Microeukaryote community composition assessed by pyrosequencing is associated with light availability and phytoplankton primary production along a lowland river

Freshwater Biology

Volumn 58, Issue 11, 2013, Pages 2401-2413

  Bradford, Tessa M ^a   Morgan, Matthew J ^a   Lorenz, Zygmunt ^a   Hartley, Diana M ^a   Hardy, Christopher M ^a   Oliver, Roderick L ^a  

^a CSIRO   (Australia)

Author keywords

18S rRNA; 454 pyrosequencing; Algae; Lowland rivers; Primary production

Indexed keywords

ALGAE; CILIOPHORA; EUKARYOTA; FUNGI; INVERTEBRATA; PROTISTA;

EID: 84884987879     PISSN: 00465070     EISSN: 13652427     Source Type: Journal    
DOI: 10.1111/fwb.12219     Document Type: Article

References (44)

1. Baldwin D.S., Colloff M.J., Rees G.N., Chariton A.A., Watson G.O. & Court L.N. et al. (2013) Impacts of inundation and drought on eukaryote biodiversity in semi-arid floodplain soils. Molecular Ecology, 22, 1746-1758.
2. Bik H.M., Porazinska D.L., Creer S., Caporaso J.G., Knight R. & Thomas W.K. (2012a) Sequencing our way towards understanding global eukaryotic biodiversity. Trends in Ecology & Evolution, 27, 233-243.
3. Bik H.M., Sung W., De Ley P., Baldwin J.G., Sharma J. & Rocha-Olivares A. et al. (2012b) Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments. Molecular Ecology, 21, 1048-1059.
4. Caporaso J.G., Kuczynski J., Stombaugh J., Bittinger K., Bushman F.D. & Costello E.K. et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7, 335-336.
5. Clarke K. & Warwick R. (2001) Change in Marine Communities: An Approach to Statistical Analysis and Interpretation, 2nd edn. PRIMER-E, Plymouth.
6. Clarke K.R. & Ainsworth M. (1993) A method of linking multivariate community structure to environmental variables. Marine Ecology-Progress Series, 92, 205-219.
7. Clarke K.R. & Gorley R.N. (2006) Primer v6: User Manual/Tutorial. PRIMER-E, Plymouth.
8. Clarke K.R. & Green R.H. (1988) Statistical design and analysis for a biological effects study. Marine Ecology-Progress Series, 46, 213-226.
9. Clarke K.R., Somerfield P.J., Airoldi L. & Warwick R.M. (2006) Exploring interactions by second-stage community analyses. Journal of Experimental Marine Biology and Ecology, 338, 179-192.
10. Creer S., Fonseca V.G., Porazinska D.L., Giblin-Davis R.M., Sung W. & Power D.M. et al. (2010) Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises. Molecular Ecology, 19, 4-20.
11. Davies P.E., Harris J.H., Hillman T.J. & Walker K.F. (2010) The Sustainable rivers audit: assessing river ecosystem health in the Murray-Darling Basin, Australia. Marine and Freshwater Research, 61, 764-777.
12. Diez B., Pedros-Alio C., Marsh T.L. & Massana R. (2001) Application of Denaturing Gradient Gel Electrophoresis (DGGE) to study the diversity of marine picoeukaryotic assemblages and comparison of DGGE with other molecular techniques. Applied and Environmental Microbiology, 67, 2942-2951.
13. Ebenezer V., Medlin L.K. & Ki J.S. (2012) Molecular detection, quantification, and diversity evaluation of microalgae. Marine Biotechnology, 14, 129-142.
14. Edgar R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 1-19.
15. Gawne B., Merrick C., Williams D.G., Rees G., Oliver R. & Bowen P.M. et al. (2007) Patterns of primary and heterotrophic productivity in an arid lowland river. River Research and Applications, 23, 1070-1087.
16. Hardy C.M., Krull E.S., Hartley D.M. & Oliver R.L. (2010) Carbon source accounting for fish using combined DNA and stable isotope analyses in a regulated lowland river weir pool. Molecular Ecology, 19, 197-212.
17. Harris G.P. (2012) Introduction to the special issue: 'Achieving ecological outcomes'. Why is translational ecology so difficult? Freshwater Biology, 57, 1-6.
18. Hebert P.D.N., Cywinska A., Ball S.L. & DeWaard J.R. (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society of London Series B-Biological Sciences, 270, 313-321.
19. Hladyz S., Nielsen D.L., Suter P.J. & Krull E.S. (2012) Temporal variations in organic carbon utilization by consumers in a lowland river. River Research and Applications, 28, 513-528.
