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Schillaci C, Perego A, Valkama E, Märker M, Saia S, Veronesi F, Lipani A, Lombardo L, Tadiello T, Gamper HA, Tedone L, Moss C, Pareja-Serrano E, Amato G, Kühl K, Dămătîrcă C, Cogato A, Mzid N, Eeswaran R, Rabelo M, Sperandio G, Bosino A, Bufalini M, Tunçay T, Ding J, Fiorentini M, Tiscornia G, Conradt S, Botta M, Acutis M. New pedotransfer approaches to predict soil bulk density using WoSIS soil data and environmental covariates in Mediterranean agro-ecosystems. Sci Total Environ 2021; 780:146609. [PMID: 34030315 DOI: 10.1016/j.scitotenv.2021.146609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/24/2021] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
For the estimation of the soil organic carbon stocks, bulk density (BD) is a fundamental parameter but measured data are usually not available especially when dealing with legacy soil data. It is possible to estimate BD by applying pedotransfer function (PTF). We applied different estimation methods with the aim to define a suitable PTF for BD of arable land for the Mediterranean Basin, which has peculiar climate features that may influence the soil carbon sequestration. To improve the existing BD estimation methods, we used a set of public climatic and topographic data along with the soil texture and organic carbon data. The present work consisted of the following steps: i) development of three PTFs models separately for top (0-0.4 m) and subsoil (0.4-1.2 m), ii) a 10-fold cross-validation, iii) model transferability using an external dataset derived from published data. The development of the new PTFs was based on the training dataset consisting of World Soil Information Service (WoSIS) soil profile data, climatic data from WorldClim at 1 km spatial resolution and Shuttle Radar Topography Mission (SRTM) digital elevation model at 30 m spatial resolution. The three PTFs models were developed using: Multiple Linear Regression stepwise (MLR-S), Multiple Linear Regression backward stepwise (MLR-BS), and Artificial Neural Network (ANN). The predictions of the newly developed PTFs were compared with the BD calculated using the PTF proposed by Manrique and Jones (MJ) and the modelled BD derived from the global SoilGrids dataset. For the topsoil training dataset (N = 129), MLR-S, MLR-BS and ANN had a R2 0.35, 0.58 and 0.86, respectively. For the model transferability, the three PTFs applied to the external topsoil dataset (N = 59), achieved R2 values of 0.06, 0.03 and 0.41. For the subsoil training dataset (N = 180), MLR-S, MLR-BS and ANN the R2 values were 0.36, 0.46 and 0.83, respectively. When applied to the external subsoil dataset (N = 29), the R2 values were 0.05, 0.06 and 0.41. The cross-validation for both top and subsoil dataset, resulted in an intermediate performance compared to calibration and validation with the external dataset. The new ANN PTF outperformed MLR-S, MLR-BS, MJ and SoilGrids approaches for estimating BD. Further improvements may be achieved by additionally considering the time of sampling, agricultural soil management and cultivation practices in predictive models.
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Affiliation(s)
- Calogero Schillaci
- Department of Agricultural and Environmental Science, University of Milan, Via Celoria 2, Milan, Italy
| | - Alessia Perego
- Department of Agricultural and Environmental Science, University of Milan, Via Celoria 2, Milan, Italy.
