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MacColl KA, Tosi M, Chagnon PL, MacDougall AS, Dunfield KE, Maherali H. Prairie restoration promotes the abundance and diversity of mutualistic arbuscular mycorrhizal fungi. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2024:e2981. [PMID: 38738945 DOI: 10.1002/eap.2981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 01/12/2024] [Accepted: 03/14/2024] [Indexed: 05/14/2024]
Abstract
Predicting how biological communities assemble in restored ecosystems can assist in conservation efforts, but most research has focused on plants, with relatively little attention paid to soil microbial organisms that plants interact with. Arbuscular mycorrhizal (AM) fungi are an ecologically significant functional group of soil microbes that form mutualistic symbioses with plants and could therefore respond positively to plant community restoration. To evaluate the effects of plant community restoration on AM fungi, we compared AM fungal abundance, species richness, and community composition of five annually cultivated, conventionally managed agricultural fields with paired adjacent retired agricultural fields that had undergone prairie restoration 5-9 years prior to sampling. We hypothesized that restoration stimulates AM fungal abundance and species richness, particularly for disturbance-sensitive taxa, and that gains of new taxa would not displace AM fungal species present prior to restoration due to legacy effects. AM fungal abundance was quantified by measuring soil spore density and root colonization. AM fungal species richness and community composition were determined in soils and plant roots using DNA high-throughput sequencing. Soil spore density was 2.3 times higher in restored prairies compared to agricultural fields, but AM fungal root colonization did not differ between land use types. AM fungal species richness was 2.7 and 1.4 times higher in restored prairies versus agricultural fields for soil and roots, respectively. The abundance of Glomeraceae, a disturbance-tolerant family, decreased by 25% from agricultural to restored prairie soils but did not differ in plant roots. The abundance of Claroideoglomeraceae and Diversisporaceae, both disturbance-sensitive families, was 4.6 and 3.2 times higher in restored prairie versus agricultural soils, respectively. Species turnover was higher than expected relative to a null model, indicating that AM fungal species were gained by replacement. Our findings demonstrate that restoration can promote a relatively rapid increase in the abundance and diversity of soil microbial communities that had been degraded by decades of intensive land use, and community compositional change can be predicted by the disturbance tolerance of soil microbial taxonomic and functional groups.
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Affiliation(s)
- Kevin A MacColl
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Micaela Tosi
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Pierre-Luc Chagnon
- Institut de recherche en biologie végétale, Université de Montréal, Montréal, Quebec, Canada
| | - Andrew S MacDougall
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Kari E Dunfield
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Hafiz Maherali
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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Peng Z, Johnson NC, Jansa J, Han J, Fang Z, Zhang Y, Jiang S, Xi H, Mao L, Pan J, Zhang Q, Feng H, Fan T, Zhang J, Liu Y. Mycorrhizal effects on crop yield and soil ecosystem functions in a long-term tillage and fertilization experiment. THE NEW PHYTOLOGIST 2024; 242:1798-1813. [PMID: 38155454 DOI: 10.1111/nph.19493] [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: 09/19/2023] [Accepted: 12/04/2023] [Indexed: 12/30/2023]
Abstract
It is well understood that agricultural management influences arbuscular mycorrhizal (AM) fungi, but there is controversy about whether farmers should manage for AM symbiosis. We assessed AM fungal communities colonizing wheat roots for three consecutive years in a long-term (> 14 yr) tillage and fertilization experiment. Relationships among mycorrhizas, crop performance, and soil ecosystem functions were quantified. Tillage, fertilizers and continuous monoculture all reduced AM fungal richness and shifted community composition toward dominance of a few ruderal taxa. Rhizophagus and Dominikia were depressed by tillage and/or fertilization, and their abundances as well as AM fungal richness correlated positively with soil aggregate stability and nutrient cycling functions across all or no-tilled samples. In the field, wheat yield was unrelated to AM fungal abundance and correlated negatively with AM fungal richness. In a complementary glasshouse study, wheat biomass was enhanced by soil inoculum from unfertilized, no-till plots while neutral to depressed growth was observed in wheat inoculated with soils from fertilized and conventionally tilled plots. This study demonstrates contrasting impacts of low-input and conventional agricultural practices on AM symbiosis and highlights the importance of considering both crop yield and soil ecosystem functions when managing mycorrhizas for more sustainable agroecosystems.
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Affiliation(s)
- Zhenling Peng
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Nancy Collins Johnson
- School of Earth and Sustainability, Northern Arizona University, Flagstaff, AZ, 86001, USA
| | - Jan Jansa
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220, Prague, Czech Republic
| | - Jiayao Han
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Zhou Fang
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yali Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Shengjing Jiang
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Hao Xi
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Lin Mao
- College of Life Sciences, Northwest Normal University, Lanzhou, 730070, China
| | - Jianbin Pan
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Qi Zhang
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Huyuan Feng
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Tinglu Fan
- Dryland Agriculture Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Jianjun Zhang
- Dryland Agriculture Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Yongjun Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
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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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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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Beta Diversity of Arbuscular Mycorrhizal Communities Increases in Time after Crop Establishment of Peruvian Sacha Inchi ( Plukenetia volubilis). J Fungi (Basel) 2023; 9:jof9020194. [PMID: 36836309 PMCID: PMC9966307 DOI: 10.3390/jof9020194] [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: 12/24/2022] [Revised: 01/22/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
(1) Background: Beta diversity, i.e., the variance in species compositions across communities, has been pointed out as a main factor for explaining ecosystem functioning. However, few studies have directly tested the effect of crop establishment on beta diversity. We studied beta diversity patterns of arbuscular mycorrhizal (AM) fungal communities associated to sacha inchi (Plukenetia volubilis) after crop establishment. (2) Methods: We molecularly characterized the AM fungal communities associated to roots of sacha inchi in plots after different times of crop establishment, from less than one year to older than three. We analyzed the patterns of alpha, beta, and phylogenetic diversity, and the sources of variation of AM fungal community composition. (3) Results: Beta diversity increased in the older plots, but no temporal effect in alpha or phylogenetic diversity was found. The AM fungal community composition was driven by environmental factors (altitude and soil conditions). A part of this variation could be attributed to differences between sampled locations (expressed as geographic coordinates). Crop age, in turn, affected the composition with no interactions with the environmental conditions or spatial location. (4) Conclusions: These results point out towards a certain recovery of the soil microbiota after sacha inchi establishment. This fact could be attributed to the low-impact management associated to this tropical crop.
