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Pedrazzini C, Rehner SA, Strasser H, Zemp N, Holderegger R, Widmer F, Enkerli J. Clonal genomic population structure of Beauveria brongniartii and Beauveria pseudobassiana: Pathogens of the common European cockchafer (Melolontha melolontha L.). Environ Microbiol 2024; 26:e16612. [PMID: 38622804 DOI: 10.1111/1462-2920.16612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 03/07/2024] [Indexed: 04/17/2024]
Abstract
Beauveria brongniartii is a fungal pathogen that infects the beetle Melolontha melolontha, a significant agricultural pest in Europe. While research has primarily focused on the use of B. brongniartii for controlling M. melolontha, the genomic structure of the B. brongniartii population remains unknown. This includes whether its structure is influenced by its interaction with M. melolontha, the timing of beetle-swarming flights, geographical factors, or reproductive mode. To address this, we analysed genome-wide SNPs to infer the population genomics of Beauveria spp., which were isolated from infected M. melolontha adults in an Alpine region. Surprisingly, only one-third of the isolates were identified as B. brongniartii, while two-thirds were distributed among cryptic taxa within B. pseudobassiana, a fungal species not previously recognized as a pathogen of M. melolontha. Given the prevalence of B. pseudobassiana, we conducted analyses on both species. We found no spatial or temporal genomic patterns within either species and no correlation with the population structure of M. melolontha, suggesting that the dispersal of the fungi is independent of the beetle. Both species exhibited clonal population structures, with B. brongniartii fixed for one mating type and B. pseudobassiana displaying both mating types. This implies that factors other than mating compatibility limit sexual reproduction. We conclude that the population genomic structure of Beauveria spp. is primarily influenced by predominant asexual reproduction and dispersal.
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Affiliation(s)
- Chiara Pedrazzini
- Molecular Ecology, Agroscope, Zürich, Switzerland
- Institute of Environmental Systems Science, ETH, Zürich, Switzerland
| | - Stephen A Rehner
- Mycology and Nematology Genetic Diversity and Biology Laboratory, United States Department of Agriculture USDA, Beltsville, Maryland, USA
| | - Hermann Strasser
- Institute of Microbiology, Leopold-Franzens University Innsbruck, Innsbruck, Austria
| | - Niklaus Zemp
- Genetic Diversity Centre (GDC), ETH, Zürich, Switzerland
| | - Rolf Holderegger
- Institute of Environmental Systems Science, ETH, Zürich, Switzerland
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | | | - Jürg Enkerli
- Molecular Ecology, Agroscope, Zürich, Switzerland
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2
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Wolf S, Collatz J, Enkerli J, Widmer F, Romeis J. Assessing potential hybridization between a hypothetical gene drive-modified Drosophila suzukii and nontarget Drosophila species. Risk Anal 2023; 43:1921-1932. [PMID: 36693350 DOI: 10.1111/risa.14096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 10/03/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Genetically engineered gene drives (geGD) are potentially powerful tools for suppressing or even eradicating populations of pest insects. Before living geGD insects can be released into the environment, they must pass an environmental risk assessment to ensure that their release will not cause unacceptable harm to non-targeted entities of the environment. A key research question concerns the likelihood that nontarget species will acquire the functional GD elements; such acquisition could lead to reduced abundance or loss of those species and to a disruption of the ecosystem services they provide. The main route for gene flow is through hybridization between the geGD insect strain and closely related species that co-occur in the area of release and its expected dispersal. Using the invasive spotted-wing drosophila, Drosophila suzukii, as a case study, we provide a generally applicable strategy on how a combination of interspecific hybridization experiments, behavioral observations, and molecular genetic analyses can be used to assess the potential for hybridization.
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Affiliation(s)
- Sarah Wolf
- Research Division Agroecology and Environment, Agroscope, Zürich, Switzerland
- Institute for Plant Sciences, University of Bern, Bern, Switzerland
| | - Jana Collatz
- Research Division Agroecology and Environment, Agroscope, Zürich, Switzerland
| | - Jürg Enkerli
- Molecular Ecology, Agroscope, Zürich, Switzerland
| | | | - Jörg Romeis
- Research Division Agroecology and Environment, Agroscope, Zürich, Switzerland
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3
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Pedrazzini C, Strasser H, Zemp N, Holderegger R, Widmer F, Enkerli J. Spatial and temporal patterns in the population genomics of the European cockchafer Melolontha melolontha in the Alpine region. Evol Appl 2023; 16:1586-1597. [PMID: 37752964 PMCID: PMC10519412 DOI: 10.1111/eva.13588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 08/04/2023] [Accepted: 08/12/2023] [Indexed: 09/28/2023] Open
Abstract
The European cockchafer Melolontha melolontha is an agricultural pest in many European countries. Populations have a synchronized 3 or 4 years life cycle, leading to temporally isolated populations. Despite the economic importance and availability of comprehensive historical as well as current records on cockchafer occurrence, population genomic analyses of M. melolontha are missing. For example, the effects of geographic separation caused by the mountainous terrain of the Alps and of temporal isolation on the genomic structure of M. melolontha still remain unknown. To address this gap, we genotyped 475 M. melolontha adults collected during 3 years from 35 sites in a central Alpine region. Subsequent population structure analyses discriminated two main genetic clusters, i.e., the South Tyrol cluster including collections located southeast of the Alpine mountain range, and a northwestern alpine cluster with all the other collections, reflecting distinct evolutionary history and geographic barriers. The "passo di Resia" linking South and North Tyrol represented a regional contact zone of the two genetic clusters, highlighting genomic differentiation between the collections from the northern and southern regions. Although the collections from northwestern Italy were assigned to the northwestern alpine genetic cluster, they displayed evidence of admixture with the South Tyrolean genetic cluster, suggesting shared ancestry. A linear mixed model confirmed that both geographic distance and, to a lower extent, also temporal isolation had a significant effect on the genetic distance among M. melolontha populations. These effects may be attributed to limited dispersal capacity and reproductive isolation resulting from synchronized and non-synchronized swarming flights, respectively. This study contributes to the understanding of the phylogeography of an organism that is recognized as an agricultural problem and provides significant information on the population genomics of insect species with prolonged temporally shifted and locally synchronized life cycles.
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Affiliation(s)
- Chiara Pedrazzini
- Molecular Ecology, AgroscopeZürichSwitzerland
- Institute of Environmental Systems ScienceETHZürichSwitzerland
| | - Hermann Strasser
- Institute of MicrobiologyLeopold‐Franzens University InnsbruckInnsbruckAustria
| | - Niklaus Zemp
- Genetic Diversity Centre (GDC)ETHZürichSwitzerland
| | - Rolf Holderegger
- Institute of Environmental Systems ScienceETHZürichSwitzerland
- Swiss Federal Research Institute WSLBirmensdorfSwitzerland
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Fox A, Widmer F, Lüscher A. Soil microbial community structures are shaped by agricultural systems revealing little temporal variation. Environ Res 2022; 214:113915. [PMID: 35940233 PMCID: PMC9492858 DOI: 10.1016/j.envres.2022.113915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/06/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Many studies in soil microbial ecology are undertaken with a single sampling event, with the influence of temporal progression rarely being considered. Under field conditions, soil samples were taken from different agricultural systems; a sown grassland to maize rotation (MC), an intensively managed permanent grassland (INT), as well as extensively managed permanent grasslands with high (EXT_HP), low to sufficient (EXT_LP) and deficient available P (EXT_DP), six times throughout the 2017 growing season. Thus, this study aimed to determine if any differences in soil microbiome structures between both sharply contrasting (MC - INT - EXT), slightly differing (EXT_HP - EXT_DP) and quite similar (EXT_HP - EXT_LP and EXT_LP - EXT_DP) agricultural systems persist through changing growth conditions within the growing season. For both fungal and bacterial community structure, the influence of agricultural system (CV = 0.256, P < 0.001 and CV = 0.145, P < 0.01, respectively) was much greater than that of temporal progression (√CV = 0.065 and 0.042, respectively, both P < 0.001). Importantly, nearly all agricultural systems persistently harbored significantly distinct fungal community structures across each of the six sampling events (all at least P < 0.05). There were not as many pairwise differences in bacterial community structure between the agricultural systems, but some did persist (MC and EXT_HP ∼ EXT_DP, all P < 0.001). Additionally, persistent indicator fungal OTUs (IndVal >0.7, P ≤ 0.05) associated to each agricultural system (except EXT_LP) were found in each of the six sampling events. These results highlight the temporal stability of pairwise differences in soil microbiome structures between established agricultural systems through changing plant growth conditions, even between those with a comparable management regime. This is a highly relevant finding in informing the sampling strategy of studies in soil microbial ecology as well as for designing efficient soil biodiversity monitoring systems.
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Affiliation(s)
- A Fox
- Forage Production and Grassland Systems, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland; Molecular Ecology, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
| | - F Widmer
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
| | - A Lüscher
- Forage Production and Grassland Systems, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland.
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Gschwend F, Hartmann M, Mayerhofer J, Hug AS, Enkerli J, Gubler A, Meuli RG, Frey B, Widmer F. Site and land-use associations of soil bacteria and fungi define core and indicative taxa. FEMS Microbiol Ecol 2022; 97:fiab165. [PMID: 34940884 PMCID: PMC8752248 DOI: 10.1093/femsec/fiab165] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/21/2021] [Indexed: 11/13/2022] Open
Abstract
Soil microbial diversity has major influences on ecosystem functions and services. However, due to its complexity and uneven distribution of abundant and rare taxa, quantification of soil microbial diversity remains challenging and thereby impeding its integration into long-term monitoring programs. Using metabarcoding, we analyzed soil bacterial and fungal communities at 30 long-term soil monitoring sites from the three land-use types arable land, permanent grassland, and forest with a yearly sampling between snowmelt and first fertilization over five years. Unlike soil microbial biomass and alpha-diversity, microbial community compositions and structures were site- and land-use-specific with CAP reclassification success rates of 100%. The temporally stable site core communities included 38.5% of bacterial and 33.1% of fungal OTUs covering 95.9% and 93.2% of relative abundances. We characterized bacterial and fungal core communities and their land-use associations at the family-level. In general, fungal families revealed stronger land-use associations as compared to bacteria. This is likely due to a stronger vegetation effect on fungal core taxa, while bacterial core taxa were stronger related to soil properties. The assessment of core communities can be used to form cultivation-independent reference lists of microbial taxa, which may facilitate the development of microbial indicators for soil quality and the use of soil microbiota for long-term soil biomonitoring.
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Affiliation(s)
- Florian Gschwend
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Martin Hartmann
- Sustainable Agroecosystems, Institute of Agricultural Sciences, Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 2, CH-8092 Zürich, Switzerland
| | - Johanna Mayerhofer
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Anna-Sofia Hug
- Swiss Soil Monitoring Network NABO, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Jürg Enkerli
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Andreas Gubler
- Swiss Soil Monitoring Network NABO, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Reto G Meuli
- Swiss Soil Monitoring Network NABO, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
| | - Franco Widmer
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
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6
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Fox A, Widmer F, Barreiro A, Jongen M, Musyoki M, Vieira Â, Zimmermann J, Cruz C, Dimitrova-Mårtensson LM, Rasche F, Silva L, Lüscher A. Small-scale agricultural grassland management can affect soil fungal community structure as much as continental scale geographic patterns. FEMS Microbiol Ecol 2021; 97:6430861. [PMID: 34792119 PMCID: PMC8684450 DOI: 10.1093/femsec/fiab148] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/16/2021] [Indexed: 11/25/2022] Open
Abstract
A European transect was established, ranging from Sweden to the Azores, to determine the relative influence of geographic factors and agricultural small-scale management on the grassland soil microbiome. Within each of five countries (factor ‘Country’), which maximized a range of geographic factors, two differing growth condition regions (factor ‘GCR’) were selected: a favorable region with conditions allowing for high plant biomass production and a contrasting less favorable region with a markedly lower potential. Within each region, grasslands of contrasting management intensities (factor ‘MI’) were defined: intensive and extensive, from which soil samples were collected. Across the transect, ‘MI’ was a strong differentiator of fungal community structure, having a comparable effect to continental scale geographic factors (‘Country’). ‘MI’ was also a highly significant driver of bacterial community structure, but ‘Country’ was clearly the stronger driver. For both, ‘GCR’ was the weakest driver. Also at the regional level, strong effects of MI occurred on various measures of the soil microbiome (i.e. OTU richness, management-associated indicator OTUs), though the effects were largely regional-specific. Our results illustrate the decisive influence of grassland MI on soil microbial community structure, over both regional and continental scales, and, thus, highlight the importance of preserving rare extensive grasslands.
