Abstract
The extensive use of copper fungicides has resulted in significant non-target effects on soil microbial communities. However, the documented effects are often variable and contradictory, depending on the methods used to assess them. In this study, we examined the effects of copper accumulation in surface soils on microbial catabolic activity, active biomass and composition, and sensitive bacterial species. The community-level catabolic profiles (CLCPs) showed that both normal (50 mg CuSO4 kg−1 soil) and high dosages (tenfold rate) of CuSO4 significantly increased the catabolic diversity of gram-positive bacteria, while the high dosage increased the overall catabolic activity of gram-negative bacteria. The phospholipid fatty acid (PLFA) analysis showed that the high dosage reduced the biomass of gram-positive bacteria by 27% but did not affect that of gram-negative bacteria. In comparison, the normal and high dosages decreased the fungal biomass by 34% and 58%, respectively. Furthermore, 16S rRNA-denaturing gradient gel electrophoresis (DGGE) fingerprint revealed that more than two-thirds of identified bands belonged to gram-negative bacteria. Some Cu-resistant gram-negative bacterial genera, such as Actinobacterium, Pseudomonas, and Proteobacterium, were detected in the soil to which the high dosage of CuSO4 had been applied. In conclusion, an excess application of CuSO4 increased the catabolic diversity of gram-positive bacteria and induced resistance in gram-negative bacteria, whereas the active fungal community displayed a dosage-dependent response to CuSO4 and can thus be used as a sensitive indicator of copper contamination.
Similar content being viewed by others
Data availability
The availability of data and materials is on account of personal request.
References
Adrees M, Ali S, Rizwan M, Ibrahim M, Abbas F, Farid M, Zia-ur-Rehman M, Irshad MK, Bharwana SA (2015) The effect of excess copper on growth and physiology of important food crops: a review. Environ Sci Pollut Res 22:8148–8162. https://doi.org/10.1007/s11356-015-4496-5
Aponte H, Herrera W, Cameron C, Black H, Meier S, Paolini J, Tapia Y, Cornejo P (2020) Alteration of enzyme activities and functional diversity of a soil contaminated with copper and arsenic. Ecotox Environ Safe 192.https://doi.org/10.1016/j.ecoenv.2020.110264
Aponte H, Mondaca P, Santander C, Meier S, Paolini J, Butler B, Rojas C, Diez MC, Cornejo P (2021) Enzyme activities and microbial functional diversity in metal(loid) contaminated soils near to a copper smelter. Sci Total Environ 779:146423. https://doi.org/10.1016/j.scitotenv.2021.146423
Bååth E (1989) Effects of heavy metals in soil on microbial processes and populations (a review). Water Air Soil Pollut 47:335–379. https://doi.org/10.1007/BF00279331
Berg J, Tom-Petersen A, Nybroe O (2005) Copper amendment of agricultural soil selects for bacterial antibiotic resistance in the field. Lett Appl Microbiol 40:146–151. https://doi.org/10.1111/j.1472-765X.2004.01650.x
Berg J, Brandt KK, Al-Soud WA, Holm PE, Hansen LH, Sørensen SJ, Nybroe O (2012) Selection for Cu-tolerant bacterial communities with altered composition, but unaltered richness, via long-term Cu exposure. Appl Environ Microbiol 78:7438–7446. https://doi.org/10.1128/AEM.01071-12
Blagodatskaya E, Kuzyakov Y (2013) Active microorganisms in soil: critical review of estimation criteria and approaches. Soil Biol Biochem 67:192–211. https://doi.org/10.1016/j.soilbio.2013.08.024
Borymski S, Cycoń M, Beckmann M, Mur LAJ, Piotrowska-Seget Z (2018) Plant species and heavy metals affect biodiversity of microbial communities associated with metal-tolerant plants in metalliferous soils. Front Microbiol 9.https://doi.org/10.3389/fmicb.2018.01425
Cowan DA, Ramond JB, Makhalanyane TP, De Maayer P (2015) Metagenomics of extreme environments. Curr Opin Microbiol 25:97–102. https://doi.org/10.1016/j.mib.2015.05.005
Cristiano B, Panos P, Emanuele L, Jen-How H, Alberto O, Arwyn J, Oihane F-U, Pasquale B, Luca M (2018) Copper distribution in European topsoils: an assessment based on LUCAS soil survey. Sci Total Environ 636:282–298. https://doi.org/10.1016/j.scitotenv.2018.04.268
Dell’Amico E, Mazzocchi M, Cavalca L, Allievi L, Andreoni V (2008) Assessment of bacterial community structure in a long-term copper-polluted ex-vineyard soil. Microbiol Res 163:671–683. https://doi.org/10.1016/j.micres.2006.09.003
Fierer N (2017) Embracing the unknown: disentangling the complexities of the soil microbiome. Nat Rev Microbiol 15:579–590. https://doi.org/10.1038/nrmicro.2017.87
Flores, A. G., Pope, C. R., & Unger, V. M. (2013). Structural biology of copper transport. In Metals in Cells (pp. 175–182). John Wiley & Sons.
