Metagenomic insights into functional traits variation and coupling effects on the anammox community during reactor start-up

Adav, 2009, Proteolytic activity in stored aerobic granular sludge and structural integrity, Bioresour. Technol., 100, 68, 10.1016/j.biortech.2008.05.045 APHA. A, 1999 Barreto, 2005, Identification of a gene cluster for the formation of extracellular polysaccharide precursors in the chemolithoautotroph Acidithiobacillus ferrooxidans, Appl. Environ. Microbiol., 71, 2902, 10.1128/AEM.71.6.2902-2909.2005 Bastian, 2009 Bhattacharjee, 2017, Whole-community metagenomics in two different anammox configurations: process performance and community structure, Environ. Sci. Technol., 51, 4317, 10.1021/acs.est.6b05855 Boleij, 2018, Identification of glycoproteins isolated from extracellular polymeric substances of full-scale anammox granular sludge, Environ. Sci. Technol., 52, 13127, 10.1021/acs.est.8b03180 Chen, 2016, Successful start-up of the anammox process: influence of the seeding strategy on performance and granule properties, Bioresour. Technol., 211, 594, 10.1016/j.biortech.2016.03.139 Ciesielski, 2018, The metagenomic approach to characterization of the microbial community shift during the long-term cultivation of anammox-enriched granular sludge, J. Appl. Genet., 59, 109, 10.1007/s13353-017-0418-1 Ding, 2018, Anaerobic ammonium oxidation (Anammox) with planktonic cells in a redox-stable semicontinuous stirred-tank reactor, Environ. Sci. Technol., 52, 5671, 10.1021/acs.est.7b05979 Feng, 2011, Variations of both bacterial community and extracellular polymers: the inducements of increase of cell hydrophobicity from biofloc to aerobic granule sludge, Bioresour. Technol., 102, 6421, 10.1016/j.biortech.2011.03.046 Feng, 2018, Microbial transcript and metabolome analysis uncover discrepant metabolic pathways in autotrophic and mixotrophic anammox consortia, Water Res., 128, 402, 10.1016/j.watres.2017.10.069 Ferreira, 2010, Distribution of cepacian biosynthesis genes among environmental and clinical Burkholderia strains and role of cepacian exopolysaccharide in resistance to stress conditions, Appl. Environ. Microbiol., 76, 441, 10.1128/AEM.01828-09 Gao, 2011, Aerobic granular sludge: characterization, mechanism of granulation and application to wastewater treatment, Crit. Rev. Biotechnol., 31, 137, 10.3109/07388551.2010.497961 Ge, 2015, Detection of nitrifiers and evaluation of partial nitrification for wastewater treatment: a review, Chemosphere, 140, 85, 10.1016/j.chemosphere.2015.02.004 Gonzalez-Gil, 2015, Microbial community composition and ultrastructure of granules from a full-scale anammox reactor, Microb. Ecol., 70, 118, 10.1007/s00248-014-0546-7 Gonzalez-Martinez, 2016, Performance and bacterial community dynamics of a CANON bioreactor acclimated from high to low operational temperatures, Chem. Eng. J., 287, 557, 10.1016/j.cej.2015.11.081 Gonzalez-Silva, 2017, Changes in the microbial community of an anammox consortium during adaptation to marine conditions revealed by 454 pyrosequencing, Appl. Microbiol. Biotechnol., 101, 5149, 10.1007/s00253-017-8160-5 Graaf, 1996, Autotrophic growth of anaerobic ammonium-oxidizing micro-organisms in a fluidized bed reactor, Microbiology, 142, 2187, 10.1099/13500872-142-8-2187 Gulhane, 2017, Study of microbial community plasticity for anaerobic digestion of vegetable waste in Anaerobic Baffled Reactor, Renew. Energy, 101, 59, 10.1016/j.renene.2016.08.021 Guo, 2016, Metagenomic analysis of anammox communities in three different microbial aggregates, Environ. Microbiol., 18, 2979, 10.1111/1462-2920.13132 Guo, 2018, A metabolomic view of how low nitrogen strength favors anammox biomass yield and nitrogen removal capability, Water Res., 143, 387, 10.1016/j.watres.2018.06.052 Hou, 2015, Role of extracellular polymeric substance in determining the high aggregation ability ofanammox sludge, Water Res., 75, 51, 10.1016/j.watres.2015.02.031 Huson, 2011, Integrative