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Ren D, Guo K, Sun Q, Zhu B, Qin L. Variations in Rhizospheric and Endophytic Root Fungal Communities of Scrophularia ningpoensis in Different Producing Areas. Curr Microbiol 2023; 80:323. [PMID: 37594529 DOI: 10.1007/s00284-023-03439-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/03/2023] [Indexed: 08/19/2023]
Abstract
Few studies have examined the association of factors associated with soil fertility and composition with the structure of microbial communities in the rhizosphere and endosphere. Hence, this study aimed to explore the effects of geographical differences on fungal communities in the roots of Scrophularia ningpoensis and the relationship between the fungal communities and secondary metabolic components in the host plant. We found that there was greater diversity in the fungal communities of the rhizosphere compartment than in endosphere communities. Ascomycota and Basidiomycota were dominant among the endosphere fungi, whereas Mortierellomycota was distributed in the rhizosphere. The composition of bulk soil obtained from different producing areas was significantly different, and the correlation between the rhizospheric and physicochemical compartments of the soil was higher than that observed with the endophytic compartment. Redundancy analysis and canonical correspondence analysis of the rhizospheric and endophytic samples revealed that the organic matter, total organic carbon, total nitrogen, and Hg levels were adequately correlated with the composition of rhizospheric and endophytic fungal communities. Multiple linear regression analyses facilitated the identification of potentially beneficial fungi whose abundance was correlated with levels of secondary metabolites, such as harpagide and harpagoside. These fungi could potentially provide valuable information regarding the use of S. ningpoensis in the medicinal plant industry.
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Affiliation(s)
- Dan Ren
- School of Pharmaceutical Sciences, Zhejiang Chinese Medicial University, Hangzhou, 310053, China
| | - Kunyuan Guo
- School of Biological Science and Technology, Hubei Minzu University, Enshi, 445000, China
| | - Qingmei Sun
- School of Pharmaceutical Sciences, Zhejiang Chinese Medicial University, Hangzhou, 310053, China
| | - Bo Zhu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medicial University, Hangzhou, 310053, China.
| | - Luping Qin
- School of Pharmaceutical Sciences, Zhejiang Chinese Medicial University, Hangzhou, 310053, China.
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Park I, Seo YS, Mannaa M. Recruitment of the rhizo-microbiome army: assembly determinants and engineering of the rhizosphere microbiome as a key to unlocking plant potential. Front Microbiol 2023; 14:1163832. [PMID: 37213524 PMCID: PMC10196466 DOI: 10.3389/fmicb.2023.1163832] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/11/2023] [Indexed: 05/23/2023] Open
Abstract
The viable community of microorganisms in the rhizosphere significantly impacts the physiological development and vitality of plants. The assembly and functional capacity of the rhizosphere microbiome are greatly influenced by various factors within the rhizosphere. The primary factors are the host plant genotype, developmental stage and status, soil properties, and resident microbiota. These factors drive the composition, dynamics, and activity of the rhizosphere microbiome. This review addresses the intricate interplay between these factors and how it facilitates the recruitment of specific microbes by the host plant to support plant growth and resilience under stress. This review also explores current methods for engineering and manipulating the rhizosphere microbiome, including host plant-mediated manipulation, soil-related methods, and microbe-mediated methods. Advanced techniques to harness the plant's ability to recruit useful microbes and the promising use of rhizo-microbiome transplantation are highlighted. The goal of this review is to provide valuable insights into the current knowledge, which will facilitate the development of cutting-edge strategies for manipulating the rhizosphere microbiome for enhanced plant growth and stress tolerance. The article also indicates promising avenues for future research in this field.
