Molecular study of indigenous bacterial community composition on exposure to soil arsenic concentration gradient

• Autorzy: Basu S. , Paul T. , Yadav P. , Debnath A. , Sarkar K.
• Języki publikacji: EN

Abstrakty

EN

Community structure of bacteria present in arsenic contaminated agricultural soil was studied with qPCR (quantitative PCR) and DGGE (Denaturing Gradient Gel Electrophoresis) as an indicator of extreme stresses. Copy number of six common bacterial taxa (Acidobacteria, Actinobacteria, α-, β- and γ-Proteobacteria, Firmicutes) was calculated using group specific primers of 16S rDNA. It revealed that soilcontaminated with low concentration of arsenic was dominated by both Actinobacteria and Proteobacteria but a shift towards Proteobacteria was observed with increasing arsenic concentration, and number of Actinobacteria eventually decreases. PCA (Principle Component Analysis) plot of bacterial community composition indicated a distinct resemblance among high arsenic content samples, while low arsenic content samples remained separated from others. Cluster analysis of soil parameters identifies three clusters, each of them was related to the arsenic content. Further, cluster analysis of 16S rDNA based DGGE fingerprint markedly distributed the soil bacterial populations into low (< 10 ppm) and high (> 10 ppm) arsenic content subgroups. Following analysis of diversity indices shows significant variation in bacterial community structure. MDS (Multi Dimensional Scaling) plot revealed distinction in the distribution of each sample denoting variation in bacterial diversity. Phylogenetic sequence analysis of fragments excised from DGGE gel revealed the presence of γ-Proteobacteria group across the study sites. Collectively, our experiments indicated that gradient of arsenic contamination affected the shape of the soil bacterial population by significant structural shift.

• Wydawca: -
• Czasopismo: Polish Journal of Microbiology
• Rocznik: 2017
• Tom: 66
• Numer: 2
• Opis fizyczny: p.209-221,fig.,ref.

Twórcy

autor

Basu S.

• Department of Microbiology, University of Kalyani, Nadia, West Bengal, India

autor

Paul T.

• Department of Microbiology, University of Kalyani, Nadia, West Bengal, India

autor

Yadav P.

• Department of Microbiology, University of Kalyani, Nadia, West Bengal, India

autor

Debnath A.

• Department of Agricultural Chemistry and Soil Science, BCKV, Mohanpur, Nadia, West Bengal, India

autor

Sarkar K.

