Skip to main content
Log in

Metagenomic analysis revealed the sulfur- and iron- oxidation capabilities of heterotrophic denitrifying sludge

  • Published:
Ecotoxicology Aims and scope Submit manuscript

Abstract

Heterotrophic denitrification is widely applied in wastewater treatment processes to remove nitrate. However, the ability of the heterotrophic denitrifying sludge to use inorganic matter as electron donors to perform autotrophic denitrification has rarely been investigated. In this study, we enriched heterotrophic denitrifying sludge and demonstrated its sulfur- and iron- oxidizing abilities and denitrification performance with batch experiments. Based on high-throughput sequencing of 16S rRNA genes, high diversity and abundance of sulfur-oxidizing bacteria (SOB) (e.g., Sulfuritalea, Thiobacillus, and Thiothrix) and iron (II)-oxidizing bacteria (FeOB) (e.g., Azospira and Thiobacillus) were observed. Metagenomic sequencing and genome binning results further suggested that the SOB in the heterotrophic denitrifying sludge were mainly Alphaproteobacteria and Betaproteobacteria instead of Gammaproteobacteria and Epsilonproteobacteria. The similarities of potential iron-oxidizing genes with known sequences were very low (32–51%), indicating potentially novel FeOB species in this system. The findings of this study suggested that the heterotrophic denitrifying sludge harbors diverse mixotrophic denitrifying bacterial species, and based on this finding, we proposed that organic carbon and inorganic electron donors (e.g., sulfur, thiosulfate, and iron) could be jointly used in engineering practices according to the quality and quantity of wastewater to balance the cost and efficiency of the denitrification process.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120

    Article  CAS  Google Scholar 

  • Bosch J, Lee K-Y, Jordan G, Kim K-W, Meckenstock RU (2012) Anaerobic, nitrate-dependent oxidation of pyrite nanoparticles by Thiobacillus denitrificans. Environ Sci Technol 46(4):2095–2101

    Article  CAS  Google Scholar 

  • Boutet E, Lieberherr D, Tognolli M, Schneider M, Bairoch A (2007) UniProtKB/Swiss-Prot: the manually annotated section of the UniProt KnowledgeBase. Plant Bioinform: Methods Protoc 406:89–112

  • Burgin AJ, Hamilton SK, Jones SE, Lennon JT (2012) Denitrification by sulfur-oxidizing bacteria in a eutrophic lake. Aquat Microb Ecol 66(3):283–293

    Article  Google Scholar 

  • Cabello P, Roldan MD, Moreno-Vivian C (2004) Nitrate reduction and the nitrogen cycle in archaea. Microbiology 150(11):3527–3546

    Article  CAS  Google Scholar 

  • Campos J, Carvalho S, Portela R, Mosquera-Corral A, Méndez R (2008) Kinetics of denitrification using sulphur compounds: effects of S/N ratio, endogenous and exogenous compounds. Bioresour Technol 99(5):1293–1299

    Article  CAS  Google Scholar 

  • Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI (2010) QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7(5):335–336

    Article  CAS  Google Scholar 

  • Carlson HK, Clark IC, Melnyk RA, Coates JD (2012) Toward a mechanistic understanding of anaerobic nitrate-dependent iron oxidation: balancing electron uptake and detoxification. Front microbiol 3:57

    Article  Google Scholar 

  • Chung J, Amin K, Kim S, Yoon S, Kwon K, Bae W (2014) Autotrophic denitrification of nitrate and nitrite using thiosulfate as an electron donor. Water Res 58:169–178

    Article  CAS  Google Scholar 

  • Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797

    Article  CAS  Google Scholar 

  • Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26(19):2460–2461

    Article  CAS  Google Scholar 

  • Fajardo C, Mosquera-Corral A, Campos J, Méndez R (2012) Autotrophic denitrification with sulphide in a sequencing batch reactor. J Environ Manage 113:552–556

