Energy, Ecology and Environment

, Volume 3, Issue 2, pp 102–109 | Cite as

Profiling of heavy metal(loid)-resistant bacterial community structure by metagenomic-DNA fingerprinting using PCR–DGGE for monitoring and bioremediation of contaminated environment

  • Jatindra N. Bhakta
  • Susmita Lahiri
  • Feroze A. Bhuiyna
  • Md. Rokunuzzaaman
  • Kouhei Ohonishi
  • Kozo Iwasaki
  • Bana B. Jana
Original Article
  • 432 Downloads

Abstract

Frequent exposure of microbes to hazardous metalloids/heavy metals in contaminated environment results in the development of heavy metal(loid)-resistance properties. The study attempted to assess the profile of elevated arsenic (As), cadmium (Cd) and mercury (Hg)—resistant bacterial community structures of sludge (S1, India), sludge and sediment (S2 and S3, Japan) and sediment (S4, Vietnam) samples by metagenomic-DNA fingerprinting using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR–DGGE) for monitoring and bioremediation of hazardous metal(loid) contamination in environment. The results revealed that As-resistant bacteria were dominant compared to Cd- and Hg-resistant bacteria with higher species diversity (Lysinibacillus sp., Uncultured soil bacterium clone, Staphylococcus sciuri, Bacillus fastidiosus, Bacillus niacini, Clostridium sp. and Bacillus sp.) in S1 and S4 than that of S2 and S3 samples. The occurrence of dominant As-resistant bacteria may indicate arsenic contamination in the investigated coastal habitats of India, Japan and Vietnam. The As-, Cd- and Hg-resistant bacteria/bacterial consortiums showed appreciable uptake ability of respective metal(loid) (0.042–0.125 mg As/l, 0.696–0.726 mg Cd/l and 0.34–0.412 mg Hg/l). Therefore, it might be concluded that the profiling of metalloids/heavy metal-resistant bacterial community structure by metagenomic-DNA fingerprinting using PCR–DGGE could be used to explore high metal(loid)-resistant bacteria for applying in metal(loid) bioremediation and as an indicator for monitoring hazardous metal(loid) contamination in environment.

Keywords

Metal(loid) Resistant Metagenomics Bacterial diversity Environmental contamination Bioremediation 

1 Introduction

Indiscriminate and uncontrolled discharge of hazardous heavy metal(loid) such as arsenic (As), cadmium (Cd) and mercury (Hg) by various anthropogenic as well as geogenic activities contaminates the environment posing severe health hazardous and detrimental impacts on all forms of life (Bidstrup 1964; Gupta and Gupta 1998; Bhakta 2017; Signes-Pastor et al. 2017; Hoover et al. 2017). The contamination of hazardous metalloids/heavy metals impacts on the qualitative and quantitative structures of microbial communities in the environment. Frequent exposure of microbial community to contaminated hazardous metalloids/heavy metals results in the acquisition of heavy metal(loid)-resistance properties by the process of metal(loid) homeostasis, facilitation of heavy metals mobility (Gadd 1990; Bhakta 2016, 2017), alteration of metabolic activity and diversity (Giller et al. 1998). The exploration of potential resistant bacteria from the environment for microbial heavy metal(loid) remediation is an emerging field. The heavy metal-resistant bacteria, Lactobacillus reuteri and Enterococcus faecium have been isolated from coastal sediment samples and characterized for use as hazardous metals removing agents (Bhakta et al. 2012a, b). Similarly, other studies have employed microbial species such as Escherichia coli, Bacillus subtilis, Saccharomyces boulardii, Enterococcus faecium, Staphylococcus aureus and Vibrio fluvialis to remove hazardous pollutants from aquatic environment (Min-sheng et al. 2001; Wei et al. 2009; Figueiredo et al. 2016; Saranya et al. 2017).

