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Maurice K, Laurent-Webb L, Bourceret A, Boivin S, Boukcim H, Selosse MA, Ducousso M. Networking the desert plant microbiome, bacterial and fungal symbionts structure and assortativity in co-occurrence networks. ENVIRONMENTAL MICROBIOME 2024; 19:65. [PMID: 39223675 PMCID: PMC11370318 DOI: 10.1186/s40793-024-00610-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024]
Abstract
In nature, microbes do not thrive in seclusion but are involved in complex interactions within- and between-microbial kingdoms. Among these, symbiotic associations with mycorrhizal fungi and nitrogen-fixing bacteria are namely known to improve plant health, while providing resources to benefit other microbial members. Yet, it is not clear how these microbial symbionts interact with each other or how they impact the microbiota network architecture. We used an extensive co-occurrence network analysis, including rhizosphere and roots samples from six plant species in a natural desert in AlUla region (Kingdom of Saudi Arabia) and described how these symbionts were structured within the plant microbiota network. We found that the plant species was a significant driver of its microbiota composition and also of the specificity of its interactions in networks at the microbial taxa level. Despite this specificity, a motif was conserved across all networks, i.e., mycorrhizal fungi highly covaried with other mycorrhizal fungi, especially in plant roots-this pattern is known as assortativity. This structural property might reflect their ecological niche preference or their ability to opportunistically colonize roots of plant species considered non symbiotic e.g., H. salicornicum, an Amaranthaceae. Furthermore, these results are consistent with previous findings regarding the architecture of the gut microbiome network, where a high level of assortativity at the level of bacterial and fungal orders was also identified, suggesting the existence of general rules of microbiome assembly. Otherwise, the bacterial symbionts Rhizobiales and Frankiales covaried with other bacterial and fungal members, and were highly structural to the intra- and inter-kingdom networks. Our extensive co-occurrence network analysis of plant microbiota and study of symbiont assortativity, provided further evidence on the importance of bacterial and fungal symbionts in structuring the global plant microbiota network.
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Affiliation(s)
- Kenji Maurice
- Cirad-UMR AGAP, Univ Montpellier, INRAE, 34398, Montpellier Cedex 5, France.
| | - Liam Laurent-Webb
- Institut de Systématique, Évolution, Biodiversité (UMR 7205 - CNRS, MNHN, UPMC, EPHE), Muséum National d'Histoire Naturelle, Sorbonne Universités, 57 Rue Cuvier, 75005, Paris, France
| | - Amélia Bourceret
- Institut de Systématique, Évolution, Biodiversité (UMR 7205 - CNRS, MNHN, UPMC, EPHE), Muséum National d'Histoire Naturelle, Sorbonne Universités, 57 Rue Cuvier, 75005, Paris, France
| | - Stéphane Boivin
- Department of Research and Development, VALORHIZ, Montpellier, France
| | - Hassan Boukcim
- Department of Research and Development, VALORHIZ, Montpellier, France
- ASARI, Mohammed VI Polytechnic University, Laayoune, Morocco
| | - Marc-André Selosse
- Institut de Systématique, Évolution, Biodiversité (UMR 7205 - CNRS, MNHN, UPMC, EPHE), Muséum National d'Histoire Naturelle, Sorbonne Universités, 57 Rue Cuvier, 75005, Paris, France
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307, Gdansk, Poland
- Institut Universitaire de France, Paris, France
| | - Marc Ducousso
- Cirad-UMR AGAP, Univ Montpellier, INRAE, 34398, Montpellier Cedex 5, France
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2
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Moukarzel R, Jones EE, Panda P, Larrouy J, Ramana JV, Guerin-Laguette A, Ridgway HJ. Vineyard management systems influence arbuscular mycorrhizal fungi recruitment by grapevine rootstocks in New Zealand. J Appl Microbiol 2024; 135:lxae211. [PMID: 39147565 DOI: 10.1093/jambio/lxae211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 08/08/2024] [Accepted: 08/13/2024] [Indexed: 08/17/2024]
Abstract
AIMS Arbuscular mycorrhizal fungi (AMF) can perform significant functions within sustainable agricultural ecosystems, including vineyards. Increased AMF diversity can be beneficial in promoting plant growth and increasing resilience to environmental changes. To effectively utilize AMF communities and their benefits in vineyard ecosystems, a better understanding of how management systems influence AMF community composition is needed. Moreover, it is unknown whether AMF communities in organically managed vineyards are distinct from those in conventionally managed vineyards. METHODS AND RESULTS In this study, vineyards were surveyed across the Marlborough region, New Zealand to identify the AMF communities colonizing the roots of different rootstocks grafted with Sauvignon Blanc and Pinot Noir in both conventional and organic systems. The AMF communities were identified based on spores isolated from trap cultures established with the collected grapevine roots, and by next-generation sequencing technologies (Illumina MiSeq). The identified AMF species/genera belonged to Glomeraceae, Entrophosporaceae, and Diversisporaceae. The results revealed a significant difference in AMF community composition between rootstocks and in their interaction with management systems. CONCLUSIONS These outcomes indicated that vineyard management systems influence AMF recruitment by rootstocks and some rootstocks may therefore be more suited to organic systems due to the AMF communities they support. This could provide an increased benefit to organic systems by supporting higher biodiversity.
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Affiliation(s)
- Romy Moukarzel
- Department of Pest-management and Conservation, Lincoln University, PO Box 85084, Lincoln 7647, New Zealand
| | - E Eirian Jones
- Department of Pest-management and Conservation, Lincoln University, PO Box 85084, Lincoln 7647, New Zealand
| | - Preeti Panda
- The New Zealand Institute for Plant and Food Research Ltd., Private Bag 4704, Christchurch 8140, New Zealand
| | - Justine Larrouy
- The New Zealand Institute for Plant and Food Research Ltd., Private Bag 4704, Christchurch 8140, New Zealand
| | - John V Ramana
- Bioprotection Aotearoa, School of Biological Sciences, University of Canterbury, Christchurch 8041, New Zealand
- Manaaki Whenua-Landcare Research, PO Box 69040, Lincoln 7640, New Zealand
| | | | - Hayley J Ridgway
- The New Zealand Institute for Plant and Food Research Ltd., Private Bag 4704, Christchurch 8140, New Zealand
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3
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Jiang Y, Mo XY, Liu LT, Lai GZ, Qiu GW. Changes in the Arbuscular Mycorrhizal Fungal Community in the Roots of Eucalyptus grandis Plantations at Different Ages in Southern Jiangxi, China. J Fungi (Basel) 2024; 10:404. [PMID: 38921389 PMCID: PMC11204516 DOI: 10.3390/jof10060404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/25/2024] [Accepted: 06/01/2024] [Indexed: 06/27/2024] Open
Abstract
Eucalyptus roots form symbiotic relationships with arbuscular mycorrhizal (AM) fungi in soil to enhance adaptation in challenging environments. However, the evolution of the AM fungal community along a chronosequence of eucalypt plantations and its relationship with soil properties remain unclear. In this study, we evaluated the tree growth, soil properties, and root AM fungal colonization of Eucalyptus grandis W. Hill ex Maiden plantations at different ages, identified the AM fungal community composition by high-throughput sequencing, and developed a structural equation model among trees, soil, and AM fungi. Key findings include the following: (1) The total phosphorus (P) and total potassium (K) in the soil underwent an initial reduction followed by a rise with different stand ages. (2) The rate of AM colonization decreased first and then increased. (3) The composition of the AM fungal community changed significantly with different stand ages, but there was no significant change in diversity. (4) Paraglomus and Glomus were the dominant genera, accounting for 70.1% and 21.8% of the relative abundance, respectively. (5) The dominant genera were mainly influenced by soil P, the N content, and bulk density, but the main factors were different with stand ages. The results can provide a reference for fertilizer management and microbial formulation manufacture for eucalyptus plantations.
