Microb Ecol DOI 10.1007/s00248-014-0553-8

ENVIRONMENTAL MICROBIOLOGY

Bacterial and Archaeal Communities in Sediments of the North Chinese Marginal Seas Jiwen Liu & Xiaoshou Liu & Min Wang & Yanlu Qiao & Yanfen Zheng & Xiao-Hua Zhang

Received: 13 August 2014 / Accepted: 1 December 2014 # Springer Science+Business Media New York 2014

Abstract Microbial communities of the Chinese marginal seas have rarely been reported. Here, bacterial and archaeal community structures and abundance in the surface sediment of four sea areas including the Bohai Sea (BS), North Yellow Sea (NYS), South Yellow Sea (SYS), and the north East China Sea (NECS) were surveyed by 16S ribosomal RNA (rRNA) gene pyrosequencing and quantitative PCR. The results showed that microbial communities of the four geographic areas were distinct from each other at the operational taxonomic unit (OTU) level, whereas the microbial communities of the BS, NYS, and SYS were more similar to each other than to the NECS at higher taxonomic levels. Across all samples, Bacteria were numerically dominant relative to Archaea, and among them, Gammaproteobacteria and Euryarchaeota were predominant in the BS, NYS, and SYS, while Deltaproteobacteria and Thaumarchaeota were prevalent in the NECS. The most abundant bacterial genera were putative sulfur oxidizer and sulfate reducer, suggesting that sulfur cycle processes might prevail in these areas, and the high abundance of dsrB (107–108 copies g−1) in all sites verified the dominance of sulfate reducer in the north Chinese marginal seas. The differences in sediment sources among the sampling areas were potential explanations for the observed microbial community variations. Furthermore, temperature and dissolved oxygen of bottom water were significant environmental factors in determining both bacterial and archaeal communities, whereas chlorophyll a in sediment was significant only in structuring archaeal community. This study presented an

Electronic supplementary material The online version of this article (doi:10.1007/s00248-014-0553-8) contains supplementary material, which is available to authorized users. J. Liu : X. Liu : M. Wang : Y. Qiao : Y. Zheng : X.0.98). Amplification efficiencies were 2.00, 1.95, and 1.98 for Bacteria, Archaea, and the dsrB gene, respectively. Statistical Analysis To equalize sampling efforts, sequences were randomly resampled according to the sample with the smallest read numbers using the perl script daisychopper.pl [21]. For alpha diversity, Chao I [22] and Shannon index [23], which are species richness estimator and species diversity estimator, respectively, were calculated in Mothur. Good’s

Microbial Communities in North Chinese Marginal Seas Fig. 1 Sampling map in the north Chinese marginal seas

coverage [24] was also measured to evaluate the sampling depth. For beta diversity, the Bray-Curtis dissimilaritybased dendrogram was plotted to cluster samples with similar operational taxonomic unit (OTU) composition and abundance. Principal component analysis (PCA) was performed using the R base package. Redundancy analysis (RDA) with 9999 Monte Carlo permutation tests was conducted with the “vegan” library in R to reveal the relationship between microbial assemblages and environmental factors. The relative influence of geographic distance and environmental factors on microbial community compositions was evaluated using Mantel and partial Mantel test in “vegan” library. A geographic distance matrix based on the latitude and longitude coordinates was calculated with the “sp” and “dismo” library in R. Wilcoxon signed-rank test was performed to analyze differences in environmental parameters, alpha diversity indices, qPCR, and the relative abundance of specific taxon

across all samples. All statistical analyses were performed in R using various packages [25]. The 454 sequences were deposited in the National Center for Biotechnology Information (NCBI) Short Read Archive database under accession number SRP030955.

Results Physicochemical Characteristics of Bottom Waters and Sediments The water depth of sampling sites ranged from 17.5 to 71.5 m with an average of 47.3 m. The content of Chl a in sediment ranged from 0.08 to 0.81 μg g−1 and was slightly lower in the NECS than the BS, NYS, and SYS although not significant. Sediment median size varied from 0.005 to 0.078 mm and appeared to be slightly

J. Liu et al. Table 1

Physical and chemical properties of the sampling sites

Station

Longitude

Latitude

TOM (%)

Water content (%)

Median size (mm)

Chl a (μg g−1)

pH

Salinity (psu)

DO (mg l−1)

BS1 BS2 BS3 NYS1

120° 03.830 119° 47.107 120° 11.700 122° 52.723

39° 11.037 38° 19.967 38° 20.255 38° 30.084

0.9 1.6 1.2 1.5

32.0 41.1 36.0 36.6

0.049 0.021 0.051 0.041

0.81 0.34 0.41 0.68

7.9 7.8 7.9 7.5

31.2 31.2 31.3 32.0

10.3 9.1 10.0 9.2

9.0 9.2 7.8 4.3

23.7 25 27 57

NYS2 NYS3 SYS1 SYS2 SYS3 NECS1 NECS2 NECS3

122° 36.718 123° 14.874 123° 25.459 122° 39.722 122° 20.099 122° 25.471 123° 54.594 125° 19.900

37° 58.194 38° 08.121 36° 59.300 35° 57.947 35° 00.768 31° 16.445 31° 16.629 31° 16.355

2.3 0.7 1.9 4.2 2.6 1.9 0.7 1.3

46.5 28.5 30.5 59.6 53.2 40.9 18.0 40.1

0.015 0.078 0.048 0.005 0.008 0.008 ND 0.009

0.37 0.34 0.10 0.10 0.45 0.08 ND 0.15

7.8 7.7 7.9 ND 7.9 8.0 8.0 8.0

31.7 32.0 32.7 33.6 33.6 26.9 33.3 33.1

9.2 9.5 8.6 7.9 6.9 7.7 7.7 8.0

5.0 5.2 7.3 8.5 8.8 15.0 13.2 11.2

51 63.5 71.5 64.5 61.7 17.5 51 54

Temperature (°C)

Depth (m)

TOM, water content, median size, and Chl a were measured from surface sediments, while pH, salinity, DO, and temperature were determined from bottom waters ND not done, TOM total organic matter, DO dissolved oxygen

higher in the BS and NYS than the SYS and NECS although not significant. No significant differences in TOM and water content were observed across all samples (P>0.05). Regarding the bottom water attributes, a significant difference in temperature, ranging from 4.3 to 15.0 °C, was observed with the highest value in the NECS and lowest value in the NYS, respectively (P

Bacterial and archaeal communities in sediments of the north Chinese marginal seas.

Microbial communities of the Chinese marginal seas have rarely been reported. Here, bacterial and archaeal community structures and abundance in the s...
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