Bacterial community composition of an urban river in the North West Province, South Africa, in relation to physico-chemical water quality

Environmental Science and Pollution Research

Volumn 23, Issue 6, 2016, Pages 5868-5880

  Jordaan, K ^a   Bezuidenhout, C C ^a  

^a NORTH WEST UNIVERSITY   (South Africa)

Author keywords

454 pyrosequencing; Anthropogenic; Bacterial community composition; Multivariate analysis

Indexed keywords

ABUNDANCE; ANTHROPOGENIC EFFECT; BACTERIUM; COMMUNITY COMPOSITION; FECES; FRESHWATER ECOSYSTEM; GENETIC ANALYSIS; MICROBIAL COMMUNITY; MULTIVARIATE ANALYSIS; NUTRIENT ENRICHMENT; PHYSICOCHEMICAL PROPERTY; URBAN AREA; WATER POLLUTION; WATER QUALITY;

KWAZULU-NATAL; MOOI RIVER; NORTH WEST PROVINCE; SOUTH AFRICA;

ACIDOBACTERIA; BACTERIA (MICROORGANISMS); BACTEROIDETES; BETAPROTEOBACTERIA; EPSILONPROTEOBACTERIA; VERRUCOMICROBIA;

BACTERIUM; CHEMISTRY; ENVIRONMENTAL MONITORING; MICROBIOLOGY; RIVER; SOUTH AFRICA; WATER POLLUTION; WATER QUALITY;

BACTERIA; ENVIRONMENTAL MONITORING; RIVERS; SOUTH AFRICA; WATER MICROBIOLOGY; WATER POLLUTION; WATER QUALITY;

EID: 84948132572     PISSN: 09441344     EISSN: 16147499     Source Type: Journal    
DOI: 10.1007/s11356-015-5786-7     Document Type: Article

References (88)

