Fate of extracellular antibiotic resistance genes (eARGs)—which are widespread in various environments—is dependent on gene persistence. This work examined the previously unconsidered role of environmentally relevant nanoparticles (NPs) in regulating eARG persistence. Fragments of eARG blaI were added at 2 μg/mL to batch systems containing nuclease-free water at pH 7.0, 0.1 M CaCl2 and 0.25 g of particles. Tested particles included humic acid functionalized silica nanoparticles (HASNPs) and kaolinite. After equilibration of eARG fragments and particles, pH was changed (between 1.0 and 11.0) or DNase I was added (at concentrations between 0.5 and 20 μg/mL). Remaining eARG fragment copies were characterized by the quantitative polymerase chain reaction and automated gel electrophoresis. eARGs fragments of various sizes (508, 680, and 861 bp) and both double- and single-stranded eARGs were tested. Sorption capacity of DNase I to NPs was also assessed using the Bradford assay for protein detection. Overall, particles improved eARG persistence. HASNPs protected extracellular DNA (eDNA) from breakage in low pH systems. Kaolinite provided full protection at all DNase I concentrations tested. Degradation of eARGs was significant in HASNP systems but was markedly decreased compared with particle-free systems at DNase I concentrations <10 μg/mL. DNase I sorbed significantly to HASNPs. Full protection of eARGs was observed, at DNase I concentrations <5 μg/mL, when HASNPs were adsorbed to DNase I. The impact of HASNPs on reducing degradation (at 1 μg/mL DNase I) was observed for up to 4 h. Smaller and single-stranded fragments, which have greater sorption capacities to HASNPs, were not better protected. This study establishes the ability of naturally occurring NPs to decrease the degradation of eARGs, either through sequestration of eDNA or inactivation of nucleases by particles. The ability of NPs to increase eARG persistence may have implications for the dissemination of antibiotic resistance.
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References
1.
AeschbacherK., MessikommerR., MeileL., and WenkC. (2005). Bt176 corn in poultry nutrition: Physiological characteristics and fate of recombinant plant DNA in chickens. Poult. Sci. 84, 385.
2.
BaurB., HanselmannK., SchlimmeW., and JenniB. (1996). Genetic transformation in freshwater: Escherichia coli is able to develop natural competence. Appl. Environ. Microbiol. 62, 3673.
3.
BennettP., LiveseyC., NathwaniD., ReevesD., SaundersJ., and WiseR. (2004). An assessment of the risks associated with the use of antibiotic resistance genes in genetically modified plants: Report of the Working Party of the British Society for Antimicrobial Chemotherapy. J. Antimicrob. Chemother. 53, 418.
4.
BienT.L.T., ThaoN.V., KitamuraS.I., ObayashiY., and SuzukiS. (2017). Release and constancy of an antibiotic resistance gene in seawater under grazing stress by ciliates and heterotrophic nanoflagellates. Environ. Microbiol. 32, 174.
5.
BlumS.A.E., LorenzM.G., and WackernagelW. (1997). Mechanism of retarded DNA degradation and prokaryotic origin of DNases in non sterile soils. Syst. Appl. Microbiol. 20, 513.
6.
CaiP., HuangQ., ChenW., ZhangD., WangK., JiangD., and LiangW. (2007). Soil colloids-bound plasmid DNA: Effect on transformation of E. coli and resistance to DNase I degradation. Soil Biol. Biochem. 39, 1007.
7.
CaiP., HuangQ., and ZhangX. (2006a). Interactions of DNA with clay minerals and soil colloidal particles and protection against degradation by Dnase. Environ. Sci. Technol. 40, 2971.
8.
CaiP., HuangQ., ZhangX., and ChenH. (2006b). Adsorption of DNA on clay minerals and various colloidal particles from an alfisol. Soil Biol. Biochem. 38, 471.
9.
ChowdhuryN.N., CoxA.R., and WiesnerM.R. (2021). Nanoparticles as vectors for antibiotic resistance: The association of silica nanoparticles with environmentally relevant extracellular antibiotic resistance genes. Sci. Tot. Environ. 761, 143261.
10.
CreccioC., and StotzkyG. (1988). Binding of DNA on humic acids: Effect on transformation of Bacillus subtilis and resistance to DNase. Soil Biol. Biochem. 30, 1061.
11.
DemanecheS. (2008). Antibiotic-resistant soil bacteria in transgenic plant fields. Proc. Natl. Acad. Sci. U.S.A. 105, 3957.
12.
