Articles | Volume 2, issue 2
SOIL, 2, 257–270, 2016
https://doi.org/10.5194/soil-2-257-2016
© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
SOIL, 2, 257–270, 2016
https://doi.org/10.5194/soil-2-257-2016
© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
Review article 20 Jun 2016
Review article | 20 Jun 2016
Technological advancements and their importance for nematode identification
Mohammed Ahmed et al.
Related subject area
Soils and biodiversity
Microbial communities and their predictive functional profiles in the arid soil of Saudi Arabia
Development of a soil biological quality index for soils of semi-arid tropics
What do we know about how the terrestrial multicellular soil fauna reacts to microplastic?
Soil microbial biomass and function are altered by 12 years of crop rotation
Soil denitrifier community size changes with land use change to perennial bioenergy cropping systems
Knowledge needs, available practices, and future challenges in agricultural soils
Fire affects root decomposition, soil food web structure, and carbon flow in tallgrass prairie
Case study of microarthropod communities to assess soil quality in different managed vineyards
A meta-analysis of soil biodiversity impacts on the carbon cycle
Munawwar A. Khan and Shams T. Khan
SOIL, 6, 513–521, https://doi.org/10.5194/soil-6-513-2020, https://doi.org/10.5194/soil-6-513-2020, 2020
Short summary
Short summary
Soil is a renewable resource for purposes ranging from agriculture to mineralization. Soil microbiome plays vital roles in facilitating process like providing nutrients to plants, or their mobilization for plant uptake, consequently improving plant growth and productivity. Therefore, understanding of these microbial communities and their role in soil is crucial for exploring the possibility of using microbial community inoculants for improving desert soil fertility and agricultural potential.
Selvaraj Aravindh, Chinnappan Chinnadurai, and Dananjeyan Balachandar
SOIL, 6, 483–497, https://doi.org/10.5194/soil-6-483-2020, https://doi.org/10.5194/soil-6-483-2020, 2020
Short summary
Short summary
Soil quality is important for functioning of the agricultural ecosystem to sustain productivity. It is combination of several physical, chemical, and biological attributes. In the present work, we developed a soil biological quality index, a sub-set of the soil quality index (SBQI) using six important biological variables. These variables were computed from long-term manurial experimental soils and transformed into a unitless 10-scaled SBQI. This will provide constraints of soil processes.
Frederick Büks, Nicolette Loes van Schaik, and Martin Kaupenjohann
SOIL, 6, 245–267, https://doi.org/10.5194/soil-6-245-2020, https://doi.org/10.5194/soil-6-245-2020, 2020
Short summary
Short summary
Via anthropogenic input, microplastics (MPs) today represent a part of the soil organic matter. We analyzed studies on passive translocation, active ingestion, bioaccumulation and adverse effects of MPs on multicellular soil faunal life. These studies on a wide range of soil organisms found a recurring pattern of adverse effects on motility, growth, metabolism, reproduction, mortality and gut microbiome. However, the shape and type of the experimental MP often did not match natural conditions.
Marshall D. McDaniel and A. Stuart Grandy
SOIL, 2, 583–599, https://doi.org/10.5194/soil-2-583-2016, https://doi.org/10.5194/soil-2-583-2016, 2016
Short summary
Short summary
Modern agriculture is dominated by monoculture crop production, having negative effects on soil biology. We used a 12-year crop rotation experiment to examine the effects of increasing crop diversity on soil microorganisms and their activity. Crop rotations increased microbial biomass by up to 112 %, and increased potential ability to supply nitrogen as much as 58 %, compared to monoculture corn. Collectively, our findings show that soil health is increased when crop diversity is increased.
Karen A. Thompson, Bill Deen, and Kari E. Dunfield
SOIL, 2, 523–535, https://doi.org/10.5194/soil-2-523-2016, https://doi.org/10.5194/soil-2-523-2016, 2016
Short summary
Short summary
Dedicated bioenergy crops are required for future energy production; however the effects of land use change from traditional crops to biofuel crops on soil microbial communities, which drive greenhouse gas production, are largely unknown. We used quantitative PCR to enumerate these microbial communities to assess the sustainability of different bioenergy crops, including miscanthus and corn. We found that miscanthus may be a suitable crop for bioenergy production in variable Ontario conditions.
Georgina Key, Mike G. Whitfield, Julia Cooper, Franciska T. De Vries, Martin Collison, Thanasis Dedousis, Richard Heathcote, Brendan Roth, Shamal Mohammed, Andrew Molyneux, Wim H. Van der Putten, Lynn V. Dicks, William J. Sutherland, and Richard D. Bardgett
SOIL, 2, 511–521, https://doi.org/10.5194/soil-2-511-2016, https://doi.org/10.5194/soil-2-511-2016, 2016
Short summary
Short summary
Enhancing soil health is key to providing ecosystem services and food security. There are often trade-offs to using a particular practice, or it is not fully understood. This work aimed to identify practices beneficial to soil health and gaps in our knowledge. We reviewed existing research on agricultural practices and an expert panel assessed their effectiveness. The three most beneficial practices used a mix of organic or inorganic material, cover crops, or crop rotations.
