records were represented in eDNA databases at the species level, depending on the geographic region. Discussion eDNA trnL gene sequencing data accurately represent global patterns in plant diversity and composition and thus can provide a basis for large-scale vegetation studies. Important experimental considerations for plant eDNA studies include using a sampling volume and design to maximise the number of taxa detected and optimising the sequencing depth. However, increasing the coverage of reference sequence databases would yield the most significant improvements in the accuracy of taxonomic assignments made using the P6 loop of the trnL region.
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Affiliation(s)
- Martti Vasar
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- *Correspondence: Martti Vasar,
| | - John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Siim-Kaarel Sepp
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Saleh Al-Quraishy
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - C. Guillermo Bueno
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Juan José Cantero
- Instituto Multidisciplinario de Biología Vegetal, Universidad Nacional de Córdoba, CONICET, Córdoba, Argentina
- Departamento de Biología Agrícola, Facultad de Agronomía y Veterinaria, Universidad Nacional de Río Cuarto, Córdoba, Argentina
| | | | - Guillaume Decocq
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR CNRS 7058), Jules Verne, University of Picardie, Amiens, France
| | - Rein Drenkhan
- Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Lauchlan Fraser
- Department of Natural Resource Sciences, Thompson Rivers University, Kamloops, BC, Canada
| | - Jane Oja
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Roberto Garibay-Orijel
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Inga Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Kadri Koorem
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Ladislav Mucina
- Iluka Chair in Vegetation Science and Biogeography, Harry Butler Institute, Murdoch University, Perth, WA, Australia
- Department of Geography & Environmental Studies, Stellenbosch University, Stellenbosch, South Africa
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Sergei Põlme
- Center of Mycology and Microbiology, University of Tartu, Tartu, Estonia
| | - Meelis Pärtel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Cherdchai Phosri
- Department of Biology, Nakhon Phanom University, Nakhon Phanom, Thailand
| | - Marina Semchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Tanel Vahter
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Jiři Doležal
- Institute of Botany, The Czech Academy of Sciences, Třeboň, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Aida M. Vasco Palacios
- Grupo de Microbiología Ambiental y Grupo BioMicro, Escuela de Microbiología, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Leho Tedersoo
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Center of Mycology and Microbiology, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Botany, University of Tartu, Tartu, Estonia
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11
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González Fradejas G, García de León D, Vasar M, Koorem K, Zobel M, Öpik M, Moora M, Rey Benayas JM. Hedgerows increase the diversity and modify the composition of arbuscular mycorrhizal fungi in Mediterranean agricultural landscapes. MYCORRHIZA 2022; 32:397-407. [PMID: 36087125 PMCID: PMC9561024 DOI: 10.1007/s00572-022-01090-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Sustainable agriculture is essential to address global challenges such as climate change and biodiversity loss. Hedgerows enhance aboveground biodiversity and provide ecosystem services, but little is known about their impact on soil biota. Arbuscular mycorrhizal (AM) fungi are one of the key components of belowground biodiversity. We compared the diversity and composition of AM fungal communities at four farmland sites located in Central Spain, where 132 soil samples in total were collected to assess soil physical and chemical properties and the AM fungal communities. We compared the richness (number of AM fungal taxa), taxonomic, functional, and phylogenetic diversity, and structure of the AM fungal communities across three farmland habitat types, namely hedgerows, woody crops (olive groves and vineyard), and herbaceous crops (barley, sunflower, and wheat). Our results showed positive effects of hedgerows on most diversity metrics. Almost 60% of the AM fungal taxa were shared among the three farmland habitat types. Hedgerows increased AM fungal taxonomic richness (31%) and alpha diversity (25%), and especially so compared to herbaceous crops (45% and 28%, respectively). Hedgerows harbored elevated proportions of AM fungi with non-ruderal life-history strategies. AM fungal communities were more similar between hedgerows and woody crops than between hedgerows and adjacent herbaceous crops, possibly because of differences in tillage and fertilization. Unexpectedly, hedgerows reduced phylogenetic diversity, which might be related to more selective associations of AM fungi with woody plants than with herbaceous crops. Overall, the results suggest that planting hedgerows contributes to maintain belowground diversity. Thus, European farmers should plant more hedgerows to attain the goals of the EU Biodiversity Strategy for 2030.