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Affiliation(s)
- Yao Jiang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Y.J.); (X.-Y.M.)
| | - Xiao-Yong Mo
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Y.J.); (X.-Y.M.)
| | - Li-Ting Liu
- Jiangxi Academy of Forestry, Nanchang 330000, China;
| | - Guo-Zhen Lai
- Jiangxi Academy of Forestry, Nanchang 330000, China;
| | - Guo-Wei Qiu
- Jinpenshan Forest Farm, Xinfeng 341600, China;
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Metzler P, Ksiazek-Mikenas K, Chaudhary VB. Tracking arbuscular mycorrhizal fungi to their source: active inoculation and passive dispersal differentially affect community assembly in urban soils. THE NEW PHYTOLOGIST 2024; 242:1814-1824. [PMID: 38294152 DOI: 10.1111/nph.19526] [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: 06/30/2023] [Accepted: 12/17/2023] [Indexed: 02/01/2024]
Abstract
Communities of arbuscular mycorrhizal (AM) fungi assemble passively over time via biotic and abiotic mechanisms. In degraded soils, AM fungal communities can assemble actively when humans manage mycorrhizas for ecosystem restoration. We investigated mechanisms of urban AM fungal community assembly in a 2-yr green roof experiment. We compared AM fungal communities in inoculated and uninoculated trays to samples from two potential sources: the inoculum and air. Active inoculation stimulated more distinct and diverse AM fungal communities, an effect that intensified over time. In the treatment trays, 45% of AM fungal taxa were detected in the inoculum, 2% were detected in aerial samples, 23% were detected in both inoculum and air, and 30% were not detected in either source. Passive dispersal of AM fungi likely resulted in the successful establishment of a small number of species, but active inoculation with native AM fungal species resulted in an immediate shift to a diverse and unique fungal community. When urban soils are constructed or modified by human activity, this is an opportunity for intervention with AM fungi that will persist and add diversity to that system.
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Affiliation(s)
- Paul Metzler
- Environmental Studies Department, Dartmouth College, Hanover, NH, 03755, USA
| | | | - V Bala Chaudhary
- Environmental Studies Department, Dartmouth College, Hanover, NH, 03755, USA
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Lekberg Y, Jansa J, McLeod M, DuPre ME, Holben WE, Johnson D, Koide RT, Shaw A, Zabinski C, Aldrich-Wolfe L. Carbon and phosphorus exchange rates in arbuscular mycorrhizas depend on environmental context and differ among co-occurring plants. THE NEW PHYTOLOGIST 2024; 242:1576-1588. [PMID: 38173184 DOI: 10.1111/nph.19501] [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: 06/29/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024]
Abstract
Phosphorus (P) for carbon (C) exchange is the pivotal function of arbuscular mycorrhiza (AM), but how this exchange varies with soil P availability and among co-occurring plants in complex communities is still largely unknown. We collected intact plant communities in two regions differing c. 10-fold in labile inorganic P. After a 2-month glasshouse incubation, we measured 32P transfer from AM fungi (AMF) to shoots and 13C transfer from shoots to AMF using an AMF-specific fatty acid. AMF communities were assessed using molecular methods. AMF delivered a larger proportion of total shoot P in communities from high-P soils despite similar 13C allocation to AMF in roots and soil. Within communities, 13C concentration in AMF was consistently higher in grass than in blanketflower (Gaillardia aristata Pursh) roots, that is P appeared more costly for grasses. This coincided with differences in AMF taxa composition and a trend of more vesicles (storage structures) but fewer arbuscules (exchange structures) in grass roots. Additionally, 32P-for-13C exchange ratios increased with soil P for blanketflower but not grasses. Contrary to predictions, AMF transferred proportionally more P to plants in communities from high-P soils. However, the 32P-for-13C exchange differed among co-occurring plants, suggesting differential regulation of the AM symbiosis.
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Affiliation(s)
- Ylva Lekberg
- MPG Ranch, Missoula, MT, 59801, USA
- Department of Ecosystem and Conservation Sciences, W.A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT, 59812, USA
| | - Jan Jansa
- Institute of Microbiology of the Czech Academy of Sciences, Prague, 14220, Czech Republic
| | | | | | - William E Holben
- Cellular, Molecular and Microbial Biology, University of Montana, Missoula, MT, 59812, USA
| | - David Johnson
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Roger T Koide
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Alanna Shaw
- Department of Ecosystem and Conservation Sciences, W.A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT, 59812, USA
| | - Catherine Zabinski
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA
| | - Laura Aldrich-Wolfe
- Department of Biological Sciences, North Dakota State University, Fargo, ND, 58108, USA
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Schönegger D, Moubset O, Margaria P, Menzel W, Winter S, Roumagnac P, Marais A, Candresse T. Benchmarking of virome metagenomic analysis approaches using a large, 60+ members, viral synthetic community. J Virol 2023; 97:e0130023. [PMID: 37888981 PMCID: PMC10688312 DOI: 10.1128/jvi.01300-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE We report here efforts to benchmark performance of two widespread approaches for virome analysis, which target either virion-associated nucleic acids (VANA) or highly purified double-stranded RNAs (dsRNAs). This was achieved using synthetic communities of varying complexity levels, up to a highly complex community of 72 viral agents (115 viral molecules) comprising isolates from 21 families and 61 genera of plant viruses. The results obtained confirm that the dsRNA-based approach provides a more complete representation of the RNA virome, in particular, for high complexity ones. However, for viromes of low to medium complexity, VANA appears a reasonable alternative and would be the preferred choice if analysis of DNA viruses is of importance. Several parameters impacting performance were identified as well as a direct relationship between the completeness of virome description and sample sequencing depth. The strategy, results, and tools used here should prove useful in a range of virome analysis efforts.