• Department of Microbiology, University of Kalyani, Nadia, West Bengal, India

Bibliografia

• Achour A.R., P. Bauda and P. Billard. 2007. Diversity of arsenite transporter genes from arsenic-resistant soil bacteria. Res. Microbiol. 158: 128–137.
• Aksornchu P., P. Prasertsan and V. Sobhon. 2008. Isolation of arsenic-tolerant bacteria from arsenic-contaminated soil. Songklanakarin J. Sci. Technol. 30: 95–102.
• Alele P.O., D. Sheil, Y. Surget-Groba, S. Lingling and C.H. Cannon. 2014. How does conversion of natural tropical rainforest ecosystems affect soil bacterial and fungal communities in the Nile River watershed of Uganda? PLoS ONE. 9: 1–13.
• Altschul S.F., T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller and D.J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389–3402.
• Anyanwu C.U. and C.E. Ugwu. 2010. Incidence of arsenic resistant bacteria isolated from a sewage treatment plant. Int. J. Basic Appl. Sci. 10: 43–47.
• Bachate S.P., V. Cavalca and V. Andreoni. 2009. Arsenic-resistant bacteria isolated from agricultural soils of Bangladesh and characterization of arsenate-reducing strains. J. Appl. Microbiol. 107: 145–156.
• Banerjee S., S. Datta, D. Chattyopadhyay and P. Sarkar. 2011. Arsenic accumulating and transforming bacteria isolated from contaminated soil for potential use in bioremediation. J. Environ. Sci. Heal. A. 46: 1736–1747.
• Baz S.E., M. Baz, M. Barakate, L. Hassani, A.E. Gharmali and B. Imziln. 2015. Resistance to and accumulation of heavy metals by Actinobacteria isolated from abandoned mining areas. Sci. World. J. ID: 761834.
• Bhattacharya P., G. Jacks, K.M. Ahmed, J. Routh and A.A. Khan. 2002. Arsenic in ground water of the Bengal delta plain aquifers in Bangladesh. Bull. Environ. Contam. Tox. 69: 538–545.
• Bhattacharya P., A.C. Samal, J. Majumdar and S.C. Santra. 2009. Transfer of arsenic from groundwater and paddy soil to rice plant (Oryza sativa L.): a micro level study in West Bengal, India. World. J. Agri. Sci. 5(4): 425–431.
• Black C.A. 1965. Methods of soil analysis. Part 2. Chemical and microbiological properties, American Society of Agronomy. Inc, Publisher, Madison, Wisconsin, USA.
• Blas O.J.D. and N.R. Mateos. 1996. Determination of total arsenic and selenium in soils and plants by atomic absorption spectrophotometry with hydride generation flow injection analysis coupled techniques. J. AOAC Inter. 79: 764–768.
• Bray R.H. and L.T. Kurtz. 1945. Determination of total, organic, and available forms of phosphorus in soils. Soil Sci. 59: 39–45.
• Bremner J.M. 1965. Organic forms of nitrogen. pp. 1238–1255. In: Black C.A. Part II (eds). Methods of Soil Analysis. American Society of Agronomy. Madison, Wisconsin, USA.
• Breugelmans P., P.J. D’Huys, R.D. Mot and D. Springael. 2007. Characterization of novel linuron-mineralizing bacterial consortia enriched fromlong-termlinuron-treatedagricultural soils. FEMS Microbiol. Ecol. 62: 374–385.
• Cai L., G. Liu, C. Rensing and G. Wang. 2009. Genes involved in arsenic transformation and resistance associated with different levels of arsenic-contaminated soils. BMC Microbiol. 9: 4.
• Dewis J. and F. Freitas. 1984. Physical and chemical methods of soil and water analysis, pp. 51–106. Oxford and IBH Publishing Company, New Delhi.
• Dhal P.K., E. Islam, S.K. Kazy and P. Sar. 2011. Culture-independent molecular analysis of bacterial diversity in uranium-ore/mine waste-contaminated and non-contaminated sites from uranium mines. 3Biotech. 1: 261–272.
• Fakruddin M. and K.S.B. Mannan. 2013. Methods for analyzing diversity of microbial communities in natural environments. Ceylon J. Sci. (Bio Sci). 42: 19–33.
• Fantroussi S.E., L. Verschuere, W. Verstraete and E.M. Top. 1999. Effect of phenylurea herbicides on soil microbial communities estimated by analysis of 16S rRNA gene fingerprints and community-level physiological profiles. Appl. Environ. Microbiol. 65: 982–988.
• Felczykowska A., A. Krajewska, S. Zielinska and J.M. Los. 2015. Sampling, metadata and DNA extraction-important steps in metagenomic studies. Acta. Biochim. Pol. 62:151–60.
• Fierer N., J.A. Jackson, R. Vilgalys and R.B. Jackson. 2005. Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Appl. Environ. Microbiol. 71(7): 4117–4120.