| | - Elena Valkama
- Natural Resources Institute Finland (Luke), Bioeconomy and Environment, FI-31600, Tietotie 4, Jokioinen, Finland
| | - Michael Märker
- Department of Earth and Environmental Sciences, University of Pavia, Via Ferrata, 1, 27100 Pavia, Italy
| | - Sergio Saia
- Department of Veterinary Sciences, University of Pisa, Via delle Piagge 2, Pisa 56129, Italy
| | - Fabio Veronesi
- Water Research Centre Limited, Frankland Road, Blagrove, Swindon, Wiltshire SN56 8YF, England, UK
| | - Aldo Lipani
- Department of Web Intelligence Group, University College London (UCL), 90 High Holborn, London, England, UK
| | - Luigi Lombardo
- Faculty of Geo-Information Science and Earth Observation (ITC), University of Twente, PO Box 217, Enschede AE 7500, the Netherlands
| | - Tommaso Tadiello
- Department of Agricultural and Environmental Science, University of Milan, Via Celoria 2, Milan, Italy
| | - Hannes A Gamper
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Piazza Università, 5 39100 Bolzano, Italy
| | - Luigi Tedone
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, Via Amendola 165/A-, 70126 Bari, Italy
| | - Cami Moss
- Department of Population Health, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | | | - Gabriele Amato
- Applied Physics Institute, Nello Carrara - National Research Council of Italy (IFAC-CNR), Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy
| | - Kersten Kühl
- Department of Geography, Ludwig-Maximilians-Universität München (LMU Munich), Germany
| | - Claudia Dămătîrcă
- Department of Agricultural, Forest and Food Sciences, University of Torino, largo Braccini 2, 10095 Grugliasco, Italy
| | - Alessia Cogato
- Department of Land, Environmental, Agriculture and Forestry, University of Padova, 35020 Legnaro, Italy
| | - Nada Mzid
- Department of Agriculture Forestry and Nature (DAFNE), University of Tuscia, 01100 Viterbo, Italy
| | - Rasu Eeswaran
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing MI48824, USA
| | - Marya Rabelo
- Department of Agriculture, Food and Environment, University of Pisa, via del Borghetto 80, 56124 Pisa, Italy
| | - Giorgio Sperandio
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa, 11, 25123 Brescia, Italy
| | - Alberto Bosino
- Department of Earth and Environmental Sciences, University of Pavia, Via Ferrata, 1, 27100 Pavia, Italy
| | - Margherita Bufalini
- University of Camerino, School of Science and Technology-Geology Division, Via Gentile III da Varano, Camerino 62032, Italy
| | - Tülay Tunçay
- Soil Fertilizer and Water Resources Central Research Institute, Ankara, Turkey
| | - Jianqi Ding
- Department of Biological and Ecological Sciences DEB, Università della Tuscia, Viterbo, Italy
| | - Marco Fiorentini
- Department of Agricultural, Food and Environmental Sciences (D3A), Marche Polytechnic University, Ancona, Italy
| | - Guadalupe Tiscornia
- Instituto Nacional de Investigación Agropecuaria (INIA), Unidad Agroclima y Sistemas de Información (GRAS), Ruta 48 KM10, Canelones 90200, Uruguay
| | | | - Marco Botta
- Department of Agricultural and Environmental Science, University of Milan, Via Celoria 2, Milan, Italy
| | - Marco Acutis
- Department of Agricultural and Environmental Science, University of Milan, Via Celoria 2, Milan, Italy
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Cardini A, Pellegrino E, Del Dottore E, Gamper HA, Mazzolai B, Ercoli L. HyLength: a semi-automated digital image analysis tool for measuring the length of roots and fungal hyphae of dense mycelia. Mycorrhiza 2020; 30:229-242. [PMID: 32300867 DOI: 10.1007/s00572-020-00956-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
In plant-fungus phenotyping, determining fungal hyphal and plant root lengths by digital image analysis can reduce labour and increase data reproducibility. However, the degree of software sophistication is often prohibitive and manual measuring is still used, despite being very time-consuming. We developed the HyLength tool for measuring the lengths of hyphae and roots in in vivo and in vitro systems. The HyLength was successfully validated against manual measures of roots and fungal hyphae obtained from all systems. Compared with manual methods, the HyLength underestimated Medicago sativa roots in the in vivo system and Rhizophagus irregularis hyphae in the in vitro system by about 12 cm per m and allowed to save about 1 h for a single experimental unit. As regards hyphae of R. irregularis in the in vivo system, the HyLength overestimated the length by about 21 cm per m compared with manual measures, but time saving was up to 20.5 h per single experimental unit. Finally, with hyphae of Aspergillus oryzae, the underestimation was about 8 cm per m with a time saving of about 10 min for a single germinating spore. By benchmarking the HyLength against the AnaMorf plugin of the ImageJ/Fiji, we found that the HyLength performed better for dense fungal hyphae, also strongly reducing the measuring time. The HyLength can allow measuring the length over a whole experimental unit, eliminating the error due to sub-area selection by the user and allowing processing a high number of samples. Therefore, we propose the HyLength as a useful freeware tool for measuring fungal hyphae of dense mycelia.
