Skip to main content
SpringerLink
Log in

Employing gene chip technology for monitoring and assessing soil heavy metal pollution

  • Published:
Environmental Monitoring and Assessment Aims and scope Submit manuscript

A Correction to this article was published on 28 February 2022

This article has been updated

Abstract

Soil heavy metals pollution can cause many serious environment problems because of involving a very complex pollution process for soil health. Therefore, it is very important to explore methods that can effectively evaluate heavy metal pollution. Researchers were actively looking for new ideas and new methods for evaluating and predicting levels of soil heavy metal pollution. The study on microbial communities is one of the effective methods using gene chip technology. Gene chip technology, as a high-throughput metagenomics analysis technique, has been widely used for studying the structure and function of complex microbial communities in different polluted environments from different pollutants, including the soil polluted by heavy metals. However, there is still a lack of a systematic summarization for the polluted soil by heavy metals. This paper systematically analyzed soil heavy metals pollution via reviewing previous studies on applying gene chip technology, including single species, tolerance mechanisms, enrichment mechanisms, anticipation and evaluation of soil remediation, and multi-directional analysis. The latest gene chip technologies and corresponding application cases for discovering critical species and functional genes via analyzing microbial communities and evaluating heavy metal pollution of soil were also introduced in this paper. This article can provide scientific guidance for researchers actively investigating the soil polluted by heavy metals.

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
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

Change history

References

  • Assuno, A. G. L., Schat, H., & Aarts, M. G. M. (2003). Thlaspi caerulescens, an attractive model species to study heavy metal hyperaccumulation in plants. New Phytologist. https://doi.org/10.1046/j.1469-8137.2003.00820.x

    Article  Google Scholar 

  • Azarbad, H., Niklinska, M., Laskowski, R., van Straalen, N. M., van Gestel, C. A., Zhou, J., He, Z., Wen, C., & Roling, W. F. (2015). Microbial community composition and functions are resilient to metal pollution along two forest soil gradients. FEMS Microbiology Ecology, 91(1), 1–11. https://doi.org/10.1093/femsec/fiu003

    Article  CAS  Google Scholar 

  • Azevedo, H., Azinheiro, S. G., Muñoz-Mérida, A., Castro, P. H., Huettel, B., Aarts, M. G., & Assunção, A. G. (2016). Transcriptomic profiling of Arabidopsis gene expression in response to varying micronutrient zinc supply. Genomics Data, 7, 256–258. https://doi.org/10.1016/j.gdata.2016.01.021

    Article  Google Scholar 

  • Bai, S., Li, J., He, Z., Van Nostrand, J. D., Tian, Y., Lin, G., Zhou, J., & Zheng, T. (2013). GeoChip-based analysis of the functional gene diversity and metabolic potential of soil microbial communities of mangroves. Applied Microbiology and Biotechnology, 97(15), 7035–7048. https://doi.org/10.1007/s00253-012-4496-z

    Article  CAS  Google Scholar 

  • Becher, M., Talke, I. N., Krall, L., & Krämer, U. (2003). Cross-species microarray transcript profiling reveals high constitutive expression of metal homeostasis genes in shoots of the zinc hyperaccumulator Arabidopsis halleri. Plant Journal, 37(2), 251–268. https://doi.org/10.1046/j.1365-313x.2003.01959.x

    Article  Google Scholar 

  • Black, A., Wakelin, S., Hamonts, K., Gerard, E., & Condron, L. (2019). Impacts of long term copper exposure on abundance of nitrogen cycling genes and denitrification activity in pasture soils. Applied Soil Ecology, 138, 253–261. https://doi.org/10.1016/j.apsoil.2019.03.009

    Article  Google Scholar 

  • Brodie, E. L., DeSantis, T. Z., Joyner, D. C., Baek, S. M., Larsen, J. T., Andersen, G. L., Hazen, T. C., Richardson, P. M., Herman, D. J., & Tokunaga, T. K. (2006). Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Applied and Environment Microbiology, 72(9), 6288–6298. https://doi.org/10.1128/AEM.00246-06

    Article  CAS  Google Scholar 

  • Brodie, E. L., & Lynch, S. V. (2013). Phyloarrays. John Wiley & Sons, Ltd.

