Bacterial and Archaeal Assemblages from Two Size Fractions in Submarine Groundwater Near an Industrial Zone
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection and Measurements of Chemical Parameters
2.2. DNA Extraction, PCR Amplification and Illumina MiSeq Sequencing
2.3. Sequence Data Processing, OTU Clustering, and Taxonomic Assignment
2.4. Phylogenetic Analyses
2.5. Statistical Analyses
2.6. Predictive Functional Profiling
3. Results
3.1. Site Description and Environmental Characteristics
3.2. Bacterial and Archaeal Diversity
3.3. Bacterial and Archaeal Distribution
3.4. Phylogenetic Analyses
3.4.1. Main Bacterial Groups in Two Size Fractions
3.4.2. Main Archaeal Groups in Two Size Fractions
3.5. Distinct Bacterial and Archaeal Communities in Two Size Fractions
4. Discussion
4.1. The Ecological Niches of Bathyarchaeota in Submarine Groundwater Systems
4.2. Microbial Candidate for In Situ Bioremediation in SGD
4.3. Influence of Key Microbes on SGD in Qinzhou Bay
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Site Descriptions | Environmental Chemical Parameters | ||
---|---|---|---|
Latitude | 21°43′39.92″ N | Temperature (°C) | 17.2 |
Longitude | 108°37′30.43″ E | Salinity | 0.5 |
Location | Qinzhou City, Guangxi Province | 222Rn (Bq m−3) | 4140 |
Well depth (m) | ~ 4 | DIC (mmol L−1) | 1.3 |
Characteristics of sampling site | In the Gaoshatou Village; near an industrial zone; 800 meters from the coast; garbage found | DOC (mmol L−1) | 1.0 |
NO3− (μmol L−1) | 5.2 | ||
NO2− (μmol L−1) | 0.42 | ||
Characteristics of submarine groundwater | Turbid water; smelly water | NH4+ (μmol L−1) | 4.8 |
PO43− (μmol L−1) | 0.31 | ||
SiO32− (μmol L−1) | 166 |
Method | Distance | Bacteria | Archaea | ||
---|---|---|---|---|---|
R2 | p Value | R2 | p Value | ||
PERMANOVA | Bray-Curtis | 0.51 | 0.02 | 0.78 | 0.02 |
OTU | Proportion of OTUs (%) | Closest Relatives | Similarity | |
---|---|---|---|---|
BP | BF | |||
OTU 594 | 4.7 | 21.8 | Limnohabitans australis strain MWH-BRAZ-DAM2D [35] | NR_125544 (99.2%) |
OTU 571 | 1.2 | 2.6 | Limnohabitans parvus strain II-B4 [36] | NR_125542 (98.9%) |
OTU 40 | 16.6 | 0.2 | Clone F22F60 from a Fe(II)-oxidizing, nitrate-reducing enrichment culture [37] | FN430660 (98.9%) |
OTU 1039 | 4.5 | 0.8 | Gammaproteobacterial clone SWL18 from a sludge wastewater treatment system [38] | AY528817 (99.7%) |
OTU 261 | 10.7 | 5.4 | Novosphingobium pentaromativorans strain US6-1 [39] | NR_025248 (98.4%) |
OTU 555 | 1.2 | 1.5 | Sphingopyxis soli strain BL03 [40] | NR_116739 (99.2%) |
OTU 843 | 3.1 | 2.7 | Flavobacterium chungnamense strain ARSA-103 [41] | NR_117494 (98.7%) |
OTU 591 | 0.1 | 1.6 | Flavobacterium columnare strain ATCC 23463 [42] | NR_118582 (98.4%) |
OTU | Proportion of OTUs (%) | Closest Relatives | Similarity | |
---|---|---|---|---|
AP | AF | |||
OTU 563 | 29.4 (OTU 563, 516 and 598) | 3.0 (OTU 563, 516 and 598) | Clone R5ENDA4 from low-temperature anaerobic solvent-degrading bioreactors [43] | DQ399807 (100%) |
OTU 516 | Clone ASC27 in unsaturated, petroleum-contaminated soil [44] | AB161330 (100%) | ||
OTU 598 | Clone ASC37 in unsaturated, petroleum-contaminated soil [44] | AB161337 (100%) | ||
OTU 540 | 19.5 | 3.3 | Acetoclastic methanoarchaeon Methanosaeta concilii strain GP6 [45] | NR_102903 (99.6%) |
OTU 312 | 1.1 | 3.7 | DGGE gel band VIARC-174 from the water column of Lake Vilar [46] | EU683427 (99.2%) |
