Comparison in Antibiotic Resistance Genes Carried by Bacteriophages and Bacteria in Farmland Soil Amended with Different Fertilizers

doi:10.13560/j.cnki.biotech.bull.1985.2021-1544

Abstract

Abstract:

This study is aimed to elucidate the effect of the long-term application of organic and chemical fertilizers on the diversity and abundance of antibiotic resistance genes（ARGs）carried by bacteriophages,and to compare them with ARGs carried by bacteria in farmland soil. Soil antibiotic resistance was divided into bacterial and bacteriophage fractions,and droplet digital PCR（ddPCR）was employed to analyze the abundance of 25 ARG subtypes and class I integrase gene（intl1）in DNA of soil bacteria and bacteriophages. The total abundance and detection rate of ARGs and intl1 abundance carried by bacteriophages were evidently lower than those in soil bacterial fraction. Twenty ARG subtypes were detected in bacteriophage DNA. Detection rates of target ARGs in bacteriophages were 68%,72%,and 76% in unfertilized,chemically fertilized,and organically fertilized soils,respectively. The total abundance of ARGs in bacteriophages in the soil amended with organic fertilizer was the significantly higher than that in the soil amended with chemical fertilizer and the unfertilized soil（P<0.05）,and the gene abundances of multi-drug,macrolide-lincosamide-streptogramin group B（MLSB）,and β-lactam resistance dominated bacteriophages. Apart from β-lactam resistance gene blaTEM_,the abundance of other ARG subtypes in bacteriophages was significantly lower than that in soil bacteria（P<0.05）. The significantly positive correlations of ARG abundance were observed between soil bacteria and bacteriophages under different fertilization treatments（P<0.05）. The results of redundancy analysis showed that fertilization may affect the occurrence characteristics of ARGs in bacteria and bacteriophages by changing soil pH,heavy metal and nutrient factor levels. The findings of this study indicate that bacteriophages are another important reservoir of ARGs in farmland soil besides bacteria. The application of organic fertilizer simultaneously increased the diversity and abundance of ARGs carried by soil bacteria and bacteriophages.

Key words: antibiotic resistance genes, bacteriophages, farmland soil, droplet digital PCR, redundancy analysis

HU Xue-ying, ZHANG Yue, GUO Ya-jie, QIU Tian-lei, GAO Min, SUN Xing-bin, WANG Xu-ming. Comparison in Antibiotic Resistance Genes Carried by Bacteriophages and Bacteria in Farmland Soil Amended with Different Fertilizers[J]. Biotechnology Bulletin, 2022, 38(9): 116-126.

Figures/Tables 7

References 35

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处理Treatment	施肥量Fertilizer amount/（kg· m^-2）
不施肥（CK） Without fertilizer	0
单施化肥（IF） Inorganic fertilizer amendment	Urea 0.04、（NH₄）₂HPO₄ 0.05和K₂SO₄ 0.03
单施有机肥（OF） Organic fertilizer amendment	Compost from chicken manure 2.38

处理Treatment	施肥量Fertilizer amount/（kg· m^-2）
不施肥（CK） Without fertilizer	0
单施化肥（IF） Inorganic fertilizer amendment	Urea 0.04、（NH₄）₂HPO₄ 0.05和K₂SO₄ 0.03
单施有机肥（OF） Organic fertilizer amendment	Compost from chicken manure 2.38

抗生素抗性基因亚型 ARG subtypes	细菌Bacteria			噬菌体acteriophages
抗生素抗性基因亚型 ARG subtypes	CK	IF	OF	CK	IF	OF
strA	+	+	+	-	+	+
strB	+	+	+	+	+	+
aadA-01	+	+	+	+	+	+
blaOXA-20	-	-	-	-	-	-
blaTEM	+	+	+	+	+	+
blaCTX-M	-	+	+	-	-	+
ermA	+	+	+	-	-	-
ermB	+	+	+	-	-	-
mphA-01	+	+	+	+	+	+
oleC	+	+	+	+	+	+
sul1	+	+	+	-	-	-
sul2	+	+	+	+	+	+
tetA	+	+	+	+	+	+
tetW	+	+	+	+	+	+
tetM	+	+	+	+	+	+
tetX	+	+	+	+	+	+
acrA-05	+	+	+	+	+	+
emrD	+	+	+	+	+	+
mepA	+	+	+	+	+	+
mexF	+	+	+	+	+	+
qnrA	-	-	-	-	-	-
qnrS	+	+	+	-	+	-
vanHB	+	+	+	+	+	+
vanA	+	+	+	+	+	+
mcr-1	+	+	+	+	-	+
检出率Detection rate/%	88	92	92	68	72	76
intl1	+	+	+	+	+	+

抗生素抗性基因亚型 ARG subtypes	细菌Bacteria			噬菌体acteriophages
抗生素抗性基因亚型 ARG subtypes	CK	IF	OF	CK	IF	OF
strA	+	+	+	-	+	+
strB	+	+	+	+	+	+
aadA-01	+	+	+	+	+	+
blaOXA-20	-	-	-	-	-	-
blaTEM	+	+	+	+	+	+
blaCTX-M	-	+	+	-	-	+
ermA	+	+	+	-	-	-
ermB	+	+	+	-	-	-
mphA-01	+	+	+	+	+	+
oleC	+	+	+	+	+	+
sul1	+	+	+	-	-	-
sul2	+	+	+	+	+	+
tetA	+	+	+	+	+	+
tetW	+	+	+	+	+	+
tetM	+	+	+	+	+	+
tetX	+	+	+	+	+	+
acrA-05	+	+	+	+	+	+
emrD	+	+	+	+	+	+
mepA	+	+	+	+	+	+
mexF	+	+	+	+	+	+
qnrA	-	-	-	-	-	-
qnrS	+	+	+	-	+	-
vanHB	+	+	+	+	+	+
vanA	+	+	+	+	+	+
mcr-1	+	+	+	+	-	+
检出率Detection rate/%	88	92	92	68	72	76
intl1	+	+	+	+	+	+