  • Castro-Ferreira, M. P., de Boer, T. E., Colbourne, J. K., Vooijs, R., van Gestel, C. A., van Straalen, N. M., Soares, A. M., Amorim, M. J., & Roelofs, D. (2014). Transcriptome assembly and microarray construction for Enchytraeus crypticus, a model oligochaete to assess stress response mechanisms derived from soil conditions. BMC Genomics, 15(1), 302. https://doi.org/10.1186/1471-2164-15-302

    Article  Google Scholar 

  • Cevher-Keskin, B., Yıldızhan, Y., Yüksel, B., Dalyan, E., & Memon, A. R. (2019). Characterization of differentially expressed genes to Cu stress in Brassica nigra by Arabidopsis genome arrays. Environmental Science and Pollution Research, 26(1), 299–311. https://doi.org/10.1007/s11356-018-3577-7

    Article  CAS  Google Scholar 

  • Chakraborty, R., Brodie, E. L., Nostrand, J. V., Zhou, J., & Hazen, T. C. (2008). Investigation of Cr (VI) tolerant bacteria from Cr (VI)-contaminated 100H site at Hanford, WA.

  • Chandler, D. P., Kukhtin, A., Mokhiber, R., Knickerbocker, C., Ogles, D., Rudy, G., Golova, J., Long, P., & Peacock, A. (2010). Monitoring microbial community structure and dynamics during in situ U (VI) bioremediation with a field-portable microarray analysis system. Environmental Science & Technology, 44(14), 5516–5522. https://doi.org/10.1021/es1006498

    Article  CAS  Google Scholar 

  • Cindy, S. (2015). Development of microarrays-based metagenomics technology for monitoring sulfate-reducing bacteria in subsurface environments. Glomics Inc.

  • Cong, J., Liu, X., Lu, H., Xu, H., Li, Y., Deng, Y., Li, D., & Zhang, Y. (2015). Analyses of the influencing factors of soil microbial functional gene diversity in tropical rainforest based on GeoChip 5.0. Genom Data, 5(5), 397–398. https://doi.org/10.1016/j.gdata.2015.07.010

    Article  Google Scholar 

  • Dalyan, E., Yüzbaşıoğlu, E., Keskin, B. C., Yıldızhan, Y., Memon, A., Ünal, M., & Yüksel, B. (2017). The identification of genes associated with Pb and Cd response mechanism in Brassica juncea L. by using Arabidopsis expression array. Environmental and Experimental Botany, 139, 105–115. https://doi.org/10.1016/j.envexpbot.2017.05.001

    Article  CAS  Google Scholar 

  • Dick, R., Muriel, D. B., Valeria, A., Pascal, B., Juliette, L., & Nico, V. S. (2012). Functional environmental genomics of a municipal landfill soil. Frontiers in Genetics. https://doi.org/10.3389/fgene.2012.00085

    Article  Google Scholar 

  • Epelde, L., Becerril, J. M., Kowalchuk, G. A., Deng, Y., Zhou, J., & Garbisu, C. (2010). Impact of metal pollution and Thlaspi caerulescens growth on soil microbial communities. Applied and Environment Microbiology, 76(23), 7843–7853. https://doi.org/10.1128/AEM.01045-10

    Article  CAS  Google Scholar 

  • Eyers, L., George, I., Schuler, L., Stenuit, B., Agathos, S. N., & El Fantroussi, S. (2004). Environmental genomics: Exploring the unmined richness of microbes to degrade xenobiotics. Applied Microbiology and Biotechnology, 66(2), 123–130. https://doi.org/10.1007/s00253-004-1703-6

    Article  CAS  Google Scholar 

  • Fountain, M. T., & Hopkin, S. P. (2005). Folsomia candida (Collembola): a “standard" soil arthropod. Annual Review of Entomology, 50(1), 201–222. https://doi.org/10.1146/annurev.ento.50.071803.130331