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Affiliation(s)
- A Fox
- Forage Production and Grassland Systems, Agroscope, Reckenholzstrasse 191, Zürich, Switzerland.,Molecular Ecology, Agroscope, Reckenholzstrasse 191, Zürich, Switzerland
| | - F Widmer
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, Zürich, Switzerland
| | - A Barreiro
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, P.O. Box 103, SE-230 53 Alnarp, Sweden
| | - M Jongen
- Centro de Ciência e Tecnologia do Ambiente e do Mar (MARETEC), Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisboa, Portugal
| | - M Musyoki
- University of Hohenheim, Hans-Ruthenberg-Institute, Garbenstr. 13, 70599 Stuttgart, Germany
| | - Â Vieira
- InBIO - Research Network in Biodiversity and Evolutionary Biology, Associate Laboratory, CIBIO-Açores, Faculty of Sciences and Technology, University of the Azores, Campus de Ponta Delgada, Rua da Mãe de Deus, 9500-321 Ponta Delgada, Portugal
| | - J Zimmermann
- University of Hohenheim, Hans-Ruthenberg-Institute, Garbenstr. 13, 70599 Stuttgart, Germany
| | - C Cruz
- Centro de Ecologia, Evolução e Alterações Ambientais, (cE3c), FCUL, Campo Grande, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - L-M Dimitrova-Mårtensson
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, P.O. Box 103, SE-230 53 Alnarp, Sweden
| | - F Rasche
- University of Hohenheim, Hans-Ruthenberg-Institute, Garbenstr. 13, 70599 Stuttgart, Germany
| | - L Silva
- InBIO - Research Network in Biodiversity and Evolutionary Biology, Associate Laboratory, CIBIO-Açores, Faculty of Sciences and Technology, University of the Azores, Campus de Ponta Delgada, Rua da Mãe de Deus, 9500-321 Ponta Delgada, Portugal
| | - A Lüscher
- Forage Production and Grassland Systems, Agroscope, Reckenholzstrasse 191, Zürich, Switzerland
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Pedrazzini C, Strasser H, Holderegger R, Widmer F, Enkerli J. Development of a SNP-based tool for the identification and discrimination of Melolontha melolontha and Melolontha hippocastani. Bull Entomol Res 2021; 111:511-516. [PMID: 33461630 DOI: 10.1017/s0007485320000784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The European (Melolontha melolontha L.) and Forest (M. hippocastani F.) cockchafer are widespread pests throughout Central Europe. Both species exhibit a 3-5-year life cycle and occur in temporally shifted populations, which have been monitored and documented for more than 100 years. Visual identification of adults and larvae belonging to these morphologically similar species requires expertise and, particularly in the case of larvae, is challenging and equivocal. The goal of the study was the development of an efficient and fast molecular genetic tool for the identification and discrimination of M. melolontha and M. hippocastani. We established a collection of both species from Switzerland, Austria and Northern Italy in 2016, 2017 and 2018. An approximately 1550 bp long fragment of the cytochrome c oxidase subunit 1 (CO1) mitochondrial gene was amplified and sequenced in 13 M. melolontha and 13 M. hippocastani beetles. Alignment of the new sequences with reference sequences (NCBI GenBank and BOLDSYSTEMS databases) and subsequent phylogenetic analysis revealed consistent clustering of the two species. After the identification of M. melolontha and M. hippocastani species-specific single nucleotide polymorphisms (SNPs) in the CO1 alignment, we developed an effective SNP tool based on the ABI PRISM® SNaPshot™ Multiplex Kit for the rapid and accurate species discrimination of adults and larvae.
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Affiliation(s)
- Chiara Pedrazzini
- Molecular Ecology, Agroscope, Zürich, Switzerland
- Department of Environmental Systems Science, ETH, Zürich, Switzerland
| | - Hermann Strasser
- Institute of Microbiology, Leopold-Franzens University Innsbruck, Innsbruck, Austria
| | - Rolf Holderegger
- Department of Environmental Systems Science, ETH, Zürich, Switzerland
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | | | - Jürg Enkerli
- Molecular Ecology, Agroscope, Zürich, Switzerland
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8
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Mayerhofer J, Thuerig B, Oberhaensli T, Enderle E, Lutz S, Ahrens CH, Fuchs JG, Widmer F. Indicative bacterial communities and taxa of disease-suppressing and growth-promoting composts and their associations to the rhizoplane. FEMS Microbiol Ecol 2021; 97:6373440. [PMID: 34549287 PMCID: PMC8478479 DOI: 10.1093/femsec/fiab134] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 05/08/2021] [Accepted: 09/17/2021] [Indexed: 11/13/2022] Open
Abstract
Compost applications vary in their plant growth promotion and plant disease suppression, likely due to differences in physico-chemical and biological parameters. Our hypothesis was that bacteria are important for plant growth promotion and disease suppression of composts and, therefore, composts having these traits would contain similar sets of indicative bacterial taxa. Seventeen composts prepared from five different commercial providers and different starting materials were classified accordingly with bioassays using cress plants and the pathogen Pythium ultimum. Using a metabarcoding approach, bacterial communities were assessed in bulk composts and cress rhizoplanes. Six and nine composts showed significant disease suppression or growth promotion, respectively, but these traits did not correlate. Growth promotion correlated positively with nitrate content of composts, whereas disease suppression correlated negatively with factors representing compost age. Growth promotion and disease suppression explained significant portions of variation in bacterial community structures, i.e. 11.5% and 14.7%, respectively. Among the sequence variants (SVs) associated with growth promotion, Microvirga, Acinetobacter, Streptomyces, Bradyrhizobium and Bacillus were highly promising, while in suppressive composts, Ureibacillus,Thermogutta and Sphingopyxis were most promising. Associated SVs represent the basis for developing prediction tools for growth promotion and disease suppression, a highly desired goal for targeted compost production and application.
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Affiliation(s)
| | - Barbara Thuerig
- Crop Protection and Phytopathology, FiBL Research Institute of Organic Agriculture, 5070, Frick, Switzerland
| | - Thomas Oberhaensli
- Crop Protection and Phytopathology, FiBL Research Institute of Organic Agriculture, 5070, Frick, Switzerland
| | - Eileen Enderle
- Crop Protection and Phytopathology, FiBL Research Institute of Organic Agriculture, 5070, Frick, Switzerland
| | - Stefanie Lutz
- Molecular Diagnostics, Genomics and Bioinformatics, Agroscope, 8820, Wädenswil, Switzerland
| | - Christian H Ahrens
- Molecular Diagnostics, Genomics and Bioinformatics, Agroscope, 8820, Wädenswil, Switzerland.,Bioinformatics and Proteogenomics, SIB Swiss Institute of Bioinformatics, 8820, Wädenswil, Switzerland
| | - Jacques G Fuchs
- Crop Protection and Phytopathology, FiBL Research Institute of Organic Agriculture, 5070, Frick, Switzerland
| | - Franco Widmer
- Molecular Ecology, Agroscope, 8046, Zurich, Switzerland
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Longepierre M, Widmer F, Keller T, Weisskopf P, Colombi T, Six J, Hartmann M. Limited resilience of the soil microbiome to mechanical compaction within four growing seasons of agricultural management. ISME Commun 2021; 1:44. [PMID: 36740718 PMCID: PMC9723577 DOI: 10.1038/s43705-021-00046-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023]
Abstract
Soil compaction affects many soil functions, but we have little information on the resistance and resilience of soil microorganisms to this disturbance. Here, we present data on the response of soil microbial diversity to a single compaction event and its temporal evolution under different agricultural management systems during four growing seasons. Crop yield was reduced (up to -90%) in the first two seasons after compaction, but mostly recovered in subsequent seasons. Soil compaction increased soil bulk density (+15%), and decreased air permeability (-94%) and gas diffusion (-59%), and those properties did not fully recover within four growing seasons. Soil compaction induced cropping system-dependent shifts in microbial community structures with little resilience over the four growing seasons. Microbial taxa sensitive to soil compaction were detected in all major phyla. Overall, anaerobic prokaryotes and saprotrophic fungi increased in compacted soils, whereas aerobic prokaryotes and plant-associated fungi were mostly negatively affected. Most measured properties showed large spatial variability across the replicated blocks, demonstrating the dependence of compaction effects on initial conditions. This study demonstrates that soil compaction is a disturbance that can have long-lasting effects on soil properties and soil microorganisms, but those effects are not necessarily aligned with changes in crop yield.
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Affiliation(s)
- Manon Longepierre
- Sustainable Agroecosystems, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland.
| | | | - Thomas Keller
- Soil Quality and Soil Use, Agroscope, Zurich, Switzerland
- Department of Soil and Environment, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | | | - Tino Colombi
- Department of Soil and Environment, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Johan Six
- Sustainable Agroecosystems, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Martin Hartmann
- Sustainable Agroecosystems, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland.
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10
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Gschwend F, Hartmann M, Hug AS, Enkerli J, Gubler A, Frey B, Meuli RG, Widmer F. Long-term stability of soil bacterial and fungal community structures revealed in their abundant and rare fractions. Mol Ecol 2021; 30:4305-4320. [PMID: 34160856 PMCID: PMC8456938 DOI: 10.1111/mec.16036] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 06/09/2021] [Accepted: 06/17/2021] [Indexed: 02/06/2023]
Abstract
Despite the importance of soil microorganisms for ecosystem services, long‐term surveys of their communities are largely missing. Using metabarcoding, we assessed temporal dynamics of soil bacterial and fungal communities in three land‐use types, i.e., arable land, permanent grassland, and forest, over five years. Soil microbial communities remained relatively stable and differences over time were smaller than those among sites. Temporal variability was highest in arable soils. Indications for consistent shifts in community structure over five years were only detected at one site for bacteria and at two sites for fungi, which provided further support for long‐term stability of soil microbial communities. A sliding window analysis was applied to assess the effect of OTU abundance on community structures. Partial communities with decreasing OTU abundances revealed a gradually decreasing structural similarity with entire communities. This contrasted with the steep decline of OTU abundances, as subsets of rare OTUs (<0.01%) revealed correlations of up to 0.97 and 0.81 with the entire bacterial and fungal communities. Finally, 23.4% of bacterial and 19.8% of fungal OTUs were identified as scarce, i.e., neither belonging to site‐cores nor correlating to environmental factors, while 67.3% of bacterial and 64.9% of fungal OTUs were identified as rare but not scarce. Our results demonstrate high stability of soil microbial communities in their abundant and rare fractions over five years. This provides a step towards defining site‐specific normal operating ranges of soil microbial communities, which is a prerequisite for detecting community shifts that may occur due to changing environmental conditions or anthropogenic activities.
