Next-generation sequencing and waste/wastewater treatment: a comprehensive overview

  • Jose L. SanzEmail author
  • Thorsten Köchling
Review paper


Microorganisms are responsible for the conversion and breakdown of organic compounds and contaminants in bioreactors designed for the treatment of different types of waste. Organized in highly complex communities, they are the heart of every wastewater treatment plant and solid residue landfill. The detailed characterization of these communities and their taxonomic classification based on phylogenetic data are of great utility in monitoring the responses of the system to changing operational parameters and the development and optimization of favorable conditions within the bioreactors these communities inhabit. Until recently, only a fraction of the microbial diversity could be assessed, limited by the available sequencing technology, which was not suited for a high-throughput implementation. With the introduction of the recent next-generation sequencing (NGS) methods, an enormous advance has taken place allowing researchers in microbial ecology to generate large amounts of phylogenetic data in a short time and at relatively low costs. In this review, we present and discuss how the increase in available information has influenced recent research and the results available phylogenetic data has produced in the field of wastewater treatment. Furthermore, we introduce the data processing of NGS-based experiments, which has become more complex as the millions of sequences that a single sample can yield require the effective use of computational resources and human bioinformatics skills. To address this part of modern microbial ecology, the most popular sequencing techniques, as well as data analysis workflows, are outlined in this review article.


Anaerobic reactors Activated sludge Illumina Microbial ecology Next-generation sequencing Pyrosequencing Wastewater 16S rDNA (amplicon sequencing) 



  1. Albertsen M, Hansen LBS, Saunders AM et al (2012) A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal. ISME J 6:1094–1106Google Scholar
  2. Awolusi OO, Nasr M, Kumari S, Bux F (2018) Principal component analysis for interaction of nitrifiers and wastewater environments at a full-scale activated sludge plant. Int J Environ Sci Technol 15:1477–1490. CrossRefGoogle Scholar
  3. Bailon-Salas AM, Medrano-Roldan H, Ordaz-Diaz SV-CLA et al (2017) Review of molecular techniques for the identification of bacterial communities in biological effluent treatment facilities at pulp and paper mills. BioResources 12:4384–4409Google Scholar
  4. Bakken LR (1985) Separation and purification of bacteria from soil. Appl Environ Microbiol 49:1482–1487Google Scholar
  5. Berger WH, Parker FL (1970) Diversity of planktonic foraminifera in deep-sea sediments. Science 168:1345–1347Google Scholar
  6. Bokulich NA, Subramanian S, Faith JJ et al (2013) Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods 10:57–59Google Scholar
  7. Bowers RM, Clum A, Tice H et al (2015) Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community. BMC Genom 16:856. CrossRefGoogle Scholar
  8. Braga JK, Motteran F, Silva EL, Varesche MBA (2015) Evaluation of bacterial community from anaerobic fluidized bed reactor for the removal of linear alkylbenzene sulfonate from laundry wastewater by 454-pyrosequence. Ecol Eng 82:231–240Google Scholar
  9. Bragg L, Stone G, Imelfort M et al (2012) Fast, accurate error-correction of amplicon pyrosequences using Acacia. Nat Methods 9:425–426Google Scholar
  10. Breitwieser FP, Lu J, Salzberg SL (2017) A review of methods and databases for metagenomic classification and assembly. Brief Bioinform. CrossRefGoogle Scholar
  11. Buttigieg PL, Ramette A (2014) A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses. FEMS Microbiol Ecol 90:543–550. CrossRefGoogle Scholar
  12. Cabezas A, de Araujo JC, Callejas C et al (2015) How to use molecular biology tools for the study of the anaerobic digestion process? Rev Environ Sci Biotechnol 14:555–593Google Scholar
  13. Cao SB, Li BK, Du R et al (2016) Nitrite production in a partial denitrifying upflow sludge bed (USB) reactor equipped with gas automatic circulation (GAC). Water Res 90:309–316Google Scholar
  14. Caporaso JG, Bittinger K, Bushman FD et al (2010a) PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26:266–267Google Scholar
  15. Caporaso JG, Kuczynski J, Stombaugh J et al (2010b) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336Google Scholar
  16. Cerrillo M, Morey L, Vinas M, Bonmati A (2016) Assessment of active methanogenic archaea in a methanol-fed upflow anaerobic sludge blanket reactor. Appl Microbiol Biotechnol 100:10137–10146Google Scholar
  17. Chai B, Wang Q, Kulam-Syed-Mohideen AS et al (2006) The ribosomal database project-II: the RDP pipeline. In: ASM general meetingGoogle Scholar
  18. Chao A (1984) Nonparametric estimation of the number of classes in a population. Scand J Stat 11:265–270Google Scholar
