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Skuza L, Filip E, Szućko I, Bocianowski J. SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: Secale) Species. Int J Mol Sci 2020; 21:ijms21249421. [PMID: 33321948 PMCID: PMC7762986 DOI: 10.3390/ijms21249421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 01/09/2023] Open
Abstract
Secale is a small but very diverse genus from the tribe Triticeae (family Poaceae), which includes annual, perennial, self-pollinating and open-pollinating, cultivated, weedy and wild species of various phenotypes. Despite its high economic importance, classification of this genus, comprising 3–8 species, is inconsistent. This has resulted in significantly reduced progress in the breeding of rye which could be enriched with functional traits derived from wild rye species. Our previous research has suggested the utility of non-coding sequences of chloroplast and mitochondrial DNA in studies on closely related species of the genus Secale. Here we applied the SPInDel (Species Identification by Insertions/Deletions) approach, which targets hypervariable genomic regions containing multiple insertions/deletions (indels) and exhibiting extensive length variability. We analysed a total of 140 and 210 non-coding sequences from cpDNA and mtDNA, respectively. The resulting data highlight regions which may represent useful molecular markers with respect to closely related species of the genus Secale, however, we found the chloroplast genome to be more informative. These molecular markers include non-coding regions of chloroplast DNA: atpB-rbcL and trnT-trnL and non-coding regions of mitochondrial DNA: nad1B-nad1C and rrn5/rrn18. Our results demonstrate the utility of the SPInDel concept for the characterisation of Secale species.
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Affiliation(s)
- Lidia Skuza
- Institute of Biology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland; (E.F.); (I.S.)
- The Centre for Molecular Biology and Biotechnology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland
- Correspondence:
| | - Ewa Filip
- Institute of Biology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland; (E.F.); (I.S.)
- The Centre for Molecular Biology and Biotechnology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland
| | - Izabela Szućko
- Institute of Biology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland; (E.F.); (I.S.)
- The Centre for Molecular Biology and Biotechnology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, 28 Wojska Polskiego, 60-637 Poznań, Poland;
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Mishra VK, Passari AK, Leo VV, Singh BP. Molecular Diversity and Detection of Endophytic Fungi Based on Their Antimicrobial Biosynthetic Genes. Fungal Biol 2017. [DOI: 10.1007/978-3-319-34106-4_1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Řeháková K, Chroňáková A, Krištůfek V, Kuchtová B, Čapková K, Scharfen J, Čapek P, Doležal J. Bacterial community of cushion plant Thylacospermum ceaspitosum on elevational gradient in the Himalayan cold desert. Front Microbiol 2015; 6:304. [PMID: 25932023 PMCID: PMC4399334 DOI: 10.3389/fmicb.2015.00304] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 03/27/2015] [Indexed: 11/16/2022] Open
Abstract
Although bacterial assemblages are important components of soils in arid ecosystems, the knowledge about composition, life-strategies, and environmental drivers is still fragmentary, especially in remote high-elevation mountains. We compared the quality and quantity of heterotrophic bacterial assemblages between the rhizosphere of the dominant cushion-forming plant Thylacospermum ceaspitosum and its surrounding bulk soil in two mountain ranges (East Karakoram: 4850-5250 m and Little Tibet: 5350-5850 m), in communities from cold steppes to the subnival zone in Ladakh, arid Trans-Himalaya, northwest India. Bacterial communities were characterized by molecular fingerprinting in combination with culture-dependent methods. The effects of environmental factors (elevation, mountain range, and soil physico-chemical parameters) on the bacterial community composition and structure were tested by multivariate redundancy analysis and conditional inference trees. Actinobacteria dominate the cultivable part of community and represent a major bacterial lineage of cold desert soils. The most abundant genera were Streptomyces, Arthrobacter, and Paenibacillus, representing both r- and K-strategists. The soil texture is the most important factor for the community structure and the total bacteria counts. Less abundant and diverse assemblages are found in East Karakoram with coarser soils derived from leucogranite bedrock, while more diverse assemblages in Little Tibet are associated with finer soils derived from easily weathering gneisses. Cushion rhizosphere is in general less diverse than bulk soil, and contains more r-strategists. K-strategists are more associated with the extremes of the gradient, with drought at lowest elevations (4850-5000 m) and frost at the highest elevations (5750-5850 m). The present study illuminates the composition of soil bacterial assemblages in relation to the cushion plant T. ceaspitosum in a xeric environment and brings important information about heterotrophic bacteria in Himalayan soil.