    Article  CAS  Google Scholar 

  • Gans, J., Wolinsky, M., & Dunbar, J. (2005). Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science, 309(5739), 1387–1390. https://doi.org/10.1126/science.1112665

    Article  CAS  Google Scholar 

  • Gorfer, M., Persak, H., Berger, H., Brynda, S., Bandian, D., & Strauss, J. (2009). Identification of heavy metal regulated genes from the root associated ascomycete Cadophora finlandica using a genomic microarray. Mycological Research, 113(12), 1377–1388. https://doi.org/10.1016/j.mycres.2009.09.005

    Article  CAS  Google Scholar 

  • Gu, Y., Joy, D. V. N., Liyou, W., Zhili, H., Yujia, Q., Fang-Jie, Z., Jizhong, Z., & Hauke, S. (2017). Bacterial community and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations. PLoS One, 12(5), e0176696. https://doi.org/10.1371/journal.pone.0176696

    Article  CAS  Google Scholar 

  • Hamadeh, H. K., Bushel, P. R., Jayadev, S., Martin, K., DiSorbo, O., Sieber, S., Bennett, L., Tennant, R., Stoll, R., Barrett, J. C., Blanchard, K., Paules, R. S., & Afshari, C. A. (2002). Gene expression analysis reveals chemical-specific profiles. Toxicological Sciences, 67(2), 2. https://doi.org/10.1093/toxsci/67.2.219

    Article  Google Scholar 

  • Handelsman, J., Rondon, M. R., Brady, S. F., Clardy, J., & Goodman, R. M. (1998). Molecular biological access to the chemistry of unknown soil microbes: A new frontier for natural products. Chemistry & Biology. https://doi.org/10.1016/s1074-5521(98)90108-9

    Article  Google Scholar 

  • He, Z., Deng, Y., Van Nostrand, J. D., Tu, Q., Xu, M., Hemme, C. L., Li, X., Wu, L., Gentry, T. J., Yin, Y., Liebich, J., Hazen, T. C., & Zhou, J. (2010). GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity. ISME Journal, 4(9), 1167–1179. https://doi.org/10.1038/ismej.2010.46

    Article  CAS  Google Scholar 

  • He, Z., Gentry, T. J., Schadt, C. W., Wu, L., Liebich, J., Chong, S. C., Huang, Z., Wu, W., Gu, B., Jardine, P., Criddle, C., & Zhou, J. (2007). GeoChip: A comprehensive microarray for investigating biogeochemical, ecological and environmental processes. The ISME Journal, 1(1), 67–77. https://doi.org/10.1038/ismej.2007.2

    Article  CAS  Google Scholar 

  • Hirano, T., & Tamae, K. (2011). Earthworms and soil pollutants. Sensors, 11(12), 11157–11167. https://doi.org/10.3390/s111211157

    Article  Google Scholar 

  • Hu, P., Brodie, E. L., Suzuki, Y., McAdams, H. H., & Andersen, G. L. (2005). Whole-genome transcriptional analysis of heavy metal stresses in caulobacter crescentus. Journal of Bacteriology, 187(24), 8437–8449. https://doi.org/10.1128/JB.187.24.8437-8449.2005

    Article  CAS  Google Scholar 

  • Jean-Marie, R., Michael, Z., & Erdogan, G. (2003). OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Research, 31(12), 3057–3062. https://doi.org/10.1093/nar/gkg426

    Article  Google Scholar 

  • Jiang, Z., Li, P., Wang, Y., Liu, H., Wei, D., Yuan, C., & Wang, H. (2019). Arsenic mobilization in a high arsenic groundwater revealed by metagenomic and Geochip analyses. Scientific Reports. https://doi.org/10.1038/s41598-019-49365-w

    Article  Google Scholar 

  • Jie, S., Li, M., Gan, M., Zhu, J., Yin, H., & Liu, X. (2016). Microbial functional genes enriched in the Xiangjiang River sediments with heavy metal contamination. BMC Microbiology, 16(1), 179. https://doi.org/10.1186/s12866-016-0800-x

    Article  CAS  Google Scholar 

  • Jin, M., & Li, J. W. (2008). Microarray application in environmental microbial community research. Microbiology China, 35(9), 1466–1471.

