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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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Zhong F, Fan X, Ji W, Hai Z, Hu N, Li X, Liu G, Yu C, Chen Y, Lian B, Wei H, Zhang J. Soil Fungal Community Composition and Diversity of Culturable Endophytic Fungi from Plant Roots in the Reclaimed Area of the Eastern Coast of China. J Fungi (Basel) 2022; 8:jof8020124. [PMID: 35205878 PMCID: PMC8878519 DOI: 10.3390/jof8020124] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/16/2022] [Accepted: 01/25/2022] [Indexed: 12/13/2022] Open
Abstract
As an important resource for screening microbial strains capable of conferring stress tolerance in plants, the fungal community associated with the plants grown in stressful environments has received great attention. In this study, high-throughput sequencing was employed to study the rhizosphere fungal community in the reclaimed area (i.e., sites F, H, and T) of the eastern coast of China. Moreover, endophytic fungi from the root of six plant species colonizing the investigated sites were isolated and identified. The differences in soil physicochemical parameters, fungal diversity, and community structure were detected among the sampling sites and between the seasons. Ectomycorrhizal (ECM) fungi (e.g., genera Tuber and Geopora) were dominant at site F, which was characterized by high soil total carbon (SC) and total nitrogen (SN) contents and low soil electrical conductivity (EC) value. Arbuscular mycorrhizal (AM) fungi, including genera Glomus, Rhizophagus, and Entrophospora were dominant at sites H (winter), H (summer), and T (summer), respectively. The positive relationship between the EC value and the abundance of genus Glomus indicated the ability of this AM fungus to protect plants against the salt stress. Endophytic fungi at sites F (Aspergillus and Tetracladium), H (Nigrospora), and T (Nigrospora, Coniochaeta and Zopfiella) were recognized as the biomarkers or keystone taxa, among which only genus Aspergillus was isolated from the plant roots. The aforementioned AM fungi and endophytic fungi could contribute to the promotion of plant growth in the newly reclaimed land.
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Affiliation(s)
- Fei Zhong
- School of Life Science, Nantong University, Nantong 226019, China; (W.J.); (Z.H.); (N.H.); (X.L.); (G.L.); (C.Y.); (Y.C.); (B.L.); (H.W.)
- Key Lab of Landscape Plant Genetics and Breeding, Nantong 226019, China
- Correspondence: (F.Z.); (J.Z.)
| | - Xinlei Fan
- The Key Laboratory for Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing 100083, China;
| | - Wenhui Ji
- School of Life Science, Nantong University, Nantong 226019, China; (W.J.); (Z.H.); (N.H.); (X.L.); (G.L.); (C.Y.); (Y.C.); (B.L.); (H.W.)
| | - Zhixing Hai
- School of Life Science, Nantong University, Nantong 226019, China; (W.J.); (Z.H.); (N.H.); (X.L.); (G.L.); (C.Y.); (Y.C.); (B.L.); (H.W.)
| | - Naican Hu
- School of Life Science, Nantong University, Nantong 226019, China; (W.J.); (Z.H.); (N.H.); (X.L.); (G.L.); (C.Y.); (Y.C.); (B.L.); (H.W.)
| | - Xintong Li
- School of Life Science, Nantong University, Nantong 226019, China; (W.J.); (Z.H.); (N.H.); (X.L.); (G.L.); (C.Y.); (Y.C.); (B.L.); (H.W.)
| | - Guoyuan Liu
- School of Life Science, Nantong University, Nantong 226019, China; (W.J.); (Z.H.); (N.H.); (X.L.); (G.L.); (C.Y.); (Y.C.); (B.L.); (H.W.)
- Key Lab of Landscape Plant Genetics and Breeding, Nantong 226019, China
| | - Chunmei Yu
- School of Life Science, Nantong University, Nantong 226019, China; (W.J.); (Z.H.); (N.H.); (X.L.); (G.L.); (C.Y.); (Y.C.); (B.L.); (H.W.)
- Key Lab of Landscape Plant Genetics and Breeding, Nantong 226019, China
| | - Yanhong Chen
- School of Life Science, Nantong University, Nantong 226019, China; (W.J.); (Z.H.); (N.H.); (X.L.); (G.L.); (C.Y.); (Y.C.); (B.L.); (H.W.)
- Key Lab of Landscape Plant Genetics and Breeding, Nantong 226019, China
| | - Bolin Lian
- School of Life Science, Nantong University, Nantong 226019, China; (W.J.); (Z.H.); (N.H.); (X.L.); (G.L.); (C.Y.); (Y.C.); (B.L.); (H.W.)
- Key Lab of Landscape Plant Genetics and Breeding, Nantong 226019, China
| | - Hui Wei
- School of Life Science, Nantong University, Nantong 226019, China; (W.J.); (Z.H.); (N.H.); (X.L.); (G.L.); (C.Y.); (Y.C.); (B.L.); (H.W.)