The diversified environment, especially the vast richness of soil microbial niches, is the best source of novel microorganisms with novel molecules that can provide various biotechnological applications. It is also obvious that the simple cultivation-dependent and colony screening approaches are unable to identify the majority of microorganisms present in soil, and so the vast amount of potential soil microorganisms remain unidentified., Metagenomics, the analysis of the entire genetic complement of a particular habitat (Handelsman et al. 1998, 2004) by DNA fingerprinting using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR–DGGE), has emerged as one of the key technologies (Logue et al. 2008; Kumar et al. 2015) that has allowed access to a wide diversity of individual genes and their products as well as analysis of entire operons encoding biosynthetic or degradative pathways (Handelsman 2004; Pettit 2004; Streit and Schmitz 2004; Schmeisser et al. 2007; Dinsdale et al. 2008; Kunin et al. 2008, Umar et al. 2017). As such, the metagenomic-16S rDNA/rRNA fingerprinting technology has extensively expanded our knowledge of microbial diversity and revealed that the range of soil microbial diversity is between 3000 and 11,000 genomes per gram of soil with less than 1% being accessible through cultivation techniques (Torsvik and Ovreas 2002; Curtis and Sloan 2004). Metagenomics also makes it possible to answer key ecological questions by enabling scientists to relate potential functions to specific microorganisms within multispecies soil communities by profiling microbial diversity using DNA fingerprinting (Smalla et al. 2007; Dinsdale et al. 2008; Kunin et al. 2008; Campbell et al. 2009; Martínez-Alonso et al. 2010). Very few studies have been performed on the screening of heavy metal(loid)-resistant bacteria from metagenomic soil samples using PCR–DGGE (Qing et al. 2007; Altimira et al. 2012). Additionally, taking the advantage of metal(loid)-resistant properties, microorganisms are potentially using in metal(loid) removing/uptaking process for the remediation of contaminated environment (water and soil) in recent years (Bhakta et al. 2012a, b; Sinha et al. 2012; Bhakta et al. 2014; Jafari and Cheraghi 2014; Watts et al. 2015; Carpio et al. 2016; Saranya et al. 2017).

The detailed profiling of hazardous metal(loid)-resistant bacteria in environmental samples (soil/sediment/sludge) by metagenomics technology has not been widely studied so far. Therefore, the objectives of the present study have been aimed to profile the elevated As-, Cd- and Hg-resistant bacteria by metagenomic-DNA fingerprinting using PCR–DGGE of sediment and sludge samples for exploration and determination of potential toxic and hazardous metal(loid)-resistant bacteria/bacterial consortium and application of them to remediate these hazardous metal(loid)-contaminated environment as a promising bioremediation technology.

2 Materials and methods

2.1 Study area and sampling

Generally, pollutants migrate from point and non-point sources to coastal bottleneck habitats through the runoff water carrying network of a land leading to enrichment of pollutants especially nondegradable metal(loid)s in these habitats. Therefore, microbial communities in coastal habitats may opportunistically acquire pollutant-resistant properties due to frequent exposure to concentrated pollutants. Considering this phenomena, the present study collected four environmental samples, sludge (S1) of a canal carrying agricultural runoff in a coastal region of North 24 Parganas, India (22°53′00′′N, 88°33′00′′E); sludge (S2) of a canal and sediment (S3) from a coastal region in Kochi, Japan (33°34′00′′N, 133°33′00″E); and sediment (S4) from coastal region in Da Nang, Vietnam (16°2′38″N and 108°11′58″E) (Fig. 1). Three sludge/sediment samples (0–5 mm) from each sampling station were randomly collected and blended properly. An aliquot of each sample was preserved into sterilized plastic bottles at − 20 °C for PCR–DGGE study, and another aliquot was used to measure the As, Cd and Hg content of sample using the method described by Bhakta and Munekage (2008).
Fig. 1

Map of East Asia showing the four sampling areas (S1–S4) in three investigated countries (North 24 Parganas, India; Kochi, Japan; Da Nang, Vietnam)

2.2 Metal(loid) solution

The arsenic (As), cadmium (Cd) and mercury (Hg) solutions were prepared from stock solutions of arsenic trioxide (As2O3), cadmium chloride (CdCl2) and mercuric chloride (HgCl2) (Cica-Reagent, Kanto Chemical Co., Inc., Tokyo, Japan), respectively, and sterilized before use.

2.3 Enrichment culture of resistant bacteria/bacterial consortium

The collected samples were used to generate an enrichment culture in high concentration of heavy metal(loid) containing medium for selecting As-, Cd- and Hg-resistant bacterial communities following the method described by Bhakta et al. (2012b) with required modifications. The enrichment culture employed twelve sterile test tubes grouped into three (for three heavy metal(loid)s) having four test tubes (for four samples, S1–S4) in each group (3 × 4) (Fig. 2). The three groups were provided with As (100 mg/l), Cd (100 mg/l) and Hg (20 mg/l) supplemented with tryptic soy broth (TSB) medium at the volume of 9 ml/test tube. In order to obtain high metal(loid)-resistant bacteria/bacterial consortium, the study considered As (100 mg/l) and Cd (100 mg/l) concentrations on the basis of previous experiments (Bhakta et al. 2012a, 2014), whereas a lower Hg (20 mg/l) concentration was used in the present study, since a screening experiments revealed no growth at higher Hg concentration (data not shown). The preserved samples were brought to normal temperature; 1 g of each sample was suspended in 9 ml 0.85% physiological saline and vortexed to get a homogenous suspension. One milliliter aliquot of each sample suspension was aseptically inoculated in the 9 ml As, Cd or Hg—TSB media and incubated at 37 °C for 3 days in an orbital shaker incubator. The bacterial growth in the test tube was observed visually on the 3rd day and recorded by spectrophotometer. The incubated supernatant TSB was collected from each test tube and preserved in 20% glycerol at − 20 °C for subsequent study.
Fig. 2