    CAS  Google Scholar 

  • Kang, S., Van, N. J. D., Gough, H. L., He, Z., Hazen, T. C., Stahl, D. A., & Zhou, J. (2013). Functional gene array–based analysis of microbial communities in heavy metals-contaminated lake sediments. Fems Microbiology Ecology, 86(2), 2. https://doi.org/10.1111/1574-6941.12152

    Article  CAS  Google Scholar 

  • Kawata, K., Yokoo, H., Shimazaki, R., & Okabe, S. (2007). Classification of heavy-metal toxicity by human DNA microarray analysis. Environmental Science & Technology, 41(10), 3769–3774. https://doi.org/10.1021/es062717d

    Article  CAS  Google Scholar 

  • Kuramae, E. E., Yergeau, E., Wong, L. C., Pijl, A. S., van Veen, J. A., & Kowalchuk, G. A. (2012). Soil characteristics more strongly influence soil bacterial communities than land-use type. FEMS Microbiology Ecology, 79(1), 12–24. https://doi.org/10.1111/j.1574-6941.2011.01192.x

    Article  CAS  Google Scholar 

  • Lemos, L. N., Fulthorpe, R. R., Triplett, E. W., & Roesch, L. F. (2011). Rethinking microbial diversity analysis in the high throughput sequencing era. Journal of Microbiological Methods, 86(1), 42. https://doi.org/10.1016/j.mimet.2011.03.014

    Article  CAS  Google Scholar 

  • Leydesdorff, L., Carley, S., & Rafols, I. (2012). Global maps of science based on the new web-of-science categories. Scientometrics, 94(2), 589–593. https://doi.org/10.1007/s11192-012-0784-8

    Article  Google Scholar 

  • Liang, Y., He, Z., Wu, L., Deng, Y., Li, G., & Zhou, J. (2010). Development of a common oligonucleotide reference standard for microarray data normalization and comparison across different microbial communities. Applied & Environmental Microbiology, 76(4), 1088–1094. https://doi.org/10.1128/AEM.02749-09

    Article  CAS  Google Scholar 

  • Madigan, M. T., Martinko, J. M., & Parker, J. (1996). Brock Biology of Microorganisms.

  • Memon, A. R., Yildizhan, Y., & Keskin, B. (2008). Phytoremediation of heavy metals from contaminated areas of Turkey. 4th European Bioremediation Conference Sep. pp. 3–6.

  • Mergeay, M., Monchy, S., Vallaeys, T., Auquier, V., Benotmane, A., Bertin, P., Taghavi, S., Dunn, J., Van Der Lelie, D., & Wattiez, R. (2003). Ralstonia metallidurans, a bacterium specifically adapted to toxic metals: Towards a catalogue of metal S, Vallaeys. T. FEMS Microbiology Reviews, 27(2–3), 385–410. https://doi.org/10.1016/S0168-6445(03)00045-7

    Article  CAS  Google Scholar 

  • Migeon, A., Blaudez, D., Wilkins, O., Montanini, B., Campbell, M. M., Richaud, P., Thomine, S., & Chalot, M. (2010). Genome-wide analysis of plant metal transporters, with an emphasis on poplar. Cellular and Molecular Life Sciences, 67(22), 3763–3784. https://doi.org/10.1007/s00018-010-0445-0

    Article  CAS  Google Scholar 

  • Monsieurs, P., Moors, H., Van Houdt, R., Janssen, P. J., Janssen, A., Coninx, I., Mergeay, M., & Leys, N. (2011). Heavy metal resistance in Cupriavidus metallidurans CH34 is governed by an intricate transcriptional network. BioMetals, 24(6), 1133–1151. https://doi.org/10.1007/s10534-011-9473-y

    Article  CAS  Google Scholar 

  • Montero-Palmero, M. B. (2014). Environmental impact of toxic metals and metalloids. The case of mercury. In: A transcriptomic study of the early responses of Medicago sativa to mercury, pp. 3.