E. Ashley Shaw, Karolien Denef, Cecilia Milano de Tomasel, M. Francesca Cotrufo, and Diana H. Wall
SOIL, 2, 199–210, https://doi.org/10.5194/soil-2-199-2016, https://doi.org/10.5194/soil-2-199-2016, 2016
Short summary
Short summary
We investigated fire's effects on root decomposition and carbon (C) flow to the soil food web. We used 13C-labeled dead roots buried in microcosms constructed from two burn treatment soils (annual and infrequent burn). Our results showed greater root decomposition and C flow to the soil food web for the annual burn compared to infrequent burn treatment. Thus, roots are a more important C source for decomposers in annually burned areas where surface plant litter is frequently removed by fire.
E. Gagnarli, D. Goggioli, F. Tarchi, S. Guidi, R. Nannelli, N. Vignozzi, G. Valboa, M. R. Lottero, L. Corino, and S. Simoni
SOIL, 1, 527–536, https://doi.org/10.5194/soil-1-527-2015, https://doi.org/10.5194/soil-1-527-2015, 2015
M.-A. de Graaff, J. Adkins, P. Kardol, and H. L. Throop
SOIL, 1, 257–271, https://doi.org/10.5194/soil-1-257-2015, https://doi.org/10.5194/soil-1-257-2015, 2015
Cited articles
Abebe, E., Mekete, T., and Thomas, W. K.: A critique of current methods in nematode taxonomy, Afr. J. Biotechnol., 10, 312–323, 2013.
Agatha, S. and Strüder-Kypke, M. C.: Phylogeny of the order Choreotrichida (Ciliophora, Spirotricha, Oligotrichea) as inferred from morphology, ultrastructure, ontogenesis, and SSr-RNA gene sequences, Eur. J. Protistol., 43, 37–63, 2007.
Akhtar, M. and Malik, A.: Roles of organic soil amendments and soil organisms in the biological control of plant-parasitic nematodes: a review, Bioresource Technol., 74, 35–47, 2000.
Allen, M. and Sher, S.: Taxonomic problems concerning the phytoparasitic nematodes, Annu. Rev. Phytopathol., 5, 247–262, 1967.
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J.: Basic local alignment search tool, J. Mol. Biol., 215, 403–410, https://doi.org/10.1016/S0022-2836(05)80360-2, 1990.
Bardgett, R. D. and Chan, K. F.: Experimental evidence that soil fauna enhance nutrient mineralization and plant nutrient uptake in montane grassland ecosystems, Soil Biol. Biochem., 31, 1007–1014, https://doi.org/10.1016/S0038-0717(99)00014-0, 1999.
Beccuti, M., Carrara, M., Cordero, F., Donatelli, S., and Calogero, R. A.: The structure of state-of-art gene fusion-finder algorithms, Genome Bioinform., 1, 1–6, 2013.
Bergé, J.-B. and Dalmasso, A.: Caractéristiques biochimiques de quelques populations de Meloidogyne hapla et Melodogyne spp, Cah ORSTOM. Série Biologie: Nématologie, 10, 263–271, 1975.
Bik, H. M., Porazinska, D. L., Creer, S., Caporaso, J. G., Knight, R., and Thomas, W. K.: Sequencing our way towards understanding global eukaryotic biodiversity, Trends Ecol. Evol., 27, 233–243, 2012.
Blaxter, M., Mann, J., Chapman, T., Thomas, F., Whitton, C., Floyd, R., and Abebe, E.: Defining operational taxonomic units using DNA barcode data, Philos. T. Roy. Soc. B, 360, 1935–1943, 2005.
Blaxter, M. L., De Ley, P., Garey, J. R., Liu, L. X., Scheldeman, P., Vierstraete, A., Vanfleteren, J. R., Mackey, L. Y., Dorris, M., and Frisse, L. M.: A molecular evolutionary framework for the phylum Nematoda, Nature, 392, 71–75, 1998.
Blok, V. C.: Molecular diagnostics for plant-parasitic nematodes, Proceedings of the Fourth International Congress of Nematology, June 2002, Tenerife, Spain, 195–206, 2004.
Blok, V. C.: Achievements in and future prospects for molecular diagnostics of plant-parasitic nematodes, Can. J. Plant. Pathol., 27, 176–185, 2005.
