Metagenomic Insights into Effects of Chemical Pollutants on Microbial Community Composition and Function in Estuarine Sediments Receiving Polluted River Water.

Pyrosequencing and metagenomic profiling were used to assess the phylogenetic and functional characteristics of microbial communities residing in sediments collected from the estuaries of Rivers Oujiang (OS) and Jiaojiang (JS) in the western region of the East China Sea. Another sediment sample was obtained from near the shore far from estuaries, used for contrast (CS). Characterization of estuary sediment bacterial communities showed that toxic chemicals potentially reduced the natural variability in microbial communities, while they increased the microbial metabolic enzymes and pathways. Polycyclic aromatic hydrocarbons (PAHs) and nitrobenzene were negatively correlated with the bacterial community variation. The dominant class in the sediments was Gammaproteobacteria. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) enzyme profiles, dominant enzymes were found in estuarine sediments, which increased greatly, such as 2-oxoglutarate synthase, acetolactate synthase, inorganic diphosphatase, and aconitate hydratase. In KEGG pathway profiles, most of the pathways were also dominated by specific metabolism in these sediments and showed a marked increase, for instance alanine, aspartate, and glutamate metabolism, carbon fixation pathways in prokaryotes, and aminoacyl-tRNA biosynthesis. The estuarine sediment bacterial diversity varied with the polluted river water inputs. In the estuary receiving river water from the more seriously polluted River Oujiang, the sediment bacterial community function was more severely affected.

Temporal-spatial variation of bacterial diversity in estuary sediments in the south of Zhejiang Province, China.

The winter and summer microbial community structure in sediment samples obtained from the estuaries of the wastewater-polluted River Ou (DO and XO), River Feiyun (DF and XF), and River Ao (DA and XA) in the south of Zhejiang Province in China was determined using 454 pyrosequencing. Sediment samples (DD and XD) were also correspondingly collected near the shore far from the estuaries for comparison. For the above sediments, 294,870 effective sequences were obtained to do the bacterial diversity and abundance determination. In total, 1924, 1517, 2071, 1956, 1995, 1800, 2261, and 2097 operational taxonomic units were obtained at 3 % distance cutoff in the DO, XO, DF, XF, DA, XA, DD, and XD sediments, respectively. Bacterial phylotype richness in DD was higher than the other sediments, and XO had the least richness. The most dominant class in the DA, DD, DF, DO, and XA sediments is Gammaproteobacteria. Deltaproteobacteria is the most dominant one in XD, XO, and XF. Circa 14.4 % sequences in XD were found to be affiliated with the Flavobacteriales order. Characterization of the estuarine sediment bacterial communities indicated that chemical pollution has the potential to decrease the natural variability that exists among estuary ecosystems. However, chemical pollutants did not cause clear bio-homogenization in these estuaries.

Impacts of vegetation, tidal process, and depth on the activities, abundances, and community compositions of denitrifiers in mangrove sediment.

Coastal mangrove wetland is well known to be intense in nitrogen cycling. The tidal process and plants are key factors in controlling the microbial processes in wetlands. However, mechanisms on how these factors and their interactions affect the microorganisms involved in denitrification remain poorly understood. In this study, the impacts of vegetation (bulk, Kandelia obovata, and Spartina alterniflora) and tidal process (falling tide and rising tide) on denitrification activities, abundances, and community compositions of denitrifiers in the sediments from different depths (0-5 and 5-10 cm) were investigated in a microcosm experiment. A significant enhancement of denitrification activities and gene abundances (nirS, nirK, and nosZ) in the vegetated sediments was observed. Activities and abundances were significantly higher in the 0-5-cm sediments when compared with the 5-10-cm counterparts. The effect of interaction between vegetation and tide or depth was also significant. Terminal restriction fragment length polymorphism (T-RFLP) analysis revealed that not only vegetation but also plant species had a significant impact on the community compositions of nirK denitrifiers, while the tidal process affected the community compositions of nirS and nosZ denitrifiers but not nirK denitrifiers. However, depth only significantly shaped the nirS denitrifier communities. These findings demonstrate the effects of these factors and their interactions in shaping the denitrifiers in sediments.