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Affiliation(s)
- Inmyoung Park
- School of Food and Culinary Arts, Youngsan University, Busan, Republic of Korea
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
| | - Mohamed Mannaa
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
- Department of Plant Pathology, Faculty of Agriculture, Cairo University, Giza, Egypt
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Delitte M, Caulier S, Bragard C, Desoignies N. Plant Microbiota Beyond Farming Practices: A Review. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.624203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Plants have always grown and evolved surrounded by numerous microorganisms that inhabit their environment, later termed microbiota. To enhance food production, humankind has relied on various farming practices such as irrigation, tilling, fertilization, and pest and disease management. Over the past few years, studies have highlighted the impacts of such practices, not only in terms of plant health or yields but also on the microbial communities associated with plants, which have been investigated through microbiome studies. Because some microorganisms exert beneficial traits that improve plant growth and health, understanding how to modulate microbial communities will help in developing smart farming and favor plant growth-promoting (PGP) microorganisms. With tremendous cost cuts in NGS technologies, metagenomic approaches are now affordable and have been widely used to investigate crop-associated microbiomes. Being able to engineer microbial communities in ways that benefit crop health and growth will help decrease the number of chemical inputs required. Against this background, this review explores the impacts of agricultural practices on soil- and plant-associated microbiomes, focusing on plant growth-promoting microorganisms from a metagenomic perspective.
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Zhou X, Leite MFA, Zhang Z, Tian L, Chang J, Ma L, Li X, van Veen JA, Tian C, Kuramae EE. Facilitation in the soil microbiome does not necessarily lead to niche expansion. ENVIRONMENTAL MICROBIOME 2021; 16:4. [PMID: 33902741 PMCID: PMC8067652 DOI: 10.1186/s40793-021-00373-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 01/21/2021] [Indexed: 05/24/2023]
Abstract
BACKGROUND The soil microbiome drives soil ecosystem function, and soil microbial functionality is directly linked to interactions between microbes and the soil environment. However, the context-dependent interactions in the soil microbiome remain largely unknown. RESULTS Using latent variable models (LVMs), we disentangle the biotic and abiotic interactions of soil bacteria, fungi and environmental factors using the Qinghai-Tibetan Plateau soil ecosystem as a model. Our results show that soil bacteria and fungi not only interact with each other but also shift from competition to facilitation or vice versa depending on environmental variation; that is, the nature of their interactions is context-dependent. CONCLUSIONS Overall, elevation is the environmental gradient that most promotes facilitative interactions among microbes but is not a major driver of soil microbial community composition, as evidenced by variance partitioning. The larger the tolerance of a microbe to a specific environmental gradient, the lesser likely it is to interact with other soil microbes, which suggests that facilitation does not necessarily lead to niche expansion.
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Affiliation(s)
- Xue Zhou
- College of Resources and Environment, Jilin Agricultural University, Changchun, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Márcio F A Leite
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands
| | - Zhenqing Zhang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Jingjing Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Lina Ma
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Xiujun Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Johannes A van Veen
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China.
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands.
- Ecology and biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands.
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Shi S, Chang J, Tian L, Nasir F, Ji L, Li X, Tian C. Comparative analysis of the rhizomicrobiome of the wild versus cultivated crop: insights from rice and soybean. Arch Microbiol 2019; 201:879-888. [PMID: 30963196 DOI: 10.1007/s00203-019-01638-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/11/2019] [Accepted: 02/18/2019] [Indexed: 12/30/2022]
Abstract
Plant domestication was a pivotal accomplishment in human history, which led to a reduction in genetic diversity of crop species; however, there was less research focus on how this reduced genetic diversity of crops in affecting rhizosphere microbial communities during crop domestication process. Here, we used high-throughput sequencing to explore the different effects of crops domestication on rhizosphere microbial community structure of rice (Oryza sativa L. and Oryza rufipogon Griff.) and soybean (Glycine max L. and Glycine soja Sieb. et Zucc.). Results indicated that rhizosphere fungal communities are more strongly influenced by crop domestication than bacterial communities. There was a stronger relationship for fungi and bacteria in the cultivated crops than in the wild relatives. Results also showed that the wild varieties had a higher abundance of beneficial symbionts and a lower abundance of pathogens comparing with the cultivated varieties. There was a similar tendency for both rice and soybean in rhizosphere microbial communities by comparing wild crops and their cultivated varieties. In conclusion, crop domestication had a stronger effect on the fungal communities than on the bacterial communities and had improved the microbial relationship in rhizosphere of cultivated crops.
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Affiliation(s)
- Shaohua Shi
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130102, China
| | - Jingjing Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130102, China
| | - Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130102, China
| | - Fahad Nasir
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130102, China
| | - Li Ji
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130102, China
| | - Xiujun Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130102, China
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130102, China.
