Effects of sulfamethoxazole and copper on the natural microbial community from a fertilized soil

Abstract

Cattle manure or its digestate, which often contains antibiotic residues, can be used as an organic fertilizer and copper (Cu) as a fungicide in agriculture. Consequently, both antibiotics and Cu are considered soil contaminants. In this work, microcosms were performed with soil amended with either manure or digestate with Cu and an antibiotic (sulfamethoxazole, SMX) co-presence and the planting of Lactuca sativa. After the addition of the organic amendments, a prompt increase in the microbial activity and at the same time of the sul1 and intI1 genes was observed, although ARGs generally decreased over time. In the amended and spiked microcosms, the microbial community was able to remove more than 99% of SMX in 36 days and the antibiotic did not bioaccumulate in the lettuce. Interestingly, where Cu and SMX were co-present, ARGs (particularly sul2) increased, showing how copper had a strong effect on resistance persistence in the soil. Copper also had a detrimental effect on the plant-microbiome system, affecting plant biomass and microbial activity in all conditions except in a digestate presence. When adding digestate microbial activity, biodiversity and lettuce biomass increased, with or without copper present. Not only did the microbial community favour plant growth, but lettuce also positively influenced its composition by increasing bacterial diversity and classes (e.g., Alphaproteobacteria) and genera (e.g., Bacillus), thus indicating a good-quality soil. KEY POINTS: • Cattle digestate promoted the highest microbial activity, diversity, and plant growth • Cattle digestate counteracted detrimental contaminant effects • Cu presence promoted antibiotic cross-resistance in soil.

Keywords: ARGs; Antibiotics; Cattle manure; Cattle manure digestate; Lettuce; Plant-microbiome system.

Fig. 1

a Live cell abundance (N. live cells/g dry soil). b Dehydrogenase activity (µg TPF/ g dry soil). Data are means of three independent replicates. The vertical bars represent the standard errors. The post hoc tests are reported in detail in Supplementary Material (Table S3 and Table S4)

Fig. 2

Relative gene abundances (ARGs or MGE/16S) in the various experimental conditions. The post hoc test is reported in detail in Supplementary Material (Table S5)

Fig. 3

Principal coordinate analysis (PCoA) based on the Bray–Curtis distance matrix and calculated on ASV distribution. Red points indicate the digestate-amended conditions, green points the manure-amended conditions, and blue ones the no amended conditions. The circle shape indicates no plant presence. The pink ellipse indicates the initial sampling time (3 h) and the light blue one the finale sampling time (36 days)

Fig. 4

Class relative abundances (% ASV) with an average presence > 1% in each experimental condition at 3 h (a), soil at 36 days (b), and rhizosphere at 36 days (c). Data are means of three independent replicates

Fig. 5

Heatmap for prokaryotic relative abundances at genus level in the different conditions and at the sampling times (3 h and 36 days). Genera and conditions were grouped in accordance with a hierarchical clustering dendrogram, at the top and the left side of the heatmap. Data are means of three independent replicates

Fig. 6

Total (aerial + root) biomass (dry weight, g) of the lettuce plants under experimental different conditions at the end of the experiment (36 days)