Antibiotics and Antibiotic Resistance Genes in Bulk and Rhizosphere Soils Subject to Manure Amendment and Vegetable Cultivation

Abstract

There is interest in understanding effects of amending soil with manure in a cultivation setting and if composting can provide benefits. Raw or composted manure from cattle administered with and without sulfamethazine, chlortetracycline, and tylosin was amended to loamy sand and silty clay loam soils, where lettuce (Lactuca sativa L.), radish (Raphanus sativus L.), and broccoli (Brassica oleracea L. var. italica) were cultivated and compared with those grown in soil amended with fertilizer as a control. Upon plant maturation, rhizosphere and bulk soils were analyzed for antibiotics, and sul1, ermB, tet(W), and intI1 genes were quantified. Antibiotic concentrations in compost‐amended soils were below detection limits. For soils amended with manure containing antibiotics, sulfamethazine ranged from 1.1 to 3.1 μg kg−1 in the bulk soils but was below detection limits in the rhizosphere soils. Chlortetracycline (2.8–9.3 μg kg−1) was two times lower in the rhizosphere than in the bulk soil. Levels of tylosin in the rhizosphere soil were similar to the bulk soil. Soil texture or vegetable type did not have significant influence on antibiotic concentration differences between the bulk and rhizosphere soils. Relative abundances of tet(W) and intI1 in the fertilizer‐amended soil were significantly lower than in those amended with manure or compost (p < 0.05), whereas ermB was not detected in any soils. Rhizosphere zone has no significant effect on the detected antibiotic resistance genes. It is suggested that plant roots may have a substantial effect on the fate of certain antibiotics in manure‐amended fields, but less of an effect on antibiotic resistance and mobility genes. Core Ideas Composting reduces antibiotic inputs to soils relative to direct manure application. Antibiotic concentrations in manure generally decrease in amended soils. Dissipation of sulfamethazine and chlortetracycline is enhanced in the rhizosphere. Antibiotic fate in bulk and rhizosphere soils was similar for three vegetables and two soils. Resistance and mobility genes were greater in manure ‐ than fertilizer‐amended soil.

Manure and Doxycycline Affect the Bacterial Community and Its Resistome in Lettuce Rhizosphere and Bulk Soil

“…HT-qPCR revealed that the effect of doxycycline-spiked manure on the number of enriched genes and on the fold change of enrichment was less pronounced in the rhizosphere than in bulk soil. This is in agreement with results of previous studies demonstrating smaller effects of antibiotics applied with manure in the rhizosphere (Jechalke et al, 2013a,b; Kopmann et al, 2013; Wang et al, 2015; Kang et al, 2017; Chen et al, 2018). The reduced effect might be related to an accelerated dissipation of doxycycline in the rhizosphere due to plant-enhanced microbial biotransformation processes, as suggested previously for different antibiotics (Rosendahl et al, 2012; Chen et al, 2018).…”

“…The rhizosphere is regarded as a hotspot of microbial activity and HGT, which might alter the fate and effects of doxycycline in agricultural soils (Rosendahl et al, 2011; Jechalke et al, 2013a,b; Chen et al, 2018). HT-qPCR revealed that the effect of doxycycline-spiked manure on the number of enriched genes and on the fold change of enrichment was less pronounced in the rhizosphere than in bulk soil.…”

“…Furthermore, the plant rhizosphere is considered to be a hotspot of HGT, which seems to be modulated by root growth and exudates production, increasing microbial abundance and activity (van Elsas et al, 2003; Mølbak et al, 2007; Heuer and Smalla, 2012). Accordingly, it was observed in previous studies that the fate and effects of antibiotics in the rhizosphere can differ from bulk soil (Rosendahl et al, 2011; Jechalke et al, 2013a,b; Chen et al, 2018). However, this was not shown so far for doxycycline.…”

Soil Chemistry and the One Health Initiative: Introduction to the Special Section

“…Chen et al (2018) conducted a greenhouse study to assess how cattle manure with and without composting treatment affects levels of sulfamethazine, chlortetracycline, and tylosin in soils planted to lettuce ( Lactuca sativa L.), radish ( Raphanus sativus L.), or broccoli ( Brassica oleracea L. var. italica ) seedlings.…”

“…However, the authors state that further studies are needed on how subsurface injection affects the downward transport of antibiotics to groundwater before best management recommendations can be made. Chen et al (2018) conducted a greenhouse study to assess how cattle manure with and without composting treatment affects levels of sulfamethazine, chlortetracycline, and tylosin in soils planted to lettuce (Lactuca sativa L.), radish (Raphanus sativus L.), or broccoli (Brassica oleracea L. var. italica) seedlings.…”