Experimental protocol followed for enrichment culture of As-, Cd- and Hg-resistant bacteria/bacterial consortium in four sludge/sediment samples (S1–S4) employed in study

2.4 Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR–DGGE)

One milliliter of preserved enriched cultured broth was centrifuged; supernatant was discarded leaving the metal(loid)-resistant bacterial community remaining. The total DNA of the bacteria was extracted following the methods described by Ruiz-Barba et al. (2005) and was used as a source of DNA template for PCR. The 16S rDNA fragments were amplified by PCR using the universal primers, 341F (5´-CCTACGGGAGGCAGCAG-3´) and 534R (5´-ATTACCGCGGCTGCTGG CA-3´) (Invitrogen) and the thermocycler PC818 (ASTEC program temperature control system). A GC clamp (5′-cgcccgccgcgcgcggcgggcggggcgggggcacgggggg-3′) was linked to the first primer to obtain F341-GC (5′-cgcccgccgcgcgcggcgggcggggcgggggcacggggggCCTACGGGAGGCAGCAG-3′). The PCR system (40 µl) contained 20 µl of AmpliTaq Gold® 360 Master Mix with 1 µl 360 GC Enhance (Applied Biosystems), 4 µl of each primer (341F-GC clamp and 534R), 9 µl nuclease free water and 2 µl template DNA. The thermocycle program was as follows: 95 °C for 10 min; 30 cycles of 95 °C for 30 s, 54 °C for 30 s, and 72 °C for 1 min; and a final extension step at 72 °C for 7 min. The PCR products were detected by electrophoresis on a 1.2% agarose gel, stained with ethidium bromide and visualized under UV light.

The DGGE was performed in a DGGE apparatus (Bio-Rad, Richmond, CA, USA) at 58 °C on 8% polyacrylamide gel with denaturing ranges from 30 to 50%. The electrophoresis running time was 2.5 h at 150 V. The gel (16 × 16 cm) was stained by SYBR Gold; bands were visualized using a UV transilluminator and photographed.

2.5 Identification of resistant bacterial strain

The DNA containing bands from the polyacrylamide gel were purified by polyacrylamide gel extraction kit (QIAEX® II, QIAGEN). The sequencing of purified DNA was performed using an automated DNA sequencer (Applied Biosystems, 3100-Avant Genetic Analyzer) (Bhakta et al. 2012b, 2014). This sequence was used for bacterial identification using BLAST (Basic logical alignment search tool) at NCBI and DDBJ.

2.6 Heavy metal(loid) bioremediation of resistant bacteria/bacterial consortium

The preserved resistant bacteria/bacterial consortium was cultured in TSB for 24 h at 37 °C to obtain fresh culture. Bacterial growth was not found in inoculums of the S4 and S1 samples of the Cd- and Hg-supplemented TSB, respectively. The bioremediation study was executed by measuring the heavy metal(loid) uptake of the resistant bacteria/bacterial consortium cells using the method described by Bhakta et al. (2012b). Freshly (24 h) cultured bacterial cells were harvested, centrifuged to pellet the cells and washed by sterilized milli-Q water thrice. The cells (40 mg [wet weight]) were resuspended in 10 ml of sterile 1 mg/l As, Cd or Hg solution, in triplicate. After incubation at 37 °C, samples were collected at 24 and 48 h, centrifuged to pellet cells and the supernatant was passed through a 0.25 μm filter (Advantec, Tokyo) for analysis.

The As, Cd and Hg content of the samples were analyzed using an ICP–AES (ICPS-1000IV; Shimadzu, Tokyo), an atomic absorption spectrophotometer (AA-6800; Shimadzu, Tokyo) and a RA-3 Mercury Analyzer (Nippon Instruments Corporation, Tokyo), respectively (Bhakta and Munekage 2008, 2010; Bhakta et al. 2012a, b, 2014).

3 Results and discussion

3.1 Enrichment culture of resistant bacteria/bacterial consortium

The measured concentrations of As, Cd and Hg of four sludge/sediment samples are shown in Table 1, which indicating the metal(loid)s contamination in studied habitat with some exceptions.
Table 1

As, Cd and Hg content in the sludge/sediment samples employed in study

Metal(loid) (µg/kg)

Samples

S1

S2

S3

S4

As

1938 ± 20

283 ± 11

1016 ± 35

1860 ± 10

Cd

1407 ± 12

530 ± 19

813 ± 16

108 ± 25

Hg

23 ± 3.5

207 ± 15

178 ± 22

114 ± 16

Bacterial growth from all samples was clearly observed in the TSB media provided with As (100 mg/l) except sample S2, whereas clear growth of bacteria was not visible in all samples cultured in TSB media supplemented with Cd (100 mg/l) and Hg (20 mg/l). These results suggest that S1, S3 and S4 samples contain a high number and diversity of As-resistant bacteria, whereas very few bacteria were resistant to 100 mg/l Cd and 20 mg/l Hg concentrations in the four samples. It can be conferred herein that majority microbes of employed samples were commonly high resistant to As compared to that of Cd and Hg, since the toxic impacts of Cd and Hg against microbes are probably higher than that of As, which strongly inhibit to develop the resistant properties in most of the microbes. Additionally, it is known that some species of autotrophic and heterotrophic microorganisms use arsenic oxyanions for their regeneration of energy and use arsenate as their nutrient in respiratory process (Lim et al. 2014). Therefore, number and diversity of As-resistant bacteria were higher compared to Cd- and Hg-resistant bacteria.