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Todeschini V, AitLahmidi N, Mazzucco E, Marsano F, Gosetti F, Robotti E, Bona E, Massa N, Bonneau L, Marengo E, Wipf D, Berta G, Lingua G. Impact of Beneficial Microorganisms on Strawberry Growth, Fruit Production, Nutritional Quality, and Volatilome. FRONTIERS IN PLANT SCIENCE 2018; 9:1611. [PMID: 30505312 PMCID: PMC6250784 DOI: 10.3389/fpls.2018.01611] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/17/2018] [Indexed: 05/24/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) colonize the roots of most terrestrial plant species, improving plant growth, nutrient uptake and biotic/abiotic stress resistance and tolerance. Similarly, plant growth promoting bacteria (PGPB) enhance plant fitness and production. In this study, three different AMF (Funneliformis mosseae, Septoglomus viscosum, and Rhizophagus irregularis) were used in combination with three different strains of Pseudomonas sp. (19Fv1t, 5Vm1K and Pf4) to inoculate plantlets of Fragaria × ananassa var. Eliana F1. The effects of the different fungus/bacterium combinations were assessed on plant growth parameters, fruit production and quality, including health-promoting compounds. Inoculated and uninoculated plants were maintained in a greenhouse for 4 months and irrigated with a nutrient solution at two different phosphate levels. The number of flowers and fruits were recorded weekly. At harvest, fresh and dry weights of roots and shoots, mycorrhizal colonization and concentration of leaf photosynthetic pigments were measured in each plant. The following fruit parameters were recorded: pH, titratable acids, concentration of organic acids, soluble sugars, ascorbic acids, and anthocyanidins; volatile and elemental composition were also evaluated. Data were statistically analyzed by ANOVA and PCA/PCA-DA. Mycorrhizal colonization was higher in plants inoculated with R. irregularis, followed by F. mosseae and S. viscosum. In general, AMF mostly affected the parameters associated with the vegetative portion of the plant, while PGPB were especially relevant for fruit yield and quality. The plant physiological status was differentially affected by inoculations, resulting in enhanced root and shoot biomass. Inoculation with Pf4 bacterial strain increased flower and fruit production per plant and malic acid content in fruits, while decreased the pH value, regardless of the used fungus. Inoculations affected fruit nutritional quality, increasing sugar and anthocyanin concentrations, and modulated pH, malic acid, volatile compounds and elements. In the present study, we show for the first time that strawberry fruit concentration of some elements and/or volatiles can be affected by the presence of specific beneficial soil microorganisms. In addition, our results indicated that it is possible to select the best plant-microorganism combination for field applications, and improving fruit production and quality, also in terms of health promoting properties.
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Affiliation(s)
- Valeria Todeschini
- Dipartimento di Scienze ed Innovazione Tecnologica, Università del Piemonte Orientale, Vercelli, Italy
| | - Nassima AitLahmidi
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Eleonora Mazzucco
- Dipartimento di Scienze ed Innovazione Tecnologica, Università del Piemonte Orientale, Alessandria, Italy
| | - Francesco Marsano
- Dipartimento di Scienze ed Innovazione Tecnologica, Università del Piemonte Orientale, Alessandria, Italy
| | - Fabio Gosetti
- Dipartimento di Scienze ed Innovazione Tecnologica, Università del Piemonte Orientale, Alessandria, Italy
| | - Elisa Robotti
- Dipartimento di Scienze ed Innovazione Tecnologica, Università del Piemonte Orientale, Alessandria, Italy
| | - Elisa Bona
- Dipartimento di Scienze ed Innovazione Tecnologica, Università del Piemonte Orientale, Vercelli, Italy
| | - Nadia Massa
- Dipartimento di Scienze ed Innovazione Tecnologica, Università del Piemonte Orientale, Alessandria, Italy
| | - Laurent Bonneau
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Emilio Marengo
- Dipartimento di Scienze ed Innovazione Tecnologica, Università del Piemonte Orientale, Alessandria, Italy
| | - Daniel Wipf
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Graziella Berta
- Dipartimento di Scienze ed Innovazione Tecnologica, Università del Piemonte Orientale, Alessandria, Italy
| | - Guido Lingua
- Dipartimento di Scienze ed Innovazione Tecnologica, Università del Piemonte Orientale, Alessandria, Italy
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Igiehon NO, Babalola OO. Rhizosphere Microbiome Modulators: Contributions of Nitrogen Fixing Bacteria towards Sustainable Agriculture. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15040574. [PMID: 29570619 PMCID: PMC5923616 DOI: 10.3390/ijerph15040574] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/03/2018] [Accepted: 03/19/2018] [Indexed: 02/05/2023]
Abstract
Rhizosphere microbiome which has been shown to enhance plant growth and yield are modulated or influenced by a few environmental factors such as soil type, plant cultivar, climate change and anthropogenic activities. In particular, anthropogenic activity, such as the use of nitrogen-based chemical fertilizers, is associated with environmental destruction and this calls for a more ecofriendly strategy to increase nitrogen levels in agricultural land. This feat is attainable by harnessing nitrogen-fixing endophytic and free-living rhizobacteria. Rhizobium, Pseudomonas, Azospirillum and Bacillus, have been found to have positive impacts on crops by enhancing both above and belowground biomass and could therefore play positive roles in achieving sustainable agriculture outcomes. Thus, it is necessary to study this rhizosphere microbiome with more sophisticated culture-independent techniques such as next generation sequencing (NGS) with the prospect of discovering novel bacteria with plant growth promoting traits. This review is therefore aimed at discussing factors that can modulate rhizosphere microbiome with focus on the contributions of nitrogen fixing bacteria towards sustainable agricultural development and the techniques that can be used for their study.