1. Ager D, Evans S, Li H, Lilley AK, Van der Gast CJ (2010) Anthropogenic disturbance affects the structure of bacterial communities. Environ Microbiol 12(3):670–678
2. Altmann D, Stief P, Amann R, De Beer D, Schramm A (2003) In situ distribution and activity of nitrifying bacteria in freshwater sediment. Environ Microbiol 5(9):798–803
3. Bhowal S, Chakraborty R (2011) Five novel acid-tolerant oligotrophic thiosulfate-metabolizing chemolithotrophic acid mine drainage strains affiliated with the genus Burkholderia of Betaproteobacteria and identification of two novel soxB gene homologues. Res Microbiol 162(4):436–445
4. Bricheux G, Morin L, Le Moal G, Coffe G, Balestrino D, Charbonnel N, Bohatier J, Forestier C (2013) Pyrosequencing assessment of prokaryotic and eukaryotic diversity in biofilm communities from a French river. Microbiol Open 2(3):402–414
5. Brümmer IHM, Fehr W, Wagner-Döbler I (2000) Biofilm community in polluted rivers: abundance of dominant phylogenetic groups over a complete annual cycle. Appl Environ Microb 66(7):3078–3082
6. Chen Y-G, Zhang Y-Q, Huang K, Tang S-K, Cao Y, Shi J-X, Xiao H-D, Cui X-L, Li W-J (2009) Pigmentiphaga litoralis sp. nov., a facultatively anaerobic bacterium isolated from a tidal flat sediment. Int J Syst Evol Micr 59(3):521–525
7. Chinivasagam HN, Corney BG, Wright LL, Diallo IS, Blackall PJ (2007) Detection of Arcobacter spp. in piggery effluent and effluent irrigated soils in southeast Queensland. J Appl Microbiol 103(2):418–426
8. Collado L, Inza I, Guarro J, Figueras MJ (2008) Presence of Arcobacter spp. in environmental waters correlates with high levels of fecal pollution. Environ Microbiol 10(6):1635–1640
9. Crump BC, Hobbie JE (2005) Synchrony and seasonality in bacterioplankton communities of two temperate rivers. Limnol Oceanogr 50(6):1718–1729
10. De Figueiredo DR, Pereira MJ, Moura A, Silva L, Bárrios S, Fonseca F, Henríques I, Correia A (2007) BCC over a dry winter in meso- and eutrophic Portuguese water bodies. FEMS Microbiol Ecol 59(3):638–650
11. De Figueiredo DR, Pereira MJ, Correia A (2010) Seasonal modulation of bacterioplankton community at a temperate eutrophic shallow lake. World J Microb Biot 26(6):1067–1077
12. De Figueiredo DR, Ferreira RV, Cerqueira M, Condesso De Melo T, Pereira MJ, Castro BB, Correia A (2012) Impact of water quality on bacterioplankton assemblage along Cértima River Basin (central western Portugal) assessed by PCR-DGGE and multivariate analysis. Environ Monit Assess 184(1):471–485
13. Decker CF, Hawkins RE, Simon GL (1992) Infections with Pseudomonas paucimobilis. Clin Infect Dis 14(3):783–784
14. Djordjevic Z, Folic MM, Zivic Z, Markovic V, Jankovic SM (2013) Nosocomial urinary tract infections caused by Pseudomonas aeruginosa and Acinetobacter species: sensitivity to antibiotics and risk factors. Am J Infect Control 41(12):1182–1187
15. 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 Microb 79(6):1897–1905
16. DWAF (1996) Department of Water Affairs and Forestry. South African Water Quality Guidelines, 1st ed. Volume 8: Field Guide.
17. DWAF (2009) Directorate national water resource planning. Department of Water Affairs and Forestry, South Africa, September 2009. Integrated water quality management plan for the Vaal River System: task 2: water quality status assessment of the Vaal River system. Report No. P RSA C000/00/2305/1.
18. Edwards ML, Lilley AK, Timms-Wilson TH, Thompson IP, Cooper I (2001) Characterisation of the culturable heterotrophic bacterial community in a small eutrophic lake (Priest Pot). FEMS Microbiol Ecol 35(3):295–304
19. Eiler A, Langenheder S, Bertilsson S, Tranvik LJ (2003) Heterotrophic bacterial growth efficiency and community structure at different natural organic carbon concentrations. Appl Environ Microb 69(7):3701–3709
20. Eiler A, Bertilsson S (2007) Flavobacteria blooms in four eutrophic lakes: linking population dynamics of freshwater bacterioplankton to resource availability. Appl Environ Microb 73(11):3511–3518
21. Eiler A, Heinrich F, Bertilsson S (2012) Coherent dynamics and association networks among lake bacterioplankton taxa. ISME J 6(2):330–342
