Enzymatic Activity and Microbial Diversity of Sod-Podzolic Soil Microbiota Using 16S rRNA Amplicon Sequencing following Antibiotic Exposure.

Tatiana Trifonova,Alexander Sprygin,Olga Byadovskaya,Anastasia Kosmacheva,Svetlana Chesnokova

doi:10.3390/antibiotics10080970

Abstract

Antibiotic contamination of the environment negatively affects soil fertility by disrupting natural microbial communities. Currently, the study of the effect of antibacterial drugs on soils typical in Russia, which are of great importance for agriculture, is insufficient. Despite a rapid increase in the number of metagenomic studies, this article is the first publication devoted to the microbial diversity of sod-podzolic soil and its relationship with enzymatic activity. In the present study, we use 16S rRNA metagenomic sequencing to analyze microbiota dynamics and to examine soil enzymatic activities after antibiotic treatment with benzylpenicillin, oxytetracycline, and tylosin. We found that, following treatment, urease activity was reduced regardless of the antibiotic used while nitrification activity showed no statistically significant changes (p > 0.05). Oxytetracycline and tylosin produced no effect on catalase activity but benzylpenicillin caused an increase. Benzylpenicillin and oxytetracycline increased cellulolytic activity whereas tylosin had no significant effect (p > 0.05). Microbiome profiling through 16S rRNA gene sequencing demonstrated antibiotic administration and exhibited no significant impact on bacterial abundance and species diversity (p > 0.05), thus pointing to the resilience of the soil microbial community. Oxytetracycline, benzylpenicillin, and tylosin are likely to negatively affect the enzymatic profiles in sod-podzolic soil but with a negligible influence on the bacterial composition.

Highlights

Animal husbandry intensification is associated with a rise in economic indicators and with a number of negative impacts on the environment such as the use of medicines against animal infectious diseases, including various spectrum antibiotics
We evaluated enzymatic activity and changes in the soil microbiome in response to antibiotics
Despite a rapid growth in the number of metagenomic studies, this article is the first publication devoted to the microbial diversity of sod-podzolic soil and its relationship with enzymatic activity

Summary

Introduction

Animal husbandry intensification is associated with a rise in economic indicators and with a number of negative impacts on the environment such as the use of medicines against animal infectious diseases, including various spectrum antibiotics. The antimicrobials introduced into the environment threaten natural microbial communities due to their ability to affect soil microorganisms, to change the total biomass, to affect the relative number of different groups, and to change soil enzyme activity. In this regard, the study of antibiotics as soil ecosystem pollutants has garnered considerable attention. The assessment of enzymatic activity changes and microbial diversity using metagenomics or 16S rRNA gene sequencing under the impact of antibiotic drugs provides significant diagnostic indicators in such research [6,7,8,9,10,11,12,13,14,15,16]

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Discussion

Conclusion