analysis of environmental sequences using MEGAN4, Genome Res., 21, 1552, 10.1101/gr.120618.111 Jia, 2017, Stratification of extracellular polymeric substances (EPS) for aggregated anammox microorganisms, Environ. Sci. Technol., 51, 3260, 10.1021/acs.est.6b05761 Jin, 2012, The inhibition of the anammox process: a review, Chem. Eng. J., 197, 67, 10.1016/j.cej.2012.05.014 Jin, 2017, Transient disturbance of engineered ZnO nanoparticles enhances the resistance and resilience of anammox process in wastewater treatment, Sci. Total Environ., 622–623, 402 Joshi Ju, 2015, Bacterial assembly and temporal dynamics in activated sludge of a full-scale municipal wastewater treatment plant, ISME J., 9, 683, 10.1038/ismej.2014.162 Kearns, 2018, Trait-based patterns of microbial dynamics in dormancy potential and heterotrophic strategy: case studies of resource-based and post-press succession, ISME J., 12, 2575, 10.1038/s41396-018-0194-x Kowalski, 2018, Start-up and long-term performance of anammox moving bed biofilm reactor seeded with granular biomass, Chemosphere, 200, 481, 10.1016/j.chemosphere.2018.02.130 Krause, 2017, Lanthanide-dependent cross-feeding of methane-derived carbon is linked by microbial community interactions, Proc. Natl. Acad. Sci., 114, 358, 10.1073/pnas.1619871114 Lawson, 2017, Metabolic network analysis reveals microbial community interactions in anammox granules, Nat. Commun., 8, 10.1038/ncomms15416 Lee, 2013, Microalgae-associated bacteria play a key role in the flocculation of Chlorella vulgaris, Bioresour. Technol., 131, 195, 10.1016/j.biortech.2012.11.130 Li, 2017, Mainstream up flow nitritation-anammox system with hybrid anaerobic pretreatment: long-term performance and microbial community dynamics, Water Res., 125, 298, 10.1016/j.watres.2017.08.048 Lieder, 2016, Environmental stress speeds up DNA replication in Pseudomonas putida in chemostat cultivations, Biotechnol. J., 11, 155, 10.1002/biot.201500059 López, 2008, Start-up and enrichment of a granular anammox SBR to treat high nitrogen load wastewaters, J. Chem. Technol. Biotechnol., 83, 233, 10.1002/jctb.1796 Ma, 2016, Biological nitrogen removal from sewage via anammox: recent advances, Bioresour. Technol., 200, 981, 10.1016/j.biortech.2015.10.074 Ma, 2017, Achieving mainstream nitrogen removal through coupling anammox with denitratation, Environ. Sci. Technol., 51, 8405, 10.1021/acs.est.7b01866 Metch, 2018, Metagenomic analysis of microbial communities yields insight into impacts of nanoparticle design, Nat. Nanotechnol., 13, 253, 10.1038/s41565-017-0029-3 Moss, 2018, Ladderane phospholipids form a densely packed membrane with normal hydrazine and anomalously low proton/hydroxide permeability, Proc. Natl. Acad. Sci., 115, 9098, 10.1073/pnas.1810706115 Newman, 2006, Modularity and community structure in networks, Proc. Natl. Acad. Sci. U. S. A., 103, 8577, 10.1073/pnas.0601602103 Nobu, 2015, Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor, ISME J., 9, 1710, 10.1038/ismej.2014.256 Ortiz-Álvarez, 2018, Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession, ISME J., 12, 1658, 10.1038/s41396-018-0076-2 Penttinen, 2016, Divergent genes in potential inoculant Sinorhizobium strains are related to DNA replication, recombination, and repair, J. Basic Microbiol., 56, 680, 10.1002/jobm.201500592 Rasigraf, 2014, Autotrophic carbon dioxide fixation via the Calvin-Benson-Bassham cycle by the denitrifying methanotroph “Candidatus Methylomirabilis oxyfera”, Appl. Environ. Microbiol., 80, 2451, 10.1128/AEM.04199-13 Reino, 2018, Stable long-term operation of an upflow anammox sludge bed reactor at mainstream conditions, Water Res., 128, 331, 10.1016/j.watres.2017.10.058 Rolfe, 2012, Lag phase is a distinct growth phase that prepares bacteria for exponential growth and involves transient metal accumulation, J. Bacteriol., 194, 686, 10.1128/JB.06112-11 Salter, 2014, Reagent contamination can critically impact sequence-based microbiome