Boisselier-Dubayle, M. and Gofas, S.: Genetic relationships between marine and marginalmarine populations of Cerithium species from the Mediterranean Sea, Mar. Biol., 135, 671–682, 1999.
Bongers, T.: The maturity index: an ecological measure of environmental disturbance based on nematode species composition, Oecologia, 83, 14–19, 1990.
Bongers, T. and Bongers, M.: Functional diversity of nematodes, Appl. Soil Ecol., 10, 239–251, 1998.
Bongers, T. and Ferris, H.: Nematode community structure as a bioindicator in environmental monitoring, Trends Ecol. Evol., 14, 224–228, 1999.
Bucklin, A., Steinke, D., and Blanco-Bercial, L.: DNA barcoding of marine metazoa, Ann. Rev. Mar. Sci., 3, 471–508, 2011.
Cantalapiedra-Navarrete, C., Navas-Cortés, J. A., Liébanas, G., Vovlas, N., Subbotin, S. A., Palomares-Rius, J. E., and Castillo, P.: Comparative molecular and morphological characterisations in the nematode genus Rotylenchus: Rotylenchus paravitis n. sp., an example of cryptic speciation, Zool. Anz. A, 252, 246–268, 2013.
Carneiro, R. M., Almeida, M. R. A., and Quénéhervé, P.: Enzyme phenotypes of Meloidogyne spp. populations, Nematology, 2, 645–654, 2000.
Carpenter, A., Hiatt, E., Lewis, S., and Abbott, A.: Genomic RFLP analysis of Meloidogyne arenaria race 2 populations, J. Nematol., 24, 23–28, 1992.
Carrasco-Ballesteros, S., Castillo, P., Adams, B., and Pérez-Artés, E.: Identification of Pratylenchus thornei, the cereal and legume root-lesion nematode, based on SCAR-PCR and satellite DNA, Eur. J. Plant. Pathol., 118, 115–125, 2007.
Castagnone-Sereno, P., Vanlerberghe-Masutti, F., and Leroy, F.: Genetic polymorphism between and within Meloidogyne species detected with RAPD markers, Genome, 37, 904–909, 1994.
Cenis, J.: Identification of Four Major Meloidogyne ssp. by Random Amplified Polymorphic DNA (RAPD-PCR), Phytopathology, 83, 76, 1993.
Charchar, J. and Eisenback, J.: An improved technique to prepare perineal patterns of root-knot nematodes for SEM, Nematol. Bras., 24, 245–247, 2000.
Chilton, N. B., Gasser, R. B., and Beveridge, I.: Differences in a ribosomal DNA sequence of morphologically indistinguishable species within the Hypodontus macropi complex (Nematoda: Strongyloidea), Int. J. Parasitol., 25, 647–651, 1995.
Cobb, N. A.: Nematodes and their relationships, in: Yearbook of the United States Department of Agriculture, 1914, US Government Printing Office, Washington, D.C., 457–490, 1915.
Coomans, A.: Present status and future of nematode systematics, Nematology, 4, 573–582, 2002.
Creer, S., Fonseca, V., Porazinska, D., Giblin-Davis, R., Sung, W., Power, D., Packer, M., Carvalho, G., Blaxter, M., and Lambshead, P.: Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises, Mol. Ecol., 19, 4–20, 2010.
Curran, J., McClure, M., and Webster, J.: Genotypic differentiation of Meloidogyne populations by detection of restriction fragment length difference in total DNA, J. Nematol., 18, 83–86, 1986.
Dayrat, B.: Towards integrative taxonomy, Biol. J. Linn. Soc., 85, 407–415, 2005.
Deagle, B. E., Jarman, S. N., Coissac, E., Pompanon, F., and Taberlet, P.: DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match, Biol. Lett., 10, https://doi.org/10.1098/rsbl.20140562, 2014
Decraemer, W. and Hunt, D.: Taxonomy and principal genera, in: Plant Nematology, edited by: Perry, R. and Moens, M., CABI Publishing, Wallingford, UK, 3–32, 2006.
De Ley, P.: Lost in worm space: phylogeny and morphology as road maps to nematode diversity, Nematology, 2, 9–16, 2000.
De Ley, P.: A quick tour of nematode diversity and the backbone of nematode phylogeny, in: WormBook, edited by: The Caenorhabditis elegans Research Community, https://doi.org/10.1895/wormbook.1.7.1, 2006.
De Ley, P., De Ley, I. T., Morris, K., Abebe, E., Mundo-Ocampo, M., Yoder, M., Heras, J., Waumann, D., Rocha-Olivares, A., and Burr, A. J.: An integrated approach to fast and informative morphological vouchering of nematodes for applications in molecular barcoding, Philos. T. Roy. Soc. B, 360, 1945–1958, 2005.
den Nijs, L. and van den Berg, W.: The added value of proficiency tests: choosing the proper method for extracting Meloidogyne second-stage juveniles from soil, Nematology, 15, 143– 151, 2013.