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Affiliation(s)
- Guillermo González Fradejas
- Grupo de Ecología y Restauración Forestal (FORECO), Departamento de Ciencias de La Vida, Universidad de Alcalá, Alcalá de Henares, Spain
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - David García de León
- Grupo de Ecología y Restauración Forestal (FORECO), Departamento de Ciencias de La Vida, Universidad de Alcalá, Alcalá de Henares, Spain.
| | - Martti Vasar
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Kadri Koorem
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - José María Rey Benayas
- Grupo de Ecología y Restauración Forestal (FORECO), Departamento de Ciencias de La Vida, Universidad de Alcalá, Alcalá de Henares, Spain
- Fundación Internacional para la Restauración de Ecosistemas, Madrid, Spain
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12
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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: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 02/07/2022] [Accepted: 03/30/2022] [Indexed: 02/06/2023]
Abstract
The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems. Here we provide an overview of current best practices in metabarcoding analysis of fungal communities, from experimental design through molecular and computational analyses. By reanalysing published data sets, we demonstrate that operational taxonomic units (OTUs) outperform amplified sequence variants (ASVs) in recovering fungal diversity, a finding that is particularly evident for long markers. Additionally, analysis of the full-length ITS region allows more accurate taxonomic placement of fungi and other eukaryotes compared to the ITS2 subregion. Finally, we show that specific methods for compositional data analyses provide more reliable estimates of shifts in community structure. We conclude that metabarcoding analyses of fungi are especially promising for integrating fungi into the full microbiome and broader ecosystem functioning context, recovery of novel fungal lineages and ancient organisms as well as barcoding of old specimens including type material.
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Bahram
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Lucie Zinger
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, France.,Naturalis Biodiversity Center, Leiden, The Netherlands
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Peter G Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, USA
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Vladimir Mikryukov
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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13
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Vasar M, Davison J, Sepp SK, Oja J, Al-Quraishy S, Bueno CG, Cantero JJ, Fabiano EC, Decocq G, Fraser L, Hiiesalu I, Hozzein WN, Koorem K, Moora M, Mucina L, Onipchenko V, Öpik M, Pärtel M, Phosri C, Vahter T, Tedersoo L, Zobel M. Global taxonomic and phylogenetic assembly of AM fungi. MYCORRHIZA 2022; 32:135-144. [PMID: 35138435 DOI: 10.1007/s00572-022-01072-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi are a ubiquitous group of plant symbionts, yet processes underlying their global assembly - in particular the roles of dispersal limitation and historical drivers - remain poorly understood. Because earlier studies have reported niche conservatism in AM fungi, we hypothesized that variation in taxonomic community composition (i.e., unweighted by taxon relatedness) should resemble variation in phylogenetic community composition (i.e., weighted by taxon relatedness) which reflects ancestral adaptations to historical habitat gradients. Because of the presumed strong dispersal ability of AM fungi, we also anticipated that the large-scale structure of AM fungal communities would track environmental conditions without regional discontinuity. We used recently published AM fungal sequence data (small-subunit ribosomal RNA gene) from soil samples collected worldwide to reconstruct global patterns in taxonomic and phylogenetic community variation. The taxonomic structure of AM fungal communities was primarily driven by habitat conditions, with limited regional differentiation, and there were two well-supported clusters of communities - occurring in cold and warm conditions. Phylogenetic structure was driven by the same factors, though all relationships were markedly weaker. This suggests that niche conservatism with respect to habitat associations is weakly expressed in AM fungal communities. We conclude that the composition of AM fungal communities tracks major climatic and edaphic gradients, with the effects of dispersal limitation and historic factors considerably less apparent than those of climate and soil.
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Affiliation(s)
- Martti Vasar
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia.
