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

Molecular Ecology

Volumn 22, Issue 21, 2013, Pages 5456-5471

  Darby, B J ^a,b   Todd, T C ^b   Herman, M A ^b  

^a UNIVERSITY OF NORTH DAKOTA   (United States)

^b KANSAS STATE UNIVERSITY   (United States)

Author keywords

bar coding; burning; Konza prairie; nematodes; nitrogen enrichment; tallgrass prairie

Indexed keywords

INVERTEBRATA; NEMATODA;

HELMINTH DNA; NITROGEN;

ALGORITHM; ANIMAL; ARTICLE; BAR-CODING; BURN; CHEMISTRY; CLASSIFICATION; COMPARATIVE STUDY; DISCRIMINANT ANALYSIS; DNA SEQUENCE; ECOLOGY; ECOSYSTEM; FIRE; GENE DOSAGE; GENETICS; KONZA PRAIRIE; METHODOLOGY; MULTIVARIATE ANALYSIS; NEMATODE; NITROGEN ENRICHMENT; PRINCIPAL COMPONENT ANALYSIS; RNA GENE; SOIL; TALLGRASS PRAIRIE;

BAR-CODING; BURNING; KONZA PRAIRIE; NEMATODES; NITROGEN ENRICHMENT; TALLGRASS PRAIRIE;

ALGORITHMS; ANIMALS; DISCRIMINANT ANALYSIS; DNA, HELMINTH; ECOLOGY; ECOSYSTEM; FIRES; GENE DOSAGE; GENES, RRNA; MULTIVARIATE ANALYSIS; NEMATODA; NITROGEN; PRINCIPAL COMPONENT ANALYSIS; SEQUENCE ANALYSIS, DNA; SOIL;

EID: 84886092556     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12480     Document Type: Article

References (47)