Sphingomonas polyaromaticivorans sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from an oil port water sample.

A bacterial strain (B2-7(T)) capable of degrading a wide range of polycyclic aromatic hydrocarbon compounds (2-4 rings) was isolated from a water sample taken from Botan Oil Port in Xiamen, China. The isolate was Gram-negative, short-rod-shaped, aerobic, non-motile and formed yellow-pigmented colonies on LB medium. Cells of strain B2-7(T) were catalase-positive and oxidase-negative. Optimal growth of strain B2-7(T) was observed at pH 7.0, at 26 °C and in 0.5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain B2-7(T) grouped with members of the genus Sphingomonas and it showed 16S rRNA gene sequence similarity of 95.40 % to Sphingomonas yunnanensis YIM 003(T). The major polar lipids were phosphatidylethanolamine, phosphatidylcholine and sphingoglycolipid. Q-10 and sym-homospermidine were the predominant ubiquinone and polyamine components, respectively. The major fatty acids were C(18:1)ω7c (67.2 %), C(14:0) 2-OH (10.0 %) and C(16:0) (9.6 %). The G+C content of the genomic DNA was 61.8 mol%. Based on phenotypic properties, and phylogenetic and genomic data, strain B2-7(T) represents a novel species of the genus Sphingomonas within the class Alphaproteobacteria, for which the name Sphingomonas polyaromaticivorans sp. nov. is proposed. The type strain is B2-7(T) ( = KCCM 42951(T) = JCM 16711(T)).

Diversity and abundance of anammox bacterial community in the deep-ocean surface sediment from equatorial Pacific.

The community structure and diversity of anaerobic ammonium oxidation (anammox) bacteria in the surface sediments of equatorial Pacific were investigated by phylogenic analysis of 16S rRNA and hydrazine oxidoreductase (hzo) genes and PCoA (principal coordinates analysis) statistical analysis. Results indicated that 16S rRNA and hzo sequences in the P2 (off the center of western Pacific warm pool) and P3 (in the eastern equatorial Pacific) sites all belong to the Candidatus "Scalindua", the dominate anammox bacteria in the low-temperature marine environment proved by previous studies. However, in the P1 site (in center of warm pool of western Pacific), large part of 16S rRNA gene sequences formed a separated cluster. Meanwhile, hzo gene sequences from P1 sediment also grouped into a single cluster. PCoA analysis demonstrated that the anammox community structure in the P1 has significant geographical distributional difference from that of P2, P3, and other marine environments based on 16S rRNA and hzo genes. The abundances of anammox bacteria in surface sediments of equatorial Pacific were quantified by q-PCR analysis of hzo genes, which ranged from 3.98 × 10(3) to 1.17 × 10(4) copies g(-1) dry sediments. These results suggested that a special anammox bacteria phylotypes exist in the surface sediment of the western Pacific warm pool, which adapted to the specific habitat and maybe involved in the nitrogen loss process from the fixed inventory in the habitat.

Distribution of Vibrio alginolyticus-like species in Shenzhen coastal waters, China.

We investigated the distribution of vibrios in Shenzhen coastal waters in order to obtain valuable information for the aquaculture industry and a health warning system. Quantities of vibrios from surface waters ranged from 0 to 4.40×10(4) CFUs mL(-1) in April (spring), while from 0 to 2.57×10(3) CFUs mL(-1) in September (autumn); the abundance of V. alginolyticus-like species from surface water ranged from 0 to 6.72×10(3) CFUs mL(-1) in April (spring) and from 0 to 1.28×10(3) CFUs mL(-1) in September (autumn); higher counts were observed in spring. The V. alginolyticus-like species was dominant in Shenzhen coastal waters, with the highest abundance in the clean region (stations YMK001 and GDN064) in April, suggesting that Vibrio spp. were naturally occurring bacteria in marine environments. The correlation between the abundance of vibrios (including V. alginolyticus-like species) and environmental factors varied in different regions and different seasons. There were no vibrios detected when the salinity was less than 11.15‰ in the Zhujiang River estuary, which indicated that salinity played a key role in the distribution of vibrios and V. alginolyticus-like species.