20. Junk W.J., Bayley P.B. & Sparks RE (1989) The flood pulse concept in river-floodplain systems. Special Publication of the Canadian Journal of Fisheries and Aquatic Sciences, 106, 110-127.
21. King A.J., Tonkin Z. & Lieshcke J. (2012) Short-term effects of a prolonged blackwater event on aquatic fauna in the Murray River, Australia: considerations for future events. Marine and Freshwater Research, 63, 576-586.
22. Krienitz L. & Bock C. (2012) Present state of the systematics of planktonic coccoid green algae of inland waters. Hydrobiologia, 698, 295-326.
23. Lefevre E., Roussel B., Amblard C. & Sime-Ngando T. (2008) The molecular diversity of freshwater picoeukaryotes reveals high occurrence of putative parasitoids in the plankton. PLoS ONE, 3, e2324.
24. Maheshwari B.L., Walker K.F. & Mcmahon T.A. (1995) Effects of regulation on the flow regime of the river murray, Australia. Regulated Rivers-Research & Management, 10, 15-38.
25. Meadow J.F. & Zabinski C.A. (2012) Spatial heterogeneity of eukaryotic microbial communities in an unstudied geothermal diatomaceous biological soil crust: Yellowstone National Park, WY, USA. Fems Microbiology Ecology, 82, 182-191.
26. Mitrovic S.M., Oliver R.L., Rees C., Bowling L.C. & Buckney R.T. (2003) Critical flow velocities for the growth and dominance of Anabaena circinalis in some turbid freshwater rivers. Freshwater Biology, 48, 164-174.
27. Oliver R.L. & Merrick C.J. (2006) Partitioning of river metabolism identifies phytoplankton as a major contributor in the regulated Murray River (Australia). Freshwater Biology, 51, 1131-1148.
28. Parsons M., Ransom G., Thoms M. & Norris R. (2002) Australian River Assessment System: AusRivAS Physical and Chemical Assessment Module Monitoring River Heath Initiative. Technical Report no 23, Commonwealth of Australia and University of Canberra, Canberra.
29. Pernthaler J. & Posch T. (2009) Microbial food webs. In: Encyclopedia of Inland Waters (Ed. G.E. Likens ), pp. 244-251. Academic Press Inc., San Diego, CA.
30. Price M.N., Dehal P.S. & Arkin A.P. (2010) FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE, 5, e9490.
31. Quast C., Pruesse E., Yilmaz P., Gerken J., Schweer T. & Yarza P. et al. (2012) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research, 41, D590-D596.
32. Schmid-Araya J.M. & Schmid P.E. (2000) Trophic relationships: integrating meiofauna into a realistic benthic food web. Freshwater Biology, 44, 149-163.
33. Shannon C.E. (1948) A mathematical theory of communication. Bell System Technical Journal, 27, 623-656.
34. Shokralla S., Spall J.L., Gibson J.F. & Hajibabaei M. (2012) Next-generation sequencing technologies for environmental DNA research. Molecular Ecology, 21, 1794-1805.
35. Sime-Ngando T., Lefevre E. & Gleason F.H. (2011) Hidden diversity among aquatic heterotrophic flagellates: ecological potentials of zoosporic fungi. Hydrobiologia, 659, 5-22.
36. Simpson E.H. (1949) Measurement of diversity. Nature, 163, 688-688.
37. Szabo K.E., Makk J., Kiss K.T., Eiler A., Acs E. & Toth B. et al. (2008) Sequential colonization by river periphyton analysed by microscopy and molecular fingerprinting. Freshwater Biology, 53, 1359-1371.
38. Walker K.F. (1985) A review of the ecological effects of river regulation in Australia. Hydrobiologia, 125, 111-129.
39. Walker K.F. & Thoms M.C. (1993) Environmental effects of flow regulation on the lower River Murray, Australia. Regulated Rivers-Research & Management, 8, 103-119.
40. Wilson J.J. (2010) Assessing the value of DNA barcodes and other priority gene regions for molecular phylogenetics of Lepidoptera. PLoS ONE, 5, e10525.
41. Yoccoz N.G. (2012) The future of environmental DNA in ecology. Molecular Ecology, 21, 2031-2038.
42. Yoccoz N.G., Brathen K.A., Gielly L., Haile J., Edwards M.E. & Goslar T. et al. (2012) DNA from soil mirrors plant taxonomic and growth form diversity. Molecular Ecology, 21, 3647-3655.
43. Yu D.W., Ji Y.Q., Emerson B.C., Wang X.Y., Ye C.X. & Yang C.Y. et al. (2012) Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods in Ecology and Evolution, 3, 613-623.
44. Zinger L., Gobet A. & Pommier T. (2012) Two decades of describing the unseen majority of aquatic microbial diversity. Molecular Ecology, 21, 1878-1896.