Effects of cadmium perturbation on the microbial community structure and heavy metal resistome of a tropical agricultural soil

Abstract

The effects of cadmium (Cd) contamination on the microbial community structure, soil physicochemistry and heavy metal resistome of a tropical agricultural soil were evaluated in field-moist soil microcosms. A Cd-contaminated agricultural soil (SL5) and an untreated control (SL4) were compared over a period of 5 weeks. Analysis of the physicochemical properties and heavy metals content of the two microcosms revealed a statistically significant decrease in value of the soil physicochemical parameters (P <  0.05) and concentration of heavy metals (Cd, Pb, Cr, Zn, Fe, Cu, Se) content of the agricultural soil in SL5 microcosm. Illumina shotgun sequencing of the DNA extracted from the two microcosms showed the predominance of the phyla, classes, genera and species of Proteobacteria (37.38%), Actinobacteria (35.02%), Prevotella (6.93%), and Conexibacter woesei (8.93%) in SL4, and Proteobacteria (50.50%), Alphaproteobacteria (22.28%), Methylobacterium (9.14%), and Methylobacterium radiotolerans (12,80%) in SL5, respectively. Statistically significant (P < 0.05) difference between the metagenomes was observed at genus and species delineations. Functional annotation of the two metagenomes revealed diverse heavy metal resistome for the uptake, transport, efflux and detoxification of various heavy metals. It also revealed the exclusive detection in SL5 metagenome of members of RND (resistance nodulation division) protein czcCBA efflux system (czcA, czrA, czrB), CDF (cation diffusion facilitator) transporters (czcD), and genes for enzymes that protect the microbial cells against cadmium stress (sodA, sodB, ahpC). The results obtained in this study showed that Cd contamination significantly affects the soil microbial community structure and function, modifies the heavy metal resistome, alters the soil physicochemistry and results in massive loss of some autochthonous members of the community not adapted to the Cd stress.

Keywords

Cadmium / Agricultural soil / Heavy metals / Soil microcosm / Shotgun metagenomics / Microbial community structure and function / Heavy metal resistome

References

[1] Adriano DC. Trace elements in terrestrial environments: biogeochemistry, bioavailability, and risks of metals, 2001, 2, New York: Springer, 867.

[2] Aislabie J, Deslippe JR. Dymond JR. Soil microbes and their contribution to soil services. Ecosystem services in New Zealand-conditions and trends, 2013, Lincoln: Manaaki Whenua Press, 143-161.

[3] Alloway BJ, Steinnes E. McLaughlin MJ, Singh BR. Anthropogenic additions of cadmium to soils. Cadmium in soils and plants Developments in plants and soil sciences, 1999, Dordrecht: Springer, 97-123.

[4] Altimira F, Yáñez C, Bravo G, González M, Rojas LA, Seeger M. Characterization of copper-resistant bacteria and bacterial communities from copper-polluted agricultural soils of central Chile. BMC Microbiol, 2012, 12(1): 193.

[5] Ammendola S, Cerasi M, Battistoni A. Deregulation of transition metals homeostasis is a key feature of cadmium toxicity in Salmonella. Biometals, 2014, 27: 703-714.

[6] Anton A, Grosse C, Reissmann C, Pribyl T, Nies DH. CzcD is a heavy metal ion transporter involved in regulation of heavy metal resistance in Ralstonia sp. strain CH34. J Bacteriol, 1999, 181: 6876-6881.

[7] Aramaki T, Blanc-Mathieu R, Endo H, Ohkubo K, Kanehisa M, Goto S, Ogata H (2019) KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics Btz859

[8] Banjerdkij P, Vattanaviboon P, Mongkolsuk S. Exposure to cadmium elevates expression of genes in the OxyR and OhrR regulons and induces cross-resistance to peroxide killing treatment in Xanthomonas campestris. Appl Environ Microbiol, 2005, 71(4): 1843-1849.

[9] Benavides MP, Gallego SM, Tomaro ML. Cadmium toxicity in plants. Braz J Plant Physiol, 2005, 17(1): 21-34.

[10] Bhadra B, Nanda AK, Chakraborty R. Inducible nickel resistance in a river isolate of india phylogenetically ascertained as a novel strain of Acinetobacter junii. World J Microbiol Biotechnol, 2005, 22(3): 225-232.

[11] Braz VS, Marques MV. Genes involved in cadmium resistance in Caulobacter crescentus. FEMS Microbiol Lett, 2005, 251: 289-295.

