Effects of water stratification and mixing on microbial community structure in a subtropical deep reservoir

Scientific Reports

Volumn 4, Issue , 2014, Pages

  Yu, Zheng ^a,b   Yang, Jun ^a   Amalfitano, Stefano ^c   Yu, Xiaoqing ^a   Liu, Lemian ^a  

^a Institute of Urban Environment   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c WATER RESEARCH INSTITUTE   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; CHLOROPHYLL; CHLOROPHYLL A; OXYGEN;

BACTERIUM; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; ECOSYSTEM; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MICROBIOLOGY; PH; PHYLOGENY; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEASON; TEMPERATURE;

BACTERIA; CHLOROPHYLL; DNA, BACTERIAL; ECOSYSTEM; HYDROGEN-ION CONCENTRATION; OXYGEN; PHYLOGENY; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, BACTERIAL; SEASONS; SEQUENCE ANALYSIS, DNA; TEMPERATURE; WATER MICROBIOLOGY;

EID: 84926429725     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep05821     Document Type: Article

References (49)

1. Wang, S., Qian, X., Han, B. P., Wang, Q. H. & Ding, Z. F. Physical limnology of a typical subtropical reservoir in south China. Lake Reserv. Manage. 27, 149-161 (2011).
2. Elçi, Ş. Effects of thermal stratification and mixing on reservoir water quality. Limnology 9, 135-142 (2008).
3. Becker, V., Huszar, V. L. M. & Crossetti, L. O. Responses of phytoplankton functional groups to the mixing regime in a deep subtropical reservoir. Hydrobiologia 628, 137-151 (2009).
4. Lawson, R. & Anderson, M. A. Stratification and mixing in Lake Elsinore, California: an assessment of axial flow pumps for improving water quality in a shallow eutrophic lake. Water Res. 41, 4457-4467 (2007).
5. Qian, P. Y. et al. Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing. ISME J. 5, 507-518 (2011).
6. Vandermeulen, H. Design and testing of a propeller aerator for reservoirs. Water Res. 26, 857-861 (1992).
7. Pantoja, S., Sepúlveda, J. & González, H. E. Decomposition of sinking proteinaceous material during fall in the oxygen minimum zone off northern Chile. Deep Sea Res. Pt. I 51, 55-70 (2004).
8. Coates, J. D., Cole, K. A., Chakraborty, R., O'Connor, S. M. & Achenbach, L. A. Diversity and ubiquity of bacteria capable of utilizing humic substances as electron donors for anaerobic respiration. Appl. Environ. Microbiol. 68, 2445-2452 (2002).
9. Yang, J., Yu, X. Q., Liu, L. M., Zhang, W. J. & Guo, P. Y. Algae community and trophic state of subtropical reservoirs in southeast Fujian, China. Environ. Sci. Pollut. Res. 19, 1432-1442 (2012).
10. Newton, R. J., Jones, S. E., Eiler, A., McMahon, K.D. & Bertilsson, S. A guide to the natural history of freshwater lake bacteria. Microbiol. Mol. Biol. R. 75, 14-49 (2011).
11. Liu, L. M., Yang, J., Yu, X. Q., Chen, G. J. & Yu, Z. Patterns in the composition of microbial communities from a subtropical river: Effects of environmental, spatial and temporal factors. PLoS ONE 8, e81232 (2013).
12. Lv, H., Yang, J. & Liu, L. M. Temporal pattern overwhelms spatial variability in phytoplankton communities from a subtropical water supply reservoir. Oceanol. Hydrobiol. St. 42, 420-430 (2013).
13. Xiao, L. J. et al. Succession of phytoplankton functional groups regulated by monsoonal hydrology in a large canyon-shaped reservoir. Water Res. 45, 5099-5109 (2011).
14. Borges, P. A. F., Train, S. & Rodrigues, L. C. Spatial and temporal variation of phytoplankton in two subtropical Brazilian reservoirs. Hydrobiologia 607, 63-74 (2008).
15. Laque, T., Farjalla, V., Rosado, A. & Esteves, F. Spatiotemporal variation of bacterial community composition and possible controlling factors in tropical shallow lagoons. Microb. Ecol. 59, 819-829 (2010).
16. Shade, A., Jones, S. E. & McMahon, K. D. The influence of habitat heterogeneity on freshwater bacterial community composition and dynamics. Environ. Microbiol. 10, 1057-1067 (2008).
17. Boucher, D., Jardillier, L. & Debroas, D. Succession of bacterial community composition over two consecutive years in two aquatic systems: a natural lake and a lake-reservoir. FEMS Microbiol. Ecol. 55, 79-97 (2006).
18. Hamady, M. & Knight, R. Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome. Res. 19, 1141-1152 (2009).
19. Lauber, C. L., Zhou, N., Gordon, J. I., Knight, R. & Fierer, N. Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. FEMS Microbiol. Lett. 307, 80-86 (2010).
20. Wilhelm, S. & Adrian, R. Impact of summer warming on the thermal characteristics of a polymictic lake and consequences for oxygen, nutrients and phytoplankton. Freshwater Biol. 53, 226-237 (2008).
