Keqiang Shao

Comparing sediment bacterial communities in the macrophyte-dominated and algae-dominated areas of eutrophic Lake Taihu, China.

Bacterial community structure and the effects of several environmental factors on bacterial community distribution were investigated in the sediment of the macrophyte-dominated and algae-dominated areas in a large, shallow, eutrophic freshwater lake (Lake Taihu, China). Surface sediment samples were collected at 6 sampling sites (3 sites from each of the 2 areas) on 15 February and 15 August 2009. Based on cluster analysis of the DGGE banding patterns, there were significant seasonal variations in the structure of the sediment bacterial community in the macrophyte- and algae-dominated areas, and site-specific variation within an area and between 2 areas. However, there were no significant between-area variations due to the large within-area variation. Analysis of DNA sequences showed that there were differences in the species composition of the sediment bacteria between the macrophyte- and algae-dominated area clone libraries. In the macrophyte-dominated area library, the bacterial community was dominated by Deltaproteobacteria, Verrucomicrobia, Acidobacteria, Bacteroidetes, Gammaproteobacteria, and Betaproteobacteria. OP10 was found in the library of this area but not in the algae-dominated area library. The algae-dominated area library was dominated by Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Acidobacteria. Cyanobacteria, Alphaproteobacteria, and Planctomycetes were found in this area library but not in the macrophyte-dominated area library. Canonical correspondence analysis demonstrated that total phosphorus and water temperature were the dominant environmental factors affecting bacterial community composition in the sediment.

Influence of Salinity on the Bacterial Community Composition in Lake Bosten, a Large Oligosaline Lake in Arid Northwestern China

ABSTRACT Salinity was found to be the dominating contributor controlling bacterial community composition (BCC) and the abundance of Betaproteobacteria in the oligosaline Lake Bosten. The high percentage of unclassified bacteria inhabiting this unique habitat highlights the potential ecological importance of BCC in the early stage of lake salinization and eutrophication.

The responses of the taxa composition of particle-attached bacterial community to the decomposition of Microcystis blooms.

The changes of taxa within the particle-attached bacterial assemblage during the decomposition of Microcystis blooms were investigated under darkness and anoxic condition in mesocosm experiments. During 14 days of darkness incubation, chlorophyll-a (Ch-a) concentration decreased from 2000 μg/L to 5 μg/L. Samples were collected on days 0, 2 and 14 for bacterial 16S rRNA analysis, based on rapid decreases in the Chl-a concentration of water column. The total bacterial community DNA was extracted and 16S rRNA genes were amplified by polymerase chain reaction, cloned and sequenced of selected samples. The results showed that the abundance of attached bacteria increased significantly, and the composition of the particle-attached bacterial communities varied temporally during the decomposition of Microcystis blooms. The bacterial assemblage appeared to be dominated by members of Bacteroidetes, Alphaproteobacteria and Betaproteobacteria. Shift of some genera of Alphaproteobacteria and Alphaproteobacteria was also observed. Additionally, we found that the family Sphingomonas, affiliated with Alphaproteobacteria, identified as a microcystin-degrading bacterium, dominated the particle-attached bacterial communities. The results from the present study, together with previously published data highlighted the need for more studies concerning the bacterial degradation process in order to trace the environmental fate of microcystins in field conditions.

Pyrosequencing analysis of free-living and attached bacterial communities in Meiliang Bay, Lake Taihu, a large eutrophic shallow lake in China

To elucidate the relationship between particle-attached (PA, ≥ 5.0 μm) and free-living (FL, 0.2-5.0 μm) bacterial communities, samplings were collected seasonally from November 2011 to August 2012 in Meiliang Bay, Lake Taihu, China. We used 454 pyrosequencing of 16S rRNA genes to study bacterial diversity and structure of PA and FL communities. The analysis rendered 37,985 highly qualified reads, subsequently assigned to 1755 operational taxonomic units (97% similarity) for the 8 samples. Although 27 high-level taxonomic groups were obtained, the 3 dominant phyla (Proteobacteria, Actinobacteria, and Bacteroidetes) comprised about 75.9% and 82.4% of the PA and FL fractions, respectively. Overall, we found no significant differences between community types, as indicated by ANOSIM R statistics (R = 0.063, P > 0.05) and the Parsimony test (P = 0.222). Dynamics of bacterial communities were correlated with changes in concentrations of total suspended solids (TSS) and total phosphorus (TP). In summer, a significant taxonomic overlap in the 2 size fractions was observed when Cyanobacteria, a major contributor of TSS and TP, dominated in the water, highlighting the potential rapid exchange between PA and FL bacterial populations in large shallow eutrophic lakes.