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Affiliation(s)
- Klára Řeháková
- Department of Phycology, Ecology, Institute of Botany Academy of Sciences of the Czech Republic, v. v. i. Třeboň, Czech Republic ; Department of Microbial Water Ecology, Biology Centre Academy of Sciences of the Czech Republic, v. v. i - Institute of Hydrobiology Ceske Budejovice, Czech Republic
| | - Alica Chroňáková
- Department of Soil Microbiology and Soil Chemistry, Biology Centre Academy of Sciences of the Czech Republic, v. v. i - Institute of Soil Biology České Budějovice, Czech Republic
| | - Václav Krištůfek
- Department of Soil Microbiology and Soil Chemistry, Biology Centre Academy of Sciences of the Czech Republic, v. v. i - Institute of Soil Biology České Budějovice, Czech Republic
| | - Barbora Kuchtová
- Department of Soil Microbiology and Soil Chemistry, Biology Centre Academy of Sciences of the Czech Republic, v. v. i - Institute of Soil Biology České Budějovice, Czech Republic
| | - Kateřina Čapková
- Department of Phycology, Ecology, Institute of Botany Academy of Sciences of the Czech Republic, v. v. i. Třeboň, Czech Republic ; Department of Botany, Faculty of Science, University of South Bohemia České Budějovice, Czech Republic
| | - Josef Scharfen
- Faculty Hospital and Faculty of Medicine, Institute of Clinical Microbiology, Charles University Hradec Králové, Czech Republic ; National Reference Laboratory for Pathogenic Actinomycetes, Department of Medical Microbiology and Immunology, Regional Hospital Trutnov, Inc. Trutnov, Czech Republic
| | - Petr Čapek
- Department of Botany, Faculty of Science, University of South Bohemia České Budějovice, Czech Republic
| | - Jiří Doležal
- Department of Phycology, Ecology, Institute of Botany Academy of Sciences of the Czech Republic, v. v. i. Třeboň, Czech Republic ; Department of Botany, Faculty of Science, University of South Bohemia České Budějovice, Czech Republic
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Thébault A, Clément JC, Ibanez S, Roy J, Geremia RA, Pérez CA, Buttler A, Estienne Y, Lavorel S. Nitrogen limitation and microbial diversity at the treeline. OIKOS 2014. [DOI: 10.1111/j.1600-0706.2013.00860.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Jabbar A, Gasser RB. Mutation scanning analysis of genetic variation within and among Echinococcus species: implications and future prospects. Electrophoresis 2014; 34:1852-62. [PMID: 23977679 DOI: 10.1002/elps.201300078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Adult tapeworms of the genus Echinococcus (family Taeniidae) occur in the small intestines of carnivorous definitive hosts and are transmitted to particular intermediate mammalian hosts, in which they develop as fluid-filled larvae (cysts) in internal organs (usually lung and liver), causing the disease echinococcosis. Echinococcus species are of major medical importance and also cause losses to the meat and livestock industries, mainly due to the condemnation of infected offal. Decisions regarding the treatment and control of echinococcosis rely on the accurate identification of species and population variants (strains). Conventional, phenetic methods for specific identification have some significant limitations. Despite advances in the development of molecular tools, there has been limited application of mutation scanning methods to species of Echinococcus. Here, we briefly review key genetic markers used for the identification of Echinococcus species and techniques for the analysis of genetic variation within and among populations, and the diagnosis of echinococcosis. We also discuss the benefits of utilizing mutation scanning approaches to elucidate the population genetics and epidemiology of Echinococcus species. These benefits are likely to become more evident following the complete characterization of the genomes of E. granulosus and E. multilocularis.