  19. Chen HB, Chang S (2017) Impact of temperatures on microbial community structures of sewage sludge biological hydrolysis. Bioresour Technol 245:502–510Google Scholar
  20. Chen WJ, Dai XH, Cao DW et al (2016) Performance and microbial ecology of a nitritation sequencing batch reactor treating high-strength ammonia wastewater. Sci Rep 6:35693Google Scholar
  21. Cho K, Shin SG, Kim W et al (2017) Microbial community shifts in a farm-scale anaerobic digester treating swine waste: correlations between bacteria communities associated with hydrogenotrophic methanogens and environmental conditions. Sci Total Environ 601:167–176Google Scholar
  22. Clark K, Karsch-Mizrachi I, Lipman DJ et al (2016) GenBank. Nucleic Acids Res 44:D67–D72Google Scholar
  23. Cole JR, Wang Q, Fish JA et al (2014) Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 42:D633–D642Google Scholar
  24. Cui M-H, Cui D, Liang B et al (2016) Decolorization enhancement by optimizing azo dye loading rate in an anaerobic reactor. RSC Adv 6:49995–50001Google Scholar
  25. Cydzik-Kwiatkowska A, Zielinska M (2016) Bacterial communities in full-scale wastewater treatment systems. World J Microbiol Biotechnol 32:66Google Scholar
  26. Cydzik-Kwiatkowska A, Bernat K, Zielinska M et al (2017) Aerobic granular sludge for bisphenol A (BPA) removal from wastewater. Int Biodeterior Biodegrad 122:1–11Google Scholar
  27. Dai HL, Lu XW, Peng LH et al (2017) Enrichment culture of denitrifying phosphorus removal sludge and its microbial community analysis. Environ Technol 38:2800–2810Google Scholar
  28. Dai RB, Chen XG, Xiang XY et al (2018) Understanding azo dye anaerobic bio-decolorization with artificial redox mediator supplement: considering the methane production. Bioresour Technol 249:799–808Google Scholar
  29. Daims H, Taylor MW, Wagner M (2006) Wastewater treatment: a model system for microbial ecology. Trends Biotechnol 24:483–489Google Scholar
  30. Delforno TP, Lacerda GV, Sierra-Garcia IN et al (2017a) Metagenomic analysis of the microbiome in three different bioreactor configurations applied to commercial laundry wastewater treatment. Sci Total Environ 587:389–398Google Scholar
  31. Delforno TP, Noronha GVLMF, Sakamoto IK et al (2017b) Microbial diversity of a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment: integration of 16S rRNA gene amplicon and shotgun metagenomic sequencing. Microbiol Open 6:e443Google Scholar
  32. Dennehy C, Lawlor PG, Gardiner GE et al (2017) Process stability and microbial community composition in pig manure and food waste anaerobic co-digesters operated at low HRTs. Front Environ Sci Eng 11:4Google Scholar
  33. DeSantis TZ, Hugenholtz P, Larsen N et al (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72:5069–5072Google Scholar
  34. Dhillon A, Lever M, Lloyd KG et al (2005) Methanogen diversity evidenced by molecular characterization of methyl coenzyme M reductase A (mcrA) genes in hydrothermal sediments of the Guaymas Basin. Appl Environ Microbiol 71:4592–4601Google Scholar
  35. Dong B, Tan J, Yang Y et al (2016a) Linking nitrification characteristic and microbial community structures in integrated fixed film activated sludge reactor by high-throughput sequencing. Water Sci Technol 74:354–1364Google Scholar
  36. Dong H, Dong H, Zhang Z et al (2016b) Microbial community dynamics in an anaerobic biofilm reactor treating heavy oil refinery wastewater. RSC Adv 6:107442–107451Google Scholar
  37. dos Furtado AL, Casper P (2000) Different methods for extracting bacteria from freshwater sediment and a simple method to measure bacterial production in sediment samples. J Microbiol Methods 41:249–257Google Scholar
  38. Dosta J, Vila J, Sancho I et al (2015) Two-step partial nitritation/Anammox process in granulation reactors: start-up operation and microbial characterization. J Environ Manag 164:196–205Google Scholar
  39. Dray S, Dufour AB (2007) The ade4 package: implementing the duality diagram for ecologists. J Stat Softw 22:1–20. CrossRefGoogle Scholar
  40. Du R, Peng YZ, Cao SB et al (2016) Mechanisms and microbial structure of partial denitrification with high nitrite accumulation. Appl Microbiol Biotechnol 100:2011–2021Google Scholar
  41. Du R, Cao SB, Li BK et al (2017a) Performance and microbial community analysis of a novel DEAMOX based on partial-denitrification and anammox treating ammonia and nitrate wastewaters. Water Res 108:46–56Google Scholar
  42. Du R, Cao SB, Li BK et al (2017b) Simultaneous domestic wastewater and nitrate sewage treatment by DEnitrifying AMmonium OXidation (DEAMOX) in sequencing batch reactor. Chemosphere 174:399–407Google Scholar
  43. Ducey TF, Hunt PG (2013) Microbial community analysis of swine wastewater anaerobic lagoons by next-generation DNA sequencing. Anaerobe 21:50–57Google Scholar
  44. Ecologist TM (2016) NGS field guide: overview. Accessed 31 Dec 2018
