UCC Library and UCC researchers have made this item openly available. Please let us know how this has helped you. Thanks! Title Microbial ecology of intermittently aerated sequencing batch reactors (IASBRs) for the treatment of dairy processing wastewaters Author(s) Gil Pulido, Beatriz Publication date 2019 Original citation Gil Pulido, B. 2019. Microbial ecology of intermittently aerated sequencing batch reactors (IASBRs) for the treatment of dairy processing wastewaters. PhD Thesis, University College Cork. Type of publication Doctoral thesis Rights © 2019, Beatriz Gil Pulido. http://creativecommons.org/licenses/by-nc-nd/3.0/ Embargo information Not applicable Item downloaded http://hdl.handle.net/10468/9585 from Downloaded on 2021-10-07T21:30:12Z Ollscoil na hÉireann, Corcaigh National University of Ireland, Cork Microbial ecology of Intermittently Aerated Sequencing Batch Reactors (IASBRs) for the treatment of dairy processing wastewaters Thesis presented by Beatriz Gil Pulido for the degree of Doctor of Philosophy University College Cork School of Microbiology Head of the School: Professor Gerald F. Fitzgerald Supervisors: Dr. Niall O’Leary, Prof. Alan D.W. Dobson July 2019 Contents Declaration of independence ...................................................................... 6 Acknowledgments ....................................................................................... 7 Abstract ...................................................................................................... 11 Dairy industry processing wastewaters: Biological treatments for nitrogen and phosphorus removal. .......................................................... 15 1.1 Overview of the global dairy industry .............................................. 16 1.2 The Dairy processing sector in Ireland ........................................... 20 1.3 Environmental impact of the dairy processing industry. Water consumption ............................................................................................. 21 1.4 Dairy processing wastewater .......................................................... 24 1.4.1 Composition of dairy effluents ...................................................... 27 1.4.2 Effluent emissions and discharge limits ........................................ 31 1.5 Treatment of dairy processing wastewaters .................................... 35 1.6 Biological nutrient removal processes............................................. 41 1.6.1 Biological nitrogen removal .......................................................... 43 1.6.2 Enhanced Biological Phosphorus removal (EBPR) ...................... 46 1.7 Intermittently Aerated Sequencing Batch Reactor (IASBR) technology ................................................................................................ 51 1.8 Approaches for the study of microbial diversity in wastewater treatment systems .................................................................................... 54 1.9 References ..................................................................................... 57 Evaluation of dairy processing wastewater biotreatment in an IASBR system: aeration rate impacts on performance and microbial ecology 80 Abstract ................................................................................................... 81 2.1 Introduction .......................................................................................... 81 2.2 Material and methods .......................................................................... 84 2.2.1 Dairy synthetic wastewater ........................................................... 84 2 2.2.2 Laboratory- scale IASBR system set up and operation ................ 84 2.2.3 Physicochemical profile of the IASBR .......................................... 86 2.2.4 Biomass collection and metagenomic DNA extraction ................. 87 2.2.5 Pyrosequencing and processing of 16S rRNA sequence data ..... 88 2.2.6 Predictive functional metabolic modelling ..................................... 89 2.2.7 Sequence data accession number ............................................... 89 2.3 Results .................................................................................................. 90 2.3.1 Nutrient removal performance in the IASBR ................................. 90 2.3.2 System community richness ......................................................... 91 2.3.3 Microbial ecology profiling of the bioreactor ................................. 91 2.3.4 Functional potential of the microbial communities ........................ 94 2.4 Discussion ............................................................................................ 98 2.4.1 Impact of the aeration rates in nutrient removal performance ...... 98 2.4.2 IASBR microbial community profiling ............................................ 99 2.4.3 Predictive metagenomic profiling of the IASBR microbial community metabolome ......................................................................................... 100 2.5 Conclusions ....................................................................................... 101 2.6 References .......................................................................................... 102 Microbial ecology of IASBR laboratory systems treating synthetic and industrial dairy processing wastewaters: Impact of influent characteristics on community dynamics and Comamonadaceae dominance. ............................................................................................... 110 Abstract .................................................................................................... 111 3.1 Introduction ........................................................................................ 112 3.2 Material and methods ........................................................................ 115 3.2.1 Bioreactor set-up, operation and influent wastewater ................. 115 3.2.2 Wastewater analyses ................................................................. 118 3.2.3 Sample collection, DNA extraction and pyrosequencing ............ 118 3.2.4 Sequence data analysis and taxonomy assignment ................... 119 3.2.5 Taxonomy graphs and heat maps .............................................. 120 3.2.6 Biostatistical analyses ................................................................ 120 3.2.8 Prediction of functional metagenome in the biological samples . 121 3 3.3 Results and discussion ..................................................................... 122 3.3.1 Overall performance of the bioreactors ...................................... 122 3.3.2 Cluster analysis of initial biomass and IASBRs samples ............ 123 3.3.3 α-Diversity indices and similarity of bioreactors samples ........... 124 3.3.4 Microbial ecology structure of the initial biomass and the IASBRs samples ............................................................................................... 124 3.3.5 Linkage of bacterial community structure and operational parameters .......................................................................................... 134 3.3.6 Functional gene prediction involved in nitrogen and phosphorus removal................................................................................................ 137 3.4 Conclusions ....................................................................................... 139 3.5 References .......................................................................................... 140 Bacterial community composition and nutrient remediation of a pilot- scale IASBR treating dairy wastewater .................................................. 154 Abstract .................................................................................................... 155 4.1 Introduction ........................................................................................ 156 4.2 Material and Methods ........................................................................ 160 4.2.1 Pilot-scale operation, analytical methods and sampling ............. 160 4.2.2 Metagenomic DNA extraction and sequencing ........................... 162 4.2.3 Bioinformatics pipeline and taxonomy assignment ..................... 163 4.2.4. Statistical analyses .................................................................... 164 4.3 Results and discussion ..................................................................... 165 4.3.1 Nutrient removal efficiency of the IASBR pilot-scale unit ............ 165 4.3.2 Overall bacterial community composition ................................... 167 4.3.3 Analysis of similarity and bacterial correlations with influent characteristics ..................................................................................... 172 4.4 Conclusions ....................................................................................... 177 4.5 References .......................................................................................... 178 Final conclussions .................................................................................. 190 5.1 General discussion ......................................................................... 191 5.1 Concluding remarks ....................................................................... 196 4 Additional work ........................................................................................ 200 Appendix 1...............................................................................................