Biomonitoring 2.0: A new paradigm in ecosystem assessment made possible by next-generation DNA sequencing

Molecular Ecology

Volumn 21, Issue 8, 2012, Pages 2039-2044

  Baird, Donald J ^a   Hajibabaei, Mehrdad ^b  

^a UNIVERSITY OF NEW BRUNSWICK   (Canada)

^b UNIVERSITY OF GUELPH   (Canada)

Author keywords

biodiversity discovery; biomonitoring; DNA barcoding; high throughput gene sequencing; multiple stressors

Indexed keywords

DNA;

ANIMAL; BIODIVERSITY; DNA BARCODING; ECOSYSTEM; ENVIRONMENTAL MONITORING; HIGH THROUGHPUT SEQUENCING; METHODOLOGY; REVIEW;

ANIMALS; BIODIVERSITY; DNA; DNA BARCODING, TAXONOMIC; ECOSYSTEM; ENVIRONMENTAL MONITORING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING;

EID: 84859562300     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2012.05519.x     Document Type: Review

References (30)

1. Bailly J, Fraissinet-Tachet L, Verner MC, (2007) Soil eukaryotic functional diversity: a metatranscriptomic approach. ISME Journal, 1, 632-642.
2. Baird DJ, Baker CJO, Brua RB, et al. (2011) Towards a knowledge infrastructure for traits-based ecological risk assessment. Integrated Environmental Assessment and Management, 7, 209-215.
3. Bonada N, Prat N, Resh VH, Statzner B, (2006) Developments in aquatic insect biomonitoring: a comparative analysis of recent approaches. Annual Review of Entomology, 51, 495-523.
4. Bothwell ML, Spaulding SA, (2008) Proceedings of the 2007 International Workshop on Didymosphaenia geminata. Canadian Technical Report of Fisheries and Aquatic Sciences, 2795, xxxv + 58p.
5. Bowen BW, (1999) Preserving genes, species or ecosystems? Healing the fractured foundations of conservation policy. Molecular Ecology, 8, S5-S10.
6. Butchart SM, Walpole M, Collen B, et al. (2010) Global biodiversity: indicators of recent declines. Science, 328, 1164-1168.
7. Chariton AA, Court LN, Hartley DM, et al. (2010) Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA. Frontiers in Ecology and the Environment, 8, 233-238.
8. Clarke J, Wu H-C, Jayasinghe L, et al. (2009) Continuous base identification for single-molecule nanopore DNA sequencing. Nature Nanotechnology, 4, 265-270.
9. Creer S, Fonseca VG, Pozarinska DL, et al., (2010) Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises. Molecular Ecology, 19 (Suppl 1), 4-20.
10. Dejean T, Valentini A, Duparc A, et al. (2011) Persistence of environmental DNA in freshwater ecosystems. PLoS One, 6, e23398.
11. Dequiedt S, Saby NPA, Lelievre M, et al. (2011) Biogeographical patterns of soil molecular microbial biomass as influenced by soil characteristics and management. Global Ecology and Biogeography, 20, 641-652.
12. Fitch WM, Margoliash E, (1967) Construction of phylogenetic trees. Science, 155, 279-284.
13. Hajibabaei M, Shokralla S, Zhou X, et al. (2011) Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS One, 6, e17497. doi:.
14. Harris GP, Heathwaite L, (2011) Why is achieving good ecological outcomes in rivers so difficult? Freshwater Biology, doi:.
15. Jones JI, Davy-Bowker J, Murphy JF, et al. (2010) Ecological monitoring and assessment in rivers. In: Ecology of Industrial Pollution (eds, Batty L, Hallberg KB,), pp. 126-146. Cambridge University Press, Cambridge, UK.
16. Lenat DR, Resh VH, (2001) Taxonomy and stream ecology-the benefits of genus- and species-level identifications. Journal of the North American Benthological Society, 20, 287-298.
17. Ley RE, Turnbaugh PJ, Klein S, et al. (2006) Microbial ecology: human gut microbes associated with obesity. Nature, 444, 1022-1023.
18. Magurran AE, Baillie SR, Buckland ST, et al. (2010) Long-term datasets in biodiversity research and monitoring: assessing change in ecological communities through time. Trends in Ecology and Evolution, 25, 574-582.
19. Menezes S, Baird DJ, Soares AMVM, (2010) Beyond taxonomy: a review of macroinvertebrate trait-based community descriptors as tools for freshwater biomonitoring. Journal of Applied Ecology, 47, 711-719.
20. Polz MF, Cavanaugh CM, (1998) Bias in template-to-product ratios in multitemplate PCR. Applied and Environmental Microbiology, 64, 3724-3730.
21. Reavie ED, Jicha TM, Angradi TR, et al. (2010) Algal assemblages for large river monitoring: comparison among biovolume, absolute and relative abundance metrics. Ecological Indicators, 10, 167-177.
22. Schriever CA, Liess M, (2007) Mapping ecological risk of agricultural pesticide runoff. Science of the Total Environment, 384, 264-279.
23. Shokralla S, Spall JL, Gibson JF, et al. (2012) Next-generation sequencing technologies for environmental DNA research. Molecular Ecology, 21, doi:10.1111/j.1365-294X.2012.05538.x.
24. Sogin ML, Morrison HG, Huber JA, et al. (2006) Microbial diversity in the deep sea and the underexplored 'rare biosphere'. Proceedings of the National Academy of Sciences, 103, 12115-12120.
25. Tetko IV, Livingstone DJ, Luik AI, (1995) Neural network studies. 1. Comparison of overfitting and overtraining. Journal of Chemical Information and Computing Science, 35, 826-833.
26. Urich T, Lanzén A, Qi J, et al. (2008) Simultaneous assessment of soil microbial community structure and function through analysis of the metatranscriptome. PLoS One, 3, e2527.
27. Valentini A, Miquel C, Ali Nawaz M, et al. (2009) New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach. Molecular Ecology Research, 9, 51-60.
28. Willerslev E, Cappellini E, Boomsma W, et al. (2007) Ancient biomolecules from deep ice cores reveal a forested southern Greenland. Science, 317, 111-114.
29. Wimsatt WC, (2007) Re-Engineering Philosophy for Limited Beings: Piecewise Approximations to Reality. Harvard University Press, Harvard, Connecticut.
30. Zinger L, Amaral-Zettler LA, Fuhrman JA, et al. (2011) Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems. PLoS One, 6, e24570. doi:.