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Affiliation(s)
| | - Oumaima Moubset
- CIRAD, UMR PHIM, Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Paolo Margaria
- Plant Virus Department, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Wulf Menzel
- Plant Virus Department, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Stephan Winter
- Plant Virus Department, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR BFP, Villenave d’Ornon, France
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7
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Hoosein S, Neuenkamp L, Trivedi P, Paschke MW. AM fungal-bacterial relationships: what can they tell us about ecosystem sustainability and soil functioning? FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1141963. [PMID: 37746131 PMCID: PMC10512368 DOI: 10.3389/ffunb.2023.1141963] [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: 01/11/2023] [Accepted: 07/05/2023] [Indexed: 09/26/2023]
Abstract
Considering our growing population and our continuous degradation of soil environments, understanding the fundamental ecology of soil biota and plant microbiomes will be imperative to sustaining soil systems. Arbuscular mycorrhizal (AM) fungi extend their hyphae beyond plant root zones, creating microhabitats with bacterial symbionts for nutrient acquisition through a tripartite symbiotic relationship along with plants. Nonetheless, it is unclear what drives these AM fungal-bacterial relationships and how AM fungal functional traits contribute to these relationships. By delving into the literature, we look at the drivers and complexity behind AM fungal-bacterial relationships, describe the shift needed in AM fungal research towards the inclusion of interdisciplinary tools, and discuss the utilization of bacterial datasets to provide contextual evidence behind these complex relationships, bringing insights and new hypotheses to AM fungal functional traits. From this synthesis, we gather that interdependent microbial relationships are at the foundation of understanding microbiome functionality and deciphering microbial functional traits. We suggest using pattern-based inference tools along with machine learning to elucidate AM fungal-bacterial relationship trends, along with the utilization of synthetic communities, functional gene analyses, and metabolomics to understand how AM fungal and bacterial communities facilitate communication for the survival of host plant communities. These suggestions could result in improving microbial inocula and products, as well as a better understanding of complex relationships in terrestrial ecosystems that contribute to plant-soil feedbacks.
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Affiliation(s)
- Shabana Hoosein
- Department of Forest and Rangeland Stewardship/Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States
| | - Lena Neuenkamp
- Institute of Landscape Ecology, Münster University, Münster, Germany
- Department of Ecology and Multidisciplinary Institute for Environment Studies “Ramon Margalef,” University of Alicante, Alicante, Spain
| | - Pankaj Trivedi
- Microbiome Network, Department of Agricultural Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States
| | - Mark W. Paschke
- Department of Forest and Rangeland Stewardship/Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States
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8
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Kakouridis A, Hagen JA, Kan MP, Mambelli S, Feldman LJ, Herman DJ, Weber PK, Pett‐Ridge J, Firestone MK. Routes to roots: direct evidence of water transport by arbuscular mycorrhizal fungi to host plants. THE NEW PHYTOLOGIST 2022; 236:210-221. [PMID: 35633108 PMCID: PMC9543596 DOI: 10.1111/nph.18281] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/16/2022] [Indexed: 05/19/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) can help mitigate plant responses to water stress, but it is unclear whether AMF do so by indirect mechanisms, direct water transport to roots, or a combination of the two. Here, we investigated if and how the AMF Rhizophagus intraradices transported water to the host plant Avena barbata, wild oat. We used two-compartment microcosms, isotopically labeled water, and a fluorescent dye to directly track and quantify water transport by AMF across an air gap to host plants. Plants grown with AMF that had access to a physically separated compartment containing 18 O-labeled water transpired almost twice as much as plants with AMF excluded from that compartment. Using an isotopic mixing model, we estimated that water transported by AMF across the air gap accounted for 34.6% of the water transpired by host plants. In addition, a fluorescent dye indicated that hyphae were able to transport some water via an extracytoplasmic pathway. Our study provides direct evidence that AMF can act as extensions of the root system along the soil-plant-air continuum of water movement, with plant transpiration driving water flow along hyphae outside of the hyphal cell membrane.
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Affiliation(s)
- Anne Kakouridis
- University of California BerkeleyBerkeleyCA94720USA
- Lawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | | | - Megan P. Kan
- University of California BerkeleyBerkeleyCA94720USA
- Lawrence Livermore National LaboratoryLivermoreCA94550USA
| | - Stefania Mambelli
- University of California BerkeleyBerkeleyCA94720USA
- Center for Stable Isotope BiogeochemistryBerkeleyCA94720USA
| | | | - Donald J. Herman
- University of California BerkeleyBerkeleyCA94720USA
- Lawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Peter K. Weber
- Lawrence Livermore National LaboratoryLivermoreCA94550USA
| | - Jennifer Pett‐Ridge
- Lawrence Livermore National LaboratoryLivermoreCA94550USA
- University of California MercedMercedCA95344USA
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Kajihara KT, Egan CP, Swift SOI, Wall CB, Muir CD, Hynson NA. Core arbuscular mycorrhizal fungi are predicted by their high abundance-occupancy relationship while host-specific taxa are rare and geographically structured. THE NEW PHYTOLOGIST 2022; 234:1464-1476. [PMID: 35218016 DOI: 10.1111/nph.18058] [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: 01/06/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Habitat restoration may depend on the recovery of plant microbial symbionts such as arbuscular mycorrhizal (AM) fungi, but this requires a better understanding of the rules that govern their community assembly. We examined the interactions of soil and host-associated AM fungal communities between remnant and restored patches of subtropical montane forests. While AM fungal richness did not differ between habitat types, community membership did and was influenced by geography, habitat and host. These differences were largely driven by rare host-specific AM fungi that displayed near-complete turnover between forest types, while core AM fungal taxa were highly abundant and ubiquitous. The bipartite networks in the remnant forest were more specialized and hosts more specific than in the restored forest. Host-associated AM fungal communities nested within soil communities in both habitats, but only significantly so in the restored forest. Our results provide evidence that restored and remnant forests harbour the same core fungal symbionts, while rare host-specific taxa differ, and that geography, host identity and taxonomic resolution strongly affect the observed distribution patterns of these fungi. We suggest that host-specific interactions with AM fungi, as well as spatial processes, should be explicitly considered to effectively re-establish target host and symbiont communities.
