| [1] | Abraham WR (2010) Megacities as sources for pathogenic bacteria in rivers and their fate downstream. Inter. J. Microbiol. 2011: 798282. doi: 10.1155/2011/798292
|
| [2] | United Nations (UN) (2009) Revision of World Urbanization Prospects. www.unpopulation.org.
|
| [3] | Kirchman DL (1994) The uptake of inorganic nutrients by heterotrophic bacteria. Microb. Ecol. 28: 255–271. doi: 10.1007/bf00166816
|
| [4] | Kent AD, Yannarell AC, Rusak JA, Triplett EW, McMahon KD (2007) Synchrony in aquatic microbial community dynamics. ISME J 1: 38–47. doi: 10.1038/ismej.2007.6
|
| [5] | Murray AE, Preston CM, Massana R, Taylor LT, Blakis A, et al. (1998) Seasonal and spatial variability ofbacterial and archaeal assemblages in the coastal waters near Anvers Island, Antarctica. Appl Environ Microbiol 64: 2585–2595.
|
| [6] | Lindstrom ES, Kamst-Van Agterveld MP, Zwart G (2005) Distribution of typical freshwater bacterial groups is associated with pH, temperature, and lake water retention time. Appl Environ Microbiol 71: 8201–8206. doi: 10.1128/aem.71.12.8201-8206.2005
|
| [7] | Ibekwe MA, Leddy MB, Bold RM, Graves AK (2012) Bacterial community composition in low-flowing river water with different sources of pollutants. FEMS Microbiol Ecol 79: 155. doi: 10.1111/j.1574-6941.2011.01205.x
|
| [8] | Araya R, Yamaguchi N, Tani K, Nasu M (2003) Change in the bacterial community of natural river biofilm during biodegradation of aniline-derived compounds determined by denaturing gradient gel electrophoresis Journal of Health Science. 49(5): 379–385. doi: 10.1248/jhs.49.379
|
| [9] | Echeveste P, Dachs J, Berrojalbiz N, Agusti S (2010) Decrease in the abundance and viability of oceanic phytoplankton due to trace levels of complex mixtures of organic pollutants Chemosphere, 81. (2): 161–168. doi: 10.1016/j.chemosphere.2010.06.072
|
| [10] | Caracciolo BA, Grenni P, Falconi F, Caputo MC, Ancona V, et al. (2011) Pharmaceutical waste disposal: assessment of its effects on bacterial communities in soil and groundwater. Chemistry and Ecology 27(1): 43–51. doi: 10.1080/02757540.2010.534082
|
| [11] | Huerta B, Marti E, Gros M, López P, Pompêo M, et al.. (2013) Exploring the links between antibiotic occurrence, antibiotic resistance, and bacterial communities in water supply reservoirs. Sci Total Environ. Epub 2013 Apr 13. doi:10.1016/j.scitotenv.2013.03.071.
|
| [12] | Shanks OC, Newton RJ, Kelty CA, Huse SM, Sogin ML, et al. (2013) Comparison of the microbial community structures of untreated wastewaters from different geographic locales. Appl Environ Microbiol. 79(9): 2906–13. doi: 10.1128/aem.03448-12
|
| [13] | Evison LM (1989) Comparative studies on the survival of indicator organisms and pathogens in fresh and seawater. Water Research 20: 309–315.
|
| [14] | Garnier J, Billen G, Servais P (1992) Physiological characteristics and ecological r？le of small and large sized bacteria in a polluted river (Seine River, France). Archiv für Hydrobiologie-Ergebnisse Limnologie 37: 83–94.
|
| [15] | Okpookwasili GC, Akujobi TC (1996) Bacteriological indicators of tropical water quality. Environmental Toxicology and Water Quality 11: 77–81. doi: 10.1002/(sici)1098-2256(1996)11:2<77::aid-tox1>3.0.co;2-5
|
| [16] | Crump BC, Armbrust EV, Baross JA (1999) Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia River, its estuary, and the adjacent coastal ocean. Appl. Environ. Microbiol. 65: 3192–3204.