Contamination and potential biodegradation of polycyclic aromatic hydrocarbons in mangrove sediments of Xiamen, China.

Five stations were established in the Fenglin mangrove area of Xiamen, China to determine the concentrations of polycyclic aromatic hydrocarbons (PAHs) and the numbers of PAH-degrading bacteria in surface sediments. Assessing the biodegradation potential of indigenous microorganisms and isolating the high molecule weight (HMW)-PAH degrading bacteria was also one of the aims of this work. The results showed that the total PAH concentration of sediments was 222.59 ng g(-1) dry weight, whereas the HMW-PAH benzo(a)pyrene (BaP) had the highest concentration among 16 individual PAH compounds. The variation in the numbers of PAH-degrading bacteria was 2.62 x 10(2)-5.67 x 10(4)CFU g(-1) dry weight. The addition of PAHs showed a great influence in increasing the microbial activity in mangrove sediments. A bacterial consortium, which could utilize BaP as the sole source of carbon and energy, and which was isolated from mangrove sediments and enriched in liquid medium for nearly one year degraded 32.8% of BaP after 63 days incubation.

[Bacterial community structure in intestine of the white shrimp, Litopenaeus vannamei].

The composition of bacterial community in the intestine of the white shrimp, Litopenaeus vannamei under laboratory culture condition was determined using the 16S rDNA clone library. 16s rRNA gene was amplified and a library was constructed by using the genomic DNA extracted from the bacteria in the shrimp intestine as template. 12 different RFLP patterns of the clones were obtained by restriction fragment length polymorphism analysis using Afa I and Msp I. Compared with the published sequences in GenBank database, sequencing results of cloned 16S rDNA amplicons revealed a diverse community including gamma-proteobacteria and Firmicutes in the intestine of artificial diet-fed shrimp. Results showed that the Firmicutes group can be a dominant component (75.4%) in the shrimp intestinal microflora and other clones belong to gamma-proteobacteria (24.6%) which were identified as Shewanella sp., Pantoea sp., Aranicola sp., Pseudomonas sp. and Vibrio sp., respectively. These results provide the first comprehensive description of microbial diversity of the white shrimp intestine and suggest that most of the bacteria associated with shrimp intestine are uncultured and novel species.

[Research on mangrove soil microorganisms: past, present and future].

Special Mangrove soil niches possesses valuable microbial resources. Unfortunately, up to the present, so far there is very little knowledge on the mangrove soil microbial communities. It mainly due to the limitations of research methods. Cultureindependent approaches based on 16S rRNA, 18S rRNA gene analysis open the window to study microbial diversity in mangrove soil. The progress had achieved about studying on mangrove soil microbial species diversity, metabolic diversity and treating environmental pollutions was summarized in the paper. In addition, the bright future of mangrove soil microorganisms was described.

Responses of bacterial and archaeal communities to nitrate stimulation after oil pollution in mangrove sediment revealed by Illumina sequencing.

This study aimed to investigate microbial responses to nitrate stimulation in oiled mangrove mesocosm. Both supplementary oil and nitrate changed the water and sediment chemical properties contributing to the shift of microbial communities. Denitrifying genes nirS and nirK were increased several times by the interaction of oil spiking and nitrate addition. Bacterial chao1 was reduced by oil spiking and further by nitrate stimulation, whereas archaeal chao1 was only inhibited by oil pollution on early time. Sampling depth explained most of variation and significantly impacted bacterial and archaeal communities, while oil pollution only significantly impacted bacterial communities (p<0.05). Despite explaining less variation, nitrate addition coupled with oil spiking enhanced the growth of hydrocarbon degraders in mangrove. The findings demonstrate the impacts of environmental factors and their interactions in shaping microbial communities during nitrate stimulation. Our study suggests introducing genera Desulfotignum and Marinobacter into oiled mangrove for bioaugmentation.

