Genetic Basis of Metal Resistance in Acidiphilium sp. DSM 27270 (Yenapatur)

Abstract:

Acidiphilium sp. DSM 27270 (Yenapatur) forms part of a microbial consortium isolated from copper mines in Chile, that is currently used in state of the art industrial-scale biotechnology. Its taxonomic assignment is still tentative and is metal resistance and homeostatic responses poorly characterized. Here we report the genomic taxonomy evaluation of the Yenapatur strain and the preliminary characterization of its metal resistance and homeostatic responses. The genome of Yenapatur was re-assembled, annotated and compared to other sequenced strains of the genus. Genomic signatures were derived to better define the taxonomy of the strain. The minimum inhibitory concentrations of diverse cations and anions (Cu (II), Fe (II), Mg (II), Mn (II), Zn (II), Al (III), As (III), Fe (III), chloride and nitrate) were determined. Known resistance determinants were profiled in the genome of Yenapatur and publically available sequenced Acidiphilium strains. Results are presented and discussed under the light of the operational conditions in which Yenapatur thrives.

• Periodical: Solid State Phenomena (Volume 262)
• Pages: 358-363
• DOI: https://doi.org/10.4028/www.scientific.net/SSP.262.358
• Online since: August 2017
• Authors: Francisco Issotta, Roberto A. Bobadilla-Fazzini, Ana Moya-Beltrán, Paulo C. Covarrubias, Raquel Quatrini, Patricio Martinez*
• Keywords: Acidiphilium, Bioleaching, Minimum Inhibitory Concentrations

References

[1] A. Hiraishi, J.F. Imhoff, Acidiphilium, in: W.B. Whitman (Ed. ), Bergey's Manual of Systematics of Archaea and Bacteria. Wiley Online Library, 2015, p.1–14.

DOI: 10.1002/9781118960608.gbm00877

[2] D.B. Johnson, Microbial communities and interactions in low pH environments, in: R. Quatrini, D.B. Johnson (Eds. ), Acidophiles: Life in extremely acidic environments, Caister Academic Press, UK, 2016, pp.121-137.

DOI: 10.21775/9781910190333.08

[3] R. Kermer, S. Hedrich, M. Taubert, S. Baumann, M. Schlomann, D.B. Johnson, M. von Bergen, J. Seifert, Elucidation of carbon transfer in a mixed culture of Acidiphilium cryptum and Acidithiobacillus ferrooxidans using protein-based stable isotope probing, J. Integr. OMICS 2 (2012).

DOI: 10.5584/jiomics.v2i1.85

[4] A.P. Harrison, Acidiphilium cryptum gen. nov., sp. nov., heterotrophic bacterium from acidic mineral environments, Int. J. Syst. Bacteriol. 31(1981) 327-332.

DOI: 10.1099/00207713-31-3-327

[5] R. Guay, M. Silver, Thiobacillus acidophilus sp. nov.: isolation and some physiological characteristics, Can. J. Microbiol. 21(1975) 281–288.

DOI: 10.1139/m75-040

[6] A.P. Harrison Jr., Genomic and physiological comparisons between heterotrophic thiobacilli and Acidiphilum cryptum, Thiobacillus versutus sp. nov., and Thiobacillus acidophilus nom. rev., Int. J. Syst. Bacteriol. 33 (1983) 211–217.

DOI: 10.1099/00207713-33-2-211

[7] A. Hiraishi, K.V.P. Nagashima, K. Matsuura, K. Shimada, S. Takaichi, N. Wakao. Y. Katayama, Phylogeny and photosynthetic features of Thiobacillus acidophilus and related acidophilic bacteria: its transfer to the genus Acidiphilium as Acidiphilium acidophilum comb. nov., Int. J. Syst. Bacteriol. 48 (1998).

DOI: 10.1099/00207713-48-4-1389

[8] J.H. Lobos, T.E. Chisolm, L.H. Bopp, D.S. Holmes, Acidiphilium organovorum sp. nov., an acidophilic heterotroph isolated from a Thiobacillus ferrooxidans culture, Int. J. Syst. Bacteriol. 36 (1986) 139-144.

DOI: 10.1099/00207713-36-2-139

[9] P.L. Wichlacz, R.F. Unz, T.A. Langworthy, Acidiphilium angustum sp. nov., Acidiphilium facilis sp. nov., and Acidiphilium rubrum sp. nov.: acidophilic heterotrophic bacteria isolated from acidic coal mine drainage, Int. J. Syst. Bacteriol. 36 (1986).

DOI: 10.1099/00207713-36-2-197

[10] S. Bhattacharyya, B.K. Chakrabarty, A. Das, P.N. Kundu, P.C. Banerjee, Acidiphilum symbioticum sp. nov., an acidophilic heterotrophic bacterium from Thiobacillus ferrooxidans cultures isolated from Indian mines, Can. J. Microbiol. 37 (1991).

