Abstract
Ecosystems worldwide are exposed to pollutants connected to the industrial production of pharmaceuticals. The objective of this study was to study the composition and characteristics of the soil microbial communities that had been exposed to long-term selection pressure caused by the industrial production of penicillin G. Soil samples from four sites among the penicillin G production plant were analysed using 16S rRNA profiling via Illumina MiSeq platform and were compared with the control samples from four sites outside the plant. Total metagenomic DNA from the impacted soil was also used for the preparation of E. coli T1R-based fosmid library which was consequently qualitatively tested for the presence of penicillin G acylase (PGA)–encoding genes using the method of sequence homology. Analyses of alpha diversity revealed that the long-term antibiotic presence in the soil significantly increased the microbial diversity and richness in terms of Shannon diversity index (p = 0.002) and Chao estimates (p = 0.004). Principal component analysis showed that the two types of communities (on-site and control) could be separated at the phylum, class and genus level. The on-site soil was enriched in Betaproteobacteria, Deltaproteobacteria, Gemmatimonadetes, Acidobacteria and Planctomycetia, while a significant decrease in Actinobacteria was observed. Metagenomic fosmid library revealed high hit rates in identifying PGAs (14 different genes identified) and confirmed the biotechnological potential of soils impacted by anthropogenic activity. This study offers new insights into the changes in microbial communities of soils exposed to anthropogenic activity as well as indicates that those soils may represent a hotspot for biotechnologically interesting targets.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Availability of data and material
Sequencing results were deposited online using the NCBI Submission Portal (SUB7201519).
References
Akimenko YV, Kazeev KS, Kolesnikov SI (2015) Impact assessment of soil contamination with antibiotics (for example, an ordinary chernozem). Am J Appl Sci 12:80–88. https://doi.org/10.3844/ajassp.2015.80.88
Arndt D, Xia J, Liu Y, Zhou Y, Guo AC, Cruz JA, Sinelnikov I, Budwill K, Nesbø CL, Wishart DS (2012) METAGENassist: a comprehensive web server for comparative metagenomics. Nucleic Acids Res 40:W88–W95. https://doi.org/10.1093/nar/gks497
Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R, Fierer N (2011) Examining the global distribution of dominant archaeal populations in soil. ISME J 5:908–917. https://doi.org/10.1038/ismej.2010.171
Cleary DW, Bishop AH, Zhang L, Topp E, Wellington EMH, Gaze WH (2016) Long-term antibiotic exposure in soil is associated with changes in microbial community structure and prevalence of class 1 integrons. FEMS Microbiol Ecol 92. https://doi.org/10.1093/femsec/fiw159
Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, McGarrell DM, Garrity GM, Tiedje JM (2005) The ribosomal database project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res 33:D294–D296. https://doi.org/10.1093/nar/gki038
Cycon M, Mrozik A, Piotrowska-Seget Z (2019) Antibiotics in the soil environment-degradation and their impact on microbial activity and diversity. Front Microbiol 10:338. https://doi.org/10.3389/fmicb.2019.00338
D'Costa VM, Griffiths E, Wright GD (2007) Expanding the soil antibiotic resistome: exploring environmental diversity. Curr Opin Microbiol 10:481–489. https://doi.org/10.1016/j.mib.2007.08.009
Deaguero AL, Blum JK, Bommarius AS (2012) Improving the diastereoselectivity of penicillin G acylase for ampicillin synthesis from racemic substrates. Protein Eng Des Sel 25:135–144. https://doi.org/10.1093/protein/gzr065
Delgado-Baquerizo M, Trivedi P, Trivedi C, Eldridge DJ, Reich PB, Jeffries TC, Singh BK (2017) Microbial richness and composition independently drive soil multifunctionality. Funct Ecol 31:2330–2343. https://doi.org/10.1111/1365-2435.12924
Dhariwal A, Chong J, Habib S, King IL, Agellon LB, Xia J (2017) MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data. Nucleic Acids Res 45:W180–W188. https://doi.org/10.1093/nar/gkx295
Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10:996–998. https://doi.org/10.1038/nmeth.2604
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–2200. https://doi.org/10.1093/bioinformatics/btr381
El Meouche I, Dunlop MJ (2018) Heterogeneity in efflux pump expression predisposes antibiotic-resistant cells to mutation. Science 362:686–690. https://doi.org/10.1126/science.aar7981
Gabor EM, de Vries EJ, Janssen DB (2004) Construction, characterization, and use of small-insert gene banks of DNA isolated from soil and enrichment cultures for the recovery of novel amidases. Environ Microbiol 6:948–958. https://doi.org/10.1111/j.1462-2920.2004.00643.x
