Integrating quantitative morphological and qualitative molecular methods to analyse soil nematode community responses to plant range expansion
暂无分享,去创建一个
L. Basten Snoek | Stefan Geisen | Johannes Helder | Wim H. van der Putten | Casper W. Quist | L. B. Snoek | C. Quist | S. Geisen | O. Kostenko | Henk Duyts | H. Duyts | Freddy C. ten Hooven | Olga Kostenko | Janneke Bloem | Henk Martens | Freddy C. ten Hooven | Henk Martens | J. Bloem | Johannes A. Helder | Wim H. der Putten
[1] T. Bongers,et al. Nematode diversity in agroecosystems , 1999 .
[2] W. Traunspurger. The biology and ecology of lotic nematodes , 2000 .
[3] P. Castagnone-Sereno,et al. Enzyme phenotypes and genetic diversity of root-knot nematodes parasitising musa in Brazil , 2004 .
[4] D. Neher,et al. Role of nematodes in soil health and their use as indicators. , 2001, Journal of nematology.
[5] Robert C. Edgar,et al. BIOINFORMATICS APPLICATIONS NOTE , 2001 .
[6] W. H. Putten,et al. Effects of native and exotic range‐expanding plant species on taxonomic and functional composition of nematodes in the soil food web , 2012 .
[7] R. Neilson,et al. Determination of the optimal soil sample size to accurately characterise nematode communities in soil , 2015 .
[8] T. M. Bezemer,et al. Successful range-expanding plants experience less above-ground and below-ground enemy impact , 2008, Nature.
[9] Karl Ritz,et al. Selecting biological indicators for monitoring soils: A framework for balancing scientific and technical opinion to assist policy development , 2009 .
[10] W. H. Putten,et al. Plant-feeding nematodes in coastal sand dunes: occurrence, host specificity and effects on plant growth , 2015, Plant and Soil.
[11] C. Quist,et al. Organic farming practices result in compositional shifts in nematode communities that exceed crop-related changes , 2016 .
[12] C. Heip,et al. The fate of intertidal microphytobenthos carbon: An in situ 13C‐labeling study , 2000 .
[13] Sven Rahmann,et al. Genome analysis , 2022 .
[14] Stéphane Audic,et al. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy , 2012, Nucleic Acids Res..
[15] M. Bonkowski,et al. Not all are free‐living: high‐throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa , 2015, Molecular ecology.
[16] M. Nicolaisen,et al. High-throughput sequencing of nematode communities from total soil DNA extractions , 2015, BMC Ecology.
[17] M. Bonkowski. Protozoa and plant growth: the microbial loop in soil revisited. , 2004, The New phytologist.
[18] J. Spouge,et al. CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms , 2012, PLoS biology.
[19] Daniel G. Brown,et al. PANDAseq: paired-end assembler for illumina sequences , 2012, BMC Bioinformatics.
[20] R. Giblin-Davis,et al. Plant invasions from a belowground nematocentric perspective , 2014 .
[21] M. Vincx,et al. Observations on the Feeding Ecology of Estuarine Nematodes , 1997, Journal of the Marine Biological Association of the United Kingdom.
[22] A. Vogler,et al. Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages , 2015 .
[23] H. Ferris,et al. Nematode community structure as a bioindicator in environmental monitoring. , 1999, Trends in ecology & evolution.
[24] M. Blaxter,et al. A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual , 2015, Molecular ecology.
[25] B. Griffiths,et al. Selecting cost effective and policy-relevant biological indicators for European monitoring of soil biodiversity and ecosystem function , 2016 .
[26] W. H. Putten,et al. Interspecific differences in nematode control between range-expanding plant species and their congeneric natives , 2016 .
[27] W. H. van der Putten,et al. Climate Change, Aboveground-Belowground Interactions, and Species' Range Shifts , 2012 .
[28] T. Powers. Nematode molecular diagnostics: from bands to barcodes. , 2004, Annual review of phytopathology.
[29] Ben Nichols,et al. VSEARCH: a versatile open source tool for metagenomics , 2016, PeerJ.
[30] Jun Wang,et al. Quantitative microbiome profiling links gut community variation to microbial load , 2017, Nature.
[31] R. Callaway,et al. Novel Weapons: Invasive Success and the Evolution of Increased Competitive Ability , 2004 .
[32] F. Strozzi,et al. A new primer set for DNA metabarcoding of soil Metazoa , 2016 .
[33] Mark Blaxter,et al. Molecular barcodes for soil nematode identification , 2002, Molecular ecology.
[34] M. Herman,et al. High‐throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure , 2013, Molecular ecology.
[35] B. Griffiths,et al. A novel molecular approach for rapid assessment of soil nematode assemblages – variation, validation and potential applications , 2012 .
[36] B. Griffiths,et al. A comparison of molecular methods for monitoring soil nematodes and their use as biological indicators , 2010 .
[37] L. Court,et al. Discrimination of plant-parasitic nematodes from complex soil communities using ecometagenetics. , 2014, Phytopathology.
