Abstract
The aim of the current study was to screen and identify heavy metal (chromium, cadmium, and lead) associated bacteria from petroleum-contaminated soil of district Muzaffarabad, Azad Jammu and Kashmir, Pakistan to develop ecofriendly technology for contaminated soil remediation. The petroleum-contaminated soil was collected from 99 different localities of district Muzaffarabad and the detection of heavy metals via an atomic absorption spectrometer. The isolation and identification of heavy metals-associated bacteria were done via traditional and molecular methods. Resistogram and antibiogram analysis were also performed using agar well diffusion and agar disc diffusion methods. The isolated bacteria were classified into species, i.e., B. paramycoides, B. albus, B. thuringiensis, B. velezensis, B. anthracis, B. pacificus Burkholderia arboris, Burkholderia reimsis, Burkholderia aenigmatica, and Streptococcus agalactiae. All heavy metals-associated bacteria showed resistance against both high and low concentrations of chromium while sensitive towards high and low concentrations of lead in the range of 3.0 ± 0.0 mm to 13.0 ± 0.0 mm and maximum inhibition was recorded when cadmium was used. Results revealed that some bacteria showed sensitivity towards Sulphonamides, Norfloxacin, Erythromycin, and Tobramycin. It was concluded that chromium-resistant bacteria could be used as a favorable source for chromium remediation from contaminated areas and could be used as a potential microbial filter.
Similar content being viewed by others
Availability of data and materials
Most of the data generated during this study are included in this article. However, raw data sheets are available from the corresponding as well as co-authors upon reasonable request.
References
Abioye OP, Oyewole OA, Oyeleke SB, Adeyemi MO, Orukotan AA (2018) Biosorption of lead, chromium and cadmium in tannery effluent using indigenous microorganisms. Braz J Biol Sci 5(9):25–32
Abo-Amer AE, Abu-Gharbia MA, Soltan ESM, Abd El-Raheem WM (2014) Isolation and molecular characterization of heavy metal-resistant Azotobacter chroococcum from agricultural soil and their potential application in bioremediation. Geomicrobiol J 31(7):551–561
Achal V, Kumari D, Pan X (2011) Bioremediation of chromium contaminated soil by abrown-rot fungus. Gloeophyllum Sepiarium Res J Microbiol 6(2):166
Ahemad M, Malik A (2011) Bioaccumulation of heavy metals by zinc resistant bacteria isolated from agricultural soils irrigated with wastewater. Bacteriol J 2(1):12–21
Aka NRJ, Babalola OO (2017) Identification and characterization of Cr-, Cd-, and Ni-tolerant bacteria isolated from mine tailings. Bioremediat J 21(1):1–19
Ashokkumar P, Loashini VM, Bhavya V (2017) Effect of pH, temperature and biomass on biosorption of heavy metals by Sphaerotilus natans. Int j Microbiol Mycol 6(1):32–38
Ashruta GA, Nanoty V, Bhalekar U (2014) Biosorption of heavy metals from aqueous solution using bacterial EPS. Int J Life Sci 2:373–377
Bauer AW, Perry DM, Kirby WM (1959) Single-disk antibiotic-sensitivity testing of staphylococci: an analysis of technique and results. Arc Internal Med 104(2):208–216
Bilgin M, Tulun S (2016) Removal of heavy metals (Cu, Cd and Zn) from contaminated soils using EDTA and FeCl3. Glob Nest J 18:98–107
Brown DF, Kothari D (1975) Comparison of antibiotic discs from different sources. J Clini Pathol 28(10):779–783
Chandrasekaran A, Ravisankar R, Harikrishnan N, Satapathy KK, Prasad MVR, Kanagasabapathy KV (2015) Multivariate statistical analysis of heavy metal concentration in soils of Yelagiri Hills, Tamilnadu, India-Spectroscopical 59 approach. Spectrochim Acta A Mol Biomol 137:589–600