DemanècheS., Jocteur-MonrizerL., QuiquampoixH., and SimonetP. (2001). Evaluation of biological and physical protection against nuclease degradation of clay-bound plasmid DNA. Appl. Environ. Microbiol. 67, 293.
13.
GardnerC., and GunschC. (2017). Adsorption capacity of multiple DNA sources to clay minerals and environmental soil matrices less than previously estimated. Chemosphere, 175, 45.
14.
GardnerC., VolkoffS., and GunschC. (2019). Examining the behavior of crop-derived antibiotic resistance genes in anaerobic sludge batch reactors under thermophilic conditions. Biotechnol. Bioeng. 116, 3063.
15.
GuoX.P., YangY., LuD.P., NiuZ.S., FengJ.N., ChenY.R., TouF-Y., GarnerE., XuJ., LiuM., and HochellaM.F.Jr. (2017). Biofilms as a sink for antibiotic resistance genes (ARGs) in the Yangtze Estuary. Water Res. 129, 277.
16.
HarrisonJ.B., SundayJ.M., and RogersS.M. (2019). Predicting the fate of eDNA in the environment and implications for studying biodiversity. Proc. R. Soc. B Biol. Sci. 286, 20191409.
17.
HeiatM., RanjbarR., LatifiA.M., RasaeeM.J., and FarnooshG. (2016). Essential strategies to optimize asymmetric PCR conditions as a reliable method to generate large amount of ssDNA aptamers. Biotechnol. Appl. Biochem. 64, 541.
18.
JacobsL., and CheniaH.Y. (2007). Chenia. Characterization of integrons and tetracycline resistance determinants in Aeromonas spp. isolated from South African aquaculture systems. Int. J. Food Microbiol. 114, 295.
19.
KhannaM., and StotzkyG. (1992). Transformation of Bacillus subtilis by DNA bound on montmorillonite and effect of dnase on the transforming ability of bound DNA. Appl. Environ. Microbiol. 58, 1930.
20.
Levy-BoothD., CampbellR., GuldenR., HartM., PowellJ., KlironomosJ., Peter PaulsK., SwantonC.J., TrevorsaJ.T., and DunfielddK.E. (2007). Cycling of extracellular DNA in the soil environment. Soil Biol. Biochem. 39, 2977.
21.
LorenzM., and WackernagelW. (1987). Adsorption of DNA to sand and variable degradation rates of adsorbed DNA. Appl. Environ. Microbiol. 53, 2948.
22.
LuY., XiaoY., ZhengG., LuJ., and ZhouL. (2020). Conditioning with zero-valent iron or Fe2+ activated peroxydisulfate at an acidic initial sludge pH removed intracellular antibiotic resistance genes but increased extracellular antibiotic resistance genes in sewage sludge. J. Hazard. Mater. 386.
23.
MaoD., LuoY., MathieuJ., WangQ., FengL., MuQ., FengC., and AlvarezP.J.J. (2014). Persistence of extracellular DNA in river sediment facilitates antibiotic resistance gene propagation. Environm. Sci. Technol. 48, 71.
24.
McKinneyC.W., LoftinK.A., MeyerM.T., DavisJ.G., and PrudenA. (2010). tet and sul Antibiotic resistance genes in livestock lagoons of various operation type, configuration, and antibiotic occurrence. Environ. Sci. Technol. 44, 6102.
25.
NielsenK.M., BonesA.M., and Van ElsasJ. (1997). Induced natural transformation of acinetobacter calcoaceticus in soil microcosms. Appl. Environ. Microbiol. 63, 39722977.
26.
NorwackB. (2016). Meeting the needs for released nanomaterials required for further testing—The SUN approach. Environ. Sci. Technol. 50, 2747.
27.
PagetE., MonrozierL.J., and SimonetP. (1992). Adsorption of DNA on clay minerals: Protection against DNaseI and influence on gene transfer. FEMS Microbiol. Lett. 97, 31.
28.
PagetE., and SimonetP. (1994). On the track of natural transformation in soil. FEMS Microbiol. Ecol. 15, 109.
29.
PaulJ.H., FrischerM.E., and ThurmondJ.M. (1991). Gene transfer in marine water column and sediment microcosms by natural plasmid transformation. Appl. Environ. Microbiol. 57, 1509.
PetersR., WeigelS., and BrandhoffP. (2014). Inventory of Nanotechnology Applications in the Agricultural, Feed and Food Sector. Wageningen, The Netherlands: EFSA Supporting Publications.
32.