  45. Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10:996–998Google Scholar
  46. Edgar RC, Haas BJ, Clemente JC et al (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2195–2200Google Scholar
  47. Eduok S, Hendry C, Ferguson R et al (2015) Insights into the effect of mixed engineered nanoparticles on activated sludge performance. FEMS Microbiol Ecol 91:fiv082Google Scholar
  48. Efron B, Stein C (1981) The Jackknife estimate of variance. Ann Stat 9:586–596Google Scholar
  49. Etchebehere C, Castello E, Wenzel J et al (2016) Microbial communities from 20 different hydrogen-producing reactors studied by 454 pyrosequencing. Appl Microbiol Biotechnol 100:3371–3384Google Scholar
  50. Fan XY, Gao JF, Pan KL et al (2018) Shifts in bacterial community composition and abundance of nitrifiers during aerobic granulation in two nitrifying sequencing batch reactors. Bioresour Technol 251:99–107Google Scholar
  51. Fernandez N, Sierra-Alvarez R, Field JA et al (2008) Microbial community dinamics in a chemolitotrophic denitrification reactor inoculated with methanogenic granular sludge. Chemosphere 70:462–474Google Scholar
  52. FitzGerald JA, Allen E, Wall DM et al (2015) Methanosarcina play an important role in anaerobic co-digestion of the seaweed Ulva lactuca: taxonomy and predicted metabolism of functional microbial communities. PLoS ONE 10:e0142603Google Scholar
  53. Gao P, Xu WL, Sontag P et al (2016) Correlating microbial community compositions with environmental factors in activated sludge from four full-scale municipal wastewater treatment plants in Shanghai, China. Appl Microbiol Biotechnol 100:4663–4673Google Scholar
  54. Gomes BC, Adorno MAT, Okada DY et al (2014) Analysis of a microbial community associated with polychlorinated biphenyl degradation in anaerobic batch reactors. Biodegradation 25:797–810Google Scholar
  55. Gonzalez-Martinez A, Rodriguez-Sanchez A, Lotti T et al (2016) Comparison of bacterial communities of conventional and A-stage activated sludge systems. Sci Rep 6:18786Google Scholar
  56. Good IJ (1953) The population frequencies of species and the estimation of population parameters. Biometrika 40:237–264Google Scholar
  57. Guo F, Zhang T (2012) Profiling bulking and foaming bacteria in activated sludge by high throughput sequencing. Water Res 46:2772–2782Google Scholar
  58. Guo JH, Peng YZ, Ni BJ et al (2015) Dissecting microbial community structure and methane-producing pathways of a full-scale anaerobic reactor digesting activated sludge from wastewater treatment by metagenomic sequencing. Microb Cell Fact 14:33Google Scholar
  59. Guo Y, Zeng W, Li N, Peng YZ (2018) Effect of electron acceptor on community structures of denitrifying polyphosphate accumulating organisms in anaerobic-anoxic-oxic (A(2)O) process using DNA based stable-isotope probing (DNA-SIP). Chem Eng J 334:2039–2049Google Scholar
  60. Han XM, Wang ZW, Ma JX et al (2015) Membrane bioreactors fed with different COD/N ratio wastewater: impacts on microbial community, microbial products, and membrane fouling. Environ Sci Pollut Res 22:11436–11445Google Scholar
  61. Han G, Shin SG, Lee J et al (2017) A comparative study on the process efficiencies and microbial community structures of six full-scale wet and semi-dry anaerobic digesters treating food wastes. Bioresour Technol 245:869–875Google Scholar
  62. Hannon B (1973) The structure of ecosystems. J Theor Biol 41:535–546Google Scholar
  63. Harb M, Hong PY (2017) Molecular-based detection of potentially pathogenic bacteria in membrane bioreactor (MBR) systems treating municipal wastewater: a case study. Environ Sci Pollut Res 24:5370–5380Google Scholar
  64. Hartman AL, Riddle S, McPhillips T, Eisen BLJA (2010) Introducing WATERS: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences. BMC Bioinform 11:317Google Scholar
  65. Hill MO (1973) Diversity and evenness: a unifying notation and its consequences. Ecology 54:427–432Google Scholar
  66. Hjelmsø MH, Hellmer M et al (2017) Evaluation of methods for the concentration and extraction of viruses from sewage in the context of metagenomic sequencing. PLoS ONE. CrossRefGoogle Scholar
  67. Ibarbalz FM, Figuerola ELM, Erijman L (2013) Industrial activated sludge exhibit unique bacterial community composition at high taxonomic ranks. Water Res 47:3854–3864Google Scholar
  68. Ibarbalz FM, Orellana E, Figuerola ELM, Erijman L (2016) Shotgun metagenomic profiles have a high capacity to discriminate samples of activated sludge according to wastewater type. Appl Environ Microbiol 82:5186–5196Google Scholar
  69. Inaba T, Hori T, Aizawa H et al (2017) Architecture, component, and microbiome of biofilm involved in the fouling of membrane bioreactors. NPJ Biofilms Microbiomes 3:UNSP 5Google Scholar
  70. Isazadeh S, Jauffur S, Frigon D (2016) Bacterial community assembly in activated sludge: mapping beta diversity across environmental variables. MicrobiologyOpen 5:1050–1060Google Scholar
