Skip to main content

Advertisement

SpringerLink
Log in

Identification of Arsenic Resistance Genes from Marine Sediment Metagenome

  • Original Article
  • Published:
Indian Journal of Microbiology Aims and scope Submit manuscript

Abstract

A metagenomic library of sea sediment metagenome containing 245,000 recombinant clones representing ~ 2.45 Gb of sea sediment microbial DNA was constructed. Two unique arsenic resistance clones, A7 and A12, were identified by selection on sodium arsenite containing medium. Clone A7 showed a six-fold higher resistance to arsenate [As(V)], a three-fold higher resistance to arsenite [As(III)] and significantly increased resistance to antimony [Sb(III)], while clone A12 showed increased resistance only to sodium arsenite and not to the other two metalloids. The clones harbored inserts of 8.848 Kb and 6.771 Kb, respectively. Both the clones possess A + T rich nucleotide sequence with similarity to sequences from marine psychrophilic bacteria. Sequence and transposon-mutagenesis based analysis revealed the presence of a putative arsenate reductase (ArsC), a putative arsenite efflux pump (ArsB/ACR) and a putative NADPH-dependent FMN reductase (ArsH) in both the clones and also a putative transcriptional regulatory protein (ArsR) in pA7. The increased resistance of clone A7 to As(V), As(III) and Sb(III) indicates functional expression of ArsC and ArsB proteins from pA7. The absence of increased As(V) resistance in clone A12 may be due to the expression of a possible inactive ArsC, as conserved Arg60 residue in this protein was replaced by Glu60, while the absence of Sb(III) resistance may be due to the presence of an ACR3p-type arsenite pump, which is known to lack antimony transport ability.

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

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  1. Frigaard N-U, Martinez A, Mincer TJ, DeLong EF (2006) Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea. Nature 439:847–850. doi:10.1038/nature04435

    Article  CAS  PubMed  Google Scholar 

  2. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74. doi:10.1126/science.1093857

    Article  CAS  PubMed  Google Scholar 

  3. Kannan N, Taylor SS, Zhai Y, Venter JC, Manning G (2007) Structural and functional diversity of the microbial kinome. PLoS Biol 5:e17. doi:10.1371/journal.pbio.0050017

    Article  PubMed  PubMed Central  Google Scholar 

  4. Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yoosep S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers YH, Falcón LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, Platt T, Bermingham E, Gallardo V, Tamayo-Castillo G, Ferrari MR, Strausberg RL, Nealson K, Friedman R, Frazier M, Venter JC (2007) The Sorcerer II global ocean sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 5:e77. doi:10.1371/journal.pbio.0050077

    Article  PubMed  PubMed Central  Google Scholar 

  5. Mukhopadhyay R, Rosen BP, Phung LT, Silver S (2002) Microbial arsenic: from geocycles to genes and enzymes. FEMS Microbiol Rev 26:311–325. doi:10.1111/j.1574-6976.2002.tb00617.x

    Article  CAS  PubMed  Google Scholar 

  6. Lin Y-F, Walmsley AR, Rosen BP (2006) An arsenic metallochaperone for an arsenic detoxification pump. Proc Natl Acad Sci U S A 103:15617–15622. doi:10.1073/pnas.0603974103

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Neyt C, Iriarte M, Thi VH, Cornelis GR (1997) Virulence and arsenic resistance in Yersiniae. J Bacteriol 179:612–619. doi:10.1128/jb.179.3.612-619.1997

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Sato T, Kobayashi Y (1998) The ars operon in the skin element of Bacillus subtilis confers resistance to arsenate and arsenite. J Bacteriol 180:1655–1661

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Bobrowicz P, Wysocki R, Owsianik G, Goffeau A, Ułaszewski S (1997) Isolation of three contiguous genes, ACR1, ACR2 and ACR3, involved in resistance to arsenic compounds in the yeast Saccharomyces cerevisiae. Yeast 13:819–828. doi:10.1002/(SICI)1097-0061(199707)13:9<819:AID-YEA142>3.0.CO;2-Y