|
| [17] | Sekiguchi H, Watanabe M, Nakahara T, Xu BH, Uchiyama H (2002) Succession of bacterial community structure along the Changjiang River determined by denaturing gradient gel electrophoresis and clone library analysis. Appl. Environ. Microbiol. 68: 5142–5150. doi: 10.1128/aem.68.10.5142-5150.2002
|
| [18] | Beier S, Witzel KP, Marxsen J (2008) Bacterial community composition in central European running waters examined by temperature gradient gel electrophoresis and sequence analysis of 16S rRNA genes. Appl. Environ. Microbiol. 74: 188–199. doi: 10.1128/aem.00327-07
|
| [19] | Shade A, Chiu CY, McMahon KD (2010) Seasonal and episodic lake mixing stimulate differential planktonic bacterial dynamics. Microb Ecol 59: 546–554. doi: 10.1007/s00248-009-9589-6
|
| [20] | Jaffe R (1991) Fate of hydrophobic organic pollutants in the aquatic environment: a review. Environ Pollut. 69(2–3): 237–57. doi: 10.1016/0269-7491(91)90147-o
|
| [21] | Murray K, Fisher L, Therrien J, George B, Gillespie J (2001) Assessment and use of indicator bacteria to determine sources of pollution to an urban river. J Great Lakes Res 27: 220–229. doi: 10.1016/s0380-1330(02)70566-2
|
| [22] | Servais P, Garcia-Armisen T, George I, Billen G (2007) Fecal bacteria in the rivers of the Seine drainage network (France): Sources, fate and modelling. Science of the Total Environment 375(1–3): 152–167. doi: 10.1016/j.scitotenv.2006.12.010
|
| [23] | Ouattara NK, Passerat J, Servais P (2011) Faecal contamination of water and sediment in the rivers of the Scheldt drainage network. Environ Monit Assess. 183(1–4): 243–57. doi: 10.1007/s10661-011-1918-9
|
| [24] | Kostanjsek R, Lapanje A, Drobne D, Perovi？ S, Perovi？ A, et al. (2005) Bacterial community structure analyses to assess pollution of water and sediments in the Lake Shkodra/Skadar, Balkan Peninsula. Environ Sci Pollut Res Int. 12(6): 361–8. doi: 10.1065/espr2005.07.271
|
| [25] | Li D, Yang M, Li Z, Qi R, He J, et al. (2008) Change of bacterial communities in sediments along Songhua River in Northeastern China after a nitrobenzene pollution event. FEMS Microbiol Ecol. 65(3): 494–503. doi: 10.1111/j.1574-6941.2008.00540.x
|
| [26] | Wakelin SA, Colloff MJ, Kookana R (2008) Effect of Wastewater Treatment Plant Effluent on Microbial Function and Community Structure in the Sediment of a Freshwater Stream with Variable Seasonal Flow. Appl Environ Microbiol. 74(9): 2659–2668. doi: 10.1128/aem.02348-07
|
| [27] | Zhu J, Zhang J, Li Q, Han T, Xie J, et al.. (2013) Phylogenetic analysis of bacterial community composition in sediment contaminated with multiple heavy metals from the Xiangjiang River in China. Mar Pollut Bull. pii: S0025-326X(13)00079-9.
|
| [28] | Kenzaka T, Yamaguchi N, Prapagdee B, Mikami E, Nasu M (2001) Bacterial community composition and activity in urban rivers in Thailand and Malaysia. J. Health Sci. 47: 353–361. doi: 10.1248/jhs.47.353
|
| [29] | Winter C, Hein T, Kavka G, Mach RL, Farnleitner AH (2007) Longitudinal changes in the bacterial community composition of the Danube River: a whole-river approach. Appl. Environ. Microbiol. 73: 421–431. doi: 10.1128/aem.01849-06
|
| [30] | Zhang M, Yu N, Chen L, Jiang C, Tao Y, et al. (2012) Structure and seasonal dynamics of bacterial communities in three urban rivers in China. Aquat Sci 74: 113–120. doi: 10.1007/s00027-011-0201-z
|
| [31] | Brion N, Servais P, Bauwens W, Verbanck M (2012) Past and present chemical and microbiological quality of the Zenne River. In: Wynants and Nuytten (eds) “Bridge over troubled waters”, Crosstalks, VUB press, 241–264.