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Affiliation(s)
- Alessio Cardini
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy
| | - Elisa Pellegrino
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.
| | - Emanuela Del Dottore
- Center for Micro-BioRobotics, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, 56025, Pontedera, Pisa, Italy
| | - Hannes A Gamper
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy
- Free University of Bozen-Bolzano, Faculty of Science and Technology, Universitätsplatz 5 - piazza Università 5, 39100, Bozen-Bolzano, Italy
| | - Barbara Mazzolai
- Center for Micro-BioRobotics, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, 56025, Pontedera, Pisa, Italy
| | - Laura Ercoli
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy
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Pellegrino E, Gamper HA, Ciccolini V, Ercoli L. Forage Rotations Conserve Diversity of Arbuscular Mycorrhizal Fungi and Soil Fertility. Front Microbiol 2020; 10:2969. [PMID: 31998261 PMCID: PMC6962183 DOI: 10.3389/fmicb.2019.02969] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 12/09/2019] [Indexed: 01/07/2023] Open
Abstract
In the Mediterranean, long-term impact of typical land uses on soil fertility have not been quantified yet on replicated mixed crop-livestock farms and considering the variability of soil texture. Here, we report the effects, after 15 years of practice, of two legume-winter cereal rotations, olive orchards and vineyards on microbiological and chemical indicators of soil fertility and the communities of arbuscular mycorrhizal fungi (AMF). We compare the changes among these four agricultural land-use types to woodland reference sites. Root colonization by AMF of English ryegrass (Lolium perenne L.), a grass that occurred under all land use types, was only half as heavy in biannual berseem clover (Trifolium alexandrinum L.)-winter cereal rotations than in 4-year alfalfa (Medicago sativa L.)-winter cereal rotations. In olive (Olea europaea L.) orchards and vineyards (Vitis vinifera L.), where weeds are controlled by frequent surface tillage, the AMF root colonization of ryegrass was again much lower than in the legume-cereal rotations and at the woodland reference sites. All the microbial parameters and soil organic carbon correlated most strongly with differences in occurrence and relative abundance (β-diversity) of AMF genera in soil. The soil pH and mineral nutrients in soil strongly correlated with differences in AMF root colonization and AMF genus richness (α-diversity) in soil. Diversity of AMF was much less affected by soil texture than land use, while the opposite was true for microbial and chemical soil fertility indicators. Land uses that guaranteed a continuous ground cover of herbaceous plants and that involved only infrequent tillage, such as multiyear alfalfa-winter cereal rotation, allowed members of the AMF genus Scutellospora to persist and remain abundant. On the contrary, under land uses accompanied by frequent tillage and hence discontinuous presence of herbaceous plants, such as tilled olive orchard and vineyard, members of the genus Funneliformis dominated. These results suggest that multiyear alfalfa-winter cereal rotation with active plant growth throughout the year is the least detrimental agricultural land use in soil carbon and AMF abundance and diversity, relative to the woodland reference.