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Affiliation(s)
- Nicholas Ozede Igiehon
- Food Security and Safety Niche, Faculty of Natural and Agricultural Science, Private Mail Bag X2046, North West University, Mmabatho 2735, South Africa.
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche, Faculty of Natural and Agricultural Science, Private Mail Bag X2046, North West University, Mmabatho 2735, South Africa.
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Rascovan N, Carbonetto B, Perrig D, Díaz M, Canciani W, Abalo M, Alloati J, González-Anta G, Vazquez MP. Integrated analysis of root microbiomes of soybean and wheat from agricultural fields. Sci Rep 2016; 6:28084. [PMID: 27312589 PMCID: PMC4911569 DOI: 10.1038/srep28084] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/31/2016] [Indexed: 12/02/2022] Open
Abstract
Root associated bacteria are critical for plant growth and health. Understanding the composition and role of root microbiota is crucial toward agricultural practices that are less dependent on chemical fertilization, which has known negative effects on the environment and human health. Here we analyzed the root-associated microbiomes of soybean and wheat under agricultural field conditions. We took samples from 11 different production fields across a large geographic area. We used 16S rRNA pyrosequencing to explore root microbial communities and also obtained 2,007 bacterial isolates from rhizospheres, which were tested for the presence of plant growth promoting (PGP) traits in-vitro. We observed that pH and nitrate content correlated with beta diversity variability of rhizospheric bacterial communities despite the variable field conditions. We described the dominant bacterial groups associated to roots from both crops at a large geographic scale and we found that a high proportion of them (60-70%) showed more than 97% similarity to bacteria from the isolated collection. Moreover, we observed that 55% of the screened isolates presented PGP activities in vitro. These results are a significant step forward in understanding crop-associated microbiomes and suggest that new directions can be taken to promote crop growth and health by modulating root microbiomes.
