Effects of Antibiotics on the Bacterial Community, Metabolic Functions and Antibiotic Resistance Genes in Mariculture Sediments during Enrichment Culturing
Abstract
:1. Introduction
2. Materials and Methods
2.1. Target Antibiotics
2.2. Sample Collection and Experimental Design
2.3. Bacterial Communities Based on Culture-Dependent Analysis
2.4. Culture-Independent Bacterial Community Analysis Based on ILLUMINA HIGH-THROUGHPUT 16S rRNA Gene Sequencing
2.5. Prediction of Bacterial Functions and Analysis of Antibiotic Resistance Genes
3. Results and Discussion
3.1. The Changes in the Abundances and Diversity of Cultivable Bacteria under Different Antibiotic Pressure
3.2. Taxonomic Composition of Cultivable Bacteria
3.3. Microbial Community Characteristics Based on the High-Throughput 16S rRNA Gene Amplicon Sequencing
3.3.1. Diversity and Richness of Microbial Community
3.3.2. Impact of Antibiotic on the Microbial Community at Phylum Level
3.3.3. Impact of Antibiotic on the Microbial Community at Genus Level
3.3.4. Comparative Analysis of Microbial Community Structures under Different Antibiotic Selective Pressures
3.4. Analysis of Bacterial Functions
3.5. Antibiotic Resistance Genes Analysis
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Group | Designated as | Treatment | Concentration (mg/L) | Incubation Time (days) |
---|---|---|---|---|
A | A0 | Control | - | 0 |
A1 | Control | - | 5 | |
A2 | Control | - | 12 | |
A3 | Control | - | 21 | |
A4 | Control | - | 30 | |
P | P0 | zinc bacitracin | 50 | 0 |
P1 | zinc bacitracin | 50 | 5 | |
P2 | zinc bacitracin | 50 | 12 | |
P3 | zinc bacitracin | 50 | 21 | |
P4 | zinc bacitracin | 50 | 30 | |
JP3 | zinc bacitracin, re-added on Day 12 | 50 + 50 | 21 | |
JP4 | zinc bacitracin, re-added on Day 12 | 50 + 50 | 30 | |
Q | Q0 | ciprofloxacin | 30 | 0 |
Q1 | ciprofloxacin | 30 | 5 | |
Q2 | ciprofloxacin | 30 | 12 | |
Q3 | ciprofloxacin | 30 | 21 | |
Q4 | ciprofloxacin | 30 | 30 | |
JQ3 | Ciprofloxacin, re-added on Day 12 | 30 + 30 | 21 | |
JQ4 | Ciprofloxacin, re-added on Day 12 | 30 + 30 | 30 | |
R | R0 | ampicillin sodium | 100 | 0 |
R1 | ampicillin sodium | 100 | 5 | |
R2 | ampicillin sodium | 100 | 12 | |
R3 | ampicillin sodium | 100 | 21 | |
R4 | ampicillin sodium | 100 | 30 | |
JR3 | ampicillin sodium, re-added on Day 12 | 100 + 100 | 21 | |
JR4 | ampicillin sodium, re-added on Day 12 | 100 + 100 | 30 | |
S | S0 | chloramphenicol | 30 | 0 |
S1 | chloramphenicol | 30 | 5 | |
S2 | chloramphenicol | 30 | 12 | |
S3 | chloramphenicol | 30 | 21 | |
S4 | chloramphenicol | 30 | 30 | |
JS3 | chloramphenicol, re-added on Day 12 | 30 + 30 | 21 | |
JS4 | chloramphenicol, re-added on Day 12 | 30 + 30 | 30 | |
T | T0 | tylosin | 50 | 0 |
T1 | tylosin | 50 | 5 | |
T2 | tylosin | 50 | 12 | |
T3 | tylosin | 50 | 21 | |
T4 | tylosin | 50 | 30 | |
JT3 | tylosin, re-added on Day 12 | 50 + 50 | 21 | |
JT4 | tylosin, re-added on Day 12 | 50 + 50 | 30 | |
U | U0 | tetracycline | 30 | 0 |
U1 | tetracycline | 30 | 5 | |
U2 | tetracycline | 30 | 12 | |
U3 | tetracycline | 30 | 21 | |
U4 | tetracycline | 30 | 30 | |