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Ducousso-Détrez A, Raveau R, Fontaine J, Hijri M, Lounès-Hadj Sahraoui A. Glomerales Dominate Arbuscular Mycorrhizal Fungal Communities Associated with Spontaneous Plants in Phosphate-Rich Soils of Former Rock Phosphate Mining Sites. Microorganisms 2022; 10:microorganisms10122406. [PMID: 36557659 PMCID: PMC9782746 DOI: 10.3390/microorganisms10122406] [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: 10/02/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are key drivers of soil functioning. They interact with multiple soil parameters, notably, phosphorus (P). In this work, AMF communities of native plants grown spontaneously on former mining sites either enriched (P sites) or not enriched with P (nP sites) by mining cuttings of rock phosphate (RP) were studied. No significant differences were observed in the root mycorrhizal rates of the plants when comparing P and nP sites. The assessment of AMF diversity and community structure using Illumina MiSeq metabarcoding and targeting 18S rDNA in roots and rhizospheric soils showed a total of 318 Amplicon Sequence Variants (ASVs) of Glomeromycota phylum. No significant difference in the diversity was found between P and nP sites. Glomeraceae species were largely dominant, formed a fungal core of 26 ASVs, and were persistent and abundant in all sites. In the P soils, eight ASVs were identified by indicator species analysis. A trend towards an increase in Diversisporaceae and Claroideoglomeraceae and a reduction in Paraglomeraceae and Glomeraceae were noticed. These results provide new insights into AMF ecology in former RP mining sites; they document that P concentration is a driver of AMF community structures in soils enriched in RP long term but also suggest an influence of land disturbance, ecosystem self-restoration, and AMF life history strategies as drivers of AMF community profiles.
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Affiliation(s)
- Amandine Ducousso-Détrez
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV), Université du Littoral Côte d’Opale, UR 4492, SFR Condorcet FR CNRS 3417, CEDEX, 62228 Calais, France
- Institut de Recherche en Biologie Végétale (IRBV), 3 AgroBioSciences, Université de Montréal, Montréal, QC H1X 2B2, Canada
| | - Robin Raveau
- INRAE, UMR SAVE, Bordeaux Science Agro, ISVV, 33882 Villenave d’Ornon, France
| | - Joël Fontaine
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV), Université du Littoral Côte d’Opale, UR 4492, SFR Condorcet FR CNRS 3417, CEDEX, 62228 Calais, France
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale (IRBV), 3 AgroBioSciences, Université de Montréal, Montréal, QC H1X 2B2, Canada
- African Genome Center, Mohammed VI Polytechnic University (UM6P), Ben Guerir 43150, Morocco
| | - Anissa Lounès-Hadj Sahraoui
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV), Université du Littoral Côte d’Opale, UR 4492, SFR Condorcet FR CNRS 3417, CEDEX, 62228 Calais, France
- Correspondence:
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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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Rasmussen PU, Abrego N, Roslin T, Öpik M, Sepp S, Blanchet FG, Huotari T, Hugerth LW, Tack AJM. Elevation and plant species identity jointly shape a diverse arbuscular mycorrhizal fungal community in the High Arctic. THE NEW PHYTOLOGIST 2022; 236:671-683. [PMID: 35751540 PMCID: PMC9796444 DOI: 10.1111/nph.18342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
Knowledge about the distribution and local diversity patterns of arbuscular mycorrhizal (AM) fungi are limited for extreme environments such as the Arctic, where most studies have focused on spore morphology or root colonization. We here studied the joint effects of plant species identity and elevation on AM fungal distribution and diversity. We sampled roots of 19 plant species in 18 locations in Northeast Greenland, using next generation sequencing to identify AM fungi. We studied the joint effect of plant species, elevation and selected abiotic conditions on AM fungal presence, richness and composition. We identified 29 AM fungal virtual taxa (VT), of which six represent putatively new VT. Arbuscular mycorrhizal fungal presence increased with elevation, and as vegetation cover and the active soil layer decreased. Arbuscular mycorrhizal fungal composition was shaped jointly by elevation and plant species identity. We demonstrate that the Arctic harbours a relatively species-rich and nonrandomly distributed diversity of AM fungi. Given the high diversity and general lack of knowledge exposed herein, we encourage further research into the diversity, drivers and functional role of AM fungi in the Arctic. Such insight is urgently needed for an area with some of the globally highest rates of climate change.