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Affiliation(s)
- Abdul Jabbar
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
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Roy J, Albert CH, Ibanez S, Saccone P, Zinger L, Choler P, Clément JC, Lavergne S, Geremia RA. Microbes on the cliff: alpine cushion plants structure bacterial and fungal communities. Front Microbiol 2013; 4:64. [PMID: 23543612 PMCID: PMC3608923 DOI: 10.3389/fmicb.2013.00064] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 03/05/2013] [Indexed: 11/29/2022] Open
Abstract
Plants affect the spatial distribution of soil microorganisms, but the influence of the local abiotic context is poorly documented. We investigated the effect of a single plant species, the cushion plant Silene acaulis, on habitat conditions, and microbial community. We collected soil from inside (In) and outside (Out) of the cushions on calcareous and siliceous cliffs in the French Alps along an elevation gradient (2,000–3,000 masl). The composition of the microbial communities was assessed by Capillary-Electrophoresis Single Strand Conformation Polymorphism (CE-SSCP). Univariate and multivariate analyses were conducted to characterize the response of the microbial beta-diversity to soil parameters (total C, total N, soil water content, N-NH4+,N-NO3-, and pH). Cushions affected the microbial communities, modifying soil properties. The fungal and bacterial communities did not respond to the same abiotic factors. Outside the cushions, the bacterial communities were strongly influenced by bedrock. Inside the cushions, the bacterial communities from both types of bedrock were highly similar, due to the smaller pH differences than in open areas. By contrast, the fungal communities were equally variable inside and outside of the cushions. Outside the cushions, the fungal communities responded weakly to soil pH. Inside the cushions, the fungal communities varied strongly with bedrock and elevation as well as increases in soil nutrients and water content. Furthermore, the dissimilarities in the microbial communities between the In and Out habitats increased with increasing habitat modification and environmental stress. Our results indicate that cushions act as a selective force that counteracts the influence of the bedrock and the resource limitations on the bacterial and fungal communities by buffering soil pH and enhancing soil nutrients. Cushion plants structure microbial communities, and this effect increases in stressful, acidic and nutrient-limited environments.
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Affiliation(s)
- J Roy
- UMR CNRS-UJF 5553, Laboratoire d'Ecologie Alpine, Université de Grenoble Grenoble, France
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Cordier T, Robin C, Capdevielle X, Desprez-Loustau ML, Vacher C. Spatial variability of phyllosphere fungal assemblages: genetic distance predominates over geographic distance in a European beech stand (Fagus sylvatica). FUNGAL ECOL 2012. [DOI: 10.1016/j.funeco.2011.12.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Carneiro J, Pereira F, Amorim A. SPI
n
D
el: a multifunctional workbench for species identification using insertion/deletion variants. Mol Ecol Resour 2012; 12:1190-5. [DOI: 10.1111/1755-0998.12011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 08/03/2012] [Accepted: 08/07/2012] [Indexed: 12/01/2022]
Affiliation(s)
- João Carneiro
- Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP) R. Dr. Roberto Frias s/n 4200‐465 Porto Portugal
- Faculty of Sciences University of Porto Rua do Campo Alegre, s/n 4169‐007 Porto Portugal
| | - Filipe Pereira
- Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP) R. Dr. Roberto Frias s/n 4200‐465 Porto Portugal
| | - António Amorim
- Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP) R. Dr. Roberto Frias s/n 4200‐465 Porto Portugal
- Faculty of Sciences University of Porto Rua do Campo Alegre, s/n 4169‐007 Porto Portugal
