Abia ALK, Alisoltani A, Keshri J, Ubomba‐Jaswa E. Metagenomic analysis of the bacterial communities and their functional profiles in water and sediments of the Apies River, South Africa, as a function of land use. Sci Total Environ. 2018; 616:326–334.
Ahkola H, Tuominen S, Karlsson S, Perkola N, Huttula T, Saraperä S, Arimo A, Korpijarju T, Äystö L, Fjäder P, Assmuth T, Rosendahl K, Nysten T. Presence of active pharmaceutical ingredients in the continuum of surface and groundwater used in drinking water production. Environ Sci Pollut Res. 2017; 24: 26778–26791.
Ahmed W, Staley C, Kaiser T, Sadowsky M, Kozak S, Beale D, Simpson S. Decay of sewage-associated bacterial communities in fresh and marine environmental waters and sediment. Appl Microbiol Biotechnol. 2018; 101: 1253–1266.
Baldani JI, Rouws L, Cruz LM, Olivares FL, Schmid MH. The Family Oxalobacteraceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F, editors. The Prokaryotes. Springer, Berlin, Heidelberg; 2014. p. 919- 974.
Banerji A, Bagley M, Elk M, Pilgrim E, Martinson J, Santo Domingo. Spatial and temporal dynamics of a freshwater eukaryotic plankton community revealed via 18S rRNA gene metabarcoding. Hydrobiologia. 2018; 818: 71–86.
Braun B, Schröder J, Knecht H, Szewzyk U. Unravelling the microbial community of a cold groundwater catchment system. Water Res. 2016; 107: 113–126.
Campbell MJ and Gardner MJ. Calculating confidence intervals for some non-parametric analyses. Br Med J. 1998; 296: 1454- 1456.
Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics. 2010b; 26: 266–267.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. QIIME allows analysis of high‐throughput community sequencing data. Nat Methods. 2010a; 7: 335– 336.
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci. 2011; 108 (Suppl 1):4516‐4522.
De Celis M, Belda I, Ortiz-Álvarez R, Arregui L, Marquina D, Serrano S, Santos A. Tuning up microbiome analysis to monitor WWTPs' biological reactors functioning. Sci Rep. 2020; 10(1):4079.
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a chimera‐checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006; 72: 5069– 5072.
Dhariwal A, Chong J, Habib S, King I, Agellon LB, Xia J. MicrobiomeAnalyst - a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data. Nucleic Acids Res. 2017; 45: W180-188.
Doronina N, Kaparullina E, Trotsenko Y. The Family Methylophilaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F, editors. The Prokaryotes. Springer, Berlin, Heidelberg; 2014. https://doi.org/10.1007/978-3-642-30197-1_243
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011; 27: 2194 –2200.
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010; 26(19):2460–2461.
Whitman W, Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Ludwig W, Suzuki K, editors. Bergey's Manual of Systematic Bacteriology.Vol. 5, The Actinobacteria, 2nd Edn. New York, NY: Springer; 2012.
Gülay A, Musovic S, Albrechtsen HJ, Al-Soud WA, Sørensen SJ, Smets BF. Ecological patterns, diversity and core taxa of microbial communities in groundwater-fed rapid gravity filters. ISME J. 2016; 10: 2209–2222.
Happonen M, Koivusalo H, Malve O, Perkola N, Juntunen J, Huttula T. Contamination risk of raw drinking water caused by PFOA sources along a river reach in south-western Finland. Sci Total Environ. 2016; 541: 74–82.
Hertzen L, Laatikainen T, Pitkänen T, Vlasoff T, Mälelä MJ, Vartiainen E, Haahtela T. Microbial content of drinking water in Finnish and Russian Karelia- implications for atopy prevalence. Allergy. 2007; 62: 288-292.
Hibbing ME, Fuqua C, Parsek MR, Peterson SB. Bacterial competition: surviving and thriving in the microbial jungle. Nat Rev Microbiol. 2010;8(1):15–25.
Hokajärvi A-M, Pitkänen T, Siljanen H, Nakari U, Torvinen E, Siltonen A, Miettinen IT. Occurrence of thermotolerant Campylobacter spp. and adenoviruses in Finnish bathing waters and purified sewage effluents. J Water Health. 2013; 11 (1): 120–134.