1. Baille D, Barriere A, Felix MA, (2008) Oscheius tipulae, a widespread hermaphroditic soil nematode, displays a higher genetic diversity and geographical structure than Caenorhabditis elegans. Molecular Ecology, 17, 1523-1534.
2. Bardgett RD, Cook R, Yeates GW, Denton CS, (1999) The influence of nematodes on below-ground processes in grassland ecosystems. Plant and Soil, 212, 23-33.
3. Bik HM, Porazinska DL, Creer S, et al,. (2012) Sequencing our way towards understanding global eukaryotic biodiversity. Trends in Ecology & Evolution, 27, 233-243.
4. Bongers T, (1990) The maturity index: An ecological measure of environmental disturbance based on nematode species composition. Oecologia, 83, 14-19.
5. Cock PJA, Antao T, Chang JT, et al,. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25, 1422-1423.
6. Collins SL, Knapp AK, Briggs JM, Blair JM, Steinauer EM, (1998) Modulation of Diversity by Grazing and Mowing in Native Tallgrass Prairie. Science, 280, 745-747.
7. Colwell RK, Chao A, Gotelli NJ, et al,. (2012) Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of assemblages. Journal of Plant Ecology, 5, 3-21.
8. Creer S, Fonseca VG, Porazinska DL, et al,. (2010) Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises. Molecular Ecology, 19, 4-20.
9. De Ley P, Bert W, (2002) Video Capture and Editing as a Tool for the Storage, Distribution, and Illustration of Morphological Characters of Nematodes. Journal of Nematology, 34, 296-302.
10. De Ley P, De Ley IT, Morris K, et al,. (2005) An integrated approach to fast and informative morphological vouchering of nematodes for applications in molecular barcoding. Philosophical Transactions of the Royal Society B-Biological Sciences, 360, 1945-1958.
11. Donn S, Neilson R, Griffiths B, Daniell T, (2011) Greater coverage of the phylum Nematoda in SSU rDNA studies. Biology and Fertility of Soils, 47, 333-339.
12. Edgar RC, (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2461.
13. Elser JJ, Sterner RW, Gorokhova E, et al,. (2000) Biological stoichiometry from genes to ecosystems. Ecology Letters, 3, 540-550.
14. Felix MA, Vierstraete A, Vanfleteren J, (2001) Three biological species closely related to Rhabditis (Oscheius) pseudodolichura Korner in Osche, 1952. Journal of Nematology, 33, 104-109.
15. Ferris H, Bongers T, (2006) Nematode Indicators of Organic Enrichment. Journal of Nematology, 38, 3-12.
16. Fiscus DA, Neher DA, (2002) Distinguishing sensitivity of freeliving soil nematode genera to physical and chemical disturbances. Ecological Applications, 12, 565-575.
17. Freckman DW, (1988) Bacterivorous Nematodes and Organic-Matter Decomposition. Agriculture Ecosystems & Environment, 24, 195-217.
18. Gibson DJ, Seastedt TR, Briggs JM, (1993) Management practices in tallgrass prairie: large- and small-scale experimental effects on species composition. Journal of Applied Ecology, 30, 247-255.
19. Ingham RE, Trofymow JA, Ingham ER, Coleman DC, (1985) Interactions of bacteria, fungi, and their nematode grazers: effects on nutrient cycling and plant growth. Ecological Monographs, 55, 119-140.
20. Jones KL, Todd TC, Wall-Beam JL, et al,. (2006) Molecular Approach for Assessing Responses of Microbial-Feeding Nematodes to Burning and Chronic Nitrogen Enrichment in a Native Grassland. Molecular Ecology, 15, 2601-2609.
21. Kembel SW, Wu M, Eisen JA, Green JL, (2012) Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance. PLoS Computational Biology, 8, e1002743.
22. Klappenbach JA, Dunbar JM, Schmidt TM, (2000) RRNA operon copy number reflects ecological strategies of bacteria. Applied and Environmental Microbiology, 66, 1328-1333.
23. Klappenbach JA, Saxman PR, Cole RJ, Schmidt TM, (2001) rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Research, 29, 181-184.
24. Lee C, Lee S, Shin S, Hwang S, (2008) Real-time PCR determination of rRNA gene copy number: absolute and relative quantification assays with Escherichia coli. Applied Microbiology and Biotechnology, 78, 371-376.
25. Long EO, Dawid IB, (1980) Repeated genes in eukaryotes. Annual Review of Biochemistry, 49, 727-764.
26. Martin M, (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 1.
27. McTaggart SJ, Dudycha JL, Omilian A, Crease TJ, (2007) Rates of Recombination in the Ribosomal DNA of Apomictically Propagated Daphnia obtusa Lines. Genetics, 175, 311-320.
28. Morrall D, (2006) Ecological applications of genetic algorithms. In: Ecological Informatics (ed., Recknagel F,), pp. 69-83. Springer, Berlin, Heidelberg.
29. Neher DA, (2001) Role of nematodes in soil health and their use as indicators. Journal of Nematology, 33, 161-168.
30. Ning Z, Cox AJ, Mullikin JC, (2001) SSAHA: A Fast Search Method for Large DNA Databases. Genome Research, 11, 1725-1729.
31. Orr CC, Dickerson OJ, (1966) Nematodes in True Prairie Soils of Kansas. Transactions of the Kansas Academy of Science, 69, 317-334.
32. Porazinska DL, Giblin-Davis RM, Faller L, et al,. (2009) Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity. Molecular Ecology Resources, 9, 1439-1450.
33. Porazinska DL, Giblin-Davis RM, Esquivel A, et al,. (2010) Ecometagenetics confirm high tropical rainforest nematode diversity. Molecular Ecology, 19, 5521-5530.
34. Powers TO, Todd TC, Burnell AM, et al,. (1997) The rDNA internal transcribed spacer region as a taxonomic marker for nematodes. Journal of Nematology, 29, 441-450.
35. Powers TO, Neher DA, Mullin P, et al,. (2009) Tropical nematode diversity: vertical stratification of nematode communities in a Costa Rican humid lowland rainforest. Molecular Ecology, 18, 985-996.
36. Prokopowich CD, Gregory TR, Crease TJ, (2003) The correlation between rDNA copy number and genome size in eukaryotes. Genome, 46, 48-50.
37. Pruesse E, Quast C, Knittel K, et al,. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Research, 35, 7188-7196.
38. Samson F, Knopf F, (1994) Prairie conservation in North America. BioScience, 44, 418-421.
39. Todd TC, (1996) Effects of management practices on nematode community structure in tallgrass prairie. Applied Soil Ecology, 3, 235-246.
40. Todd TC, Powers TO, Mullin PG, (2006) Sentinel nematodes of land-use change and restoration in tallgrass prairie. Journal of Nematology, 38, 20-27.
41. Vervoort MTW, Vonk JA, Mooijman PJW, et al,. (2012) SSU Ribosomal DNA-Based Monitoring of Nematode Assemblages Reveals Distinct Seasonal Fluctuations within Evolutionary Heterogeneous Feeding Guilds. PLoS ONE, 7, e47555.
42. Wardle DA, Bardgett RD, Klironomos JN, Setala H, van der Putten WH, Wall DH, (2004) Ecological linkages between aboveground and belowground biota. Science, 304, 1629-1633.
43. Weider LJ, Elser JJ, Crease TJ, et al,. (2005) The functional significance of ribosomal (r)DNA variation: impacts on the evolutionary ecology of organisms. Annual Review of Ecology, Evolution, and Systematics, 36, 219-242.
44. Yeates GW, Bongers T, de Goede RGM, Freckman DW, Georgieva SS, (1993) Feeding habits in soil nematode families and genera-An outline for soil ecologists. J. Nematology, 25, 315-331.
45. Yeates GW, Ferris H, Moens T, Van Der Putten WH, (2009) The role of nematodes in ecosystems. In: Nematodes as Environmental Indicators (eds, Wilson MJ, &, Khakouli-Duarte T,), pp. 1-44. CABI, Cambridge, Massachusetts.
46. Yoder M, De Ley IT, King IW, et al,. (2006) DESS: a Versatile Solution for Preserving Morphology and Extractable DNA of Nematodes. Nematology, 8, 367-376.
47. Zhang QF, Saghai Maroof MA, Allard RW, (1990) Effects on adaptedness of variations in ribosomal DNA copy number in populations of wild barley (Hordeum vulgare ssp. spontaneum). Proceedings of the National Academy of Sciences, 87, 8741-8745.