| | - John Davison
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Siim-Kaarel Sepp
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Jane Oja
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Saleh Al-Quraishy
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - C Guillermo Bueno
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Juan José Cantero
- CONICET, Instituto Multidisciplinario de Biología Vegetal, Universidad Nacional de Córdoba, Córdoba, Argentina
- Departamento de Biología Agrícola, Facultad de Agronomía Y Veterinaria, Universidad Nacional de Río Cuarto, Córdoba, Argentina
| | | | - Guillaume Decocq
- Ecologie et Dynamique des Systèmes Anthropisés, Jules Verne University of Picardie, Amiens, France
| | - Lauchlan Fraser
- Department of Natural Resource Sciences, Thompson Rivers University, Kamloops, BC, Canada
| | - Inga Hiiesalu
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Wael N Hozzein
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Kadri Koorem
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Mari Moora
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Ladislav Mucina
- Iluka Chair in Vegetation Science and Biogeography, Harry Butler Institute, Murdoch University, Murdoch, Perth, Australia
- Department of Geography and Environmental Studies, Stellenbosch University, Stellenbosch, South Africa
| | - Vladimir Onipchenko
- Department of Ecology and Plant Geography, Faculty of Biology, Moscow Lomonosov State University, Moscow, Russia
| | - Maarja Öpik
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Meelis Pärtel
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Cherdchai Phosri
- Department of Biology, Nakhon Phanom University, Nakhon Phanom, Thailand
| | - Tanel Vahter
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Leho Tedersoo
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Botany, University of Tartu, Tartu, Estonia
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14
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Apangu GP, Frisk CA, Petch GM, Muggia L, Pallavicini A, Hanson M, Skjøth CA. Environmental DNA reveals diversity and abundance of Alternaria species in neighbouring heterogeneous landscapes in Worcester, UK. AEROBIOLOGIA 2022; 38:457-481. [PMID: 36471880 PMCID: PMC9715499 DOI: 10.1007/s10453-022-09760-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 09/28/2022] [Indexed: 05/05/2023]
Abstract
UNLABELLED Alternaria is a pathogenic and allergenic fungus affecting 400 plant species and 334 million people globally. This study aimed at assessing the diversity of Alternaria species in airborne samples collected from closely located (7 km apart) and heterogeneous sites (rural, urban and unmanaged grassland) in Worcester and Lakeside, the UK. A secondary objective was to examine how the ITS1 subregion varies from ITS2 in Alternaria species diversity and composition. Airborne spores were collected using Burkard 7-day and multi-vial Cyclone samplers for the period 5 July 2016-9 October 2019. Air samples from the Cyclone were amplified using the ITS1and ITS2 subregions and sequenced using Illumina MiSeq platform whereas those from the Burkard sampler were identified and quantified using optical microscopy. Optical microscopy and eDNA revealed a high abundance of Alternaria in the rural, urban and unmanaged sites. ITS1 and ITS2 detected five and seven different Alternaria species at the three sampling sites, respectively. A. dactylidicola, A. metachromatica and A. infectoria were the most abundant. The rural, urban and unmanaged grassland sites had similar diversity (PERMANOVA) of the species due to similarity in land use and proximity of the sites. Overall, the study showed that heterogeneous and neighbouring sites with similar land uses can have similar Alternaria species. It also demonstrated that an eDNA approach can complement the classical optical microscopy method in providing more precise information on fungal species diversity in an environment for targeted management. Similar studies can be replicated for other allergenic and pathogenic fungi. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10453-022-09760-9.
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Affiliation(s)
- Godfrey Philliam Apangu
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester UK
- Present Address: Protecting Crops and the Environment, Rothamsted Research, West Common, Harpenden, AL5 2JQ Hertfordshire UK
| | - Carl Alexander Frisk
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester UK
- Present Address: Department of Urban Greening and Vegetation Ecology, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Geoffrey M. Petch
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester UK
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
| | - Mary Hanson
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester UK
| | - Carsten Ambelas Skjøth
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester UK
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
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15
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Liu S, Moora M, Vasar M, Zobel M, Öpik M, Koorem K. Arbuscular mycorrhizal fungi promote small-scale vegetation recovery in the forest understorey. Oecologia 2021; 197:685-697. [PMID: 34716490 DOI: 10.1007/s00442-021-05065-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 10/17/2021] [Indexed: 11/26/2022]
Abstract
Root-associating arbuscular mycorrhizal (AM) fungi foster vegetation recovery in degraded habitats. AM fungi increase nutrient availability for host plants; therefore, their importance is expected to be higher when nutrient availability is low. However, little is known about how small-scale variation in nutrient availability influences plant and AM fungal communities in a stable ecosystem. We conducted a 2-year field study in the understorey of a boreonemoral forest where we examined plant and AM fungal communities at microsites (15 cm diameter) with intact vegetation cover and at disturbed microsites where vegetation was cleared away and soil was sterilized to remove soil biota. We manipulated soil nutrient content (increased with fertilizer, unchanged, or decreased with sucrose addition) and fungal activity (natural or suppressed by fungicide addition) at these microsites. After two vegetation seasons, manipulations with nutrient content resulted in significant, although moderate, differences in the content of soil nutrients (e.g. in soil phosphorus). Suppression of fungal activity resulted in lower richness, abundance and phylogenetic diversity of AM fungal community, independently of microsite type and soil fertility level. Plant species richness and diversity decreased when fungal activity was suppressed at disturbed but not in intact microsites. The correlation between plant and AM fungal communities was not influenced by microsite type or soil fertility. We conclude that small-scale variation in soil fertility and habitat integrity does not influence the interactions between plants and AM fungi. The richness, but not composition, of AM fungal communities recovered fast after small-scale disturbance and supported the recovery of species-rich vegetation.