Derycke, S., Remerie, T., Vierstraete, A., Backeljau, T., Vanfleteren, J., Vincx, M., and Moens, T.: Mitochondrial DNA variation and cryptic speciation within the free-living marine nematode Pellioditis marina, Mar. Ecol.-Prog. Ser., 300, 91–103, 2005.
Dorris, M., De Ley, P., and Blaxter, M.: Molecular analysis of nematode diversity and the evolution of parasitism, Parasitol Today, 15, 188–193, 1999.
Drotz, M. K., Saura, A., and Nilsson, A. N.: The species delimitation problem applied to the Agabus bipustulatus complex (Coleoptera, Dytiscidae) in north Scandinavia, Biol. J. Linn. Soc., 73, 11–22, 2001.
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., and Knight, R.: UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, 27, 2194–2200, 2011.
Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., Peluso, P., Rank, D., Baybayan, P., and Bettman, B.: Real-time DNA sequencing from single polymerase molecules, Science, 323, 133–138, 2009.
Eisenback, J. D. and Hirschmann, H.: Identification of Meloidogyne Species on the Basis of Head Shape and, Stylet Morphology of the Male, J. Nematol., 13, 513–521, 1981.
Eisenback, J. D. and Hunt, D. J.: General Morphology, in: Root-knot Nematodes, edited by: Perry R. N., Moens, M., and Starr J. L., CABI, Wallingford, UK, 18–54, 2009.
Ekblom, R. and Galindo, J.: Applications of next generation sequencing in molecular ecology of non-model organisms, Heredity, 107, 1–15, 2011.
Esbenshade, P. and Triantaphyllou, A.: Use of enzyme phenotypes for identification of Meloidogyne species, J. Nematol., 17, 6–20, 1985.
Esbenshade, P. and Triantaphyllou, A.: Isozyme phenotypes for the identification of Meloidogyne species, J. Nematol., 22, 10–15, 1990.
Eves-Van Den Akker, S., Lilley, C. J., Reid, A., Pickup, J., Anderson, E., Cock, P. J. A., Blaxter, M., Urwin, P. E., Jones, J. T., and Blok, V. C.: A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual, Mol. Ecol., 24, 5842–5851, https://doi.org/10.1111/mec.13434, 2015.
Ferri, E., Barbuto, M., Bain, O., Galimberti, A., Uni, S., Guerrero, R., Ferté, H., Bandi, C., Martin, C., and Casiraghi, M.: Integrated taxonomy: traditional approach and DNA barcoding for the identification of filarioid worms and related parasites (Nematoda), Front. Zool., 6, 1–12, https://doi.org/10.1186/1742-9994-6-1, 2009.
Ferris, V., Ferris, J., Faghihi, J., and Ireholm, A.: Comparisons of isolates of Heterodera avenae using 2-D PAGE protein patterns and ribosomal DNA, J. Nematol., 26, 144–151, 1994.
Floyd, R., Abebe, E., Papert, A., and Blaxter, M.: Molecular barcodes for soil nematode identification, Mol. Ecol., 11, 839–850, 2002.
Fonseca, G., Derycke, S., and Moens, T.: Integrative taxonomy in two free-living nematode species complexes, Biol. J. Linn. Soc., 94, 737–753, 2008.
Fonseca, V. G., Carvalho, G. R., Sung, W., Johnson, H. F., Power, D. M., Neill, S. P., Packer, M., Blaxter, M. L., Lambshead, P. J. D., and Thomas, W. K.: Second-generation environmental sequencing unmasks marine metazoan biodiversity, Nat. Commun., 1, 98, 2010.
Fonseca, V. G., Nichols, B., Lallias, D., Quince, C., Carvalho, G. R., Power, D. M., and Creer, S.: Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses, Nucl. Acids Res., 40, e66, 2012.
Fourie, H., Zijlstra, C., and McDonald, A.: Identification of root-knot nematode species occurring in South Africa using the SCAR-PCR technique, Nematology, 3, 675–680, https://doi.org/10.1163/156854101753536046, 2001.
Glenn, T. C.: Field guide to next generation DNA sequencers, Mol. Ecol. Resour., 11, 759–769, 2011.
Groombridge, B.: Global biodiversity: status of the Earth's living resources, Chapman & Hall, London, UK, 1992.
Haas, B. J., Gevers, D., Earl, A. M., Feldgarden, M., Ward, D. V., Giannoukos, G., Ciulla, D., Tabbaa, D., Highlander, S. K., and Sodergren, E.: Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons, Genome Res., 21, 494–504, 2011.