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Affiliation(s)
- Elisa Pellegrino
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy
| | - Hannes A. Gamper
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy
| | | | - Laura Ercoli
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy
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Ndungu SM, Messmer MM, Ziegler D, Gamper HA, Mészáros É, Thuita M, Vanlauwe B, Frossard E, Thonar C. Cowpea ( Vigna unguiculata L. Walp) hosts several widespread bradyrhizobial root nodule symbionts across contrasting agro-ecological production areas in Kenya. Agric Ecosyst Environ 2018; 261:161-171. [PMID: 29970945 PMCID: PMC5946706 DOI: 10.1016/j.agee.2017.12.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 09/18/2017] [Accepted: 12/15/2017] [Indexed: 06/08/2023]
Abstract
Cowpea (Vigna unguiculata L. Walp.) is an important African food legume suitable for dry regions. It is the main legume in two contrasting agro-ecological regions of Kenya as an important component of crop rotations because of its relative tolerance to unpredictable drought events. This study was carried out in an effort to establish a collection of bacterial root nodule symbionts and determine their relationship to physicochemical soil parameters as well as any geographical distributional patterns. Bradyrhizobium spp. were found to be widespread in this study and several different types could be identified at each site. Unique but rare symbionts were recovered from the nodules of plants sampled in a drier in-land region, where there were also overall more different bradyrhizobia found. Plants raised in soil from uncultivated sites with a natural vegetation cover tended to also associate with more different bradyrizobia. The occurrence and abundance of different bradyrhizobia correlated with differences in soil texture and pH, but did neither with the agro-ecological origin, nor the origin from cultivated (n = 15) or uncultivated (n = 5) sites. The analytical method, protein profiling of isolated strains by Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS), provided higher resolution than 16S rRNA gene sequencing and was applied in this study for the first time to isolates recovered directly from field-collected cowpea root nodules. The method thus seems suitable for screening isolate collections on the presence of different groups, which, provided an appropriate reference database, can also be assigned to known species.
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Affiliation(s)
- Samuel Mathu Ndungu
- Institute of Agricultural Sciences, ETH Zurich Plant Nutrition group Eschikon 33, CH-8315 Lindau, Switzerland
- International Institute of Tropical Agriculture (IITA), c/o ICIPE Campus, P.O. Box 30772-00100 Nairobi, Kenya
- Research Institute of Organic Agriculture (FiBL), Ackerstrasse 113, CH-5070 Frick, Switzerland
| | - Monika M. Messmer
- Research Institute of Organic Agriculture (FiBL), Ackerstrasse 113, CH-5070 Frick, Switzerland
| | - Dominik Ziegler
- Mabritec AG, Lörracherstrasse 50, CH-4125 Riehen, Switzerland
| | - Hannes A. Gamper
- Institute of Agricultural Sciences, ETH Zurich Plant Nutrition group Eschikon 33, CH-8315 Lindau, Switzerland
| | - Éva Mészáros
- Institute of Agricultural Sciences, ETH Zurich Plant Nutrition group Eschikon 33, CH-8315 Lindau, Switzerland
| | - Moses Thuita
- International Institute of Tropical Agriculture (IITA), c/o ICIPE Campus, P.O. Box 30772-00100 Nairobi, Kenya
| | - Bernard Vanlauwe
- International Institute of Tropical Agriculture (IITA), c/o ICIPE Campus, P.O. Box 30772-00100 Nairobi, Kenya
| | - Emmanuel Frossard
- Institute of Agricultural Sciences, ETH Zurich Plant Nutrition group Eschikon 33, CH-8315 Lindau, Switzerland
| | - Cécile Thonar
- Research Institute of Organic Agriculture (FiBL), Ackerstrasse 113, CH-5070 Frick, Switzerland
- Current address: AgroBioChem Department, Gembloux Agro-Bio Tech, University of Liège, B-5030 Gembloux, Belgium
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Aghili F, Gamper HA, Eikenberg J, Khoshgoftarmanesh AH, Afyuni M, Schulin R, Jansa J, Frossard E. Green manure addition to soil increases grain zinc concentration in bread wheat. PLoS One 2014; 9:e101487. [PMID: 24999738 PMCID: PMC4084887 DOI: 10.1371/journal.pone.0101487] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 06/07/2014] [Indexed: 11/18/2022] Open
Abstract
Zinc (Zn) deficiency is a major problem for many people living on wheat-based diets. Here, we explored whether addition of green manure of red clover and sunflower to a calcareous soil or inoculating a non-indigenous arbuscular mycorrhizal fungal (AMF) strain may increase grain Zn concentration in bread wheat. For this purpose we performed a multifactorial pot experiment, in which the effects of two green manures (red clover, sunflower), ZnSO4 application, soil γ-irradiation (elimination of naturally occurring AMF), and AMF inoculation were tested. Both green manures were labeled with 65Zn radiotracer to record the Zn recoveries in the aboveground plant biomass. Application of ZnSO4 fertilizer increased grain Zn concentration from 20 to 39 mg Zn kg-1 and sole addition of green manure of sunflower to soil raised grain Zn concentration to 31 mg Zn kg-1. Adding the two together to soil increased grain Zn concentration even further to 54 mg Zn kg-1. Mixing green manure of sunflower to soil mobilized additional 48 µg Zn (kg soil)-1 for transfer to the aboveground plant biomass, compared to the total of 132 µg Zn (kg soil)-1 taken up from plain soil when neither green manure nor ZnSO4 were applied. Green manure amendments to soil also raised the DTPA-extractable Zn in soil. Inoculating a non-indigenous AMF did not increase plant Zn uptake. The study thus showed that organic matter amendments to soil can contribute to a better utilization of naturally stocked soil micronutrients, and thereby reduce any need for major external inputs.