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Affiliation(s)
- Siqiao Liu
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia.
| | - Mari Moora
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Martti Vasar
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Maarja Öpik
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Kadri Koorem
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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16
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Hoeffner K, Beylich A, Chabbi A, Cluzeau D, Dascalu D, Graefe U, Guzmán G, Hallaire V, Hanisch J, Landa BB, Linsler D, Menasseri S, Öpik M, Potthoff M, Sandor M, Scheu S, Schmelz RM, Engell I, Schrader S, Vahter T, Banse M, Nicolaï A, Plaas E, Runge T, Roslin T, Decau ML, Sepp SK, Arias-Giraldo LF, Busnot S, Roucaute M, Pérès G. Legacy effects of temporary grassland in annual crop rotation on soil ecosystem services. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 780:146140. [PMID: 34030316 DOI: 10.1016/j.scitotenv.2021.146140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/21/2021] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
The introduction of temporary grassland into an annual crop rotation is recognized to improve soil ecosystem services, and resulting legacies can be beneficial for the following crops. In this context, the aim of the present study was to evaluate legacy effects of introducing temporary grassland into an annual crop rotation on five ecosystem services (i) soil structure maintenance (aggregate stability), (ii) water regulation (saturated hydraulic conductivity), (iii) biodiversity conservation (microbial biomass and microbial metabolic activity, as well as microorganism, enchytraeid, springtail and earthworm communities), (iv) pathogen regulation (soil suppressiveness to Verticillium dahliae), and (v) forage production and quality. Three crop rotation schemes, maintained for twelve years, were compared in four random blocks, one being an annual crop rotation without grassland (0%), another with a medium percentage of grassland (50%, corresponding to 3 years of continuous grassland in the crop rotation), and a third one with a high percentage of grassland in the crop rotation (75%, corresponding to 6 years of continuous grassland in the crop rotation). The results showed that the grassland introduction into an annual crop rotation improved, whatever the duration of the grassland, soil structure maintenance and biodiversity conservation, while it decreased pathogen regulation and did not modify water regulation. Comparing the two crop rotations that included grassland, indicated a stronger beneficial grassland legacy effect for the higher proportion of grassland concerning soil structure maintenance and biodiversity conservation. By contrast, water regulation, pathogen regulation and forage production were not affected by the legacy of the 75% grassland during the rotation. Overall, our findings demonstrated the extent to which grassland legacies are affecting the current state of soil properties and possible ecosystem services provided. To improve ecosystem services, soil management should take legacy effects into account and consider longer timeframes to apply beneficial practices.
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Affiliation(s)
- Kevin Hoeffner
- UMR SAS, INRAE, INSTITUT AGRO AGROCAMPUS OUEST, 35000 Rennes, France; University of Rennes, CNRS, ECOBIO [(Ecosystèmes, biodiversité, évolution)], - UMR 6553, Rennes, France.
| | - Anneke Beylich
- IFAB Institut für Angewandte Bodenbiologie GmbH, 22337 Hamburg, Germany
| | - Abad Chabbi
- INRAE, UR P3F, Centre Poitou-Charentes, Lusignan, France; UMR ECOSYS, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Daniel Cluzeau
- University of Rennes, CNRS, ECOBIO [(Ecosystèmes, biodiversité, évolution)], - UMR 6553, Rennes, France
| | - Dumitrita Dascalu
- University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Cluj-Napoca, Romania
| | - Ulfert Graefe
- IFAB Institut für Angewandte Bodenbiologie GmbH, 22337 Hamburg, Germany
| | - Gema Guzmán
- Institute for Sustainable Agriculture, CSIC, Cordoba, Spain
| | - Vincent Hallaire
- UMR SAS, INRAE, INSTITUT AGRO AGROCAMPUS OUEST, 35000 Rennes, France
| | - Jörg Hanisch
- University of Göttingen, J.F. Blumenbach Institute of Zoology and Anthropology, 37073 Göttingen, Germany
| | - Blanca B Landa
- Institute for Sustainable Agriculture, CSIC, Cordoba, Spain