Hague, N. and Gowen, S.: Chemical control of nematodes, Principles and practice of nematode control in crops, Academic Press, Sydney, 131–178, 1987.
Handoo, Z., Nyczepir, A., Esmenjaud, D., Van der Beek, J., Castagnone-Sereno, P., Carta, L., Skantar, A., and Higgins, J.: Morphological, molecular, and differential-host characterization of Meloidogyne floridensis n. sp. (Nematoda: Meloidogynidae), a root-knot nematode parasitizing peach in Florida, J. Nematol., 36, 20–35, 2004.
Harris, T., Sandall, L., and Powers, T. O.: Identification of single Meloidogyne juveniles by polymerase chain reaction amplification of mitochondrial DNA, J. Nematol., 22, 518–524, 1990.
Hebert, P. D. and Gregory, T. R.: The promise of DNA barcoding for taxonomy, Syst. Biol., 54, 852–859, 2005.
Hebert, P. D., Cywinska, A., and Ball, S. L.: Biological identifications through DNA barcodes, P. Roy. Soc. Lond. B, 270, 313–321, 2003.
Hollingsworth, P. M., Forrest, L. L., Spouge, J. L., Hajibabaei, M., Ratnasingham, S., van der Bank, M., Chase, M. W., Cowan, R. S., Erickson, D. L., and Fazekas, A. J.: A DNA barcode for land plants, P Natl. Acad. Sci., 106, 12794–12797, 2009.
Holterman, M. H., van der Wurff, A., van den Elsen, S., van Megen, H., Bongers, T., Holovachov, O., Bakker, J., and Helder, J.: Phylum-wide analysis of SSU rDNA reveals deep phylogenetic relationships among nematodes and accelerated evolution toward crown clades, Mol. Biol. Evol., 23, 1792–1800, 2006.
Holterman, M. H., Karssen, G., Van Den Elsen, S., Van Megen, H., Bakker, J., and Helder, J.: Small subunit rDNA-based phylogeny of the Tylenchida sheds light on relationships among some high impact plant-parasitic nematodes and the evolution of plant feeding, Phytopathology, 99, 227–235, 2009.
Holterman, M. H., Oggenfuss, M., Frey, J. E., and Kiewnick, S.: Evaluation of High resolution Melting Curve Analysis as a New Tool for Root-knot Nematode Diagnostics, J. Phytopathol., 160, 59–66, 2012.
Höss, S., Claus, E., Von der Ohe, P. C., Brinke, M., Güde, H., Heininger, P., and Traunspurger, Sochová, I., Hofman, J., and Holoubek, I.: Using nematodes in soil ecotoxicology, Environ. Int., 32, 374–383, 2006.
Hu, M., Jex, A. R., Campbell, B. E., and Gasser, R. B.: Long PCR amplification of the entire mitochondrial genome from individual helminths for direct sequencing, Nat. Protoc., 2, 2339–2344, 2007.
Huber, T., Faulkner, G., and Hugenholtz, P.: Bellerophon: a program to detect chimeric sequences in multiple sequence alignments, Bioinformatics, 20, 2317–2319, 2004.
Hyman, B. C.: Molecular diagnosis of Meloidogyne species, J. Nematol., 22, 24, 1990.
Hyman, E. D.: A new method of sequencing DNA, Anal. Biochem., 174, 423–436, 1988.
Ibrahim, S., Davies, K., and Perry, R.: Identification of the root-knot nematode, Meloidogyne incognita, using monoclonal antibodies raised to non-specific esterases, Physiol. Mol. Plant. P., 49, 79–88, 1996.
Janssen, T., Karssen, G., Verhaeven, M., Coyne, D., and Bert, W.: Mitochondrial coding genome analysis of tropical root-knot nematodes (Meloidogyne) supports haplotype based diagnostics and reveals evidence of recent reticulate evolution, Sci. Rep., 6, 22591, https://doi.org/10.1038/srep22591, 2016.
Jex, A. R., Hu, M., Littlewood, D. T. J., Waeschenbach, A., and Gasser, R. B.: Using 454 technology for long-PCR based sequencing of the complete mitochondrial genome from single Haemonchus contortus (Nematoda), BMC Genomics, 9, 1, https://doi.org/10.1186/1471-2164-9-11, 2008a.
Jex, A. R., Waeschenbach, A., Littlewood, D. T. J., Hu, M., and Gasser, R. B.: The Mitochondrial Genome of Toxocara canis, Plos Neglect. Trop. D., 2, e273, https://doi.org/10.1371/journal.pntd.0000273, 2008b.
Jex, A. R., Littlewood, D. T. J., and Gasser, R. B.: Toward next-generation sequencing of mitochondrial genomes – focus on parasitic worms of animals and biotechnological implications, Biotechnol. Adv., 28, 151–159, 2010.