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Affiliation(s)
- Forough Aghili
- Institute of Agricultural Sciences, Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH) Zürich, Switzerland
| | - Hannes A. Gamper
- Institute of Agricultural Sciences, Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH) Zürich, Switzerland
| | - Jost Eikenberg
- Paul Scherrer Institute (PSI), Radioanalytics Laboratory, Villigen, Switzerland
| | - Amir H. Khoshgoftarmanesh
- College of Agriculture, Department of Soil Sciences, Isfahan University of Technology, Isfahan, Iran
| | - Majid Afyuni
- College of Agriculture, Department of Soil Sciences, Isfahan University of Technology, Isfahan, Iran
| | - Rainer Schulin
- Institute of Terrestrial Ecosystems, Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH) Zürich, Switzerland
| | - Jan Jansa
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Emmanuel Frossard
- Institute of Agricultural Sciences, Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH) Zürich, Switzerland
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Pellegrino E, Turrini A, Gamper HA, Cafà G, Bonari E, Young JPW, Giovannetti M. Establishment, persistence and effectiveness of arbuscular mycorrhizal fungal inoculants in the field revealed using molecular genetic tracing and measurement of yield components. New Phytol 2012; 194:810-822. [PMID: 22380845 DOI: 10.1111/j.1469-8137.2012.04090.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
• Inoculation of crop plants by non-native strains of arbuscular mycorrhizal (AM) fungi as bio-enhancers is promoted without clear evidence for symbiotic effectiveness and fungal persistence. To address such gaps, the forage legume Medicago sativa was inoculated in an agronomic field trial with two isolates of Funneliformis mosseae differing in their nuclear rDNA sequences from native strains. • The inoculants were traced by PCR with a novel combination of the universal fungal NS31 and Glomeromycota-specific LSUGlom1 primers which target the nuclear rDNA cistron. The amplicons were classified by restriction fragment length polymorphism and sequencing. • The two applied fungal inoculants were successfully traced and discriminated from native strains in roots sampled from the field up to 2 yr post inoculation. Moreover, field inoculation with inocula of non-native isolates of F. mosseae appeared to have stimulated root colonization and yield of M. sativa. • Proof of inoculation success and sustained positive effects on biomass production and quality of M. sativa crop plants hold promise for the role that AM fungal inoculants could play in agriculture.