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Affiliation(s)
| | - Martin Hartmann
- Sustainable Agroecosystems, Institute of Agricultural Sciences, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Anna-Sofia Hug
- Swiss Soil Monitoring Network NABO, Agroscope, Zürich, Switzerland
| | - Jürg Enkerli
- Molecular Ecology, Agroscope, Zürich, Switzerland
| | - Andreas Gubler
- Swiss Soil Monitoring Network NABO, Agroscope, Zürich, Switzerland
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Reto G Meuli
- Swiss Soil Monitoring Network NABO, Agroscope, Zürich, Switzerland
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Mayerhofer J, Wächter D, Calanca P, Kohli L, Roth T, Meuli RG, Widmer F. Environmental and Anthropogenic Factors Shape Major Bacterial Community Types Across the Complex Mountain Landscape of Switzerland. Front Microbiol 2021; 12:581430. [PMID: 33776948 PMCID: PMC7990788 DOI: 10.3389/fmicb.2021.581430] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 07/08/2020] [Accepted: 02/19/2021] [Indexed: 11/13/2022] Open
Abstract
Mountain areas harbor large climatic and geographic gradients and form numerous habitats that promote high overall biodiversity. Compared to macroorganisms, knowledge about drivers of biodiversity and distribution of soil bacteria in mountain regions is still scarce but a prerequisite for conservation of bacterial functions in soils. An important question is, whether soil bacterial communities with similar structures share environmental preferences. Using metabarcoding of the 16S rRNA gene marker, we assessed soil bacterial communities at 255 sites of a regular grid covering the mountainous landscape of Switzerland, which is characterized by close location of biogeographic regions that harbor different land-use types. Distribution of bacterial communities was mainly shaped by environmental selection, as revealed by 47.9% variance explained by environmental factors, with pH (29%) being most important. Little additional variance was explained by biogeographic regions (2.8%) and land-use types (3.3%). Cluster analysis of bacterial community structures revealed six bacterial community types (BCTs), which were associated to several biogeographic regions and land-use types but overall differed mainly in their preference for soil pH. BCT I and II occurred at neutral pH, showed distinct preferences for biogeographic regions mainly differing in elevation and nutrient availability. BCT III and IV differed only in their preferred soil pH. BCT VI occurred in most acidic soils (pH 3.6) and almost exclusively at forest sites. BCT V occurred in soils with a mean pH of 4 and differed from BCT VI in preference for lower values of organic C, total nitrogen and their ratio. Indicator species and bipartite network analyses revealed 3,998 OTUs associating to different levels of environmental factors and BCTs. Taxonomic classification revealed opposing associations of taxa deriving from the same phyla. The results revealed that pH, land-use type, biogeographic region, and nutrient availability were the main factors shaping bacterial communities across Switzerland. Indicator species and bipartite network analyses revealed environmental preferences of bacterial taxa. Combining information of environmental factors and BCTs yielded increased resolution of the factors shaping soil bacterial communities and provided an improved biodiversity framework. OTUs exclusively associated to BCTs provide a novel resource to identify unassessed environmental drivers.
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Affiliation(s)
| | - Daniel Wächter
- Swiss Soil Monitoring Network, Agroscope, Zurich, Switzerland
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12
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Mayerhofer J, Enkerli J, Widmer F. Small bias of one highly dominant taxon on community analyses using amplicon sequencing. J Microbiol Methods 2020; 178:106069. [PMID: 33007337 DOI: 10.1016/j.mimet.2020.106069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 11/16/2022]
Abstract
Amplicon sequencing allows for simultaneous assessment of inoculation success and responses of indigenous communities after microbial inoculation. However, the presence of a highly dominant taxon may bias correct assessment of communities due to dilution effects, chimera formation, or preferential amplification. Here, we present a simple test to assess these biases.
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Affiliation(s)
- Johanna Mayerhofer
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, 8046 Zürich, Switzerland.
| | - Jürg Enkerli
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, 8046 Zürich, Switzerland
| | - Franco Widmer
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, 8046 Zürich, Switzerland
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13
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Fox A, Lüscher A, Widmer F. Plant species identity drives soil microbial community structures that persist under a following crop. Ecol Evol 2020; 10:8652-8668. [PMID: 32884648 PMCID: PMC7452769 DOI: 10.1002/ece3.6560] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 02/25/2020] [Revised: 05/25/2020] [Accepted: 06/08/2020] [Indexed: 12/18/2022] Open
Abstract
Compared to monocultures, multi-species swards have demonstrated numerous positive diversity effects on aboveground plant performance, such as yield, N concentration, and even legacy effects on a following crop. Whether such diversity effects are seen in the soil microbiome is currently unclear. In a field experiment, we analyzed the effect that three plant species (a grass, forb, and legume), and mixtures of these, had on soil fungal and bacterial community structures, as well as their associated legacy effects under a following crop, the grass Lolium multiflorum. We utilized six sward types, three monocultures (Lolium perenne, Cichorium intybus and Trifolium pratense), two bi-species mixtures, and a mixture of the three species. Soil samples were taken from these swards in March (at the end of a three year conditioning phase) and in June, August, and September after L. multiflorum was established, that is, the legacy samplings. When present, the differing monocultures had a significant effect on various aspects of the fungal community: structure, OTU richness, the relative abundance of the phylum Glomeromycota, and indicator OTUs. The effect on bacterial community structure was not as strong. In the multi-species swards, a blending of individual plant species monoculture effects (identity effect) was seen in (a) fungal and bacterial community structure and (b) fungal OTU richness and the relative abundance of the Glomeromycota. This would indicate that plant species identity, rather than diversity effects (i.e., the interactions among the plant species), was the stronger determinant. During the legacy samplings, structural patterns in the fungal and bacterial communities associated with the previous swards were retained, but the effect faded with time. These results highlight that plant species identity can be a strong driver of soil microbial community structures. They also suggest that their legacy effect on the soil microbiome may play a crucial role in following crop performance.
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Affiliation(s)
- Aaron Fox
- Forage Production and Grassland SystemsAgroscopeZürichSwitzerland
- Molecular EcologyAgroscopeZürichSwitzerland
| | - Andreas Lüscher
- Forage Production and Grassland SystemsAgroscopeZürichSwitzerland
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14
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Lutz S, Thuerig B, Oberhaensli T, Mayerhofer J, Fuchs JG, Widmer F, Freimoser FM, Ahrens CH. Harnessing the Microbiomes of Suppressive Composts for Plant Protection: From Metagenomes to Beneficial Microorganisms and Reliable Diagnostics. Front Microbiol 2020; 11:1810. [PMID: 32849417 PMCID: PMC7406687 DOI: 10.3389/fmicb.2020.01810] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [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: 01/27/2020] [Accepted: 07/09/2020] [Indexed: 01/20/2023] Open
Abstract
Soil-borne diseases cause significant yield losses worldwide, are difficult to treat and often only limited options for disease management are available. It has long been known that compost amendments, which are routinely applied in organic and integrated farming as a part of good agricultural practice to close nutrient cycles, can convey a protective effect. Yet, the targeted use of composts against soil-borne diseases is hampered by the unpredictability of the efficacy. Several studies have identified and/or isolated beneficial microorganisms (i.e., bacteria, oomycetes, and fungi) from disease suppressive composts capable of suppressing pathogens (e.g., Pythium and Fusarium) in various crops (e.g., tomato, lettuce, and cucumber), and some of them have been developed into commercial products. Yet, there is growing evidence that synthetic or complex microbial consortia can be more effective in controlling diseases than single strains, but the underlying molecular mechanisms are poorly understood. Currently, a major bottleneck concerns the lack of functional assays to identify the most potent beneficial microorganisms and/or key microbial consortia from complex soil and compost microbiomes, which can harbor tens of thousands of species. This focused review describes microorganisms, which have been isolated from, amended to or found to be abundant in disease-suppressive composts and for which a beneficial effect has been documented. We point out opportunities to increasingly harness compost microbiomes for plant protection through an integrated systems approach that combines the power of functional assays to isolate biocontrol and plant growth promoting strains and further prioritize them, with functional genomics approaches that have been successfully applied in other fields of microbiome research. These include detailed metagenomics studies (i.e., amplicon and shotgun sequencing) to achieve a better understanding of the complex system compost and to identify members of taxa enriched in suppressive composts. Whole-genome sequencing and complete assembly of key isolates and their subsequent functional profiling can elucidate the mechanisms of action of biocontrol strains. Integrating the benefits of these approaches will bring the long-term goals of employing microorganisms for a sustainable control of plant pathogens and developing reliable diagnostic assays to assess the suppressiveness of composts within reach.
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Affiliation(s)
- Stefanie Lutz
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.,SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Barbara Thuerig
- Research Institute of Organic Agriculture (FiBL), Department of Crop Sciences, Frick, Switzerland
| | - Thomas Oberhaensli
- Research Institute of Organic Agriculture (FiBL), Department of Crop Sciences, Frick, Switzerland
| | | | - Jacques G Fuchs
- Research Institute of Organic Agriculture (FiBL), Department of Crop Sciences, Frick, Switzerland
| | - Franco Widmer
- Agroscope, Research Group Molecular Ecology, Zurich, Switzerland
| | - Florian M Freimoser
- Agroscope, Research Group Phytopathology and Zoology in Fruit and Vegetable Production, Wädenswil, Switzerland
| | - Christian H Ahrens
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.,SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
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Romeis J, Widmer F. Assessing the Risks of Topically Applied dsRNA-Based Products to Non-target Arthropods. Front Plant Sci 2020; 11:679. [PMID: 32582240 PMCID: PMC7289159 DOI: 10.3389/fpls.2020.00679] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 04/30/2020] [Indexed: 05/17/2023]
Abstract
RNA interference (RNAi) is a powerful technology that offers new opportunities for pest control through silencing of genes that are essential for the survival of arthropod pests. The approach relies on sequence-specificity of applied double-stranded (ds) RNA that can be designed to have a very narrow spectrum of both the target gene product (RNA) as well as the target organism, and thus allowing highly targeted pest control. Successful RNAi has been reported from a number of arthropod species belonging to various orders. Pest control may be achieved by applying dsRNA as foliar sprays. One of the main concerns related to the use of dsRNA is adverse environmental effects particularly on valued non-target species. Arthropods form an important part of the biodiversity in agricultural landscapes and contribute important ecosystem services. Consequently, environmental risk assessment (ERA) for potential impacts that plant protection products may have on valued non-target arthropods is legally required prior to their placement on the market. We describe how problem formulation can be used to set the context and to develop plausible pathways on how the application of dsRNA-based products could harm valued non-target arthropod species, such as those contributing to biological pest control. The current knowledge regarding the exposure to and the hazard posed by dsRNA in spray products for non-target arthropods is reviewed and suggestions are provided on how to select the most suitable test species and to conduct laboratory-based toxicity studies that provide robust, reliable and interpretable results to support the ERA.
