Abstract
The effect of antibiotics on the diversity and functioning of indigenous microorganisms in the environment has attracted much attention. In this study, effects of exposure to six different antibiotics on the bacterial community, metabolic functions and antibiotic resistance genes (ARGs) in marine sediments during enrichment culturing were investigated. Classical culture-dependent method and high-throughput 16S rRNA gene sequencing method were both applied. In the culture-dependent analysis, the obtained 1549 isolates belonged to four phyla (Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria) and 155 genera. Proteobacteria and Firmicutes were the dominant phyla. The diversity and abundance of obtained bacteria after antibiotic processing exhibited different degrees of decrease. Enrichment culturing for different time could also affect the bacterial community composition. Some genera of bacteria were not isolated in the control group, but they could be isolated in the antibiotic-treated groups. In high-throughput 16S rRNA gene amplicon sequencing analyses, all the effective reads were clustered into 2822 OTUs at 97% similarity cutoff; they were annotated to 49 phyla, 103 class, 220 orders, 347 families, 624 genera and 1122 species. An alpha diversity analysis indicated that the community diversity and richness decreased under antibiotic exposure. The changes at the genus level were much more obvious. Only 48 genera of 129 genera were shared by all the samples. A total of 29 genera which were not detected in the initial control sample could be detected in at least one antibiotic-treated group. SIMPER analysis showed that OTU2543 and OTU1450 were the most common taxa to the dissimilarity of bacterial community between antibiotic-treated groups and the control group. OTU2034 and OUT2543 were the most contributive taxa to dissimilarity of groups incubating for different time. Metabolism was the predominant bacterial function. A total of 30 ARGs were detected in the samples. This study mainly focused on the changes of microbiota under the selective pressure of antibiotics for different time and the results demonstrated that the antibiotic could affect the bacterial diversity and richness in the marine ecosystem.
Highlights
Antibiotics have been widely used in the human medical field, the aquaculture, the animal husbandry and agriculture, to prevent various infections and stimulate the growth of animals and plants since their discovery [1,2,3,4,5]
Comparing the samples at time 0 (A0, P0, Q0, R0, S0, T0, U0), exposure to antibiotics could make the concentration of cultivable bacteria decrease in different degree, suggesting that the antibiotics had a negative effect on the microbial community
When the antibiotics were re-added on Day 12 to consolidate the selective pressure, the cultivable bacteria in the samples collected on Day 21 were less than that of samples without re-adding antibiotics
Summary
Antibiotics have been widely used in the human medical field, the aquaculture, the animal husbandry and agriculture, to prevent various infections and stimulate the growth of animals and plants since their discovery [1,2,3,4,5]. Due to the increasing consumption of antibiotics globally in recent years [6], they have caused extensive concern They have been largely released into the environments by improper disposal or excretion by humans and animals [7,8,9], and cause chemical pollution, and result in the dissemination of antibiotic resistance genes (ARGs) and epidemic of antibiotic resistant bacteria—or even multiresistant bacteria [10,11]. This is a serious and growing threat to ecosystems, human and animal health [1,12,13]. With the increasing use of antibiotics, the potential threat to environment cannot be neglected [21,22,23]
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