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Affiliation(s)
- Kacie T Kajihara
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, 1993 East-West Road, Honolulu, HI, 96822, USA
| | - Cameron P Egan
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, 1993 East-West Road, Honolulu, HI, 96822, USA
- Department of Biology, Okanagan College, 1000 KLO Road, Kelowna, BC, VIY 4X8, Canada
| | - Sean O I Swift
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, 1993 East-West Road, Honolulu, HI, 96822, USA
| | - Christopher B Wall
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, 1993 East-West Road, Honolulu, HI, 96822, USA
- Biological Sciences, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Christopher D Muir
- School of Life Sciences, University of Hawai'i at Mānoa, 2538 McCarthy Mall, Honolulu, HI, 96822, USA
| | - Nicole A Hynson
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, 1993 East-West Road, Honolulu, HI, 96822, USA
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10
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Matzen SL, Lobo GP, Fakra SC, Kakouridis A, Nico PS, Pallud CE. Arsenic hyperaccumulator Pteris vittata shows reduced biomass in soils with high arsenic and low nutrient availability, leading to increased arsenic leaching from soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151803. [PMID: 34808151 DOI: 10.1016/j.scitotenv.2021.151803] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/06/2021] [Accepted: 11/15/2021] [Indexed: 06/13/2023]
Abstract
Plant-soil interactions affect arsenic and nutrient availability in arsenic-contaminated soils, with implications for arsenic uptake and tolerance in plants, and leaching from soil. In 22-week column experiments, we grew the arsenic hyperaccumulating fern Pteris vittata in a coarse- and a medium-textured soil to determine the effects of phosphorus fertilization and mycorrhizal fungi inoculation on P. vittata arsenic uptake and arsenic leaching. We investigated soil arsenic speciation using synchrotron-based spectromicroscopy. Greater soil arsenic availability and lower nutrient content in the coarse-textured soil were associated with greater fern arsenic uptake, lower biomass (apparently a metabolic cost of tolerance), and arsenic leaching from soil, due to lower transpiration. P. vittata hyperaccumulated arsenic from coarse- but not medium-textured soil. Mass of plant-accumulated arsenic was 1.2 to 2.4 times greater, but aboveground biomass was 74% smaller, in ferns growing in coarse-textured soil. In the presence of ferns, mean arsenic loss by leaching was 195% greater from coarse- compared to the medium-textured soil, and lower across both soils compared to the absence of ferns. In the medium-textured soil arsenic concentrations in leachate were higher in the presence of ferns. Fern arsenic uptake was always greater than loss by leaching. Most arsenic (>66%) accumulated in P. vittata appeared of rhizosphere origin. In the medium-textured soil with more clay and higher nutrient content, successful iron scavenging increased arsenic release from soil for leaching, but transpiration curtailed leaching.
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Affiliation(s)
- S L Matzen
- Department of Environmental Science, Policy, and Management, University of California-Berkeley, 130 Mulford Hall, Berkeley, CA 94720, USA
| | - G P Lobo
- Civil and Environmental Engineering, University of California-Berkeley, 410 O'Brien Hall, Berkeley, CA 94720, USA
| | - S C Fakra
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - A Kakouridis
- Department of Environmental Science, Policy, and Management, University of California-Berkeley, 130 Mulford Hall, Berkeley, CA 94720, USA
| | - P S Nico
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - C E Pallud
- Department of Environmental Science, Policy, and Management, University of California-Berkeley, 130 Mulford Hall, Berkeley, CA 94720, USA.
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11
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Tedersoo L, Bahram M, Zinger L, Nilsson RH, Kennedy PG, Yang T, Anslan S, Mikryukov V. Best practices in metabarcoding of fungi: From experimental design to results. Mol Ecol 2022; 31:2769-2795. [PMID: 35395127 DOI: 10.1111/mec.16460] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 02/07/2022] [Accepted: 03/30/2022] [Indexed: 02/06/2023]
Abstract
The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems. Here we provide an overview of current best practices in metabarcoding analysis of fungal communities, from experimental design through molecular and computational analyses. By reanalysing published data sets, we demonstrate that operational taxonomic units (OTUs) outperform amplified sequence variants (ASVs) in recovering fungal diversity, a finding that is particularly evident for long markers. Additionally, analysis of the full-length ITS region allows more accurate taxonomic placement of fungi and other eukaryotes compared to the ITS2 subregion. Finally, we show that specific methods for compositional data analyses provide more reliable estimates of shifts in community structure. We conclude that metabarcoding analyses of fungi are especially promising for integrating fungi into the full microbiome and broader ecosystem functioning context, recovery of novel fungal lineages and ancient organisms as well as barcoding of old specimens including type material.
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Bahram
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Lucie Zinger
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, France.,Naturalis Biodiversity Center, Leiden, The Netherlands
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Peter G Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, USA
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Vladimir Mikryukov
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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12
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Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP. Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 2022; 88:1-33. [PMID: 35585929 PMCID: PMC8924126 DOI: 10.3897/mycokeys.88.77106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/25/2022] [Indexed: 12/17/2022] Open
Abstract
Full taxonomic characterisation of fungal communities is necessary for establishing ecological associations and early detection of pathogens and invasive species. Complex communities of fungi are regularly characterised by metabarcoding using the Internal Transcribed Spacer (ITS) and the Large-Subunit (LSU) gene of the rRNA locus, but reliance on a single short sequence fragment limits the confidence of identification. Here we link metabarcoding from the ITS2 and LSU D1-D2 regions to characterise fungal communities associated with bark beetles (Scolytinae), the likely vectors of several tree pathogens. Both markers revealed similar patterns of overall species richness and response to key variables (beetle species, forest type), but identification against the respective reference databases using various taxonomic classifiers revealed poor resolution towards lower taxonomic levels, especially the species level. Thus, Operational Taxonomic Units (OTUs) could not be linked via taxonomic classifiers across ITS and LSU fragments. However, using phylogenetic trees (focused on the epidemiologically important Sordariomycetes) we placed OTUs obtained with either marker relative to reference sequences of the entire rRNA cistron that includes both loci and demonstrated the largely similar phylogenetic distribution of ITS and LSU-derived OTUs. Sensitivity analysis of congruence in both markers suggested the biologically most defensible threshold values for OTU delimitation in Sordariomycetes to be 98% for ITS2 and 99% for LSU D1-D2. Studies of fungal communities using the canonical ITS barcode require corroboration across additional loci. Phylogenetic analysis of OTU sequences aligned to the full rRNA cistron shows higher success rate and greater accuracy of species identification compared to probabilistic taxonomic classifiers.
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13
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Kuang J, Han S, Chen Y, Bates CT, Wang P, Shu W. Root-associated fungal community reflects host spatial co-occurrence patterns in a subtropical forest. ISME COMMUNICATIONS 2021; 1:65. [PMID: 36755184 PMCID: PMC9723750 DOI: 10.1038/s43705-021-00072-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 11/09/2022]
Abstract
Plant roots harbor and interact with diverse fungal species. By changing these belowground fungal communities, focal plants can affect the performance of surrounding individuals and the outcome of coexistence. Although highly host related, the roles of these root-associated fungal communities per se in host plant spatial co-occurrence is largely unknown. Here, we evaluated the host dependency of root-associated communities for 39-plant species spatially mapped throughout a 50-ha subtropical forest plot with relevant environmental properties. In addition, we explored whether the differentiation in root fungal associations among plant species can reflect their observed co-occurrence patterns. We demonstrated a strong host-dependency by discriminating the differentiation of root-associated fungal communities regardless of background soil heterogeneity. Furthermore, Random Forest modeling indicated that these nonrandom root fungal associations significantly increased our ability to explain spatial co-occurrence patterns, and to a greater degree than the relative abundance, phylogenetic relatedness, and functional traits of the host plants. Our results further suggested that plants harbor more abundant shared, "generalist" pathogens are likely segregated, while hosting more abundant unique, "specialist" ectomycorrhizal fungi might be an important strategy for promoting spatial aggregation, particularly between early established trees and the heterospecific adults. Together, we provide a conceptual and testable approach to integrate this host-dependent root fungal "fingerprinting" into the plant diversity patterns. We highlight that this approach is complementary to the classic cultivation-based scheme and can deepen our understanding of the community-level effect from overall fungi and its contribution to the pairwise plant dynamics in local species-rich communities.