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Affiliation(s)
- Pil U. Rasmussen
- Department of Ecology, Environment and Plant SciencesStockholm UniversitySE‐106 91StockholmSweden
- The National Research Centre for the Working Environment105 Lersø ParkalléDK‐2100CopenhagenDenmark
| | - Nerea Abrego
- Department of Agricultural SciencesUniversity of HelsinkiPO Box 27, (Latokartanonkaari 5)HelsinkiFI‐00014Finland
| | - Tomas Roslin
- Department of Agricultural SciencesUniversity of HelsinkiPO Box 27, (Latokartanonkaari 5)HelsinkiFI‐00014Finland
- Department of EcologySwedish University of Agricultural SciencesBox 7044UppsalaSE‐750 07Sweden
| | - Maarja Öpik
- Department of BotanyUniversity of Tartu40 Lai StreetTartu51005Estonia
| | - Siim‐Kaarel Sepp
- Department of BotanyUniversity of Tartu40 Lai StreetTartu51005Estonia
| | - F. Guillaume Blanchet
- Département de Biologie, Faculté des SciencesUniversité de Sherbrooke2500 Boulevard UniversitéSherbrookeQCJ1K 2R1Canada
- Département de Mathématiques, Faculté des SciencesUniversité de Sherbrooke2500 Boulevard UniversitéSherbrookeQCJ1K 2R1Canada
- Département des Sciences de la Santé Communautaire, Faculté de Médecine et des Sciences de la SantéUniversité de Sherbrooke3001 12 Avenue NordSherbrookeQCJ1H 5N4Canada
| | - Tea Huotari
- Department of Agricultural SciencesUniversity of HelsinkiPO Box 27, (Latokartanonkaari 5)HelsinkiFI‐00014Finland
| | - Luisa W. Hugerth
- Department of Molecular, Tumor and Cell Biology, Science for Life Laboratory, Center for Translational Microbiome ResearchKarolinska InstitutetSE‐171 65SolnaSweden
| | - Ayco J. M. Tack
- Department of Ecology, Environment and Plant SciencesStockholm UniversitySE‐106 91StockholmSweden
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Albornoz FE, Ryan MH, Bending GD, Hilton S, Dickie IA, Gleeson DB, Standish RJ. Agricultural land-use favours Mucoromycotinian, but not Glomeromycotinian, arbuscular mycorrhizal fungi across ten biomes. THE NEW PHYTOLOGIST 2022; 233:1369-1382. [PMID: 34618929 DOI: 10.1111/nph.17780] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 09/19/2021] [Indexed: 05/26/2023]
Abstract
Globally, agricultural land-use negatively affects soil biota that contribute to ecosystem functions such as nutrient cycling, yet arbuscular mycorrhizal fungi (AMF) are promoted as essential components of agroecosystems. Arbuscular mycorrhizal fungi include Glomeromycotinian AMF (G-AMF) and the arbuscule-producing fine root endophytes, recently re-classified into the Endogonales order within Mucoromycotina. The correct classification of Mucoromycotinian AMF (M-AMF) and the availability of new molecular tools can guide research to better the understanding of their diversity and ecology. To investigate the impact on G-AMF and M-AMF of agricultural land-use at a continental scale, we sampled DNA from paired farm and native sites across 10 Australian biomes. Glomeromycotinian AMF were present in both native and farm sites in all biomes. Putative M-AMF were favoured by farm sites, rare or absent in native sites, and almost entirely absent in tropical biomes. Temperature, rainfall, and soil pH were strong drivers of richness and community composition of both groups, and plant richness was an important mediator. Both fungal groups occupy different, but overlapping, ecological niches, with M-AMF thriving in temperate agricultural landscapes. Our findings invite exploration of the origin and spread of M-AMF and continued efforts to resolve the phylogeny of this newly reclassified group of AMF.
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Affiliation(s)
- Felipe E Albornoz
- Commonwealth Scientific and Industrial Research Organisation, Land and Water, Wembley, WA, 6913, Australia
- Institute of Agriculture, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Hwy, Crawley (Perth), WA, 6009, Australia
| | - Megan H Ryan
- Institute of Agriculture, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Hwy, Crawley (Perth), WA, 6009, Australia
| | - Gary D Bending
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Sally Hilton
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Ian A Dickie
- Bio-Protection Research Centre, School of Biological Science, University of Canterbury, Christchurch, 8041, New Zealand
| | - Deirdre B Gleeson
- Institute of Agriculture, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Hwy, Crawley (Perth), WA, 6009, Australia
| | - Rachel J Standish
- Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
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Davison J, Moora M, Semchenko M, Adenan SB, Ahmed T, Akhmetzhanova AA, Alatalo JM, Al-Quraishy S, Andriyanova E, Anslan S, Bahram M, Batbaatar A, Brown C, Bueno CG, Cahill J, Cantero JJ, Casper BB, Cherosov M, Chideh S, Coelho AP, Coghill M, Decocq G, Dudov S, Fabiano EC, Fedosov VE, Fraser L, Glassman SI, Helm A, Henry HAL, Hérault B, Hiiesalu I, Hiiesalu I, Hozzein WN, Kohout P, Kõljalg U, Koorem K, Laanisto L, Mander Ü, Mucina L, Munyampundu JP, Neuenkamp L, Niinemets Ü, Nyamukondiwa C, Oja J, Onipchenko V, Pärtel M, Phosri C, Põlme S, Püssa K, Ronk A, Saitta A, Semboli O, Sepp SK, Seregin A, Sudheer S, Peña-Venegas CP, Paz C, Vahter T, Vasar M, Veraart AJ, Tedersoo L, Zobel M, Öpik M. Temperature and pH define the realised niche space of arbuscular mycorrhizal fungi. THE NEW PHYTOLOGIST 2021; 231:763-776. [PMID: 33507570 DOI: 10.1111/nph.17240] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 01/19/2021] [Indexed: 05/26/2023]
Abstract
The arbuscular mycorrhizal (AM) fungi are a globally distributed group of soil organisms that play critical roles in ecosystem function. However, the ecological niches of individual AM fungal taxa are poorly understood. We collected > 300 soil samples from natural ecosystems worldwide and modelled the realised niches of AM fungal virtual taxa (VT; approximately species-level phylogroups). We found that environmental and spatial variables jointly explained VT distribution worldwide, with temperature and pH being the most important abiotic drivers, and spatial effects generally occurring at local to regional scales. While dispersal limitation could explain some variation in VT distribution, VT relative abundance was almost exclusively driven by environmental variables. Several environmental and spatial effects on VT distribution and relative abundance were correlated with phylogeny, indicating that closely related VT exhibit similar niche optima and widths. Major clades within the Glomeraceae exhibited distinct niche optima, Acaulosporaceae generally had niche optima in low pH and low temperature conditions, and Gigasporaceae generally had niche optima in high precipitation conditions. Identification of the realised niche space occupied by individual and phylogenetic groups of soil microbial taxa provides a basis for building detailed hypotheses about how soil communities respond to gradients and manipulation in ecosystems worldwide.