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Affiliation(s)
- Jörg Romeis
- Research Division Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Franco Widmer
- Competence Division Method Development and Analytics, Agroscope, Zurich, Switzerland
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Haller S, Widmer F, Siegfried BD, Zhuo X, Romeis J. Responses of two ladybird beetle species (Coleoptera: Coccinellidae) to dietary RNAi. Pest Manag Sci 2019; 75:2652-2662. [PMID: 30729648 DOI: 10.1002/ps.5370] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 10/22/2018] [Revised: 01/10/2019] [Accepted: 02/04/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND One concern with the adoption of RNAi-based genetically engineered (GE) crops is the potential harm to valued non-target organisms. Species of Coccinellidae (Coleoptera) are important natural enemies and might be exposed to the insecticidal dsRNA produced by the plant. To assess their susceptibility to dietary RNAi, we fed Adalia bipunctata and Coccinella septempunctata with a dsRNA designed to target the vATPase A of the western corn rootworm, Diabrotica virgifera virgifera (Dvv dsRNA). Specific dsRNAs designed to target the vATPase A of the two ladybird beetle species served as positive controls. RESULTS Our results revealed that both species were sensitive to dietary RNAi when ingesting their own dsRNAs, with C. septempunctata being more sensitive than A. bipunctata. Dvv dsRNA also adversely affected the two ladybird beetles as indicated by a significantly (but marginally) prolonged developmental time for A. bipunctata and a significantly reduced survival rate for C. septempunctata. These results, however, were obtained at Dvv dsRNA concentrations that were orders of magnitude higher than expected to occur in the field. Gene expression analyses confirmed the bioactivity of the dsRNA treatments and the results from the feeding bioassays. These results are consistent with the bioinformatics analyses, which revealed a higher number of 21-nucleotide-long matches, a requirement for effective RNAi, of the Dvv dsRNA with the vATPase A of C. septempunctata (34 matches) than with that of A. bipunctata (six matches). CONCLUSION Feeding bioassays revealed that two ladybird species are responsive to dietary RNAi. The two species, however, differed in their sensitivity. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Simone Haller
- Research Division Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Franco Widmer
- Competence Division Method Development and Analytics, Agroscope, Zurich, Switzerland
| | - Blair D Siegfried
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
| | - Xuguo Zhuo
- Department of Entomology, University of Kentucky, Lexington, KY, USA
| | - Jörg Romeis
- Research Division Agroecology and Environment, Agroscope, Zurich, Switzerland
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Knorst V, Byrne S, Yates S, Asp T, Widmer F, Studer B, Kölliker R. Pooled DNA sequencing to identify SNPs associated with a major QTL for bacterial wilt resistance in Italian ryegrass (Lolium multiflorum Lam.). Theor Appl Genet 2019; 132:947-958. [PMID: 30506318 PMCID: PMC6449324 DOI: 10.1007/s00122-018-3250-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/23/2018] [Indexed: 05/27/2023]
Abstract
SNPs and candidate genes associated with bacterial wilt resistance in Italian ryegrass were identified by sequencing the parental plants and pooled F1 progeny of a segregating population. Italian ryegrass (Lolium multiflorum Lam.) is one of the most important forage grass species in temperate regions. Its yield, quality and persistency can significantly be reduced by bacterial wilt, a serious disease caused by Xanthomonas translucens pv. graminis. Although a major QTL for bacterial wilt resistance has previously been reported, detailed knowledge on underlying genes and DNA markers to allow for efficient resistance breeding strategies is currently not available. We used pooled DNA sequencing to characterize a major QTL for bacterial wilt resistance of Italian ryegrass and to develop inexpensive sequence-based markers to efficiently target resistance alleles for marker-assisted recurrent selection. From the mapping population segregating for the QTL, DNA of 44 of the most resistant and 44 of the most susceptible F1 individuals was pooled and sequenced using the Illumina HiSeq 2000 platform. Allele frequencies of 18 × 106 single nucleotide polymorphisms (SNP) were determined in the resistant and susceptible pool. A total of 271 SNPs on 140 scaffold sequences of the reference parental genome showed significantly different allele frequencies in both pools. We converted 44 selected SNPs to KASP™ markers, genetically mapped these proximal to the major QTL and thus validated their association with bacterial wilt resistance. This study highlights the power of pooled DNA sequencing to efficiently target binary traits in biparental mapping populations. It delivers genome sequence data, SNP markers and potential candidate genes which will allow to implement marker-assisted strategies to fix bacterial wilt resistance in outcrossing breeding populations of Italian ryegrass.
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Affiliation(s)
- Verena Knorst
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Universitätsstrasse 2, 8092, Zurich, Switzerland
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, 8046, Zurich, Switzerland
| | - Stephen Byrne
- Crops Science Department, Teagasc, Oak Park, Carlow, R93 XE12, Ireland
| | - Steven Yates
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Universitätsstrasse 2, 8092, Zurich, Switzerland
| | - Torben Asp
- Department of Molecular Biology and Genetics, Section for Crop Genetics and Biotechnology, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Franco Widmer
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, 8046, Zurich, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Universitätsstrasse 2, 8092, Zurich, Switzerland
| | - Roland Kölliker
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Universitätsstrasse 2, 8092, Zurich, Switzerland.
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, 8046, Zurich, Switzerland.
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Hunziker L, Radovanovic D, Jeger R, Pedrazzini G, Cuculi F, Urban P, Erne P, Rickli H, Pilgrim T, Hess F, Simon R, Hangartner P, Hufschmid U, Hornig B, Altwegg L, Trummler S, Windecker S, Rueff T, Loretan P, Roethlisberger C, Evéquoz D, Mang G, Ryser D, Müller P, Jecker R, Kistler W, Hongler T, Stäuble S, Freiwald G, Schmid H, Stauffer J, Cook S, Bietenhard K, Roffi M, Wojtyna W, Schönenberger R, Simonin C, Waldburger R, Schmidli M, Federspiel B, Weiss E, Marty H, Weber K, Zender H, Poepping I, Hugi A, Koltai E, Iglesias J, Erne P, Heimes T, Jordan B, Pagnamenta A, Feraud P, Beretta E, Stettler C, Repond F, Widmer F, Heimgartner C, Polikar R, Bassetti S, Iselin H, Giger M, Egger P, Kaeslin T, Fischer A, Herren T, Eichhorn P, Neumeier C, Flury G, Girod G, Vogel R, Niggli B, Yoon S, Nossen J, Stoller U, Veragut U, Bächli E, Weber A, Schmidt D, Hellermann J, Eriksson U, Fischer T, Peter M, Gasser S, Fatio R, Vogt M, Ramsay D, Wyss C, Bertel O, Maggiorini M, Eberli F, Christen S. Twenty-Year Trends in the Incidence and Outcome of Cardiogenic Shock in AMIS Plus Registry. Circ Cardiovasc Interv 2019; 12:e007293. [DOI: 10.1161/circinterventions.118.007293] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Lukas Hunziker
- Department of Cardiology, Bern University Hospital, Switzerland (L.H., T.P.)
| | - Dragana Radovanovic
- AMIS Plus Data Center, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Switzerland (D.R.)
| | - Raban Jeger
- Division of Cardiology, University Hospital Basel, Switzerland (R.J.)
| | | | - Florim Cuculi
- Heart Centre Lucerne, Luzerner Kantonsspital, Switzerland (F.C.)
| | - Philip Urban
- Cardiology Department, La Tour Hospital, Geneva, Switzerland (P.U.)
| | - Paul Erne
- Department of Biomedicine, University of Basel, Switzerland (P.E.)
| | - Hans Rickli
- Department of Cardiology, Kantonsspital St. Gallen, Switzerland (H.R.)
| | - Thomas Pilgrim
- Department of Cardiology, Bern University Hospital, Switzerland (L.H., T.P.)
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Mayerhofer J, Lutz A, Dennert F, Rehner SA, Kepler RM, Widmer F, Enkerli J. A species-specific multiplexed PCR amplicon assay for distinguishing between Metarhizium anisopliae, M. brunneum, M. pingshaense and M. robertsii. J Invertebr Pathol 2019; 161:23-28. [PMID: 30641044 DOI: 10.1016/j.jip.2019.01.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 01/07/2019] [Accepted: 01/09/2019] [Indexed: 02/01/2023]
Abstract
The fungal species Metarhizium pingshaense, M. anisopliae, M. robertsii, and M. brunneum, a monophyletic group informally referred to as the PARB species complex, are well known facultative entomopathogens, including many commercialized strains used for biological pest control. Accurate and expedient species identification of Metarhizium isolates represents an important first step when addressing ecological as well as application-related questions involving these fungi. To this end, a species-specific multiplexed polymerase chain reaction (PCR) assay was developed for identification and discrimination among Metarhizium PARB complex species, based on unique sequence signature differences within the nuclear ribosomal intergenic spacer (rIGS) and nuclear intergenic spacer regions MzFG546 and MzIGS2. Species-specificities of the four primer pairs were assessed following a three-step approach including: (1) in silico verification of sequence signatures by BLASTN searches against publically available genome and amplicon sequence data, (2) corroboration of assay specificity and robustness by performing test PCR amplifications against a taxonomically curated reference strain collection of 68 Metarhizium strains representing 12 species, and (3) testing against a field collection of 19 unknown Metarhizium isolates from soil of a Swiss meadow. The specificity of these four primer pairs provide an efficient means to detect and discriminate PARB species in studies targeting ecological aspects of indigenous isolates, as well as efficacy, persistence and potential non-target effects of applied biocontrol strains.
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Affiliation(s)
| | - Andy Lutz
- Molecular Ecology, Agroscope, 8046 Zurich, Switzerland
| | - Francesca Dennert
- Molecular Ecology, Agroscope, 8046 Zurich, Switzerland; Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - Stephen A Rehner
- Systematic Mycology and Nematology Genomic Diversity and Biology Laboratory, USDA-ARS, Beltsville, MD 20705-2350, USA
| | - Ryan M Kepler
- Systematic Mycology and Nematology Genomic Diversity and Biology Laboratory, USDA-ARS, Beltsville, MD 20705-2350, USA
| | - Franco Widmer
- Molecular Ecology, Agroscope, 8046 Zurich, Switzerland
| | - Jürg Enkerli
- Molecular Ecology, Agroscope, 8046 Zurich, Switzerland.
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Schmalz G, Berisha L, Wendorff H, Widmer F, Marcinkowski A, Teschler H, Sommerwerck U, Haak R, Kollmar O, Ziebolz D. Association of time under immunosuppression and different immunosuppressive medication on periodontal parameters and selected bacteria of patients after solid organ transplantation. Med Oral Patol Oral Cir Bucal 2018; 23:e326-e334. [PMID: 29680846 PMCID: PMC5945244 DOI: 10.4317/medoral.22238] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 12/18/2017] [Indexed: 02/03/2023] Open
Abstract
Background Aim of this study was to investigate the association of the time under immunosuppression and different immunosuppressive medication on periodontal parameters and selected periodontal pathogenic bacteria of immunosuppressed patients after solid organ transplantation (SOT). Material and Methods 169 Patients after SOT (lung, liver or kidney) were included and divided into subgroups according their time under (0-1, 1-3, 3-6, 6-10 and >10 years) and form of immunosuppression (Tacrolimus, Cyclosporine, Mycophenolate, Glucocorticoids, Sirolimus and monotherapy vs. combination). Periodontal probing depth (PPD) and clinical attachment loss (CAL) were assessed. Periodontal disease severity was classified as healthy/mild, moderate or severe periodontitis. Subgingival biofilm samples were investigated for eleven selected potentially periodontal pathogenic bacteria using polymerasechainreaction. Results The mean PPD and CAL as well as prevalence of Treponema denticola and Capnocytophaga species was shown to be different but heterogeneous depending on time under immunosuppression (p<0.05). Furthermore, only the medication with Cyclosporine was found to show worse periodontal condition compared to patients without Cyclosporine (p<0.05). Prevalence of Porphyromonas gingivalis, Tannerella forsythia and Fusobacterium nucleatum was reduced and prevalence of Parvimonas micra and Capnocytophaga species was increased in patients under immunosuppression with Glucocorticoids, Mycophenolate as well as combination therapy. Conclusions Time under and form of immunosuppression might have an impact on the clinical periodontal and microbiological parameters of patients after SOT. Patients under Cyclosporine medication should receive increased attention. Differences in subgingival biofilm, but not in clinical parameters were found for Glucocorticoids, Mycophenolate and combination therapy, making the clinical relevance of this finding unclear. Key words:Immunosuppression, organ transplantation, periodontitis, periodontal bacteria.