• Gafan G.P., V.S. Lucas, G.J. Roberts, A. Petrie, M. Wilson and D.A. Spratt. 2005. Statistical analyses of complex denaturing gradient gel electrophoresis profiles. J. Clin. Microbiol. 43: 3971–3978.
• Ghodsi H., M. Hoodaji, A. Tahmourespour and M.M. Gheisari. 2011. Investigation of bioremediation of arsenic by bacteria isolated from contaminated soil. Afr. J. Microbiol. Res. 5: 5889–5895.
• Ghosh D., P. Bhadury and J. Routh. 2014. Diversity of arsenite oxidizing bacterial communities in arsenic-rich deltaic aquifers in West Bengal, India. Front. Microbiol. 5: 1–14.
• Gillan D.C., B. Danis, P. Pernet, G. Joly and P. Dubois. 2005. Structure of sediment-associated microbial communities along a heavy-metal contamination gradient in the marine environment. Appl. Environ. Microbiol. 71: 679–690.
• Goswami R., S. Mukherjee, V.S. Rana, D.R. Saha, R. Raman, P.K. Padhy and S. Mazumder. 2015. Isolation and characterization of arsenic-resistant bacteria from contaminated water-bodies in West Bengal, India, Geomicrobiol. J. 32:17–26.
• Guha Mazumder D.N. 2003. Chronic arsenic toxicity: clinical features, epidemiology, and treatment: experience in West Bengal. J. Environ. Sci. Health. A Tox. Hazard. Subst. Environ. Eng. 38(1): 141–163.
• Hanway J.J. and H. Heidel. 1952. Soil analyses methods as used in Iowa State College Soil Testing Laboratory. Iowa. Agri. 57: 1–31.
• Hedrick D.B., A. Peacock, J.R. Stephen, S.J. Macnaughton, J. Bruggemann and D.C. White. 2000. Measuring soil microbial community diversity using polar lipid fatty acid and denaturing gradient gel electrophoresis data. J. Microbiol. Meth. 41: 235–248.
• Heikens A., G.M. Panaullah and A.A. Meharg. 2007. Arsenic behavior from ground water and soil to crops. Rev. Environ. Contam. Toxicol. 189: 43–87.
• Hossain M.A., M.K. Sengupta, S. Ahamed, M.M. Rahman, D. Mondal, D. Lodh, B. Das, B. Nayak, B.K. Roy, A. Mukherjee and others. 2005. Ineffectiveness and poor reliability of arsenic removal plants in West Bengal, India. Environ. Sci. Technol. 39: 4300–4306.
• Huang J., X. Sheng, L. He, Z. Huang, Q. Wang and Z. Zhang. 2013. Characterization of depth-related changes in bacterial community compositions and functions of a paddy soil profile. FEMS Microbiol. Lett. 347: 33–42.
• Islam E. and P. Sar. 2011. Molecular assessment on impact of uranium ore contamination in soil bacterial diversity. Int. Biodeterioration. Biodegrad. 65: 1043–1051.
• Jackson M.L. 1973. Soil Chemical Analysis. Prentice Hall of India Private Limited, New Delhi.
• Lee C., S. Lee, S.G. Shin and S. Hwang. 2008. Real-time PCR determination of rRNA gene copy number: absolute and relative quantification assays with Escherichia coli. Appl. Microbiol. Biotechnol. 78: 371–376.
• Maiwore J., N.L. Tatsadjieu, T. Goli, D. Montet and C.M.F. Mbofung. 2012. Influence of technological treatments on bacterial communities in tilapia (Oreochromis niloticus) as determined by 16S rDNA fingerprinting using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Afr. J. Biotechnol. 11: 8586–8593.
• Majumder A., S. Ghosh, N. Saha, S.C. Kole and S. Sarkar. 2013. Arsenic accumulating bacteria isolated from soil for possible application in bioremediation. J. Environ. Biol. 34: 841–846.
• Mallick I., S.T. Hossain, S. Sinha and S.K. Mukherjee. 2014. Brevibacillus sp. KUMAs2, a bacterial isolate for possible bio’ remediation of arsenic in rhizosphere. Ecotox. Environ. Safe. 107: 236–244.
• Mccaig A.E., L.A. Glover and J.I. Prosser. 1999. Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. Appl. Environ. Microbiol. 65: 1721–1730.
• Moura A., M. Tacao, I. Henriques, J. Dias, P. Ferreira and A. Correia. 2009. Characterization of bacterial diversity in two aerated lagoons of a waste water treatment plant using PCR-DGGE analysis. Microbiol. Res. 164: 560–569.
• Muhling M., J. Woolven-Allen, J.C. Murrell and I. Joint. 2008. Improved group-specific PCR primers for denaturing gradient gel electrophoresis analysis of the genetic diversity of complex microbial communities. ISME J. 2: 379–392.
• Mukherjee A.B and P. Bhattacharya. 2001. Arsenic in ground water in the Bengal Delta Plain: slow poisoning in Bangladesh. Environ. Rev. 9: 189–220.
