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Frontiers of Earth Science

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ISSN 2095-0209(Online)

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Front Earth Sci    0, Vol. Issue () : 373-382    https://doi.org/10.1007/s11707-012-0324-0
RESEARCH ARTICLE
Abundance and diversity of candidate division JS1- and Chloroflexi-related bacteria in cold seep sediments of the northern South China Sea
Yong ZHANG1,2, Xin SU1,2(), Fang CHEN3, Lu JIAO1,2, Hongchen JIANG4(), Hailiang DONG1,5, Guochun DING6
1. State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China; 2. School of Ocean Sciences, China University of Geosciences, Beijing 100083, China; 3. Guangzhou Marine Geology Survey, Guangzhou 510075, China; 4. State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; 5. Department of Geology and Environmental Earth Science, Miami University, Oxford, OH 45056, USA; 6. Julius Kühn-Institut (JKI)-Federal Research Centre for Cultivated Plants, Braunschweig 38104, Germany
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Abstract

Candidate division JS1-and Chloroflexi-related bacteria are ubiquitous in various deep marine sediments worldwide, yet almost nothing is known about their abundance and diversity in cold seep sediments. Here, we investigated the abundance and diversity of JS1- and Chloroflexi-related bacteria in a cold seep marine sediment core collected from the northern South China Sea (SCS) with the employment of quantitative polymerase chain reaction (qPCR) and 16S rRNA gene phylogenetic analyses. The qPCR results showed that 16S rRNA gene copies per gram of sediments for the total bacteria and JS1- and Chloroflexi-related bacteria were at magnitudes of 108 and 106, respectively. The relative abundance of JS1- and Chloroflexi-related 16S rRNA genes to that of total bacteria was 0.07%–8.78% throughout the core. Phylogenetic analyses showed that the JS-1 related clone sequences were dominant throughout the core. Our study provided insights into abundance and diversity of JS1- and Chloroflexi-related bacteria in the northern SCS cold seep sediments.
Keywords candidate division JS1      Chloroflexi      cold seep sediments      South China Sea     
Corresponding Author(s): SU Xin,Email:xsu@cugb.edu.cn; JIANG Hongchen,Email:hongchen.jiang@gmail.com   
Issue Date: 05 December 2012
 Cite this article:   
Yong ZHANG,Xin SU,Fang CHEN, et al. Abundance and diversity of candidate division JS1- and Chloroflexi-related bacteria in cold seep sediments of the northern South China Sea[J]. Front Earth Sci, 0, (): 373-382.
 URL:  
https://academic.hep.com.cn/fesci/EN/10.1007/s11707-012-0324-0
https://academic.hep.com.cn/fesci/EN/Y0/V/I/373
Fig.1  Sampling site (?) of the cold seep gravity core from Haiyang 4 Area of the northern South China Sea
ConstituentMethodReferences
AmmoniumTitrationGrasshoff et al.(1999)
TOCLiu (1996)
Hydrogen sulphideSpectrophotometryGrasshoff et al. (1999)
Phosphate
Headspace methaneGas chromatographyNiew?hner et al. (1998)
Sulfate, chlorideIon chromatographyhttp://wwwodp.tamu.edu/publications/notes/tn15/f_chem3.html
Tab.1  Methods used for geochemical analyses
Sample number16S rRNA gene copies per gram of sediments
Total bacteria (107)Total JCa) (105)Total JC/Total bacteriab)/%
DSH1186.71 (±16.94)19.10 (±1.48)0.10 (±0.01)
DSH217.41 (±9.70)36.06 (±18.95)3.00 (±2.86)
DSH3728.80 (±25.40)6.08 (±1.25)0.08 (±0.00)
DSH469.09 (±11.75)5.26 (±2.09)0.07 (±0.03)
DSH53.82 (±2.62)4.71 (±2.03)2.32 (±2.31)
DSH64.34 (±3.41)3.68 (±2.53)2.21 (±3.00)
DSH72.49 (±1.29)0.75 (±0.11)0.41 (±0.25)
DSH80.84 (±0.20)7.25 (±1.41)8.78 (±3.11)
DSH92.16 (±0.11)4.02 (±4.02)1.87 (±2.16)
DSH101.20 (±0.10)1.72 (±0.07)1.57 (±0.19)
DSH112.53 (±0.93)15.60 (±8.88)7.14 (±5.84)
DSH123.17 (±1.46)1.24 (±0.33)0.49 (±0.31)
Tab.2  qPCR-based 16S rRNA gene abundances of total bacteria and JS1- and -related bacteria in cold seep sediments of the northern SCS
Sample numberDepth/ (cmbsf)SO42-/(mM)CH4/ (μM)H2S/ (μM)NH4+/(μM)HPO4-(μΜ)Cl-/(mM)TOC/%
DSH15-1029.12.0506.606.005550.51
DSH250-5528.22.32039.716.695510.51
DSH3100-10528.32.53040.676.695580.56
DSH4150-15528.72.61028.543.595560.65
DSH5200-20528.61.59045.824.915570.58
DSH6250-25528.61.77048.265.535560.79
DSH7300-30528.52.4914.8056.293.985540.61
DSH8350-35528.43.7417.2066.414.055540.61
DSH9400-40525.85.455.6092.156.315560.50
DSH10450-45521.48.081276.80100.4010.125540.55
DSH11500-50515.312.731824.00179.8016.195460.59
DSH12550-55512.620.341612.00203.1017.675490.56
Tab.3  Geochemical parameters of the sediment core
Fig.2  DNA copy numbers of the 16S rRNA genes of the total bacteria (●) and JS1- and -related bacteria (?) in the cold seep sediment core from the northern SCS
Clone libraryNumber of clone sequences
No. of total clone sequences obtainedJS1-related bacteriaAnaerolineae-related bacteriaOther bacteria
DSH15443 (80%)7 (13%)4 (7%)
DSH34723 (49%)6 (13%)18 (38%)
DSH54428 (64%)016 (36%)
DSH74724 (51%)2 (4%)21 (45%)
DSH95048 (98%)02 (4%)
DSH125352 (98%)01 (2%)
Tab.4  Clone library analyses of JS1- and -related bacteria in cold seep sediments from northern SCS
Fig.3  Neighbor-Joining tree showing the phylogenetic relationships of candidate division JS1 and -related bacteria 16S rRNA gene sequences cloned a cold seep sediment core from of the northern SCS. Sequences obtained in this study are marked in bold. One representative clone type within each phylotype is shown, and the number of clones within each phylotype is shown after the GenBank accession number. Bootstrap values of>50% (for 1000 iterations) are shown.
Environmental variablesTotal bacteriaa)Total JCb)OTU levelMajor group level
rPrPrPrP
CH4-0.1050.3340.1560.2100.4640.2060.0560.400
Cl--0.1360.1990.0040.4330.3700.2470.1040.400
HPO4--0.1580.1320.0840.2650.4540.2880.0340.400
H2S-0.0820.3290.1250.2330.5040.158-0.0020.600
NH4+0.1140.1840.1620.1590.5820.0560.1010.200
SO42--0.0900.3210.1220.2120.4820.1600.0580.400
TOC-0.1120.321-0.1510.251-0.4540.047-0.2580.400
Tab.5  Simple Mantel tests for similarity between biotic and environmental matrices in cold seep sediments from the northern SCS
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