  71. Jabari L, Gannoun H, Khelifi E et al (2016) Bacterial ecology of abattoir wastewater treated by an anaerobic digestor. Braz J Microbiol 47:73–84Google Scholar
  72. Jang HM, Ha JH, Park JM et al (2015) Comprehensive microbial analysis of combined mesophilic anaerobic-thermophilic aerobic process treating high-strength food wastewater. Water Res 73:291–303Google Scholar
  73. Jang HM, Ha JH, Kim MS et al (2016) Effect of increased load of high-strength food wastewater in thermophilic and mesophilic anaerobic co-digestion of waste activated sludge on bacterial community structure. Water Res 99:140–148Google Scholar
  74. Jeong E, Im WT, Kim DH et al (2014) Different susceptibilities of bacterial community to silver nanoparticles in wastewater treatment systems. J Environ Sci Health Part A Toxic Hazard Subst Environ Eng 49:685–693Google Scholar
  75. Jiang XT, Guo F, Zhang T (2016) Population dynamics of bulking and foaming bacteria in a full-scale wastewater treatment plant over five years. Sci Rep 6:24180Google Scholar
  76. Jiang Y, Wei L, Yang K et al (2017) Rapid formation of aniline-degrading aerobic granular sludge and investigation of its microbial community succession. J Clean Prod 166:1235–1243Google Scholar
  77. Jost L (2006) Entropy and diversity. Oikos 113:363–375Google Scholar
  78. Ju F, Xia Y, Guo F et al (2014) Taxonomic relatedness shapes bacterial assembly in activated sludge of globally distributed wastewater treatment plants. Environ Microbiol 16:2421–2432Google Scholar
  79. Jünemann S, Kleinbölting N, Jaenicke S et al (2017) Bioinformatics for NGS-based metagenomics and the application to biogas research. J Biotechnol 261:10–23. CrossRefGoogle Scholar
  80. Keating C, Chin JP, Hughes D et al (2016) Biological phosphorus removal during high-rate, low-temperature, anaerobic digestion of wastewater. Front Microbiol 7:226Google Scholar
  81. Kembel SW, Wu M, Eisen JA, Green JL (2012) Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS ONE 8:e1002743Google Scholar
  82. Kim TS, Kim HS, Kwon S, Park HD (2011) Nitrifying bacterial community structure of a full-scale integrated fixed-film activated sludge process as investigated by pyrosequencing. J Microbiol Biotechnol 21:293–298Google Scholar
  83. Kim S, Bae J, Choi O et al (2014) A pilot scale two-stage anaerobic digester treating (FWL): performance and microbial structure analysis using pyrosequencing. Process Biochem 49:301–308Google Scholar
  84. Kim D-H, Lee M-K, Hwang Y et al (2016) Microbial granulation for lactic acid production. Biotechnol Bioeng 113:101–111Google Scholar
  85. Kindt R, Coe R (2005) Tree diversity analysis. A manual and software for common statistical methods for ecological and biodiversity studies. World Agroforestry Centre (ICRAF), Nairobi (Kenya)Google Scholar
  86. Krober M, Bekel T, Diaz NN et al (2009) Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. J Biotechnol 142:38–49Google Scholar
  87. Kumar S, Carlsen T, Mevik B-H et al (2011) CLOTU: an online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation. BMC Bioinform 12:182. CrossRefGoogle Scholar
  88. Lemarchand K, Berthiaume F, Maynard C et al (2005) Optimization of microbial DNA extraction and purification from raw wastewater samples for downstream pathogen detection by microarrays. J Microbiol Methods 63:115–126. CrossRefGoogle Scholar
  89. Lettinga G (2014) My anaerobic sustainability story. Lettinga Foundation, Hardinxveld-GiessendamGoogle Scholar
  90. Li JB, Rui JP, Pei ZJ et al (2014) Straw- and slurry-associated prokaryotic communities differ during co-fermentation of straw and swine manure. Appl Microbiol Biotechnol 98:4771–4780Google Scholar
  91. Li C, Zhang Z, Li Y, Cao JS (2015a) Study on dyeing wastewater treatment at high temperature by MBBR and the thermotolerant mechanism based on its microbial analysis. Process Biochem 50:1934–1941Google Scholar
  92. Li JB, Rui JP, Yao MJ et al (2015b) Substrate type and free ammonia determine bacterial community structure in full-scale mesophilic anaerobic digesters treating cattle or swine manure. Front Microbiol 6:1337Google Scholar
  93. Li YF, Nelson MC, Chen PH et al (2015c) Comparison of the microbial communities in solid-state anaerobic digestion (SS-AD) reactors operated at mesophilic and thermophilic temperatures. Appl Microbiol Biotechnol 99:969–980Google Scholar
  94. Li DP, Li B, Wang QR et al (2016a) Toxicity of TiO2 nanoparticle to denitrifying strain CFY1 and the impact on microbial community structures in activated sludge. Chemosphere 144:1334–1341Google Scholar
  95. Li L, He Q, Ma Y et al (2016b) A mesophilic anaerobic digester for treating food waste: process stability and microbial community analysis using pyrosequencing. Microb Cell Factories 15:65Google Scholar
  96. Li P, Wang YJ, Zuo JE et al (2017a) Nitrogen removal and N2O accumulation during hydrogenotrophic denitrification: influence of environmental factors and microbial community characteristics. Environ Sci Technol 51:870–879Google Scholar