  • Moore, C. M., Gaballa, A., Hui, M., Ye, R. W., & Helmann, J. D. (2005). Genetic and physiological responses of Bacillus subtilis to metal ion stress. Molecular Microbiology, 57(1), 27–40. https://doi.org/10.1111/j.1365-2958.2005.04642.x

    Article  CAS  Google Scholar 

  • Nelson, D. L., & Cox, M. M. (2005). Lehninger Principles of Biochemistry. Lehninger principles of biochemistry.

  • Nota, B., Timmermans, M. J., Franken, O., Montagne-Wajer, K., Mariën, J., Boer, M. E. D., Boer, T. E. D., Ylstra, B., Straalen, N. M. V., & Roelofs, D. (2008). Gene expression analysis of collembola in cadmium containing soil. Environmental Science & Technology, 42(21), 8152–8157. https://doi.org/10.1021/es801472r

    Article  CAS  Google Scholar 

  • Nota, B., Verweij, R. A., Molenaar, D., Ylstra, B., van Straalen, N. M., & Roelofs, D. (2010). Gene expression analysis reveals a gene set discriminatory to different metals in soil. Toxicological Sciences, 115(1), 34–40. https://doi.org/10.1093/toxsci/kfq043

    Article  CAS  Google Scholar 

  • Ochsner, U. A., Wilderman, P. J., Vasil, A. I., & Vasil, M. L. (2002). GeneChip® expression analysis of the iron starvation response in Pseudomonas aeruginosa: Identification of novel pyoverdine biosynthesis genes. Molecular Microbiology, 45(5), 1277–1287. https://doi.org/10.1046/j.1365-2958.2002.03084.x

    Article  CAS  Google Scholar 

  • Olsson-Francis, K., Van Houdt, R., Mergeay, M., Leys, N., & Cockell, C. S. (2010). Microarray analysis of a microbe-mineral interaction. Geobiology, 8(5), 446–456. https://doi.org/10.1111/j.1472-4669.2010.00253.x

    Article  CAS  Google Scholar 

  • Pathak, A., Shanker, R., Garg, S. K., & Manickam, N. (2011). Profiling of biodegradation and bacterial 16S rRNA genes in diverse contaminated ecosystems using 60-mer oligonucleotide microarray. Applied Microbiology and Biotechnology, 90(5), 1739–1754. https://doi.org/10.1007/s00253-011-3268-5

    Article  CAS  Google Scholar 

  • Plessl, M., Rigola, D., Hassinen, V., Aarts, M. G., Schat, H., & Ernst, D. (2005). Transcription profiling of the metal-hyperaccumulator Thlaspi caerulescens (J. & C. PRESL). Zeitschrift Für Naturforschung C, 60(3–4), 216–223. https://doi.org/10.1515/znc-2005-3-406

    Article  CAS  Google Scholar 

  • Rastogi, G., Barua, S., Sani, R. K., & Peyton, B. M. (2011). Investigation of microbial populations in the extremely metal-contaminated Coeur d’Alene River sediments. Microbial Ecology, 62(1), 1–13. https://doi.org/10.1007/s00248-011-9810-2

    Article  Google Scholar 

  • Rastogi, G., Osman, S., Vaishampayan, P. A., Andersen, G. L., Stetler, L. D., & Sani, R. K. (2010). Microbial diversity in uranium mining-impacted soils as revealed by high-density 16S microarray and clone library. Microbial Ecology, 59(1), 94–108. https://doi.org/10.1007/s00248-009-9598-5