Decomposition of Microcystis blooms: implications for the structure of the sediment bacterial community, as assessed by a mesocosm experiment in Lake Taihu, China.

The effect of decomposition of Microcystis blooms on the sediment bacterial communities was investigated in a 14‐day mesocosm experiments under dark and anoxic condition with three differing levels of Microcystis spp. biomass (from 20 to 2000 µg L−1) as measured by chlorophyll‐a (Chl‐a) concentration in the water column. Sediment samples were collected on days 0 and 14 for bacterial community composition (BCC) analysis, based on rapid decreases in the Chl‐a concentration of water column. The BCC was determined by denaturing gradient gel electrophoresis and sequencing of predominant bands. The results showed that after Microcystis decomposition (day 14), the bacterial phylotype diversity in the sediment increased in enclosures with added Microcystis, and the relative abundance of bacteria affiliated with Bacteroidetes and Verrucomicrobia strongly increased. Canonical correspondence analysis showed that organic matter and Chl‐a contributed significantly to the changes in sediment bacterial communities during Microcystis decomposition. The present results demonstrate Microcystis decomposition may directly and indirectly influence the BCC of the sediment.

Bacterial community changes along a salinity gradient in a Chinese wetland

We analyzed the composition and diversity of a bacterial community to determine its response to increasing salinity in the Xiangsi Lake wetland in the arid region of northwest China. We studied 12 sites, ranging from freshwater to saltwater habitats, using polymerase chain reaction (PCR)-based terminal restriction fragment length polymorphism (T-RFLP) and sequencing of the 16S rRNA genes of 5 selected samples. Cluster analysis and phylogenetic analysis revealed that the bacterial community changed significantly in response to increased salinity within the small-scale wetland (50.8 km(2)). Detailed analysis showed that (i) Betaproteobacteria can maintain balanced growth over a salinity range (from 0.34 to 6.86 g/L) through intergenus changes in community structure, followed by a sharp decrease in relative abundance (from 62.2% to 16.0%) when salinity reaches 26.18 g/L; (ii) salt-sensitive and halophobic taxa were progressively replaced by halotolerant and halophilic taxa with increasing salinity; (iii) bacterial diversity was lowest at intermediate salinity levels (6.86 g/L); and (iv) an increasing percentage of unclassified bacterial taxa were found with increasing salinity. This study has implications to improve understanding of bacterial community response to water salinization.

Impacts of different salinities on bacterial biofilm communities in fresh water

Natural and anthropogenic salinization continuously impacts inland aquatic ecosystems. Associated bacterial biofilms respond rapidly to environmental conditions and are potential bioindicators for changes in water quality. This study evaluates the effects of different salinity concentrations (0.3‰-10‰) on bacterial biofilms communities grown in fresh water from Lake Bosten. Bacterial communities associated with biofilms were analyzed using terminal restriction fragment length polymorphism and clone library analyses of 16S rRNA genes. Results indicated that the attached bacterial community composition (ABCC) changed over several weeks of biofilm growth, but all followed similar bacterial successional trends in the different salinity groups. Detailed analysis showed the following. (i) ABCC did not differ (P > 0.05) in the low-salinity groups (0.3‰-3.5‰), which may be related to the lower osmotic pressure and the shorter time scale (weeks) of their present habitats. (ii) There were significant differences between the oligosaline (3.5‰) and saline (10‰) groups (P < 0.05). In particular, genus Flavobacterium became dominant in attached bacterial communities in the saline groups. The higher abundance of genus Flavobacterium was possibly due to the biological and metabolic characteristics of the bacteria. (iii) Some bacterial taxa can maintain the higher abundance within attached bacteria in the entire process of biofilms growth, such as the genera Hydrogenophaga and Methyloversatilis in Betaproteobacteria and the family Sphingomonadaceae in Alphaproteobacteria. These data suggested that the bacterial successional trends within biofilms seem almost unaffected by salinity (0.3‰-10‰), but ABCC in saline groups (10‰) are notably changed.

Comparative analysis of alkaline phosphatase-encoding genes (phoX) in two contrasting zones of Lake Taihu.