Contamination of soil, leaves and vegetables by polychlorinated biphenyls in Xiamen region, China.

The paper aimed to identify the primary of polychlorinated biphenyls(PCBs) in the Jiulong River Estuary, investigate the spatial distribution of PCBs contamination in the environment, localize the atmospheric source and evaluate ongoing PCBs emissions by analyzing soil samples collected along the Jiulong River region. In addition, the accumulation of PCBs in the human food chain was quantified by analyzing leaf of orange trees and vegetable samples collected along a gradient of soil/atmospheric contamination moving away from the source. Consequently, the impact on the human health and the ecosystem was quantified, different management options were proposed to reduce this impact and to carry out research on organic contaminants along the Jiulong River and Xiamen region.

Biological activity of a red-tide alga--A. tamarense under co-cultured condition with bacteria.

The relationship between Alexandrium tamarense (Lebour) Balech, one of red-tide alga, and two strains of marine bacteria, Bacillius megaterium (S7) and B. halmapulus (S10) isolated from Xiamen Western Sea, was investigated by evaluating the growth state of A. tamarense and the variation of beta-glucosidase activity in co-culture system. The results showed the growth and multiplication of the alga were related with the concentration, genus speciality of the bacteria, and growth stage of the alga itself. The growth of A. tamarense was obviously inhibited by S7 and S10 at high concentration. Either inhibition or promotion contributed much more clearly in earlier than in later stage of the growth of the alga. Furthermore, there was a roughly similar variation trend of the activity of extra-cellular enzyme, beta-glucosidase, in the water of the separately co-cultured bacteria S7 and S10 with the alga. The beta-glucosidase activity (beta-GlcA) rapidly increased during the later algal growth accompanying the increase of the lysis of the alga cells. The obvious inhibition of A. tamarense by marine bacteria at high concentration and evident increase of beta-GlcA in co-colture system would help us in better understanding the relationship between red-tide alga and bacteria, and also enlightenedus the possible use of bacteria in the bio-control of red-tide.

Brominated flame retardants in mangrove sediments of the Pearl River Estuary, South China: spatial distribution, temporal trend and mass inventory.

Sediments were collected from three mangrove wetlands in the Pearl River Estuary (PRE) of South China to investigate spatial and temporal distributions of polybrominated diphenyl ethers (PBDEs), decabromodiphenyl ethane (DBDPE) and 1,2-bis(2,4,6-tribromophenoxy)ethane (BTBPE). Concentrations of ΣPBDEs, DBDPE and BTBPE in mangrove sediments of the PRE ranged from 1.25-206, 0.364-34.9, and not detected-0.794 ng g(-1) dry weight, respectively. The highest concentrations of ΣPBDEs, DBDPE and BTBPE were found at the mangrove wetland from Shenzhen, followed by Zhuhai and Guangzhou, showing the dependence on the proximity to urban areas. PBDEs were the predominant brominated flame retardants (BFRs) in mangrove sediments. The concentrations of ΣPBDEs, DBDPE and BTBPE in sediment cores showed an increasing trend from the bottom to top layers, reflecting the increasing usage of these BFRs. The inventories of ΣPBDEs, DBDPE and BTBPE in mangrove sediments were 1962, 245, and 4.10 ng cm(-2), respectively. This is the first study to report the occurrence of DBDPE and BTBPE in mangrove ecosystems.

Biosorption of C.I. Direct Blue 199 from aqueous solution by nonviable Aspergillus niger.