[12] Bruins MR, Kapil S, Oehme FW. Microbial resistance to metals in the environment. Ecotoxicol Environ Saf, 2000, 45: 198-207.

[13] Cheema S, Lavania M, Lal B. Impact of petroleum hydrocarbon contamination on the indigenous microbial community. Ann Microbiol, 2015, 66: 359-369.

[14] De Marco P, Pacheco CC, Figueiredo AR, Moradas-Ferreira P. Novel pollutant-resistant methylotrophic bacteria for use in bioremediation. FEMS Microbiol Lett, 2004, 234: 75-80.

[15] Dourado MN, Andreote FD, Dini-Andreote F, Conti R, Araujo JM, Araujo WL. Analysis of the 16S rRNA and mxaF genes revealing insights into Methylobacterium niche-specific plant association. Gen Mol Biol, 2012, 35(1): 142-148.

[16] Dourado MN, Neves AAC, Santos DS, Araujo WL. Biotechnological and agronomic potential of endophytic pink-pigmented methylotrophic Methylobacterium spp. Biomed Res Int, 2015, 2015: 909016.

[17] Edwards JR, Prozialeck WC. Cadmium, diabetes and chronic kidney disease. Toxicol Appl Pharmacol, 2009, 238(3): 289-293.

[18] Fashola MO, Ngole-Jeme VM, Babalola OO. Heavy metal pollution from gold mines: environmental effects and bacterial strategies for resistance. Int J Environ Res Public Health, 2016, 13: 1047.

[19] Feng G, Xie T, Wang X, Bai J, . Metagenomic analysis of microbial community and function involved in cd-contaminated soil. BMC Microbiol, 2018, 18: 1.

[20] Ferianc P, Farewell A, Nystrom T. The cadmium-stress stimulon of Escherichia coli K-12. Microbiology, 1998, 144: 1045-1050.

[21] Fernandes VC, Albergaria JT, Oliva-Teles T, Delerue-Matos C, de Marco P. Dual augmentation foe aerobic bioremediation of MTBE and TCE pollution in heavy metal-contaminated soil. Biodegradation, 2009, 20(3): 375-382.

[22] Fortuniak A, Zadzinski R, Bilinski T, Bartosz G. Glutathione depletion in the yeast Saccharomyces cerevisiae. Biochem Mol Biol Int, 1996, 38: 901-910.

[23] Franke S, Grass G, Rensing C, Nies DH. Molecular analysis of the copper-transporting efflux system CusCFBA of Escherichia coli. J Bacteriol, 2003, 185: 3804-3812.

[24] Grass G, Fan B, Rosen BP, Franke S, Nies DH, Rensing C. ZitB (YbgR), a member of the cation diffusion facilitator family, is an additional zinc transporter in Escherichia coli. J Bacteriol, 2001, 183: 4664-4667.

[25] Gray CW, McLaren RG, Roberts AHC, Condron LM. Sorption and desorption of cadmium from some New Zealand soils: effect of pH and contact time. Australian J Soil Res, 1998, 36: 199-216.

[26] Gray CW, McLaren RG, Roberts AHC, Condron LM. Effect of soil pH on cadmium phytoavailability in some New Zealand soils. N Z J Crop Hortic Sci, 1999, 27: 169-179.

[27] Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev, 2004, 68: 669-678.

[28] Hassan MT, van der Lelie D, Springael D, Romling U, Ahmed N, Mergeay M. Identification of a gene cluster, czr, involved in cadmium and zinc resistance in Pseudomonas aeruginosa. Gene, 1999, 238: 417-425.

[29] Hu N, Zhao B. Key genes involved in heavy-metal resistance in Pseudomonas putida CD2. FEMS Microbiol Lett, 2007, 267: 17-22.

[30] Hu P, Brodie EL, Suzuki Y, McAdams HH, Andersen GL. Whole-genome transcriptional analysis of heavy metal stresses in Caulobacter crescentus. J Bacteriol, 2005, 187: 8437-8449.

[31] Imai I, Siegel SM. A specific response to toxic cadmium levels in red kidney bean embryos. Physiol Plant, 1973, 29: 118-120.

[32] Jones P, Kortenkamp A, O’Brien P, Wang G, Yang G. Evidence for the generation of hydroxyl radicals from a chromium(V) intermediate isolated from the reaction of chromate with glutathione. Arch Biochem Biophys, 1991, 286: 652-655.