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Affiliation(s)
- Elisa Pellegrino
- Institute of Life Sciences, Scuola Superiore Sant'Anna, P.za Martiri della Libertà 33, 56127 Pisa, Italy
- Department of Crop Plant Biology, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Alessandra Turrini
- Department of Crop Plant Biology, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Hannes A Gamper
- Department of Environmental Sciences, University of Basel, Hebelstrasse 1, 4056 Basel, Switzerland
- Group of Plant Nutrition, Institute of Agricultural Sciences, Swiss Federal Institute of Technology Zurich, Eschikon 33, 8315 Lindau (ZH), Switzerland
| | - Giovanni Cafà
- Department of Crop Plant Biology, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Enrico Bonari
- Institute of Life Sciences, Scuola Superiore Sant'Anna, P.za Martiri della Libertà 33, 56127 Pisa, Italy
| | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK
| | - Manuela Giovannetti
- Department of Crop Plant Biology, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
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Blum M, Gamper HA, Waldner M, Sierotzki H, Gisi U. The cellulose synthase 3 (CesA3) gene of oomycetes: structure, phylogeny and influence on sensitivity to carboxylic acid amide (CAA) fungicides. Fungal Biol 2012; 116:529-42. [PMID: 22483051 DOI: 10.1016/j.funbio.2012.02.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 01/16/2012] [Accepted: 02/06/2012] [Indexed: 11/17/2022]
Abstract
Proper disease control is very important to minimize yield losses caused by oomycetes in many crops. Today, oomycete control is partially achieved by breeding for resistance, but mainly by application of single-site mode of action fungicides including the carboxylic acid amides (CAAs). Despite having mostly specific targets, fungicidal activity can differ even in species belonging to the same phylum but the underlying mechanisms are often poorly understood. In an attempt to elucidate the phylogenetic basis and underlying molecular mechanism of sensitivity and tolerance to CAAs, the cellulose synthase 3 (CesA3) gene was isolated and characterized, encoding the target site of this fungicide class. The CesA3 gene was present in all 25 species included in this study representing the orders Albuginales, Leptomitales, Peronosporales, Pythiales, Rhipidiales and Saprolegniales, and based on phylogenetic analyses, enabled good resolution of all the different taxonomic orders. Sensitivity assays using the CAA fungicide mandipropamid (MPD) demonstrated that only species belonging to the Peronosporales were inhibited by the fungicide. Molecular data provided evidence, that the observed difference in sensitivity to CAAs between Peronosporales and CAA tolerant species is most likely caused by an inherent amino acid configuration at position 1109 in CesA3 possibly affecting fungicide binding. The present study not only succeeded in linking CAA sensitivity of various oomycetes to the inherent CesA3 target site configuration, but could also relate it to the broader phylogenetic context.
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Affiliation(s)
- Mathias Blum
- Institute of Botany, Section Plant Physiology, University of Basel, Basel, Switzerland.
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Verbruggen E, Röling WFM, Gamper HA, Kowalchuk GA, Verhoef HA, van der Heijden MGA. Positive effects of organic farming on below-ground mutualists: large-scale comparison of mycorrhizal fungal communities in agricultural soils. New Phytol 2010; 186:968-979. [PMID: 20345633 DOI: 10.1111/j.1469-8137.2010.03230.x] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
*The impact of various agricultural practices on soil biodiversity and, in particular, on arbuscular mycorrhizal fungi (AMF), is still poorly understood, although AMF can provide benefit to plants and ecosystems. Here, we tested whether organic farming enhances AMF diversity and whether AMF communities from organically managed fields are more similar to those of species-rich grasslands or conventionally managed fields. *To address this issue, the AMF community composition was assessed in 26 arable fields (13 pairs of organically and conventionally managed fields) and five semi-natural grasslands, all on sandy soil. Terminal restriction fragment length polymorphism community fingerprinting was used to characterize AMF community composition. *The average number of AMF taxa was highest in grasslands (8.8), intermediate in organically managed fields (6.4) and significantly lower in conventionally managed fields (3.9). Moreover, AMF richness increased significantly with the time since conversion to organic agriculture. AMF communities of organically managed fields were also more similar to those of natural grasslands when compared with those under conventional management, and were less uniform than their conventional counterparts, as expressed by higher beta-diversity (between-site diversity). *We suggest that organic management in agro-ecosystems contributes to the restoration and maintenance of these important below-ground mutualists.