The capacity and mechanism with which nonviable Aspergillus niger removed the textile dye, C.I. Direct Blue 199, from aqueous solution was investigated using different parameters, such as initial dye concentration, pH and temperature. In batch experiments, the biosorption capacity increased with decrease in pH, and the maximum dye uptake capacity of the biosorbent was 29.96 mg g(-1) at 400 mg L(-1) dye concentration and 45 degrees C. The Langmuir and Freundlich models were able to describe the biosorption equilibrium of C.I. Direct Blue 199 onto the fungal biomass. Biosorption followed a pseudo-second order kinetic model with high correlation coefficients (r(2)>0.99). Thermodynamic studies revealed that the biosorption process was successful, spontaneous and endothermic in nature.

[Distribution and activity of marine bacterioplankton at frequent HAB area of East China Sea].

The distribution, activity and community structure of bacterioplankton in surface water were investigated at frequent harmful algae blooms (HABs) area in East China Sea (28 degrees-30.7 degrees N) from April to May, 2006. The abundance of bacterioplankton was determined by using the DAPI (4, 6-diamidino-2-phenylindole) direct count (DDC) method. The beta-glucosidase and aminopeptidase activity were measured with fluorogenic model substrates. And the bacterial community structure was analyzed by PCR-DGGE. Results showed that bacterial abundance in northern of the sampling area was much more than that in southern of the sampling area. It ranged from 5.85 x 10(4) cells x mL(-1) to 9.26 x 10(5) cells x mL(-1). And there was the highest value area outer the costal of Zhou Shan Island. The average aminopeptidase activity was 3.6 times of beta-glucosidase activity which was 0. 023 micromol x (L x h) (-1) in this area. The beta-glucosidase activity in >5 microm fraction contributed 47.4% of the total, and that of the aminopeptidase activity was 44.24% of the total. Bacterial extracellular enzyme activity had a higher average value in southern of the sampling area. This indicated that the bacterial activity had no direct relationship with bacterial abundance. Bacterial diversity and community structure differed from each sampling station. There were more divers in northern sampling area. The results suggested that the human being activity and continental inputting organic matters played a key role on the distribution of bacterial abundance. The distribution of bacterial extracellular enzyme activity was mainly affected by the Taiwan warm current. And it was the complicated unknown factors that caused the difference of the bacterial community structure and diversity from each sampling station. Obviously, it needed further work to enhance the knowledge of the ecological function of the bacterioplankton at frequent HABs area of the coastal water in East China Sea.

Biological decolorization of the reactive dyes Reactive Black 5 by a novel isolated bacterial strain Enterobacter sp. EC3.

Studies were carried out on the decolorization of the reactive dye Reactive Black 5 by a newly isolated bacterium, EC3. Phenotypic characterization and phylogenetic analysis based on 16S rDNA sequence comparisons indicate that this strain belonged to the genus Enterobacter. The optimal conditions for the decolorizing activity of Enterobacter sp. EC3 were anaerobic conditions with glucose supplementation, at pH 7.0, and 37 degrees C. The maximum decolorization efficiency against Reactive Black 5 achieved in this study was 92.56%. Ultra-violet and visible (UV-vis) analyses before and after decolorization and the colorless bacterial biomass after decolorization suggested that decolorization was due to biodegradation, rather than inactive surface adsorption. The bacterial strain also showed a strong ability to decolorize various reactive textile dyes, including both azo and anthraquinone dyes. To our knowledge, it is the first time that a bacterial strain of Enterobacter sp. has been reported with decolorizing ability against both azo and anthraquinone dyes.

[16S rDNA clone library analysis of microbial diversity associated with the PSP-producing dinoflagellate Alexandrium tamarense].