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Affiliation(s)
- Jialiang Kuang
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, China.
| | - Shun Han
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Yongjian Chen
- Department of Environmental Science, University of Arizona, Tucson, AZ, USA
| | - Colin T Bates
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Pandeng Wang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, China
| | - Wensheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, China.
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14
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Reynolds NK, Jusino MA, Stajich JE, Smith ME. Understudied, underrepresented, and unknown: Methodological biases that limit detection of early diverging fungi from environmental samples. Mol Ecol Resour 2021; 22:1065-1085. [PMID: 34695878 DOI: 10.1111/1755-0998.13540] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 01/04/2023]
Abstract
Metabarcoding is an important tool for understanding fungal communities. The internal transcribed spacer (ITS) rDNA is the accepted fungal barcode but has known problems. The large subunit (LSU) rDNA has also been used to investigate fungal communities but available LSU metabarcoding primers were mostly designed to target Dikarya (Ascomycota + Basidiomycota) with little attention to early diverging fungi (EDF). However, evidence from multiple studies suggests that EDF comprise a large portion of unknown diversity in community sampling. Here, we investigate how DNA marker choice and methodological biases impact recovery of EDF from environmental samples. We focused on one EDF lineage, Zoopagomycota, as an example. We evaluated three primer sets (ITS1F/ITS2, LROR/LR3, and LR3 paired with new primer LR22F) to amplify and sequence a Zoopagomycota mock community and a set of 146 environmental samples with Illumina MiSeq. We compared two taxonomy assignment methods and created an LSU reference database compatible with AMPtk software. The two taxonomy assignment methods recovered strikingly different communities of fungi and EDF. Target fragment length variation exacerbated PCR amplification biases and influenced downstream taxonomic assignments, but this effect was greater for EDF than Dikarya. To improve identification of LSU amplicons we performed phylogenetic reconstruction and illustrate the advantages of this critical tool for investigating identified and unidentified sequences. Our results suggest much of the EDF community may be missed or misidentified with "standard" metabarcoding approaches and modified techniques are needed to understand the role of these taxa in a broader ecological context.
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Affiliation(s)
- Nicole K Reynolds
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Michelle A Jusino
- Center for Forest Mycology Research, USDA Forest Service, Northern Research Station, Madison, Wisconsin, USA
| | - Jason E Stajich
- Department of Plant Pathology & Microbiology and Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California, USA
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
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15
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Šmilauer P, Košnar J, Kotilínek M, Pecháčková S, Šmilauerová M. Host age and surrounding vegetation affect the community and colonization rates of arbuscular mycorrhizal fungi in a temperate grassland. THE NEW PHYTOLOGIST 2021; 232:290-302. [PMID: 34115391 DOI: 10.1111/nph.17550] [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: 05/04/2021] [Accepted: 06/08/2021] [Indexed: 05/04/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are important symbionts for the majority of terrestrial vascular plants, yet the drivers of the compositional variation in AMF communities need to be better understood. What effects does the ontogenetic stage of host plants have and do these effects differ between plant functional groups? Are the AMF communities modified by the properties of surrounding vegetation, such as the proportion of different functional groups or nonmycorrhizal plants ? We addressed these questions in a temperate grassland and studied AMF communities using next-generation sequencing and light microscopy, evaluating their composition, taxonomic, phylogenetic and functional diversity, functional traits and root colonization levels. We found important differences between AMF communities and their diversity between seedlings and adults which are larger than the differences among host species or between functional groups. The proportion of nonmycorrhizal plants in the surrounding affected AMF community composition and increased its richness. Our results highlight the need for further investigating the existence of a common mycelial networks. The decision to use seedlings for experimental work can affect the results more than the chosen host species.
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Affiliation(s)
- Petr Šmilauer
- Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, 370 05, Czech Republic
| | - Jiří Košnar
- Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, 370 05, Czech Republic
| | - Milan Kotilínek
- Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, 370 05, Czech Republic
| | - Sylvie Pecháčková
- The West Bohemian Museum, Kopeckého Sady 2, Plzeň, 301 00, Czech Republic
| | - Marie Šmilauerová
- Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, 370 05, Czech Republic
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16
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Šmilauer P, Šmilauerová M, Kotilínek M, Košnar J. Arbuscular mycorrhizal fungal communities of forbs and C3 grasses respond differently to cultivation and elevated nutrients. MYCORRHIZA 2021; 31:455-470. [PMID: 34050407 DOI: 10.1007/s00572-021-01036-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/17/2021] [Indexed: 06/12/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) represent important players in the structure and function of many ecosystems. Yet, we learn about their roles mostly from greenhouse-based experiments, with results subjected to cultivation bias. This study explores multiple aspects of this bias and separates the effect of increased nutrient availability from other cultivation specifics. For 15 grassland plant species from two functional groups (C3 grasses vs dicotyledonous forbs), we compared AMF communities of adults collected from non-manipulated vegetation with those in plants grown in a greenhouse. Nutrient availability was comparable to field conditions or experimentally elevated. We evaluated changes in AMF community composition, diversity, root colonisation, and the averages of functional traits characterising hyphal soil exploration. Additionally, we use the data from the greenhouse experiment to propose a new plant functional trait-the change of AMF colonisation in response to nutrient surplus. The AMF community differed profoundly between field-collected and greenhouse-grown plants, with a larger change of its composition in grass species, and AMF community composition in grasses also responded more to fertilisation than in forbs. Taxonomic and phylogenetic diversity declined more in forbs under cultivation (particularly with elevated nutrients), because in their roots, the AMF taxa from families other than Glomeraceae largely disappeared. A decline in AMF colonisation was not caused by greenhouse cultivation itself but selectively by the elevation of nutrient availability, particularly in grass host species. We demonstrate that the extent of decrease in AMF colonisation with elevated nutrients is a useful plant functional trait explaining an observed response of the plant community to manipulation.