Frostegård A, Bååth E (1996) The use of phospholipid fatty acid analysis to estimate bacterial and fungal biomass in soil. Biol Fertil Soils 22:59–65. https://doi.org/10.1007/BF00384433
Frostegård Å, Bååth E, Tunlio A (1993) Shifts in the structure of soil microbial communities in limed forests as revealed by phospholipid fatty acid analysis. Soil Biol Biochem 25:723–730. https://doi.org/10.1016/0038-0717(93)90113-P
Frostegård Å, Tunlid A, Bååth E (1996) Changes in microbial community structure during long-term incubation in two soils experimentally contaminated with metals. Soil Biol Biochem 28:55–63. https://doi.org/10.1016/0038-0717(95)00100-X
Gadd GM (2010) Metals, minerals and microbes: geomicrobiology and bioremediation. Microbiology 156:609–643. https://doi.org/10.1099/mic.0.037143-0
Garland JL, Mills AL (1991) Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization. Appl Environ Microbiol 57:2351–2359. https://doi.org/10.1128/AEM.57.8.2351-2359.1991
Heděnec P, Cajthaml T, Pižl V, Márialigeti K, Tóth E, Borsodi AK, Chroňáková A, Krištůfek V, Frouz J (2020) Long-term effects of earthworms (Lumbricus rubellus Hoffmeister, 1843) on activity and composition of soil microbial community under laboratory conditions. Appl Soil Ecol 150:103463. https://doi.org/10.1016/j.apsoil.2019.103463
Huang CY, Schulte E (1985) Digestion of plant tissue for analysis by ICP emission spectroscopy. Commun Soil Sci Plant Anal 16:943–958. https://doi.org/10.1080/00103628509367657
LaPara TM, Nakatsu CH, Pantea L, Alleman JE (2000) Phylogenetic analysis of bacterial communities in mesophilic and thermophilic bioreactors treating pharmaceutical wastewater. Appl Environ Microbiol 66:3951–3959. https://doi.org/10.1128/AEM.66.9.3951-3959.2000
Li YC, Li YF, Chang SX, Liang X, Qin H, Chen JH, Xu QF (2017) Linking soil fungal community structure and function to soil organic carbon chemical composition in intensively managed subtropical bamboo forests. Soil Biol Biochem 107:19–31. https://doi.org/10.1016/j.soilbio.2016.12.024
Li YC, Li YF, Chang SX, Yang YF, Fu SL, Jiang PK, Luo Y, Yang M, Chen ZH, Hu SD, Zhao MX, Liang X, Xu QF, Zhou GM, Zhou JZ (2018) Biochar reduces soil heterotrophic respiration in a subtropical plantation through increasing soil organic carbon recalcitrancy and decreasing carbon-degrading microbial activity. Soil Biol Biochem 122:173–185. https://doi.org/10.1016/j.soilbio.2018.04.019
Liang C, Fujinuma R, Balser TC (2008) Comparing PLFA and amino sugars for microbial analysis in an Upper Michigan old growth forest. Soil Biol Biochem 40:2063–2065. https://doi.org/10.1016/j.soilbio.2008.01.022
Liu YH, Li YC, Hua XM, Müller K, Wang HL, Yang TY, Wang Q, Peng X, Wang MC, Pang YJ, Qi JL, Yang YH (2018) Glyphosate application increased catabolic activity of gram-negative bacteria but impaired soil fungal community. Environ Sci Pollut Res 25:14762–14772. https://doi.org/10.1007/s11356-018-1676-0
Mackie KA, Mueller T, Kandeler E (2012) Remediation of copper in vineyards-a mini review. Environ Pollut 167:16–26. https://doi.org/10.1016/j.envpol.2012.03.023
Malhotra K, Sharma P, Capalash N (2004) Copper and dyes enhance laccase production in γ-proteobacterium JB. Biotechnol Lett 26:1047–1050. https://doi.org/10.1023/B:BILE.0000032959.10370.18