Jones, P., Ambler, D., and Robinson, M.: The application of monoclonal antibodies to the diagnosis of plant pathogens and pests, Proc. Brighton Crop., 1988, 767–776, 1988.
Karssen, G., Van Hoenselaar, T., Verkerk-Bakker, B., and Janssen, R.: Species identification of cyst and root-knot nematodes from potato by electrophoresis of individual females, Electrophoresis, 16, 105–109, 1995.
Kerry, B. R.: Rhizosphere interactions and the exploitation of microbial agents for the biological control of plant-parasitic nematodes, Annu. Rev. Phytopathol., 38, 423–441, 2000.
Kiewnick, S., Holterman, M., van den Elsen, S., van Megen, H., Frey, J. E., and Helder, J.: Comparison of two short DNA barcoding loci (COI and COII) and two longer ribosomal DNA genes (SSU & LSU rRNA) for specimen identification among quarantine root-knot nematodes (Meloidogyne spp.) and their close relatives, Eur. J. Plant. Pathol., 140, 97–110, 2014.
Lahaye, R., Van der Bank, M., Bogarin, D.,Warner, J., Pupulin, F., Gigot, G., Maurin, O., Duthoit, S., Barraclough, T. G., and Savolainen, V.: DNA barcoding the floras of biodiversity hotspots, P. Natl. Acad. Sci., 105, 2923–2928, 2008.
Lallias, D., Hiddink, J. G., Fonseca, V. G., Gaspar, J. M., Sung, W., Neill, S. P., Barnes, N., Ferrero, T., Hall, N., and Lambshead, P. J. D.: Environmental metabarcoding reveals heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems, ISME J., 9, 1208–1221, 2015.
Lambshead, P.: Marine nematode diversity, in: Advances and Perspectives: Nematode Morphology, Physiology and Ecology, edited by: Chen, W. Y., Chen, S. Y., and Dickson, S. W., CABI Publishing, Wallingford, UK, 438–468, 2004.
Marché, L., Valette, S., Grenier, E., and Mugniéry, D.: Intra-species DNA polymorphism in the tobacco cyst nematode complex (Globodera tabacum) using AFLP, Genome, 44, 941–946, 2001.
Marcussen, T.: Evolution, phylogeography, and taxonomy within the Viola alba complex (Violaceae), Plant. Syst. Evol., 237, 51–74, 2003.
Mardis, E. R.: Next-generation DNA sequencing methods, Annu. Rev. Genomics Hum. Genet., 9, 387–402, 2008.
Markmann, M. and Tautz, D.: Reverse taxonomy: an approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences, Philos. T. Roy. Soc. B, 360, 1917–1924, 2005.
Mayr, E. and Ashlock, P. D.: The Science of Taxonomy, in: Principles of Systematic Zoology, McGraw-Hill, New York, 1–14, 1991.
McCarter, J. P.: Cell Biology of Plant Nematode Parasitism, edited by: Berg, R. H. and Taylor, C. G., Springer, Berlin, Heidelberg, 239–267, 2009.
Metzker, M. L.: Emerging technologies in DNA sequencing, Genome Res., 15, 1767–1776, 2005.
Nakamura, K., Oshima, T., Morimoto, T., Ikeda, S., Yoshikawa, H., Shiwa, Y., Ishikawa, S., Linak, M. C., Hirai, A., and Takahashi, H.: Sequence-specific error profile of Illumina sequencers, Nucleic Acids Res., 39, e90, https://doi.org/10.1093/nar/gkr344, 2011.
Neher, D. A.: Role of nematodes in soil health and their use as indicators, J. Nematol, 33, 161–168, 2001.
Ntalli, N. G. and Menkissoglu-Spiroudi, U.: Pesticides of botanical origin: a promising tool in plant protection, in: Pesticides – Formulations, Effects, Fate, edited by: Stoytcheva, M., In-Tech, Shanghai, China, 3–24, 2011.
Orgiazzi, A., Dunbar, M. B., Panagos, P., de Groot, G. A., and Lemanceau, P.: Soil biodiversity and DNA barcodes: opportunities and challenges, Soil. Biol. Biochem., 80, 244–250, 2015.
Payan, L. and Dickson, D.: Comparison of populations of Pratylenchus brachyurus based on isozyme phenotypes, J. Nematol., 22, 538–545, 1990.
Perera, M. R., Taylor, S. P., Vanstone, V. A., and Jones, M. G.: Protein biomarkers to distinguish oat and lucerne races of the stem nematode, Ditylenchus dipsaci, with quarantine significance for Western Australia, Nematology, 11, 555–563, 2009.