3.2 Analysis of PCR–DGGE

The DGGE analysis demonstrated variations in the intensity of DNA bands in the four samples incubated in the three heavy metal(loid). High-intensity DNA bands (A, C, D, E, F, G and H) were found in the S1, S3 and S4 samples, whereas only faint A and D bands was observed in the S2 sample cultured in 100 mg/l As medium (Fig. 3). Only one kind of faint B DNA band was found in the S1, S2 and S3 samples cultured in 100 mg/l Cd medium, whereas two types of faint DNA bands (B and G) were found in the S2, S3 and S4 samples cultured in 20 mg/l Hg medium (Fig. 3). This analysis of PCR–DGGE band intensity indicated the quantitative (numerical) variation in the heavy metal(loid)-resistant bacterial populations. It may be concluded that As-resistant bacterial species (A, C, D, E, F, G and H) were dominant in all samples except S2, whereas only one Cd-resistant bacterium (B) was dominant in all samples except S4, and two Hg-resistant bacteria (B and G) were dominant in all samples except S1. This is equivalent to previous analysis where bacteria isolated from sewage sludge and coastal sediment showed higher As and Pb resistance capacity but not significant Cd resistance (Bhakta et al. 2010, 2012b).
Fig. 3

Metagenomic–DNA fingerprinting pattern of As-, Cd- and Hg-resistant bacteria/bacterial consortium from four sludge/sediment samples (S1–S4) using PCR–DGGE. The different bands (A–H) of metagenomic–DNA fingerprint indicate the different bacteria strains identified by 16S rDNA sequencing

The results of PCR–DGGE analysis showed that eight resistant bacterial strains A, B, C, D, E, F, G and H were found in samples S1, S2, S3 and S4. Of the eight, 7 types of bacterial strains were appeared as As-resistant. The As-resistant strain A was found in all samples and F appeared in S1, S3, S4 samples, whereas strains C, D and G were exclusively found in S1 and strains E and H were exclusive in sample S4. Only one Cd-resistant strain B was detected in S1, S2 and S3 samples. The strains B and G were appeared as Hg-resistant in S2, S3 and S4 samples. These results indicated that the diversity of As-resistant bacterial species was significantly greater compared to the Cd- and Hg-resistant bacterial species diversity in the four samples. Generally, heavy metal(loid) contamination of the environment is greatly responsible for acquiring the resistance properties of bacteria in the sample investigated. Considering this fact, therefore, the presence of dominant As-resistant bacteria indicates arsenic contamination in the investigated areas of India, coastal area of Japan, and Vietnam, whereas the sludge collected from area S2 in Japan may not be As contaminated due to no apparent As-resistant bacterial dominance and diversity. The bacterial community studied by DGGE revealed that heavy metal contamination in marine sediments changes the bacterial community structure (Yao et al. 2017) and in agricultural soils close to copper and zinc smelters may provoke changes in the composition of soil bacterial community and a decrease of the bacterial diversity (Li et al. 2006; Wang et al. 2007; Altimira et al. 2012). However, changes in the soil bacterial community exposed to heavy metals may vary depending of soil properties, heavy metal bioavailability and the indigenous microbial groups in soil (Ranjard et al. 2006). Bhakta et al. (2012a, b) postulated that microbial communities of coastal sediments and sewage sludge samples acquire resistance properties due to frequent exposure to various heavy metals transported by runoff water. The PCR–DGGE also revealed that the strain B is resistant to both Cd and Hg, while strain G is resistant to both As and Hg, whereas all remaining strains are resistant to only As. This indicated that the strain B and G have acquired multi heavy metal(loid)-resistance ability. Bhakta et al. (2012b) and Qing et al. (2007) also showed high multi-resistance ability of bacteria.

Irrespective of heavy metal(loid) specificity, S1, S2, S3 and S4 samples collectively contain six (A, B, C, D, F and G), three (A, B and G), four (A. B, F and G) and six (A, B, E, F, G and H) bacterial strains, respectively. This clearly suggested that S1 and S4 samples have higher bacterial diversity than the S2 and S3 samples. The high dominance and diversity of bacterial species in the canal sludge of India and coastal sediment of Vietnam samples may be due to the effect of the tropical zones. Bhakta et al. (2012b) revealed that coastal sediments and sewage sludge are the rich source of heavy metal(loid)-resistant bacteria.