- Key Lab of Landscape Plant Genetics and Breeding, Nantong 226019, China
| | - Jian Zhang
- School of Life Science, Nantong University, Nantong 226019, China; (W.J.); (Z.H.); (N.H.); (X.L.); (G.L.); (C.Y.); (Y.C.); (B.L.); (H.W.)
- Key Lab of Landscape Plant Genetics and Breeding, Nantong 226019, China
- Correspondence: (F.Z.); (J.Z.)
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3
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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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Czaplicki LM, Redfern LK, Cooper EM, Ferguson PL, Vilgalys R, Gunsch CK. Investigating the mycobiome of the Holcomb Creosote Superfund Site. CHEMOSPHERE 2020; 252:126208. [PMID: 32229362 PMCID: PMC7242165 DOI: 10.1016/j.chemosphere.2020.126208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 12/20/2019] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
Even though many fungi are known to degrade a range of organic chemicals and may be advantageous for targeting hydrophobic chemicals with low bioavailability due to their ability to secrete extracellular enzymes, fungi are not commonly leveraged in the context of bioremediation. Here we sought to examine the fungal microbiome (mycobiome) at a model creosote polluted site to determine if fungi were prevalent under high PAH contamination conditions as well as to identify potential mycostimulation targets. Several significant positive associations were detected between OTUs and mid-to high-molecular weight PAHs. Several OTUs were closely related to taxa that have previously been identified in culture-based studies as PAH degraders. In particular, members belonging to the Ascomycota phylum were the most diverse at higher PAH concentrations suggesting this phylum may be promising biostimulation targets. There were nearly three times more positive correlations as compared to negative correlations, suggesting that creosote-tolerance is more common than creosote-sensitivity in the fungal community. Future work including shotgun metagenomic analysis would help confirm the presence of specific degradation genes. Overall this study suggests that mycobiome and bacterial microbiome analyses should be performed in parallel to devise the most optimal in situ biostimulation treatment strategies.
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Affiliation(s)
- Lauren M Czaplicki
- Pratt School of Engineering, Department of Civil and Environmental Engineering, Duke University, Durham, NC, 27713, USA
| | - Lauren K Redfern
- Pratt School of Engineering, Department of Civil and Environmental Engineering, Duke University, Durham, NC, 27713, USA
| | - Ellen M Cooper
- Nicholas School of the Environment, Duke University, Durham, NC, 27713, USA
| | - P Lee Ferguson
- Nicholas School of the Environment, Duke University, Durham, NC, 27713, USA
| | - Rytas Vilgalys
- Department of Biology, Duke University, Durham, NC, 27713, USA
| | - Claudia K Gunsch
- Pratt School of Engineering, Department of Civil and Environmental Engineering, Duke University, Durham, NC, 27713, USA.
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Větrovský T, Morais D, Kohout P, Lepinay C, Algora C, Awokunle Hollá S, Bahnmann BD, Bílohnědá K, Brabcová V, D'Alò F, Human ZR, Jomura M, Kolařík M, Kvasničková J, Lladó S, López-Mondéjar R, Martinović T, Mašínová T, Meszárošová L, Michalčíková L, Michalová T, Mundra S, Navrátilová D, Odriozola I, Piché-Choquette S, Štursová M, Švec K, Tláskal V, Urbanová M, Vlk L, Voříšková J, Žifčáková L, Baldrian P. GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies. Sci Data 2020; 7:228. [PMID: 32661237 PMCID: PMC7359306 DOI: 10.1038/s41597-020-0567-7] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/05/2020] [Indexed: 02/08/2023] Open
Abstract
Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com . The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.
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Affiliation(s)
- Tomáš Větrovský
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Daniel Morais
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Kohout
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Clémentine Lepinay
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Camelia Algora
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sandra Awokunle Hollá
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Barbara Doreen Bahnmann
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Květa Bílohnědá
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vendula Brabcová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Federica D'Alò
- Laboratory of Systematic Botany and Mycology, University of Tuscia, Largo dell'Università snc, Viterbo, 01100, Italy
| | - Zander Rainier Human
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Mayuko Jomura
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Miroslav Kolařík
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Jana Kvasničková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Salvador Lladó
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Rubén López-Mondéjar
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tijana Martinović
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tereza Mašínová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lenka Meszárošová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lenka Michalčíková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tereza Michalová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sunil Mundra
- Department of Biology, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
- Section for Genetics and Evolutionary Biology, University of Oslo, Blindernveien 31, 0316, Oslo, Norway
| | - Diana Navrátilová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Iñaki Odriozola
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sarah Piché-Choquette
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Martina Štursová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Karel Švec
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vojtěch Tláskal
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Michaela Urbanová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lukáš Vlk
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Jana Voříšková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lucia Žifčáková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.