  97. Li RR, Duan N, Zhang YH et al (2017b) Anaerobic co-digestion of chicken manure and microalgae Chlorella sp.: methane potential, microbial diversity and synergistic impact evaluation. Waste Manag 68:120–127Google Scholar
  98. Liao RH, Li Y, Yu XM et al (2014) Performance and microbial diversity of an expanded granular sludge bed reactor for high sulfate and nitrate waste brine treatment. J Environ Sci 26:717–725Google Scholar
  99. Lim S, Kim S, Yeon KM et al (2012) Correlation between microbial community structure and biofouling in a laboratory scale membrane bioreactor with synthetic wastewater. Desalination 287:209–215Google Scholar
  100. Liu Z, Lozupone C, Hamady M et al (2007) Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res 35:e120. CrossRefGoogle Scholar
  101. Liu CS, Zhao CC, Wang AJ et al (2015a) Denitrifying sulfide removal process on high-salinity wastewaters. Appl Microbiol Biotechnol 99:6463–6469Google Scholar
  102. Liu Z, Dang Y, Li C, Sun DZ (2015b) Inhibitory effect of high NH4 + -N concentration on anaerobic biotreatment of fresh leachate from a municipal solid waste incineration plant. Waste Manag 43:188–195Google Scholar
  103. Liu ZY, Yu SL, Heedeung P et al (2016) Impact of titanium dioxide nanoparticles on the bacterial communities of biological activated carbon filter intended for drinking water treatment. Environ Sci Pollut Res 23:15574–15583Google Scholar
  104. Liu T, Mao YJ, Shi YP, Quan X (2017) Start-up and bacterial community compositions of partial nitrification in moving bed biofilm reactor. Appl Microbiol Biotechnol 101:2563–2574Google Scholar
  105. Liu Y, Huang L, Dong G et al (2018) Enhanced granulation and methane recovery at low load by downflow sludge circulation in anaerobic treatment of domestic wastewater. Bioresour Technol 249:851–857Google Scholar
  106. Louca S, Doebeli M, Parfrey LW (2018) Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem. Microbiome 6:41Google Scholar
  107. Lu Q, Yi J, Yang DH (2016) Comparative analysis of performance and microbial characteristics between high-solid and low-solid anaerobic digestion of sewage sludge under mesophilic conditions. J Microbiol Biotechnol 26:110–119Google Scholar
  108. Lucas R, Kuchenbuch A, Fetzer I et al (2015) Long-term monitoring reveals stable and remarkably similar microbial communities in parallel full-scale biogas reactors digesting energy crops. FEMS Microbiol Ecol 91:fiv004Google Scholar
  109. Lv XM, Shao MF, Li CL et al (2014) A comparative study of the bacterial community in denitrifying and traditional enhanced biological phosphorus removal processes. Microbes Environ 29:261–268Google Scholar
  110. Ma JX, Wang ZW, Yang Y et al (2013) Correlating microbial community structure and composition with aeration intensity in submerged membrane bioreactors by 454 high-throughput pyrosequencing. Water Res 47:859–869Google Scholar
  111. Ma JX, Wang ZW, Zang LL et al (2015a) Occurrence and fate of potential pathogenic bacteria as revealed by pyrosequencing in a full-scale membrane bioreactor treating restaurant wastewater. RSC Adv 5:24469–24478Google Scholar
  112. Ma K-L, Li X-K, Wang K et al (2015b) 454-Pyrosequencing reveals microbial community structure and composition in a mesophilic UAFB system treating PTA wastewater. Curr Microbiol 71:551–558Google Scholar
  113. Mao YP, Wang ZP, Li LG et al (2016) Exploring the shift in structure and function of microbial communities performing biological phosphorus removal. PLoS ONE 11:e0161506Google Scholar
  114. Matheson CD, Gurney C, Esau N, Lehto R (2010) Assessing PCR inhibition from humic substances. Open Enzyme Inhib J 3:38–45Google Scholar
  115. Motteran F, Braga JK, Silva EL, Varesche MBA (2017) Kinetics of methane production and biodegradation of linear alkylbenzene sulfonate from laundry wastewater anaerobic batch reactors. J Environ Sci Health Part A Toxic Hazard Subst Environ Eng 51:1288–1302Google Scholar
  116. Nair HP, Vincent H, Bhat SG (2014) Evaluation of five in situ lysis protocols for PCR amenable metagenomic DNA from mangrove soils. Biotechnol Rep 4:134–138Google Scholar
  117. Nilakanta H, Drews KL, Firrell S et al (2014) A review of software for analyzing molecular sequences. BMC Res Notes 7:830Google Scholar
  118. Niu LH, Zhang X, Li Y et al (2017) Elevational characteristics of the archaeal community in full-scale activated sludge wastewater treatment plants at a 3660-m elevational scale. Water Sci Technol 76:531–541Google Scholar
  119. Nyvad B, Crielaard W, Mira A et al (2013) Dental caries from a molecular microbiological perspective. Caries Res 47:89–102Google Scholar
  120. Okada DY, Delforno TP, Etchebehere C, Varesche MBA (2014) Evaluation of the microbial community of upflow anaerobic sludge blanket reactors used for the removal and degradation of linear alkylbenzene sulfonate by pyrosequencing. Int Biodeterioration Biodegrad 96:63–70Google Scholar