[38] D. Porazinska,et al. Do tropical rain forest soils have greater nematode diversity than High Arctic tundra? A metagenetic comparison of Malaysia and Svalbard , 2016 .
[39] Rob Knight,et al. UCHIME improves sensitivity and speed of chimera detection , 2011, Bioinform..
[40] P. Urwin,et al. Transgenic Potatoes for Potato Cyst Nematode Control Can Replace Pesticide Use without Impact on Soil Quality , 2012, PloS one.
[41] Micah,et al. Soil protistology rebooted: 30 fundamental questions to start with , 2017 .
[42] D. Trudgill,et al. Utility of nematode community analysis as an integrated measure of the functional state of soils: perspectives and challenges , 1999, Plant and Soil.
[43] B. K. Ellis,et al. The role of micro‐organisms in the ecological connectivity of running waters , 1998 .
[44] T. Cavalier-smith,et al. Helkesimastix marina n. sp. (Cercozoa: Sainouroidea superfam. n.) a gliding zooflagellate of novel ultrastructure and unusual ciliary behaviour. , 2009, Protist.
[45] Wolfgang Nentwig,et al. Alien species in a warmer world: risks and opportunities. , 2009, Trends in ecology & evolution.
[46] R. Knight,et al. Sequencing our way towards understanding global eukaryotic biodiversity. , 2012, Trends in ecology & evolution.
[47] M. Bonkowski,et al. Methodological advances to study the diversity of soil protists and their functioning in soil food webs , 2017 .
[48] James R. Cole,et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis , 2013, Nucleic Acids Res..
[49] G. Yohe,et al. A globally coherent fingerprint of climate change impacts across natural systems , 2003, Nature.
[50] Abraham E. Tucker,et al. Evaluating high‐throughput sequencing as a method for metagenomic analysis of nematode diversity , 2009, Molecular ecology resources.
[51] Hadley Wickham,et al. ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .
[52] Alex C Rodriguez,et al. Soil biota and exotic plant invasion , 2004, Nature.
[53] U. Göbel,et al. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. , 1997, FEMS microbiology reviews.
[54] S. Geisen. Thorough high-throughput sequencing analyses unravels huge diversities of soil parasitic protists. , 2016, Environmental microbiology.
[55] C. Mulder,et al. SSU Ribosomal DNA-Based Monitoring of Nematode Assemblages Reveals Distinct Seasonal Fluctuations within Evolutionary Heterogeneous Feeding Guilds , 2012, PloS one.
[56] M. Tenuta,et al. Reflections on plant and soil nematode ecology: past, present and future. , 2012, Journal of nematology.
[57] M. Crawley,et al. Exotic plant invasions and the enemy release hypothesis , 2002 .
[58] B. Griffiths,et al. Molecular sequencing and morphological analysis of a nematode community , 2006 .
[59] B. Griffiths,et al. The need for standardisation: Exemplified by a description of the diversity, community structure and ecological indices of soil nematodes , 2018 .
[60] S. Scheu,et al. Possible mechanisms underlying abundance and diversity responses of nematode communities to plant diversity , 2017 .
[61] P. Garbeva,et al. Belowground Plant–Herbivore Interactions Vary among Climate-Driven Range-Expanding Plant Species with Different Degrees of Novel Chemistry , 2017, Front. Plant Sci..
[62] D. Neher. Ecology of plant and free-living nematodes in natural and agricultural soil. , 2010, Annual review of phytopathology.
[63] J. Prosser. Dispersing misconceptions and identifying opportunities for the use of 'omics' in soil microbial ecology , 2015, Nature Reviews Microbiology.
[64] R. Giblin-Davis,et al. Ecometagenetics confirm high tropical rainforest nematode diversity , 2010, Molecular ecology.
[65] C. Ettema,et al. Soil nematode diversity: species coexistence and ecosystem function. , 1998, Journal of nematology.
[66] L. Noble,et al. Assessment of nematode biodiversity using DGGE of 18S rDNA following extraction of nematodes from soil , 2004 .
[67] Tom Bongers,et al. The maturity index: an ecological measure of environmental disturbance based on nematode species composition , 1990, Oecologia.
[68] R. Giblin-Davis,et al. Reproducibility of read numbers in high‐throughput sequencing analysis of nematode community composition and structure , 2009, Molecular ecology resources.
[69] T. Bongers,et al. Functional diversity of nematodes , 1998 .
[70] Anders F. Andersson,et al. Systematic Design of 18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia , 2014, PloS one.
[71] Top-down control of root-feeding nematodes in range-expanding and congeneric native plant species , 2015 .
[72] J. C. Moore,et al. The detrital food web in a shortgrass prairie , 1987, Biology and Fertility of Soils.
[73] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[74] T. Bongers,et al. Feeding habits in soil nematode families and genera-an outline for soil ecologists. , 1993, Journal of nematology.
[75] T. Stoeck,et al. Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions. , 2011, Environmental microbiology.