Malik AA, Chowdhury S, Schlager V, Oliver A, Puissant J, Vazquez PGM, Jehmlich N, von Bergen M, Griffiths RI, Gleixner G (2016) Soil fungal:bacterial ratios are linked to altered carbon cycling. Front Microbiol 7.https://doi.org/10.3389/fmicb.2016.01247
Martínez-Iñigo MJ, Pérez-Sanz A, Ortiz I, Alonso J, Alarcón R, García P, Lobo MC (2009) Bulk soil and rhizosphere bacterial community PCR–DGGE profiles and β-galactosidase activity as indicators of biological quality in soils contaminated by heavy metals and cultivated with Silene vulgaris (Moench) Garcke. Chemosphere 75:1376–1381. https://doi.org/10.1016/j.chemosphere.2009.03.014
McGarvey JA, Miller WG, Sanchez S, Stanker L (2004) Identification of bacterial populations in dairy wastewaters by use of 16S rRNA gene sequences and other genetic markers. Appl Environ Microbiol 70:4267–4275. https://doi.org/10.1128/AEM.70.7.4267-4275.2004
McTee M, Bullington L, Rillig MC, Ramsey PW (2019) Do soil bacterial communities respond differently to abrupt or gradual additions of copper? FEMS Microbiol Ecol 95.https://doi.org/10.1093/femsec/fiy212
Miotto A, Ceretta CA, Girotto E, Trentin G, Kaminski J, De Conti L, Moreno T, Elena B, Brunetto G (2017) Copper accumulation and availability in sandy, acid, vineyard soils. Commun Soil Sci Plant Anal 48:1167–1183. https://doi.org/10.1080/00103624.2017.1341908
Nunes I, Jacquiod S, Brejnrod A, Holm PE, Johansen A, Brandt KK, Priemé A, Sørensen SJ (2016) Coping with copper: legacy effect of copper on potential activity of soil bacteria following a century of exposure. FEMS Microbiol Ecol 92.https://doi.org/10.1093/femsec/fiw175
Rajapaksha RMCP, Tobor-Kapłon MA, Bååth E (2004) Metal toxicity affects fungal and bacterial activities in soil differently. Appl Environ Microbiol 70:2966–2973. https://doi.org/10.1128/AEM.70.5.2966-2973.2004
Rehman M, Liu LJ, Wang Q, Saleem MH, Bashir S, Ullah S, Peng DX (2019) Copper environmental toxicology, recent advances, and future outlook: a review. Environ Sci Pollut Res 26:18003–18016. https://doi.org/10.1007/s11356-019-05073-6
Staddon WJ, Duchesne LC, Trevors JT (1997) Microbial diversity and community structure of postdisturbance forest soils as determined by sole-carbon-source utilization patterns. Microb Ecol 34:125–130. https://doi.org/10.1007/s002489900042
Tong ZH, Bischoff M, Nies L, Applegate B, Turco RF (2007) Impact of fullerene (C60) on a soil microbial community. Environ Sci Technol 41:2985–2991. https://doi.org/10.1021/es061953l
Vance ED, Brookes PC, Jenkinson DS (1987) An extraction method for measuring soil microbial biomass C. Soil Biol Biochem 19:703–707. https://doi.org/10.1016/0038-0717(87)90052-6
Vavoulidou E, Avramides EJ, Papadopoulos P, Dimirkou A, Charoulis A, Konstantinidou-Doltsinis S (2005) Copper content in agricultural soils related to cropping systems in different regions of greece. Commun Soil Sci Plant Anal 36:759–773. https://doi.org/10.1081/CSS-200043367
Vogeler I, Vachey A, Deurer M, Bolan N (2008) Impact of plants on the microbial activity in soils with high and low levels of copper. Eur J Soil Biol 44:92–100. https://doi.org/10.1016/j.ejsobi.2007.12.001