The composition of bacterial community in the Alexandrium tamarense culture was determined by analyzing the 16S rDNA clone libraries. 16S rRNA gene was amplified by using the total DNA extracted from the A. tamarense culture at three growth stages as templates. 34 different restriction fragment length polymorphism (RFLP) patterns of the clones were obtained from the three libraries. Clones representing each RFLP patterns were sequenced and phylogenetic analysis revealed that the Proteobacteria and the Bacteroidetes group can be the dominant component in the phycosphere microflora. Results showed that in the lag phase, alpha-Proteobacteria (36.4%), gamma-Proteobacteria (27.3%) and Bacteroidetes (27.3%) were the dominant group; in the late-exponential phase, the clones belonged to alpha-Proteobacteria (53.3%), beta-Proteobacteria (13.3%), gamma-Proteobacteria (6.7%), and Bacteroidetes (26.7%); and in the stationary phase, the community was comprised of alpha-Proteobacteria (47.8%), beta-Proteobacteria (8.7%), gamma-Proteobacteria (21.7%), delta-Proteobacteria (4.3%) and Bacteroidetes (17.4%). The results also suggest that a part of the bacteria associated with A. tamarense are uncultured and novel species. And these bacteria may play a major role in regulating the processes of algal bloom initiation, maintenance and decline. So these results may provide us great academic and practical importance in controlling the algal blooms by microbes.

[Construction of large fragment metagenome library of natural mangrove soil].

Applying our optimized direct extraction method, the percentage of large fragment DNA in the total extracted mangrove soil DNA was significant increased. The large fragment metagenome library derived from natural mangrove soil over four seasons was successfully constructed by the optimized DNA extraction and electro elution purification method. All of the clones had recombinant Cosmids and each differed in their fragment profiles when Cosmid DNA was extracted from 12 randomly picked colonies and digested with BamHI. The average insert size for this library was larger than 35 kbp. This culturing-independent library at least encompassed 335 Mbp valuable genetic information of mangrove soil microbes. It allowed mining of valuable intertidal microbial resource to become a reality. It is a recommended method for those researchers who have still not circumvented the large insert environmental libraries or for those beginning research in this field, so as to avoid them attempting repetitive, fussy work.

Distribution of Vibrio alginolyticus-like species in Shenzhen coastal waters, China

We investigated the distribution of vibrios in Shenzhen coastal waters in order to obtain valuable information for the aquaculture industry and a health warning system. Quantities of vibrios from surface waters ranged from 0 to 4.40×10(4) CFUs mL-1 in April (spring), while from 0 to 2.57×10³ CFUs mL-1 in September (autumn); the abundance of V. alginolyticus-like species from surface water ranged from 0 to 6.72×10³ CFUs mL-1 in April (spring) and from 0 to 1.28×10³ CFUs mL-1 in September (autumn); higher counts were observed in spring. The V. alginolyticus-like species was dominant in Shenzhen coastal waters, with the highest abundance in the clean region (stations YMK001 and GDN064) in April, suggesting that Vibrio spp. were naturally occurring bacteria in marine environments. The correlation between the abundance of vibrios (including V. alginolyticus-like species) and environmental factors varied in different regions and different seasons. There were no vibrios detected when the salinity was less than 11.15‰ in the Zhujiang River estuary, which indicated that salinity played a key role in the distribution of vibrios and V. alginolyticus-like species.

Distribution of Vibrio alginolyticus-like species in Shenzhen coastal waters, China

We investigated the distribution of vibrios in Shenzhen coastal waters in order to obtain valuable information for the aquaculture industry and a health warning system. Quantities of vibrios from surface waters ranged from 0 to 4.40×10(4) CFUs mL-1 in April (spring), while from 0 to 2.57×10³ CFUs mL-1 in September (autumn); the abundance of V. alginolyticus-like species from surface water ranged from 0 to 6.72×10³ CFUs mL-1 in April (spring) and from 0 to 1.28×10³ CFUs mL-1 in September (autumn); higher counts were observed in spring. The V. alginolyticus-like species was dominant in Shenzhen coastal waters, with the highest abundance in the clean region (stations YMK001 and GDN064) in April, suggesting that Vibrio spp. were naturally occurring bacteria in marine environments. The correlation between the abundance of vibrios (including V. alginolyticus-like species) and environmental factors varied in different regions and different seasons. There were no vibrios detected when the salinity was less than 11.15ë in the Zhujiang River estuary, which indicated that salinity played a key role in the distribution of vibrios and V. alginolyticus-like species.