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Badin AL, Mustafa T, Bertrand C, Monier A, Delolme C, Geremia RA, Bedell JP. Microbial communities of urban stormwater sediments: the phylogenetic structure of bacterial communities varies with porosity. FEMS Microbiol Ecol 2012; 81:324-38. [DOI: 10.1111/j.1574-6941.2012.01354.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 02/24/2012] [Accepted: 02/24/2012] [Indexed: 11/29/2022] Open
Affiliation(s)
- Anne-Laure Badin
- Université de Lyon, Lyon, France Université Lyon1, Villeurbanne, France ENTPE, Vaulx-en-velin, France CNRS, UMR 5023, Laboratoire Ecologie des Hydrosystèmes Naturels et Anthropisés; Villeurbanne; France
| | - Tarfa Mustafa
- Laboratoire d'Ecologie Alpine; CNRS UMR 5553; Université Joseph Fourier; Grenoble 1, Grenoble; France
| | - Cédric Bertrand
- Laboratoire de Chimie des Biomolécules et de l'Environnement - EA 4215; Université de Perpignan Via Domitia; Perpignan; France
| | - Armelle Monier
- Laboratoire d'Ecologie Alpine; CNRS UMR 5553; Université Joseph Fourier; Grenoble 1, Grenoble; France
| | - Cécile Delolme
- Université de Lyon, Lyon, France Université Lyon1, Villeurbanne, France ENTPE, Vaulx-en-velin, France CNRS, UMR 5023, Laboratoire Ecologie des Hydrosystèmes Naturels et Anthropisés; Villeurbanne; France
| | - Roberto A. Geremia
- Laboratoire d'Ecologie Alpine; CNRS UMR 5553; Université Joseph Fourier; Grenoble 1, Grenoble; France
| | - Jean-Philippe Bedell
- Université de Lyon, Lyon, France Université Lyon1, Villeurbanne, France ENTPE, Vaulx-en-velin, France CNRS, UMR 5023, Laboratoire Ecologie des Hydrosystèmes Naturels et Anthropisés; Villeurbanne; France
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Krüger D, Kapturska D, Fischer C, Daniel R, Wubet T. Diversity measures in environmental sequences are highly dependent on alignment quality--data from ITS and new LSU primers targeting basidiomycetes. PLoS One 2012; 7:e32139. [PMID: 22363808 PMCID: PMC3283731 DOI: 10.1371/journal.pone.0032139] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 01/23/2012] [Indexed: 02/04/2023] Open
Abstract
The ribosomal DNA comprised of the ITS1-5.8S-ITS2 regions is widely used as a fungal marker in molecular ecology and systematics but cannot be aligned with confidence across genetically distant taxa. In order to study the diversity of Agaricomycotina in forest soils, we designed primers targeting the more alignable 28S (LSU) gene, which should be more useful for phylogenetic analyses of the detected taxa. This paper compares the performance of the established ITS1F/4B primer pair, which targets basidiomycetes, to that of two new pairs. Key factors in the comparison were the diversity covered, off-target amplification, rarefaction at different Operational Taxonomic Unit (OTU) cutoff levels, sensitivity of the method used to process the alignment to missing data and insecure positional homology, and the congruence of monophyletic clades with OTU assignments and BLAST-derived OTU names. The ITS primer pair yielded no off-target amplification but also exhibited the least fidelity to the expected phylogenetic groups. The LSU primers give complementary pictures of diversity, but were more sensitive to modifications of the alignment such as the removal of difficult-to align stretches. The LSU primers also yielded greater numbers of singletons but also had a greater tendency to produce OTUs containing sequences from a wider variety of species as judged by BLAST similarity. We introduced some new parameters to describe alignment heterogeneity based on Shannon entropy and the extent and contents of the OTUs in a phylogenetic tree space. Our results suggest that ITS should not be used when calculating phylogenetic trees from genetically distant sequences obtained from environmental DNA extractions and that it is inadvisable to define OTUs on the basis of very heterogeneous alignments.
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Affiliation(s)
- Dirk Krüger
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany.