  121. Oksanen J, Blanchet FG, Friendly M et al (2018) vegan: community ecology package.
  122. Orellana E, Davies-Sala C, Guerrero L, Vardé I, Altina M, Lorenzo MC, Figuerola EL, Pontiggia RM, Erijman L (2019) Microbiome network analysis of co-occurrence patterns in anaerobic co-digestion of sewage sludge and food waste. Water Sci Technol 79:1956–1965Google Scholar
  123. Ouyang E, Lu Y, Ouyang J, Wang L, Wang X (2017) Bacterial community analysis of anoxic/aeration (A/O) system in a combined process for gibberellin wastewater treatment. PLoS ONE. CrossRefGoogle Scholar
  124. Pan F, Zhong XH, Xia DS et al (2017) Nanoscale zero-valent iron/persulfate enhanced upflow anaerobic sludge blanket reactor for dye removal: insight into microbial metabolism and microbial community. Sci Rep 7:44626Google Scholar
  125. Pan KL, Gao JF, Li HY et al (2018) Ammonia-oxidizing bacteria dominate ammonia oxidation in a full-scale wastewater treatment plant revealed by DNA-based stable isotope probing. Bioresour Technol 256:152–159Google Scholar
  126. Peng XX, Guo F, Ju F, Zhang T (2015) Shifts in the microbial community, nitrifiers and denitrifiers in the biofilm in a full-scale rotating biological contactor. Environ Sci Technol 48:8044–8052Google Scholar
  127. Persson F, Suarez C, Hermansson M et al (2017) Community structure of partial nitritation-anammox biofilms at decreasing substrate concentrations and low temperature. Microb Biotechnol 10:761–772Google Scholar
  128. Quast C, Pruesse E, Yilmaz P et al (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590–D596Google Scholar
  129. Quince C, Lanzén A, Curtis TP et al (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 6:639–641Google Scholar
  130. Quintela-Baluja M, Abouelnaga M, Romalde J, Su JQ, Yu Y, Gomez-Lopez M, Smets B, Zhu YG, Graham DW (2019) Spatial ecology of a wastewater network defines the antibiotic resistance genes in downstream receiving waters. Water Res 162:347–357Google Scholar
  131. Rademacher A, Zakrzewski M, Schlüter A et al (2012) Characterization of microbial biofilms in a thermophilic biogas system by high-throughput metagenome sequencing. FEMS Microbiol Ecol 79:785–799Google Scholar
  132. Ramette A (2007) Multivariate analyses in microbial ecology. FEMS Microbiol Ecol 62:142–160. CrossRefGoogle Scholar
  133. Ramirez-Vargas R, Serrano-Silva N, Navarro-Noya YE et al (2015) 454 pyrosequencing-based characterization of the bacterial consortia in a well established nitrifying reactor. Water Sci Technol 72:990–997Google Scholar
  134. Ranasinghe PD, Satoh H, Oshiki M et al (2012) Revealing microbial community structures in large- and small-scale activated sludge systems by barcoded pyrosequencing of 16S rRNA gene. Water Sci Technol 66:2155–2161Google Scholar
  135. Rasool K, Mahmoud KA, Lee DS (2015) Influence of co-substrate on textile wastewater treatment and microbial community changes in the anaerobic biological sulfate reduction process. J Hazard Mater 299:453–461Google Scholar
  136. Reeder J, Knight R (2010) Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distribution. Nat Methods 7:668–669Google Scholar
  137. Rodríguez N, Sanz JL (1998) Response of an anaerobic granular sludge to chlorinated aliphatic hydrocarbons in different conditions. J Ferment Bioeng 86:226–232Google Scholar
  138. Rodríguez E, García-Encina P, Stams AJM et al (2015) Meta-omics approaches to understand and improve wastewater treatment systems. Rev Environ Sci Biotechnol 14:385–406Google Scholar
  139. Sanz JL, Köchling T (2007) Molecular biology techniques used in wastewater treatment: an overview. Process Biochem 42:119–133Google Scholar
  140. Saunders AM, Albertsen M, Vollertsen J, Nielsen PH (2016) The activated sludge ecosystem contains a core community of abundant organisms. ISME J 10:11–20Google Scholar
  141. Schloss PD, Westcott SL, Ryabin T et al (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541Google Scholar
  142. Schlüter A, Bekel T, Diaz NN et al (2008) The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology. J Biotechnol 136:77–90Google Scholar
  143. Shan L, Zhang Z, Yu Y et al (2017) Performance of CSTR-EGSB-SBR system for treating sulfate-rich cellulosic ethanol wastewater and microbial community analysis. Environ Sci Pollut Res 24:14387–14395Google Scholar
  144. Shannon CE (1948) A mathematical theory of communication. Bell Syst Tech J 27:379–423. CrossRefGoogle Scholar
  145. Shokralla S, Spall JL, Gibson JF, Hajibabaei M (2012) Next-generation sequencing technologies for environmental DNA research. Mol Ecol 21:1794–1805Google Scholar
  146. Simpson EH (1949) Measurement of diversity. Nature 163:688Google Scholar
  147. Sivagurunathan P, Anburajan P, Kumar G et al (2016) High-rate hydrogen production from galactose in an upflow anaerobic sludge blanket reactor (UASBr). RSC Adv 6:59823–59833Google Scholar
  148. Smith AM, Sharma D, Lappin-Scott H et al (2014) Microbial community structure of a pilot-scale thermophilic anaerobic digester treating poultry litter. Appl Microbiol Biotechnol 98:2321–2334Google Scholar
  149. Su C, Lu Y, Qin J et al (2017) Performance and microbial community structure characterization of a CIC anaerobic reactor for the treatment of cassava wastewater. Ecol Eng 108:114–122Google Scholar
  150. Sun HH, Yu P, Li QL et al (2017) Transformation of anaerobic granules into aerobic granules and the succession of bacterial community. Appl Microbiol Biotechnol 101:7703–7713Google Scholar
  151. Sundberg C, Al-Soud WA, Larsson M et al (2013) 454 pyrosequencing analyses of bacterial and archaeal richness in 21 full-scale biogas digesters. FEMS Microbiol Ecol 85:612–626Google Scholar