    Article  CAS  Google Scholar 

  • Federation WE, Association APH (2005) Standard methods for the examination of water and wastewater. American Public Health Association (APHA), Washington, DC, USA

    Google Scholar 

  • Friedrich CG, Quentmeier A, Bardischewsky F, Rother D, Kraft R, Kostka S, Prinz H (2000) Novel genes coding for lithotrophic sulfur oxidation of Paracoccus pantotrophus GB17. J Bacteriol 182(17):4677–4687

    Article  CAS  Google Scholar 

  • Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59(3):307–321

    Article  CAS  Google Scholar 

  • Hedrich S, Schlömann M, Johnson DB (2011) The iron-oxidizing proteobacteria. Microbiology 157(6):1551–1564

    Article  CAS  Google Scholar 

  • He S, Tominski C, Kappler A, Behrens S, Roden EE (2016) Metagenomic analyses of the autotrophic Fe (II)-oxidizing, nitrate-reducing enrichment culture KS. Appl Environ Microbiol 82(9):2656–2668

    Article  CAS  Google Scholar 

  • Heylen K, Vanparys B, Wittebolle L, Verstraete W, Boon N, De Vos P (2006) Cultivation of denitrifying bacteria: optimization of isolation conditions and diversity study. Appl Environ Microbiol 72(4):2637–2643

    Article  CAS  Google Scholar 

  • Huang N, Wang T, Wang W-L, Wu Q-Y, Li A, Hu H-Y (2017) UV/chlorine as an advanced oxidation process for the degradation of benzalkonium chloride: Synergistic effect, transformation products and toxicity evaluation. Water Res 114:246–253

    Article  CAS  Google Scholar 

  • Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform 11(1):119

    Article  CAS  Google Scholar 

  • Ilbert M, Bonnefoy V (2013) Insight into the evolution of the iron oxidation pathways. Biochimica et Biophysica Acta (BBA)-Bioenergetics 1827(2):161–175

    Article  CAS  Google Scholar 

  • Ishii S, Joikai K, Otsuka S, Senoo K, Okabe S (2016) Denitrification and nitrate-dependent Fe(II) oxidation in various Pseudogulbenkiania strains. Microbes Environ 31(3):293–298

    Article  Google Scholar 

  • Kanehisa M, Sato Y, Morishima K (2016) BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 428(4):726–731

    Article  CAS  Google Scholar 

  • Kang DD, Froula J, Egan R, Wang Z (2015) MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3:e1165

    Article  CAS  Google Scholar 

  • Kim I, Oh S, Bum M, Lee J, Lee S (2002) Monitoring the denitrification of wastewater containing high concentrations of nitrate with methanol in a sulfur-packed reactor. Appl Microbiol Biotechnol 59(1):91–96

    Article  CAS  Google Scholar 

  • Laufer K, Røy H, Jørgensen BB, Kappler A (2016) Evidence for the existence of autotrophic nitrate-reducing Fe(II)-oxidizing bacteria in marine coastal sediment. Appl Environ Microbiol 82(20):6120–6131

    Article  CAS  Google Scholar 

  • Liu B, Zhang F, Feng X, Liu Y, Yan X, Zhang X, Wang L, Zhao L (2005) Thauera and Azoarcus as functionally important genera in a denitrifying quinoline-removal bioreactor as revealed by microbial community structure comparison. FEMS Microbiol Ecol. 55(2):274–286

    Article  Google Scholar 

  • Liu H, Jiang W, Wan D, Qu J (2009) Study of a combined heterotrophic and sulfur autotrophic denitrification technology for removal of nitrate in water. J Hazard Mater 169(1):23–28

    Article  CAS  Google Scholar 

  • Liu T, Xia X, Liu S, Mou X, Qiu Y (2013) Acceleration of denitrification in turbid rivers due to denitrification occurring on suspended sediment in oxic waters. Environ Sci Technol 47(9):4053–4061

