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Enrichment of denitratating bacteria from a methylotrophic denitrifying culture

  • Environmental biotechnology
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Abstract

Denitratation (nitrite produced from nitrate), has the potential applications in wastewater treatment by combining with ANAMMOX process. The occurrence of denitratation has been shown to be effected qualitatively by various parameters in the environment. A more quantitative understanding can be obtained using enrichment cultures in lab-scale experiments, yet information on the enrichment of functional microorganisms responsible for denitratation is lacking. In this study, a stable denitratation-dominated culture was obtained from methylotrophic denitrifying culture. The results showed that, besides the substitution of acetate for methanol, the lasting starvation following saturation of electron donor was another pivotal selection pressure that favored the growth of denitratating bacteria, which was supported by the distinctive physiological strategy involving the higher growth rate combining with larger poly-hydroxybutyrate (PHB) accumulation at sufficient electron donor situation and then manage the stress of electron donor starvation by consumpiton of the PHB. High-throughput 16S rRNA gene sequencing analysis indicated that non-methylotrophic Halomonas campisalis (48.1 %) and Halomonas campaniensis (30.4 %) dominated in the denitratating community. Moreover the denitratation was driven by the nitrate inhibiting the nirS transcription in the Halomonas species.

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References

  • Ahn YH (2006) Sustainable nitrogen elimination biotechnologies: a review. Process Biochem 41:1709–1721

    Article  CAS  Google Scholar 

  • Anderson AJ, Dawes EA (1990) Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates. Microbiol Rev 54:450–472

    CAS  PubMed  PubMed Central  Google Scholar 

  • Anthony C (2011) How half a century of research was required to understand bacterial growth on C1 and C2 compounds; the story of the serine cycle and the ethylmalonyl-CoA pathway. Sci Prog 94(Pt 2):109–137

    Article  CAS  PubMed  Google Scholar 

  • APHA (2005) Standard methods for the examination of water and wastewater, 21st edn. American Public Health Association, Washington

    Google Scholar 

  • Baytshtok V, Lu H, Park H, Kim S, Yu R, Chandran K (2009) Impact of varying electron donors on the molecular microbial ecology and biokinetics of methylotrophic denitrifying bacteria. Biotechnol Bioeng 102:1527–1536

    Article  CAS  PubMed  Google Scholar 

  • Brandes JA, Devol AH, Deutsch C (2007) New developments in the marine nitrogen cycle. Chem Rev 107:577–589

    Article  CAS  PubMed  Google Scholar 

  • Cao SB, Wang SY, Peng YZ, Wu CC, Du R, Gong LX, Ma B (2013) Achieving partial denitrification with sludge fermentation liquid as carbon source: the effect of seeding sludge. Bioresour Technol 149:570–574

    Article  CAS  PubMed  Google Scholar 

  • Cao SB, Li BK, Du R, Ren NQ, Peng YZ (2016) Nitrite production in a partial denitrifying upflow sludge bed (USB) reactor equipped with gas automatic recirculation (GAC). Wat Res 90:309–316

    Article  CAS  Google Scholar 

  • Drysdale G, Kasan H, Bux F (2001) Assessment of denitrification by the ordinary heterotrophic organisms in anNDBEPR activated sludge sytem. Water Sci Technol 43:147–154

    CAS  PubMed  Google Scholar 

  • Du R, Peng YZ, Cao SB, Wang SY, Wu CC (2015) Advanced nitrogen removal from wastewater by combining anammox with partial denitrification. Bioresour Technol 179:497–504

    Article  CAS  PubMed  Google Scholar 

  • Gerber, M., Span, R (2008) An analysis of available mathematical models for anaerobic digestion of organic substances for production of biogas. In: Proc. IGRC: Paris

  • Gong LX, Huo MX, Yang Q, Li J, Ma B, Zhu RL, Wang SY, Peng YZ (2013) Performance of heterotrophic partial denitrification under feast-famine condition of electron donor: a case study using acetate as external carbon source. Bioresour Technol 133:263–269

    Article  CAS  PubMed  Google Scholar 

  • Grady CPLJ, Daigger GT, Lim HC (1999) Biological wastewater treatment. Marcel Dekker, New York