  152. Szabo E, Liebana R, Hermansson M et al (2017) Comparison of the bacterial community composition in the granular and the suspended phase of sequencing batch reactors. AMB Express 7:168Google Scholar
  153. Team RDC (2008) R: a language and environment for statistical computing. R Foundation for Statistical Computing, ViennaGoogle Scholar
  154. Tian HL, Zhao JY, Zhang HY et al (2015a) Bacterial community shift along with the changes in operational conditions in a membrane-aerated biofilm reactor. Appl Microbiol Biotechnol 99:3279–3290Google Scholar
  155. Tian M, Zhao FQ, Shen X et al (2015b) The first metagenome of activated sludge from full-scale anaerobic/anoxic/oxic (A2O) nitrogen and phosphorus removal reactor using Illumina sequencing. J Environ Sci 35:181–190Google Scholar
  156. Torres K, Alvarez-Hornos FJ, San-Valero P et al (2018) Granulation and microbial community dynamics in the chitosan-supplemented anaerobic treatment of wastewater polluted with organic solvents. Water Res 130:376–387Google Scholar
  157. Tuan NN, Chang YC, Yu CP, Huang SL (2014) Multiple approaches to characterize the microbial community in a thermophilic anaerobic digester running on swine manure: a case study. Microbiol Res 169:717–724Google Scholar
  158. Vetrovsky T, Baldrian P (2013) The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS ONE 8:e57923Google Scholar
  159. Vrieze JD, Pinto AJ, Sloan WT, Ijaz UZ (2018) The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool. Microbiome 6:63Google Scholar
  160. Walden C, Carbonero F, Zhang W (2017) Assessing impacts of DNA extraction methods on next generation sequencing of water and wastewater samples. J Microbiol Methods 141:10–16Google Scholar
  161. Wang XH, Hu M, Xia Y et al (2012) Pyrosequencing analysis of bacterial diversity in 14 wastewater treatment systems in China. Appl Microbiol Biotechnol 78:7042–7047Google Scholar
  162. Wang HY, He QL, Chen D et al (2015) Microbial community in a hydrogenotrophic denitrification reactor based on pyrosequencing. Appl Microbiol Biotechnol 99:10829–10837Google Scholar
  163. Wang JF, Qian FY, Liu XP et al (2016a) Cultivation and characteristics of partial nitrification granular sludge in a sequencing batch reactor inoculated with heterotrophic granules. Appl Microbiol Biotechnol 100:9381–9391Google Scholar
  164. Wang P, Yu ZS, Qi R, Zhang HX (2016b) Detailed comparison of bacterial communities during seasonal sludge bulking in a municipal wastewater treatment plant. Water Res 105:157–166Google Scholar
  165. Wang ST, Wang WQ, Zhang ZR, You H (2016c) The impact of zinc oxide nanoparticles on phosphorus removal and the microbial community in activated sludge in an SBR. RSC Adv 6:96706–96713Google Scholar
  166. Wang XC, Shen JM, Chen ZL et al (2016d) Removal of pharmaceuticals from synthetic wastewater in an aerobic granular sludge membrane bioreactor and determination of the bioreactor microbial diversity. Appl Microbiol Biotechnol 100:8213–8223Google Scholar
  167. Wang S, Li ZW, Gao MC et al (2017a) Long-term effects of cupric oxide nanoparticles (CuO NPs) on the performance, microbial community and enzymatic activity of activated sludge in a sequencing batch reactor. J Environ Manag 187:330–339Google Scholar
  168. Wang S, Li ZW, Gao MC et al (2017b) Long-term effects of nickel oxide nanoparticles on performance, microbial enzymatic activity, and microbial community of a sequencing batch reactor. Chemosphere 169:387–395Google Scholar
  169. Wen X, Gong BZ, Zhou J et al (2017) Efficient simultaneous partial nitrification, anammox and denitrification (SNAD) system equipped with a real-time dissolved oxygen (DO) intelligent control system and microbial community shifts of different substrate concentrations. Water Res 119:201–211Google Scholar
  170. Westerholm M, Crauwels S, Geel MV et al (2016) Microwave and ultrasound pre-treatments influence microbial community structure and digester performance in anaerobic digestion of waste activated sludge. Appl Microbiol Biotechnol 100:5339–5352Google Scholar
  171. Wolters B, Ding GC, Kreuzig R, Smalla K (2016) Full-scale mesophilic biogas plants using manure as C-source: bacterial community shifts along the process cause changes in the abundance of resistance genes and mobile genetic elements. FEMS Microbiol Ecol 92:fiv163Google Scholar
  172. Wu SJ, Dang Y, Qiu B et al (2015) Effective treatment of fermentation wastewater containing high concentration of sulfate by two-stage expanded granular sludge bed reactors. Int Biodeteriation Biodegrad 104:15–20Google Scholar
  173. Xiao X, Li TT, Lu XR et al (2018) A simple method for assaying anaerobic biodegradation of dyes. Bioresour Technol 251:204–209Google Scholar
  174. Xue Y, Zhao H, Ge L et al (2015) Comparison of the performance of waste leachate treatment in submerged and recirculated membrane bioreactors. Int Biodeteriation Biodegrad 102:73–80Google Scholar
  175. Yang Y, Quensen J, Mathieu J et al (2014a) Pyrosequencing reveals higher impact of silver nanoparticles than Ag + on the microbial community structure of activated sludge. Water Res 48:317–325Google Scholar
  176. Yang Y, Yu K, Xia Y et al (2014b) Metagenomic analysis of sludge from full-scale anaerobic digesters operated in municipal wastewater treatment plants. Appl Microbiol Biotechnol 98:5709–5718Google Scholar
  177. Yang B, Xu H, Wang J et al (2017) Bacterial and archaeal community distribution and stabilization of anaerobic sludge in a strengthen circulation anaerobic (SCA) reactor for municipal wastewater treatment. Bioresour Technol 244:750–758Google Scholar