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Affiliation(s)
- John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Marina Semchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
- School of Earth and Environmental Sciences, University of Manchester, Manchester,, M13 9PL, UK
| | | | - Talaat Ahmed
- Environmental Science Centre, Qatar University, Doha, 2713, Qatar
| | - Asem A Akhmetzhanova
- Department of Ecology and Plant Geography, Faculty of Biology, Moscow Lomonsov State University, Moscow, 119991, Russia
| | - Juha M Alatalo
- Environmental Science Centre, Qatar University, Doha, 2713, Qatar
| | - Saleh Al-Quraishy
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Elena Andriyanova
- Institute of Biological Problems of the North Far East Branch of Russian Academy of Sciences, Magadan, 685000, Russia
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, 756 51, Sweden
| | - Amgaa Batbaatar
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Charlotte Brown
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - C Guillermo Bueno
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - James Cahill
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Juan José Cantero
- Instituto Multidisciplinario de Biología Vegetal, Universidad Nacional de Córdoba, CONICET, Córdoba, X5000HUA, Argentina
- Departamento de Biología Agrícola, Facultad de Agronomía y Veterinaria, Universidad Nacional de Río Cuarto, Córdoba, X5804BYA, Argentina
| | - Brenda B Casper
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104-4544, USA
| | - Mikhail Cherosov
- Institute of Biological Problems of the Cryolithozone, Siberian Branch of the Russian Academy of Sciences, Yakutsk, 677000, Russia
| | - Saida Chideh
- Département de Recherche en Sciences de l'Environnement, Université de Djibouti, Private bag 1904, Djibouti, Djibouti
| | - Ana P Coelho
- Department of Biology and CESAM, University of Aveiro, Aveiro, 3810-193, Portugal
| | - Matthew Coghill
- Department of Natural Resource Sciences, Thompson Rivers University, Kamloops, BC, V2C 0C8, Canada
| | - Guillaume Decocq
- Ecologie et Dynamique des Systèmes Anthropisés, Jules Verne University of Picardie, Amiens, F-80037, France
| | - Sergey Dudov
- Department of Ecology and Plant Geography, Faculty of Biology, Moscow Lomonsov State University, Moscow, 119991, Russia
| | - Ezequiel Chimbioputo Fabiano
- Department of Wildlife Management and Ecotourism, University of Namibia, Private bag 1096, Katima Mulilo, Namibia
| | - Vladimir E Fedosov
- Department of Ecology and Plant Geography, Faculty of Biology, Moscow Lomonsov State University, Moscow, 119991, Russia
- Botanical Garden-Institute FEB RAS, Vladivostok, 690024, Russia
| | - Lauchlan Fraser
- Department of Natural Resource Sciences, Thompson Rivers University, Kamloops, BC, V2C 0C8, Canada
| | - Sydney I Glassman
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Aveliina Helm
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Hugh A L Henry
- Department of Biology, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Bruno Hérault
- CIRAD, UPR Forêts et Sociétés, Yamoussoukro, Côte d'Ivoire
- Forêts et Sociétés, Université de Montpellier, CIRAD, Montpellier, 34000, France
- Institut National Polytechnique Félix Houphouët-Boigny, INP-HB, Yamoussoukro, Côte d'Ivoire
| | - Indrek Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Inga Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Wael N Hozzein
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Bani Suwayf, 62511, Egypt
| | - Petr Kohout
- Institute of Microbiology, Czech Academy of Science, Prague, 14220, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, 12843, Czechia
| | - Urmas Kõljalg
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Kadri Koorem
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Lauri Laanisto
- Chair of Biodiversity and Nature Tourism, Estonian University of Life Sciences, Tartu, 51006, Estonia
| | - Ülo Mander
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Ladislav Mucina
- Iluka Chair in Vegetation Science and Biogeography, Harry Butler Institute, Murdoch University, Murdoch, Perth, WA, 6150, Australia
- Department of Geography & Environmental Studies, Stellenbosch University, Stellenbosch, 7602, South Africa
| | - Jean-Pierre Munyampundu
- School of Science, College of Science and Technology, University of Rwanda, Kigali, 3900, Rwanda
| | - Lena Neuenkamp
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
- Institute of Plant Sciences, University of Bern, Bern, 3013, Switzerland
| | - Ülo Niinemets
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, Tartu, 51006, Estonia
| | - Casper Nyamukondiwa
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private bag 16, Palapye, Botswana
| | - Jane Oja
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Vladimir Onipchenko
- Department of Ecology and Plant Geography, Faculty of Biology, Moscow Lomonsov State University, Moscow, 119991, Russia
| | - Meelis Pärtel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Cherdchai Phosri
- Department of Biology, Nakhon Phanom University, Nakhon Phanom, 48000, Thailand
| | - Sergei Põlme
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
- Natural History Museum, University of Tartu, Tartu, 51014, Estonia
| | - Kersti Püssa
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Argo Ronk
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104-4544, USA
| | - Alessandro Saitta
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Palermo, 90128, Italy
| | - Olivia Semboli
- Center of Studies and Research on Pharmacopoeia and Traditional African Medicine, University of Bangui, Bangui, Central African Republic
| | - Siim-Kaarel Sepp
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Alexey Seregin
- Department of Ecology and Plant Geography, Faculty of Biology, Moscow Lomonsov State University, Moscow, 119991, Russia
| | - Surya Sudheer
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Clara P Peña-Venegas
- Instituto Amazónico de Investigaciones Científicas Sinchi, Leticia, Amazonas, 910001, Colombia
| | - Claudia Paz
- Departamento de Biodiversidade, Universidade Estadual Paulista, Rio Claro, São Paulo, 13506-900, Brazil
| | - Tanel Vahter
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Martti Vasar
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Annelies J Veraart
- Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Nijmegen, 6525AJ, the Netherlands
