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Heterotrophic Denitrification and Paracoccus spp. as Tools for Bioremediation

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Microbial Models: From Environmental to Industrial Sustainability

Part of the book series: Microorganisms for Sustainability ((MICRO,volume 1))

Abstract

Denitrifiers comprise a metabolically diverse group of microbes used as a resource for environmental engineering, due to their ability to perform anaerobic respiration. The main use of denitrification in environmental sustainability is the removal of nitrate and nitrite in water treatment plants.

Heterotrophic denitrifiers are those that use organic molecules as C sources, including pollutants, a trait that makes them as a potential tool for many bioremediation processes. A notorious advantage of denitrifiers over other microorganisms is that they are able to degrade pollutants in anaerobic environments, which extend their potential usefulness.

In this chapter, recent advances regarding the use of heterotrophic denitrifiers in environmental sustainability will be discussed. We end the chapter discussing the singularities of denitrifying strains of the genus Paracoccus and their potentiality in environmental sustainability.

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References

  • Bai Y, Sun Q, Zhao C et al (2008) Microbial degradation and metabolic pathway of pyridine by a Paracoccus sp. strain BW001. Biodegradation 19:915–926

    Article  CAS  PubMed  Google Scholar 

  • Bell LC, Richardson DJ, Ferguson SJ (1990) Periplasmic and membrane-bound respiratory nitrate reductases in Thiosphaera pantotropha: the periplasmic enzyme catalyzes the first step in aerobic denitrification. FEBS Lett 265:85–87

    Article  CAS  PubMed  Google Scholar 

  • Blackburne R, Yuan Z, Keller J (2008) Demonstration of nitrogen removal via nitrite in a sequencing batch reactor treating domestic wastewater. Water Res 42:2166–2176

    Article  CAS  PubMed  Google Scholar 

  • Borden AK, Brusseau ML, Carroll KC et al (2012) Ethanol addition for enhancing denitrification at the uranium mill tailing site in Monument Valley, AZ. Water Air Soil Pollut 223:755–763

    Article  CAS  Google Scholar 

  • Burt TP, Matchett LS, Goulding KWT et al (1999) Denitrification in riparian buffer zones: the role of floodplain hydrology. Hydrol Process 13:1451–1463

    Article  Google Scholar 

  • Cai S, Li X, Cai T et al (2013) Degradation of piperazine by Paracoccus sp. TOH isolated from activated sludge. Bioresour Technol 130:536–542

    Article  CAS  PubMed  Google Scholar 

  • Calderer M, Gibert O, Martí V et al (2010) Denitrification in presence of acetate and glucose for bioremediation of nitrate-contaminated groundwater. Environ Technol 31:799–814

    Article  CAS  PubMed  Google Scholar 

  • Carroll KC, Jordan FL, Glenn EP et al (2009) Comparison of nitrate attenuation characterization methods at the Uranium mill tailing site in Monument Valley, Arizona. J Hydrol 378:72–81

    Article  CAS  Google Scholar 

  • Courtens ENP, Vlaeminck SE, Vilchez-Vargas R et al (2014) Trade-off between mesophilic and thermophilic denitrification: rates vs. sludge production, settleability and stability. Water Res 63:234–244

    Article  CAS  PubMed  Google Scholar 

  • da Silva MLB, Corseuil HX (2012) Groundwater microbial analysis to assess enhanced BTEX biodegradation by nitrate injection at a gasohol-contaminated site. Int Biodeterior Biodegrad 67:21–27

    Article  CAS  Google Scholar 

  • de la Rúa A, González-López J, Gómez Nieto MA (2008) Influence of temperature on inoculation and startup of a groundwater-denitrifying submerged filter. Environ Eng Sci 25:265–274

    Article  CAS  Google Scholar 

  • Durant ND, Wilson LP, Bouwer EJ (1995) Microcosm studies of subsurface PAH-degrading bacteria from a former manufactured gas plant. J Contam Hydrol 17:213–237

    Article  CAS  Google Scholar 

  • Edwards NT (1983) Polycyclic aromatic hydrocarbons (PAH’s) in the terrestrial environment—a review. J Environ Qual 12:427–441