Chang JS, Kim YH, Kim KW (2008) The ars genotype characterization of arsenic resistant bacteria from arsenic-contaminated gold–silver mines in the Republic of Korea. Appl Microbiol Biotechnol APPL 80(1):155–165
Chatterjee S, Chatterjee NC, Dutta S (2012) Bioreduction of chromium (VI) to chromium (III) by a novel yeast strain Rhodotorula mucilaginosa (MTCC 9315). Afr J Biotechnol 11(83):14920–14929
Chen LC, Zhu Y, Papandreou G, Schroff F, Adam H (2018) Encoder-decoder with atrous separable convolution for semantic image segmentation. In Proceedings of the European conference on computer vision (ECCV) pp 801–818
Chinedu E, Chukwuemeka CK (2018) Oil spillage and heavy metals toxicity risk in the Niger Delta. Nigeria J Health Pollut 8(19):180905
De J, Ramaiah N, Vardanyan L (2008) Detoxification of toxic heavy metals by marine bacteria highly resistant to mercury. Mar Biotechnol 10(4):471–477
de la Cueva SC, Rodríguez CH, Cruz NOS, Contreras JAR, Miranda JL (2016) Changes in bacterial populations during bioremediation of soil contaminated with petroleum hydrocarbons. Water Air Soil Pollut 227:1–12
Di Cesare A, Eckert EM, D’Urso S, Bertoni R, Gillan DC, Wattiez R, Corno G (2016) Co-occurrence of integrase 1, antibiotic and heavy metal resistance genes in municipal wastewater treatment plants. Water Res 94:208–214
Dixit R, Wasiullah MD, Pandiyan K, Singh UB, Sahu A, Shukla R, Singh BP, Rai JP, Sharma PK et al (2015) Bioremediation of heavy metals from soil and aquatic environment: an overview of principles and criteria of fundamental processes. Sustainability 7(2):2189–2212
Duruibe JO, Ogwuegbu MOC, Egwurugwu JN (2007) Heavy metal pollution and human biotoxic effects. IJPS 2(5):112–118
Ekperusi OA, Aigbodion IF (2015) Bioremediation of heavy metals and petroleum hydrocarbons in diesel contaminated soil with the earthworm. Springerplus 4(1):1–13
Galal TM, Gharib FA, Ghazi SM, Mansour KH (2017) Phytostabilization of heavy metals by the emergent macrophyte Vossia cuspidata (Roxb.) Griff.: a 61 phytoremediation approach. Int J Phytoremediation 19(11):992999
Gautam RK, Mudhoo A, Lofrano G, Chattopadhyaya MC (2014) Biomass-derived biosorbents for metal ions sequestration: adsorbent modification and activation methods and adsorbent regeneration. J Environ Chem Eng 2(1):239–259
Guerra AM, Aimedieu P, Bornert M, Cui YJ, Tang AM, Sun Z, Bernier F (2018) Analysis of the structural changes of a pellet/powder bentonite mixture upon wetting by X-ray computed microtomography. Appl Clay Sci 165:164–169
Hammer KA, Carson CF, Riley TV (1999) Antimicrobial activity of essential oils and other plant extracts. J Appl Microbiol 86(6):985–990
Hu HW, Wang JT, Li J, Li JJ, Ma YB, Chen D, He JZ (2016) Field-based evidence for copper contamination induced changes of antibiotic resistance in agricultural soils. Environ Microbiol 18(11):3896–3909
Huan L, Haixia Z, Longhua W, Anna L, Fang-Jie Z, Wenzhong X (2017) Heavy metal ATPase 3 (HMA3) confers cadmium hypertolerance on the cadmium/zinc hyperaccumulator Sedum plumbizincicola. New Phytol 15:687–698
Huang D, Hu C, Zeng G, Cheng M, Xu P, Gong X, Wang R, Xue W (2016) Combination of Fenton processes and biotreatment for wastewater treatment and soil remediation. Sci Total Environ 574:1599–1610
Huerta B, Marti E, Gros M, López P, Pompêo M, Armengol J, Marcé R (2013) Exploring the links between antibiotic occurrence, antibiotic resistance, and bacterial communities in water supply reservoirs. Sci Total Environ 456:161–170