    Article  CAS  Google Scholar 

  • Li Y, Zhang Y, Zhao Z, Sun S, Quan X, Zhao H (2016) Enhancement of sludge granulation in hydrolytic acidogenesis by denitrification. Appl Microbiol Biotechnol 100(7):3313–3320

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Meier DV, Pjevac P, Bach W, Hourdez S, Girguis PR, Vidoudez C, Amann R, Meyerdierks A (2017) Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents. ISME J 11:1545–1558

    Article  CAS  Google Scholar 

  • Mora M, Guisasola A, Gamisans X, Gabriel D (2014) Examining thiosulfate-driven autotrophic denitrification through respirometry. Chemosphere 113:1–8

    Article  CAS  Google Scholar 

  • Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25(7):1043–1055

    Article  CAS  Google Scholar 

  • Pokorna D, Zabranska J (2015) Sulfur-oxidizing bacteria in environmental technology. Biotechnol Adv 33(6):1246–1259

    Article  CAS  Google Scholar 

  • Sahinkaya E, Kilic A, Duygulu B (2014) Pilot and full scale applications of sulfur-based autotrophic denitrification process for nitrate removal from activated sludge process effluent. Water Res 60:210–217

    Article  CAS  Google Scholar 

  • Shao M-F, Zhang T, Fang HH-P (2010) Sulfur-driven autotrophic denitrification: diversity, biochemistry, and engineering applications. Appl Microbiol Biotechnol 88(5):1027–1042

    Article  CAS  Google Scholar 

  • Shoun H, Kim D-H, Uchiyama H, Sugiyama J (1992) Denitrification by fungi. FEMS Microbiol Lett 94(3):277–281

    Article  CAS  Google Scholar 

  • Sierra-Alvarez R, Beristain-Cardoso R, Salazar M, Gómez J, Razo-Flores E, Field JA (2007) Chemolithotrophic denitrification with elemental sulfur for groundwater treatment. Water Res 41(6):1253–1262

    Article  CAS  Google Scholar 

  • Sun Y, Shen D, Zhou X, Shi N, Tian Y (2016) Microbial diversity and community structure of denitrifying biological filters operated with different carbon sources. SpringerPlus 5(1):1752

    Article  CAS  Google Scholar 

  • Varaljay VA, Satagopan S, North JA, Witte B, Dourado MN, Anantharaman K, Arbing MA, McCann SH, Oremland RS, Banfield JF (2016) Functional metagenomic selection of ribulose 1, 5‐bisphosphate carboxylase/oxygenase from uncultivated bacteria. Environ Microbiol 18(4):1187–1199

    Article  CAS  Google Scholar 

  • Wang R, Zheng P, Zhang M, Zhao H-P, Ji J-Y, Zhou X-X, Li W (2015) Bioaugmentation of nitrate-dependent anaerobic ferrous oxidation by heterotrophic denitrifying sludge addition: a promising way for promotion of chemoautotrophic denitrification. Bioresour Technol 197:410–415

    Article  CAS  Google Scholar 

  • Xia X, Jia Z, Liu T, Zhang S, Zhang L (2016) Coupled nitrification-denitrification caused by suspended sediment (SPS) in rivers: importance of SPS size and composition. Environ Sci Technol 51(1):212–221

    Article  CAS  Google Scholar 

  • Zhang M, Zheng P, Li W, Wang R, Ding S, Abbas G (2015) Performance of nitrate-dependent anaerobic ferrous oxidizing (NAFO) process: a novel prospective technology for autotrophic denitrification. Bioresour Technol 179:543–548

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by the Jiangsu Provincial Key Research and Development Program (BE2019635), the National Natural Science Foundation of China (51608256) and the Open Fund of Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (KHK1804), A Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Lin Ye.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Huang, K., Li, Q., Sun, H. et al. Metagenomic analysis revealed the sulfur- and iron- oxidation capabilities of heterotrophic denitrifying sludge. Ecotoxicology 30, 1399–1407 (2021). https://doi.org/10.1007/s10646-020-02307-z

Download citation

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10646-020-02307-z

Keywords

Navigation