[33] Júnior CAL, Mazzafera P, Arruda MAZ. A comparative ionomic approach focusing on cadmium effects in sunflowers (Helianthus annuus L). Environ Exp Bot, 2014, 107: 180-186.

[34] Kachur AV, Koch CJ, Biaglow JE. Mechanism of copper-catalyzed oxidation of glutathione. Free Radic Res, 1998, 28: 259-269.

[35] Khan S, Rehman S, Khan A, Khan M, Shah M. Soil and vegetables enrichment with heavy metals from geological sources in Gilgit, northern Pakistan. Ecotoxicol Environ Safety, 2010, 73: 1820-1827.

[36] Khan MIR, Nazir F, Asgher M, Per TS, Khan NA. Selenium and sulfur influence ethylene formation and alleviate cadmium-induced oxidative stress by improving proline and glutathione production in wheat. J Plant Physiol, 2015, 173: 9-18.

[37] Khan A, Khan S, Alam M, Khan MA, Aamir M, Qamar Z, Rehman ZU, Perveen S. Toxic metal interactions affect the bioaccumulation and dietary intake of macro- and micro-nutrients. Chemosphere, 2016, 146: 121-128.

[38] Khan S, Munir S, Sajjad M, Li G. Urban park soil contamination by potentially harmful elements and human health risk in Peshawar City, Khyber Pakhtunkhwa, Pakistan. J Geochem Explor, 2016, 165: 102-110.

[39] Khan MA, Khan S, Khan A, Alam M. Soil contamination with cadmium, consequences and remediation using organic amendments. Sci Total Environ, 2017, 601–602: 1591-1605.

[40] Kwak M-J, Jeong H, Madhaiyan M, . Genome information of Methylobacterium oryzae, a plant-probiotic methylotroph in the phyllosphere. PLoS ONE, 2014, 9(9): e106704.

[41] Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie-2. Nat Methods, 2012, 9(4): 357-359.

[42] Larkin MJ, Kulakov LA, Allen CC. Biodegradation and Rhodococcus—masters of catabolic versatility. Curr Opin Biotechnol, 2005, 16: 282-290.

[43] Lee SW, Glickmann E, Cooksey DA. Chromosomal locus for cadmium resistance in Pseudomonas putida consisting of a cadmium-transporting ATPase and a MerR family response regulator. Appl Environ Microbiol, 2001, 67: 1437-1444.

[44] Legatzki A, Grass G, Anton A, Rensing C, Nies DH. Interplay of the Czc system and two P-type ATPases in conferring metal resistance to Ralstonia metallidurans. J Bacteriol, 2003, 185: 4354-4361.

[45] Li P-E, Lo C-C, Anderson JJ, . Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform. Nucleic Acids Res, 2017, 45(1): 67-80.

[46] Lo C-C, Chain PSG. Rapid evaluation and quality control of next generation sequencing data with FaQCs. BMC Bioinform, 2014, 15: 366.

[47] Lopez-Mill’a’n AF, Sagardoy R, Solanas M, Abadia A, Abadia J. Cadmium toxicity in tomato (Lycopersicon esculentum) plants grown in hydroponics. Environ Exp Bot, 2009, 65: 376-385.

[48] Liu J, Zhang H, Zhang Y, Chai T. Silicon attenuates cadmium toxicity in Solanum nigrum L. by reducing cadmium uptake and oxidative stress. Plant Physiol Biochem, 2013, 68: 1-7.

[49] Madhaiyan M, Poonguzhali S, Sa T. Characterization of 1-aminocyclopropane-1-carboxylate (ACC) deaminase containing Methylobacterium oryzae and interactions with auxins and ACC regulation of ethylene in canola (Brassica campestris). Planta, 2007, 226(4): 867-876.

[50] Marchler-Bauer A, Derbyshire MK, Gonzales NR, . CDD: NCBI’s conserved domain database. Nucleic Acids Res, 2015, 43(D): 222-226.

[51] Marschner P. Marschner’s Mineral Nutrition of Higher Plants, 2012, 3, London: Academic Press.

[52] Mielke HW, Adams JL, Chaney RL, Mielke PW Jr, Ravikumar VC. The pattern of cadmium in the environment of five Minnesota cities. Environ Geochem Health, 1991, 13(1): 29-34.