3.3 Identification of resistant strain

The BLAST homology search of amplified 16S rDNA nucleotide sequence from the resistant strains revealed similarity to Lysinibacillus sp. (A), uncultured Lactobacillaceae bacterium (B), an uncultured soil bacterium clone (C), Staphylococcus sciuri (D), Bacillus fastidiosus (E), Bacillus niacin (F), Clostridium sp. (G) and Bacillus sp. (H). Bacillus cereus and Enterobacter cloacae were previously identified as Cd-resistant bacterial strains from soil of Pb–Zn tailing in a suburb of Beijing City (Quing et al. 2007). A number various heavy metal(loid)-resistant Lactobacillus sp., Bacillus sp. and Enterococcus sp. have also been isolated from coastal sediments and sludge samples of India, Japan and Vietnam (Bhakta et al. 2012a, b), Enterobacter sp. and Klebsiella pneumoniae from wastewater (Abbas et al. 2014), and Vibrio fluvialis from industrial effluents (Saranya et al. 2017). Figueiredo et al. (2016) identified aerobic Hg-resistant in the Tagus Estuary (Portugal) for Hg bioremediation.

3.4 Heavy metal(loid) bioremediation of resistant bacteria/bacterial consortium

The removal efficiency of As, Cd and Hg by the corresponding metal(loid)-resistant bacteria/bacterial consortium isolated from each sample is shown in Fig. 4. Cd-resistant bacteria/bacterial consortiums revealed highest respective metal(loid) removal efficiency compared to that of the As- and Hg-resistant bacteria/bacterial consortiums and showed the following order of metal(loid) removal efficiency of respective resistant bacteria/bacterial consortiums: Cd > Hg > As. It implies that Cd-resistant bacteria/bacterial consortiums acquired excellent respective metal(loid) removing capacity than that of the other two, As- and Hg-resistant bacteria/bacterial consortiums, since cellular mechanism of Cd-resistant bacteria/bacterial consortiums in removing and tackling respective metal(loid) is probably efficient than As- and Hg-resistant bacteria/bacterial consortiums studied herein.
Fig. 4

As, Cd and Hg removal properties of As-, Cd- and Hg-resistant bacteria/bacterial consortia obtained by enrichment culture of four sludge/sediment samples (S1–S4)

In case of As, As-resistant bacteria/bacterial consortium of S1 removed higher percentage (90–190%) of As compared to that of the As-resistant bacteria/bacterial consortiums of S2, S3 and S4, which might be due to the presence of the high dominance and diversity of As-resistant bacterial species and especially for the presence of uncultured soil bacterium clone (C) in S1 as proved from the enrichment culture and PCR–DGGE analysis. There was no remarkable Cd or Hg removal difference among S1, S2 and S3 of Cd or among S2, S3 and S4 of Hg-resistant bacteria/bacterial consortiums obtained from samples. Since only uncultured Lactobacillaceae was found as Cd-resistant bacterium in S1, S2 and S3 samples, which showed almost similar Cd removal rate in Cd bioremediation study, and in Hg removal study, almost similar amount of Hg removal was estimated in S2, S3 and S4 samples by uncultured Lactobacillaceae bacterium and Clostridium sp. constituting Hg-resistant bacterial consortium. The heavy metal(loid) (As, Cd and Hg) removal performances of corresponding metal(loid)-resistant bacteria/bacterial consortium were temporally increased (Fig. 4). The above results also imply that the resistant bacteria/bacterial consortium can survive in high heavy metal(loid) contaminated environment and can remove appreciable amounts of heavy metal(loid) from ambience probably due to having higher uptake and resistance capacity, which might play a pivotal role in bioremediation process of metalloid and/or heavy metal in environment (Mejias Carpio et al. 2016; Kvasnova et al. 2017). The metal(loid)-resistant bacteria, in particular a mixed consortia are therefore a promising tool to remove metals from an aqueous phase (Bhakta et al. 2012a, b, 2014; Carpio et al. 2014; O’Brien and Buckling 2015; Abbas et al. 2015; Mejias Carpio et al. 2016; Kvasnova et al. 2017). Indeed, Singh et al. (2012) proposed mixed bacterial consortia as an emerging tool to remove hazardous trace metals.