21. Lane, D. J. 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds). Nucleic Acid Techniques in Bacterial Systematics. John Wiley and Sons: Chichester. pp 115-175 (1991).
22. Bustin, S. A. et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin. Chem. 55, 611-622 (2009).
23. Humblot, C. & Guyot, J. P. Pyrosequencing of tagged 16S rRNA Gene amplicons for rapid deciphering of the microbiomes of fermented foods such as Pearl Millet slurries. Appl. Environ. Microbiol. 75, 4354-4361 (2009).
24. Vilo, C. & Dong, Q. Evaluation of the RDP classifier accuracy using 16S rRNA gene variable regions. Metagenomics 1, 1-5 (2012).
25. Hoffmann, C. et al. DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. Nucleic. Acids. Res. 35, e91 (2007).
26. Gontcharova, V. et al. Black box chimera check (B2C2): awindows-based software for batch depletion of chimeras from bacterial 16S rRNA gene datasets. Open Microbiol. J. 4, 47-52 (2010).
27. Crawford, P. A. et al. Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation. Proc. Nat. Acad. Sci. USA 106, 11276-11281 (2009).
28. Haegeman, B. et al. Robust estimation of microbial diversity in theory and in practice. ISME J. 7, 1092-1101 (2013).
29. Lozupone, C. & Knight, R. Uni Frac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71, 8228-8235 (2005).
30. Xu, M. Y. et al. Responses of microbial community functional structures to pilotscale uranium in situ bioremediation. ISME J. 4, 1060-1070 (2010).
31. Bienhold, C., Boetius, A. & Ramette, A. The energy-diversity relationship of complex bacterial communities in Arctic deep-sea sediments. ISME J. 6, 724-732 (2012).
32. Sawall, Y., Richter, C. & Ramette, A. Effects of eutrophication, seasonality and macrofouling on the diversity of bacterial biofilms in equatorial coral reefs. PLoS ONE 7, e39951 (2012).
33. Becker, V., Huszar, V.L.M., Naselli-Flores, L. & Padis ÁK, J. Phytoplankton equilibrium phases during thermal stratification in a deep subtropical reservoir. Freshwater Biol. 53, 952-963 (2008).
34. Berdjeb, L., Ghiglione, J. F. & Jacquet, S. Bottom-up versus top-down control of hypo-and epilimnion free-living bacterial community structures in two neighboring freshwater lakes. Appl. Environ. Microbiol. 77, 3591-3599 (2011).
35. Cantin, A., Beisner, B. E., Gunn, J. M., Prairie, Y. T. & Winter, J. G. Effects of thermocline deepening on lake plankton communities. Can. J. Fish. Aquat. Sci. 68, 260-276 (2011).
36. Ghiglione, J. F. et al. Pole-to-pole biogeography of surface and deep marine bacterial communities. Proc. Nat. Acad. Sci. USA 109, 17633-17638 (2012).
37. Fazi, S., Vázquez, E., Casamayor, E. O., Amalfitano, S. & Butturini, A. Stream hydrological fragmentation drives bacterioplankton community composition. PLoS ONE 8, e64109 (2013).
38. Connell, J. Diversity in tropical rain forests and coral reefs. Science 199, 1302-1310 (1978).
39. Li, Z. et al. Responses of phytoplankton diversity to physical disturbance under manual operation in a large reservoir, China. Hydrobiologia 684, 45-56 (2012).
40. Rheims, H., Felske, A., Seufert, S. & Stackebrandt, E. Molecular monitoring of an uncultured group of the class Actinobacteria in two terrestrial environments. J. Microbiol. Meth. 36, 65-75 (1999).
41. Glöckner, F. O. et al. Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. Appl. Environ. Microbiol. 66, 5053-5065 (2000).
42. Pinhassi, J. & Berman, T. Differential growth response of colony-forming α- and γ-proteobacteria in dilution culture and nutrient addition experiments from Lake Kinneret (Israel), the eastern Mediterranean Sea, and the Gulf of Eilat. Appl. Environ. Microbiol. 69, 199-211 (2003).
43. Yu, Z. et al. Water stratification affects the microeukaryotic community in a subtropical deep reservoir. J. Eukaryot. Microbiol. 61, 126-133 (2014).
44. Rigosi, A. & Rueda, F. J. Hydraulic control of short-term successional changes in the phytoplankton assemblage in stratified reservoirs. Ecol. Eng. 44, 216-226 (2012).
45. Weston, N. B. & Joye, S. B. Temperature-driven decoupling of key phases of organic matter degradation in marine sediments. Proc. Natl. Acad. Sci. USA 102, 17036-17040 (2005).
46. Shade, A. et al. Resistance, resilience and recovery: aquatic bacterial dynamics after water column disturbance. Environ. Microbiol. 13, 2752-2767 (2011).
47. Shade, A. et al. Lake microbial communities are resilient after a whole-ecosystem disturbance. ISME J. 6, 2153-2167 (2012).
48. Boehrer, B. & Schultze, M. Stratification of lakes. Rev. Geophys. 46, RG2005 (2008).
49. Comeau, A. M., Harding, T., Galand, P. E., Vincent, W. F. & Lovejoy, C. Vertical distribution of microbial communities in a perennially stratified Arctic lake with saline, anoxic bottom waters. Sci. Rep. 2, 604 (2012).