Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection, Processing, and eDNA Isolation
2.2. Sequencing and Prediction of 16S rRNA Data
2.3. Metagenome Predictions from 16S rRNA Data
2.4. 16S rRNA Sequence Assembly and Statistical Analysis
3. Results
3.1. Differences in Taxonomic Richness between Sand Mining vs. Control Microbial Communities
3.2. Differences in Composition and Diversity of Microbial Seawater Community between Sand Mining vs. Control Sites
3.3. Differences in Composition and Diversity of Microbial Sediment Community between Sand Mining vs. Control Sites
4. Discussion
5. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Site ID | Latitude; Longitude | Sample Type | Samples | Sampling Period | Read Counts | Total Base Pair Counts |
---|---|---|---|---|---|---|
Site12 | 34°15.05′ N; 128°23.68′ E | Control | Surface | April 2015 (Spring) | 876,484 | 263,821,684 |
Middle | 904,794 | 272,342,994 | ||||
Deep | 865,924 | 260,643,124 | ||||
Site21 | 34°11.55′ N; 128°22.55′ E | Sand mining | Surface | 887,080 | 267,011,080 | |
Middle | 574,816 | 173,019,616 | ||||
Deep | 511,724 | 154,028,924 | ||||
Site12 | 34°15.05′ N; 128°23.68′ E | Control | Sediment | 845,526 | 254,503,326 | |
Site21 | 34°11.55′ N; 128°22.55′ E | Sand mining | Sediment | 741,150 | 223,086,150 | |
Site12 | 34°15.05′ N; 128°23.68′ E | Control | Surface | October 2015 (Autumn) | 845,526 | 254,503,326 |
Middle | 1,260,066 | 379,279,866 | ||||
Deep | 1,039,742 | 312,962,342 | ||||
Site SM | 34°11.17′ N; 128°24.50′ E | Sand mining | Surface | 1,135,076 | 341,657,876 | |
Middle | 1,052,748 | 316,877,148 | ||||
Deep | 1,133,566 | 341,203,366 | ||||
Site SM | Sand mining | Sediment | 1,090,470 | 328,231,470 | ||
Sediment | 1,496,222 | 450,362,822 | ||||
Sediment | 1,955,034 | 588,465,234 |
Sample | Class | Family | Genus |
---|---|---|---|
Surface water | Cenarchaeales | Cenarchaeaceae | - |
Flavobacteriales | Flavobacteriaceae | Mesonia | |
Ignavibacteriales | Ignavibacteriaceae | - | |
Kordiimonadales | Kordiimonadaceae | - | |
Burkholderiales | Alcaligenaceae | - | |
Alteromonadales | Alteromonadaceae | Marinobacter | |
Alteromonadales | Idiomarinaceae | Pseudidiomarina | |
Oceanospirillales | Alcanivoracaceae | Alcanivorax | |
Oceanospirillales | Halomonadaceae | Cobetia | |
Marinicellales | Marinicellaceae | Marinicella | |
Middle water | Bacteroidia | Bacteroidaceae | Bacteroides |
Bacteroidia | Porphyromonadaceae | Parabacteroides | |
Flavobacteriia | Flavobacteriaceae | Cellulophaga | |
Flavobacteriia | Weeksellaceae | - | |
Clostridia | Lachnospiraceae | Lachnospira | |
Clostridia | Veillonellaceae | Succiniclasticum | |
Clostridia | Acidaminobacteraceae | Fusibacter | |
Fusobacteriia | Fusobacteriaceae | Propionigenium | |
Alphaproteobacteria | Erythrobacteraceae | - | |
Alphaproteobacteria | Sphingomonadaceae | Novosphingobium | |
Deltaproteobacteria | Desulfarculaceae | - | |
Deltaproteobacteria | Desulfobacteraceae | Desulfofaba | |
Deep water | Actinobacteria | Micrococcaceae | Micrococcus |
Cytophagia | Amoebophilaceae | Ucs1325 | |
Chlamydiia | Simkaniaceae | - | |
Ignavibacteria | lheB3-7 | - | |
Synechococcophycideae | Synechococcaceae | - | |