    Google Scholar 

  • Granger J, Ward BB (2003) Accumulation of nitrogen oxides in copper-limited cultures of denitrifying bacteria. Limnol & Oceanogr 48:313–318

    Article  CAS  Google Scholar 

  • Hallin S, Lindgren PE (1999) PCR detection of genes encodingnitrite reductase in denitrifying bacteria. Appl Environ Microbiol 65:1652–1657

    CAS  PubMed  PubMed Central  Google Scholar 

  • Haroon MF, Hu SH, Shi Y, Imelfort M, Keller J, Hugenholtz P, Yuan ZG, Tyson GW (2013) Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature 500:567–570

    Article  CAS  PubMed  Google Scholar 

  • He JZ, Shen JP, Zhang LM, Zhu YG, Zheng YM, Xu MG, Di HJ (2007) Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environ Microbiol 9:2364–2374

    Article  CAS  PubMed  Google Scholar 

  • Jiang YM, Chen YG, Zheng X (2009) Efficient Polyhydroxyalkanoates production from a waste-activated sludge alkaline fermentation liquid by activated sludge submitted to the aerobic feeding and discharge process. Environ. Sci. Technol. 43:7734–7741

    Article  CAS  PubMed  Google Scholar 

  • Kalyuzhnyi S, Gladchenko M, Kang H, Mulder A, Versprille A (2008) Development and optimisation of VFA driven DEAMOX process for treatment of strong nitrogenous anaerobic effluents. Water Sci Technol 57:323–328

    Article  CAS  PubMed  Google Scholar 

  • Kartal B, Kuypers MMM, Lavik G, Schalk J, den Camp HJMO, Jetten MSM, Strous M (2007) Anammox bacteria disguised as denitrifiers: nitrate reduction to dinitrogen gas via nitrite and ammonium. Environ Microbiol 9:635–642

    Article  CAS  PubMed  Google Scholar 

  • Kawata Y, Jin YX, Nojiri M (2013) Efficient secretion of (R)-3-hydroxybutyric acid from Halomonas sp. KM-1 cultured with saccharified Japanese cedar under microaerobic conditions. Bioresour Technol 140:443–445

    Article  CAS  PubMed  Google Scholar 

  • Kraft B, Strous M, Tegetmeyer HE (2011) Microbial nitrate respiration - genes, enzymes and environmental distribution. J Biotechnol 155:104–117

    Article  CAS  PubMed  Google Scholar 

  • Kraft B, Tegetmeyer HE, Sharma R, Klotz MG, Ferdelman TG, Hettich RL, Geelhoed JS, Strous M (2014) The environmental controls that govern the end product of bacterial nitrate respiration. Science 345:676–679

    Article  CAS  PubMed  Google Scholar 

  • Lai CY, Yang XE, Tang YN, Rittmann BE, Zhao HP (2014) Nitrate shaped the Selenate-reducing microbial Community in a Hydrogen-Based Biofilm Reactor. Environ. Sci. Technol. 48:3395–3402

    Article  CAS  PubMed  Google Scholar 

  • Lai CY, Wen LL, Zhang Y, Luo SS, Wang QY, Luo YH, Chen R, Yang XE, Rittmann BE, Zhao HP (2016) Autotrophic antimonate bio-reduction using hydrogen as the electron donor. Water Res 88:467–474

    Article  CAS  PubMed  Google Scholar 

  • Lane DJ, Weisburg WG, Barns SM (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703

    Article  PubMed  PubMed Central  Google Scholar 

  • Lee SY (1996) Bacterial polyhydroxyalkanoates. Biotechnol Bioeng 49:1–14

    Article  CAS  PubMed  Google Scholar 

  • Li W, Zheng P, Wang L, Zhang M, Lu H, Xing YJ, Zhang JQ, Wang R, Song J, Ghulam A (2013) Physical characteristics and formation mechanism of denitrifying granular sludge in high-load reactor. Bioresour Technol 142:683–687