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Affiliation(s)
- G Schmalz
- University Leipzig, Dept. of Cariology, Endodontology and Periodontology, Liebigstr. 12, D 04103 Leipzig, Germany,
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Affiliation(s)
- Cameron Wagg
- Department of Evolutionary Biology and Environmental SciencesUniversity of Zürich Zürich Switzerland
- Institute of EcologyUniversity of Jena Jena Germany
| | - Jan‐Hendrik Dudenhöffer
- Chair of Nature Conservation and Landscape EcologyInstitute of Earth and Environmental SciencesUniversity of Freiburg Freiburg Germany
| | - Franco Widmer
- Molecular Ecology, AgroscopeInstitute for Sustainability Sciences Zürich Switzerland
| | - Marcel G. A. Heijden
- Department of Evolutionary Biology and Environmental SciencesUniversity of Zürich Zürich Switzerland
- Plant‐Soil Interactions, AgroscopeInstitute for Sustainability Sciences Zürich Switzerland
- Plant‐Microbe InteractionsInstitute of Environmental BiologyFaculty of Science Utrecht The Netherlands
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Mayerhofer J, Eckard S, Hartmann M, Grabenweger G, Widmer F, Leuchtmann A, Enkerli J. Assessing effects of the entomopathogenic fungus Metarhizium brunneum on soil microbial communities in Agriotes spp. biological pest control. FEMS Microbiol Ecol 2017; 93:4111146. [PMID: 28961941 PMCID: PMC5812499 DOI: 10.1093/femsec/fix117] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/08/2017] [Indexed: 12/15/2022] Open
Abstract
The release of large quantities of microorganisms to soil for purposes such as pest control or plant growth promotion may affect the indigenous soil microbial communities. In our study, we investigated potential effects of Metarhizium brunneum ART2825 on soil fungi and prokaryota in bulk soil using high-throughput sequencing of ribosomal markers. Different formulations of this strain, and combinations of the fungus with garlic as efficacy-enhancing agent, were tested over 4 months in a pot and a field experiment carried out for biological control of Agriotes spp. in potatoes. A biocontrol effect was observed only in the pot experiment, i.e. the application of FCBK resulted in 77% efficacy. Colony counts combined with genotyping and marker sequence abundance confirmed the successful establishment of the applied strain. Only the formulated applied strain caused small shifts in fungal communities in the pot experiment. Treatment effects were in the same range as the effects caused by barley kernels, the carrier of the FCBK formulation and temporal effects. Garlic treatments and time affected prokaryotic communities. In the field experiment, only spatial differences affected fungal and prokaryotic communities. Our findings suggest that M. brunneum may not adversely affect soil microbial communities.
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Affiliation(s)
| | - Sonja Eckard
- Ecology of Noxious and Beneficial Organisms, Agroscope, CH-8046 Zurich, Switzerland
| | - Martin Hartmann
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, CH-8903 Birmensdorf, Switzerland
| | - Giselher Grabenweger
- Ecology of Noxious and Beneficial Organisms, Agroscope, CH-8046 Zurich, Switzerland
| | - Franco Widmer
- Molecular Ecology, Agroscope, CH-8046 Zurich, Switzerland
| | - Adrian Leuchtmann
- Plant Ecological Genetics, Institute of Integrative Biology, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Jürg Enkerli
- Molecular Ecology, Agroscope, CH-8046 Zurich, Switzerland
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Hersemann L, Wibberg D, Blom J, Goesmann A, Widmer F, Vorhölter FJ, Kölliker R. Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis. BMC Genomics 2017; 18:35. [PMID: 28056815 PMCID: PMC5217246 DOI: 10.1186/s12864-016-3422-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 12/14/2016] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Xanthomonas translucens pathovars differ in their individual host ranges among Poaceae. As the causal agent of bacterial wilt in Italian ryegrass (Lolium multiflorum Lam.), X. translucens pv. graminis (Xtg) is one of the most important bacterial pathogens in temperate grassland regions. The genomes of six Xtg strains from Switzerland, Norway, and New Zealand were sequenced in order to gain insight into conserved genomic traits from organisms covering a wide geographical range. Subsequent comparative analysis with previously published genome data of seven non-graminis X. translucens strains including the pathovars arrhenatheri, poae, phlei, cerealis, undulosa, and translucens was conducted to identify candidate genes linked to the host adaptation of Xtg to Italian ryegrass. RESULTS Phylogenetic analysis revealed a tight clustering of Xtg strains, which were found to share a large core genome. Conserved genomic traits included a non-canonical type III secretion system (T3SS) and a type IV pilus (T4P), which both revealed distinct primary structures of the pilins when compared to the non-graminis X. translucens strains. Xtg-specific traits that had no homologues in the other X. translucens strains were further found to comprise several hypothetical proteins, a TonB-dependent receptor, transporters, and effector proteins as well as toxin-antitoxin systems and DNA methyltransferases. While a nearly complete flagellar gene cluster was identified in one of the sequenced Xtg strains, phenotypic analysis pointed to swimming-deficiency as a common trait of the pathovar graminis. CONCLUSION Our study suggests that host adaptation of X. translucens pv. graminis may be conferred by a combination of pathovar-specific effector proteins, regulatory mechanisms, and adapted nutrient acquisition. Sequence deviations of pathogen-associated molecular patterns (PAMPs), as observed for the pilins of the T4P and T3SS, are moreover likely to impede perception by the plant defense machinery and thus facilitate successful host colonization of Italian ryegrass.
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Affiliation(s)
| | - Daniel Wibberg
- Center for Biotechnology, Bielefeld University, 33615, Bielefeld, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Franco Widmer
- Molecular Ecology, Agroscope, 8046, Zurich, Switzerland
| | - Frank-Jörg Vorhölter
- Center for Biotechnology, Bielefeld University, 33615, Bielefeld, Germany
- MVZ Dr. Eberhard & Partner Dortmund, 44137, Dortmund, Germany
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Kempf K, Malisch C, Grieder C, Widmer F, Kölliker R. Marker-trait association analysis for agronomic and compositional traits in sainfoin (Onobrychis viciifolia). Genet Mol Res 2017; 16:gmr-16-01-gmr.16019483. [DOI: 10.4238/gmr16019483] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Moll J, Okupnik A, Gogos A, Knauer K, Bucheli TD, van der Heijden MGA, Widmer F. Effects of Titanium Dioxide Nanoparticles on Red Clover and Its Rhizobial Symbiont. PLoS One 2016; 11:e0155111. [PMID: 27171465 PMCID: PMC4865228 DOI: 10.1371/journal.pone.0155111] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 04/25/2016] [Indexed: 12/03/2022] Open
Abstract
Titanium dioxide nanoparticles (TiO2 NPs) are in consideration to be used in plant protection products. Before these products can be placed on the market, ecotoxicological tests have to be performed. In this study, the nitrogen fixing bacterium Rhizobium trifolii and red clover were exposed to two TiO2 NPs, i.e., P25, E171 and a non-nanomaterial TiO2. Growth of both organisms individually and their symbiotic root nodulation were investigated in liquid and hydroponic systems. While 23 and 18 mg l-1 of E171 and non-nanomaterial TiO2 decreased the growth rate of R. trifolii by 43 and 23% respectively, P25 did not cause effects. Shoot length of red clover decreased between 41 and 62% for all tested TiO2 NPs. In 21% of the TiO2 NP treated plants, no nodules were found. At high concentrations certain TiO2 NPs impaired R. trifolii as well as red clover growth and their symbiosis in the hydroponic systems.
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Affiliation(s)
- Janine Moll
- Institute for Sustainability Sciences ISS, Agroscope, Zurich, Switzerland
- Plant-Microbe-Interactions, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Annette Okupnik
- Institute for Sustainability Sciences ISS, Agroscope, Zurich, Switzerland
| | - Alexander Gogos
- Institute for Sustainability Sciences ISS, Agroscope, Zurich, Switzerland
| | - Katja Knauer
- Federal Office for Agriculture FOAG, Berne, Switzerland
| | - Thomas D. Bucheli
- Institute for Sustainability Sciences ISS, Agroscope, Zurich, Switzerland
| | - Marcel G. A. van der Heijden
- Institute for Sustainability Sciences ISS, Agroscope, Zurich, Switzerland
- Plant-Microbe-Interactions, Department of Biology, Utrecht University, Utrecht, the Netherlands
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Franco Widmer
- Institute for Sustainability Sciences ISS, Agroscope, Zurich, Switzerland
- * E-mail:
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Moll J, Gogos A, Bucheli TD, Widmer F, van der Heijden MGA. Effect of nanoparticles on red clover and its symbiotic microorganisms. J Nanobiotechnology 2016; 14:36. [PMID: 27161241 PMCID: PMC4862186 DOI: 10.1186/s12951-016-0188-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 04/22/2016] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Nanoparticles are produced and used worldwide and are released to the environment, e.g., into soil systems. Titanium dioxide (TiO2) nanoparticles (NPs), carbon nanotubes (CNTs) and cerium dioxide (CeO2) NPs are among the ten most produced NPs and it is therefore important to test, whether these NPs affect plants and symbiotic microorganisms that help plants to acquire nutrients. In this part of a joint companion study, we spiked an agricultural soil with TiO2 NPs, multi walled CNTs (MWCNTs), and CeO2 NPs and we examined effects of these NP on red clover, biological nitrogen fixation by rhizobia and on root colonization of arbuscular mycorrhizal fungi (AMF). We also tested whether effects depended on the concentrations of the applied NPs. RESULTS Plant biomass and AMF root colonization were not negatively affected by NP exposure. The number of flowers was statistically lower in pots treated with 3 mg kg(-1) MWCNT, and nitrogen fixation slightly increased at 3000 mg kg(-1) MWCNT. CONCLUSIONS This study revealed that red clover was more sensitive to MWCNTs than TiO2 and CeO2 NPs. Further studies are necessary for finding general patterns and investigating mechanisms behind the effects of NPs on plants and plant symbionts.