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Martin Zobel
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
- Department of Botany, University of Tartu, Tartu, 51005, Estonia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
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11
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Vasar M, Davison J, Neuenkamp L, Sepp SK, Young JPW, Moora M, Öpik M. User-friendly bioinformatics pipeline gDAT (graphical downstream analysis tool) for analysing rDNA sequences. Mol Ecol Resour 2021; 21:1380-1392. [PMID: 33527735 DOI: 10.1111/1755-0998.13340] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/19/2021] [Accepted: 01/21/2021] [Indexed: 01/04/2023]
Abstract
High-throughput sequencing (HTS) of multiple organisms in parallel (metabarcoding) has become a routine and cost-effective method for the analysis of microbial communities in environmental samples. However, careful data treatment is required to identify potential errors in HTS data, and the large volume of data generated by HTS requires in-house experience with command line tools for downstream analysis. This paper introduces a pipeline that incorporates the most common command line tools into an easy-to-use graphical interface-gDAT. By using the Python scripting language, the pipeline is compatible with the latest Windows, macOS and Linux operating systems. The pipeline supports analysis of Sanger, 454, IonTorrent, Illumina and PacBio sequences, allows custom modification of quality filtering steps, and implements both open and closed-reference operational taxonomic unit-picking for sequence identification. Predefined parameters are optimized for analysis of small subunit (SSU) rRNA gene amplicons from arbuscular mycorrhizal fungi, but the pipeline is widely applicable to metabarcoding studies targeting a broad range of organisms. The pipeline was additionally tested with data using general eukaryotic primers from the SSU gene region and fungal primers from the internal transcribed spacer (ITS) marker region. We describe the pipeline design and evaluate its performance and speed by conducting analysis of example data sets using different marker regions sequenced on Illumina platforms. The graphical interface, with the option to use the command line if needed, provides an accessible tool for rapid data analysis with repeatability and logging capabilities. Keeping the software open-source maximizes code accessibility, allowing scrutiny and bug fixes by the community.
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Affiliation(s)
- Martti Vasar
- Department of Botany, University of Tartu, Tartu, Estonia
| | - John Davison
- Department of Botany, University of Tartu, Tartu, Estonia
| | - Lena Neuenkamp
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | | | | | - Mari Moora
- Department of Botany, University of Tartu, Tartu, Estonia
| | - Maarja Öpik
- Department of Botany, University of Tartu, Tartu, Estonia
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12
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Arbuscular Mycorrhizal Fungal Communities in the Soils of Desert Habitats. Microorganisms 2021; 9:microorganisms9020229. [PMID: 33499315 PMCID: PMC7912695 DOI: 10.3390/microorganisms9020229] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 12/25/2022] Open
Abstract
Deserts cover a significant proportion of the Earth’s surface and continue to expand as a consequence of climate change. Mutualistic arbuscular mycorrhizal (AM) fungi are functionally important plant root symbionts, and may be particularly important in drought stressed systems such as deserts. Here we provide a first molecular characterization of the AM fungi occurring in several desert ecosystems worldwide. We sequenced AM fungal DNA from soil samples collected from deserts in six different regions of the globe using the primer pair WANDA-AML2 with Illumina MiSeq. We recorded altogether 50 AM fungal phylotypes. Glomeraceae was the most common family, while Claroideoglomeraceae, Diversisporaceae and Acaulosporaceae were represented with lower frequency and abundance. The most diverse site, with 35 virtual taxa (VT), was in the Israeli Negev desert. Sites representing harsh conditions yielded relatively few reads and low richness estimates, for example, a Saudi Arabian desert site where only three Diversispora VT were recorded. The AM fungal taxa recorded in the desert soils are mostly geographically and ecologically widespread. However, in four sites out of six, communities comprised more desert-affiliated taxa (according to the MaarjAM database) than expected at random. AM fungal VT present in samples were phylogenetically clustered compared with the global taxon pool, suggesting that nonrandom assembly processes, notably habitat filtering, may have shaped desert fungal assemblages.
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13
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Neuenkamp L, Zobel M, Koorem K, Jairus T, Davison J, Öpik M, Vasar M, Moora M. Light availability and light demand of plants shape the arbuscular mycorrhizal fungal communities in their roots. Ecol Lett 2020; 24:426-437. [PMID: 33319429 DOI: 10.1111/ele.13656] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 01/01/2023]
Abstract
Plants involved in the arbuscular mycorrhizal (AM) symbiosis trade photosynthetically derived carbon for fungal-provided soil nutrients. However, little is known about how plant light demand and ambient light conditions influence root-associating AM fungal communities. We conducted a manipulative field experiment to test whether plants' shade-tolerance influences their root AM fungal communities in open and shaded grassland sites. We found similar light-dependent shifts in AM fungal community structure for experimental bait plant roots and the surrounding soil. Yet, deviation from the surrounding soil towards lower AM fungal beta-diversity in the roots of shade-intolerant plants in shade suggested preferential carbon allocation to specific AM fungi in conditions where plant-assimilated carbon available to fungi was limited. We conclude that favourable environmental conditions widen the plant biotic niche, as demonstrated here with optimal light availability reducing plants' selectivity for specific AM fungi, and promote compatibility with a larger number of AM fungal taxa.