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Garland S, James TY, Blair D, Berger L, Skerratt LF. Polymorphic repetitive loci of the amphibian pathogen Batrachochytrium dendrobatidis. DISEASES OF AQUATIC ORGANISMS 2011; 97:1-9. [PMID: 22235589 DOI: 10.3354/dao02396] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Batrachochytrium dendrobatidis (Bd), the cause of a fatal fungal skin disease of amphibians that has led to massive die-offs, global declines and extinctions, has spread internationally as a pandemic clone with low genetic diversity. A need exists to develop highly polymorphic markers to determine centers of origin and patterns of spread to assist in the development of management strategies. Comparison of paralogous sequences, obtained from the 2 sequenced Bd genomes, indicates useful levels of inter-strain polymorphism in repetitive fragments. We assessed 6 repetitive loci for variation within and among Australian isolates using standard fragment analysis and capillary electrophoresis-single strand conformation polymorphism (CE-SSCP) analysis. Confirmation of inter-isolate polymorphism was achieved for 2 marker systems, highlighting the potential of repetitive loci for the development of polymorphic markers in Bd. In addition, we found that repetitive loci in Bd include possible orthologs of virulence-related genes from pathogenic fungi.
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Affiliation(s)
- Stephen Garland
- Amphibian Disease Ecology Group, Tropical Medicine and Rehabilitation Sciences, James Cook University, Townsville, Queensland 4811, Australia,
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Gulija TK, Ivancic-Jelecki J, Šantak M, Forcic D. Comparative analysis of CE-SSCP to standard RFLP-CE-FLA method in quantification of known viral variants within an RNA virus quasispecies. Electrophoresis 2011; 32:1852-9. [DOI: 10.1002/elps.201100010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Zinger L, Lejon DPH, Baptist F, Bouasria A, Aubert S, Geremia RA, Choler P. Contrasting diversity patterns of crenarchaeal, bacterial and fungal soil communities in an alpine landscape. PLoS One 2011; 6:e19950. [PMID: 21589876 PMCID: PMC3093402 DOI: 10.1371/journal.pone.0019950] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 04/07/2011] [Indexed: 12/02/2022] Open
Abstract
Background The advent of molecular techniques in microbial ecology has aroused interest in gaining an understanding about the spatial distribution of regional pools of soil microbes and the main drivers responsible of these spatial patterns. Here, we assessed the distribution of crenarcheal, bacterial and fungal communities in an alpine landscape displaying high turnover in plant species over short distances. Our aim is to determine the relative contribution of plant species composition, environmental conditions, and geographic isolation on microbial community distribution. Methodology/Principal Findings Eleven types of habitats that best represent the landscape heterogeneity were investigated. Crenarchaeal, bacterial and fungal communities were described by means of Single Strand Conformation Polymorphism. Relationships between microbial beta diversity patterns were examined by using Bray-Curtis dissimilarities and Principal Coordinate Analyses. Distance-based redundancy analyses and variation partitioning were used to estimate the relative contributions of different drivers on microbial beta diversity. Microbial communities tended to be habitat-specific and did not display significant spatial autocorrelation. Microbial beta diversity correlated with soil pH. Fungal beta-diversity was mainly related to soil organic matter. Though the effect of plant species composition was significant for all microbial groups, it was much stronger for Fungi. In contrast, geographic distances did not have any effect on microbial beta diversity. Conclusions/Significance Microbial communities exhibit non-random spatial patterns of diversity in alpine landscapes. Crenarcheal, bacterial and fungal community turnover is high and associated with plant species composition through different set of soil variables, but is not caused by geographical isolation.
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Affiliation(s)
- Lucie Zinger
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université de Grenoble, Grenoble, France.