Ghannam RB, Schaerer LG, Butler TM, Techtmann SM (2020) Biogeographic patterns in members of globally distributed and dominant taxa found in port microbial communities. mSphere 5. https://doi.org/10.1128/mSphere.00481-19
Grulich M, Štěpánek V, Kyslík P (2013) Perspectives and industrial potential of PGA selectivity and promiscuity. Biotechnol Adv 31:1458–1472. https://doi.org/10.1016/j.biotechadv.2013.07.005
Katoh K, Asimenos G, Toh H (2009) Multiple alignment of DNA sequences with MAFFT. J Bioinform Seq Anal 537:39–64. https://doi.org/10.1007/978-1-59745-251-9_3
Klein EY, Van Boeckel TP, Martinez EM, Pant S, Gandra S, Levin SA, Goossens H, Laxminarayan R (2018) Global increase and geographic convergence in antibiotic consumption between 2000 and 2015. Proc Natl Acad Sci USA 115:E3463–E3470. https://doi.org/10.1073/pnas.1717295115
Kotik M (2009) Novel genes retrieved from environmental DNA by polymerase chain reaction: current genome-walking techniques for future metagenome applications. J Biotechnol 144:75–82. https://doi.org/10.1016/j.jbiotec.2009.08.013
Kraemer SA, Ramachandran A, Perron GG (2019) Antibiotic pollution in the environment: from microbial ecology to public policy. Microorganisms 7:180. https://doi.org/10.3390/microorganisms7060180
Larsson DG, de Pedro C, Paxeus N (2007) Effluent from drug manufactures contains extremely high levels of pharmaceuticals. J Hazard Mater 148:751–755. https://doi.org/10.1016/j.jhazmat.2007.07.008
Li D, Qi R, Yang M, Zhang Y, Yu T (2011) Bacterial community characteristics under long-term antibiotic selection pressures. Water Res 45:6063–6073. https://doi.org/10.1016/j.watres.2011.09.002
Liu Z, Lozupone C, Hamady M, Bushman FD, Knight R (2007) Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res 35:e120. https://doi.org/10.1093/nar/gkm541
Lopatto E, Choi J, Colina A, Ma L, Howe A, Hinsa-Leasure S (2019) Characterizing the soil microbiome and quantifying antibiotic resistance gene dynamics in agricultural soil following swine CAFO manure application. PLoS One 14:e0220770. https://doi.org/10.1371/journal.pone.0220770
Maiques E, Ubeda C, Campoy S, Salvador N, Lasa I, Novick RP, Barbé J, Penadés JR (2006) beta-lactam antibiotics induce the SOS response and horizontal transfer of virulence factors in Staphylococcus aureus. J Bacteriol 188:2726–2729. https://doi.org/10.1128/JB.188.7.2726-2729.2006
Marešová H, Plačková M, Grulich M, Kyslík P (2014) Current state and perspectives of penicillin G acylase-based biocatalyses. Appl Microbiol Biotechnol 98:2867–2879. https://doi.org/10.1007/s00253-013-5492-7
Martínez JL (2017) Effect of antibiotics on bacterial populations: a multi-hierarchical selection process. F1000Res 6:51–51. https://doi.org/10.12688/f1000research.9685.1
Nesme J, Simonet P (2015) The soil resistome: a critical review on antibiotic resistance origins, ecology and dissemination potential in telluric bacteria. Environ Microbiol 17:913–930. https://doi.org/10.1111/1462-2920.12631
Novo A, Andre S, Viana P, Nunes OC, Manaia CM (2013) Antibiotic resistance, antimicrobial residues and bacterial community composition in urban wastewater. Water Res 47:1875–1887. https://doi.org/10.1016/j.watres.2013.01.010
Payá Pérez A, Rodríguez N (2018) Status of local soil contamination in Europe. Revision of the indicator ‘Progress in the management contaminated sites in Europe’. JRC Sci Hub. https://doi.org/10.2760/503827
Petrovich ML, Zilberman A, Kaplan A, Eliraz GR, Wang Y, Langenfeld K, Duhaime M, Wigginton K, Poretsky R, Avisar D, Wells GF (2020) Microbial and viral communities and their antibiotic resistance genes throughout a hospital wastewater treatment system. Front Microbiol 11:153. https://doi.org/10.3389/fmicb.2020.00153
Raddadi N, Cherif A, Daffonchio D, Neifar M, Fava F (2015) Biotechnological applications of extremophiles, extremozymes and extremolytes. Appl Microbiol Biotechnol 99:7907–7913. https://doi.org/10.1007/s00253-015-6874-9
Rogers PD, Liu TT, Barker KS, Hilliard GM, English BK, Thornton J, Swiatlo E, McDaniel LS (2007) Gene expression profiling of the response of Streptococcus pneumoniae to penicillin. J Antimicrob Chemother 59:616–626. https://doi.org/10.1093/jac/dkl560
Roose-Amsaleg C, Brygoo Y, Harry M (2004) Ascomycete diversity in soil-feeding termite nests and soils from a tropical rainforest. Environ Microbiol 6:462–469. https://doi.org/10.1111/j.1462-2920.2004.00579.x
Segata N, Huttenhower C (2011) Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies. PLoS One 6:e24704. https://doi.org/10.1371/journal.pone.0024704
Shen X, Jin G, Zhao Y, Shao X (2020) Prevalence and distribution analysis of antibiotic resistance genes in a large-scale aquaculture environment. Sci Total Environ 711:134626. https://doi.org/10.1016/j.scitotenv.2019.134626
Shestakov SV (2012) Impact of metagenomics on biotechnological development. Appl Biochem Microbiol 48:705–715. https://doi.org/10.1134/S0003683812090050