22. Evtushenko LI, Dorofeeva LV, Subbotin SA, Cole JR, Tiedje JM (2000) Leifsonia poae gen. nov., sp. nov., isolated from nematode galls on Poa annua, and reclassification of ‘Corynebacterium aquaticum’ Leifson 1962 as Leifsonia aquatica (ex Leifson 1962) gen. nov., nom. rev., comb. nov. and Clavibacter xyli Davis et al. 1984 with two subspecies as Leifsonia xyli (Davis et al. 1984) gen. nov., comb. nov. Int J Syst Evol Micr 50(1):371–380
23. Fong TT, Mansfield LS, Wilson DL, Schwab DJ, Molloy SL, Rose JB (2007) Massive microbiological groundwater contamination associated with a waterborne outbreak in Lake Erie, South Bass Island, Ohio. Environ Health Persp 115(6):856–864
24. Ford TE (2000) Response of marine microbial communities to anthropogenic stress. J Aquat Ecosyst Stress Recovery 7(1):75–89
25. Gavigan J-A, Leonard MM, Dobson ADW (1999) Regulation of polyphosphate kinase gene expression in Acinetobacter baumannii 252. Microbiology 145(10):2931–2937
26. Ghosh M, Verma SC, Mengoni A, Tripathi AK (2004) Enrichment and identification of bacteria capable of reducing chemical oxygen demand of anaerobically treated molasses spent wash. J Appl Microbiol 96(6):1278–1286
27. Goñi-Urriza M, Capdepuy M, RAymond N, Quentin C, Caumette P (1999) Impact of an urban effluent on the bacterial community structure in the Arga River, Spain, with special reference to culturable Gram-negative rods. Can J Microbiol 45(10):826–832
28. Haller L, Tonolla M, Zopfi J, Peduzzi R, Wildi W, Poté J (2011) Composition of bacterial and archaeal communities in freshwater sediments with different contamination levels (Lake Geneva, Switzerland). Water Res 45(3):1213–1228
29. HDA (2012) The Housing Development Agency. Informal settlement status, South Africa
30. Ho HT, Lipman LJ, Gaastra W (2006) Arcobacter, what is known and unknown about a potential foodborne zoonotic agent! Vet Microbiol 115(1–3):1–13
31. Horňák K, Jezbera J, Šimek K (2008) Effects of a Microcystis aeruginosa bloom and bacterivory on bacterial abundance and activity in a eutrophic reservoir. Aquat Microb Ecol 52(2):107–117
32. Iwegbue CMA, Arimoro FO, Nwajei GE, Eguavoen OI (2012) Concentrations and distribution of trace metals in water and streambed sediments of Orogodo River, Southern Nigeria. Soil Sediment Contam 21(3):382–406
33. Jordaan K, Bezuidenhout CC (2013) The impact of physico-chemical water quality parameters on bacterial diversity in the Vaal River, South Africa. Water SA 39(3):365–376
34. Kalwasińska A, Kęsy J, Donderski W, Lalke–POrczyk E (2008) Biodegradation of carbendazim by planktonic and benthic bacteria of eutrophic lake Chełmżyńskie. Pol J Environ Stud 17(4):515–523
35. Kamjunke N, Buttner O, Jager CG, Marcus H, Von Tumpling W, Halbedel S, Norf H, Brauns M, Baborowski M, Wild R, Borchardt D, Weitere M (2013) Biogeochmical patterns in a river network along a land use gradient. Environ Monit Assess 185(11):9221–36
36. Kirchman DL (2012) Processes in microbial ecology. Oxford University Press, New York
37. Kisand V, Cuadros R, Wikner J (2002) Phylogeny of culturable estuarine bacteria catabolizing riverine organic matter in the northern Baltic Sea. Appl Environ Microb 68(1):379–388
38. Kisand V, Andersson N, Wikner J (2005) Bacterial freshwater species successfully immigrate to the brackish water environment in the northern Baltic. Limnol Oceanogr 50:945–956
39. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. John Wiley & Sons, New York, pp 115–175
40. Laque T, Farjalla VF, Rosado AS, Esteves FA (2010) Spatiotemporal variation of bacterial community composition and possible controlling factors in tropical shallow lagoons. Microbial Ecol 59(4):819–829
41. Larsen PE, Field D, Gilbert JA (2012) Predicting bacterial community assemblages using an artificial neural network approach. Nat Methods 9:621–625
42. Lee J-S, Shin YK, Yoon J-H, Takeuchi M, Pyun Y-R, Park Y-H (2001) Sphingomonas aquatilis sp. nov., Sphingomonas koreensis sp. nov. and Sphingomonas taejonensis sp. nov., yellow-pigmented bacteria isolated from natural mineral water. Int J Syst Evol Micr 51(4):1491–1498
43. Li W, Shen Z, Tian T, Liu R, Qiu J (2012) Temporal variation of heavy metal pollution in urban stormwater runoff. Front Environ Sci En 6(5):692–700