    Article  CAS  Google Scholar 

  • Rivas, L. A., García-Villadangos, M., Moreno-Paz, M., Cruz-Gil, P., Gómez-Elvira, J., & Parro, V. (2008). A 200-antibody microarray biochip for environmental monitoring: Searching for universal microbial biomarkers through immunoprofiling. Analytical Chemistry, 80(21), 7970–7979. https://doi.org/10.1021/ac8008093

    Article  CAS  Google Scholar 

  • Roelofs, D., Janssens, T. K., Timmermans, M. J., Nota, B., Marien, J., Bochdanovits, Z., Ylstra, B., & Van Straalen, N. M. (2009). Adaptive differences in gene expression associated with heavy metal tolerance in the soil arthropod Orchesella cincta. Molecular Ecology, 18(15), 3227–3239. https://doi.org/10.1111/j.1365-294X.2009.04261.x

    Article  CAS  Google Scholar 

  • Roh, S. W., Abell, G. C. J., Kim, K. -H., Nam, Y. -D., & Bae, J. -W. (2010). Comparing microarrays and next-generation sequencing technologies for microbial ecology research. Trends in Biotechnology, 28(6), 291–299. https://doi.org/10.1016/j.tibtech.2010.03.001

    Article  CAS  Google Scholar 

  • Roy, S. V., Vanbroekhoven, K., Dejonghe, W., & Diels, L. (2006). Immobilization of heavy metals in the saturated zone by sorption and in situ bioprecipitation processes. Hydrometallurgy, 83(1), 195–203. https://doi.org/10.1016/j.hydromet.2006.03.024

    Article  CAS  Google Scholar 

  • Sánchez-Fortún, M., Ouled-Cheikh, J., Jover, C., García-Tarrasón, M., Carrasco, J. L., & Sanpera, C. (2020). Following up mercury pollution in the Ebro Delta (NE Spain): Audouin’s gull fledglings as model organisms to elucidate anthropogenic impacts on the environment. Environmental Pollution, 266, 115232. https://doi.org/10.1016/j.envpol.2020.115232

    Article  CAS  Google Scholar 

  • Shalon, D., Smith, S. J., & Brown, P. O. (1996). A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Research, 6(7), 639–645. https://doi.org/10.1101/gr.6.7.639

    Article  CAS  Google Scholar 

  • Shen, L., Liu, X., & Qiu, G. (2008). Gene function and microbial community structure in sulfide minerals bioleaching system based on microarray analysis. Chinese Journal of Biotechnology, 24(6), 968–974. https://doi.org/10.3724/SP.J.1005.2008.00568

    Article  CAS  Google Scholar 

  • Singh, B. K., Quince, C., Macdonald, C. A., Khachane, A., Thomas, N., Al-Soud, W. A., Sørensen, S. J., He, Z., White, D., Sinclair, A., Crooks, B., Zhou, J., & Campbell, C. D. (2014). Loss of microbial diversity in soils is coincident with reductions in some specialized functions. Environmental Microbiology, 16(8), 2408–2420. https://doi.org/10.1111/1462-2920.12353

    Article  Google Scholar 

  • Sitte, J., Löffler, S., Burkhardt, E.-M., Goldfarb, K. C., Büchel, G., Hazen, T. C., & Küsel, K. (2015). Metals other than uranium affected microbial community composition in a historical uranium-mining site. Environmental Science and Pollution Research, 22(24), 19326–19341. https://doi.org/10.1007/s11356-015-4791-1

    Article  CAS  Google Scholar 

  • Small, J., Call, D. R., Brockman, F. J., Straub, T. M., & Chandler, D. P. (2001). Direct Detection of 16S rRNA in Soil Extracts by Using Oligonucleotide Microarrays. Applied & Environmental Microbiology, 67(10), 4708–4716. https://doi.org/10.1128/Aem.67.10.4708-4716.2001

    Article  CAS  Google Scholar 

  • Stone, J., Burgos, W., Royer, R., & Dempsey, B. (2006). Impact of zinc on biological Fe(III) and nitrate reduction by Shewanella putrefaciens CN32. Environmental Engineering Science, 23(4), 691–704. https://doi.org/10.1089/ees.2006.23.691

    Article  CAS  Google Scholar 

  • Sun, Y. J., & Zhang, H. C. (2013). Application of functional gene chip in research of soil microecology. South-to-North Water Transfers and Water Science & Technology, 11(01), 93–96.