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Assessment of soil fungal diversity in different alpine tundra habitats by means of pyrosequencing. FUNGAL DIVERS 2011. [DOI: 10.1007/s13225-011-0101-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Badin AL, Monier A, Volatier L, Geremia RA, Delolme C, Bedell JP. Structural stability, microbial biomass and community composition of sediments affected by the hydric dynamics of an urban stormwater infiltration basin. Dynamics of physical and microbial characteristics of stormwater sediment. MICROBIAL ECOLOGY 2011; 61:885-897. [PMID: 21431934 DOI: 10.1007/s00248-011-9829-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2010] [Accepted: 02/09/2011] [Indexed: 05/30/2023]
Abstract
The sedimentary layer deposited at the surface of stormwater infiltration basins is highly organic and multicontaminated. It undergoes considerable moisture content fluctuations due to the drying and inundation cycles (called hydric dynamics) of these basins. Little is known about the microflora of the sediments and its dynamics; hence, the purpose of this study is to describe the physicochemical and biological characteristics of the sediments at different hydric statuses of the infiltration basin. Sediments were sampled at five time points following rain events and dry periods. They were characterized by physical (aggregation), chemical (nutrients and heavy metals), and biological (total, bacterial and fungal biomasses, and genotypic fingerprints of total bacterial and fungal communities) parameters. Data were processed using statistical analyses which indicated that heavy metal (1,841 μg/g dry weight (DW)) and organic matter (11%) remained stable through time. By contrast, aggregation, nutrient content (NH₄⁺, 53-717 μg/g DW), pH (6.9-7.4), and biological parameters were shown to vary with sediment water content and sediment biomass, and were higher consecutive to stormwater flows into the basin (up to 7 mg C/g DW) than during dry periods (0.6 mg C/g DW). Coinertia analysis revealed that the structure of the bacterial communities is driven by the hydric dynamics of the infiltration basin, although no such trend was found for fungal communities. Hydric dynamics more than rain events appear to be more relevant for explaining variations of aggregation, microbial biomass, and shift in the microbial community composition. We concluded that the hydric dynamics of stormwater infiltration basins greatly affects the structural stability of the sedimentary layer, the biomass of the microbial community living in it and its dynamics. The decrease in aggregation consecutive to rewetting probably enhances access to organic matter (OM), explaining the consecutive release of NH₄⁺, the bloom of the microbial biomass, and the change in structure of the bacterial community. These results open new perspectives for basin management since the risk of OM and pollutant transfer to the aquifer is greatly affected by alternating dry and flood periods.
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Michelland RJ, Monteils V, Combes S, Cauquil L, Gidenne T, Fortun-Lamothe L. Comparison of the archaeal community in the fermentative compartment and faeces of the cow and the rabbit. Anaerobe 2010; 16:396-401. [PMID: 20417714 DOI: 10.1016/j.anaerobe.2010.04.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 03/18/2010] [Accepted: 04/15/2010] [Indexed: 12/01/2022]
Abstract
The archaeal community in the fermentative compartment and faeces of the cow and the rabbit were compared by analysis capillary electrophoresis single-stranded conformation polymorphism (CE-SSCP) profiles of 16S rRNA genes. Ruminal and faecal contents were sampled in five cows for three weeks. Hard and soft faeces were collected in 14 rabbits for three consecutive weeks and caecal contents were sampled in the third week. The archaeal community differed according to the host species (ANOSIM-R=0.53 and 0.72 respectively for the comparison of the fermentative compartments and faeces; P<0.001) and to the location within the digestive tract of both species (ANOSIM-R=0.37, 0.52 respectively for the cow and the rabbit; P<0.001). In both species, the archaeal community of the digestive tract was stable over weeks and varied very little between individual animals. The structure (NS) and the richness index (9.9+/-2.7, 10.1+/-3.1 respectively, NS) of the archaeal community were similar for the caecal content and the soft faeces which permitted to use the latter as a representative indicator.