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Affiliation(s)
- Nicolás Rascovan
- Instituto de Agrobiotecnología de Rosario (INDEAR), Ocampo 210 bis (2000), Predio CCT Rosario, Santa Fe, Argentina
| | - Belén Carbonetto
- Instituto de Agrobiotecnología de Rosario (INDEAR), Ocampo 210 bis (2000), Predio CCT Rosario, Santa Fe, Argentina
| | - Diego Perrig
- Rizobacter Argentina S. A, Argentina, Avda. Pte. Dr. Arturo Frondizi No. 1150-Calle No. 1, Parque Industrial, CP B2702HDA-Pergamino (Bs.As), Argentina
| | - Marisa Díaz
- Rizobacter Argentina S. A, Argentina, Avda. Pte. Dr. Arturo Frondizi No. 1150-Calle No. 1, Parque Industrial, CP B2702HDA-Pergamino (Bs.As), Argentina
| | - Wilter Canciani
- Rizobacter Argentina S. A, Argentina, Avda. Pte. Dr. Arturo Frondizi No. 1150-Calle No. 1, Parque Industrial, CP B2702HDA-Pergamino (Bs.As), Argentina
| | - Matías Abalo
- Rizobacter Argentina S. A, Argentina, Avda. Pte. Dr. Arturo Frondizi No. 1150-Calle No. 1, Parque Industrial, CP B2702HDA-Pergamino (Bs.As), Argentina
| | - Julieta Alloati
- Instituto de Agrobiotecnología de Rosario (INDEAR), Ocampo 210 bis (2000), Predio CCT Rosario, Santa Fe, Argentina
| | - Gustavo González-Anta
- Rizobacter Argentina S. A, Argentina, Avda. Pte. Dr. Arturo Frondizi No. 1150-Calle No. 1, Parque Industrial, CP B2702HDA-Pergamino (Bs.As), Argentina
| | - Martín P. Vazquez
- Instituto de Agrobiotecnología de Rosario (INDEAR), Ocampo 210 bis (2000), Predio CCT Rosario, Santa Fe, Argentina
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Soil Characteristics Driving Arbuscular Mycorrhizal Fungal Communities in Semiarid Mediterranean Soils. Appl Environ Microbiol 2016; 82:3348-3356. [PMID: 27016567 DOI: 10.1128/aem.03982-15] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 03/21/2016] [Indexed: 01/29/2023] Open
Abstract
UNLABELLED We investigated communities of arbuscular mycorrhizal fungi (AMF) in the roots and the rhizosphere soil of Brachypodium retusum in six different natural soils under field conditions. We explored phylogenetic patterns of AMF composition using indicator species analyses to find AMF associated with a given habitat (root versus rhizosphere) or soil type. We tested whether the AMF characteristics of different habitats or contrasting soils were more closely related than expected by chance. Then we used principal-component analysis and multivariate analysis of variance to test for the relative contribution of each factor in explaining the variation in fungal community composition. Finally, we used redundancy analysis to identify the soil properties that significantly explained the differences in AMF communities across soil types. The results pointed out a tendency of AMF communities in roots to be closely related and different from those in the rhizosphere soil. The indicator species analyses revealed AMF associated with rhizosphere soil and the root habitat. Soil type also determined the distribution of AMF communities in soils, and this effect could not be attributed to a single soil characteristic, as at least three soil properties related to microbial activity, i.e., pH and levels of two micronutrients (Mn and Zn), played significant roles in triggering AMF populations. IMPORTANCE Communities of arbuscular mycorrhizal fungi (AMF) are main components of soil biota that can determine the productivity of ecosystems. These fungal assemblages vary across host plants and ecosystems, but the main ecological processes that shape the structures of these communities are still largely unknown. A field study in six different soil types from semiarid areas revealed that AMF communities are significantly influenced by habitat (soil versus roots) and soil type. In addition, three soil properties related to microbiological activity (i.e., pH and manganese and zinc levels) were the main factors triggering the distribution of AMF. These results contribute to a better understanding of the ecological factors that can shape AMF communities, an important soil microbial group that affects multiple ecosystem functions.
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10
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The Cry1Ab Protein Has Minor Effects on the Arbuscular Mycorrhizal Fungal Communities after Five Seasons of Continuous Bt Maize Cultivation. PLoS One 2015; 10:e0146041. [PMID: 26717324 PMCID: PMC4696834 DOI: 10.1371/journal.pone.0146041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/11/2015] [Indexed: 11/19/2022] Open
Abstract
The cultivation of genetically modified plants (GMP) has raised concerns regarding the plants’ ecological safety. A greenhouse experiment was conducted to assess the impact of five seasons of continuous Bt (Bacillus thuringiensis) maize cultivation on the colonisation and community structure of the non-target organisms arbuscular mycorrhizal fungi (AMF) in the maize roots, bulk soils and rhizospheric soils using the terminal restriction fragment length polymorphism (T-RFLP) analysis of the 28S ribosomal DNA and sequencing methods. AMF colonisation was significantly higher in the two Bt maize lines that express Cry1Ab, 5422Bt1 (event Bt11) and 5422CBCL (MON810) than in the non-Bt isoline 5422. No significant differences were observed in the diversity of the AMF community between the roots, bulk soils and rhizospheric soils of the Bt and non-Bt maize cultivars. The AMF genus Glomus was dominant in most of the samples, as detected by DNA sequencing. A clustering analysis based on the DNA sequence data suggested that the sample types (i.e., the samples from the roots, bulk soils or rhizospheric soils) might have greater influence on the AMF community phylotypes than the maize cultivars. This study indicated that the Cry1Ab protein has minor effects on the AMF communities after five seasons of continuous Bt maize cultivation.