|
| [32] | Porter KG, Feig YS (1980) The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceanog. 25: 943–948. doi: 10.4319/lo.1980.25.5.0943
|
| [33] | Llirós M, Casamayor EO, Borrego C (2008) High archaeal richness in the water column of a freshwater sulfurous karstic lake along an interannual study. FEMS Microbiol Ecol. 66: 331–342. doi: 10.1111/j.1574-6941.2008.00583.x
|
| [34] | Callaway TR, Dowd SE, Wolcott RD, Sun Y, Mcreynolds JL, et al. (2009) Evaluation of the bacterial diversity in cecal contents of laying hens fed various molting diets by using bacterial tagencoded FLX amplicon pyrosequencing. Poult Sci (88) 298–302. doi: 10.3382/ps.2008-00222
|
| [35] | Smith DM, Snow DE, Rees E, Zischkau AM, Hanson JD, et al. (2010) Evaluation of the bacterial diversity of pressure ulcers using bTEFAP pyrosequencing. BMC Med Genomics 3: 41. doi: 10.1186/1755-8794-3-41
|
| [36] | Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIIME improves sensitivity and speed of chimera detection. Oxford Journal of Bioinformatics 27(16): 2194–2200. doi: 10.1093/bioinformatics/btr381
|
| [37] | Clarke KR, Gorley RN (2006) PRIMER V6: User Manual/Tutorial. Plymouth, UK: PRIMER-E.
|
| [38] | Clarke KR, Warwick RM (2001) Change in Marine Communities: An Approach to Statistical Analysis and Interpretation, PRIMERE Ldt, Plymouth, UK.
|
| [39] | R Development Core Team (2011) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0.
|
| [40] | Oksanen J, Blanchet FG, Kindt R, Legendre P, O’Hara RB, et al.. (2011) vegan: Community Ecology Package. R package version 1.17–8.
|
| [41] | David R (2010) labdsv: Ordination and Multivariate Analysis for Ecology. R package version 1.4–1.
|
| [42] | Peres-Neto PR, Legendre P, Dray S, Borcard D (2006) Variation partitioning of species data matrices: estimation and comparison of fractions. Ecology 87: 2614–2625. doi: 10.1890/0012-9658(2006)87[2614:vposdm]2.0.co;2
|
| [43] | Weithman AS, Haas MA (1984) Effects of dissolved-oxygen depletion on the rainbow trout fishery in Lake Taneycomo, Missouri. Trans. Am. Fish. Soc. 113: 109–124. doi: 10.1577/1548-8659(1984)113<109:eoddot>2.0.co;2
|
| [44] | Ademoroti CMA (1996) Mini water Development in Ibadan. Environmental Chemistry and Toxicology 1st Edition Foludex Press Ibadan, Nigeria. 70–121.
|
| [45] | Garnier J, Servais P, Billen G (1992b) Bacterioplankton in the Seine River: impact of the Parisian urban effluents. Can. J. Microbiol. 38: 56–64. doi: 10.1139/m92-009
|
| [46] | Hu M, Wang X, Wen X, Xia Y (2012) Microbial community structures in different wastewater treatment plants as revealed by 454-pyrosequencing analysis. Bioresource Technology 117: 72–79. doi: 10.1016/j.biortech.2012.04.061
|
| [47] | Methé BA, Hiorns WD, Zehr JP (1998) Contrasts between marine and freshwater bacterial community composition: Analyses of communities in Lake George and six other Adirondack lakes. Limnol Oceanogr 43: 368–374. doi: 10.4319/lo.1998.43.2.0368
|
| [48] | Drury B, Rosi-Marshall E, Kelly JJ (2013) Wastewater treatment effluent reduces the abundance and diversity of benthic bacterial communities in urban and suburban rivers. Appl Environ Microbiol. 79(6): 1897–905. doi: 10.1128/aem.03527-12
|
| [49] | Van der Gucht K, Sabbe K, De Meester L, Vloemans N, Zwart G, et al. (2001) Contrasting bacterioplankton community composition and seasonal dynamics in two neighbouring hypertrophic freshwater lakes. Environ. Microbiol. 3: 680–690. doi: 10.1046/j.1462-2920.2001.00242.x
|