4 Conclusions

This study has drawn the following conclusions of As-, Cd- and Hg-resistant bacterial community structure of the investigated habitats: (1) the dominance and diversities of As-resistant bacterial species were higher in the investigated samples compared to Cd- and Hg-resistant bacterial species diversities and (2) the dominance and diversities of As-resistant bacterial species in the canal sludge of India and coastal sediment of Vietnam were greater than the remaining samples. The dominant As-resistant bacteria, therefore, indicated arsenic contamination in the investigated habitat of India, coastal habitat of Japan and Vietnam which is also proved by high As content in samples. The metal(loid) uptake properties of the identified resistant bacteria/bacterial consortia demonstrated their potential application for heavy metal(loid) bioremediation. It can be concluded that the profiling of heavy metal(loid)-resistant bacterial community structure of a habitat by metagenomic-DNA fingerprinting using PCR–DGGE is an excellent tool to explore novel heavy metal(loid)-resistant bacteria/bacterial consortia for applying in metal(loid) bioremediation and as an alternative indicator for monitoring and identifying heavy metal(loid) contamination in the environment (water and soil).

Notes

Acknowledgements

Authors are grateful to Japan Society for the promotion of Science (JSPS) for sponsoring research fund and fellowship (FY2009 JSPS postdoctoral fellowship) to Dr. Bhakta to carry out the study. Authors are also especially grateful to Dr. J. K. Pittman for reviewing the manuscript.

Compliance with ethical standards

Conflicts of interest

The authors declare that they have no conflict of interest.