• Olioso D., M. Boaretti, M. Ligozzi, G.L. Cascio and R. Fontana. 2007. Detection and quantification of hepatitis B virus DNA by SYBR green real-time polymerase chain reaction. Eur. J. Clin. Microbiol. Infect. Dis. 26:43–50.
• Paul D., S.K. Kazy, A.K. Gupta, T. Pal and P. Sar. 2015. Diversity, metabolic properties and arsenic mobilization potential of indigenous bacteria in arsenic contaminated groundwater of West Bengal, India. PLoS ONE 10(3): e0118735.
• Piper C.S. 1966. Soil and plant analysis. Hans Publishers, Bombay, India.
• Philippot L., D. Tscherko, D. Bru and E. Kandeler. 2011. Distribution of high bacterial taxa across the chronosequence of two alpine glacier forelands. Microb. Ecol. 61: 303–312.
• Pogacic T., N. Kelava, S. Zamberlin, I. Dolencic-Spehar and D. Samarzija. 2010. Methods for culture-independent identification of lactic acid bacteria in dairy products. Food. Technol. Biotechnol. 48(1): 3–10.
• Rahman M.A., H. Hasegawa, M.M. Rahman, M.A. Rahman and M.A.M. Miah. 2007. Accumulation of arsenic in tissues of rice plant (Oryza sativaL.) and its distribution in fractions of rice grain. Chemosphere. 69: 942–948.
• Ranjard L., F. Poly and S. Nazaret. 2000. Monitoring complex bacterial communities using culture-independent molecular techniques: application to soil environment. Res. Microbiol. 151: 167–177.
• Saitou N. and M. Nei. 1987. The neighbor-joining method: a new me-thod for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406–425.
• Schabereiter-Gurtner C., W. Lubitz and S. Rolleke. 2003. Application of broad-range 16S rRNA PCR amplification and DGGE fingerprinting for detection of tick-infecting bacteria. J. Microbiol. Meth. 52: 251–260.
• Schmidt A., G. Haferburg, M. Sineriz, D. Merten, G. Buchel and E. Kothe. 2005. Heavy metal resistance mechanisms in Actinobacteria for survival in AMD contaminated soils. Chem. Erde Geochem. 65(S1):131–144.
• Sharma R, R. Ranjan, R.K. Kapardar, A. Grover. 2005. ‘Unculturable’ bacterial diversity: An untapped resource. Curr. Sci. 89: 72–77.
• Sheik C.S., T.W. Mitchell, F.Z. Rizvi, Y. Rehman, M. Faisal, S. Hasnain, M.J. McInerney and L.R. Krumholz. 2012. Exposure of soil microbial communities to chromium and arsenic alters their diversity and structure. PLoS ONE 7(6): e40059.
• Shrivastava A., A. Barla, H. Yadav and S. Bose. 2014. Arsenic contamination in shallow groundwater and agricultural soil of Chakdaha block, West Bengal, India. Front. Environ. Sci. 2: 1–9.
• Singh N. 2011. Bioremediation of arsenic by bacteria isolated from arsenic contaminated marine environment of Goa harbor of India. Int. J. Pharm. Bio. Sci. 2: 629–639.
• Smalla K., G. Wieland, A. Buchner, A. Zock, J. Parzy, S. Kaiser, N. Roskot, H. Heuer, G. Berg. 2001. Bulk and rhizosphere soil bacterial communities studied by denaturing gradient Gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl. Environ. Microbiol. 67: 4742–4751.
• Smit E., P. Leeflang, S. Gommans, J.V.D. Broek, S.V. Mil and K. Wernars. 2001. Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Appl. Environ. Microbiol. 67: 2284–2291.
• Sobolev D. and M.F.T. Begonia. 2008. Effects of heavy metal contamination upon soil microbes: lead-induced changes in general and denitrifying microbial communities as evidenced by molecular markers. Int. J. Environ. Res. Public Health. 5: 450–456.
• Thompson J.D., D.G. Higgins and T.J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic. Acids Res. 22: 4673-4680.
• Vartoukian S.R., R.M. Palmer and W.G. Wade. 2010. Strategies for culture of ‘unculturable’ bacteria. FEMS Microbiol. Lett. 309: 1–7.
• Xiong J., L. Wu, S. Tu, J.D.V. Nostrand, Z. He, J. Zhou and V. Wang. 2010. Microbial communities and functional genes associated with soil arsenic contamination and the rhizosphere of the arsenic hyperaccumulating plant Pteris vittata L. Appl. Environ. Microbiol. 76: 7277–7284.
• Yuan S., D.B. Cohen, J. Ravel, Z. Abdo, L.J. Forney. 2012. Evaluation of methods for the extraction and purification of DNA from the human microbiome. PLoS ONE 11(9): e0163148.
• Yu Z. and M. Morrison. 2004. Comparisons of different hypervariable regions of rrs genes for use in fingerprinting of microbial communities by PCR-denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 70: 4800–4806.

Identyfikatory

DOI

10.5604/01.3001.0010.7838