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11
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Diversity, richness and degree of colonization of arbuscular mycorrhizal fungi in coconut cultivated along with intercrops in high productive zone of Kerala, India. Symbiosis 2015. [DOI: 10.1007/s13199-015-0326-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Boyer LR, Brain P, Xu XM, Jeffries P. Inoculation of drought-stressed strawberry with a mixed inoculum of two arbuscular mycorrhizal fungi: effects on population dynamics of fungal species in roots and consequential plant tolerance to water deficiency. MYCORRHIZA 2015; 25:215-27. [PMID: 25186649 DOI: 10.1007/s00572-014-0603-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 08/25/2014] [Indexed: 05/24/2023]
Abstract
The effect of inoculation with two arbuscular mycorrhizal fungi (AMF) on growth and drought tolerance of cultivated strawberry (Fragaria × ananassa) was studied. Three treatments (a single treatment either of Funneliformis mosseae BEG25, Funneliformis geosporus BEG11 or a 50:50 mixed inoculation treatment of both species) were compared to uninoculated plants. Species-specific primers for qPCR quantification of F. geosporus and F. mosseae DNA were developed to quantify the relative abundance of each fungus in roots of strawberry under different conditions of water stress. Co-occupation of the same root by both species was shown to commonly occur, but their relative abundance varied with water stress (reduced irrigation of up to 40%). Greater root colonisation was observed microscopically under water stress, but this increased colonisation was often accompanied with decreased amounts of fungal DNA in the root. F. mosseae tended to become more abundant under water stress relative to F. geosporus. There was significant correlation in the fungal colonisation measurements from the microscopic and qPCR methods under some conditions, but the nature of this relationship varied greatly with AMF inoculum and abiotic conditions. Single-species inoculation treatments gave similar benefits to the host to the mixed inoculation treatment regardless of irrigation regime; here, amount of colonisation was of greater importance than functional diversity. The addition of AMF inocula to plants subjected to reduced irrigation restored plant growth to the same or higher values as the non-mycorrhizal, fully-watered plants. The water use efficiency of plants was greater under the regulated deficit irrigation (RDI) regime and in AMF-inoculated plants, but there were no significant differences between plants inoculated with the single or combined inoculum. This study demonstrated that the increase in plant growth was directly influenced by an increase in root colonisation by AMF when individual plants were examined.
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Affiliation(s)
- Louisa Robinson Boyer
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK,
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Nallanchakravarthula S, Mahmood S, Alström S, Finlay RD. Influence of soil type, cultivar and Verticillium dahliae on the structure of the root and rhizosphere soil fungal microbiome of strawberry. PLoS One 2014; 9:e111455. [PMID: 25347069 PMCID: PMC4210224 DOI: 10.1371/journal.pone.0111455] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 10/02/2014] [Indexed: 12/31/2022] Open
Abstract
Sustainable management of crop productivity and health necessitates improved understanding of the ways in which rhizosphere microbial populations interact with each other, with plant roots and their abiotic environment. In this study we examined the effects of different soils and cultivars, and the presence of a soil-borne fungal pathogen, Verticillium dahliae, on the fungal microbiome of the rhizosphere soil and roots of strawberry plants, using high-throughput pyrosequencing. Fungal communities of the roots of two cultivars, Honeoye and Florence, were statistically distinct from those in the rhizosphere soil of the same plants, with little overlap. Roots of plants growing in two contrasting field soils had high relative abundance of Leptodontidium sp. C2 BESC 319 g whereas rhizosphere soil was characterised by high relative abundance of Trichosporon dulcitum or Cryptococcus terreus, depending upon the soil type. Differences between different cultivars were not as clear. Inoculation with the pathogen V. dahliae had a significant influence on community structure, generally decreasing the number of rhizosphere soil- and root-inhabiting fungi. Leptodontidium sp. C2 BESC 319 g was the dominant fungus responding positively to inoculation with V. dahliae. The results suggest that 1) plant roots select microorganisms from the wider rhizosphere pool, 2) that both rhizosphere soil and root inhabiting fungal communities are influenced by V. dahliae and 3) that soil type has a stronger influence on both of these communities than cultivar.