    Article  CAS  PubMed  Google Scholar 

  • Li W, Zheng P, Guo J, Ji JY, Zhang M, Zhang ZH, Zhan EC, Abbas G (2014) Characteristics of self-alkalization in high-rate denitrifying automatic circulation (DAC) reactor fed with methanol and sodium acetate. Bioresour Technol 154:44–50

    Article  CAS  PubMed  Google Scholar 

  • Li W, Shan XY, Wang ZY, Lin XY, Li CX, Cai CY, Abbas G, Zhang M, Shen LD, Hu ZQ, Zhao HP, Zheng P (2016) Effect of self-alkalization on nitrite accumulation in a high-rate denitrification system: performance, microflora and enzymatic activities. Water Res 88:758–765

    Article  CAS  PubMed  Google Scholar 

  • Liu BB, Mao YJ, Bergaust L, Bakken LR, Frostegard A (2013) Strains in the genus Thauera exhibit remarkably different denitrification regulatory phenotypes. Environ Microbiol 15:2816–2828

    CAS  PubMed  Google Scholar 

  • Louzeiro NR, Mavinic DS, Oldham WK, Meisen A, Gardner IS (2003) Process control and design considerations for methanol-induced denitrification in a sequencing batch reactor. Environ Technol 24(2):161–169

    Article  CAS  PubMed  Google Scholar 

  • Lu HJ, Chandran K (2010) Diagnosis and quantification of glycerol assimilating denitrifying bacteria in an integrated fixed-film activated sludge reactor via 13C DNA stable-isotope probing. Environ Sci Technol 44:8943–8949

    Article  CAS  PubMed  Google Scholar 

  • Lu HJ, Chandran K, Stensel D (2014) Microbial ecology of denitrification in biological wastewater treatment. Water Res 64:237–254

    Article  CAS  PubMed  Google Scholar 

  • Mata JA, Martinez-Canovas J, Quesada E, Bejar V (2002) A detailed phenotypic characterisation of the type strains of Halomonas species. Syst & Appl Microbiol 25:360–375

    Article  CAS  Google Scholar 

  • McCarty, P.L., Beck, L., Amant, P.S (1969) Biological denitrification of wastewater by addition of organic materials. Proceeding of the 24th Industrial Waste Conference. Purdue University, Lafayette, IN

  • Michotey V, Méjean V, Bonin P (2000) Comparison of methodsfor quantification of cytochrome cd1-denitrifying bacteria inenvironmental marine samples. Appl Environ Microbiol 66:1564–1571

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700

    CAS  PubMed  PubMed Central  Google Scholar 

  • Peyton BM, Mormile MR, Petersen JN (2001) Nitrate reduction with Halomonas campisalis: kinetics of dentrification at pH 9 AND 12.5 % NaCl. Water Res 35:4237–4242

    Article  CAS  PubMed  Google Scholar 

  • Quan ZX, Rhee SK, Zuo JE, Yang Y, Bae JW, Park JR, Lee ST, Park YH (2008) Diversity of ammonium-oxidizing bacteria in a granular sludge anaerobic ammonium-oxidizing (anammox) reactor. Environ Microbiol 10:3130–3139

    Article  CAS  PubMed  Google Scholar 

  • Quillaguamán J, Delgado O, Mattiasson B, Hatti-Kaul R (2006) Poly (beta-hydroxybutyrate) production by a moderate halophile, Halomonas boliviensis LC1. Enzyme & Microb Tech 38:148–154

    Article  CAS  Google Scholar 

  • Quillaguamán J, Doan-Van T, Guzmán H, Guzmán D, Martín J, Akaraonye E, Hatti-Kaul R (2008) Poly(3-hydroxybutyrate) production by Halomonas boliviensis in fed-batch culture. Appl Microbiol Biotechnol 78:227–232

    Article  CAS  PubMed  Google Scholar 

  • Rivera-Terceros P, Tito-Claros E, Torrico S, Carballo S, Doan VT, Quillaguaman J (2015) Production of poly(3-hydroxybutyrate) by Halomonas boliviensis in an air-lift reactor. J Biol Res 22:1–9