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Affiliation(s)
- Petr Šmilauer
- Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-370 05, České Budějovice, Czech Republic.
| | - Marie Šmilauerová
- Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-370 05, České Budějovice, Czech Republic
| | - Milan Kotilínek
- Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-370 05, České Budějovice, Czech Republic
| | - Jiří Košnar
- Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-370 05, České Budějovice, Czech Republic
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17
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Bullington LS, Lekberg Y, Larkin BG. Insufficient sampling constrains our characterization of plant microbiomes. Sci Rep 2021; 11:3645. [PMID: 33574436 PMCID: PMC7878899 DOI: 10.1038/s41598-021-83153-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/29/2021] [Indexed: 12/14/2022] Open
Abstract
Plants host diverse microbial communities, but there is little consensus on how we sample these communities, and this has unknown consequences. Using root and leaf tissue from showy milkweed (Asclepias speciosa), we compared two common sampling strategies: (1) homogenizing after subsampling (30 mg), and (2) homogenizing bulk tissue before subsampling (30 mg). We targeted bacteria, arbuscular mycorrhizal (AM) fungi and non-AM fungi in roots, and foliar fungal endophytes (FFE) in leaves. We further extracted DNA from all of the leaf tissue collected to determine the extent of undersampling of FFE, and sampled FFE twice across the season using strategy one to assess temporal dynamics. All microbial groups except AM fungi differed in composition between the two sampling strategies. Community overlap increased when rare taxa were removed, but FFE and bacterial communities still differed between strategies, with largely non-overlapping communities within individual plants. Increasing the extraction mass 10 × increased FFE richness ~ 10 ×, confirming the severe undersampling indicated in the sampling comparisons. Still, seasonal patterns in FFEs were apparent, suggesting that strong drivers are identified despite severe undersampling. Our findings highlight that current sampling practices poorly characterize many microbial groups, and increased sampling intensity is necessary for increase reproducibility and to identify subtler patterns in microbial distributions.
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Affiliation(s)
- Lorinda S Bullington
- MPG Ranch, Missoula, MT, 59801, USA.
- Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, 59812, USA.
| | - Ylva Lekberg
- MPG Ranch, Missoula, MT, 59801, USA
- Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, 59812, USA
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18
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Banchi E, Ametrano CG, Tordoni E, Stanković D, Ongaro S, Tretiach M, Pallavicini A, Muggia L. Environmental DNA assessment of airborne plant and fungal seasonal diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 738:140249. [PMID: 32806340 DOI: 10.1016/j.scitotenv.2020.140249] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/25/2020] [Accepted: 06/14/2020] [Indexed: 05/06/2023]
Abstract
Environmental DNA (eDNA) metabarcoding and metagenomics analyses can improve taxonomic resolution in biodiversity studies. Only recently, these techniques have been applied in aerobiology, to target bacteria, fungi and plants in airborne samples. Here, we present a nine-month aerobiological study applying eDNA metabarcoding in which we analyzed simultaneously airborne diversity and variation of fungi and plants across five locations in North and Central Italy. We correlated species composition with the ecological characteristics of the sites and the seasons. The most abundant taxa among all sites and seasons were the fungal genera Cladosporium, Alternaria, and Epicoccum and the plant genera Brassica, Corylus, Cupressus and Linum, the latter being much more variable among sites. PERMANOVA and indicator species analyses showed that the plant diversity from air samples is significantly correlated with seasons, while that of fungi varied according to the interaction between seasons and sites. The results consolidate the performance of a new eDNA metabarcoding pipeline for the simultaneous amplification and analysis of airborne plant and fungal particles. They also highlight the promising complementarity of this approach with more traditional biomonitoring frameworks and routine reports of air quality provided by environmental agencies.
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Affiliation(s)
- Elisa Banchi
- Department of Life Sciences, University of Trieste, via Giorgieri 10, I-34127 Trieste, Italy; National Institute of Oceanography and Applied Geophysics - OGS, via Piccard 54, I-34151 Trieste, Italy
| | - Claudio G Ametrano
- Department of Life Sciences, University of Trieste, via Giorgieri 10, I-34127 Trieste, Italy
| | - Enrico Tordoni
- Department of Life Sciences, University of Trieste, via Giorgieri 10, I-34127 Trieste, Italy
| | - David Stanković
- Department of Life Sciences, University of Trieste, via Giorgieri 10, I-34127 Trieste, Italy; Marine Biology Station, National Institute of Biology, Fornače 41, SLO-6330 Piran, Slovenia
| | - Silvia Ongaro
- Department of Life Sciences, University of Trieste, via Giorgieri 10, I-34127 Trieste, Italy
| | - Mauro Tretiach
- Department of Life Sciences, University of Trieste, via Giorgieri 10, I-34127 Trieste, Italy
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, via Giorgieri 10, I-34127 Trieste, Italy; National Institute of Oceanography and Applied Geophysics - OGS, via Piccard 54, I-34151 Trieste, Italy.
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, via Giorgieri 10, I-34127 Trieste, Italy.
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19
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Wall CB, Egan CP, Swift SIO, Hynson NA. Three decades post-reforestation has not led to the reassembly of arbuscular mycorrhizal fungal communities associated with remnant primary forests. Mol Ecol 2020; 29:4234-4247. [PMID: 32885507 DOI: 10.1111/mec.15624] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 01/04/2023]
Abstract
The negative effects of deforestation can potentially be ameliorated through ecological restoration. However, reforestation alone may not reassemble the same ecological communities or functions as primary forests. In part, this failure may be owed to forest ecosystems inherently involving complex interactions among guilds of organisms. Plants, which structure forest food webs, rely on intimate associations with symbiotic microbes such as root-inhabiting mycorrhizal fungi. Here, we leverage a large-scale reforestation project on Hawai'i Island underway for over three decades to assess whether arbuscular mycorrhizal (AM) fungal communities have concurrently been restored. The reference ecosystem for this restoration project is a remnant montane native Hawaiian forest that provides critical habitat for endangered birds. We sampled soils from 12 plots within remnant and restored forest patches and characterized AM fungal communities using high-throughput amplicon sequencing. While some AM fungal community metrics were comparable between remnant and restored forest (e.g. species richness), other key characteristics were not. Specifically, community membership and the identity of AM fungal keystone species differed between the two habitat types, as well as the primary environmental factors influencing community composition. Remnant forest AM fungal communities were strongly associated with soil chemical properties, especially pH, while restored forest communities were influenced by the spatial proximity to remnant forests. We posit that combined, these differences in soil AM fungal communities could be negatively affecting the recruitment of native plant hosts and that future restoration efforts should consider plant-microbe interactions as an important facet of forest health.