Petersen, D. and Vrain, T.: Rapid identification of Meloidogyne chitwoodi, M. hapla, and M. fallax using PCR primers to amplify their ribosomal intergenic spacer, Fund. Appl. Nematol., 19, 601–605, 1996.
Porazinska, D. L., Giblin-Davis, R. M., Faller, L., Farmerie, W., Kanzaki, N., Morris, K., Powers, T. O., Tucker, A. E., Sung, W., and Thomas, W. K.: Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity, Mol. Ecol. Resour., 9, 1439–1450, 2009.
Porazinska, D. L., Giblin-Davis, R. M., Sung, W., and Thomas, W. K.: Linking operational clustered taxonomic units (OCTUs) from parallel ultra sequencing (PUS) to nematode species, Zootaxa, 2427, 55–63, 2010.
Porazinska, D. L., Giblin-Davis, R. M., Sung, W., and Thomas, W. K.: The nature and frequency of chimeras in eukaryotic metagenetic samples, J. Nematol., 44, 18–25, 2012.
Powers, T.: Nematode molecular diagnostics: from bands to barcodes, Annu. Rev. Phytopathol., 42, 367–383, 2004.
Powers, T. O. and Fleming, C. C.: Biochemical and molecular characterization, in: The physiology and biochemistry of free-living and plant-parasitic nematodes, edited by: Perry, R. and Wright, D., CABI Publishing, Wallingford, UK, 355–380, 1998.
Powers, T. O., Mullin, P., Harris, T., Sutton, L., and Higgins, R.: Incorporating molecular identification of Meloidogyne spp. into a large-scale regional nematode survey, J. Nematol., 37, 226–235, 2005.
Quail, M. A., Smith, M., Coupland, P., Otto, T. D., Harris, S. R., Connor, T. R., Bertoni, A., Swerdlow, H. P., and Gu, Y.: A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers, BMC Genomics, 13, 1, 2012.
Ristau, K., Steinfartz, S., and Traunspurger, W.: First evidence of cryptic species diversity and significant population structure in a widespread freshwater nematode morphospecies (Tobrilus gracilis), Mol. Ecol., 22, 4562–4575, 2013.
Rothberg, J. M., Hinz, W., Rearick, T. M., Schultz, J., Mileski, W., Davey, M., Leamon, J. H., Johnson, K., Milgrew, M. J., and Edwards, M.: An integrated semiconductor device enabling non-optical genome sequencing, Nature, 475, 348–352, 2011.
Sapkota, R. and Nicolaisen, M.: High-throughput sequencing of nematode communities from total soil DNA extractions, BMC Ecol., 15, 1–8, https://doi.org/10.1186/s12898-014-0034-4, 2015.
Sasser, J. N.: Identification and host-parasite relationships of certain root-knot nematodes (Meloidogyne spp.), Technical Bulletin, A-77, Maryland Agricultural Experiment Station, Maryland, 31 pp., 1954.
Sasser, J. N. and Carter, C. C.: Root-knot nematodes (Meloidogyne spp.): Identification, morphological and physiological variation, host range, ecology, and control, Nematology in the southern region of the United States, South. Cooperat. Ser. Bull., 276, 21–32, 1982.
Schots, A., Gommers, F. J., Bakker, J., and Egberts, E.: Serological differentiation of plantparasitic nematode species with polyclonal and monoclonal antibodies, J. Nematol., 22, 16– 23, 1990.
Schroder, J., Bailey, J., Conway, T., and Zobel, J.: Reference-free validation of short read data, PLoS One, 5, e12681, https://doi.org/10.1371/journal.pone.0012681, 2010.
Semblat, J., Wajnberg, E., Dalmasso, A., Abad, P., and Castagnone-Sereno, P.: High-resolution DNA fingerprinting of parthenogenetic root-knot nematodes using AFLP analysis, Mol. Ecol., 7, 119–125, 1998.
Shaw, A. J. and Allen, B.: Phylogenetic relationships, morphological incongruence, and geographic speciation in the Fontinalaceae (Bryophyta), Mol. Phylogenet. Evol., 16, 225–237, 2000.
Sites Jr., J. W. and Marshall, J. C.: Operational criteria for delimiting species, Annu. Rev. Ecol. Evol. Syst., 35, 199–227, 2004.
Sochová, I., Hofman, J., and Holoubek, I.: Using nematodes in soil ecotoxicology, Environ. Int., 32, 374–383, 2006.
Subbotin, S. and Moens, M.: Molecular diagnostics of plant-parasitic nematodes, in: Plant Nematology, edited by: Perry, R. and Moens, M., CABI Wallingford, UK, 33–58, 2007.