    Article  CAS  Google Scholar 

  • European Commission. The nitrates directive. http://ec.europa.eu/environment/water/water-nitrates/index_en.html

    Google Scholar 

  • Geng Y, Deng Y, Chen F et al (2015) Biodegradation of isopropanol by a solvent-tolerant Paracoccus denitrificans strain. Prep Biochem Biotechnol 45:491–499

    Article  CAS  PubMed  Google Scholar 

  • Gibert O, Pomierny S, Rowe I et al (2008) Selection of organic substrates as potential reactive materials for use in a denitrification permeable reactive barrier (PRB). Bioresour Technol 99:7587–7596

    Article  CAS  PubMed  Google Scholar 

  • Gómez MA, González-López J, Hontoria-García E (2000) Influence of carbon source on nitrate removal of contaminated groundwater in a denitrifying submerged filter. J Hazard Mater 80:69–80

    Article  PubMed  Google Scholar 

  • Graf DRH, Jones CM, Hallin S (2014) Intergenomic comparisons highlight modularity of the denitrification pathway and underpin the importance of community structure for N2O emissions. PLoS One 9

    Google Scholar 

  • Greenan CM, Moorman TB, Kaspar TC et al (2006) Comparing carbon substrates for denitrification of subsurface drainage water. J Environ Qual 35:824–829

    Article  CAS  PubMed  Google Scholar 

  • Guo CL, Zhou HW, Wong YS et al (2005) Isolation of PAH-degrading bacteria from mangrove sediments and their biodegradation potential. Mar Pollut Bull 51:1054–1061

    Article  CAS  PubMed  Google Scholar 

  • Guo J, Peng Y, Huang H et al (2010) Short- and long-term effects of temperature on partial nitrification in a sequencing batch reactor treating domestic wastewater. J Hazard Mater 179:471–479

    Article  CAS  PubMed  Google Scholar 

  • Habe H, Omori T (2003) Genetics of polycyclic aromatic hydrocarbon metabolism in diverse aerobic bacteria. Biosci Biotechnol Biochem 67:225–243

    Article  CAS  PubMed  Google Scholar 

  • Hasinger M, Scherr KE, Lundaa T et al (2012) Changes in iso- and n-alkane distribution during biodegradation of crude oil under nitrate and sulphate reducing conditions. J Biotechnol 157:490–498

    Article  CAS  PubMed  Google Scholar 

  • He Z, Wang J, Zhang X et al (2015) Nitrogen removal from wastewater by anaerobic methane-driven denitrification in a lab-scale reactor: heterotrophic denitrifiers associated with denitrifying methanotrophs. Appl Microbiol Biotechnol 99:10853–10860

    Article  CAS  PubMed  Google Scholar 

  • Hino T, Matsumoto Y, Nagano S et al (2010) Structural basis of biological N2O generation by bacterial nitric oxide reductase. Science 330:1666–1670

    Article  CAS  PubMed  Google Scholar 

  • Huang Y, Long X-E, Chapman SJ et al (2014) Acidophilic denitrifiers dominate the N2O production in a 100-year-old tea orchard soil. Environ Sci Pollut Res 22:4173–4182

    Article  CAS  Google Scholar 

  • Jia KZ, Cui ZL, He J et al (2006) Isolation and characterization of a denitrifying monocrotophos-degrading Paracoccus sp. M-1. FEMS Microbiol Lett 263:155–162

    Article  CAS  PubMed  Google Scholar 

  • Jones CM, Stres B, Rosenquist M et al (2008) Phylogenetic analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes reveal a complex evolutionary history for denitrification. Mol Biol Evol 25:1955–1966

    Article  CAS  PubMed  Google Scholar 

  • Jones CM, Spor A, Brennan FP et al (2014) Recently identified microbial guild mediates soil N2O sink capacity. Nat Clim Chang 4:801–805

    Article  CAS  Google Scholar 

  • Kao C-M, Borden RC (1997) Site specific variability in BTEX biodegradation under denitrifying conditions. Groundwater 35:305–311

    Article  CAS  Google Scholar 

  • Kelly DP, Rainey FA, Wood AP (2006) The genus Paracoccus. The Prokaryotes. Springer, New York, 2006, p 232–49