Voloudakis AE, Bender CL, Cooksey DA (1993) Similarity between copper resistance genes from Xanthomonas campestris and Pseudomonas syringae. Appl Environ Microbiol 59:1627–1634. https://doi.org/10.1128/AEM.59.5.1627-1634.1993
Vukicevich E, Lowery T, Bowen P, Úrbez-Torres JR, Hart M (2016) Cover crops to increase soil microbial diversity and mitigate decline in perennial agriculture. A Review Agron Sustain Dev 36:48. https://doi.org/10.1007/s13593-016-0385-7
Wang MC, Liu YH, Wang Q, Gong M, Hua XM, Pang YJ, Hu SJ, Yang YH (2008) Impacts of methamidophos on the biochemical, catabolic, and genetic characteristics of soil microbial communities. Soil Biol Biochem 40:778–788. https://doi.org/10.1016/j.soilbio.2007.10.012
White DC, Findlay RH (1988) Biochemical markers for measurement of predation effects on the biomass, community structure, nutritional status, and metabolic activity of microbial biofilms. Hydrobiologia 159:119–132. https://doi.org/10.1007/BF00007373
Wightwick AM, Salzman SA, Reichman SM, Allinson G, Menzies NW (2013) Effects of copper fungicide residues on the microbial function of vineyard soils. Environ Sci Pollut Res 20:1574–1585. https://doi.org/10.1007/s11356-012-1114-7
Wittebolle L, Marzorati M, Clement L, Balloi A, Daffonchio D, Heylen K, De Vos P, Verstraete W, Boon N (2009) Initial community evenness favours functionality under selective stress. Nature 458:623–626. https://doi.org/10.1038/nature07840
Zhou JZ, Bruns MA, Tiedje JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62:316–322. https://doi.org/10.1128/AEM.62.2.316-322.1996
Acknowledgements
We thank Jianfang Feng from State Key Laboratory of Pollution Control and Resource Reuse in the School of Environment of Nanjing University for her assistance with the GC-MS analysis. We are very grateful to Mr. Robert Luan and Dr. Muhammad Fahad Sardar for their helpful comments in composing the manuscript.
Funding
This work was financially supported by the National Natural Science Foundation of China (NSFC) (31870495, 31372140, 40371071), the Program for Changjiang Scholars and Innovative Research Team in University (IRT_14R27), and the Fundamental Research Funds for the Central Universities (No. 020814380002).
Author information
Authors and Affiliations
Contributions
YHY and ZH acquired funds, designed, and supervised the research. MKY, YHL1, YHL2, ZLW, AYF, and YCL performed the experimental work and analyzed the data. MKY, YCL, and YHY wrote the manuscript. All discussed the results and edited/commented on the manuscript.
Corresponding authors
Ethics declarations
Ethics approval and consent to participate
The manuscript was reviewed by all authors, as well as ethical approved for publication and consents to participate.
Consent to publish
All authors approved publication of this manuscript.
Competing interests
The authors declare no competing interests.
Additional information
Responsible Editor: Robert Duran
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.
Rights and permissions
About this article
Cite this article
Yang, M., Liu, Y., Liao, Y. et al. Excess copper promotes catabolic activity of gram-positive bacteria and resistance of gram-negative bacteria but inhibits fungal community in soil. Environ Sci Pollut Res 29, 22602–22612 (2022). https://doi.org/10.1007/s11356-021-17510-6
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11356-021-17510-6