Table 2.

Antibiotics and ARGs found in soil-plant systems (1–4 columns) and effects in terms of soil and plant microbiome shifts (5–6 columns).

Antibiotics		ARGs		Microbial Composition		References
Soil	Plant	Soil	Plant Microbiome	Soil	Plant Microbiome
ABs: 2.5 mg/kg each enrofloxacin (ENR) ciprofloxacin (CIP) sulfamethazine (SMZ) sulfamethoxazole (SMX) doxycycline (DOX) chlortetracycline hydrochloride (CTCC) lincomycin (LIN)	Lettuce: SMX: 0.044 mg/kg fresh weight LIN: 0.051 mg/kg fresh weight SMZ: 0.021 mg/kg fresh weight	-	-	-	-	[81]
Sulfamethoxazole (SMX) 100 mg/kg 200 mg/kg 300 mg/kg	Lettuce: 0.084 mg/kg 0.181 mg/kg 0.503 mg/kg	sul1 sul2 tetM tetA/P tet34 tetG1 tetG2 qnrS1 qnrS2 cmlA1 floR	-	Control soil microbial community dominated by: Gaiella, Streptomyces, Sphingomonas Soil + SMX dominated by: Lysobacter, Bacillus	-	[86]
-	-	beta-lactam, aminoglycoside, MLSB, tetracyclinesulphonamide, FCA, vancomycin, MGEs	beta-lactam, aminoglycoside, MLSB, tetracycline, sulphonamid, FCA, vancomycin, MGEs	Soil: Actinobacteria and Deltaproteobacteria increase, Cyanobacteria decrease in AB presence	Root endophytes: Alphaproteobacteria increase and Gammaproteobacteria decrease; Phyllosphere: Actinobacteria decrease	[100]
Swine manure added to the soil and doxycycline (DOX): 84.02 µg/kg sulfamethoxazole (SMX): 86.41 µg/kg tilmicosin (TIL): 69.37 µg/kg	Lettuce	tetA; tetG; tetM; tetX, intI1	Phyllosphere: sul2; tetA; tetG; tetM; tetQ; ermC intI1; intI2 Endosphere: tetQ; tetL; tetA; tetO; tetX; intI1; intI2	Fluviicola, Cohnella, Alcanivorax bacteria correlated with ARGs	Phyllosphere: Pseudomonas, Clostridium_IV correlated with ARGs Endosphere: Chelativorans, Halomonas	[101]
ABs: 7.5 mg/kg each Sulfamethoxazole (SMX) Ciprofloxacin (CIP) Enrofloxacin (ENR)	Lettuce: CIP bioaccumulation, with significantly higher values in manure amended than digestate condition	sul2 aac-(6′)-Ib-cr qepA	Rhizosphere: sul2 aac-(6′)-Ib-cr qepA Phyllosphere: sul1 sul2 aac-(6′)-Ib-cr qepA sul1 tnpA	Significant increase in Bacilli and Bacteroida in antibiotic and manure amended conditions Significant decrease in Actinobacteria and Alphaproteobacteria	Rhizosphere: significant decrease in Actinobacteria, Alphaproteobacteria and Bacilli in antibiotic and manure amended conditions Phyllosphere: significant increase in Bacilli and Gammaproteobacteria in antibiotic and manure amended conditions	[30]
Oxytetracycline (OTC) Streptomycin (STR) Calculated soil concentration of 59.45 mg/kg at 74 days	Cherry radish: Significantly higher presence of STR in plant tissue in comparison with OTC Phyllosphere: STR 0.3 mg/kg OTC 0.003 mg/kg Fruits: STR 0.2 mg/kg OTC 0.005 mg/kg Soil STR 0 mg/kg OTC 0.007 mg/kg	-	-	At 74 days no more Firmicutes detected and general decrease in Actinobacteria. Increase in Poteobacteria and Chloroflexi in OTC condition; decrease in Actinobcteria. Increase in Gemmatimonadetes in STR condition	At 74 days Phyllosphere: decrease in Bacterioidetes. Increase in Cyanobacteria and decrease in Firmicutes in antibiotic conditions. Fruits: increase in Actinobacteria in OTC condition. Root Endophytes: increase in Chloroflexi. Increase in Proteobacteria and Actinobacteria in OTC and STR conditions, respectively	[102]