Huang K, Mao Y, Zhao F, Zhang X, Ju F, Ye L, Wang Y, Li B, Ren H, Zhang T. Free-living bacterial and potential bacterial pathogens in sewage treatment plants. Appl Microbiol Biotechnol. 2018; 102: 2455-2464.
Hubbe MA, Metts JR, Hermosilla D, Blanco MA, Yerushlmi L, Haghighat F, Lindholm-Lehto P, Khodaparast Z, Kamali M, Elliott A. Wastewater treatment and reclamation: a review of pulp and paper industry practices and opportunities. BioResources. 2016; 11(3): 7953-8091.
Huys G. The Family Aeromonadaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F, editors. The Prokaryotes. Springer, Berlin, Heidelberg; 2014.
Ibekwe AM, Leddy MB, Bold RM, Graves AK. Bacterial community composition in low-flowing river water with different sources of pollutants. FEMS Microbiol Ecol. 2012; 79: 155–166.
Inkinen J, Jayaprakash B, Santo Domingo JW, Keinänen-Toivola MM, Ryu H, Pitkänen T. Diversity of ribosomal 16S DNA- and RNA-based bacterial community in an office building drinking water system. J Appl Microbiol. 2016;120: 1723–1738.
Jin D, Kong X, Cui B, Jin S, Xie Y, Wang X, Deng Y. 2018. Bacterial communities and potential waterborne pathogens within the typical urban surface waters. Sci Rep. 2018; 8:13368.
Jokela P, Eskola T, Heinonen T, Tanttu U, Tyrväinen J, Artimo A. Raw water quality and pretreatment in managed aquifer recharge for drinking water production in Finland. Water. 2017; 9: 138.
Jordaan K, Comeau AM, Khasa DP, Bezuidenhout CC. An integrated insight into the response of bacterial communities to anthropogenic contaminants in a river: A case study of the Wonderfonteinspruit catchment area, South Africa. PLoS ONE. 2019;14(5): e0216758.
Kielak AM, Barreto CC, Kowalchuk GA, Veen JA, Kuramae EE. The ecology of Acidobacteria: moving beyond genes and genomes. Front Microbiol. 2016; 7:744.
Koo H, Hakim JA, Morrow CD, Eipers PG, Davila A, Andersen DT, Bej AK. Comparison of two bioinformatics tools used to characterize the microbial diversity and predicted functional attributes of microbial mats from Lake Oberse, Antarctica. J Microbiol Methods. 2017; 140: 15–22.
Korajkic A, Parfrey LW, McMinn BR, Baeza YV, VanTeuren W, Knight R, Shanks OC. Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi river water. Water Res. 2015; 69: 30–39.
Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Thurber RLV, Knight R, Beiko RG, Huttenhower C. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 2013; 31: 814–821.
Lastovica AJ, On SLW, Zhang L. The Family Campylobacteraceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F, editors. The Prokaryotes. Springer, Berlin, Heidelberg, 2014.
Li Q, Yu S, Li L, Liu G, Gu Z, Liu M, Liu Z, Ye Y, Xia Q, Ren L. Microbial communities shaped by treatment processes in a drinking water treatment plant and their contribution and threat to drinking water safety. Front Microbiol. 2017; 8: Article 2465.
Liu Y, Tong T, Li B, Xie S. Dynamics of bacterial communities in a river water treatment wetland. Ann Microbiol. 2019; 69: 637–645.
Ma X, Li G, Chen R, Yu Y, Tao H, Zhang G, Shi B. Revealing the changes of bacterial community from water source to consumers tap: A full-scale investigation in eastern city of China. J Environ Sci. 2020; 87: 331–340.
Magoc T and Salzberg SL. FLASH: Fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2010; 27 (21): 2957–2963.
McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012; 6(3): 610–618.
Morris EK, Carusto T, Buscot F, Fischer M, Hancock C, Maier TS, Meiners T, Müller C, Obermaier E, Prati D, Socher SA, Sonnemann I, Waschke N, Wuet T, Wurst S, Rillig MC. Choosing and using diversity indices: insights for ecological applications from the German Biodiversity Exploratories. Ecol Evol. 2014; 4(18): 3514– 3524.