    Google Scholar 

  • Teng, Y., Luo, Y. M., & Li, Z. G. (2006). Microbial diversity in polluted soils: An overview. Acta Pedologica Sinica, 43(6), 1018–1026. https://doi.org/10.11766/trxb200512080620

  • Ueno, D., Milner, M. J., Yamaji, N., Yokosho, K., Koyama, E., Clemencia Zambrano, M., Kaskie, M., Ebbs, S., Kochian, L. V., & Ma, J. F. (2011). Elevated expression of TcHMA3 plays a key role in the extreme Cd tolerance in a Cd-hyperaccumulating ecotype of Thlaspi caerulescens. The Plant Journal, 66(5), 852–862. https://doi.org/10.1111/j.1365-313X.2011.04548.x

    Article  CAS  Google Scholar 

  • Van Eck, N. J., & Waltman, L. (2010). Software survey: VOSviewer, a computer program for bibliometric mapping. Scientometrics, 84(2), 523–538. https://doi.org/10.1007/s11192-009-0146-3

    Article  Google Scholar 

  • Wan, J., Tokunaga, T. K., Brodie, E., Wang, Z., Zheng, Z., Herman, D., Hazen, T. C., Firestone, M. K., & Sutton, S. R. (2005). Reoxidation of bioreduced uranium under reducing conditions. Environmental Science & Technology, 39(16), 6162–6169. https://doi.org/10.1021/es048236g

    Article  CAS  Google Scholar 

  • Wang, J. J., & Hou, P. Q. (2008). Gene chip technology. Preventive Medicine Tribune, 14(3), 285–287.

    Google Scholar 

  • Weber, M., Harada, E., Vess, C., Roepenack-Lahaye, E. V., & Clemens, S. (2004). Comparative microarray analysis of Arabidopsis thaliana and Arabidopsis halleri roots identifies nicotianamine synthase, a ZIP transporter and other genes as potential metal hyperaccumulation factors. The Plant Journal, 37(2), 269–281. https://doi.org/10.1046/j.1365-313X.2003.01960.x

    Article  CAS  Google Scholar 

  • Wei, Z., Hao, Z., Li, X., Guan, Z., Cai, Y., & Liao, X. (2019). The effects of phytoremediation on soil bacterial communities in an abandoned mine site of rare earth elements. Science of the Total Environment, 670, 950–960. https://doi.org/10.1016/j.scitotenv.2019.03.118

    Article  CAS  Google Scholar 

  • Wu, F., You, Y. Q., Werner, D., Jiao, S., Hu, J., Zhang, X. Y., Wan, Y., Liu, J. F., Wang, B., & Wang, X. L. (2020). Carbon nanomaterials affect carbon cycle-related functions of the soil microbial community and the coupling of nutrient cycles. Journal of Hazardous Materials. https://doi.org/10.1016/j.jhazmat.2020.122144

    Article  Google Scholar 

  • Xie, J., He, Z., Liu, X., Liu, X., Van Nostrand, J. D., Deng, Y., Wu, L., Zhou, J., & Qiu, G. (2011). GeoChip-based analysis of the functional gene diversity and metabolic potential of microbial communities in acid mine drainage. Applied & Environmental Microbiology, 77(3), 991–999. https://doi.org/10.1128/AEM.01798-10

    Article  CAS  Google Scholar 

  • Xiong, J., He, Z., Van Nostrand, J. D., Luo, G., Tu, S., Zhou, J., & Wang, G. (2012). Assessing the microbial community and functional genes in a vertical soil profile with long-term arsenic contamination. PLoS One, 7(11), e50507. https://doi.org/10.1371/journal.pone.0050507