Smit E, Leeflang P, Gommans S, van den Broek J, van Mil S, Wernars K (2001) Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Appl Environ Microbiol 67:2284–2291. https://doi.org/10.1128/AEM.67.5.2284-2291.2001
Thiele-Bruhn S, Beck IC (2005) Effects of sulfonamide and tetracycline antibiotics on soil microbial activity and microbial biomass. Chemosphere 59:457–465. https://doi.org/10.1016/j.chemosphere.2005.01.023
Tishkov VI, Savin SS, Yasnaya AS (2010) Protein engineering of penicillin acylase. Acta Nat 2:47–61
Větrovský T, Baldrian P (2013a) Analysis of soil fungal communities by amplicon pyrosequencing: current approaches to data analysis and the introduction of the pipeline SEED. Biol Fertil Soils 49:1027–1037. https://doi.org/10.1007/s00374-013-0801-y
Větrovský T, Baldrian P (2013b) The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS One 8:e57923. https://doi.org/10.1371/journal.pone.0057923
Wei Z, Hu X, Li X, Zhang Y, Jiang L, Li J, Guan Z, Cai Y, Liao X (2017) The rhizospheric microbial community structure and diversity of deciduous and evergreen forests in Taihu Lake area, China. PLoS One 12:e0174411. https://doi.org/10.1371/journal.pone.0174411
Wolińska A, Górniak D, Zielenkiewicz U, Kuźniar A, Izak D, Banach A, Blaszczyk M (2019) Actinobacteria structure in autogenic, hydrogenic and lithogenic cultivated and non-cultivated soils: a culture-independent approach. Agronomy 9:598. https://doi.org/10.3390/agronomy9100598
Wrenbeck EE, Azouz LR, Whitehead TA (2017) Single-mutation fitness landscapes for an enzyme on multiple substrates reveal specificity is globally encoded. Nat Commun 8:15695–15695. https://doi.org/10.1038/ncomms15695
Wu Q, Zhao X, Peng S, Wang L, Zhao X (2018) Risk assessment and effect of penicillin-G on bacterial diversity in drinking water. IOP Conf Ser Earth Environ Sci 113:012156. https://doi.org/10.1088/1755-
You X, Wu D, Wei H, Xie B, Lu J (2018) Fluoroquinolones and beta-lactam antibiotics and antibiotic resistance genes in autumn leachates of seven major municipal solid waste landfills in China. Environ Int 113:162–169. https://doi.org/10.1016/j.envint.2018.02.002
Zhang Z, Schwartz S, Wagner L, Miller W (2000) A greedy algorithm for aligning DNA sequences. J Comput Biol 7:203–214. https://doi.org/10.1089/10665270050081478
Zhang Q, Xu H, Zhao J, Zeng R (2014) Expression and characterization of a thermostable penicillin G acylase from an environmental metagenomic library. Biotechnol Lett 36:617–625. https://doi.org/10.1007/s10529-013-1403-3
Zhang Q, Kang O, Jabeen S, Dick WA (2017) Alterations in soil microbial communities caused by treatments with penicillin or neomycin. Environ Sci Pollut R 24:18651–18662. https://doi.org/10.1007/s11356-017-9530-3
Zhang B, Wu X, Tai X, Sun L, Wu M, Zhang W, Chen X, Zhang G, Chen T, Liu G, Dyson P (2019) Variation in actinobacterial community composition and potential function in different soil ecosystems belonging to the arid Heihe River basin of northwest China. Front Microbiol 10. https://doi.org/10.3389/fmicb.2019.02209
Acknowledgement
The authors gratefully acknowledge the support of the Grant Agency of Charles University in Prague, Czech Republic, project GA UK No. 1470414, and the support of the Institute of Microbiology of the Czech Academy of Sciences, long-term research development project RVO 61388971.
Funding
This project was financially supported by the Grant Agency of Charles University in Prague, Czech Republic, project GA UK No. 1470414, and by the Institute of Microbiology of the Czech Academy of Sciences, long-term research development project RVO 61388971.
Author information
Authors and Affiliations
Contributions
MB, HM and APa designed the experiments. MB, APi and MH performed sampling and laboratory analyses. APi and MH performed sequencing data processing; MB performed statistical analyses and interpreted the data. MB wrote the manuscript. MB, PK and VS conceived of the study. PK, HM, APa and VS supervised the research. All authors read and approved the manuscript.
Corresponding author
Ethics declarations
Conflicts of interest
The authors declare that they have no conflict of interests.
Ethics approval
This article does not contain any studies with human participants or animals performed by any of the authors.
Consent to participate
Not applicable.
Consent for publication
Not applicable.
Code availability
Not applicable.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
ESM 1
(DOCX 8342 kb)
Rights and permissions
About this article
Cite this article
Borčinová, M., Pitkina, A., Marešová, H. et al. Characteristics of microbial community of soil subjected to industrial production of antibiotics. Folia Microbiol 65, 1061–1072 (2020). https://doi.org/10.1007/s12223-020-00819-z
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12223-020-00819-z