Yanying Zhang

Phylogenetic diversity of nitrogen-fixing bacteria in mangrove sediments assessed by PCR-denaturing gradient gel electrophoresis

Culture-independent PCR–denaturing gradient gel electrophoresis (DGGE) was employed to assess the composition of diazotroph species from the sediments of three mangrove ecosystem sites in Sanya, Hainan Island, China. A strategy of removing humic acids prior to DNA extraction was conducted, then total community DNA was extracted using the soil DNA kit successfully for nifH PCR amplification, which simplified the current procedure and resulted in good DGGE profiles. The results revealed a novel nitrogen-fixing bacterial profile and fundamental diazotrophic biodiversity in mangrove sediments, as reflected by the numerous bands present DGGE patterns. Canonical correspondence analysis (CCA) revealed that the sediments organic carbon concentration and available soil potassium accounted for a significant amount of the variability in the nitrogen-fixing bacterial community composition. The predominant DGGE bands were sequenced, yielding 31 different nifH sequences, which were used in phylogenetic reconstructions. Most sequences were from Proteobacteria, e.g. α, γ, β, δ-subdivisions, and characterized by sequences of members of genera Azotobacter, Desulfuromonas, Sphingomonas, Geobacter, Pseudomonas, Bradyrhizobium and Derxia. These results significantly expand our knowledge of the nitrogen-fixing bacterial diversity of the mangrove environment.

Seasonal Variation of Water Quality and Phytoplankton Response Patterns in Daya Bay, China

Data collected from 12 stations in Daya Bay in different seasons in 2002 revealed the relation between water quality and phytoplankton response patterns. The results showed that Daya Bay could be divided into wet and dry seasons by multivariate statistical analysis. Principal component analysis indicated that temperature, chlorophyll a and nutrients were important components during the wet season (summer and autumn). The salinity and dissolved oxygen were the main environmental factors in the dry season (winter and spring). According to non-metric multidimensional scaling, there was a shift from the large diatoms in the dry season to the smaller line-chain taxa in the wet season with the condition of a high dissolved inorganic nitrogen and nitrogen to phosphorous concentration ratio. Nutrient changes can thus alter the phytoplankton community composition and biomass, especially near the aquaculture farm areas. There was no evidence of an effect of thermal water from the nearby nuclear power plants on the observed changes in phytoplankton community and biomass in 2002.

Mangrovibacterium diazotrophicum gen. nov., sp. nov., a nitrogen-fixing bacterium isolated from a mangrove sediment, and proposal of Prolixibacteraceae fam. nov.

A nitrogen-fixing bacterium, designated strain SCSIO N0430(T), was isolated from a mangrove sediment sample. Analysis of the sequence of the nifH gene responsible for nitrogen fixation in this strain indicated a close relationship to an uncultured bacterium ZNZ-D11 (GenBank accession no. JF896696). 16S rRNA gene sequence analysis revealed that this isolate had less than 93 % similarity to its closest relative, Sunxiuqinia elliptica DQHS4(T). A phylogenetic tree reconstructed based on 16S rRNA gene sequences revealed that strain SCSIO N0430(T) was a member of the phylum Bacteroidetes. Chemotaxonomic and physiological characteristics, including phospholipids and major fatty acids, readily distinguished the isolate from established members of the phylum Bacteroidetes. It is concluded that strain SCSIO N0430(T) represents a novel genus and species, for which the name Mangrovibacterium diazotrophicum gen. nov., sp. nov. is proposed, with the type strain of the species SCSIO N0430(T) ( = KCTC 32129(T) = DSM 27148(T) = JCM 19152(T)). Based on phylogenetic characteristics and 16S rRNA gene signature nucleotide patterns, the three genera Sunxiuqinia, Prolixibacter and Mangrovibacterium are proposed to make up a novel family, Prolixibacteraceae fam. nov., in the order Bacteroidales.

