Assessing bacterial diversity and antibiotic resistance dynamics in wastewater effluent-irrigated soil and vegetables in a microcosm setting

Abstract

Water scarcity is one of the main challenges in sustainable agricultural development particularly in developing countries therefore, irrigation of food crops with wastewater effluent has become a common practice in order to meet the growing food demand. The aim of this study was to determine the impact of wastewater irrigation on bacterial community and antibiotic resistance dynamics in soil and vegetables in an agricultural setting. To determine bacterial diversity, occurrence and overall dynamics of antibiotic resistant genes (ARGs) in effluent irrigated soil and vegetables, 16S rRNA gene metagenomics, shotgun metagenomics and molecular PCR technique were utilized. A shift in bacterial community profile was observed as notable reduction in proteobacteria and increase in firmicutes phyla from the microcosm soil following wastewater effluent irrigation. Shotgun metagenomics revealed diverse ARGs belonging to at least nine different classes of antibiotics in the effluent wastewater. However, only bla _TEM (beta-lactamase) and aadA (aminoglycoside) resistance gene sequences were identified in microcosm soil following irrigation and only bla _TEM was detected on effluent irrigated vegetable surfaces (spinach and beetroots). From the study, only bla _TEM gene was identified across all samples; effluent wastewater, effluent-treated soil, and vegetables. The data suggests a possible dissemination and persistence of the beta-lactamase bla _TEM gene from effluent wastewater into agricultural soil and vegetables. This study enhances our understanding of antibiotic resistance spread and highlights the importance of monitoring antibiotic resistance in agro-systems, which is critical for informing policies aimed at sustainable use of wastewater effluent in water-stressed countries.

Keywords: Agriculture; Antibiotic resistant genes; Metagenomics; Microcosm; Wastewater effluent.

Figure 1

Microcosm experimental design. A; Experimental microplots showing vegetables that were sown and irrigated using PWWTP effluent. B; Control microplots showing vegetables that were sown and irrigated using tap water. C: Untreated microplots.

Figure 2

Taxonomic classification comparison based on Proteobacteria found in PWWTP effluent, untreated soil and effluent irrigated soil.

Figure 3

Taxonomic classification comparison based on Firmicutes found in PWWTP effluent, untreated soil and effluent irrigated soil.

Figure 4

PCR amplification of targeted bla_TEM gene. Key – L; 1KB DNA Ladder, NC; Negative control, PC; Positive control, 1; Wastewater effluent irrigated soil after 30 days, 2; Wastewater effluent irrigated soil after 60 days, 3; Wastewater effluent irrigated soil after 90 days, 4; Spinach at harvest, 5: Beetroot at harvest, 6; Wastewater effluent 7; Untreated soil.