Metagenomic Analysis for Evaluating Change in Bacterial Diversity in TPH-Contaminated Soil after Soil Remediation
Abstract
:1. Introduction
2. Materials and Methods
2.1. Soil Sampling and Sample Description
2.2. Soil Chemical Properties and Total Petroleum Hydrocarbon (TPH) Analysis
2.3. Metagenomic Analysis
2.3.1. DNA Extraction, Polymerase Chain Reaction (PCR) Amplification, and 16S rRNA Gene Amplicon Sequencing
2.3.2. Bioinformatic Analysis
2.4. Data Analysis
3. Results and Discussion
3.1. Soil Chemical Properties and TPH Concentration
3.2. Soil Bacterial Diversity Analysis
3.3. Varied Bacterial Distribution in Soil
3.4. Effect of TPH-Degrading Bacteria in Contaminated and Remediated Soil
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Treatment | pH | Electric Conductivity (EC) | Soil Organic Matter (SOM) | Available Phosphorus (Av.P) | Cation Exchange Capacity (CEC) | Total Nitrogen (TN) | TPH |
---|---|---|---|---|---|---|---|
1:5 | dS m−1 | % | mg kg−1 | cmolc kg−1 | % | mg kg−1 | |
Control | 6.23 ± 0.58 b | 0.38 ± 0.06 a | 1.54 ± 0.04 a | 24.6 ± 11.2 a | 14.9 ± 4.00 b | 0.90 ± 0.36 a | 77 ± 17 b |
CS | 6.22 ± 0.69 b | 0.29 ± 0.10 a | 0.90 ± 0.22 b | 21.7 ± 12.1 a | 8.91 ± 2.90 c | 0.09 ± 0.09 b | 2,690 ± 680 a |
SW | 7.23 ± 0.11 a | 0.11 ± 0.02 b | 0.81 ± 0.02 b | 2.86 ± 1.57 b | 11.7 ± 2.40 bc | 0.13 ± 0.16 b | 111 ± 39 b |
LF | 6.90 ± 0.06 ab | 0.28 ± 0.10 a | 1.06 ± 0.01 b | 18.7 ± 0.10 a | 37.4 ± 0.80 a | 0.93 ± 0.38 a | 249 ± 39 b |
Sample Group | Reads | Good’s Coverage (%) | OTUs | Chao1 | Shannon |
---|---|---|---|---|---|
Control | 14,907 ± 2188 d | 97.99 ± 0.12 | 1265 ± 308 a | 1475 ± 340 a | 8.58 ± 0.62 a |
CS | 35,782 ± 12,110 a | 99.95 ± 0.03 | 296 ± 13 c | 308 ± 24 c | 4.76 ± 1.30 c |
SW | 29,979 ± 5923 b | 99.94 ± 0.08 | 305 ± 47 c | 316 ± 63 c | 5.94 ± 0.57 b |
LF | 21,345 ± 3826 c | 98.99 ± 0.16 | 815 ± 111 b | 1000 ± 101 b | 7.06 ± 0.29 b |
Phylum | Genus | Relative Abundance (%) | |||
---|---|---|---|---|---|
Class | Control | CS | SW | LF | |
Actinobacteria | |||||
Actinobacteria | Corynebacterium | 0.01 | 0.85 | 1.20 | - |
Dietzia | - | 0.08 | - | - | |
Kocuria | 0.06 | 0.10 | - | - | |
Microbacterium | 0.02 | 0.31 | 0.03 | 0.01 | |
Micrococcus | - | 0.33 | 0.05 | - | |
Nocardioides | 0.90 | 1.41 | 0.82 | 0.24 | |
Rhodococcus | - | - | 0.01 | 0.05 | |
Streptomyces | 1.49 | 0.04 | 0.08 | 0.11 | |
Bacteroidetes | |||||
Flavobacteriia | Chryseobacterium | - | 0.01 | 0.08 | - |
Flavobacterium | 0.03 | 0.04 | 0.09 | - | |
Firmicutes | |||||
Bacilli | Bacillus | 0.26 | 0.29 | 0.32 | 0.93 |
Paenibacillus | 0.02 | 0.06 | - | 0.04 | |
Staphylococcus | 0.03 | 1.37 | 3.39 | - | |
Streptococcus | - | 0.52 | 0.92 | - | |
Proteobacteria | |||||
Alphaproteobacteria | Azospirillum | 0.05 | 0.06 | 0.13 | 0.43 |
Methylobacterium | 0.17 | 0.19 | 0.13 | 0.01 | |
Paracoccus | - | 0.77 | 0.03 | - | |
Rhizobium | 0.24 | 0.09 | 0.52 | 0.02 | |
Betaproteobacteria | Acidovorax | 0.07 | 0.60 | 0.99 | 0.02 |
Burkholderia | 0.25 | - | - | 0.01 | |
Gammaproteobacteria | Acinetobacter | 0.03 | 2.92 | 5.54 | - |
Alkanindiges | - | 0.07 | 0.01 | - | |
Immundisolibacter | 0.02 | 1.82 | 3.26 | 8.63 | |
Pseudomonas | 0.15 | 1.72 | 3.38 | 0.05 | |
Pseudoxanthomonas | 0.10 | 2.85 | 0.96 | - | |
Rhodanobacter | 0.01 | 0.64 | 0.21 | 1.70 | |
Stenotrophomonas | 0.04 | 0.03 | 0.10 | - | |
Thermomonas | 0.10 | 3.44 | 1.25 | 0.04 | |
Total | 4.05 | 20.61 | 23.49 | 12.29 |
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Kim, J.-W.; Hong, Y.-K.; Kim, H.-S.; Oh, E.-J.; Park, Y.-H.; Kim, S.-C. Metagenomic Analysis for Evaluating Change in Bacterial Diversity in TPH-Contaminated Soil after Soil Remediation. Toxics 2021, 9, 319. https://doi.org/10.3390/toxics9120319
Kim J-W, Hong Y-K, Kim H-S, Oh E-J, Park Y-H, Kim S-C. Metagenomic Analysis for Evaluating Change in Bacterial Diversity in TPH-Contaminated Soil after Soil Remediation. Toxics. 2021; 9(12):319. https://doi.org/10.3390/toxics9120319
Chicago/Turabian StyleKim, Jin-Wook, Young-Kyu Hong, Hyuck-Soo Kim, Eun-Ji Oh, Yong-Ha Park, and Sung-Chul Kim. 2021. "Metagenomic Analysis for Evaluating Change in Bacterial Diversity in TPH-Contaminated Soil after Soil Remediation" Toxics 9, no. 12: 319. https://doi.org/10.3390/toxics9120319