    Google Scholar 

  • Kim SG, Bae HS, Lee ST (2001) A novel denitrifying bacterial isolate that degrades trimethylamine both aerobically and anaerobically via two different pathways. Arch Microbiol 176:271–277

    Article  CAS  PubMed  Google Scholar 

  • Li K, Wang S, Shi Y et al (2011) Genome sequence of Paracoccus sp. strain TRP, a chlorpyrifos biodegrader. J Bacteriol 193:1786–1787

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lin YF, Jing SR, Wang TW et al (2002) Effects of macrophytes and external carbon sources on nitrate removal from groundwater in constructed wetlands. Environ Pollut 119:413–420

    Article  CAS  PubMed  Google Scholar 

  • Lofrano G, Brown J (2010) Wastewater management through the ages: a history of mankind. Sci Total Environ 408:5254–5264

    Article  CAS  PubMed  Google Scholar 

  • Long LM, Schipper LA, Bruesewitz DA (2011) Long-term nitrate removal in a denitrification wall. Agric Ecosyst Environ 140:514–520

    Article  CAS  Google Scholar 

  • Long A, Song B, Fridey K et al (2015) Detection and diversity of copper containing nitrite reductase genes (nirK) in prokaryotic and fungal communities of agricultural soils. FEMS Microbiol Ecol 91:1–9

    Article  PubMed  Google Scholar 

  • Ludwig W, Mittenhuber G, Friedrich CG (1993) Transfer of Thiosphaera pantotropha to Paracoccus denitrificans. Int J Syst Bacteriol 43:363–367

    Article  CAS  PubMed  Google Scholar 

  • Lyles C, Boopathy R, Fontenot Q et al (2008) Biological treatment of shrimp aquaculture wastewater using a sequencing batch reactor. Appl Biochem Biotechnol 151:474–479

    Article  CAS  PubMed  Google Scholar 

  • Martínez S, Cuervo-López FM, Gomez J (2007) Toluene mineralization by denitrification in an up flow anaerobic sludge blanket (UASB) reactor. Bioresour Technol 98:1717–1723

    Article  CAS  PubMed  Google Scholar 

  • Moreno B, Gómez MA, González-López J et al (2005) Inoculation of a submerged filter for biological denitrification of nitrate polluted groundwater: a comparative study. J Hazard Mater 117:141–147

    Article  CAS  PubMed  Google Scholar 

  • Neef A, Zaglauer A, Meier H et al (1996) Population analysis in a denitrifying sand filter: conventional and in situ identification of Paracoccus spp. in methanol-fed biofilms. Appl Environ Microbiol 62:4329–4339

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nielsen M, Schreiber L, Finster K et al (2015) Draft genome sequence of Bacillus azotoformans MEV2011, a (Co-) denitrifying strain unable to grow with oxygen. Stand Genomic Sci 10:23

    Article  PubMed  PubMed Central  Google Scholar 

  • Nisha KN, Devi V, Varalakshmi P et al (2015) Biodegradation and utilization of dimethylformamide by biofilm forming Paracoccus sp. strains MKU1 and MKU2. Bioresour Technol 188:9–13

    Article  CAS  PubMed  Google Scholar 

  • Offre P, Spang A, Schleper C (2013) Archaea in biogeochemical cycles. Annu Rev Microbiol 67:437–457

    Article  CAS  PubMed  Google Scholar 

  • Orellana LH, Rodriguez-R LM, Higgins S et al (2014) Detecting nitrous oxide reductase (nosZ) genes in soil metagenomes: method development and implications for the nitrogen cycle. MBio 5:e01193–14

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Palmer K, Drake HL, Horn MA (2010) Association of novel and highly diverse acid-tolerant denitrifiers with N2O fluxes of an acidic fen. Appl Environ Microbiol 76:1125–1134

    Article  CAS  PubMed  Google Scholar 

  • Philippot L (2002) Denitrifying genes in bacterial and Archaeal genomes. Biochim Biophys Acta 1577:355–376

    Article  CAS  PubMed  Google Scholar 

  • Powlson DS, Addiscott TM, Benjamin N et al (2008) When does nitrate become a risk for humans? J Environ Qual 37:291–295