PietramellaraG., AscherJ., BogogniF., CeccheriniM., GuerriG., and NanipieriP. (2008). Extracellular DNA in soil and sediment: Fate and ecological relevance. Biol. Fertil. Soils, 45, 219.
33.
PietramellaraG., AscherJ., CeccheriniM., NannipieriP., and WenderothD. (2007). Adsorption of pure and dirty bacterial DNA on clay minerals and their transformation frequency. Biol. Fertil. Soils, 43, 731.
34.
PolyF., ChenouC., SimonetP., RouillerJ., and Jocteur-MonrizerL. (2000). Differences between linear chromosomal and supercoiled plas mid DNA in their mechanisms and extent of adsorption on clay minerals. Langmuir, 16, 1233.
35.
PotéJ., CeccheriniM.T., VanV.T., RosselliW., WildiW., SimonetP., and VogelT.M. (2003). Fate and transport of antibiotic resistance genes in saturated soil columns. Eur. J. Soil Biol. 39, 65.
36.
PradoA.G.S., PertusattiJ., and NunesA.R. (2011). Aspects of protonation and deprotonation of humic scid durface on molecular conformation. J. Braz. Chem. Soc. 22, 1478.
37.
PrudenA., PeiR., StorteboomH., and CarlsonK.H. (2006). Antibiotic resistance genes as emerging contaminants: Studies in northern Colorado. Environ. Sci. Technol. 40, 7445.
38.
RizzoL., ManaiaC., MerlinC., SchwartzT., DagotC., PloyM.C., MichaelI., and Fatta-KassinosD. (2013). Urban wastewater treatment plants as hotspots for antibiotic resistant bacteria and genes spread into the environment: A review. Sci. Tot. Environ. 447, 345.
39.
SaekiK., IhyoY., SakaiM., and KunitoT. (2010). Strong adsorption of DNA molecules on humic acids. Environ. Chem. Lett. 9, 505.
40.
SchwabF., ZhaiG., KernM., TurnerA., SchnoorJ.L., and WiesnerM. (2015). Barriers, pathways and processes for uptake, translocation and accumulation of nanomaterials in plants—Critical review. Nanotoxicology, 10, 257.
41.
SlaterL., NtarlagiannisD., and WishartD. (2006). On the relationship between induced polarization and surface area in metal–sand and clay–sand mixtures. Geophysics, 71, A1.
42.
StewartG.J., and SinigallianoC.D. (1990). Detection of horizontal gene transfer by natural transformation in native and introduced species of bacteria in marine and synthetic sediments. Appl. Environ. Microbiol. 56, 1818.
43.
VikeslandP., PrudenA., AlvarezP., AgaD., BergmanH., LiX.-D., ManaiaC.M., NambiI., WiggintonK., ZhangT., and ZhuY.-G. (2017). Toward a comprehensive strategy to mitigate dissemination of environmental sources of antibiotic resistance. Environ. Sci. Technol. 51, 13061.
44.
WangD.N., LiuL., QiuZ.G., ShenZ.Q., GuoX., YangD., LiJ., LiuW-L., JinM., and LiJ-W. (2016). A new adsorption-elution technique for the concentration of aquatic extracellular antibiotic resistance genes from large volumes of water. Water Res. 92, 188.
45.
WiesnerM., LowryG., AlvarezP., DionysiouD., and BiswasP. (2006) Assessing the risks of manufactured nanomaterials. Environ. Sci. Technol. 40, 4336.
46.
XiC., ZhangY., MarrsC.F., YeW., SimonC., FoxmanB., and NriaguJ. (2009). Prevalence of antibiotic resistance in drinking water treatment and distribution systems. Appl. Environ. Microbiol. 75, 5714.
47.
YinJ., ZhangD., ZhaoJ., WangX., ZhuH., and WangC. (2014). Meso- and micro-porous composite carbons derived from humic acid for supercapacitors. Electrochim. Acta, 136, 504.
48.
YuanK., WangX., ChenX., ZhaoZ., FangL., ChenB., JiangJ., LuanT., and ChenB. (2019). Occurrence of antibiotic resistance genes in extracellular and intracellular DNA from sediments collected from two types of aquaculture farms. Chemosphere, 234, 234.
49.
ZhangY., LiA., DaiT., LiF., XieH., ChenL., and WenD. (2018). Cell-free DNA: A neglected source for antibiotic resistance genes spreading from WWTPs. Environ. Sci. Technol. 52, 248.
50.
ZhuB. (2006). Degradation of plasmid and plant DNA in water microcosms monitored by natural transformation and real-time polymerase chain reaction (PCR). Water Res. 40, 3231.
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