| | - Deborah Linsler
- University of Göttingen, Centre of Biodiversity and Sustainable Land Use, 37077 Göttingen, Germany
| | - Safya Menasseri
- UMR SAS, INRAE, INSTITUT AGRO AGROCAMPUS OUEST, 35000 Rennes, France
| | - Maarja Öpik
- Department of Botany, University of Tartu, Lai 40, EE-51005 Tartu, Estonia
| | - Martin Potthoff
- University of Göttingen, Centre of Biodiversity and Sustainable Land Use, 37077 Göttingen, Germany
| | - Mignon Sandor
- University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Cluj-Napoca, Romania
| | - Stefan Scheu
- University of Göttingen, J.F. Blumenbach Institute of Zoology and Anthropology, 37073 Göttingen, Germany
| | - Rüdiger M Schmelz
- IFAB Institut für Angewandte Bodenbiologie GmbH, 22337 Hamburg, Germany
| | - Ilka Engell
- University of Göttingen, Centre of Biodiversity and Sustainable Land Use, 37077 Göttingen, Germany
| | - Stefan Schrader
- Johann Heinrich von Thünen-Institute, Institute of Biodiversity, Braunschweig, Germany
| | - Tanel Vahter
- Department of Botany, University of Tartu, Lai 40, EE-51005 Tartu, Estonia
| | - Martin Banse
- Johann Heinrich von Thünen-Institute, Institute of Market Analysis, Braunschweig, Germany
| | - Annegret Nicolaï
- UMR SAS, INRAE, INSTITUT AGRO AGROCAMPUS OUEST, 35000 Rennes, France; University of Rennes, CNRS, ECOBIO [(Ecosystèmes, biodiversité, évolution)], - UMR 6553, Rennes, France
| | - Elke Plaas
- University of Göttingen, Centre of Biodiversity and Sustainable Land Use, 37077 Göttingen, Germany; University of Göttingen, Department for Agricultural Economics and Rural Development, Göttingen, Germany
| | - Tania Runge
- Johann Heinrich von Thünen-Institute, Institute of Market Analysis, Braunschweig, Germany
| | - Tomas Roslin
- Swedish University of Agricultural Sciences, Department of Ecology, Uppsala, Sweden
| | | | - Siim-Kaarel Sepp
- Department of Botany, University of Tartu, Lai 40, EE-51005 Tartu, Estonia
| | | | - Sylvain Busnot
- UMR SAS, INRAE, INSTITUT AGRO AGROCAMPUS OUEST, 35000 Rennes, France
| | - Marc Roucaute
- UMR SAS, INRAE, INSTITUT AGRO AGROCAMPUS OUEST, 35000 Rennes, France
| | - Guénola Pérès
- UMR SAS, INRAE, INSTITUT AGRO AGROCAMPUS OUEST, 35000 Rennes, France
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17
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Frew A, Price JN, Oja J, Vasar M, Öpik M. Impacts of elevated atmospheric CO 2 on arbuscular mycorrhizal fungi and their role in moderating plant allometric partitioning. MYCORRHIZA 2021; 31:423-430. [PMID: 33674909 DOI: 10.1007/s00572-021-01025-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/18/2021] [Indexed: 06/12/2023]
Abstract
Elevated atmospheric CO2 concentration (eCO2) effects on plants depend on several factors including plant photosynthetic physiology (e.g. C3, C4), soil nutrient availability and plants' co-evolved soil-dwelling fungal symbionts, namely arbuscular mycorrhizal (AM) fungi. Complicated interactions among these components will determine the outcomes for plants. Therefore, clearer understanding is needed of how plant growth and nutrient uptake, along with root-colonising AM fungal communities, are simultaneously impacted by eCO2. We conducted a factorial growth chamber experiment with a C3 and a C4 grass species (± AM fungi and ± eCO2). We found that eCO2 increased plant biomass allocation towards the roots, but only in plants without AM fungi, potentially associated with an eCO2-driven increase in plant nutrient requirements. Furthermore, our data suggest a difference in the identities of root-colonising fungal taxa between ambient CO2 and eCO2 treatments, particularly in the C4 grass species, although this was not statistically significant. As AM fungi are ubiquitous partners of grasses, their response to increasing atmospheric CO2 is likely to have important consequences for how grassland ecosystems respond to global change.
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Affiliation(s)
- Adam Frew
- Centre for Crop Health, School of Sciences, University of Southern Queensland, Toowoomba, QLD, Australia.
- Institute for Land, Water and Society, Charles Sturt University, Albury, NSW, Australia.
| | - Jodi N Price
- Institute for Land, Water and Society, Charles Sturt University, Albury, NSW, Australia
| | - Jane Oja
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Martti Vasar
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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