    Article  CAS  PubMed  Google Scholar 

  • Qu D, Zhao Y, Sun J et al (2015) BTEX biodegradation and its nitrogen removal potential by a newly isolated Pseudomonas thivervalensis MAH1. Can J Microbiol 61:691–699

    Article  CAS  PubMed  Google Scholar 

  • Rivett MO, Buss SR, Morgan P et al (2008) Nitrate attenuation in groundwater: a review of biogeochemical controlling processes. Water Res 42:4215–4232

    Article  CAS  PubMed  Google Scholar 

  • Robertson LA, van Niel EW, Torremans RAM et al (1988) Simultaneous nitrification and denitrification in aerobic chemostat cultures of Thiosphaera pantotropha. Appl Environ Microbiol 54:2812–2818

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ruiz G, Jeison D, Rubilar O et al (2006) Nitrification-denitrification via nitrite accumulation for nitrogen removal from wastewaters. Bioresour Technol 97:330–335

    Article  CAS  PubMed  Google Scholar 

  • Sanford RA, Wagner DD, Wu Q et al (2012) Unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils. Proc Natl Acad Sci U S A 109:19709–19714

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Santal AR, Singh NP, Saharan BS (2016) A novel application of Paracoccus pantotrophus for the decolorization of melanoidins from distillery effluent under static conditions. J Environ Manage 169:78–83

    Article  CAS  PubMed  Google Scholar 

  • Santoshkumar M, Veeranagouda Y, Lee K et al (2011) Utilization of aliphatic nitrile by Paracoccus sp. SKG isolated from chemical waste samples. Int Biodeterior Biodegrad 65:153–159

    Article  CAS  Google Scholar 

  • Scherer MM, Richter S, Valentine RL et al (2000) Chemistry and microbiology of permeable reactive barriers for In situ groundwater clean up. Crit Rev Microbiol 26:221–264

    Article  CAS  PubMed  Google Scholar 

  • Schipper L, Vojvodić-Vuković M (1998) Nitrate removal from groundwater using a denitrification wall amended with sawdust: field trial. J Environ Qual 27:664–668

    Article  CAS  Google Scholar 

  • Schipper LA, Barkle GF, Hadfield JC et al (2004) Hydraulic constraints on the performance of a groundwater denitrification wall for nitrate removal from shallow groundwater. J Contam Hydrol 69:263–279

    Article  CAS  PubMed  Google Scholar 

  • Schmidt CA, Clark MW (2012) Efficacy of a denitrification wall to treat continuously high nitrate loads. Ecol Eng 42:203–211

    Article  Google Scholar 

  • Shi Z, Zhang Y, Zhou J et al (2013) Biological removal of nitrate and ammonium under aerobic atmosphere by Paracoccus versutus LYM. Bioresour Technol 148:144–148

    Article  CAS  PubMed  Google Scholar 

  • Shipin OV, Lee SH, Chiemchaisri C et al (2007) Piggery wastewater treatment in a tropical climate: biological and chemical treatment options. Environ Technol 28:329–337

    Article  CAS  PubMed  Google Scholar 

  • Shoun H, Kim D-H, Uchiyama H et al (1992) Denitrification by fungi. FEMS Microbiol Lett 94:277–282

    Article  CAS  Google Scholar 

  • Siddavattam D, Karegoudar TB, Mudde SK et al (2011) Genome of a novel isolate of Paracoccus denitrificans capable of degrading N, N-Dimethylformamide. J Bacteriol 193:5598–5599

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Singh S, Kang SH, Mulchandani A et al (2008) Bioremediation: environmental clean-up through pathway engineering. Curr Opin Biotechnol 19:437–444

    Article  CAS  PubMed  Google Scholar 

  • Sivonen K (1996) Cyanobacterial toxins and toxin production. Phycologia 35:12–24

    Article  Google Scholar 

  • Sorokin DY, Gijs Kuenen J, Jetten MSM (2001) Denitrification at extremely high pH values by the alkaliphilic, obligately chemolithoautotrophic, sulfur-oxidizing bacterium Thioalkalivibrio denitrificans strain ALJD. Arch Microbiol 175:94–101