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Affiliation(s)
- Lena Neuenkamp
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia.,Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, 3013, Switzerland
| | - Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Kadri Koorem
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Teele Jairus
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Martti Vasar
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
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14
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Davison J, García de León D, Zobel M, Moora M, Bueno CG, Barceló M, Gerz M, León D, Meng Y, Pillar VD, Sepp SK, Soudzilovaskaia NA, Tedersoo L, Vaessen S, Vahter T, Winck B, Öpik M. Plant functional groups associate with distinct arbuscular mycorrhizal fungal communities. THE NEW PHYTOLOGIST 2020; 226:1117-1128. [PMID: 31943225 DOI: 10.1111/nph.16423] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/24/2019] [Indexed: 05/26/2023]
Abstract
The benefits of the arbuscular mycorrhizal (AM) symbiosis between plants and fungi are modulated by the functional characteristics of both partners. However, it is unknown to what extent functionally distinct groups of plants naturally associate with different AM fungi. We reanalysed 14 high-throughput sequencing data sets describing AM fungal communities associating with plant individuals (2427) belonging to 297 species. We examined how root-associating AM fungal communities varied between plants with different growth forms, photosynthetic pathways, CSR (competitor, stress-tolerator, ruderal) strategies, mycorrhizal statuses and N-fixing statuses. AM fungal community composition differed in relation to all studied plant functional groups. Grasses, C4 and nonruderal plants were characterised by high AM fungal alpha diversity, while C4 , ruderal and obligately mycorrhizal plants were characterised by high beta diversity. The phylogenetic diversity of AM fungi, a potential surrogate for functional diversity, was higher among forbs than other plant growth forms. Putatively ruderal (previously cultured) AM fungi were disproportionately associated with forbs and ruderal plants. There was phylogenetic correlation among AM fungi in the degree of association with different plant growth forms and photosynthetic pathways. Associated AM fungal communities constitute an important component of plant ecological strategies. Functionally different plants associate with distinct AM fungal communities, linking mycorrhizal associations with functional diversity in ecosystems.
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Affiliation(s)
- John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - David García de León
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
- Department of Life Sciences, University of Alcalá, Alcalá de Henares, 28805, Spain
| | - Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
- College of Science, King Saud University, Riyadh, 11451, Kingdom of Saudi Arabia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - C Guillermo Bueno
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Milagros Barceló
- Environmental Biology Department, Institute of Environmental Sciences Leiden University, Einsteinweg 2, Leiden, 2333CC, the Netherlands
| | - Maret Gerz
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Daniela León
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Yiming Meng
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Valerio D Pillar
- Department of Ecology, Universidade Federal do Rio Grande do Sul, 9500, Porto Alegre, 91501-970, Brazil
| | - Siim-Kaarel Sepp
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Nadejda A Soudzilovaskaia
- Environmental Biology Department, Institute of Environmental Sciences Leiden University, Einsteinweg 2, Leiden, 2333CC, the Netherlands
| | - Leho Tedersoo
- Natural History Museum, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia
| | - Stijn Vaessen
- Environmental Biology Department, Institute of Environmental Sciences Leiden University, Einsteinweg 2, Leiden, 2333CC, the Netherlands
| | - Tanel Vahter
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Bruna Winck
- Department of Ecology, Universidade Federal do Rio Grande do Sul, 9500, Porto Alegre, 91501-970, Brazil
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
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15
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Wang Z, Li Y, Li T, Zhao D, Liao Y. Conservation tillage decreases selection pressure on community assembly in the rhizosphere of arbuscular mycorrhizal fungi. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 710:136326. [PMID: 31923682 DOI: 10.1016/j.scitotenv.2019.136326] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/21/2019] [Accepted: 12/23/2019] [Indexed: 06/10/2023]
Abstract
Different tillage practices elicit various degrees of soil disturbance and significantly affect the community structure of soil microbes, especially rhizosphere microbes. However, little is known about the effects of tillage on community assembly and composition in the rhizosphere of arbuscular mycorrhizal fungi (RAMF). In this study, we investigated wheat RAMF communities under long-term different tillage patterns in an agroecosystem. The results showed that soil disturbance caused by tillage resulted in significant changes in RAMF communities, and this change varied with the degree of disturbance. Soil total nitrogen was the most relevant abiotic factor to RAMF communities. Notably, as a biotic selection factor, we found that cohesion of communities could also explain the changes in RAMF taxonomic and phylogenetic composition, which have not been revealed by other studies. Meanwhile, by analyzing the RAMF community assembly process under tillage practices, we found that stochastic processes dominated the assembly of RAMF communities under different tillage practices, and with the reduction of disturbance degree, the process occupied an increasingly important position. Overall, the structure and assembly process of the RAMF community in the rhizosphere varied with the degree of soil disturbance caused by tillage. These findings may provide more insights on underground processes and aid in the development of conservation tillage as a sustainable agricultural practice.