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Affiliation(s)
- Erik Verbruggen
- Department of Ecological Science, Faculty of Earth and Life Sciences, VU University Amsterdam, the Netherlands
| | - Wilfred F M Röling
- Molecular Cell Physiology, Faculty of Earth and Life Sciences, VU University Amsterdam, the Netherlands
| | - Hannes A Gamper
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Boterhoeksestraat 48, 6666 GA Heteren, Heteren, the Netherlands
- Botanical Institute, University of Basel, Hebelstrasse 1, CH-4056 Basel, Switzerland
| | - George A Kowalchuk
- Department of Ecological Science, Faculty of Earth and Life Sciences, VU University Amsterdam, the Netherlands
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Boterhoeksestraat 48, 6666 GA Heteren, Heteren, the Netherlands
| | - Herman A Verhoef
- Department of Ecological Science, Faculty of Earth and Life Sciences, VU University Amsterdam, the Netherlands
| | - Marcel G A van der Heijden
- Department of Ecological Science, Faculty of Earth and Life Sciences, VU University Amsterdam, the Netherlands
- Ecological Farming Systems, Research Station ART, Agroscope Reckenholz Tänikon, Zürich, Switzerland
- Plant-Microbe Interactions, Institute of Environmental Biology, Faculty of Science, Utrecht University, 3508 TB, Utrecht, the Netherlands
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van de Voorde TFJ, van der Putten WH, Gamper HA, Hol WHG, Bezemer TM. Comparing arbuscular mycorrhizal communities of individual plants in a grassland biodiversity experiment. New Phytol 2010; 186:746-754. [PMID: 20298485 DOI: 10.1111/j.1469-8137.2010.03216.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Plants differ greatly in the soil organisms colonizing their roots. However, how soil organism assemblages of individual plant roots can be influenced by plant community properties remains poorly understood. We determined the composition of arbuscular mycorrhizal fungi (AMF) in Jacobaea vulgaris plants, using terminal restriction fragment length polymorphism (T-RFLP). The plants were collected from an experimental field site with sown and unsown plant communities. Natural colonization was allowed for 10 yr in sown and unsown plots. Unsown plant communities were more diverse and spatially heterogeneous than sown ones. Arbuscular mycorrhizal fungi diversity did not differ between sown and unsown plant communities, but there was higher AMF assemblage dissimilarity between individual plants in the unsown plant communities. When we grew J. vulgaris in field soil that was homogenized after collection in order to rule out spatial variation, no differences in AMF dissimilarity between sown and unsown plots were found. Our study shows that experimental manipulation of plant communities in the field, and hence plant community assembly history, can influence the AMF communities of individual plants growing in those plant communities. This awareness is important when interpreting results from field surveys and experimental ecological studies in relation to plant-symbiont interactions.
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Affiliation(s)
- Tess F J van de Voorde
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 40, 6666 ZG Heteren, The Netherlands.
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Abstract
Arbuscular mycorrhizal (AM) fungi form symbiotic associations with the roots of most plants, thereby mediating nutrient and carbon fluxes, plant performance, and ecosystem dynamics. Although considerable effort has been expended to understand the keystone ecological position of AM symbioses, most studies have been limited in scope to recording organism occurrences and identities, as determined from morphological characters and (mainly) ribosomal sequence markers. In order to overcome these restrictions and circumvent the shortcomings of culture- and phylogeny-based approaches, we propose a shift toward plant and fungal protein-encoding genes as more immediate indicators of mycorrhizal contributions to ecological processes. A number of candidate target genes, involved in the uptake of phosphorus and nitrogen, carbon cycling, and overall metabolic activity, are proposed. We discuss the advantages and disadvantages of future protein-encoding gene marker and current (phylo-) taxonomic approaches for studying the impact of AM fungi on plant growth and ecosystem functioning. Approaches based on protein-encoding genes are expected to open opportunities to advance the mechanistic understanding of ecological roles of mycorrhizas in natural and managed ecosystems.
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Affiliation(s)
- Hannes A Gamper
- Botanical Institute, University of Basel, Hebelstrasse 1, CH-4056 Basel, Switzerland.