[53] Mohamed AA, Castagna A, Ranieri A, Sanita di Toppi L. Cadmium tolerance in Brassica juncea roots and shoots is affected by antioxidant status and phytochelatin biosynthesis. Plant Physiol Biochem, 2012, 57: 15-22.

[54] Mongkolsuk S, Helmann JD. Regulation of inducible peroxide stress responses. Mol Microbiol, 2002, 45: 9-15.

[55] Montecchia MS, Tosi M, Soria MA, Vogrig JA, Sydorenko O, Correa OS. Pyrosequencing reveals changes in soil bacterial communities after conversion of Yungas forests to agriculture. PLoS ONE, 2015, 10: e0119426.

[56] Moynihan M, Peterson KE, Cantoral A, . Dietary predictors of urinary cadmium among pregnant women and children. Sci Total Environ, 2017, 575: 1255-1262.

[57] Nawab J, Khan S, Aamir M, Shamshad I, Qamar Z, Din I, Huang Q. Organic amendments impact the availability of heavy metal(loid)s in mine-impacted soil and their phytoremediation by Penisitum americanum and Sorghum bicolor. Environ Sci Pollut Res, 2016, 23(3): 2381-2390.

[58] Nies DH. CzcR and CzcD, gene products affecting regulation of resistance to cobalt, zinc, and cadmium (czc system) in Alcaligenes eutrophus. J Bacteriol, 1992, 174: 8102-8110.

[59] Nies DH. The cobalt, zinc, and cadmium efflux system CzcABC from Alcaligenes eutrophus functions as a cation-proton antiporter in Escherichia coli. J Bacteriol, 1995, 177: 2707-2712.

[60] Nies D. Microbial heavy-metal resistance. Appl Microbiol Biotechnol, 1999, 51: 730-750.

[61] Nies DH. Efflux-mediated heavy metal resistance in prokaryotes. FEMS Microbiol Rev, 2003, 27: 313-339.

[62] Nies DH, Silver S. Plasmid-determined inducible efflux is responsible for resistance to cadmium, zinc, and cobalt in Alcaligenes eutrophus. J Bacteriol, 1989, 171: 896-900.

[63] Nies DH, Nies A, Chu L, Silver S. Expression and nucleotide sequence of a plasmid determined divalent cation efflux system from Alcaligenes eutrophus. Proc Natl Acad Sci USA, 1989, 86: 7351-7355.

[64] Noguchi H, Park J, Takagi T. MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Res, 2006, 34(19): 5623-5630.

[65] Nucifora G, Chu L, Misra TK, Silver S. Cadmium resistance from Staphylococcus aureus plasmid pI258 cadA gene results from a cadmium efflux ATPase. Proc Natl Acad Sci USA, 1989, 86: 3544-3548.

[66] Oulas A, Pavloudi G, Polymanakou P, Pavlopoulus GA, Papanikolaou N, Kotoulas G, Arvanitidis C, Iliopoulus I. Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. Bioinform Biol Insights, 2015, 9: 75-88.

[67] Pal C, Bengtsson-Palme J, Rensing C, Kristiansson E, Larsson DG. BacMet: antibacterial biocide and metal resistance genes database. Nucleic Acids Res, 2014, 42(1): 737-743.

[68] Peng Y, Leung HC, Yiu SM, Chin FY. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics, 2012, 28(11): 1420-1428.

[69] Rai PK, Lee SS, Zhang M, Tsang YF, Kim K-H. Heavy metals in food crops: health risks, fate, mechanisms, and management. Environ Int, 2019, 125: 365-385.

[70] Rensing C, Mitra B, Rosen BP. The zntA gene of Escherichia coli encodes a Zn(II)- translocating P-type ATPase. Proc Natl Acad Sci USA, 1997, 94: 14326-14331.

[71] Rensing C, Ghosh M, Rosen BP. Families of soft-metal-ion-transporting ATPases. J Bacteriol, 1999, 181: 5891-5897.

[72] Rhee SK, Liu X, Wu L, Chong SC, Wan X, Zhou J. Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl Environ Microbiol, 2004, 70(7): 4303-4317.

[73] Salam LB. Detection of carbohydrate-active enzymes and genes in a spent engine oil-perturbed agricultural soil. Bull Natl Res Cent, 2018, 42: 10.

[74] Salam LB, Ishaq A. Biostimulation potentials of corn steep liquor in enhanced hydrocarbon degradation in chronically polluted soil. Biotech, 2019, 9: 46.