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Affiliation(s)
- Ziting Wang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, PR China; State Key Laboratory for Conservation & Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi 530004, PR China; Guangxi Key Laboratory of Sugarcane Biology, Nanning, Guangxi 530004, PR China
| | - Yüze Li
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Tong Li
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Deqiang Zhao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Yuncheng Liao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
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16
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Pellegrino E, Gamper HA, Ciccolini V, Ercoli L. Forage Rotations Conserve Diversity of Arbuscular Mycorrhizal Fungi and Soil Fertility. Front Microbiol 2020; 10:2969. [PMID: 31998261 PMCID: PMC6962183 DOI: 10.3389/fmicb.2019.02969] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 12/09/2019] [Indexed: 01/07/2023] Open
Abstract
In the Mediterranean, long-term impact of typical land uses on soil fertility have not been quantified yet on replicated mixed crop-livestock farms and considering the variability of soil texture. Here, we report the effects, after 15 years of practice, of two legume-winter cereal rotations, olive orchards and vineyards on microbiological and chemical indicators of soil fertility and the communities of arbuscular mycorrhizal fungi (AMF). We compare the changes among these four agricultural land-use types to woodland reference sites. Root colonization by AMF of English ryegrass (Lolium perenne L.), a grass that occurred under all land use types, was only half as heavy in biannual berseem clover (Trifolium alexandrinum L.)-winter cereal rotations than in 4-year alfalfa (Medicago sativa L.)-winter cereal rotations. In olive (Olea europaea L.) orchards and vineyards (Vitis vinifera L.), where weeds are controlled by frequent surface tillage, the AMF root colonization of ryegrass was again much lower than in the legume-cereal rotations and at the woodland reference sites. All the microbial parameters and soil organic carbon correlated most strongly with differences in occurrence and relative abundance (β-diversity) of AMF genera in soil. The soil pH and mineral nutrients in soil strongly correlated with differences in AMF root colonization and AMF genus richness (α-diversity) in soil. Diversity of AMF was much less affected by soil texture than land use, while the opposite was true for microbial and chemical soil fertility indicators. Land uses that guaranteed a continuous ground cover of herbaceous plants and that involved only infrequent tillage, such as multiyear alfalfa-winter cereal rotation, allowed members of the AMF genus Scutellospora to persist and remain abundant. On the contrary, under land uses accompanied by frequent tillage and hence discontinuous presence of herbaceous plants, such as tilled olive orchard and vineyard, members of the genus Funneliformis dominated. These results suggest that multiyear alfalfa-winter cereal rotation with active plant growth throughout the year is the least detrimental agricultural land use in soil carbon and AMF abundance and diversity, relative to the woodland reference.
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Affiliation(s)
- Elisa Pellegrino
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy
| | - Hannes A. Gamper
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy
| | | | - Laura Ercoli
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy
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Atunnisa R, Ezawa T. Nestedness in Arbuscular Mycorrhizal Fungal Communities in a Volcanic Ecosystem: Selection of Disturbance-tolerant Fungi along an Elevation Gradient. Microbes Environ 2019; 34:327-333. [PMID: 31413228 PMCID: PMC6759341 DOI: 10.1264/jsme2.me19073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Arbuscular mycorrhizal (AM) fungi play a significant role in the establishment and resilience of vegetation in harsh environments, such as volcanic slopes, in which soil is frequently disturbed by ash falling and erosion. We characterized AM fungal communities associated with a pioneer grass in a volcanic slope based on the disturbance tolerance of the fungi, addressing the hypothesis that soil disturbance is a major ecological filter for AM fungi in volcanic ecosystems and, thus, fungi that are more tolerant to soil disturbance are selected at higher elevations (i.e. nearer to the crater). Paired soil-core samples were collected from the rhizosphere of Miscanthus sinensis between the vegetation limit and forest limit on a volcanic slope and used in a trap culture with M. sinensis seedlings, in which one of the paired samples was sieved to destroy hyphal networks (disturbance treatment), while the other was not (intact treatment). Seedlings were grown in a greenhouse for two months, and the roots were subjected to molecular analysis of fungal communities. AM fungal diversity decreased with increasing elevations, in which nested structure was observed. Community dissimilarity between the disturbed and intact communities decreased with increasing elevations, suggesting that communities at higher elevations were more robust against soil disturbance. These results suggest that AM fungi that are more tolerant to soil disturbance are more widely distributed across the ecosystem, that is, they are generalists. The wide distribution of disturbance-tolerant fungi may have significant implications for the rapid resilience of vegetation after disturbance in the ecosystem.
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Gerz M, Bueno CG, Ozinga WA, Zobel M, Moora M. Responses of plant community mycorrhization to anthropogenic influence depend on the habitat and mycorrhizal type. OIKOS 2019. [DOI: 10.1111/oik.06272] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maret Gerz
- Dept of Botany, Inst. of Ecology and Earth Sciences, Univ. of Tartu Lai 40 EE‐Tartu 51005 Estonia
| | - C. Guillermo Bueno
- Dept of Botany, Inst. of Ecology and Earth Sciences, Univ. of Tartu Lai 40 EE‐Tartu 51005 Estonia
| | - Wim A. Ozinga
- Experimental Plant Ecology, Inst. for Water and Wetland Research, Radboud Univ. Nijmegen Nijmegen the Netherlands
- Forest and Landscape Ecology, Wageningen Environmental Research (Alterra) Wageningen the Netherlands
| | - Martin Zobel
- Dept of Botany, Inst. of Ecology and Earth Sciences, Univ. of Tartu Lai 40 EE‐Tartu 51005 Estonia
| | - Mari Moora
- Dept of Botany, Inst. of Ecology and Earth Sciences, Univ. of Tartu Lai 40 EE‐Tartu 51005 Estonia
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Andrew C, Büntgen U, Egli S, Senn‐Irlet B, Grytnes J, Heilmann‐Clausen J, Boddy L, Bässler C, Gange AC, Heegaard E, Høiland K, Kirk PM, Krisai‐Greilhüber I, Kuyper TW, Kauserud H. Open-source data reveal how collections-based fungal diversity is sensitive to global change. APPLICATIONS IN PLANT SCIENCES 2019; 7:e01227. [PMID: 30937219 PMCID: PMC6426159 DOI: 10.1002/aps3.1227] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 10/29/2018] [Indexed: 05/30/2023]
Abstract
PREMISE OF THE STUDY Fungal diversity (richness) trends at large scales are in urgent need of investigation, especially through novel situations that combine long-term observational with environmental and remotely sensed open-source data. METHODS We modeled fungal richness, with collections-based records of saprotrophic (decaying) and ectomycorrhizal (plant mutualistic) fungi, using an array of environmental variables across geographical gradients from northern to central Europe. Temporal differences in covariables granted insight into the impacts of the shorter- versus longer-term environment on fungal richness. RESULTS Fungal richness varied significantly across different land-use types, with highest richness in forests and lowest in urban areas. Latitudinal trends supported a unimodal pattern in diversity across Europe. Temperature, both annual mean and range, was positively correlated with richness, indicating the importance of seasonality in increasing richness amounts. Precipitation seasonality notably affected saprotrophic fungal diversity (a unimodal relationship), as did daily precipitation of the collection day (negatively correlated). Ectomycorrhizal fungal richness differed from that of saprotrophs by being positively associated with tree species richness. DISCUSSION Our results demonstrate that fungal richness is strongly correlated with land use and climate conditions, especially concerning seasonality, and that ongoing global change processes will affect fungal richness patterns at large scales.