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Affiliation(s)
- Janine Moll
- />Agroscope, Institute for Sustainability Sciences ISS, 8046 Zurich, Switzerland
- />Plant-Microbe-Interactions, Department of Biology, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Alexander Gogos
- />Agroscope, Institute for Sustainability Sciences ISS, 8046 Zurich, Switzerland
| | - Thomas D. Bucheli
- />Agroscope, Institute for Sustainability Sciences ISS, 8046 Zurich, Switzerland
| | - Franco Widmer
- />Agroscope, Institute for Sustainability Sciences ISS, 8046 Zurich, Switzerland
| | - Marcel G. A. van der Heijden
- />Agroscope, Institute for Sustainability Sciences ISS, 8046 Zurich, Switzerland
- />Plant-Microbe-Interactions, Department of Biology, Utrecht University, 3508 TB Utrecht, The Netherlands
- />Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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Nesme J, Achouak W, Agathos SN, Bailey M, Baldrian P, Brunel D, Frostegård Å, Heulin T, Jansson JK, Jurkevitch E, Kruus KL, Kowalchuk GA, Lagares A, Lappin-Scott HM, Lemanceau P, Le Paslier D, Mandic-Mulec I, Murrell JC, Myrold DD, Nalin R, Nannipieri P, Neufeld JD, O'Gara F, Parnell JJ, Pühler A, Pylro V, Ramos JL, Roesch LFW, Schloter M, Schleper C, Sczyrba A, Sessitsch A, Sjöling S, Sørensen J, Sørensen SJ, Tebbe CC, Topp E, Tsiamis G, van Elsas JD, van Keulen G, Widmer F, Wagner M, Zhang T, Zhang X, Zhao L, Zhu YG, Vogel TM, Simonet P. Back to the Future of Soil Metagenomics. Front Microbiol 2016; 7:73. [PMID: 26903960 PMCID: PMC4748112 DOI: 10.3389/fmicb.2016.00073] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 01/15/2016] [Indexed: 11/13/2022] Open
Affiliation(s)
- Joseph Nesme
- Environmental Microbial Genomics Group, Laboratoire Ampère, Centre National de la Recherche Scientifique, UMR5005, Institut National de la Recherche Agronomique, USC1407, Ecole Centrale de Lyon, Université de LyonEcully, France; Research Unit for Environmental Genomics, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)Neuherberg, Germany
| | - Wafa Achouak
- Aix-Marseille Université, CEA, Centre National de la Recherche Scientifique, Laboratoire d'Écologie Microbienne de la Rhizosphère et Environnements Extrêmes, UMR 7265, Biologie Végétale et de Microbiologie Environnementales Saint-Paul-lez-Durance, France
| | - Spiros N Agathos
- Earth and Life Institute, Catholic University of LouvainLouvain-la-Neuve, Belgium; School of Life Sciences and Biotechnology, Yachay Tech UniversityUrcuquí, Ecuador
| | - Mark Bailey
- Natural Environment Research Council, Centre for Ecology and Hydrology Oxford, UK
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences Praha, Czech Republic
| | - Dominique Brunel
- Institut National de la Recherche Agronomique, US1279, Etude du Polymorphisme des Génomes Végétaux, CEA, Institut de Génomique, Centre National de Génotypage Evry, France
| | - Åsa Frostegård
- NMBU Nitrogen Group, Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences Aas, Norway
| | - Thierry Heulin
- Aix-Marseille Université, CEA, Centre National de la Recherche Scientifique, Laboratoire d'Écologie Microbienne de la Rhizosphère et Environnements Extrêmes, UMR 7265, Biologie Végétale et de Microbiologie Environnementales Saint-Paul-lez-Durance, France
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory Richland, WA, USA
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, The Faculty of Agriculture, Food and Environment, The Otto Warburg-Minerva Center in Agricultural Biotechnology, The Hebrew University of Jerusalem Rehovot, Israel
| | - Kristiina L Kruus
- Enzymology of Renewable Biomass, VTT, Technical Research Centre of Finland Espoo, Finland
| | - George A Kowalchuk
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University Utrecht, Netherlands
| | - Antonio Lagares
- Departamento de Ciencia Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Centro Científico Tecnológico-Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de La Plata La Plata, Argentina
| | | | - Philippe Lemanceau
- Institut National de la Recherche Agronomique, UMR 1347, Agroécologie, Université de Bourgogne Dijon, France
| | - Denis Le Paslier
- CEA/Direction des sciences du vivant/Institut de Génomique. Genoscope, Centre National de la Recherche Scientifiue UMR 8030, Université d'Evry Val d'Essonne Evry, France
| | - Ines Mandic-Mulec
- Department of Food Science and Technology, Biotechnical Faculty- University of Ljubljana Ljubljana, Slovenia
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia Norwich, UK
| | - David D Myrold
- Department of Crop and Soil Science, Oregon State University Corvallis, OR, USA
| | | | - Paolo Nannipieri
- Department of Agrifood and Environmental Science, University of Florence Florence, Italy
| | - Josh D Neufeld
- Department of Biology, University of Waterloo Waterloo, ON, Canada
| | - Fergal O'Gara
- BIOMERIT Research Centre, School of Microbiology, National University of IrelandCork, Ireland; School of Biomedical Science, Curtin UniversityPerth, WA, Australia
| | - John J Parnell
- National Ecological Observatory Network Boulder, CO, USA
| | - Alfred Pühler
- Center for Biotechnology, Institute for Genome Research and Systems Biology, Genome Research of Industrial Microorganisms, Bielefeld University Bielefeld, Germany
| | - Victor Pylro
- Genomics and Computational Biology Group, René Rachou Research Centre - CPqRR/FIOCRUZ Belo Horizonte, Brazil
| | - Juan L Ramos
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
| | | | - Michael Schloter
- Research Unit for Environmental Genomics, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) Neuherberg, Germany
| | - Christa Schleper
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna Vienna, Austria
| | - Alexander Sczyrba
- Center for Biotechnology and Faculty of Technology, Computational Metagenomics, Bielefeld University Bielefeld, Germany
| | - Angela Sessitsch
- Health and Environment Department, Bioresources, AIT Austrian Institute of Technology GmbH Tulln, Austria
| | - Sara Sjöling
- School of Natural Sciences and Environmental Studies, Södertörn University Huddinge, Sweden
| | - Jan Sørensen
- Section of Genetics and Microbiology, Department of Plant and Environmental Microbiology, University of Copenhagen Frederiksberg, Denmark
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | | | - Edward Topp
- Agriculture and Agri-Food Canada, Department of Biology, University of Western Ontario London, ON, Canada
| | - George Tsiamis
- Department of Environmental and Natural Resources Management, University of Patras Agrinio, Greece
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen Groningen, Netherlands
| | - Geertje van Keulen
- Institute of Life Science, Medical School, Swansea University Swansea, UK
| | - Franco Widmer
- Molecular Ecology, Institute for Sustainability Sciences, Agroscope Zürich, Switzerland
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna Vienna, Austria
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong Hong Kong, China
| | - Xiaojun Zhang
- Group of Microbial Ecology and Ecogenomics, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Liping Zhao
- Group of Microbial Ecology and Ecogenomics, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Yong-Guan Zhu
- Institute of Urban Environment, Chinese Academy of Sciences Xiamen, China
| | - Timothy M Vogel
- Environmental Microbial Genomics Group, Laboratoire Ampère, Centre National de la Recherche Scientifique, UMR5005, Institut National de la Recherche Agronomique, USC1407, Ecole Centrale de Lyon, Université de Lyon Ecully, France
| | - Pascal Simonet
- Institute of Life Science, Medical School, Swansea University Swansea, UK
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Frey B, Rime T, Phillips M, Stierli B, Hajdas I, Widmer F, Hartmann M. Microbial diversity in European alpine permafrost and active layers. FEMS Microbiol Ecol 2016; 92:fiw018. [DOI: 10.1093/femsec/fiw018] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2016] [Indexed: 01/08/2023] Open
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Kempf K, Grieder C, Walter A, Widmer F, Reinhard S, Kölliker R. Evidence and consequences of self-fertilisation in the predominantly outbreeding forage legume Onobrychis viciifolia. BMC Genet 2015; 16:117. [PMID: 26446757 PMCID: PMC4596305 DOI: 10.1186/s12863-015-0275-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 10/02/2015] [Indexed: 12/02/2022] Open
Abstract
Background Sainfoin (Onobrychis viciifolia) is a promising alternative forage plant of good quality, moderate nutrient demand and a high content of polyphenolic compounds. Its poor adoption is caused by the limited availability of well performing varieties. Sainfoin is characterised as tetraploid and mainly outcrossing, but the extent of self-fertilisation and its consequences was not investigated so far. This study aimed at assessing the rate of self-fertilisation in sainfoin under different pollination regimes and at analysing the consequences on plant performance in order to assist future breeding efforts. Methods The self-fertilisation rate was assessed in three sainfoin populations with artificially directed pollination (ADP) and in three populations with non-directed pollination (NDP). Dominant SRAP (sequence-related amplified polymorphism) and codominant SSR (simple sequence repeats) markers were used to detect self-fertilisation in sainfoin for the first time based on molecular marker data. Results High rates of self-fertilisation of up to 64.8 % were observed for ADP populations in contrast to only up to 3.9 % for NDP populations. Self-fertilisation in ADP populations led to a reduction in plant height, plant vigour and, most severely, for seed yield. Conclusions Although sainfoin is predominantly outcrossing, self-fertilisation can occur to a high degree under conditions of limited pollen availability. These results will influence future breeding efforts because precautions have to be taken when crossing breeding material. The resulting inbreeding depression can lead to reduced performance in self-fertilised offspring. Nevertheless the possibility of self-fertilisation also offers new ways for hybrid breeding based on the development of homogenous inbred lines. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0275-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katharina Kempf
- Molecular Ecology, Agroscope Reckenholz ISS, Reckenholzstrasse 191, 8046, Zurich, Switzerland. .,Crop Science, ETH Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland.
| | - Christoph Grieder
- Fodder Plant Breeding, Agroscope Reckenholz ISS, Reckenholzstrasse 191, 8046, Zurich, Switzerland.
| | - Achim Walter
- Crop Science, ETH Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland.
| | - Franco Widmer
- Molecular Ecology, Agroscope Reckenholz ISS, Reckenholzstrasse 191, 8046, Zurich, Switzerland.
| | - Sonja Reinhard
- Molecular Ecology, Agroscope Reckenholz ISS, Reckenholzstrasse 191, 8046, Zurich, Switzerland.
| | - Roland Kölliker
- Molecular Ecology, Agroscope Reckenholz ISS, Reckenholzstrasse 191, 8046, Zurich, Switzerland.
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Steinwender BM, Enkerli J, Widmer F, Eilenberg J, Kristensen HL, Bidochka MJ, Meyling NV. Root isolations of Metarhizium spp. from crops reflect diversity in the soil and indicate no plant specificity. J Invertebr Pathol 2015; 132:142-148. [PMID: 26407950 DOI: 10.1016/j.jip.2015.09.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 09/14/2015] [Accepted: 09/21/2015] [Indexed: 10/23/2022]
Abstract
Metarhizium spp. have recently been shown to be associated with the roots of different plants. Here we evaluated which Metarhizium species were associated with roots of oat (Avena sativa), rye (Secale cereale) and cabbage (Brassica oleracea), common crop plants in Denmark. Thirty-six root samples from each of the three crops were collected within an area of approximately 3ha. The roots were rinsed with sterile water, homogenized and the homogenate plated onto selective media. A subset of 126 Metarhizium isolates were identified to species by sequencing of the 5' end of the gene translation elongation factor 1-alpha and characterized by simple sequence repeat (SSR) analysis of 14 different loci. Metarhizium brunneum was the most common species isolated from plant roots (84.1% of all isolates), while M. robertsii (11.1%) and M. majus (4.8%) comprised the remainder. The SSR analysis revealed that six multilocus genotypes (MLGs) were present among the M. brunneum and M. robertsii isolates, respectively. A single MLG of M. brunneum represented 66.7%, 79.1% and 79.2% of the total isolates obtained from oat, rye and cabbage, respectively. The isolation of Metarhizium spp. and their MLGs from roots revealed a comparable community composition as previously reported from the same agroecosystem when insect baiting of soil samples was used as isolating technique. No specific MLG association with a certain crop was found. This study highlights the diversity of Metarhizium spp. found in the rhizosphere of different crops within a single agroecosystem and suggests that plants either recruit fungal associates from the surrounding soil environment or even govern the composition of Metarhizium populations.
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Affiliation(s)
- Bernhardt M Steinwender
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C., Denmark.
| | - Jürg Enkerli
- Molecular Ecology, Institute for Sustainability Sciences, Agroscope, Reckenholzstrasse 191, 8046 Zürich, Switzerland
| | - Franco Widmer
- Molecular Ecology, Institute for Sustainability Sciences, Agroscope, Reckenholzstrasse 191, 8046 Zürich, Switzerland
| | - Jørgen Eilenberg
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C., Denmark
| | - Hanne L Kristensen
- Department of Food Science, Aarhus University, Kirstinebjergvej 10, DK-5792 Aarslev, Denmark
| | - Michael J Bidochka
- Department of Biology, Brock University, St. Catharines, ON L2S 3A1, Canada
| | - Nicolai V Meyling
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C., Denmark
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Hartmann M, Frey B, Mayer J, Mäder P, Widmer F. Distinct soil microbial diversity under long-term organic and conventional farming. ISME J 2015; 9:1177-94. [PMID: 25350160 PMCID: PMC4409162 DOI: 10.1038/ismej.2014.210] [Citation(s) in RCA: 446] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 09/05/2014] [Accepted: 09/23/2014] [Indexed: 02/01/2023]
Abstract
Low-input agricultural systems aim at reducing the use of synthetic fertilizers and pesticides in order to improve sustainable production and ecosystem health. Despite the integral role of the soil microbiome in agricultural production, we still have a limited understanding of the complex response of microbial diversity to organic and conventional farming. Here we report on the structural response of the soil microbiome to more than two decades of different agricultural management in a long-term field experiment using a high-throughput pyrosequencing approach of bacterial and fungal ribosomal markers. Organic farming increased richness, decreased evenness, reduced dispersion and shifted the structure of the soil microbiota when compared with conventionally managed soils under exclusively mineral fertilization. This effect was largely attributed to the use and quality of organic fertilizers, as differences became smaller when conventionally managed soils under an integrated fertilization scheme were examined. The impact of the plant protection regime, characterized by moderate and targeted application of pesticides, was of subordinate importance. Systems not receiving manure harboured a dispersed and functionally versatile community characterized by presumably oligotrophic organisms adapted to nutrient-limited environments. Systems receiving organic fertilizer were characterized by specific microbial guilds known to be involved in degradation of complex organic compounds such as manure and compost. The throughput and resolution of the sequencing approach permitted to detect specific structural shifts at the level of individual microbial taxa that harbours a novel potential for managing the soil environment by means of promoting beneficial and suppressing detrimental organisms.