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Rodríguez-Caballero G, Caravaca F, Díaz G, Torres P, Roldán A. The invader Carpobrotus edulis promotes a specific rhizosphere microbiome across globally distributed coastal ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 719:137347. [PMID: 32120096 DOI: 10.1016/j.scitotenv.2020.137347] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 06/10/2023]
Abstract
The importance of plant-microbe interactions to the success of invasive plants has rarely been studied at a global scale. Carpobrotus edulis (L.) N. E. Br is an aggressive invader in many areas around the world, forming dense mats in coastal environments. In an approach at a large geographical scale, over a wide latitudinal and climatic range, we tested the ability of C. edulis to alter the local bacterial and fungal community structure and microbial activity in eight invaded coastal locations. The factors invasiveness and geographical location had a significant effect on the soil microbiota, the microbial community composition and structure from the rhizosphere of native and C. edulis plants being distinct in every location. The effect of the invader on all the chemical, physico-chemical, and microbiological properties studied depended on the invaded location. The soil bacterial and fungal community composition and structure were related to the soil available nutrients and mean annual rainfall, and those of the soil bacterial community were also linked to the soil respiration and latitude. Overall, our results reveal that the ability of the invader C. edulis to alter soil microbial community structure harboring a specific microbiome was widespread across a large invaded range - leading to concurring changes in the rhizosphere microbial functioning, such as nutrient cycling.
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Affiliation(s)
- G Rodríguez-Caballero
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation. P.O. Box 164, Campus de Espinardo, 30100 Murcia, Spain
| | - F Caravaca
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation. P.O. Box 164, Campus de Espinardo, 30100 Murcia, Spain.
| | - G Díaz
- Universidad Miguel Hernández de Elche. Department of Applied Biology, Avda. Ferrocarril, s/n. Edf. Laboratorios, 03202 Elche, Alicante, Spain
| | - P Torres
- Universidad Miguel Hernández de Elche. Department of Applied Biology, Avda. Ferrocarril, s/n. Edf. Laboratorios, 03202 Elche, Alicante, Spain
| | - A Roldán
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation. P.O. Box 164, Campus de Espinardo, 30100 Murcia, Spain
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DeBellis T, Kembel SW, Lessard JP. Shared mycorrhizae but distinct communities of other root-associated microbes on co-occurring native and invasive maples. PeerJ 2019; 7:e7295. [PMID: 31392089 PMCID: PMC6677121 DOI: 10.7717/peerj.7295] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/14/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Biological invasions are major drivers of environmental change that can significantly alter ecosystem function and diversity. In plants, soil microbes play an important role in plant establishment and growth; however, relatively little is known about the role they might play in biological invasions. A first step to assess whether root microbes may be playing a role in the invasion process is to find out if invasive plants host different microbes than neighbouring native plant species. METHODS In this study we investigated differences in root associated microbes of native sugar maple (Acer saccharum Marsh.) and exotic Norway maple (A. platanoides L.) collected from a forested reserve in eastern Canada. We used microscopy to examine root fungi and high-throughput sequencing to characterize the bacterial, fungal and arbuscular mycorrhizal communities of both maple species over one growing season. RESULTS We found differences in root associated bacterial and fungal communities between host species. Norway maple had a higher bacterial and fungal OTU (operational taxonomic units) richness compared to sugar maple, and the indicator species analysis revealed that nine fungal OTUs and three bacterial OTUs had a significant preference for sugar maple. The dominant bacterial phyla found on the roots of both maple species were Actinobacteria and Proteobacteria. The most common fungal orders associated with the Norway maple roots (in descending order) were Helotiales, Agaricales, Pleosporales, Hypocreales, Trechisporales while the Agaricales, Pleosporales, Helotiales, Capnodiales and Hypocreales were the dominant orders present in the sugar maple roots. Dark septate fungi colonization levels were higher in the sugar maple, but no differences in arbuscular mycorrhizal fungal communities and colonization rates were detected between maple species. DISCUSSION Our findings show that two congeneric plant species grown in close proximity can harbor distinct root microbial communities. These findings provide further support for the importance of plant species in structuring root associated microbe communities. The high colonization levels observed in Norway maple demonstrates its compatibility with arbuscular mycorrhizal fungi in the introduced range. Plant-associated microbial communities can affect host fitness and function in many ways; therefore, the observed differences suggest a possibility that biotic interactions can influence the dynamics between native and invasive species.