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Affiliation(s)
- Rory Julien Michelland
- Institut National de la Recherche Agronomique-UMR 1289, Tissus Animaux, Nutrition, Digestion, Ecosystème et Métabolisme, Castanet-Tolosan, France
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Pegard A, Miquel C, Valentini A, Coissac E, Bouvier F, François D, Taberlet P, Engel E, Pompanon F. Universal DNA-based methods for assessing the diet of grazing livestock and wildlife from feces. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2009; 57:5700-5706. [PMID: 19566081 DOI: 10.1021/jf803680c] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Because of the demand for controlling livestock diets, two methods that characterize the DNA of plants present in feces were developed. After DNA extraction from fecal samples, a short fragment of the chloroplastic trnL intron was amplified by PCR using a universal primer pair for plants. The first method generates a signature that is the electrophoretic migration pattern of the PCR product. The second method consists of sequencing several hundred DNA fragments from the PCR product through pyrosequencing. These methods were validated with a blind analysis of feces from concentrate- and pasture-fed lambs. The signature method allowed differentiation of the two diets and confirmed the presence of concentrate in one of them. The pyrosequencing method allowed the identification of up to 25 taxa in a diet. These methods are complementary to the chemical methods already used. They could be applied to the control of diets and the study of food preferences.
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Affiliation(s)
- Anthony Pegard
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, Grenoble Cedex 9, France
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Microbial diversity in alpine tundra soils correlates with snow cover dynamics. ISME JOURNAL 2009; 3:850-9. [PMID: 19322246 DOI: 10.1038/ismej.2009.20] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The temporal and spatial snow cover dynamics is the primary factor controlling the plant communities' composition and biogeochemical cycles in arctic and alpine tundra. However, the relationships between the distribution of snow and the diversity of soil microbial communities remain largely unexplored. Over a period of 2 years, we monitored soil microbial communities at three sites, including contiguous alpine meadows of late and early snowmelt locations (LSM and ESM, respectively). Bacterial and fungal communities were characterized by using molecular fingerprinting and cloning/sequencing of microbial ribosomal DNA extracted from the soil. Herein, we show that the spatial and temporal distribution of snow strongly correlates with microbial community composition. High seasonal contrast in ESM is associated with marked seasonal shifts for bacterial communities; whereas less contrasted seasons because of long-lasting snowpack in LSM is associated with increased fungal diversity. Finally, our results indicate that, similar to plant communities, microbial communities exhibit important shifts in composition at two extremes of the snow cover gradient. However, winter conditions lead to the convergence of microbial communities independently of snow cover presence. This study provides new insights into the distribution of microbial communities in alpine tundra in relation to snow cover dynamics, and may be helpful in predicting the future of microbial communities and biogeochemical cycles in arctic and alpine tundra in the context of a warmer climate.
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Valentini A, Pompanon F, Taberlet P. DNA barcoding for ecologists. Trends Ecol Evol 2008; 24:110-7. [PMID: 19100655 DOI: 10.1016/j.tree.2008.09.011] [Citation(s) in RCA: 527] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2007] [Revised: 08/26/2008] [Accepted: 09/08/2008] [Indexed: 12/14/2022]
Abstract
DNA barcoding - taxon identification using a standardized DNA region - has received much attention recently, and is being further developed through an international initiative. We anticipate that DNA barcoding techniques will be increasingly used by ecologists. They will be able to not only identify a single species from a specimen or an organism's remains but also determine the species composition of environmental samples. Short DNA fragments persist in the environment and might allow an assessment of local biodiversity from soil or water. Even DNA-based diet composition can be estimated using fecal samples. Here we review the new avenues offered to ecologists by DNA barcoding, particularly in the context of new sequencing technologies.
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Affiliation(s)
- Alice Valentini
- Laboratoire d'Ecologie Alpine, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
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Baptist F, Zinger L, Clement JC, Gallet C, Guillemin R, Martins JMF, Sage L, Shahnavaz B, Choler P, Geremia R. Tannin impacts on microbial diversity and the functioning of alpine soils: a multidisciplinary approach. Environ Microbiol 2008; 10:799-809. [DOI: 10.1111/j.1462-2920.2007.01504.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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