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Affiliation(s)
- Martin Hartmann
- Molecular Ecology, Institute for Sustainability Sciences, Agroscope, Zurich, Switzerland
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Jochen Mayer
- Nutrient Flows, Institute for Sustainability Sciences, Agroscope, Zurich, Switzerland
| | - Paul Mäder
- Department of Soil Sciences, Research Institute of Organic Agriculture, Frick, Switzerland
| | - Franco Widmer
- Molecular Ecology, Institute for Sustainability Sciences, Agroscope, Zurich, Switzerland
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Rime T, Hartmann M, Brunner I, Widmer F, Zeyer J, Frey B. Vertical distribution of the soil microbiota along a successional gradient in a glacier forefield. Mol Ecol 2015; 24:1091-108. [DOI: 10.1111/mec.13051] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 12/16/2014] [Accepted: 12/17/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Thomas Rime
- Forest Soils and Biogeochemistry; Swiss Federal Research Institute WSL; 8903 Birmensdorf Switzerland
| | - Martin Hartmann
- Forest Soils and Biogeochemistry; Swiss Federal Research Institute WSL; 8903 Birmensdorf Switzerland
- Molecular Ecology; Institute for Sustainability Sciences; Agroscope 8046 Zürich Switzerland
| | - Ivano Brunner
- Forest Soils and Biogeochemistry; Swiss Federal Research Institute WSL; 8903 Birmensdorf Switzerland
| | - Franco Widmer
- Molecular Ecology; Institute for Sustainability Sciences; Agroscope 8046 Zürich Switzerland
| | - Josef Zeyer
- Institute of Biogeochemistry and Pollutant Dynamics; Federal Institute of Technology (ETH Zürich); 8092 Zürich Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry; Swiss Federal Research Institute WSL; 8903 Birmensdorf Switzerland
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Affiliation(s)
- Cameron Wagg
- Inst. for Sustainability Sciences, Agroscope; Reckenholzstrasse 191 CH-8046 Zürich Switzerland
- Inst. of Evolutionary Biology and Environmental Studies, Univ. of Zürich; Winterthurestrasse 190 CH-8057 Zürich Switzerland
| | - Beat Boller
- Inst. for Sustainability Sciences, Agroscope; Reckenholzstrasse 191 CH-8046 Zürich Switzerland
| | - Salome Schneider
- Inst. for Sustainability Sciences, Agroscope; Reckenholzstrasse 191 CH-8046 Zürich Switzerland
- Dept of Microbiology; Swedish Univ. of Agricultural Sciences; SE-750 07 Uppsala Sweden
| | - Franco Widmer
- Inst. for Sustainability Sciences, Agroscope; Reckenholzstrasse 191 CH-8046 Zürich Switzerland
| | - Marcel G. A. van der Heijden
- Inst. for Sustainability Sciences, Agroscope; Reckenholzstrasse 191 CH-8046 Zürich Switzerland
- Inst. of Evolutionary Biology and Environmental Studies, Univ. of Zürich; Winterthurestrasse 190 CH-8057 Zürich Switzerland
- Inst. of Environmental Biology, Faculty of Science, Utrecht Univ.; NL-3508 TC, Utrecht the Netherlands
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Steinwender BM, Enkerli J, Widmer F, Eilenberg J, Thorup-Kristensen K, Meyling NV. Molecular diversity of the entomopathogenic fungal Metarhizium community within an agroecosystem. J Invertebr Pathol 2014; 123:6-12. [DOI: 10.1016/j.jip.2014.09.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 08/27/2014] [Accepted: 09/03/2014] [Indexed: 10/24/2022]
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Wagg C, Bender SF, Widmer F, van der Heijden MGA. Soil biodiversity and soil community composition determine ecosystem multifunctionality. Proc Natl Acad Sci U S A 2014; 111:5266-70. [PMID: 24639507 PMCID: PMC3986181 DOI: 10.1073/pnas.1320054111] [Citation(s) in RCA: 730] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Biodiversity loss has become a global concern as evidence accumulates that it will negatively affect ecosystem services on which society depends. So far, most studies have focused on the ecological consequences of above-ground biodiversity loss; yet a large part of Earth's biodiversity is literally hidden below ground. Whether reductions of biodiversity in soil communities below ground have consequences for the overall performance of an ecosystem remains unresolved. It is important to investigate this in view of recent observations that soil biodiversity is declining and that soil communities are changing upon land use intensification. We established soil communities differing in composition and diversity and tested their impact on eight ecosystem functions in model grassland communities. We show that soil biodiversity loss and simplification of soil community composition impair multiple ecosystem functions, including plant diversity, decomposition, nutrient retention, and nutrient cycling. The average response of all measured ecosystem functions (ecosystem multifunctionality) exhibited a strong positive linear relationship to indicators of soil biodiversity, suggesting that soil community composition is a key factor in regulating ecosystem functioning. Our results indicate that changes in soil communities and the loss of soil biodiversity threaten ecosystem multifunctionality and sustainability.
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Affiliation(s)
- Cameron Wagg
- Plant Soil Interactions and
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, CH 8057 Zürich, Switzerland; and
| | - S. Franz Bender
- Plant Soil Interactions and
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, CH 8057 Zürich, Switzerland; and
| | - Franco Widmer
- Molecular Ecology, Institute for Sustainability Sciences, Agroscope, CH 8046 Zürich, Switzerland
| | - Marcel G. A. van der Heijden
- Plant Soil Interactions and
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, CH 8057 Zürich, Switzerland; and
- Plant–Microbe Interactions, Institute of Environmental Biology, Faculty of Science, Utrecht University, 3508 TC, Utrecht, The Netherlands
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Last L, Widmer F, Fjellstad W, Stoyanova S, Kölliker R. Genetic diversity of natural orchardgrass (Dactylis glomerata L.) populations in three regions in Europe. BMC Genet 2013; 14:102. [PMID: 24165514 PMCID: PMC4231346 DOI: 10.1186/1471-2156-14-102] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 10/08/2013] [Indexed: 11/29/2022] Open
Abstract
Background Dactylis glomerata (orchardgrass or cocksfoot) is a forage crop of agronomic importance comprising high phenotypic plasticity and variability. Although the genus Dactylis has been studied quite well within the past century, little is known about the genetic diversity and population patterns of natural populations from geographically distinct grassland regions in Europe. The objectives of this study were to test the ploidy level of 59 natural and semi-natural populations of D. glomerata, to investigate genetic diversity, differentiation patterns within and among the three geographic regions, and to evaluate selected populations for their value as genetic resources. Results Among 1861 plants from 20 Swiss, 20 Bulgarian and 19 Norwegian populations of D. glomerata, exclusively tetraploid individuals were identified based on 29 SSR markers. The average expected heterozygosity (HE,C) ranged from 0.44 to 0.59 and was highest in the Norwegian region. The total number of rare alleles was high, accounting for 59.9% of the amplified alleles. 80.82% of the investigated individuals could be assigned to their respective geographic region based on allele frequencies. Average genetic distances were low despite large geographic distances and ranged from D = 0.09 to 0.29 among populations. Conclusions All three case study regions revealed high genetic variability of tetraploid D. glomerata within selected populations and numerous rare and localized alleles which were geographically unique. The large, permanent grassland patches in Bulgaria provided a high genetic diversity, while fragmented, semi-natural grassland in the Norwegian region provided a high amount of rare, localized alleles, which have to be considered in conservation and breeding strategies. Therefore, the selected grassland populations investigated conserve a large pool of genetic resources and provide valuable sources for forage crop breeding programs.
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Affiliation(s)
| | | | | | | | - Roland Kölliker
- Agroscope Reckenholz-Tänikon Research Station ART, Reckenholzstrasse 191, Zurich 8046, Switzerland.
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Hartmann M, Niklaus PA, Zimmermann S, Schmutz S, Kremer J, Abarenkov K, Lüscher P, Widmer F, Frey B. Resistance and resilience of the forest soil microbiome to logging-associated compaction. ISME J 2013; 8:226-44. [PMID: 24030594 DOI: 10.1038/ismej.2013.141] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 07/15/2013] [Accepted: 07/15/2013] [Indexed: 02/01/2023]
Abstract
Soil compaction is a major disturbance associated with logging, but we lack a fundamental understanding of how this affects the soil microbiome. We assessed the structural resistance and resilience of the microbiome using a high-throughput pyrosequencing approach in differently compacted soils at two forest sites and correlated these findings with changes in soil physical properties and functions. Alterations in soil porosity after compaction strongly limited the air and water conductivity. Compaction significantly reduced abundance, increased diversity, and persistently altered the structure of the microbiota. Fungi were less resistant and resilient than bacteria; clayey soils were less resistant and resilient than sandy soils. The strongest effects were observed in soils with unfavorable moisture conditions, where air and water conductivities dropped well below 10% of their initial value. Maximum impact was observed around 6-12 months after compaction, and microbial communities showed resilience in lightly but not in severely compacted soils 4 years post disturbance. Bacteria capable of anaerobic respiration, including sulfate, sulfur, and metal reducers of the Proteobacteria and Firmicutes, were significantly associated with compacted soils. Compaction detrimentally affected ectomycorrhizal species, whereas saprobic and parasitic fungi proportionally increased in compacted soils. Structural shifts in the microbiota were accompanied by significant changes in soil processes, resulting in reduced carbon dioxide, and increased methane and nitrous oxide emissions from compacted soils. This study demonstrates that physical soil disturbance during logging induces profound and long-lasting changes in the soil microbiome and associated soil functions, raising awareness regarding sustainable management of economically driven logging operations.
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Affiliation(s)
- Martin Hartmann
- 1] Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland [2] Molecular Ecology, Research Station Agroscope Reckenholz-Tänikon ART, Zurich, Switzerland
| | - Pascal A Niklaus
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Stephan Zimmermann
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Stefan Schmutz
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Johann Kremer
- Forest Work Science and Applied Informatics, Technical University of Munich, Freising, Germany
| | | | - Peter Lüscher
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Franco Widmer
- Molecular Ecology, Research Station Agroscope Reckenholz-Tänikon ART, Zurich, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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Wichmann F, Vorhölter FJ, Hersemann L, Widmer F, Blom J, Niehaus K, Reinhard S, Conradin C, Kölliker R. The noncanonical type III secretion system of Xanthomonas translucens pv. graminis is essential for forage grass infection. Mol Plant Pathol 2013; 14:576-88. [PMID: 23578314 PMCID: PMC6638798 DOI: 10.1111/mpp.12030] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Xanthomonas translucens pv. graminis (Xtg) is a gammaproteobacterium that causes bacterial wilt on a wide range of forage grasses. To gain insight into the host-pathogen interaction and to identify the virulence factors of Xtg, we compared a draft genome sequence of one isolate (Xtg29) with other Xanthomonas spp. with sequenced genomes. The type III secretion system (T3SS) encoding a protein transport system for type III effector (T3E) proteins represents one of the most important virulence factors of Xanthomonas spp. In contrast with other Xanthomonas spp. assigned to clade 1 on the basis of phylogenetic analyses, we identified an hrp (hypersensitive response and pathogenicity) gene cluster encoding T3SS components and a representative set of 35 genes encoding putative T3Es in the genome of Xtg29. The T3SS was shown to be divergent from the hrp gene clusters of other sequenced Xanthomonas spp. Xtg mutants deficient in T3SS regulating and structural genes were constructed to clarify the role of the T3SS in forage grass colonization. Italian ryegrass infection with these mutants led to significantly reduced symptoms (P < 0.05) relative to plants infected with the wild-type strain. This showed that the T3SS is required for symptom evocation. In planta multiplication of the T3SS mutants was not impaired significantly relative to the wild-type, indicating that the T3SS is not required for survival until 14 days post-infection. This study represents the first major step to understanding the bacterial colonization strategies deployed by Xtg and may assist in the identification of resistance (R) genes in forage grasses.