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Affiliation(s)
- Christopher B Wall
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Cameron P Egan
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, USA.,Department of Biology, Okanagan College, Kelowna, BC, Canada
| | - Sean I O Swift
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Nicole A Hynson
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, USA
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20
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Londoño DMM, Meyer E, da Silva KJ, Hernández AG, de Armas RD, Soares LM, Stürmer SL, Nodari RO, Soares CRFS, Lovato PE. Root colonization and arbuscular mycorrhizal fungal community composition in a genetically modified maize, its non-modified isoline, and a landrace. MYCORRHIZA 2020; 30:611-621. [PMID: 32556837 DOI: 10.1007/s00572-020-00969-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
The use of genetically modified (GM) plants has increased in recent decades, but there are uncertainties about their effects on soil microbial communities. Aiming to quantify root colonization and characterize arbuscular mycorrhizal fungi (AMF) communities associated with roots and rhizosphere soil of different maize genotypes, a field trial was carried out in Southern Brazil with three maize genotypes as follows: a GM hybrid (DKB 240 VTPRO), its non-modified isoline (DKB 240), and a landrace (Pixurum). Soil samples were collected to evaluate the occurrence of AMF during the growth of corn genotypes at sowing and V3 (vegetative), R1 (flowering), and R3 (grain formation) stages of the crop. The occurrence of AMF was determined by the morphological identification of spores, and by analyzing AMF community composition in soil and roots of maize, using PCR-DGGE. The GM genotype of maize promoted lower mycorrhizal colonization in the vegetative stage and had lower sporulation at grain development than the conventional hybrid and the landrace maize. Twenty AMF morphotypes were identified and 13 were associated with all maize genotypes. The genera Acaulospora, Glomus, and Dentiscutata had the largest numbers of species. There were no differences in AMF community composition due to maize genotypes or genetic modification, but crop phenological stages affected AMF communities associated with maize roots.
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Affiliation(s)
- Diana Marcela Morales Londoño
- Departamento de Engenharia Rural, Centro de Ciências Agrarias, Universidade Federal de Santa Catarina. Rodovia Admar Gonzaga, 1346, Florianópolis, Santa Catarina, CEP: 88034-001, Brazil
| | - Edenilson Meyer
- Departamento de Engenharia Rural, Centro de Ciências Agrarias, Universidade Federal de Santa Catarina. Rodovia Admar Gonzaga, 1346, Florianópolis, Santa Catarina, CEP: 88034-001, Brazil
| | - Kelly Justin da Silva
- Centro Universitário Católica de Santa Catarina - Joinville, Campus Joinville. Rua Visconde de Taunay 427, Joinville, Santa Catarina, CEP 89203-005, Brazil
| | - Anabel González Hernández
- Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina. Campus Reitor João David Ferreira Lima, Florianópolis, Santa Catarina, CEP 88040-900, Brazil
| | - Rafael Dutra de Armas
- Centro Universitário Católica de Santa Catarina - Joinville, Campus Joinville. Rua Visconde de Taunay 427, Joinville, Santa Catarina, CEP 89203-005, Brazil
| | - Luis Macedo Soares
- Departamento de Ecologia e Zoologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina. Campus Reitor João David Ferreira Lima, Florianópolis, Santa Catarina, CEP 88040-900, Brazil
| | - Sidney Luiz Stürmer
- Departamento de Ciencias Naturais, Centro de Ciencias Exatas e Naturais, Fundação Universidade Regional de Blumenau. Rua Antonio da Veiga, 140, Centro, Blumenau, Santa Catarina, CEP 89030-903, Brazil
| | - Rubens Onofre Nodari
- Departamento de Fitotecnia, Centro de Ciências Agrárias Universidade Federal de Santa Catarina. Rodovia Admar Gonzaga, 1346, Bloco B, Itacorubi, Florianópolis, Santa Catarina, CEP 88040-900, Brazil
| | - Cláudio Roberto Fonsêca Sousa Soares
- Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina. Campus Reitor João David Ferreira Lima, Florianópolis, Santa Catarina, CEP 88040-900, Brazil
| | - Paulo Emilio Lovato
- Departamento de Engenharia Rural, Centro de Ciências Agrarias, Universidade Federal de Santa Catarina. Rodovia Admar Gonzaga, 1346, Florianópolis, Santa Catarina, CEP: 88034-001, Brazil.
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21
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New MiSeq based strategy exposed plant-preferential arbuscular mycorrhizal fungal communities in arid soils of Mexico. Symbiosis 2020. [DOI: 10.1007/s13199-020-00698-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
AbstractArbuscular mycorrhizal fungi (AMF) are obligate symbionts of c. 80% of land plants, having enormous ecological and economic impact, as they often improve crop plant nutrition and yield. DNA-based identification with molecular markers is used to analyze AM fungal communities in the field, but reaching species level taxonomic resolution remains challenging. Thus, currently there is no consensus on how to analyze high-throughput sequences and assign them into species. Here, a new sequencing strategy combined with taxonomic affiliations implemented with an evolutionary placement algorithm (EPA) was established. It is based on sequencing a c. 450 bp region of the large subunit (LSU) ribosomal rRNA gene with the MiSeq-Illumina platform. The method is suitable for the discrimination of closely related AMF species and was used to study host-AMF preferences in roots of Pequin pepper, soybean and orange at one location in the arid northeast of Mexico. Twenty AM fungal species from 13 genera were detected. Phylogenetic affiliation of reads to species revealed crop preferential associations. In Pequin pepper roots, several Rhizophagus species represented most of the community, Rhizophagus clarus being the most abundant. The soybean AM fungal community was dominated by Rhizophagus irregularis and Funneliformis mosseae and that of orange by several species of Dominikia, some of them only found in this crop. Unraveling the AMF-plant preferences of important crops by an affordable and robust sequencing method, combined with phylotaxonomic AMF species resolution, is an important tool to obtain taxonomic units that are meaningful in both biological and ecological studies.
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22
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Delavaux CS, Bever JD, Karppinen EM, Bainard LD. Keeping it cool: Soil sample cold pack storage and DNA shipment up to 1 month does not impact metabarcoding results. Ecol Evol 2020; 10:4652-4664. [PMID: 32551050 PMCID: PMC7297747 DOI: 10.1002/ece3.6219] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 02/17/2020] [Accepted: 03/06/2020] [Indexed: 01/30/2023] Open
Abstract
With the advances of sequencing tools, the fields of environmental microbiology and soil ecology have been transformed. Today, the unculturable majority of soil microbes can be sequenced. Although these tools give us tremendous power and open many doors to answer important questions, we must understand how sample processing may impact our results and interpretations. Here, we test the impacts of four soil storage methods on downstream amplicon metabarcoding and qPCR analyses for fungi and bacteria. We further investigate the impact of thaw time on extracted DNA to determine a safe length of time during which this can occur with minimal impact on study results. Overall, we find that storage using standard cold packs with subsequent storage at -20°C is little different than immediate storage in liquid nitrogen, suggesting that the historical and current method is adequate. We further find evidence that storage at room temperature or with aid of RNAlater can lead to changes in community composition and in the case of RNAlater, lower gene copies. We therefore advise against these storage methods for metabarcoding analyses. Finally, we show that over 1 month, DNA extract thaw time does not impact diversity or qPCR metrics. We hope that this work will help researchers working with soil bacteria and fungi make informed decisions about soil storage and transport to ensure repeatability and accuracy of results and interpretations.