Limnetic habitats that are dominated by either algae or macrophytes represent the 2 dominant ecosystems in shallow lakes. We assessed seasonal variations in the diversity and abundance of alkaline phosphate-encoding genes (phoX) in these 2 zones of Lake Taihu, which is a large, shallow, eutrophic lake in China. There was no significant difference in seasonal mean phoX diversity between the 2 zones, whereas the seasonal mean phoX abundance in the macrophyte-dominated region was higher than that in the algae-dominated region. The bulk of the genotypes in the 2 regions were most similar to the alphaproteobacterial and betaproteobacterial phoX. Genotypes most similar to phoX affiliated with Betaproteobacteria were present with greater diversity in the macrophyte-dominated zone than in the algae-dominated zone. In the algae-dominated zone, the relative proportion of genotypes most similar to cyanobacterial phoX was highest (38.8%) in summer. In addition to the different genotype structures and environmental factors between the 2 stable states, the lower gene abundances and higher alkaline phosphatase activities in Meiliang Bay in summer than those in Xukou Bay reveals different organophosphate-mineralizing modes in these 2 contrasting habitats.

Bacterial Community Composition in Oligosaline Lake Bosten: Low Overlap of Betaproteobacteria and Bacteroidetes with Freshwater Ecosystems.

Oligosaline lakes in arid regions provide indispensable water resources for humans; however, information on the bacterial community composition (BCC) of this ecosystem is limited. In the present study, we explored seasonal and vertical variations in BCC in Lake Bosten, a unique oligosaline lake (1.2‰ salinity) in arid, northwestern China, using denaturing gradient gel electrophoresis and 16S rRNA gene sequencing. We obtained 544 clones and 98 operational taxonomic units (OTUs) from six clone libraries. The top 10 OTUs represented 59.4% of the entire bacterial community. Betaproteobacteria (22.1%), Gammaproteobacteria (19.9%), Bacteroidetes (18.8%), and Firmicutes (11.4%) dominated in Lake Bosten. Although seasonal variations were recorded in BCC, the vertical changes observed were not significant. Water temperature and salinity were the most important factors shaping the dynamics of BCC. A low degree of overlap was observed in BCC between Lake Bosten and freshwater ecosystems, especially for Betaproteobacteria and Bacteroidetes. An RDP seqmatch analysis showed that 169 sequences (31%) were novel bacterial sequences (<97% similarity to the closest sequences in GenBank), which suggested that specific indigenous bacteria inhabit this oligosaline environment. Our results support bacterial endemicity being more common than previously considered, particularly in oligosaline lakes. An analysis of these communities may reveal how bacteria respond to increases in salinity and nutrients in the early stage of salinization and eutrophication.

Effects of Trophic Status and Temperature on Communities of Sedimentary Ammonia Oxidizers in Lake Taihu

To probe the responsiveness of ammonia oxidizers to environmental factors along different seasons in eutrophic lakes, we investigated the seasonal distribution of community structure and abundance of ammonia oxidizers in relation to the environmental factors in sediments within eutrophic Lake Taihu. We used terminal restriction fragment length polymorphism and real-time PCR to target the molecular biomarker gene of ammonia monooxygenase subunit A. Both phylogenetic analyses and the dominant terminal restriction fragments showed that archaeal ammonia oxidizers belonged to the Crenarchaeota Group I.1a and Crenarchaeota Group I.1b, while bacterial ammonia oxidizers included both Nitrosomonas-like and Nitrosospira-like species. The bacterial ammonia oxidizers were more diverse but less abundant than the ammonia-oxidizing archaea. Significant spatial differences in the ammonia-oxidizing archaeal community structure and abundance were found between the algae-dominated and the macrophyte-dominated regions, which suggest sedimentary trophic status is an important influence. In contrast, there was no significant correlation between bacterial ammonia oxidizer communities and sedimentary trophic status. There were pronounced seasonal variations in ammonia-oxidizing bacterial community structures, reflected by the absence of the Nitrosospira-like species in August and their presence in other months. Both the abundances of archaeal and bacterial ammonia oxidizers were highest in February. The correlation analyses between prokaryotic ammonia oxidizer communities and the investigated physicochemical variables demonstrated that the overlying water temperature was the dominant factor influencing the seasonal variations in ammonia oxidizer community structure and abundance. Supplemental materials are available for this article. Go to the publishers online edition of Geomicrobiology Journal to view the supplemental file.