analyses, bioRxiv, 12, 87 Sekiguchi, 2003, Anaerolinea thermophila gen. nov., sp. nov. and Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain bacteria at the subphylum level, Int. J. Syst. Evol. Microbiol., 53, 1843, 10.1099/ijs.0.02699-0 Silva, 2017, Regulator LdhR and D-lactate dehydrogenase LdhA of Burkholderia multivorans play roles in carbon overflow and in planktonic cellular aggregate formation, Appl. Environ. Microbiol., 83, 10.1128/AEM.01343-17 Sonthiphand, 2014, Biogeography of anaerobic ammonia-oxidizing (anammox) bacteria, Front. Microbiol., 5, 399, 10.3389/fmicb.2014.00399 Speth, 2016, Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system, Nat. Commun., 7, 11172, 10.1038/ncomms11172 Strous, 1998, The sequencing batch reactor as a powerful tool for the study of slowly growing anaerobic ammonium-oxidizing microorganisms, Appl. Microbiol. Biotechnol., 50, 589, 10.1007/s002530051340 Tang, 2009, Start-up and inhibition analysis of the Anammox process seeded with anaerobic granular sludge, J. Ind. Microbiol. Biotechnol., 36, 1093, 10.1007/s10295-009-0593-0 Tang, 2018, Metabolomics uncovers the regulatory pathway of acyl-homoserine lactones-based quorum sensing in anammox consortia, Environ. Sci. Technol., 52, 2206, 10.1021/acs.est.7b05699 Ummalyma, 2017, Bioflocculation: an alternative strategy for harvesting of microalgae-an overview, Bioresour. Technol., 242, 227, 10.1016/j.biortech.2017.02.097 Vander Heiden, 2009, Understanding the Warburg effect: the metabolic requirements of cell proliferation, Science, 324, 1029, 10.1126/science.1160809 Xia, 2015, Phylogeny-structured carbohydrate metabolism across microbiomes collected from different units in wastewater treatment process, Biotechnol. Biofuels, 8, 172, 10.1186/s13068-015-0348-2 Xie, 2011, KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases, Nucleic Acids Res., 39, 316, 10.1093/nar/gkr483 Xie, 2018, Achieving high-level nitrogen removal in mainstream by coupling anammox with denitrifying anaerobic methane oxidation in a membrane biofilm reactor, Water Res., 131, 196, 10.1016/j.watres.2017.12.037 Xing, 2016, Influence of preservation temperature on the characteristics of anaerobic ammonium oxidation (anammox) granular sludge, Appl. Microbiol. Biotechnol., 100, 4637, 10.1007/s00253-016-7292-3 Xu, 2019, The revolution of performance, sludge characteristics and microbial community of anammox biogranules under long-term NiO NPs exposure, Sci. Total Environ., 649, 440, 10.1016/j.scitotenv.2018.08.386 Yang, 2011, High-rate nitrogen removal by the Anammox process at ambient temperature, Bioresour. Technol., 102, 672, 10.1016/j.biortech.2010.08.039 Yang, 2013, The evolution of Anammox performance and granular sludge characteristics under the stress of phenol, Bioresour. Technol., 137, 332, 10.1016/j.biortech.2013.03.145 Yang, 2013, Exploring variation of antibiotic resistance genes in activatedSludge over a four-year period through a metagenomic approach, Environ. Sci. Technol., 47, 10197, 10.1021/es4017365 Zhang, 2019, Long-term effects of N-acyl-homoserine lactone-based quorum sensing on the characteristics of ANAMMOX granules in high-loaded reactors, Chemosphere, 218, 632, 10.1016/j.chemosphere.2018.11.170 Zhao, 2014, Pyrosequencing analysis of bacterial community and assembly in activated sludge samples from different geographic regions in China, Appl. Microbiol. Biotechnol., 98, 9119, 10.1007/s00253-014-5920-3 Zhao, 2018, Insight into the aggregation capacity of anammox consortia during reactor start-up, Environ. Sci. Technol., 52, 3685, 10.1021/acs.est.7b06553 Zhu, 2014, Anaerobic ammonium oxidation in polyvinyl alcohol and sodium alginate immobilized biomass system: a potential tool to maintain anammox biomass in application, Water Sci. Technol., 69, 718, 10.2166/wst.2013.762 Zhu, 2018, Anammox granular sludge in low-ammonium sewage treatment: not bigger size driving better performance, Water Res., 142, 147, 10.1016/j.watres.2018.05.048