    Article  CAS  PubMed  Google Scholar 

  • Takaya N, Catalan-Sakairi MAB, Sakaguchi Y et al (2003) Aerobic denitrifying bacteria that produce low levels of nitrous oxide. Appl Environ Microbiol 69:3152–3157

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wakida FT, Lerner DN (2005) Non-agricultural sources of groundwater nitrate: a review and case study. Water Res 39:3–16

    Article  CAS  PubMed  Google Scholar 

  • Wang LK, Li Y (2009) Sequencing batch reactors. Biological treatment processes. Springer, New York, p 459–511

    Google Scholar 

  • Wang Q, Feng C, Zhao Y et al (2009) Denitrification of nitrate contaminated groundwater with a fiber-based biofilm reactor. Bioresour Technol 100:2223–2227

    Article  CAS  PubMed  Google Scholar 

  • Wang Y, Wan R, Zhang S et al (2012) Anthracene biodegradation under nitrate-reducing condition and associated microbial community changes. Biotechnol Bioprocess Eng 17:371–376

    Article  CAS  Google Scholar 

  • Wilcke W (2000) Polycyclic aromatic hydrocarbons (PAHs) in soil — a review. J Plant Nutr Soil Sci 163:229–248

    Article  CAS  Google Scholar 

  • World Health Organization (2011) Nitrate and nitrite in drinking-water. Backgr Doc Dev WHO Guid Drink Qual 2011:23

    Google Scholar 

  • Wu C, Chen Z, Liu X et al (2007) Nitrification-denitrification via nitrite in SBR using real-time control strategy when treating domestic wastewater. Biochem Eng J 36:87–92

    Article  CAS  Google Scholar 

  • Xu G, Zheng W, Li Y et al (2008) Biodegradation of chlorpyrifos and 3,5,6-trichloro-2-pyridinol by a newly isolated Paracoccus sp. strain TRP. Int Biodeterior Biodegrad 62:51–56

    Article  CAS  Google Scholar 

  • Yamato N, Kimura K, Miyoshi T et al (2006) Difference in membrane fouling in membrane bioreactors (MBRs) caused by membrane polymer materials. J Membr Sci 280:911–919

    Article  CAS  Google Scholar 

  • Yang X, Ye J, Lyu L et al (2013) Anaerobic biodegradation of pyrene by Paracoccus denitrificans under various nitrate/nitrite-reducing conditions. Water Air Soil Pollut 224:1–10

    Google Scholar 

  • Yongzhen P, Shouyou G, Shuying W et al (2007) Partial nitrification from domestic wastewater by aeration control at ambient temperature. Chin J Chem Eng 15:115–121

    Article  Google Scholar 

  • Yue W, Xiong M, Li F et al (2015) The isolation and characterization of the novel chlorothalonil-degrading strain Paracoccus sp. XF-3 and the cloning of the chd gene. J Biosci Bioeng 120:544–548

    Article  CAS  PubMed  Google Scholar 

  • Zumft WG (1997) Cell biology and molecular basis of denitrification. Microbiol Mol Biol Rev 61:533–616

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

This work was supported by Consejo Sectorial de Investigación Científica (CSIC—UdelaR), Comisión Académica de Posgrado (CAP-UdelaR).

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  1. Laboratorio de Microbiología, Facultad de Agronomía, Universidad de la República, Av. Gral. Eugenio Garzón 809, Montevideo, 12900, Uruguay

    Gastón Azziz, Gabriela Illarze & Pilar Irisarri

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  1. Gastón Azziz
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  2. Gabriela Illarze
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Correspondence to Gastón Azziz .

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  1. Biochemistry and Molecular Biology Section, Faculty of Sciences, Universidad de la República, Montevideo, Uruguay

    Susana Castro-Sowinski

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Azziz, G., Illarze, G., Irisarri, P. (2016). Heterotrophic Denitrification and Paracoccus spp. as Tools for Bioremediation. In: Castro-Sowinski, S. (eds) Microbial Models: From Environmental to Industrial Sustainability. Microorganisms for Sustainability, vol 1. Springer, Singapore. https://doi.org/10.1007/978-981-10-2555-6_10

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