Chemometry use in the evaluation of the sanya bay water quality

In this study, chemometric method is employed to identify anthropogenic effects on the water quality in Sanya Bay, South China Sea, and its marine and natural characteristics. Principal component analysis has extracted the four latent factors, thus explaining 85.52% of the total variance. Cluster analysis and principal component analysis have identified three different patterns of water quality based on anthropogenic effects and marine characteristics: Cluster I located in the outer and middle parts of the bay, Cluster II close to downtown Sanya, Cluster III located in the Sanya River estuary. In terms of the temporal pattern, principal component analysis and cluster analysis have distinguished the dry season from November to the following April, and the rainy season from May to October. The temporal pattern is related to climate and natural characteristics. The similarity index between variables and scores of samples can further distinguish the contribution of the variables to the samples. Both the polluting sources external to the Sanya River and the water from the South China Sea exercise an important influence on the water quality in Sanya Bay. These results may be valuable for socioeconomic development and human health in the Sanya Bay area.

The diversity of coral associated bacteria and the environmental factors affect their community variation

Coral associated bacterial community potentially has functions relating to coral health, nutrition and disease. Culture-free, 16S rRNA based techniques were used to compare the bacterial community of coral tissue, mucus and seawater around coral, and to investigate the relationship between the coral-associated bacterial communities and environmental variables. The diversity of coral associated bacterial communities was very high, and their composition different from seawater. Coral tissue and mucus had a coral associated bacterial community with higher abundances of Gammaproteobacteria. However, bacterial community in seawater had a higher abundance of Cyanobacteria. Different populations were also found in mucus and tissue from the same coral fragment, and the abundant bacterial species associated with coral tissue was very different from those found in coral mucus. The microbial diversity and OTUs of coral tissue were much higher than those of coral mucus. Bacterial communities of corals from more human activities site have higher diversity and evenness; and the structure of bacterial communities were significantly different from the corals collected from other sites. The composition of bacterial communities associated with same coral species varied with season’s changes, geographic differences, and coastal pollution. Unique bacterial groups found in the coral samples from more human activities location were significant positively correlated to chemical oxygen demand. These coral specific bacteria lead to coral disease or adjust to form new function structure for the adaption of different surrounding needs further research.

Fungal Community Successions in Rhizosphere Sediment of Seagrasses Enhalus acoroides under PAHs Stress.

Seagrass meadows represent one of the highest productive marine ecosystems and are of great ecological and economic values. Recently, they have been confronted with worldwide decline. Fungi play important roles in sustaining the ecosystem health as degraders of polycyclic aromatic hydrocarbons (PAHs), but fewer studies have been conducted in seagrass ecosystems. Hence, we investigated the dynamic variations of the fungal community succession under PAH stress in rhizosphere sediment of seagrasses Enhalus acoroides in this study. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), quantitative PCR (qPCR) and a clone library have been employed to analyze the fungal community’s shifts. Sequencing results of DGGE and the clone library showed that the predominant species belong to phyla Ascomycota and Basidiomycota. The abundance of three groups decreased sharply over the incubation period, whereas they demonstrated different fungal diversity patterns. Both the exposure time and the PAH concentrations affected the microbial diversity as assessed by PCR-DGGE analysis. Redundancy analysis (RDA) indicated that significant factors driving community shifts were ammonium and pH (p < 0.05). Significant amounts of the variations (31.1%) were explained by pH and ammonium, illustrating that those two parameters were the most likely ones to influence or be influenced by the fungal communities’ changes. Investigation results also indicated that fungal communities in seagrass meadow were very sensitive to PAH-induced stress and may be used as potential indicators for the PAH contamination.