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Affiliation(s)
- Tonia DeBellis
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Department of Biology, Dawson College, Montreal, Quebec, Canada
| | - Steven W. Kembel
- Département des sciences Biologiques, Université du Québec à Montréal, Montréal, Québec, Canada
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8
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Rodríguez-Caballero G, Caravaca F, Roldán A. The unspecificity of the relationships between the invasive Pennisetum setaceum and mycorrhizal fungi may provide advantages during its establishment at semiarid Mediterranean sites. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 630:1464-1471. [PMID: 29554765 DOI: 10.1016/j.scitotenv.2018.02.321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 02/27/2018] [Accepted: 02/27/2018] [Indexed: 05/12/2023]
Abstract
The involvement of mutualistic plant-fungal interactions in invasion processes, especially in some climatic regions including semiarid areas, has not been sufficiently investigated. We compared the arbuscular mycorrhizal fungi (AMF) communities hosted by the invasive plant Pennisetum setaceum with those from the co-occurring native Hyparrhenia hirta at five Mediterranean semiarid locations with different edaphic characteristics. Illumina technology was used to investigate the AMF communities in the roots. The subsequent multivariate analysis showed that native and non-native host plants shared a similar AMF community, whereas the invaded locations differed in AMF communities harbored in the plant roots. The indicator species analysis revealed the absence of indicator virtual taxa for the fungal communities of the roots of native or invasive plants. In contrast, different numbers of indicator species were recorded in different sampling locations. According to the canonical correspondence analysis, the variability in the AMF communities between sampling sites was related to changes in soil total carbon, electrical conductivity, respiration, and protease and urease activities. These findings reveal the unspecificity of P. setaceum in relation to its association with the AMF community encountered in the invaded locations, which could have facilitated its successful establishment and spread.
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Affiliation(s)
- G Rodríguez-Caballero
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation, P.O. Box 164, Campus de Espinardo, 30100 Murcia, (Spain).
| | - F Caravaca
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation, P.O. Box 164, Campus de Espinardo, 30100 Murcia, (Spain)
| | - A Roldán
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation, P.O. Box 164, Campus de Espinardo, 30100 Murcia, (Spain)
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Vasar M, Andreson R, Davison J, Jairus T, Moora M, Remm M, Young JPW, Zobel M, Öpik M. Increased sequencing depth does not increase captured diversity of arbuscular mycorrhizal fungi. MYCORRHIZA 2017; 27:761-773. [PMID: 28730541 DOI: 10.1007/s00572-017-0791-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/12/2017] [Indexed: 05/26/2023]
Abstract
The arrival of 454 sequencing represented a major breakthrough by allowing deeper sequencing of environmental samples than was possible with existing Sanger approaches. Illumina MiSeq provides a further increase in sequencing depth but shorter read length compared with 454 sequencing. We explored whether Illumina sequencing improves estimates of arbuscular mycorrhizal (AM) fungal richness in plant root samples, compared with 454 sequencing. We identified AM fungi in root samples by sequencing amplicons of the SSU rRNA gene with 454 and Illumina MiSeq paired-end sequencing. In addition, we sequenced metagenomic DNA without prior PCR amplification. Amplicon-based Illumina sequencing yielded two orders of magnitude higher sequencing depth per sample than 454 sequencing. Initial analysis with minimal quality control recorded five times higher AM fungal richness per sample with Illumina sequencing. Additional quality control of Illumina samples, including restriction of the marker region to the most variable amplicon fragment, revealed AM fungal richness values close to those produced by 454 sequencing. Furthermore, AM fungal richness estimates were not correlated with sequencing depth between 300 and 30,000 reads per sample, suggesting that the lower end of this range is sufficient for adequate description of AM fungal communities. By contrast, metagenomic Illumina sequencing yielded very few AM fungal reads and taxa and was dominated by plant DNA, suggesting that AM fungal DNA is present at prohibitively low abundance in colonised root samples. In conclusion, Illumina MiSeq sequencing yielded higher sequencing depth, but similar richness of AM fungi in root samples, compared with 454 sequencing.
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Affiliation(s)
- Martti Vasar
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai Str, 51005, Tartu, Estonia.
| | - Reidar Andreson
- Institute of Molecular and Cell Biology, University of Tartu, 23b Riia Str, 51010, Tartu, Estonia
- Estonian Biocentre, 23b Riia Str, 51010, Tartu, Estonia
| | - John Davison
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai Str, 51005, Tartu, Estonia
| | - Teele Jairus
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai Str, 51005, Tartu, Estonia
| | - Mari Moora
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai Str, 51005, Tartu, Estonia
| | - Maido Remm
- Institute of Molecular and Cell Biology, University of Tartu, 23b Riia Str, 51010, Tartu, Estonia
| | - J P W Young
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Martin Zobel
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai Str, 51005, Tartu, Estonia
| | - Maarja Öpik
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai Str, 51005, Tartu, Estonia
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