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11
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Gamper HA, Walker C, Schüßler A. Diversispora celata sp. nov: molecular ecology and phylotaxonomy of an inconspicuous arbuscular mycorrhizal fungus. New Phytol 2009; 182:495-506. [PMID: 19338635 DOI: 10.1111/j.1469-8137.2008.02750.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The increasing numbers of taxonomically unassigned phylotypes reported in molecular ecological studies contrast with the few formally described arbuscular mycorrhizal fungi (AMF; Glomeromycota). Here, a species new to science with Glomus-like spores is phylogenetically, morphologically and ecologically characterized. From single spore isolates of a previously recognized member of the Diversisporaceae from Swiss agricultural grassland, 17 new nuclear internal transcribed spacer (ITS), large subunit (LSU) and small subunit (SSU) ribosomal RNA (rRNA) gene sequences were determined and compared with 14 newly generated sequences of two close relatives and public database sequences, including environmental sequences, of known geographic origin. SSU ribosomal DNA (rDNA) sequence signatures and phylogenies based on ITS, LSU and SSU rDNA sequences show that the fungus belongs to the genus Diversispora. It is described as Diversispora celata sp. nov. Comparison with environmental sequences in the public domain confirmed its molecular genetic distinctiveness and revealed a cross-continental distribution of close relatives. The value of combining morphology and phylogeny to characterize AMF was reinforced by the morphological similarity to other species and the inconspicuous nature of D. celata spores and mycorrhizas. Inclusion of all three nuclear rDNA regions in species descriptions will facilitate species determination from environmental phylotypes.
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Affiliation(s)
- Hannes A Gamper
- Netherlands Institute of Ecology (NIOO-KNAW) - Centre for Terrestrial Ecology, Department of Terrestrial Microbial Ecology, Boterhoeksestraat 48, PO Box 40, 6666 ZG Heteren, The Netherlands
| | - Christopher Walker
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Arthur Schüßler
- Genetics, Department of Biology I, Ludwig-Maximilian-University Munich, Großhadernerstrasse 4, 82152 Planegg-Martinsried, Munich, Germany
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Croll D, Corradi N, Gamper HA, Sanders IR. Multilocus genotyping of arbuscular mycorrhizal fungi and marker suitability for population genetics. New Phytol 2008; 180:564-568. [PMID: 18684159 DOI: 10.1111/j.1469-8137.2008.02602.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- Daniel Croll
- Department of Ecology & Evolution, Biophore Building, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Nicolas Corradi
- Department of Ecology & Evolution, Biophore Building, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Hannes A Gamper
- Netherlands Institute of Ecology, Center for Terrestrial Ecology, Boterhoeksestraat 48, PO Box 40, NL-6666 ZG, Heteren, The Netherlands
| | - Ian R Sanders
- Department of Ecology & Evolution, Biophore Building, University of Lausanne, CH-1015 Lausanne, Switzerland
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Croll D, Wille L, Gamper HA, Mathimaran N, Lammers PJ, Corradi N, Sanders IR. Genetic diversity and host plant preferences revealed by simple sequence repeat and mitochondrial markers in a population of the arbuscular mycorrhizal fungus Glomus intraradices. New Phytol 2008; 178:672-87. [PMID: 18298433 DOI: 10.1111/j.1469-8137.2008.02381.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are important symbionts of plants that improve plant nutrient acquisition and promote plant diversity. Although within-species genetic differences among AMF have been shown to differentially affect plant growth, very little is actually known about the degree of genetic diversity in AMF populations. This is largely because of difficulties in isolation and cultivation of the fungi in a clean system allowing reliable genotyping to be performed. A population of the arbuscular mycorrhizal fungus Glomus intraradices growing in an in vitro cultivation system was studied using newly developed simple sequence repeat (SSR), nuclear gene intron and mitochondrial ribosomal gene intron markers. The markers revealed a strong differentiation at the nuclear and mitochondrial level among isolates. Genotypes were nonrandomly distributed among four plots showing genetic subdivisions in the field. Meanwhile, identical genotypes were found in geographically distant locations. AMF genotypes showed significant preferences to different host plant species (Glycine max, Helianthus annuus and Allium porrum) used before the fungal in vitro culture establishment. Host plants in a field could provide a heterogeneous environment favouring certain genotypes. Such preferences may partly explain within-population patterns of genetic diversity.
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Affiliation(s)
- Daniel Croll
- Department of Ecology & Evolution, Biophore Building, University of Lausanne, CH-1015 Lausanne, Switzerland
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