JU3 | tetracycline, re-added on Day 12 | 30 + 30 | 21 | |
JU4 | tetracycline, re-added on Day 12 | 30 + 30 | 30 |
Sample No. | Enrichment Time (d) | Number of Strains | Taxonomic Composition | ||
---|---|---|---|---|---|
Phyla | Genera | Species | |||
Control | 372 | 4 | 76 | 145 | |
A0 | 0 | 55 | 4 | 28 | 43 |
A1 | 5 | 58 | 4 | 18 | 32 |
A2 | 12 | 82 | 4 | 27 | 44 |
A3 | 21 | 98 | 4 | 35 | 63 |
A4 | 30 | 79 | 4 | 31 | 55 |
Exposure to zinc bacitracin (P) | 254 | 4 | 67 | 137 | |
P0 | 0 | 35 | 2 | 19 | 28 |
P1 | 5 | 16 | 4 | 12 | 14 |
P2 | 12 | 28 | 4 | 16 | 20 |
P3 | 21 | 50 | 4 | 24 | 36 |
JP3 | 21 | 44 | 4 | 22 | 35 |
P4 | 30 | 21 | 3 | 13 | 21 |
JP4 | 30 | 60 | 4 | 24 | 40 |
Exposure to ciprofloxacin (Q) | 134 | 4 | 37 | 67 | |
Q0 | 0 | 7 | 1 | 2 | 2 |
Q1 | 5 | 16 | 3 | 5 | 11 |
Q2 | 12 | 34 | 4 | 17 | 23 |
Q3 | 21 | 25 | 4 | 13 | 18 |
JQ3 | 21 | 24 | 4 | 12 | 18 |
Q4 | 30 | 14 | 4 | 9 | 10 |
JQ4 | 30 | 14 | 4 | 13 | 14 |
Exposure to ampicillin sodium (R) | 156 | 4 | 46 | 83 | |
R0 | 0 | 15 | 3 | 12 | 13 |
R1 | 5 | 17 | 2 | 7 | 11 |
R2 | 12 | 31 | 4 | 11 | 19 |
R3 | 21 | 29 | 4 | 15 | 23 |
JR3 | 21 | 26 | 4 | 15 | 18 |
R4 | 30 | 19 | 3 | 14 | 17 |
JR4 | 30 | 19 | 4 | 13 | 18 |
Exposure to chloramphenicol (S) | 190 | 4 | 48 | 85 | |
S0 | 0 | 5 | 2 | 3 | 3 |
S1 | 5 | 17 | 3 | 6 | 10 |
S2 | 12 | 39 | 4 | 17 | 27 |
S3 | 21 | 31 | 4 | 16 | 24 |
JS3 | 21 | 58 | 4 | 23 | 36 |
S4 | 30 | 20 | 4 | 15 | 17 |
JS4 | 30 | 20 | 3 | 12 | 15 |
Exposure to tylosin (T) | 250 | 4 | 58 | 117 | |
T0 | 0 | 5 | 1 | 2 | 34 |
T1 | 5 | 22 | 4 | 10 | 14 |
T2 | 12 | 31 | 2 | 11 | 23 |
T3 | 21 | 39 | 3 | 12 | 25 |
JT3 | 21 | 59 | 3 | 27 | 43 |
T4 | 30 | 44 | 4 | 18 | 26 |
JT4 | 30 | 50 | 4 | 21 | 37 |
Exposure to tetracycline (U) | 193 | 4 | 51 | 93 | |
U0 | 0 | 42 | 4 | 25 | 33 |
U1 | 5 | 19 | 4 | 8 | 9 |
U2 | 12 | 25 | 4 | 12 | 19 |
U3 | 21 | 30 | 3 | 12 | 17 |
JU3 | 21 | 39 | 4 | 19 | 28 |
U4 | 30 | 10 | 4 | 10 | 10 |
JU4 | 30 | 28 | 4 | 15 | 21 |
Treatment | Sample ID | OTUs Number | Sobs | Shannon | Simpson | Ace | Chao | Coverage |
---|---|---|---|---|---|---|---|---|
Control (A) | A0 | 1972 | 1972 | 5.966149 | 0.007343 | 2190.212 | 2169.367 | 0.991121 |
A1 | 850 | 850 | 3.488607 | 0.080376 | 1869.999 | 1467.281 | 0.990808 | |
A2 | 987 | 987 | 3.530338 | 0.082274 | 1879.859 | 1570.807 | 0.990654 | |
A3 | 1335 | 1335 | 4.175985 | 0.057538 | 2343.172 | 1923.443 | 0.991536 | |
A4 | 1110 | 1110 | 3.934633 | 0.08665 | 1898.589 | 1602.39 | 0.989918 | |
Zinc bacitracin (P) | P1 | 787 | 787 | 3.465812 | 0.076074 | 1802.525 | 1404.236 | 0.990751 |
P2 | 946 | 946 | 3.290489 | 0.106069 | 1908.711 | 1466.348 | 0.991175 | |
P3 | 894 | 894 | 3.602227 | 0.09099 | 1979.937 | 1553.758 | 0.989684 | |
JP3 | 1094 | 896 | 3.45138 | 0.10768 | 1867.263 | 1485.578 | 0.991722 | |
P4 | 896 | 1094 | 3.521291 | 0.116067 | 1636.944 | 1644.864 | 0.991047 | |
JP4 | 806 | 806 | 3.2706 | 0.119642 | 1719.658 | 1370.8 | 0.992001 | |
Ciprofloxacin (Q) | Q1 | 712 | 712 | 2.778247 | 0.138909 | 1695.499 | 1234.447 | 0.991287 |
Q2 | 1254 | 1254 | 3.623877 | 0.109462 | 2287.941 | 1910.64 | 0.989922 | |