Taberlet, P., Coissac, E., Pompanon, F., Brochmann, C., and Willerslev, E.: Towards next generation biodiversity assessment using DNA metabarcoding, Mol. Ecol., 21, 2045–2050, 2012.
Tastet, C., Val, F., Lesage, M., Renault, L., Marché, L., Bossis, M., and Mugniéry, D.: Application of a putative fatty-acid binding protein to discriminate serologically the two European quarantine root-knot nematodes, Meloidogyne chitwoodi and M. fallax, from other Meloidogyne species, Eur. J. Plant Pathol., 107, 821–832, 2001.
Tietjen, J. H.: Ecology of deep-sea nematodes from the Puerto Rico Trench area and Hatteras Abyssal Plain, Deep-Sea Res. Pt. A, 36, 1579–1594, 1989.
Tripathi, A. M., Tyagi, A., Kumar, A., Singh, A., Singh, S., Chaudhary, L. B., and Roy, S.: The internal transcribed spacer (ITS) region and trnhH-psbA are suitable candidateloci for DNA barcoding of tropical tree species of India, PloS one, 8, e57934, https://doi.org/10.1371/journal.pone.0057934, 2013.
Valentini, A., Pompanon, F., and Taberlet, P.: DNA barcoding for ecologists, Trends Ecol. Evol., 24, 110–117, 2009.
van Megen, H., van den Elsen, S., Holterman, M., Karssen, G., Mooyman, P., Bongers, T., Holovachov, O., Bakker, J., and Helder, J.: A phylogenetic tree of nematodes based on about 1200 full-length small subunit ribosomal DNA sequences, Nematology, 11, 927–950, 2009.
Vovlas, N., Troccoli, A., Palomares-Rius, J. E., De Luca, F., Liébanas, G., Landa, B. B., Subbotin, S. A., and Castillo, P.: Ditylenchus gigas n. sp. parasitizing broad bean: a new stem nematode singled out from the Ditylenchus dipsaci species complex using a polyphasic approach with molecular phylogeny, Plant Pathol., 60, 762–775, 2011.
Waite, I. S., O'Donnell, A. G., Harrison, A., Davies, J. T., Colvan, S. R., Ekschmitt, K., Dogan, H., Wolters, V., Bongers, T., and Bongers, M.: Design and evaluation of nematode 18S rDNA primers for PCR and denaturing gradient gel electrophoresis (DGGE) of soil community DNA, Soil Biol. Biochem., 35, 1165–1173, 2003.
Wardle, D., Yeates, G., Barker, G., and Bonner, K.: The influence of plant litter diversity on decomposer abundance and diversity, Soil Biol. Biochem., 38, 1052–1062, https://doi.org/10.1016/j.soilbio.2005.09.003, 2006.
Williams, S.: Species boundaries in the starfish genus Linckia, Mar. Biol., 136, 137–148, 2000.
Wilson, E. O.: A global biodiversity map, Science, 289, 2279–2279, 2000.
Wilson, M. J. and Khakouli-Duarte, T.: Nematodes as environmental indicators, CABI Publishing, Wallingford, UK, 326 pp., 2009.
Yeates, G. W.: Variation in soil nematode diversity under pasture with soil and year, Soil Biol. Biochem., 16, 95–102, 1984.
Yeates, G. W.: Nematodes as soil indicators: functional and biodiversity aspects, Biol. Fert. Soils, 37, 199–210, 2003.
Yeates, G. W., Bongers, T., De Goede, R., Freckman, D., and Georgieva, S.: Feeding habits in soil nematode families and genera – an outline for soil ecologists, J. Nematol., 25, 315–331, 1993.
Zhou, X., Li, Y., Liu, S., Yang, Q., Su, X., Zhou, L., Tang, M., Fu, R., Li, J., and Huang, Q.: Ultradeep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification, GigaScience, 2, 1–12, 2013.
Zijlstra, C.: Identification of Meloidogyne chitwoodi, M. fallax and M. hapla based on SCAR PCR: a powerful way of enabling reliable identification of populations or individuals that share common traits, Eur. J. Plant. Pathol., 106, 283–290, 2000.
Zijlstra, C., Donkers-Venne, D. T., and Fargette, M.: Identification of Meloidogyne incognita, M. javanica and M. arenaria using sequence characterised amplified region (SCAR) based PCR assays, Nematology, 2, 847–853, 2000.
Short summary
This review covers the history and advances made in the area of nematode taxonomy. It highlights the success and limitations of the classical approach to nematode taxonomy and provides reader with a bit of background to the applications of protein and DNA-based methods for identification nematodes. The review also outlines the pros and cons of the use of DNA barcoding in nematology and explains how DNA metabarcoding has been applied in nematology through next-generation sequencing.
This review covers the history and advances made in the area of nematode taxonomy. It highlights...