    Article  CAS  PubMed  Google Scholar 

  10. Qin J, Rosen BP, Zhang Y, Wang G, Franke S, Rensing C (2006) Arsenic detoxification and evolution of trimethylarsine gas by a microbial arsenite S-adenosylmethionine methyltransferase. Proc Natl Acad Sci U S A 103:2075–2080. doi:10.1073/pnas.0506836103

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Yang HC, Cheng J, Finan TM, Rosen BP, Bhattacharjee H (2005) Novel pathway for arsenic detoxification in the legume symbiont Sinorhizobium meliloti. J Bacteriol 187:6991–6997. doi:10.1128/JB.187.20.6991-6997.2005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Takeuchi M, Kawahata H, Gupta LP, Kita N, Morishita Y, Ono Y, Komai T (2007) Arsenic resistance and removal by marine and non-marine bacteria. J Biotechnol 127:434–442. doi:10.1016/j.jbiotec.2006.07.018

    Article  CAS  PubMed  Google Scholar 

  13. Schloss PD, Girard RA, Martin T, Edwards J, Thrash JC (2016) Status of the archaeal and bacterial census: an update. MBio 7:e00201–e00216. doi:10.1128/mBio.00201-16

    Article  PubMed  PubMed Central  Google Scholar 

  14. Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNeil IA, Minor C, Tiong CL, Gilman M, Osburne MS, Clardy J, Handelsman J, Goodman RM (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66:2541–2547. doi:10.1128/AEM.66.6.2541-2547.2000

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Cai L, Yu K, Yang Y, Chen BW, Li XD, Zhang T (2013) Metagenomic exploration reveals high levels of microbial arsenic metabolism genes in activated sludge and coastal sediments. Appl Microbiol Biotechnol 97:9579–9588. doi:10.1007/s00253-012-4678-8

    Article  CAS  PubMed  Google Scholar 

  16. Bertin PN, Heinrich-Salmeron A, Pelletier E, Goulhen-Chollet F, Arsène-Ploetze F, Gallien S, Lauga B, Casiot C, Calteau A, Vallenet D, Bonnefoy V, Bruneel O, Chane-Woon-Ming B, Cleiss-Arnold J, Duran R, Elbaz-Poulichet F, Fonknechten N, Giloteaux L, Halter D, Koechler S, Marchal M, Mornico D, Schaeffer C, Smith AA, Van Dorsselaer A, Weissenbach J, Médigue C, Le Paslier D (2011) Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta- and proteo-genomics. ISME J 5:1735–1747. doi:10.1038/ismej.2011.51

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Xiao KQ, Li LG, Ma LP, Zhang SY, Bao P, Zhang T, Zhu YG (2016) Metagenomic analysis revealed highly diverse microbial arsenic metabolism genes in paddy soils with low-arsenic contents. Environ Pollut 211:1–8. doi:10.1016/j.envpol.2015.12.023

    Article  CAS  PubMed  Google Scholar 

  18. Plewniak F, Koechler S, Navet B, Dugat-Bony E, Bouchez O, Peyret P, Séby F, Battaglia-Brunet F, Bertin PN (2013) Metagenomic insights into microbial metabolism affecting arsenic dispersion in Mediterranean marine sediments. Mol Ecol 22:4870–4883. doi:10.1111/mec.12432

    Article  CAS  PubMed  Google Scholar 

  19. Luo J, Bai Y, Liang J, Qu J (2014) Metagenomic approach reveals variation of microbes with arsenic and antimony metabolism genes from highly contaminated soil. PLoS One 9:e108185. doi:10.1371/journal.pone.0108185

    Article  PubMed  PubMed Central  Google Scholar 

  20. Gu Y, Van Nostrand JD, Wu L, He Z, Qin Y, Zhao F, Zhou J (2017) Bacterial community and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations. PLoS One 12:e0176696. doi:10.1371/journal.pone.0176696

    Article  PubMed  PubMed Central  Google Scholar 

  21. Das S, Sankar S, Yadav RNS, Barooah M (2017) Genomics Data A metagenomic approach to decipher the indigenous microbial communities of arsenic contaminated groundwater of Assam. Genomics Data 12:89–96. doi:10.1016/j.gdata.2017.03.013