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Affiliation(s)
- Fabienne Wichmann
- Agroscope Reckenholz-Tänikon Research Station ART, Reckenholzstrasse 191, 8046 Zurich, Switzerland
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Shabarova T, Widmer F, Pernthaler J. Mass effects meet species sorting: transformations of microbial assemblages in epiphreatic subsurface karst water pools. Environ Microbiol 2013; 15:2476-88. [PMID: 23614967 DOI: 10.1111/1462-2920.12124] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 02/21/2013] [Accepted: 02/25/2013] [Indexed: 11/29/2022]
Abstract
We investigated the transformations of the microbial communities in epiphreatic karst cave pools with different flooding frequencies. Fingerprinting of 16S rRNA genes was combined with microscopic and sequence analysis to examine if source water would transport comparable microbial inocula into the pools at consecutive flood events, and to assess possible effects of residence time on the microbial assemblages during stagnant periods. Variability in the concentrations of dissolved organic carbon and conductivity indicated differences between floods and changes of pool water over time. High numbers of Betaproteobacteria affiliated with Methylophilaceae and Comamonadaceae were introduced into the pools during floodings. While the former persisted in the pools, the latter exhibited considerable microdiversification. These Betaproteobacteria might thus represent core microbial groups in karst water. A decrease in the estimated total diversity of the remaining bacterial taxa was apparent after a few weeks of residence: Some were favoured by stagnant conditions, whereas the majority was rapidly outcompeted. Thus, the microbial communities consisted of different components governed by complementary assembly mechanisms (dispersal versus environmental filtering) upon introduction into the pools. High overlap of temporary and persistent community members between samplings from two winters, moreover, reflected the seasonal recurrence of the studied microbial assemblages.
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Affiliation(s)
- Tanja Shabarova
- Limnological Station, Institute of Plant Biology, University of Zurich, Seestr. 187, CH-8802, Kilchberg, Switzerland
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Jordan M, Eppenberger HM, Sucker H, Widmer F, Einsele A. Interactions between animal cells and gas bubbles: The influence of serum and pluronic F68 on the physical properties of the bubble surface. Biotechnol Bioeng 2012; 43:446-54. [PMID: 18615740 DOI: 10.1002/bit.260430603] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We describe a method by which the degree of bubble saturation can be determined by measuring the velocity of single bubbles at different heights from the bubble source in pure water containing increasing concentrations of surfactants. The highest rising velocities were measured in pure water. Addition of surfactants caused a concentration-dependent and height-dependent decrease in bubble velocity; thus, bubbles are covered with surfactants as they rise, and the distance traveled until saturation is reached decreases with increased concentration of surfactant. Pluronic F68 is a potent effector of bubble saturation, 500 times more active than serum. At Pluronic F68 concentrations of 0.1% (w/v), bubbles are saturated essentially at their source. The effect of bubble saturation on the interactions between animal cells and gas bubbles was investigated by using light microscopy and a micromanipulator. In the absence of surfactants, bubbles had a killing effect on cells; hybridoma cells and Chinese hamster ovary (CHO) cells were ruptured when coming into contact with a bubble. Bubbles only partially covered by surfactants adsorbed the cells. The adsorbed cells were not damaged and they also could survive subsequent detachment. Saturated bubbles, on the other hand, did not show any interactions with cells. It is concluded that the protective effect of serum and Pluronic F68 in sparged cultivation systems is based on covering the medium-bubble interface with surfaceactive components and that cell death occurs either after contact of cells with an uncovered bubble or by adsorption of cells through partially saturated bubbles and subsequent transport of cells into the foam region. (c) 1994 John Wiley & Sons, Inc.
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Affiliation(s)
- M Jordan
- Institute for Cell Biology, Swiss Federal Institute of Technology (ETH) 8093 Zürich, Switzerland
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Duffy B, Walsh F, Pelludat C, Holliger E, Oulevet C, Widmer F. ENVIRONMENTAL MONITORING OF ANTIBIOTIC RESISTANCE AND IMPACT OF STREPTOMYCIN USE ON ORCHARD BACTERIAL COMMUNITIES. ACTA ACUST UNITED AC 2011. [DOI: 10.17660/actahortic.2011.896.71] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Wichmann F, Asp T, Widmer F, Kölliker R. Transcriptional responses of Italian ryegrass during interaction with Xanthomonas translucens pv. graminis reveal novel candidate genes for bacterial wilt resistance. Theor Appl Genet 2011; 122:567-579. [PMID: 20976589 DOI: 10.1007/s00122-010-1470-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Accepted: 10/11/2010] [Indexed: 05/30/2023]
Abstract
Xanthomonas translucens pv. graminis (Xtg) causes bacterial wilt, a severe disease of forage grasses such as Italian ryegrass (Lolium multiflorum Lam.). In order to gain a more detailed understanding of the genetic control of resistance mechanisms and to provide prerequisites for marker assisted selection, the partial transcriptomes of two Italian ryegrass genotypes, one resistant and one susceptible to bacterial wilt were compared at four time points after Xtg infection. A cDNA microarray developed from a perennial ryegrass (Lolium perenne) expressed sequence tag set consisting of 9,990 unique genes was used for transcriptome analysis in Italian ryegrass. An average of 4,487 (45%) of the perennial ryegrass sequences spotted on the cDNA microarray were detected by cross-hybridisation to Italian ryegrass. Transcriptome analyses of the resistant versus the susceptible genotype revealed substantial gene expression differences (>1,200) indicating that great gene expression differences between different Italian ryegrass genotypes exist which potentially contribute to the observed phenotypic divergence in Xtg resistance between the two genotypes. In the resistant genotype, several genes differentially expressed after Xtg inoculation were identified which revealed similarities to transcriptional changes triggered by pathogen-associated molecular patterns in other plant-pathogen interactions. These genes represent candidate genes of particular interest for the development of tools for marker assisted resistance breeding.
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Affiliation(s)
- Fabienne Wichmann
- Agroscope Reckenholz-Tänikon Research Station ART, Reckenholzstrasse 191, Zurich, Switzerland
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Fournier A, Widmer F, Enkerli J. Development of a single-nucleotide polymorphism (SNP) assay for genotyping of Pandora neoaphidis. Fungal Biol 2010; 114:498-506. [DOI: 10.1016/j.funbio.2010.03.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Revised: 03/24/2010] [Accepted: 03/24/2010] [Indexed: 11/28/2022]
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Oulevey C, Widmer F, Kölliker R, Enkerli J. An optimized microsatellite marker set for detection of Metarhizium anisopliae genotype diversity on field and regional scales. ACTA ACUST UNITED AC 2009; 113:1016-24. [DOI: 10.1016/j.mycres.2009.06.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Revised: 04/28/2009] [Accepted: 06/12/2009] [Indexed: 11/16/2022]
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Enkerli J, Ghormade V, Oulevey C, Widmer F. PCR-RFLP analysis of chitinase genes enables efficient genotyping of Metarhizium anisopliae var. anisopliae. J Invertebr Pathol 2009; 102:185-8. [PMID: 19682457 DOI: 10.1016/j.jip.2009.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Revised: 05/18/2009] [Accepted: 08/07/2009] [Indexed: 10/20/2022]
Abstract
A new genotyping tool has been developed and evaluated for Metarhizium anisopliae var. anisopliae. The tool is based on Restriction Fragment Length Polymorphism (RFLP) analysis of three chitinase genes that are functionally linked to insect-pathogenicity of this fungus. It allowed for discrimination of 14 genotypes among 22 M. anisopliae var. anisopliae strains of a world wide collection. Analyses revealed that the approach may also be applicable to other Metarhizium varieties. The new tool will be useful for genetic characterization of M. anisopliae var. anisopliae strains, and it is applicable for laboratories with limited access to molecular diagnostic equipment.
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Affiliation(s)
- Jürg Enkerli
- Agroscope Reckenholz-Tänikon Research Station ART, Reckenholzstrasse 191, 8046 Zürich, Switzerland.
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Schneider S, Enkerli J, Widmer F. A generally applicable assay for the quantification of inhibitory effects on PCR. J Microbiol Methods 2009; 78:351-3. [PMID: 19540882 DOI: 10.1016/j.mimet.2009.06.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Revised: 06/10/2009] [Accepted: 06/10/2009] [Indexed: 11/28/2022]
Abstract
PCR amplification of target genes from environmental DNA extracts can suffer from PCR inhibition, caused by co-extracted substances. No simple assay has been available to quantify this inhibition. Therefore, a generally applicable PCR inhibition-assay was developed, which allows determination of statistically significant inhibition of PCR. This information is important when documenting quality of DNA in environmental extracts used as template for PCR.
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Affiliation(s)
- Salome Schneider
- Molecular Ecology, Agroscope Reckenholz-Tänikon Research Station ART, Reckenholzstrasse 191, 8046 Zürich, Switzerland
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Kölliker R, Bassin S, Schneider D, Widmer F, Fuhrer J. Elevated ozone affects the genetic composition of Plantago lanceolata L. populations. Environ Pollut 2008; 152:380-6. [PMID: 17658204 DOI: 10.1016/j.envpol.2007.06.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2007] [Revised: 05/16/2007] [Accepted: 06/10/2007] [Indexed: 05/16/2023]
Abstract
The genetic composition and diversity of Plantago lanceolata L. populations were analysed using amplified fragment length polymorphism (AFLP) as well as simple sequence repeat (SSR) markers to test for differences in an old semi-natural grassland after five years of treatment with ambient or elevated ozone (O3) using a free-air fumigation system. Genetic diversity in populations exposed to elevated O3 was slightly higher than in populations sampled from control plots. This effect was significant for AFLP-based measures of diversity and for SSR markers based on observed heterozygosity. Also, a small but significant difference in genetic composition between O3 treatments was detected by analysis of molecular variance and redundancy analysis. The results show that micro-evolutionary processes could take place in response to long-term elevated O3 exposure in highly diverse populations of outbreeding plant species.
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Affiliation(s)
- Roland Kölliker
- Molecular Ecology and Air Pollution/Climate Groups, Agroscope Reckenholz-Tänikon Research Station ART, CH-8046 Zurich, Switzerland.
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Frey B, Pesaro M, Rüdt A, Widmer F. Resilience of the rhizosphere Pseudomonas and ammonia-oxidizing bacterial populations during phytoextraction of heavy metal polluted soil with poplar. Environ Microbiol 2008; 10:1433-49. [DOI: 10.1111/j.1462-2920.2007.01556.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Terminal restriction fragment length polymorphism (T-RFLP) analysis is commonly used for profiling microbial communities in various environments. However, it may suffer from biases during the analytic process. This study addressed the potential of T-RFLP profiles (1) to reflect real community structures and diversities, as well as (2) to reliably detect changing components of microbial community structures. For this purpose, defined artificial communities of 30 SSU rRNA gene clones, derived from nine bacterial phyla, were used. PCR amplification efficiency was one primary bias with a maximum variability factor of 3.5 among clones. PCR downstream analyses such as enzymatic restriction and capillary electrophoresis introduced a maximum bias factor of 4 to terminal restriction fragment (T-RF) signal intensities, resulting in a total maximum bias factor of 14 in the final T-RFLP profiles. In addition, the quotient between amplification efficiency and T-RF size allowed predicting T-RF abundances in the profiles with high accuracy. Although these biases impaired detection of real community structures, the relative changes in structures and diversities were reliably reflected in the T-RFLP profiles. These data support the suitability of T-RFLP profiling for monitoring effects on microbial communities.
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Affiliation(s)
- Martin Hartmann
- Molecular Ecology, Agroscope Reckenholz-Tänikon Research Station ART, Reckenholzstrasse 191, Zurich, Switzerland
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