[75] Salam LB, Obayori OS. Structural and functional metagenomics analyses of a tropical agricultural soil. Spanish J Soil Sci, 2019, 9(1): 1-23.

[76] Salam LB, Obayori OS, Raji SA. Biodegradation of used engine oil by a methylotrophic bacterium, Methylobacterium Mesophilicum isolated from tropical hydrocarbon-contaminated soil. Petrol Sci Technol, 2015, 33(2): 186-195.

[77] Salam LB, Obayori OS, Nwaokorie FO, Suleiman A, Mustapha R. Metagenomic insights into effects of spent engine oil perturbation on the microbial community composition and function in a tropical agricultural soil. Environ Sci Pollut Res, 2017, 24: 7139-7159.

[78] Salam LB, Ilori MO, Amund OO, LiiMien Y, Nojiri H. Characterization of bacterial community structure in a hydrocarbon-contaminated tropical African soil. Environ Technol, 2018, 39(7): 939-951.

[79] Salam LB, Shomope H, Ummi Z, Bukar F. Mercury contamination imposes structural shift on the microbial community of an agricultural soil. Bull Natl Res Cent, 2019, 43: 163.

[80] Satarug S, Baker JR, Reilly PE, Moore MR, Williams DJ. Changes in zinc and copper homeostasis in human livers and kidneys associated with exposure to environmental cadmium. Hum Exp Toxicol, 2001, 20: 205-213.

[81] Scherer J, Nies DH. CzcP is a novel efflux system contributing to transition metal resistance in Cupriavidus metallidurans CH34. Mol Microbiol, 2009, 73: 601-621.

[82] Schloss PD, Westcott SL, Ryabin T, . Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009, 75(23): 7537-7541.

[83] Steinnes E, Friedland AJ. Metal contamination of natural surface soils from long-range atmospheric transport: existing and missing knowledge. Environ Rev, 2006, 14: 169-186.

[84] Stohs SJ, Bagchi D. Oxidative mechanisms in the toxicity of metal-ions. Free Radic Biol Med, 1995, 18: 321-336.

[85] Stohs SJ, Bagchi D, Hassoun E, Bagchi M. Oxidative mechanisms in the toxicity of metal ions. Free Radic Biol Med, 2001, 18: 321-336.

[86] Toppi LSD, Gabbrielli R. Response to cadmium in higher plants. Environ Exp Bot, 1999, 41(2): 105-130.

[87] Törönen P, Medlar A, Holm L. PANNZER2: a rapid functional annotation webserver. Nucleic Acids Res, 2018, 46(W1): W84-W88.

[88] Trivedi P, Delgado-Baquerizo M, Anderson IC, Singh BK. Response of soil properties and microbial communities to agriculture: implications for primary productivity and health indicators. Front Plant Sci, 2016, 7: 990.

[89] Valencia EY, Braz VS, Guzzo C, Marques MV. Two RND proteins involved in heavy metal efflux in Caulobacter crescentus belong to separate clusters within proteobacteria. BMC Microbiol, 2013, 13: 79.

[90] Vallee BL, Ulmer DD. Biochemical effects of mercury, cadmium and lead. Annu Rev Biochem, 1972, 41: 91-128.

[91] Waisberg M, Joseph P, Hale B, Beyersmann D. Molecular and cellular mechanisms of cadmium carcinogenesis. Toxicol, 2003, 192(2–3): 95-117.

[92] WHO/FAO (2001). Codex alimentarius commission. Food additives and contaminants. Joint FAO/WHO Food Standards Programme, ALINORM 10/12A

[93] Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol, 2014, 15(3): R46.

[94] Xiong A, Jayaswal RK. Molecular characterization of a chromosomal determinant conferring resistance to zinc and cobalt ions in Staphylococcus aureus. J Bacteriol, 1998, 180: 4024-4029.

[95] Yazdankhah A, Moradi S, Amirmahmoodi S, Abbasian M, Shoja SE. Enhanced sorption of cadmium ion on highly ordered nanoporous carbon by using different surfactant modification. Microporous Mesoporous Mater, 2010, 133: 45-53.

[96] Yin C, Mueth N, Hulbert S. Bacterial community on wheat grown under long-term conventional tillage and no-till in the Pacific Northwest of the United States. Phytobiomes J, 2017, 1(2): 83-90.