44. Lin S, Wang Y, Lin J, Quan C (2014) Response of planktonic and benthic microbial community to urban pollution from sewage discharge in Jilin reach of the second Songhua River, China. Clean – Soil Air Water 42(10):1376–1383
45. Lindström ES, Vrede K, Leskinen E (2004) Response of a member of the Verrucomicrobia, among the dominating bacteria in a hypolimnion, to increased phosphorus availability. J Plankton Res 26(2):241–246
46. Lindström 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 Microb 71(12):8201–8206
47. Liu Z, Huang S, Sun G, Xu Z, Xu M (2012) Phylogenetic diversity, composition and distribution of bacterioplankton community in the Dongjiang River, China. FEMS Microbiol Ecol 80(1):30–44
48. Lu X-M, Lu P-Z (2014) Characterization of bacterial communities in sediments receiving various wastewater effluents with high-throughput sequencing analysis. Microbial Ecol 67(3):612–623
49. Madhaiyan M, Poonguzhali S, Saravanan VS, Hari K, Lee K-C, Lee J-S (2013) Duganella sacchari sp. nov. and Duganella radices sp. nov., two novel species isolated from rhizosphere of field-grown sugar cane. Int J Syst Evol Micr 63:1126–1131
50. Magee JG, Ward AC (2012) Genus I. Mycobacterium. In: Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Suzuki K, Ludwig W, Whitman B (eds) Bergey’s manual of systematic bacteriology, vol 5, 2nd edn. The Actinobacteria. Springer, New York, pp 312–375
51. Marcel KA, Antoinette AA, Mireille D (2002) Isolation and characterization of Aeromonas species from an eutrophic tropical estuary. Mar Pollut Bull 44(12):1341–1344
52. Markúsdóttir M, Heiðmarsson S, Eyþórsdótti A, Magnússon KP, Vilhelmsson O (2013) The natural and anthropogenic microbiota of Glerá, a sub-arctic river in northeastern Iceland. Int Biodeter Biodegr 84:192–203
53. Martinuzzi S, Januchowski-Hartley SR, Pracheil BM, McIntyre PB, Plantinga AJ, Lewis DJ, Lewis DJ, Radeloff VC (2014) Threats and opportunities for freshwater conservation under future land use change scenarios in the United States. Glob Change Biol 20(1):113–24
54. Mckinney ML (2006) Urbanization as a major cause of biotic homogenization. Biol Conserv 127(3):247–260
55. Mclellan SL, Huse SM, Mueller-Spitz SR, Andreishcheva EN, Sogin ML (2010) Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent. Environ Microbiol 12(2):378–392
56. Newton RJ, Jones SE, Eiler A, Mcmahon K, Bertilsson S (2011) A guide to the natural history of freshwater lake bacteria. Microbiol Mol Biol Rev 75(1):14–49
57. O’Driscoll M, Clinton S, Jefferson A, Manda A, McMillan S (2010) Urbanization effects on watershed hydrology and in-stream processes in the southern United States. Water 2(3):605–648
58. Paerl HW, Dyble J, Moisander PH, Noble RT, Piehler MF, Pinckney JL, Steppe TF, Twomey L, Valdes LM (2003) Microbial indicators of aquatic ecosystems change: current applications to eutrophication studies. FEMS Microbiol Ecol 46(3):233–246
59. Paissé S, Coulon F, Goñi-Urriza M, Peperzak L, McGenity TJ, Duran R (2008) Structure of bacterial communities along a hydrocarbon contamination gradient in a coastal sediment. FEMS Microbiol Ecol 66(2):295–305
60. Parker JL, Shaw JG (2011) Aeromonas spp. clinical microbiology and disease. J Infect 62(2):109–118
61. Paver SF, Kent AD (2010) Temporal patterns in glycolate-utilizing bacterial community composition correlate with phytoplankton population dynamics in humic lakes. Microbial Ecol 60(2):406–418
62. Pereira RM, DA Silveira EL, Scaquitto DC, Pedrinho EAN, Val-Moraes SP, Wickert E, Carareto-Alves LM (2006) Molecular characterization of bacterial populations of different soils. Braz J Microbiol 37(4):439–447
63. Pesce S, Fajon C, Bardot C, Bonnemoy F, Portelli C, Bohatier J (2008) Longitudinal changes in microbial planktonic communities of a French river in relation to pesticide and nutrient inputs. Aquat Toxicol 86(3):352–360
64. Pinyakong O, Habe H, Omori T (2003) The unique aromatic catabolic genes in sphingomonads degrading polycyclic aromatic hydrocarbons (PAHs). J Gen Appl Microbiol 49(1):1–19
65. Rice EW, Baird RB, Eaton AD, Clesceri LS (2012). Standard methods for the examination of water and wastewater, 22nd ed. American Public Health Association, American Water Works Association, Water Environment Federation