    Article  PubMed  PubMed Central  Google Scholar 

  22. Chauhan NS, Ranjan R, Purohit HJ, Kalia VC, Sharma R (2009) Identification of genes conferring arsenic resistance to Escherichia coli from an effluent treatment plant sludge metagenomic library. FEMS Microbiol Ecol 67:130–139. doi:10.1111/j.1574-6941.2008.00613.x

    Article  CAS  PubMed  Google Scholar 

  23. Morgante V, Mirete S, de Figueras CG, Postigo Cacho M, González-Pastor JE (2015) Exploring the diversity of arsenic resistance genes from acid mine drainage microorganisms. Environ Microbiol 17:1910–1925. doi:10.1111/1462-2920.12505

    Article  CAS  PubMed  Google Scholar 

  24. Sambrook J, Russell DW, David W (2001) Molecular cloning : a laboratory manual. Cold Spring Harbor Laboratory Press, NY

    Google Scholar 

  25. Liu J, Gladysheva TB, Lee L, Rosen BP (1995) Identification of an essential cysteinyl residue in the ArsC arsenate reductase of plasmid R773. Biochemistry 34:13472–13476. doi:10.1021/bi00041a026

    Article  CAS  PubMed  Google Scholar 

  26. Tusnády GE, Simon I (2001) The HMMTOP transmembrane topology prediction server. Bioinformatics 17:849–850. doi:10.1093/bioinformatics/17.9.849

    Article  PubMed  Google Scholar 

  27. Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol. doi:10.1093/molbev/msw054

    PubMed Central  Google Scholar 

  28. Qin QL, Li Y, Zhang YJ, Zhou ZM, Zhang WX, Chen XL, Zhang XY, Zhou BC, Wang L, Zhang YZ (2011) Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913. ISME J 5:274–284. doi:10.1038/ismej.2010.103

    Article  PubMed  Google Scholar 

  29. Moghadam MS, Albersmeier A, Winkler A, Cimmino L, Rise K, Hohmann-Marriott MF, Kalinowski J, Rückert C, Wentzel A, Lale R (2016) Isolation and genome sequencing of four Arctic marine Psychrobacter strains exhibiting multicopper oxidase activity. BMC Genom 17:117. doi:10.1186/s12864-016-2445-4

    Article  Google Scholar 

  30. DeMel S, Shi J, Martin P, Rosen BP, Edwards BFP (2004) Arginine 60 in the ArsC arsenate reductase of E. coli plasmid R773 determines the chemical nature of the bound As(III) product. Protein Sci 13:2330–2340. doi:10.1110/ps.04787204

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Xu C, Shi W, Rosen BP (1996) The chromosomal arsR gene of Escherichia coli encodes a trans-acting metalloregulatory protein. J Biol Chem 271:2427–2432. doi:10.1074/jbc.271.5.2427

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We gratefully acknowledge Director, I.G.I.B. for support. NSC acknowledges UGC for research fellowships. This work was supported by Department of Biotechnology grant BT/PR/8662/BCE/08/508/2007.

Funding

This study was funded by Department of Biotechnology (DBT) Grant BT/PR/8662/BCE/08/508/2007.

Author information

Author notes

  1. Nar Singh Chauhan

    Present address: Department of Biochemistry, Maharishi Dayanand University, Rohtak, Haryana, India

Authors and Affiliations

  1. CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Sukhdev Vihar, Mathura Road, Delhi, 110020, India

    Nar Singh Chauhan, Sonam Nain & Rakesh Sharma

  2. Academy of Scientific and Industrial Research (AcSIR), New Delhi, India

    Sonam Nain & Rakesh Sharma

Authors
  1. Nar Singh Chauhan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sonam Nain
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Rakesh Sharma
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Rakesh Sharma.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 18 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chauhan, N.S., Nain, S. & Sharma, R. Identification of Arsenic Resistance Genes from Marine Sediment Metagenome. Indian J Microbiol 57, 299–306 (2017). https://doi.org/10.1007/s12088-017-0658-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12088-017-0658-0

Keywords

Search

Navigation