References

  1. Abbas SZ, Riaz M, Ramzan N, Zahid MT, Shakoori FR, Rafatullah M (2014) Isolation and characterization of arsenic resistant bacteria from wastewater. Braz J Microbiol 45:1309–1315CrossRefGoogle Scholar
  2. Abbas SZ, Rafatullah M, Ismail N, Lalung J (2015) Isolation and characterization of Cd-resistant bacteria from industrial wastewater. Desalin Water Treat 56:1037–1046CrossRefGoogle Scholar
  3. Altimira F, Yáñez C, Bravo G, González M, Rojas LA, Seeger M (2012) Characterization of copper–resistant bacteria and bacterial communities from copper–polluted agricultural soils of central Chile. BMC Microbiol 12:193CrossRefGoogle Scholar
  4. Bhakta JN (2016) Microbial response against metal toxicity. In: Rathoure AK, Dhatwalia VK (eds) Toxicity and waste management using bioremediation. IGI Global, PA, pp 75–96.  https://doi.org/10.4018/978-1-4666-9734-8.ch004 CrossRefGoogle Scholar
  5. Bhakta JN (2017) Metal toxicity in microorganism. In: Bhakta JN (ed) Handbook of research on inventive bioremediation techniques. IGI Global, PA, pp 1–23.  https://doi.org/10.4018/978-1-5225-2325-3.ch001 CrossRefGoogle Scholar
  6. Bhakta JN, Munekage Y (2008) Role of ecosystem components in Cd removal process of aquatic ecosystem. Ecol Eng 32:274–280CrossRefGoogle Scholar
  7. Bhakta JN, Munekage Y (2010) Mercury removal by some soils of Japan from aquatic environment. Environ Eng Manag J 9(4):503–510Google Scholar
  8. Bhakta JN, Ohnishi K, Munekage Y, Iwasaki K (2010) Isolation and probiotic characterization of arsenic–resistant lactic acid bacteria for uptaking arsenic. Int J Chem Biol Eng 3:4Google Scholar
  9. Bhakta JN, Munekage Y, Ohnishi K, Jana BB (2012a) Isolation and identification of cadmium and lead resistant lactic acid bacteria for applying as metal removing probiotic. Int J Environ Sci Technol 9:433–440CrossRefGoogle Scholar
  10. Bhakta JN, Ohnishi K, Munekage Y, Iwasaki K, Wei M (2012b) Characterization of lactic acid bacteria–based probiotics as heavy metals sorbents. J Appl Microbiol 112:1193–1206CrossRefGoogle Scholar
  11. Bhakta JN, Munekage Y, Ohnishi K, Jana BB, Balcazar JL (2014) Isolation and characterization of cadmium and arsenic absorbing bacteria for bioremediation. Water Air Soil Pollut 225(10):2151.  https://doi.org/10.1007/s11270-014-2151-2 CrossRefGoogle Scholar
  12. Bidstrup PC (1964) Toxicity of mercury and its compounds. Elsevier, AmsterdamGoogle Scholar
  13. Campbell JH, Clark JS, John CZ (2009) PCR–DGGE comparison of bacterial community structure in fresh and archived soils sampled along a Chihuahuan Desert elevational gradient. Microb Ecol 57(2):261–266CrossRefGoogle Scholar
  14. Carpio IE, Machado-Santelli G, Sakata SK, Ferreira Filho SS, Rodrigues DF (2014) Copper removal using a heavy-metal resistant microbial consortium in a fixed-bed reactor. Water Res 62:156–166CrossRefGoogle Scholar
  15. Carpio IEM, Franco DC, Sato MIZ, Sakata S, Pellizari VH, Ferreira Filho SS, Rodrigues DF (2016) Biostimulation of metal-resistant microbial consortium to remove zinc from contaminated environments. Sci Total Environ 550:670–675.  https://doi.org/10.1016/j.scitotenv.2016.01.149 CrossRefGoogle Scholar
  16. Curtis TP, Sloan WT (2004) Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology. Curr Opin Microbiol 7:221–226CrossRefGoogle Scholar
  17. Dinsdale EA, Edwards RA, Hall D et al (2008) Functional metagenomic profiling of nine biomes. Nature 452:629–632CrossRefGoogle Scholar
  18. Figueiredo NL, Canário J, O’Driscoll NJ, Duarte A, Carvalho C (2016) Aerobic Mercury-resistant bacteria alter Mercury speciation and retention in the Tagus Estuary (Portugal). Ecotoxicol Environ Saf 124:60–67CrossRefGoogle Scholar
  19. Gadd GM (1990) Heavy metal accumulation by bacteria and other microorganisms. Experientia 46:834–840CrossRefGoogle Scholar
  20. Giller K, Witter E, McGrath SP (1998) Toxicity of heavy metals to microorganisms and microbial processes in agricultural soils: a review. Soil Biol Biochem 30:1389–1414CrossRefGoogle Scholar
  21. Gupta UC, Gupta SC (1998) Trace element toxicity relationships to crop production and livestock and human health: implications for management. Commun Soil Sci Plant Anal 29(11–14):1491–1522CrossRefGoogle Scholar
  22. Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669–685CrossRefGoogle Scholar
  23. Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5:R245–R249CrossRefGoogle Scholar
  24. Hoover J, Gonzales M, Shuey C, Barney Y, Lewis J (2017) Elevated arsenic and uranium concentrations in unregulated water sources on the Navajo Nation, USA. Expo Health 9:113–124.  https://doi.org/10.1007/s12403-016-0226-6 CrossRefGoogle Scholar
  25. Jafari SA, Cheraghi S (2014) Mercury removal from aqueous solution by dried biomass of indigenous Vibrio parahaemolyticus PG02: kinetic, equilibrium, and thermodynamic studies. Int Biodeterior Biodegrad 92:12–19CrossRefGoogle Scholar
  26. Kumar S, Krishnani KK, Bhushan B, Brahmane MP (2015) Metagenomics: retrospect and prospects in high throughput age. Biotech Res Int 2015, Article ID 121735, p 13. https://dx.doi.org/10.1155/2015/121735
  27. Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P (2008) A bioinformatician’s guide to metagenomics. Microbiol Mol Biol Rev 72:557–578CrossRefGoogle Scholar
  28. Kvasnova S, Hamarová L, Pristaš P (2017) Zinc bioaccumulation by microbial consortium isolated from nickel smelter sludge disposal site. Nova Biotechnol Chim 16:48–53.  https://doi.org/10.1515/nbec-2017-0007 Google Scholar