66. Rickard AH, McBain AJ, Ledder RG, Handley PS, Gilbert P (2003) Coaggregation between freshwater bacteria within biofilm and planktonic communities. FEMS Microbiol Lett 220(1):133–140
67. SABS (2010) South African Bureau of Standards, Water–Nitrate and nitrite content. 2nd ed. Standards South Africa
68. Sartory DP, Grobbelaar JU (1984) Extraction of chlorophyll a from freshwater phytoplankton for spectrophotometric analysis. Hydrobologia 114(3):177–187
69. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing MOTHUR: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microb 75(23):7537–7541
70. Schloss PD, Gevers D, Westcott SL (2011) Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PloS ONE 6:e27310
71. Sigee DC (2005) Freshwater microbiology: biodiversity and dynamic interactions of microorganisms in the aquatic environment. John Wiley & Sons, England
72. Šimek K, Horňák K, Jezbera J, Nedoma J, Znachor P, Hejzlar J, Sed’a J (2008) Spatio-temporal patterns of bacterioplankton production and community composition related to phytoplankton composition and protistan bacterivory in a dam reservoir. Aquat Microb Ecol 51(3):249–262
73. Singh J, Behal A, Singla N, Joshi A, Birbian N, Singh S, Bali V, Batra N (2009) Metagenomics: concept, methodology, ecological inference and recent advances. Biotechnol J 4(4):480–494
74. Spring S, Wagner M, Schumann P, Kämpfer 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. Int J Syst Evol Micr 55(2):621–629
75. Stabili L, Cavallo RA (2011) Microbial pollution indicators and culturable heterotrophic bacteria in a Mediterranean area (Southern Adriatic Sea Italian coasts). J Sea Res 65(4):461–469
76. Stats SA (2011) Census 2011. http://www.statssa.gov.za/census2011/default.asp. Accessed 10 February 2013.
77. Struthers M, Wong J, Janda JM (1996) An initial appraisal of the clinical significance of Roseomonas species associated with human infections. Clin Infect Dis 23(4):729–733
78. Táncsics A, Szabó I, Baka E, Szoboszlay S, Kukolya J, Kriszt B, Márialigeti K (2010) Investigation of catechol 2,3-dioxygenase and 16S rRNA gene diversity in hypoxic, petroleum hydrocarbon contaminated groundwater. Syst Appl Microbiol 33(7):398–406
79. Van der Gucht K, Vandekerckhove T, Vloemans N, Cousin S, Muylaert K, Sabbe K, Gillis M, Declerk S, De Meester L, Vyverman W (2005) Characterization of bacterial communities in four freshwater lakes differing in nutrient load and food web structure. FEMS Microbiol Ecol 53(2):205–220
80. Van der Walt IJ, Winde F, Nell B (2002) Integrated catchment management: the Mooi River (North West Province, South Africa) as a case study. Cuadernos de Investigación Geográfica 28:109–126
81. Vishnivetskaya TA, Mosher JJ, Palumbo AV, Yang ZK, Podar M, Brown SD, Brooks SC, Gu B, Southworth GR, Drake MM, Brandt CC, Elias DA (2011) Mercury and other heavy metals influence bacterial community structure in contaminated Tennessee streams. Appl Environ Microb 77(1):302–311
82. Wakelin SA, Colloff MJ, Kookana RS (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 Microb 74(9):2659–2668
83. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microb 73(16):5261–5267
84. Yergeau E, Lawrence JR, Sanschagrin S, Waiser MJ, Korber DR, Greera CW (2012) Next-generation sequencing of microbial communities in the Athabasca River and its tributaries in relation to oil sands mining activities. Appl Environ Microb 78(21):7626–7637
85. Yi H, Li Z, Shuying Z, Shuguang X (2011) Comparison of bacterioplankton communities in three heavily polluted streams in China. Biomed Environ Sci 24(2):140–145
86. Zafiriou OC, Joussot-Dubien J, Zepp RG, Zika RG (1984) Photochemistry of natural waters. Environ Sci Technol 18(12):358A–371A
87. Zampini M, Stevens PR, Pachebat JA, Kingston-Smith A, Mur LAJ, Hayes F (2015) RapGene: a fast and accurate strategy for synthetic gene assembly in Escherichia coli. Scientific Reports 5:11302. doi:10.1038/srep11302
88. Zarraonaindia I, Smith DP, Gilbert JA (2013) Beyond the genome: community-level analysis of the microbial world. Biol Philos 28(2):261–282