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Affiliation(s)
- Carrie Andrew
- Swiss Federal Research Institute WSLCH‐8903BirmensdorfSwitzerland
- Section for Genetics and Evolutionary Biology (EVOGENE)University of OsloBlindernveien 310316OsloNorway
| | - Ulf Büntgen
- Swiss Federal Research Institute WSLCH‐8903BirmensdorfSwitzerland
- Department of GeographyUniversity of CambridgeCB2 3ENCambridgeUnited Kingom
- Global Change Research Centre and Masaryk University613 00BrnoCzech Republic
| | - Simon Egli
- Swiss Federal Research Institute WSLCH‐8903BirmensdorfSwitzerland
| | | | - John‐Arvid Grytnes
- Department of Biological SciencesUniversity of BergenP.O. Box 7803N‐5020BergenNorway
| | - Jacob Heilmann‐Clausen
- Centre for Macroecology, Evolution and ClimateNatural History Museum of DenmarkUniversity of CopenhagenDK‐2100CopenhagenDenmark
| | - Lynne Boddy
- School of BiosciencesCardiff UniversityMuseum AvenueCardiffCF10 3AXUnited Kingdom
| | - Claus Bässler
- Bavarian Forest National ParkFreyunger Str. 294481GrafenauGermany
- Chair for Terrestrial EcologyTechnical University of MunichHans‐Carl‐von‐Carlowitz‐Platz 285354FreisingGermany
| | - Alan C. Gange
- School of Biological SciencesRoyal HollowayUniversity of LondonEghamSurreyTW20 0EXUnited Kingdom
| | - Einar Heegaard
- Forestry and Forest ResourcesNorwegian Institute of Bioeconomy ResearchFanaflaten 4N‐5244FanaNorway
| | - Klaus Høiland
- Section for Genetics and Evolutionary Biology (EVOGENE)University of OsloBlindernveien 310316OsloNorway
| | - Paul M. Kirk
- Mycology SectionJodrell LaboratoryRoyal Botanic GardenKew, RichmondSurreyTW9 3DSUnited Kingdom
| | | | - Thomas W. Kuyper
- Department of Soil QualityWageningen UniversityP.O. Box 476700 AAWageningenThe Netherlands
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EVOGENE)University of OsloBlindernveien 310316OsloNorway
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Cotton TEA. Arbuscular mycorrhizal fungal communities and global change: an uncertain future. FEMS Microbiol Ecol 2018; 94:5096018. [DOI: 10.1093/femsec/fiy179] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 09/10/2018] [Indexed: 01/13/2023] Open
Affiliation(s)
- TE Anne Cotton
- Department of Animal and Plant Sciences, Alfred Denny Building, Western Bank, The University of Sheffield, Sheffield, South Yorkshire, S10 2TN, UK
- Plant Production and Protection (P3) Institute for Translational Plant and Soil Biology, Department of Animal and Plant Sciences, Alfred Denny Building, Western Bank, The University of Sheffield, Sheffield, South Yorkshire, S10 2TN, UK
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Arbuscular mycorrhizal fungal communities in tropical rain forest are resilient to slash-and-burn agriculture. JOURNAL OF TROPICAL ECOLOGY 2018. [DOI: 10.1017/s0266467418000184] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract:Certain forestry and agricultural practices are known to affect arbuscular mycorrhizal (AM) fungal communities, but the effects of deforestation – including slash-and-burn management and other more severe disturbances – in tropical rain forests are poorly understood. We addressed the effects of anthropogenic disturbance on rain-forest AM fungal communities in French Guiana, by comparing mature tropical rain forest, slash-and-burn (5 y old) and clearcut areas (8 y old). A total of 36 soil samples were collected in six plots and sequenced using a high throughput 454-pyrosequencing platform. A total of 32649 sequences from 103 AM fungal virtual taxa (VT) were recorded. Whereas alpha diversity of AM fungi did not decrease due to land-use intensification, with average richness ranging from 17 to 21 taxa per plot, beta diversity (average distance to multivariate centroid) dropped by 28% from 0.46 in rain forest to 0.33 under clearcutting. AM fungal community composition was correlated with land use and soil chemical properties. Clearcut areas were characterized by the more frequent occurrence of specialist AM fungi, compared with mature forest or slash-and-burn areas. Specifically, clearcuts contained the highest proportions of VT that were geographic (21%), habitat (31%), abundance (97%) or host (97%) specialists based on VT metadata contained in the MaarjAM database. This suggests that certain AM fungi with narrow ecological niches have traits that allow them to exploit conditions of severe disturbance. In conclusion, slash-and-burn management appears to allow diverse AM fungal communities to persist, and may favour regeneration of tropical rain forest after abandonment. More severe disturbance in the form of clearcutting resulted in marked changes in AM fungal communities.
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