  29. Li Z, Xu J, Tang C, Wu J, Muhammad A, Wang H (2006) Application of 16S rRNA PCR amplification and DGGE fingerprinting for detection of shift microbial community diversity in Cu–, Zn– and Cd–contaminated paddy soil. Chemosphere 62:1374–1380CrossRefGoogle Scholar
  30. Lim KT, Shukor MY, Wasoh H (2014) Physical, chemical, and biological methods for the removal of arsenic compounds. BioMed Res Int 2014, Article ID 503784, p 9. https://dx.doi.org/10.1155/2014/503784
  31. Logue JB, Bürgmann H, Robinson CT (2008) Progress in the ecological genetics and biodiversity of freshwater bacteria. Bioscience 58:103–113.  https://doi.org/10.1641/B580205 CrossRefGoogle Scholar
  32. Martínez-Alonso M, Escolano J, Montesinos E, Gaju N (2010) Diversity of the bacterial community in the surface soil of a pear orchard based on 16S rRNA gene analysis. Int Microbiol 13(3):123–134Google Scholar
  33. Min-sheng H, Jing P, Le-ping Z (2001) Removal of heavy metals from aqueous solutions using bacteria. J Shanghai Univ 5(3):253–259CrossRefGoogle Scholar
  34. O’Brien S, Buckling A (2015) Hijacking the social lives of microbial populations to clean up heavy metal contamination. EMBO Rep 16:1241–1245CrossRefGoogle Scholar
  35. Pettit RK (2004) Soil DNA libraries for anticancer drug discovery. Cancer Chemother Pharmacol 54:1–6CrossRefGoogle Scholar
  36. Qing H, Min-Na D, Hong-Yan Q, Xiang-Ming X, Guo-Qiang Z, Min Y (2007) Detection, isolation, and identi cation of cadmium–resistant bacteria based on PCR–DGGE. J Environ Sci 19:1114–1119CrossRefGoogle Scholar
  37. Ranjard L, Echairi A, Nowak V, Lejon D, Nouaim R, Chaussod R (2006) Field and microcosm experiments to evaluate the effects of agricultural Cu treatment on the density and genetic structure of microbial communities in two different soils. FEMS Microbiol Ecol 58:303–315CrossRefGoogle Scholar
  38. Ruiz-Barba JL, Maldonado A, Jiménez-Díaz R (2005) Small–scale total DNA extraction from bacteria and yeast for PCR applications. Anal Biochem 347:333–335CrossRefGoogle Scholar
  39. Saranya K, Sundaramanickam A, Shekhar S, Swaminathan S, Balasubramanian T (2017) Bioremediation of mercury by Vibrio fluvialis screened from industrial effluents. BioMed Res Int, Article ID 6509648, 6 pages. https://dx.doi.org/10.1155/2017/6509648
  40. Schmeisser C, Steele H, Streit WR (2007) Metagenomics, biotechnology with non–culturable microbes. Appl Microbiol Biotechnol 75:955–962CrossRefGoogle Scholar
  41. Signes-Pastor AJ, Carey M, Vioque J, Navarrete-Mun˜oz EM, Rodrıguez-Dehli C, Tardon A, Begon˜a-Zubero M, Santa-Marina L, Vrijheid M, Casas M, Llop S, Gonzalez-Palacios S, Meharg AA (2017) Urinary arsenic speciation in children and pregnant women from Spain. Expo Health 9:105–111.  https://doi.org/10.1007/s12403-016-0225-7 CrossRefGoogle Scholar
  42. Singh PK, Singh AL, Kumar A, Singh MP (2012) Mixed bacterial consortium as an emerging tool to remove hazardous trace metals from coal. Fuel 102:227–230CrossRefGoogle Scholar
  43. Sinha A, Pant KK, Khare SK (2012) Studies on mercury bioremediation by alginate immobilized mercury tolerant Bacillus cereus cells. Int Biodeterior Biodegrad 71:1–8CrossRefGoogle Scholar
  44. Smalla K, Oros-Sichler M, Milling A, Heuer H, Baumgarte S, Becker R, Neuber G, Kropf S, Ulrich A, Tebbe CC (2007) Bacterial diversity of soils assessed by DGGE, T-RFLP and SSCP fingerprints of PCR–amplified 16S rRNA gene fragments: do the different methods provide similar results? J Microbiol Methods 69(3):470–479CrossRefGoogle Scholar
  45. Streit WR, Schmitz RA (2004) Metagenomics—the key to the uncultured microbes. Curr Opin Microbiol 7:492–498CrossRefGoogle Scholar
  46. Torsvik V, Ovreas L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240–245CrossRefGoogle Scholar
  47. Umar AF, Tahir F, Agbo EB (2017) Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR–DGGE) profile of bacterial community from agricultural soils in Bauchi, North-East Nigeria. Adv Microbiol 7:480–486CrossRefGoogle Scholar
  48. Wang Y, Shi J, Wang H, Lin Q, Chen X, Chen Y (2007) The influence of soil heavy metals pollution on soil microbial biomass, enzyme activity, and community composition near a copper smelter. Ecotoxicol Environ Saf 67:75–81CrossRefGoogle Scholar
  49. Watts MP, Khijniak TV, Boothman C, Lloyd JR (2015) Treatment of alkaline Cr(VI)-contaminated leachate with an alkaliphilic metal-reducing bacterium. Appl Environ Microbiol 81(16): eScholarID:268368Google Scholar
  50. Wei G, Fan L, Zhu W, Fu Y, Yu J, Tang M (2009) Isolation and characterization of the heavy metal resistant bacteria CCNWRS33–2 isolated from root nodule of Lepedeza cuneata in gold mine tailings in China. J Hazard Mater 162:50–56CrossRefGoogle Scholar
  51. Yao X-F, Zhang J-M, Tian L, Guob J-H (2017) The effect of heavy metal contamination on the bacterial community structure at Jiaozhou Bay, China. Braz J Microbiol 48:71–78.  https://doi.org/10.1016/j.bjm.2016.09.007 CrossRefGoogle Scholar

Copyright information

© Joint Center on Global Change and Earth System Science of the University of Maryland and Beijing Normal University and Springer-Verlag GmbH Germany, part of Springer Nature 2017

Authors and Affiliations

  • Jatindra N. Bhakta
    • 1
  • Susmita Lahiri
    • 1
  • Feroze A. Bhuiyna
    • 2
  • Md. Rokunuzzaaman
    • 2
  • Kouhei Ohonishi
    • 2
  • Kozo Iwasaki
    • 3
  • Bana B. Jana
    • 1
  1. 1.Department of Ecological Studies & International Centre for Ecological EngineeringUniversity of KalyaniKalyaniIndia
  2. 2.Research Institute of Molecular Genetics, Faculty of AgricultureKochi UniversityNankokuJapan
  3. 3.Life and Environmental Medical Science Cluster, Faculty of AgricultureUniversity of KochiNankokuJapan

Personalised recommendations