  178. Yang B, Wang M, Wang JF et al (2018) Mechanism of high contaminant removal performance in the expanded granular sludge blanket (EGSB) reactor involved with granular activated carbon for low-strength wastewater treatment. Chem Eng J 334:1176–1185Google Scholar
  179. Ye L, Zhang T (2011) Pathogenic bacteria in sewage treatment plants as revealed by 454 Pyrosequencing. Environ Sci Technol 45:7173–7179Google Scholar
  180. Ye L, Zhang T (2013) Bacterial communities in different sections of a municipal wastewater treatment plant revealed by 16S rDNA 454 pyrosequencing. Appl Microbiol Biotechnol 97:2681–2690Google Scholar
  181. Yeates C, Gillings MR (1998) Rapid purification of DNA from soil for molecular biodiversity analysis. Lett Appl Microbiol 27:49–53Google Scholar
  182. Yeates C, Gillings MR, Davison AD et al (1997) PCR amplification of crude microbial DNA extracted from soil. Lett Appl Microbiol 25:303–307Google Scholar
  183. Yi J, Dong B, Jin JW, Dai XH (2014) Effect of increasing total solids contents on anaerobic digestion of food waste under mesophilic conditions: performance and microbial characteristics analysis. PLoS ONE 9:e102548Google Scholar
  184. Yu HG, Wang QY, Wang ZW et al (2014) Start-up of an anaerobic dynamic membrane digester for waste activated sludge digestion: temporal variations in microbial communities. PLoS ONE 9:e93710Google Scholar
  185. Yu B, Zhang DL, Shan AD et al (2015) Methane-rich biogas production from waste-activated sludge with the addition of ferric chloride under a thermophilic anaerobic digestion system. RSC Adv 5:38538–38546Google Scholar
  186. Yu D, Li C, Wang L et al (2016a) Multiple effects of trace elements on methanogenesis in a two-phase anaerobic membrane bioreactor treating starch wastewater. Appl Microbiol Biotechnol 100:6631–6642Google Scholar
  187. Yu HG, Wang ZW, Zhu ZCWNCW (2016b) Enhanced waste activated sludge digestion using a submerged anaerobic dynamic membrane bioreactor: performance, sludge characteristics and microbial community. Sci Rep 6:20111Google Scholar
  188. Zeng Q, Hao TW, Mackey HR et al (2017) Alkaline textile wastewater biotreatment: a sulfate-reducing granular sludge based lab-scale study. J Hazard Mater 332:104–111Google Scholar
  189. Zhang T, Ye L, Tong AHY et al (2011) Ammonia-oxidizing archaea and ammonia-oxidizing bacteria in six full-scale wastewater treatment bioreactors. Appl Microbiol Biotechnol 91:1215–1225Google Scholar
  190. Zhang T, Shao MF, Ye L (2012) 454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants. ISME J 6:1137–1147Google Scholar
  191. Zhang Y, Hu M, Li P et al (2015a) Analysis of trichloroethylene removal and bacterial community function based on pH-adjusted in an upflow anaerobic sludge blanket reactor. Appl Microbiol Biotechnol 99:9289–9297Google Scholar
  192. Zhang Y, Hu M, Li P et al (2015b) Trichloroethylene removal and bacterial variations in the up-flow anaerobic sludge blanket reactor in response to temperature shifts. Appl Microbiol Biotechnol 99:6091–6102Google Scholar
  193. Zhang Y, Wang X, Hu M, Li P (2015c) Effect of hydraulic retention time (HRT) on the biodegradation of trichloroethylene wastewater and anaerobic bacterial community in the UASB reactor. Appl Microbiol Biotechnol 99:1977–1987Google Scholar
  194. Zhang BY, Zhao HY, Yu HR et al (2016a) Evaluation of biogas production performance and Archaeal microbial dynamics of corn straw during anaerobic co-digestion with cattle manure liquid. J Microbiol Biotechnol 26:739–747Google Scholar
  195. Zhang Y, Zhen Y, Mi T et al (2016b) Molecular characterization of sulfate-reducing bacteria community in surface sediments from the adjacent area of Changjiang Estuary. J Ocean Univ China 15:107–116Google Scholar
  196. Zhang JX, Loh KC, Lee J et al (2017) Three-stage anaerobic co-digestion of food waste and horse manure. Sci Rep 7:1269Google Scholar
  197. Zhao JW, Gui L, Wang QL et al (2017) Aged refuse enhances anaerobic digestion of waste activated sludge. Water Res 123:724–733Google Scholar
  198. Zhou J, Yang J, Yu Q et al (2017a) Different organic loading rates on the biogas production during the anaerobic digestion of rice straw: a pilot study. Bioresour Technol 244:865–871Google Scholar
  199. Zhou WL, Li Y, Liu X et al (2017b) Comparison of microbial communities in different sulfur-based autotrophic denitrification reactors. Appl Microbiol Biotechnol 101:447–453Google Scholar
  200. Zhu S, Wu H, Zhou L, Wei C (2017a) The resilience of microbial community involved in coking wastewater treatment system. J Next Gener Seq Appl 4:1000142Google Scholar
  201. Zhu XY, Kougias PG, Treu L et al (2017b) Microbial community changes in methanogenic granules during the transition from mesophilic to thermophilic conditions. Appl Microbiol Biotechnol 101:1313–1322Google Scholar
  202. Ziganshin AM, Liebetrau J, Proter J, Kleinsteuber S (2013) Microbial community structure and dynamics during anaerobic digestion of various agricultural waste materials. Appl Microbiol Biotechnol 97:5161–5174Google Scholar
  203. Ziganshin AM, Ziganshina EE, Kleinsteuber S, Nikolausz M (2016) Comparative analysis of methanogenic communities in different laboratory-scale anaerobic digesters. Archaea 2016:3401272Google Scholar

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© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Molecular Biology DepartmentAutonoma University of MadridMadridSpain

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