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Affiliation(s)
- Camille S. Delavaux
- Department of Ecology and Evolutionary BiologyThe University of KansasLawrenceKSUSA
- Kansas Biological SurveyThe University of KansasLawrenceKSUSA
| | - James D. Bever
- Department of Ecology and Evolutionary BiologyThe University of KansasLawrenceKSUSA
- Kansas Biological SurveyThe University of KansasLawrenceKSUSA
| | - Erin M. Karppinen
- Swift Current Research and Development CentreAgriculture and Agri‐Food CanadaSwift CurrentSKCanada
| | - Luke D. Bainard
- Swift Current Research and Development CentreAgriculture and Agri‐Food CanadaSwift CurrentSKCanada
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Schreiner RP. Depth structures the community of arbuscular mycorrhizal fungi amplified from grapevine (Vitis vinifera L.) roots. MYCORRHIZA 2020; 30:149-160. [PMID: 31993741 DOI: 10.1007/s00572-020-00930-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/02/2020] [Indexed: 06/10/2023]
Abstract
The diversity of arbuscular mycorrhizal fungi (AMF) associating with grapevines has been determined previously, yet little is known of how the community in roots is shaped by depth in the soil or where roots occur in different management zones of the vineyard (vine row versus alley). The influence of depth, management zone, and time of year on the community of AMF in grape roots was examined. I also tested the potential influence of the alley vegetation on AMF in grapevines by comparing the taxa amplified from roots of other plants retrieved from the alley surface soil to those from grapevines growing in the same zone. Depth shaped the AMF community in grapevine roots more than the management zone based on dissimilarity among all grapevine samples. Time of the growing season did not, although AMF taxa richness was greater in grapevine roots collected in late summer (veraison) than it was in late spring (bloom). The number of abundant AMF taxa in grapevine roots from the uppermost soil depth in the vine row was substantially lower in late spring than in late summer, and this was related to high soil nitrate in late spring. The alley vegetation comprised primarily grass, and clover plants harbored a different AMF community in roots than did intermingled grapevine roots. The change in the AMF community in a single perennial host (grape) that occurred with depth in this study resulted from a shift among common taxa as opposed to the appearance of unique taxa in the subsoil.
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Affiliation(s)
- R Paul Schreiner
- USDA-ARS, Horticultural Crops Research Laboratory, 3420 NW Orchard Avenue, Corvallis, Oregon, 97330, USA.
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Faggioli V, Menoyo E, Geml J, Kemppainen M, Pardo A, Salazar MJ, Becerra AG. Soil lead pollution modifies the structure of arbuscular mycorrhizal fungal communities. MYCORRHIZA 2019; 29:363-373. [PMID: 31016370 DOI: 10.1007/s00572-019-00895-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 04/08/2019] [Indexed: 05/09/2023]
Abstract
The impact of lead (Pb) pollution on native communities of arbuscular mycorrhizal fungi (AMF) was assessed in soil samples from the surroundings of an abandoned Pb smelting factory. To consider the influence of host identity, bulk soil surrounding plant roots soil samples of predominant plant species (Sorghum halepense, Bidens pilosa, and Tagetes minuta) growing in Pb-polluted soils and in an uncontaminated site were selected. Molecular diversity was assessed by sequencing the 18S rDNA region with primers specific to AMF (AMV4.5NF/AMDGR) using Illumina MiSeq. A total of 115 virtual taxa (VT) of AMF were identified in this survey. Plant species did not affect AMF diversity patterns. However, soil Pb content was negatively correlated with VT richness per sample. Paraglomeraceae and Glomeraceae were the predominant families while Acaulosporaceae, Ambisporaceae, Archaeosporaceae, Claroideoglomeraceae, Diversisporaceae, and Gigasporaceae were less abundant. Acaulosporaceae and Glomeraceae were negatively affected by soil Pb, but Paraglomeraceae relative abundance increased under increasing soil Pb content. Overall, 26 indicator taxa were identified; four of them were previously reported in Pb-polluted soils (VT060; VT222; VT004; VT380); and five corresponded to cultured spores of Scutellospora castaneae (VT041), Diversispora spp. and Tricispora nevadensis (VT060), Diversispora epigaea (VT061), Glomus proliferum (VT099), and Gl. indicum (VT222). Even though AMF were present in Pb-polluted soils, community structure was strongly altered via the differential responses of taxonomic groups of AMF to Pb pollution. These taxon-specific differences in tolerance to soil Pb content should be considered for future phytoremediation strategies based on the selection and utilization of native Glomeromycota.
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Affiliation(s)
- Valeria Faggioli
- Instituto Nacional de Tecnología Agropecuaria, EEA Marcos Juárez, Ruta 12 km 36, 2580, Marcos Juárez, Argentina
| | - Eugenia Menoyo
- Grupo de Estudios Ambientales (GEA), Instituto de Matemática Aplicada San Luis (IMASL)-CONICET, Universidad Nacional de San Luis, Ejército de los Andes 950, 5700, San Luis, Argentina
| | - József Geml
- Biodiversity Dynamics Research Group, Naturalis Biodiversity Center, Vondellaan 55, 2332 AA, Leiden, The Netherlands
| | - Minna Kemppainen
- Laboratorio de Micología Molecular, Instituto de Microbiología Básica y Aplicada (IMBA), Departamento de Ciencia y Tecnología, y CONICET, Universidad Nacional de Quilmes, Roque Sáenz Peña, 352, Bernal, Provincia de Buenos Aires, Argentina
| | - Alejandro Pardo
- Laboratorio de Micología Molecular, Instituto de Microbiología Básica y Aplicada (IMBA), Departamento de Ciencia y Tecnología, y CONICET, Universidad Nacional de Quilmes, Roque Sáenz Peña, 352, Bernal, Provincia de Buenos Aires, Argentina
| | - M Julieta Salazar
- Instituto Multidisciplinario de Biología Vegetal (IMBIV)-CONICET, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Av. Vélez Sársfield, 1611, Córdoba, Argentina
| | - Alejandra G Becerra
- Instituto Multidisciplinario de Biología Vegetal (IMBIV)-CONICET, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Av. Vélez Sársfield, 1611, Córdoba, Argentina.
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Cruz-Paredes C, Frøslev TG, Michelsen A, Bang-Andreasen T, Hansen M, Ingerslev M, Skov S, Wallander H, Kjøller R. Wood ash application in a managed Norway spruce plantation did not affect ectomycorrhizal diversity or N retention capacity. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2018.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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