| [50] | Crump BC, Hobbie J (2005) Synchrony and seasonality in bacterioplankton communities of two temperate rivers. Limnol. Oceanogr. 50(6): 1718–1729. doi: 10.4319/lo.2005.50.6.1718
|
| [51] | Newton RJ, Jones SE, Eiler A, McMahon KD, Bertilsson S (2011) A guide to the natural history of freshwater lake bacteria. Microbiol Mol Biol Rev 75: 14–49. doi: 10.1128/mmbr.00028-10
|
| [52] | Lamy D, Obernosterer I, Laghdass M, Artigas LF, Breton E, et al. (2009) Temporal changes of major bacterial groups and bacterial heterotrophic activity during a Phaeocystis globosa bloom in the eastern English Channel. Aquat. Microb. Ecol. 58: 95–107. doi: 10.3354/ame01359
|
| [53] | Gilbert JA, Field D, Swift P, Thomas S, Cummings D, et al. (2010) The taxonomic and functional diversity of microbes at a temperate coastal site: a ‘multiomic’ study of seasonal and diel temporal variation. PLoS One 5: e15545. doi: 10.1371/journal.pone.0015545
|
| [54] | Ghiglione JF, Murray AE (2012) Pronounced summer to winter differences and higher winter time richness in coastal Antarctic marine bacterioplankton. Environmental Microbiology 14(3): 617–629. doi: 10.1111/j.1462-2920.2011.02601.x
|
| [55] | Nielsen PH, Mielczarek AT, Kragelund C, Nielsen JL, Saunders AM, et al. (2010) A conceptual ecosystem model of microbial communities in enhanced biological phosphorus removal plants. Water Res 44: 5070–5088. doi: 10.1016/j.watres.2010.07.036
|
| [56] | Eikelboom D (1975) Filementous Organisms observed in activated sludge. Water Research 9: 365–388. doi: 10.1016/0043-1354(75)90182-7
|
| [57] | Kotay SM, Datta T, Choi J, Goel R (2011) Biocontrol of biomass bulking caused by Haliscomenobacter hydrossis using a newly isolated lytic bacteriophage. Water Res. 45(2): 694–704. doi: 10.1016/j.watres.2010.08.038
|
| [58] | Finneran KT, Johnsen CV, Lovley DR (2003) Rhodoferax ferrireducens sp. nov., a psychrotolerant, facultatively anaerobic bacterium that oxidizes acetate with the reduction of Fe(III). Int. J. Sys. Evol. Microbiol. 53: 669–673. doi: 10.1099/ijs.0.02298-0
|
| [59] | Belanchea L, Valdea JJ, Comas J, Rodab IR, Poch M (2000) Prediction of the bulking phenomenon in wastewater treatment plants. Artificial Intelligence in Engineering 14: 307–317. doi: 10.1016/s0954-1810(00)00012-1
|
| [60] | Moreno Y, Botella S, Alonso JL, Ferrús MA, Hernández M, et al. (2003) Specific Detection of Arcobacter and Campylobacter Strains in Water and Sewage by PCR and Fluorescent In situ Hybridization. Appl Environ Microb 69: 1181–1186. doi: 10.1128/aem.69.2.1181-1186.2003
|
| [61] | Starliper C (2011) Bacterial coldwater diseased fished by Flavobacterium psychrophilum. J. Adv. Res. 2(2): 97–108. doi: 10.1016/j.jare.2010.04.001
|
| [62] | Spring S, Wagner M, Schumann P, K？mpfer P (2005) Malikia granosa gen. nov., sp. nov., a novel polyhydroxyalkanoate- and polyphosphate-accumulating bacterium isolated from activated sludge, and reclassification of Pseudomonas spinosa as Malikia spinosa comb. nov. IJSEM 55(2): 621–629. doi: 10.1099/ijs.0.63356-0
|
| [63] | Yannarell AC, Kent AD, Lauster GH, Kratz TK, Triplett EW (2003) Temporal patterns in bacterial communities in three temperate lakes of different trophic status. Microb. Ecol. 46: 391–405. doi: 10.1007/s00248-003-1008-9
|
| [64] | Allison G (2004) The influence of species diversity and tress intensity on community resistance and resilience. Ecological Monographs 74: 117–134 doi:10.1890/02-068.
|
| [65] | Berga M, Székely A, Langenheder S (2012) Effects of disturbance intensity and frequency on bacterial community composition and function. PLoS ONE 7(5): e36959 doi:10.1371/journal.pone.0036959.
|