Idodo-Umeh G, Ogbeibu AE (2010) Bioaccumulation of the heavy metals in cassava tubers and plantain fruits grown in soils impacted with petroleum and non-petroleum activities. Res J Environ Sci 4(1):33–41
Igiri BE, Okoduwa SI, Idoko GO, Akabuogu EP, Adeyi AO, Ejiogu IK (2018) Toxicity and bioremediation of heavy metals contaminated ecosystem from tannery wastewater: a review. J Toxicol 2018
Jafari SA, Cheraghi S, Mirbakhsh M, Mirza R, Maryamabadi A (2015) Employing response surface methodology for optimization of mercury bioremediation by Vibrio parahaemolyticus PG02 in coastal sediments of Bushehr Iran. CLEAN–Soil Air Water 43(1):118–126
Jayakumar K, Rajesh M, Baskaran L, Vijayarengan P (2013) Changes in nutritional metabolism of tomato (Lycopersicon esculantum Mill.) plants exposed to increasing concentration of cobalt chloride. Int J Food Sci Nutr 4(2):62–69
Jinadasa N, Collins D, Holford P, Milham PJ, Conroy JP (2016) Reactions to cadmium stress in a cadmium-tolerant variety of cabbage (Brassica oleracea L.): is cadmium tolerance necessarily desirable in food crops. ESPR 23(6):5296–5306
Karakagh RM, Chorom M, Motamedi H, Kalkhajeh YK, Oustan S (2012) Biosorption of Cd and Ni by inactivated bacteria isolated from agricultural soil treated with sewage sludge. Ecohydrol Hydrobiol 12(3):191–198
Khusro A, Preetam Raj JP, Panicker SG (2014) Multiple heavy metals response and antibiotic sensitivity pattern of Bacillus subtilis strain KPA. J Chem Pharm Res 6:532–538
Kim HS, Kim YJ, Seo YR (2015a) An overview of carcinogenic heavy metal: molecular toxicity mechanism and prevention. J Cancer Prev 20(4):232
Kim IH, Choi JH, Joo JO, Kim YK, Choi JW, Oh BK (2015b) Development of a microbe-zeolite carrier for the effective elimination of heavy metals from seawater. J Microbiol Biotechnol 25(9):1542–1546
Ksheminska H, Fedorovych D, Honchar T, Ivash M, Gonchar M (2008) Yeast tolerance to chromium depends on extracellular chromate reduction and Cr (III) chelation. Food Technol Biotechnol 46(4):419–426
Kumar R, Bhatia D, Singh R, Rani S, Bishnoi NR (2011) Sorption of heavy metals from electroplating effluent using immobilized biomass Trichoderma viride in a continuous packed-bed column. Int Biodeterior Biodegradation 65(8):1133–1139
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X. Molecular Evolutionary Genetics Analysis across Computing Platforms Mol Bio Evo 35:1547–1549
Kumaran NS, Sundaramanicam A, Bragadeeswaran S (2011) Adsorption studies on heavy metals by isolated cyanobacterial strain (nostoc sp.) from uppanar estuarine water, southeast coast of India. J Appl Sci 7(11):16091615
Lakkireddy K, Kües U (2017) Bulk isolation of basidiospores from wild mushrooms by electrostatic attraction with low risk of microbial contaminations. AMB Express 7(1):1–22
Li P, Li J, Feng X, Li J, Hao Y, Zhang J, Wang B (2019) Metal-organic frameworks with photocatalytic bactericidal activity for integrated air cleaning. Nat Commun 10:1–10
Lianwen L, Wei L, Weiping S, Mingxin G (2018) Remediation techniques for heavy metal-contaminated soils: principles and applicability. Sci Total Environ 633:206–219
Luna JM, Rufino RD, Sarubbo LA (2016) Biosurfactant from Candida sphaerica UCP0995 exhibiting heavy metal remediation properties. Process Saf Environ Prot 102:558–566
Ma L, Wang Q, Islam SM, Liu Y, Ma S, Kanatzidis MG (2016) Highly selective and efficient removal of heavy metals by layered double hydroxide intercalated with the MoS42–ion. J Amer Chem Soci 138:2858–2866