DOI: 10.1139/m91-012

[11] N. Wakao, N. Nagasawa, T. Matsuura, H. Matsukura, T. Matsumoto, A. Hiraishi, Y. Sakurai, H. Shiota, Acidiphilium multivorum sp. nov., an acidophilic chemoorganotrophic bacterium from pyritic acid mine drainage, J. Gen. Appl. Microbiol. 40 (1994).

DOI: 10.2323/jgam.40.143

[12] K. Okamura, A. Kawai, N. Wakao, T. Yamada, A. Hiraishi, Acidiphilium iwatense sp. nov., isolated from an acid mine drainage treatment plant, and emendation of the genus Acidiphilium, Int. J. Syst. Evol. Microbiol. 65 (2015) 42-48.

DOI: 10.1099/ijs.0.065052-0

[13] N.R. Mahapatra, S. Ghosh, C. Deb, P.C. Banerjee, Resistance to cadmium and zinc in Acidiphilium symbioticum KM2 is plasmid mediated, Curr. Microbiol. 45 (2002), 180.

DOI: 10.1007/s00284-001-0113-6

[14] S. Itoh, M. Iwaki, N. Wakao, A. Aoki, K. Tazaki, Accumulation of Fe, Cr and Ni metals inside cells of acidophilic bacterium Acidiphilium rubrum that produced Zn containing bacteriochlorophyll a, Plant Cell Physiol. 39 (1998) 740.

DOI: 10.1093/oxfordjournals.pcp.a029428

[15] N.R. Mahapatra, P.C. Banerjee, Extreme tolerance to cadmium and high resistance to copper, nickel and zinc in different Acidiphilium strains, Lett. Appl. Microbiol. 23 (1996) 393.

DOI: 10.1111/j.1472-765x.1996.tb01344.x

[16] M. Latorre, M.P. Cortés, D. Travisany, A. Di Genova, M. Budinich, A. Reyes-Jara, C. Hödar, M. González, P. Parada, R.A. Bobadilla-Fazzini, V. Cambiazo, A. Maass. The bioleaching potential of a bacterial consortium, Biores Technol. 218 (2016).

DOI: 10.1016/j.biortech.2016.07.012

[17] F. Issotta, P.A. Galleguillos, A. Moya-Beltrán, C.S. Davis-Belmar, G. Rautenbach, P.C. Covarrubias, M. Acosta, F.J. Ossandon, Y. Contador , D.S. Holmes, S. Marín-Eliantonio, R. Quatrini, C. Demergasso, Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile, Stand. Genomic. Sci. 11 (2016).

DOI: 10.1186/s40793-016-0142-1

[18] J. Goris, K.T. Konstantinidis, J.A. Klappenbach, T. Coenye, P. Vandamme, J.M. Tiedje, DNA-DNA hybridization values and their relationship to whole-genome sequence similarities, Int. J. Syst. Evol. Microbiol. 57 (2007) 81-91.

DOI: 10.1099/ijs.0.64483-0

[19] J.P. Meier-Kolthoff, A.F. Auch, H.P. Klenk, M. Göker, Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics. 14 (2013) 60.

DOI: 10.1186/1471-2105-14-60

[20] J.P. Meier-Kolthoff, R.L. Hahnke, J. Petersen, C. Scheuner, V. Michael, A. Fiebig, C. Rohde, M. Rohde, B. Fartmann, L.A. Goodwin, O. Chertkov, T.B.K. Reddy, A. Pati, N.N. Ivanova, V. Markowitz, N.C. Kyrpides, T. Woyke, M. Göker, H.P. Klenk,. Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy, Stand. Genomic. Sci. 9(2014).

DOI: 10.1186/1944-3277-9-2

[21] K. Katoh, D.M. Standley, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol. Biol. Evol. 30 (2013) 772–80.

DOI: 10.1093/molbev/mst010

[22] S. Kumar, G. Stecher, K. Tamura, MEGA7: Molecular Evolutionary Genetics Analysis Version 7. 0 for Bigger Datasets, Mol. Biol. Evol. 33 (2016) 1870–1874.

DOI: 10.1093/molbev/msw054

[23] J.P. Huelsenbeck, F. Ronquist, MRBAYES: Bayesian inference of phylogenetic trees, Bioinformatics 17 (2001) 754–755.

DOI: 10.1093/bioinformatics/17.8.754

[24] J. Sukumaran, M.T. Holder, DendroPy: a Python library for phylogenetic computing, Bioinformatics 26 (2010) 1569–1571.

DOI: 10.1093/bioinformatics/btq228

[25] K. Suzuki, N. Wakao, Y. Sakurai, T. Kimura, K. Sakka, K. Ohmiya, Transformation of Escherichia coli with a large plasmid of Acidiphilium multivorum AIU 301 encoding arsenic resistance, Appl. Environ. Microbiol. 63 (1997) 2089–(2091).

DOI: 10.1128/aem.63.5.2089-2091.1997