OTU 458 | 3.2 | 7.4 | Clone WsL03b13_109f from groundwater of a volcanic mountain, Mt. Fuji (Unpublished) | AB794582 (98.4%) |
OTU 536 | 1.8 | 5.7 | Clone LL_ADT_15 from low-level bank soil of the River Rhine [47] | AM503273 (98.8%) |
OTU 541 | 0.5 | 2.3 | Clone gwa2_scaffold_29719 from an aquifer adjacent to Colorado River [48] | KP308734 (87.0%) |
OTU 449 | 16.3 | 41.4 | VIARC-45 retrieved from the water column of Lake Vilar [46] | AM697998 (92.5%) |
Pathway | Relative Abundance | Definition | |
---|---|---|---|
>0.45 μm Size Fraction | 0.2–0.45 μm Fraction | ||
ko00351 | 0.00 | 0.00 | 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation |
ko00361 | 0.22 | 0.21 | Chlorocyclohexane and chlorobenzene degradation |
ko00362 | 1.31 | 1.55 | Benzoate degradation |
ko00363 | 0.19 | 0.23 | Bisphenol degradation |
ko00364 | 0.13 | 0.12 | Fluorobenzoate degradation |
ko00621 | 0.21 | 0.18 | Dioxin degradation |
ko00622 | 0.20 | 0.15 | Xylene degradation |
ko00623 | 0.34 | 0.34 | Toluene degradation |
ko00624 | 0.27 | 0.29 | Polycyclic aromatic hydrocarbon degradation |
ko00625 | 0.50 | 0.52 | Chloroalkane and chloroalkene degradation |
ko00626 | 0.48 | 0.54 | Naphthalene degradation |
ko00627 | 0.88 | 1.09 | Aminobenzoate degradation |
ko00633 | 0.16 | 0.13 | Nitrotoluene degradation |
ko00642 | 0.22 | 0.18 | Ethylbenzene degradation |
ko00643 | 0.20 | 0.20 | Styrene degradation |
ko00791 | 0.10 | 0.10 | Atrazine degradation |
ko00903 | 0.76 | 0.92 | Limonene and pinene degradation |
ko00930 | 0.56 | 0.70 | Caprolactam degradation |
Total | 6.73 | 7.46 |
Pathway | Relative Abundance | Definition | |
---|---|---|---|
>0.45 μm Size Fraction | 0.2–0.45 μm Fraction | ||
ko00281 | 0.19 | 0.25 | Geraniol degradation |
ko00361 | 0.01 | 0.03 | Chlorocyclohexane and chlorobenzene degradation |
ko00362 | 0.49 | 0.53 | Benzoate degradation |
ko00363 | 0.01 | 0.04 | Bisphenol degradation |
ko00364 | 0.00 | 0.01 | Fluorobenzoate degradation |
ko00621 | 0.01 | 0.03 | Dioxin degradation |
ko00622 | 0.00 | 0.01 | Xylene degradation |
ko00623 | 0.33 | 0.29 | Toluene degradation |
ko00624 | 0.11 | 0.12 | Polycyclic aromatic hydrocarbon degradation |
ko00625 | 0.17 | 0.23 | Chloroalkane and chloroalkene degradation |
ko00626 | 0.05 | 0.11 | Naphthalene degradation |
ko00627 | 0.23 | 0.29 | Aminobenzoate degradation |
ko00630 | 1.03 | 1.05 | Glyoxylate and dicarboxylate metabolism |
ko00633 | 0.87 | 0.77 | Nitrotoluene degradation |
ko00642 | 0.01 | 0.02 | Ethylbenzene degradation |
ko00643 | 0.01 | 0.03 | Styrene degradation |
ko00791 | 0.00 | 0.02 | Atrazine degradation |
ko00903 | 0.27 | 0.29 | Limonene and pinene degradation |
ko00930 | 0.18 | 0.20 | Caprolactam degradation |
Total | 3.97 | 4.31 |
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Chen, X.; Ye, Q.; Du, J.; Zhang, J. Bacterial and Archaeal Assemblages from Two Size Fractions in Submarine Groundwater Near an Industrial Zone. Water 2019, 11, 1261. https://doi.org/10.3390/w11061261
Chen X, Ye Q, Du J, Zhang J. Bacterial and Archaeal Assemblages from Two Size Fractions in Submarine Groundwater Near an Industrial Zone. Water. 2019; 11(6):1261. https://doi.org/10.3390/w11061261
Chicago/Turabian StyleChen, Xiaogang, Qi Ye, Jinzhou Du, and Jing Zhang. 2019. "Bacterial and Archaeal Assemblages from Two Size Fractions in Submarine Groundwater Near an Industrial Zone" Water 11, no. 6: 1261. https://doi.org/10.3390/w11061261