    Article  CAS  Google Scholar 

  • Yokoi, T., Kaku, Y., Suzuki, H., Ohta, M., Ikuta, H., Isaka, K., Sumino, T., & Wagatsuma, M. (2007). “FloraArray” for screening of specific DNA probes representing the characteristics of a certain microbial community. FEMS Microbiology Letters, 273(2), 166–171. https://doi.org/10.1111/j.1574-6968.2007.00799.x

    Article  CAS  Google Scholar 

  • Yu, Z., He, Z., Tao, X., Zhou, J., Yang, Y., Zhao, M., Zhang, X., Zheng, Z., Yuan, T., & Liu, P. (2016). The shifts of sediment microbial community phylogenetic and functional structures during chromium (VI) reduction. Ecotoxicology, 25(10), 1759–1770. https://doi.org/10.1007/s10646-016-1719-6

    Article  CAS  Google Scholar 

  • Zhang, H. B., Duan, C. Q., & Qu, L. H. (2003). Culture independent methods for studies on microbial ecology of soils. Chinese Journal of Ecology, 22(5), 131–136.

    Google Scholar 

  • Zhang, Y., Zhang, S. G., Qi, L. W., Chen, X. Q., Chen, R. Y., & Song, W. Q. (2006). Poplar as a model for Forest Tree in genome research. Chinese Bulletin of Botany.

  • Zhang, Y. G., Li, D. Q., & Xiao, Q. M. (2004). Microarrays and their application to environmental microorganisms. Acta Microbiologica Sinica, 44(3), 406–410. https://doi.org/10.1360/biodiv.050058

    Article  Google Scholar 

  • Zhou, J., He, Z., Yang, Y., Deng, Y., Tringe, S. G., & Alvarez-Cohen, L. (2015). High-throughput metagenomic technologies for complex microbial community analysis: Open and closed formats. Mbio, 6(1), e02288-e2314. https://doi.org/10.1128/mbio.02288-14

    Article  CAS  Google Scholar 

  • Zhou, J. Z., Xue, K., Xie, J. P., Deng, Y., & Luo, Y. (2012). Microbial mediation of carbon-cycle feedbacks to climate warming. Nature Climate Change, 2(2), 106–110. https://doi.org/10.1038/Nclimate1331

    Article  CAS  Google Scholar 

  • Zou, Y., Ning, D. L., Huang, Y., Liang, Y. T., Wang, H., Duan, L., Yuan, T., He, Z. L., Yang, Y. F., Xue, K., Van Nostrand, J. D., & Zhou, J. Z. (2020). Functional structures of soil microbial community relate to contrasting N2O emission patterns from a highly acidified forest. Science of the Total Environment. https://doi.org/10.1016/j.scitotenv.2020.138504

    Article  Google Scholar 

Download references

Funding

This work was supported by Key laboratory of Degraded and Unused Land Consolidation Engineering, and the Ministry of Natural and Resources (Grant No. SXDJ2019).

Author information

Authors and Affiliations

  1. College of Hehai, Chongqing University of Technology, Chongqing, 400717, China

    ZiChun Lu

  2. Key Laboratory of Degraded and Unused Land Consolidation Engineering, the Ministry of Natural and Resources, Xi’an, Shanxi, 710075, China

    HaiFeng Su

  3. Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing, 400714, China

    HaiFeng Su

Authors
  1. ZiChun Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. HaiFeng Su
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

HFS participated in the conception, design, data collection and analysis, and drafted the manuscript. ZCL assisted the laboratory work, results interpretation, and manuscript revision.

Corresponding author

Correspondence to HaiFeng Su.

Ethics declarations

Conflict of interest

The authors declare no conflict of interest.

Additional information

Publisher's Note

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

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 6903 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Lu, Z., Su, H. Employing gene chip technology for monitoring and assessing soil heavy metal pollution. Environ Monit Assess 194, 2 (2022). https://doi.org/10.1007/s10661-021-09650-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s10661-021-09650-6

Keywords

Search

Navigation