Bacilli | Streptococcaceae | Streptococcus | |
Alphaproteobacteria | Kiloniellaceae | Thalassospira | |
Alphaproteobacteria | Rhodospirillaceae | - | |
Alphaproteobacteria | Erythrobacteraceae | Erythrobacter | |
Deltaproteobacteria | Desulfarculaceae | - | |
Deltaproteobacteria | Desulfobacteraceae | Desulfosarcina | |
Deltaproteobacteria | Syntrophaceae | Desulfobacca | |
Gammaproteobacteria | Coxiellaceae | Coxiella | |
Gammaproteobacteria | Halomonadaceae | Haererehalobacter | |
Gammaproteobacteria | Oceanospirillaceae | Oleibacter | |
PRR-12 | KSB4 | - |
Sample | Class | Family | Genus |
---|---|---|---|
Bottom sediments | Actinobacteria | Bifidobacteriaceae | Bifidobacterium |
Fimbriimonadia | Fimbriimonadaceae | - | |
Bacteroidia | Bacteroidaceae | Bacteroides | |
Flavobacteriia | Cryomorphaceae | - | |
Flavobacteriia | Cryomorphaceae | Cryomorpha | |
Flavobacteriia | Cryomorphaceae | Owenweeksia | |
Rhodothermi | Balneolaceae | Balneola | |
Synechococcophycideae | Synechococcaceae | Prochlorococcus | |
Bacilli | Planococcaceae | Sporosarcina | |
Bacilli | Thermoactinomycetaceae | - | |
Clostridia | Clostridiaceae | Alkaliphilus | |
Clostridia | Clostridiaceae | Geosporobacter | |
Clostridia | Lachnospiraceae | - | |
Clostridia | Lachnospiraceae | Coprococcus | |
Clostridia | Lachnospiraceae | Lachnospira | |
Clostridia | Peptostreptococcaceae | - | |
Clostridia | Ruminococcaceae | Faecalibacterium | |
Clostridia | Ruminococcaceae | Ruminococcus | |
Clostridia | Veillonellaceae | Dialister | |
Clostridia | Veillonellaceae | Megamonas | |
Clostridia | Acidaminobacteraceae | - | |
Fusobacteriia | Fusobacteriaceae | u114 | |
Alphaproteobacteria | Methylocystaceae | Pleomorphomonas | |
Alphaproteobacteria | Rhodobiaceae | Afifella | |
Alphaproteobacteria | Rhodobacteraceae | Marivita | |
Alphaproteobacteria | Rhodobacteraceae | Thalassobius | |
Alphaproteobacteria | Rhodospirillaceae | Novispirillum | |
Alphaproteobacteria | Rhodospirillaceae | Rhodospirillum | |
Alphaproteobacteria | AEGEAN_112 | - | |
Deltaproteobacteria | S25_1238 | - | |
Deltaproteobacteria | SAR324 | - | |
Gammaproteobacteria | Psychromonadaceae | - | |
Gammaproteobacteria | Legionellaceae | Legionella | |
Gammaproteobacteria | Legionellaceae | Tatlockia | |
Gammaproteobacteria | Oceanospirillaceae | Oleispira | |
AB16 | A714017 | SargSea-WGS | |
Mollicutes | Mycoplasmataceae | Candidatus Hepatoplasma |
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Won, N.-I.; Kim, K.-H.; Kang, J.H.; Park, S.R.; Lee, H.J. Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis. Int. J. Environ. Res. Public Health 2017, 14, 130. https://doi.org/10.3390/ijerph14020130
Won N-I, Kim K-H, Kang JH, Park SR, Lee HJ. Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis. International Journal of Environmental Research and Public Health. 2017; 14(2):130. https://doi.org/10.3390/ijerph14020130
Chicago/Turabian StyleWon, Nam-Il, Ki-Hwan Kim, Ji Hyoun Kang, Sang Rul Park, and Hyuk Je Lee. 2017. "Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis" International Journal of Environmental Research and Public Health 14, no. 2: 130. https://doi.org/10.3390/ijerph14020130