Q3 | 884 | 884 | 3.248321 | 0.1079 | 1773.738 | 1409.007 | 0.991538 | |
JQ3 | 1058 | 1058 | 3.047219 | 0.130086 | 2114.434 | 1634.563 | 0.992718 | |
Q4 | 941 | 941 | 2.855148 | 0.175216 | 1936.621 | 1600.519 | 0.99218 | |
JQ4 | 1030 | 1030 | 3.279126 | 0.122727 | 1858.773 | 1586.065 | 0.99266 | |
Ampicillin sodium (R) | R1 | 830 | 830 | 2.853027 | 0.166461 | 1729.973 | 1333.879 | 0.991071 |
R2 | 885 | 885 | 3.427011 | 0.073872 | 2260.472 | 1544.065 | 0.990153 | |
R3 | 1133 | 1133 | 3.584233 | 0.072941 | 2253.065 | 1797.837 | 0.992216 | |
JR3 | 762 | 762 | 3.175357 | 0.115644 | 1755.871 | 1290.186 | 0.993518 | |
R4 | 793 | 793 | 3.473673 | 0.070351 | 2043.293 | 1423.629 | 0.991592 | |
JR4 | 856 | 856 | 3.860091 | 0.048022 | 1680.427 | 1397.525 | 0.991285 | |
Chloramphenicol (S) | S1 | 705 | 705 | 2.904588 | 0.129851 | 2197.763 | 1459.063 | 0.992152 |
S2 | 982 | 982 | 3.618378 | 0.069773 | 1780.536 | 1528.923 | 0.992284 | |
S3 | 776 | 776 | 3.318475 | 0.099976 | 1577.62 | 1306.472 | 0.992443 | |
JS3 | 826 | 826 | 3.72379 | 0.066223 | 1766.24 | 1423.3 | 0.990486 | |
S4 | 1056 | 1056 | 3.737706 | 0.074712 | 1965.486 | 1692 | 0.99179 | |
JS4 | 709 | 709 | 3.23018 | 0.09656 | 1629.057 | 1183 | 0.992223 | |
Tylosin (T) | T1 | 1240 | 1240 | 3.111999 | 0.156664 | 2279.861 | 1936.444 | 0.987293 |
T2 | 1519 | 1519 | 4.406583 | 0.045868 | 1989.912 | 1937.915 | 0.988868 | |
T3 | 700 | 700 | 2.380128 | 0.187307 | 1584.71 | 1165.124 | 0.9944 | |
JT3 | 656 | 656 | 2.568263 | 0.231294 | 1831.557 | 1269.085 | 0.992333 | |
T4 | 1138 | 1138 | 3.452094 | 0.077866 | 1690.838 | 1601.896 | 0.992349 | |
JT4 | 706 | 706 | 2.336018 | 0.204594 | 2000.348 | 1395.545 | 0.99165 | |
Tetracycline (U) | U1 | 1021 | 1021 | 3.614356 | 0.069014 | 2029.165 | 1648.687 | 0.988888 |
U2 | 1070 | 1070 | 3.699218 | 0.067774 | 1978.579 | 1598.746 | 0.990355 | |
U3 | 945 | 945 | 3.048431 | 0.145983 | 1429.909 | 1384.833 | 0.993129 | |
JU3 | 901 | 901 | 2.861111 | 0.169415 | 1873.211 | 1480.333 | 0.993019 | |
U4 | 730 | 730 | 2.761487 | 0.147617 | 1719.237 | 1280.225 | 0.99187 | |
JU4 | 811 | 811 | 2.829413 | 0.137191 | 1585.21 | 1257.515 | 0.993866 |
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Ye, M.-Q.; Chen, G.-J.; Du, Z.-J. Effects of Antibiotics on the Bacterial Community, Metabolic Functions and Antibiotic Resistance Genes in Mariculture Sediments during Enrichment Culturing. J. Mar. Sci. Eng. 2020, 8, 604. https://doi.org/10.3390/jmse8080604
Ye M-Q, Chen G-J, Du Z-J. Effects of Antibiotics on the Bacterial Community, Metabolic Functions and Antibiotic Resistance Genes in Mariculture Sediments during Enrichment Culturing. Journal of Marine Science and Engineering. 2020; 8(8):604. https://doi.org/10.3390/jmse8080604
Chicago/Turabian StyleYe, Meng-Qi, Guan-Jun Chen, and Zong-Jun Du. 2020. "Effects of Antibiotics on the Bacterial Community, Metabolic Functions and Antibiotic Resistance Genes in Mariculture Sediments during Enrichment Culturing" Journal of Marine Science and Engineering 8, no. 8: 604. https://doi.org/10.3390/jmse8080604