Cultivation-dependent analysis of the microbial diversity associated with the seagrass meadows in Xincun Bay, South China Sea

Microbial communities have largely existed in the seagrass meadows. A total of 496 strains of the bacteria in the seagrass meadows, which belonged to 50 genera, were obtained by the plate cultivation method from three sites of Xincun Bay, South China Sea. The results showed that Bacillales and Vibrionales accounted for the highest proportions of organisms in all communities. The diversity of the bacteria in the sediment was higher than that associated with seagrass. Thalassia hemperichii possessed the highest abundance of bacteria, followed by Enhalus acoroides and Cymodocea rotundata. Robust seasonal dynamics in microbial community composition were also observed. It was found that microbial activities were closely tied to the growth stage of the seagrass. The microbial distribution was the lowest in site 3. The abundance of the bacteria was linked to the interactions between bacteria and plants, the condition of plant and even the coastal water quality and the nutrition level in the sediment.

Illumina-based analysis the microbial diversity associated with Thalassia hemprichii in Xincun Bay, South China Sea

In order to increase our understanding of the microbial diversity associated with seagrass Thalassia hemprichii in Xincun Bay, South China Sea, 16S rRNA gene was identified by highthrough sequencing method. Bacteria associated with seagrass T. hemprichii belonged to 37 phyla, 99 classes. The diversity of bacteria associated with seagrass was similar among the geographically linked coastal locations of Xincun Bay. Proteobacteria was the dominant bacteria and the α-proteobacteria had adapted to the seagrass ecological niche. As well, α-proteobacteria and Pseudomonadales were associated microflora in seagrass meadows, but the interaction between the bacteria and plant is needed to further research. Burkholderiales and Verrucomicrobiae indicated the influence of the bay from anthropogenic activities. Further, Cyanobacteria could imply the difference of the nutrient conditions in the sites. γ-proteobacteria, Desulfobacterales and Pirellulales played a role in the cycle of sulfur, organic mineralization and meadow ecosystem, respectively. In addition, the less abundance bacteria species have key functions in the seagrass meadows, but there is lack knowledge of the interaction of the seagrass and less abundance bacteria species. Microbial communities can response to surroundings and play key functions in the biochemical cycle.

Identification of coastal water quality by self-organizing map in Sanya Bay, South China Sea

A self-organizing map (SOM) was utilized to identify the effects caused by human activities on water quality in Sanya Bay, South China Sea. Spatial pattern is mainly related to anthropogenic activities and hydrodynamic conditions. Water quality in Sanya Bay was divided into two groups by SOM: S1 and S2 were in east parts of Sanya Bay (Sanya River Estuary), which are areas of human activity, while the rest of the monitoring sites were in the south, central and northern parts of Sanya Bay, which are areas that have water exchanges from South China Sea. The results of this study may provide information on spatial patterns in Sanya Bay.

Diversity analysis of diazotrophs associated with corals from Xisha and Sanya, South China Sea

In recent years, many studies have shown an increase in coral associated microbial biodiversity in coral diseases. However, the variation of coral diazotroph, which plays an important role in the nitrogen cycle, is still unclear. To explore the changes of nitrogen fixing microbial communities, we analyzed the diversity of nitrogen-fixing bacteria associated with corals in healthy vs. diseased conditions, and corals from two different locations (Xisha and Sanya). The diversity of nitrogen-fixing bacteria associated with two coral species, Porites lutea and Pocillopora damicornis were assessed using cloning and sequencing of the nitrogenase gene nifH. Phylogenetic analysis indicated coral associated diazotrophs community structure varied in different coral species: Chlorobi dominated in Porites lutea, while Alphaproteobacteria and Gammaproteobacteria were the most abundant nitrogen-fixing bacteria in Pocillopora damicornis. The dominant group of nitrogen-fixing bacteria was Chlorobi in healthy Porites lutea, but Cyanobacteria predominated in diseased ones. Moreover, the dominant nitrogen-fixing bacteria Gammaproteobacteria was replaced by Alphaproteobacteria in coral Pocillopora damicornis, from open sea to the coast. The diseased and coastal corals contained higher diversity of nitrogen-fixing bacteria than the healthy and open ocean corals. In conclusion, the nitrogen-fixing bacteria community structure shifted in response to the variation of coral species, coral health status and surrounding environments.