Manivasagaperumal R, Balamurugan S, Thiyagarajan G, Sekar J (2011) Effect of zinc on germination, seedling growth and biochemical content of cluster bean (Cyamopsis tetragonoloba (L.) Taub). Curr Plant Biol 2(5):11–15
Martínez Álvarez LM, Lo Balbo A, Mac Cormack WP, Ruberto LAM (2015) Bioremediation of a petroleum hydrocarbon-contaminated Antarctic soil: optimization of a biostimulation strategy using response-surface methodology (RSM). Cold Reg Sci Technol 119:61–67
Mosa KA, Saadoun I, Kumar K, Helmy M, Dhankher OP (2016) Potential biotechnological strategies for the cleanup of heavy metals and metalloids. Front Plant Sci 7:303
Muhlbachova G, Sagova-Mareckova M, Omelka M, Szakova J, Tlustos P (2015) The influence of soil organic carbon on interactions between microbial parameters and metal concentrations at a long-term contaminated site. Sci Total Environ 502:218–223
Naseer A, Andleeb S, Basit A, Abbasi WA, Ejaz S, Ali S, Ali NM (2022) Phylogenetic illustration of Eisenia fetida associated vermi-bacteria involved in heavy metals remediation and retaining plant growth promoting traits. J Oleo Sci 71(8):1241–1252
Okolo NV, Olowolafe EA, Akawu I, Okoduwa SIR (2016) Effects of industrial effluents on soil resources in Challawa industrial area. Kano, Nigeria Glob Ecol Conserv 5(1):1–10
Pacwa-Płociniczak M, Płaza GA, Poliwoda A, Piotrowska-Seget Z (2014) Characterization of hydrocarbon-degrading and biosurfactant-producing Pseudomonas sp. P-1 strain as a potential tool for bioremediation of petroleum-contaminated soil. Environ Sci Pollut Res 21(15):9385–9395
Parvathi K, Nagendran R, Nareshkumar R (2007) Effect of pH on chromium biosorption by chemically treated Saccharomyces.
Puyen ZM, Villagrasa E, Maldonado J, Diestra E, Esteve I, Solé A (2012) Biosorption of lead and copper by heavy-metal tolerant Micrococcus luteus DE2008. Bioresour Technol 126:233–237
Rajkumar M, Ae N, Prasad MNV, Freitas H (2010) Potential of siderophore-producing bacteria for improving heavy metal phytoextraction. Trends Biotechnol 28(3):142–149
Rehman A, Anjum MS (2011) Multiple metal tolerance and biosorption of cadmium by Candida tropicalis isolated from industrial effluents: glutathione as detoxifying agent. Environ Monit Assess 174(1):585–595
Rezania S, Taib SM, Din MFM, Dahalan FA, Kamyab H (2016) Comprehensive review on phytotechnology: heavy metals removal by diverse aquatic plants species from wastewater. J Hazard Mater 318:587–599
Rios JL, Recio MC, Villar A (1988) Screening methods for natural products with antimicrobial activity: a review of the literature. J Ethnopharmacol 23(2–3):127–149
Rodriguez-Mozaz S, Chamorro S, Marti E, Huerta B, Gros M, Sànchez-Melsió A, Balcázar JL (2015) Occurrence of antibiotics and antibiotic resistance genes in hospital and urban wastewaters and their impact on the receiving river. Water Res 69:234–242
Sarah GH, Thaura GH (2021) Heavy metals in soils and the remediation potential of bacteria associated with the plant microbiome. Frontiers Environ Sci 9:604216
Seeley HW, Vandemark PJ, Lee JJ (2001) Microbes in action: a laboratory manual of microbiology, W.H. Freeman and Company, New York, NY, USA, 4th edition
Siddiquee S, Rovina K, Azad SA, Naher L, Suryani S, Chaikaew P (2015) Heavy metal contaminants removal from wastewater using the potential filamentous fungi biomass: a review. J Microb Biochem Technol 7(6):384–395
Singh N, Verma T, Gaur R (2013) Detoxification of hexavalent chromium by an indigenous facultative anaerobic Bacillus cereus strain isolated from tannery effluent. Afr J Biotechnol 12(10)