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Affiliation(s)
- Srivathsa Nallanchakravarthula
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
| | - Shahid Mahmood
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sadhna Alström
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Roger D. Finlay
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Alguacil MDM, Torrecillas E, Lozano Z, Torres MP, Roldán A. Prunus persica crop management differentially promotes arbuscular mycorrhizal fungi diversity in a tropical agro-ecosystem. PLoS One 2014; 9:e88454. [PMID: 24520389 PMCID: PMC3919774 DOI: 10.1371/journal.pone.0088454] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 01/12/2014] [Indexed: 11/18/2022] Open
Abstract
Due to the important role of arbuscular mycorrhizal fungi (AMF) in ecosystem functioning, determination of the effect of management practices on the AMF diversity in agricultural soils is essential for the sustainability of these agro-ecosystems. The objective of this study was to compare the AMF diversity in Prunus persica roots under two types of fertilisation (inorganic, with or without manure) combined with integrated or chemical pest management in a Venezuelan agro-ecosystem. The AM fungal small-subunit (SSU) rRNA genes were subjected to PCR, cloning, sequencing and phylogenetic analyses. Twenty-one different phylotypes were identified: 15 belonged to the genus Glomus, one to Claroideoglomus, two to Paraglomus, one to Acaulospora, one to Scutellospora and one to Archaeospora. The distribution of the AMF community composition differed as a consequence of the treatment effects. The treatment combining organic and inorganic fertilisation with chemical pest control had the highest AMF richness and the treatment combining inorganic fertilisation with chemical pest had the lowest. The real causes and effects of these differences in the AMF community are very difficult to establish, since the crop management regimes tested were composed of several interacting factors. In conclusion, the crop management practices can exert a significant influence on the populations of AMF. The treatment combining organic and inorganic fertilisation with chemical pest control appears to be the most suitable agricultural management strategy with respect to improving the AMF diversity in this crop under tropical conditions, and thus for maintaining the agricultural and environmental sustainability of this agro-ecosystem.
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Affiliation(s)
- Maria del Mar Alguacil
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation, Campus de Espinardo, Murcia, Spain
| | - Emma Torrecillas
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation, Campus de Espinardo, Murcia, Spain
| | - Zenaida Lozano
- Universidad Central de Venezuela (UCV), Facultad de Agronomía, Instituto de Edafología, El Limón, Campus Universitario, Maracay, Venezuela
| | - Maria Pilar Torres
- Departamento de Biología Aplicada, Area de Botánica, Universidad Miguel Hernández, Elche, Alicante, Spain
| | - Antonio Roldán
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation, Campus de Espinardo, Murcia, Spain
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Dai M, Bainard LD, Hamel C, Gan Y, Lynch D. Impact of land use on arbuscular mycorrhizal fungal communities in rural Canada. Appl Environ Microbiol 2013; 79:6719-29. [PMID: 23995929 PMCID: PMC3811508 DOI: 10.1128/aem.01333-13] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 08/20/2013] [Indexed: 11/20/2022] Open
Abstract
The influence of land use on soil bio-resources is largely unknown. We examined the communities of arbuscular mycorrhizal (AM) fungi in wheat-growing cropland, natural areas, and seminatural areas along roads. We sampled the Canadian prairie extensively (317 sites) and sampled 20 sites in the Atlantic maritime ecozone for comparison. The proportions of the different AM fungal taxa in the communities found at these sites varied with land use type and ecozones, based on pyrosequencing of 18S rRNA gene (rDNA) amplicons, but the lists of AM fungal taxa obtained from the different land use types and ecozones were very similar. In the prairie, the Glomeraceae family was the most abundant and diverse family of Glomeromycota, followed by the Claroideoglomeraceae, but in the Atlantic maritime ecozone, the Claroideoglomeraceae family was most abundant. In the prairie, species richness and Shannon's diversity index were highest in roadsides, whereas cropland had a higher degree of species richness than roadsides in the Atlantic maritime ecozone. The frequencies of occurrence of the different AM fungal taxa in croplands in the prairie and Atlantic maritime ecozones were highly correlated, but the AM fungal communities in these ecozones had different structures. We conclude that the AM fungal resources of soils are resilient to disturbance and that the richness of AM fungi under cropland management has been maintained, despite evidence of a structural shift imposed by this type of land use. Roadsides in the Canadian prairie are a good repository for the conservation of AM fungal diversity.