    Google Scholar 

  • Schmittgen TD, Livak KJ (2008) Analyzing real-time PCR data by the comparative CT method. Nat Protoc 3:1101–1108

    Article  CAS  PubMed  Google Scholar 

  • Strohm TO, Griffin B, Zumft WG, Schink B (2007) Growth yields in bacterial denitrification and nitrate ammonification. Appl Environ Microbiol 73:1420–1424

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sumino T, Isaka K, Ikuta H, Saiki Y, Yokota T (2006) Nitrogen removal from wastewater using simultaneous nitrate reduction and anaerobic ammonium oxidation in single reactor. J Biosci Bioeng 102:346–351

    Article  CAS  PubMed  Google Scholar 

  • Tan D, Xue YS, Aibaidula G, Chen GQ (2011) Unsterile and continuous production of polyhydroxybutyrate by Halomonas TD01. Bioresour Technol 102:8130–8136

    Article  CAS  PubMed  Google Scholar 

  • Tang CJ, Zheng P, Wang CH, Mahmood Q (2010) Suppression of anaerobic ammonium oxidizers under high organic content in high-rate Anammox UASB reactor. Bioresour Technol 101:1762–1768

    Article  CAS  PubMed  Google Scholar 

  • Thamdrup B, Dalsgaard T (2002) Production of N2 through anaerobic ammonium oxidation coupled to nitrate reduction in marine sediments. Appl Environ Microbiol 68:1312–1318

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Throbäck IN, Enwall K, Jarvis A, Hallin S (2004) Reassessing PCR primers targeting nirS, nirK and nosZ genes for communitysurveys of denitrifying bacteria with DGGE. FEMS Microbiol Ecol 49:401–417

    Article  CAS  PubMed  Google Scholar 

  • van den Berg EM, van Dongen U, Abbas B, van Loosdrecht MCM (2015) Enrichment of DNRA bacteria in a continuous culture. ISME J 9:2153–2161

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • van der Star WRL, Miclea AI, van Dongen UGJM, Muyzer G, Picioreanu C, van Loosdrecht MCM (2008) The membrane bioreactor: a novel tool to grow anammox bacteria as free cells. Biotechnol Bioeng 101:286–294

    Article  CAS  PubMed  Google Scholar 

  • van Rijn J, Tal Y, Barak Y (1996) Influence of volatile fatty acids on nitrite accumulation by a pseudomonas stutzeri strain isolated from a denitrifying fluidized bed reactor. Appl Environ Microbiol 62:2615–2620

    PubMed  PubMed Central  Google Scholar 

  • Waki M, Yasuda T, Fukumoto Y, Kuroda K, Suzuki K (2013) Effect of electron donors on anammox coupling with nitrate reduction for removing nitrogen from nitrate and ammonium. Bioresour Technol 130:592–598

    Article  CAS  PubMed  Google Scholar 

  • Wuchter CB, Abbas MJL, Coolen L, Herfort J, van Bleijswijk P, Timmers M, Strous E, Teira GJ, Herndl JJ, Middelburg S, Schouten JS, Damste S (2006) Archaeal nitrification in the ocean. PNAS 103:12317–12322

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu B, Enfors SO (1996) Modeling of nitrite accumulation by the denitrifying bacterium pseudomonas stutzeri. J Ferment Bioeng 82:56–60

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This research was supported by the National Science and Technology Support Program (2013BAD21B04). the Key Science and Technology Innovation Team Grant of Zhejiang (2013TD12), Shanghai Tongji Gao Tingyao Environmental Science and Technology Development Foundation, Zhejiang College Students’ Science and Technology Innovation Program.

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Correspondence to Ping Zheng.

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The authors declare that they have no conflict of interest. This article does not contain any studies with human participants or animals performed by any of the authors. Informed consent was obtained from all individual participants included in the study.

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Li, W., Lin, XY., Chen, JJ. et al. Enrichment of denitratating bacteria from a methylotrophic denitrifying culture. Appl Microbiol Biotechnol 100, 10203–10213 (2016). https://doi.org/10.1007/s00253-016-7859-z

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  • DOI: https://doi.org/10.1007/s00253-016-7859-z

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