Smith E, Thavamani P, Ramadass K, Naidu R, Srivastava P, Megharaj M (2015) Remediation trials for hydrocarbon-contaminated soils in arid environments: evaluation of bioslurry and biopiling techniques. Int Biodeterior Biodegradation 101:56–65
Somasegaran P, Hoben HJ (1994) Quantifying the growth of rhizobia. Handbook for Rhizobia Springer New York NY 47–57
Srivastava S, Agrawal SB, Mondal MK (2015) A review on progress of heavy metal removal using adsorbents of microbial and plant origin. Environ Sci Pollut Res 22(20):15386–15415
Su C (2014) A review on heavy metal contamination in the soil worldwide: situation, impact and remediation techniques. Environ Skep Crit 3:24–38
Sumiahadi A, Acar R (2018) A review of phytoremediation technology: heavy metals uptake by plants. Earth Env Sci 142:12–23
Sun Y (2009) On-site management of International Petroleum Cooperation Projects. Natural Gas Exploration and Development 32(2):69–73
Tamura K, Nei M (1993) Estimation of the Number of Nucleotide Substitutions in the Control Region of Mitochondrial DNA in Humans and Chimpanzees Mol Bio Evo 10:512–526
Taştan BE, Ertuğrul S, Dönmez G (2010) Effective bioremoval of reactive dye and heavy metals by Aspergillus versicolor. Bioresour Technol 101(3):870–876
Tremblay MS, Aubert S, Barnes JD, Saunders TJ, Carson V, Latimer-Cheung AE, Chinapaw MJ (2017) Sedentary behavior research network (SBRN)–terminology consensus project process and outcome. IJBNPA 14(1):1–17
Verma S, Kuila A (2019) Bioremediation of heavy metals by microbial process. Environ Technol Innov 14:100369
Wakelin S, Gerard E, Black A, Hamonts K, Condron L, Yuan T, O’Callaghan M (2014) Mechanisms of pollution induced community tolerance in a soil microbial community exposed to Cu. Environ Pollut 190:1–9
Wan J, Zhang C, Zeng G, Huang D, Hu L, Huang C, Wang L (2016) Synthesis and evaluation of a new class of stabilized nano-chlorapatite for Pb immobilization in sediment. J Hazard Mater 320:278–288
Yang T, Chen M, Wang J (2015) Genetic and chemical modification of cells for selective separation and analysis of heavy metals of biological or environmental significance. TrAC, Trends Anal Chem 66:90–102
Zheng X, Chen L, Chen M, Chen J, Li X (2019) Functional metagenomics to mine soil microbiome for novel cadmium resistance genetic determinants. Pedosphere 29(3):298–310
Zhu S, Meng Q, Wang L, Zhang J, Song Y, Jin H, Yang B (2013) Highly photoluminescent carbon dots for multicolor patterning, sensors, and bioimaging. Angew Chem 125(14):4045–4049
Author information
Authors and Affiliations
Contributions
Saiqa Andleeb conceived the idea, designed the experiments, analyzed and interpreted the results, and was a major contributor to manuscript writing. Abdul Basit, Fahad Kiyani, and Anum Naseer performed all the experiments and wrote the first draft of the manuscript. Iram Liaqat helped in bioinformatics tools for phylogenetic data analysis. Shaukat Ali, Aisha Nazir, and Nasra Ashraf contributed to formal analysis, interpreted results, and manuscript review.
Corresponding author
Ethics declarations
Consent for publication
Not applicable.
Consent to participate
Not applicable.
Competing interests
The authors declare no competing interests.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Basit, A., Andleeb, S., Liaqat, I. et al. Characterization of heavy metal-associated bacteria from petroleum-contaminated soil and their resistogram and antibiogram analysis. Folia Microbiol (2024). https://doi.org/10.1007/s12223-024-01135-6
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s12223-024-01135-6