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Affiliation(s)
- Mulan Dai
- Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, Swift Current, Saskatchewan, Canada
| | - Luke D. Bainard
- Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, Swift Current, Saskatchewan, Canada
| | - Chantal Hamel
- Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, Swift Current, Saskatchewan, Canada
| | - Yantai Gan
- Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, Swift Current, Saskatchewan, Canada
| | - Derek Lynch
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, Canada
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17
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Impact of land use on arbuscular mycorrhizal fungal communities in rural Canada. Appl Environ Microbiol 2013. [PMID: 23995929 DOI: 10.1128/aem.01333‐13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The influence of land use on soil bio-resources is largely unknown. We examined the communities of arbuscular mycorrhizal (AM) fungi in wheat-growing cropland, natural areas, and seminatural areas along roads. We sampled the Canadian prairie extensively (317 sites) and sampled 20 sites in the Atlantic maritime ecozone for comparison. The proportions of the different AM fungal taxa in the communities found at these sites varied with land use type and ecozones, based on pyrosequencing of 18S rRNA gene (rDNA) amplicons, but the lists of AM fungal taxa obtained from the different land use types and ecozones were very similar. In the prairie, the Glomeraceae family was the most abundant and diverse family of Glomeromycota, followed by the Claroideoglomeraceae, but in the Atlantic maritime ecozone, the Claroideoglomeraceae family was most abundant. In the prairie, species richness and Shannon's diversity index were highest in roadsides, whereas cropland had a higher degree of species richness than roadsides in the Atlantic maritime ecozone. The frequencies of occurrence of the different AM fungal taxa in croplands in the prairie and Atlantic maritime ecozones were highly correlated, but the AM fungal communities in these ecozones had different structures. We conclude that the AM fungal resources of soils are resilient to disturbance and that the richness of AM fungi under cropland management has been maintained, despite evidence of a structural shift imposed by this type of land use. Roadsides in the Canadian prairie are a good repository for the conservation of AM fungal diversity.
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Stürmer SL, Stürmer R, Pasqualini D. Taxonomic diversity and community structure of arbuscular mycorrhizal fungi (Phylum Glomeromycota) in three maritime sand dunes in Santa Catarina state, south Brazil. FUNGAL ECOL 2013. [DOI: 10.1016/j.funeco.2012.10.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Torrecillas E, Alguacil MM, Roldán A. Host preferences of arbuscular mycorrhizal fungi colonizing annual herbaceous plant species in semiarid Mediterranean prairies. Appl Environ Microbiol 2012; 78:6180-6. [PMID: 22752164 PMCID: PMC3416610 DOI: 10.1128/aem.01287-12] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 06/20/2012] [Indexed: 11/20/2022] Open
Abstract
In this study, we have analyzed and compared the diversities of the arbuscular mycorrhizal fungi (AMF) colonizing the roots of five annual herbaceous species (Hieracium vulgare, Stipa capensis, Anagallis arvensis, Carduus tenuiflorus, and Avena barbata) and a perennial herbaceous species (Brachypodium retusum). Our goal was to determine the differences in the communities of the AMF among these six plant species belonging to different families, using B. retusum as a reference. The AMF small-subunit rRNA genes (SSU) were subjected to nested PCR, cloning, sequencing, and phylogenetic analysis. Thirty-six AMF phylotypes, belonging to Glomus group A, Glomus group B, Diversispora, Paraglomus, and Ambispora, were identified. Five sequence groups identified in this study clustered to known glomalean species or isolates: group Glomus G27 to Glomus intraradices, group Glomus G19 to Glomus iranicum, group Glomus G10 to Glomus mosseae, group Glomus G1 to Glomus lamellosum/etunicatum/luteum, and group Ambispora 1 to Ambispora fennica. The six plant species studied hosted different AMF communities. A certain trend of AMF specificity was observed when grouping plant species by taxonomic families, highlighting the importance of protecting and even promoting the native annual vegetation in order to maintain the biodiversity and productivity of these extreme ecosystems.
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Affiliation(s)
- E Torrecillas
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation, Campus de Espinardo, Murcia, Spain
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