Morris RM, Rappé MS, Connon SA, Vergin KL, Siebold WA, Carlson CA, Giovannoni SJ. SAR11 clade dominates ocean surface bacterioplankton communities. Nature. 2020; 420 (6917): 806–810.
Oren A. The Family Rhodocyclaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F(eds) The Prokaryotes. Springer, Berlin, Heidelberg, 2014.
Pan F, Liu W, Yu Y, Yin X, Wang Q, Zheng Z, Wu M, Zhao D, Zhang Q, Lei X, Xia D. The effects of manganese oxide octahedral molecular sieve chitosan microspheres on sludge bacterial community structures during sewage biological treatment. Sci Rep. 2016; 6: 37518.
Pérez-Cataluña A, Salas-Massó N, Diéguez AL, Balboa S, Lema A, Romalde JL, Figueras MJ. Revisiting the taxonomy of the genus Arcobacter: Getting order from the chaos. Front Microbiol. 2018; 9: 2077.
Pitkänen T, Ryu H, Elk M, Hokajärvi A-M, Siponen S, Vepsäläinen A, Räsänen P, Santo Domingo JW. Detection of fecal bacteria and source tracking identifiers in environmental waters using rRNA-based RT-qPCR and rDNA-based qPCR assays. Environ Sci Technol. 2013; 47(23): 13611–13620.
Prest EI, Hammes F, van Loosdrecht MCM, Vrouwendelder JS. Biological stability of drinking water: controlling factors, methods, and challenges. Front Microbiol. 2016; 7: 45.
Ramette A. Multivariate analysis in microbial ecology. FEMS Microbio Ecol. 2007; 62(2): 142–160.
Savio D, Sinclair L, Lijaz UZ, Parajka J, Reischer GH, Sadler P, Blaschke AP, Blöschl G, Mach RL, Kirchner AKT, Farnleitner AH, Eiler A. Bacterial diversity along a 2600 km river continuum. Environ Microbial. 2015; 17 (12): 4994–5007.
Staley C, Gould TJ, Wang P, Phillips J, Cotner JB, Sadowsk MJ. Core functional traits of bacterial communities in the Upper Mississippi River show limited variation in response to land cover. Front Microbiol. 2014; 5: 414.
Teixeira LM and Merquior VLC. The Family Moraxellaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F, editors. The Prokaryotes. Springer, Berlin, Heidelberg, 2014.
Wang L, Zhang J, Li H, Yang H, Peng C, Peng Z, Lu L. Shift in the microbial community composition of surface water and sediment along an urban river. Sci Total Environ. 2018;627: 600–612.
Wang Y, Yang J, Liu L, Yu Z. Quantifying the effects of geographical and environmental factors on distribution of stream bacterioplankton within nature reserves of Fujian, China. Environ Sci Pollut Res. 2015; 22:11010–11021.
Willems A. The Family Comamonadaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F, editors. The Prokaryotes. Springer, Berlin, Heidelberg, 2014.
Payment P, Sartory DP, Reasoner DJ.The history and use of HPC in drinking-water quality management. In J Bartram, J Cotruvo, M Exner, C Fricker, and A Glasmacher, editors. Heterotrophic plate counts and drinking-water safety. IWA Publishing, London; 2003. p. 20–49.
Wu H, Li Y, Zhang W, Wang C, Wang P, Niu L, Du J, Gao Y. Bacterial community composition and function shift with the aggravation of water quality in a heavily polluted river. J Environ Manage. 2019; 237:433–441.
Ye L and Zhang T. Pathogenic bacteria in sewage treatment plants as revealed by 454 Pyrosequencing. Environ Sci Technol. 2011; 45:7173–7179.
Yu Z, Yang J, Amalfitano S, Yu X, Liu L. Effects of water stratification and mixing on microbial community structure in a subtropical deep reservoir. Sci Rep. 2014; 4:5821.
Zeglin LH. Stream microbial diversity in response to environmental changes: review and synthesis of existing research. Front Microbiol. 2015; 6: Article 454.