Plankton community composition in the Three Gorges Reservoir Region revealed by PCR-dGGE and its relationships with environmental factors

Global profiling of ribosomal protein acetylation reveals essentiality of acetylation homeostasis in maintaining ribosome assembly and function

Acetylation is a global post-translational modification that regulates various cellular processes. Bacterial acetylomic studies have revealed extensive acetylation of ribosomal proteins. However, the role of acetylation in regulating ribosome function remains poorly understood. In this study, we systematically profiled ribosomal protein acetylation and identified a total of 289 acetylated lysine residues in 52 ribosomal proteins (r-proteins) from Salmonella Typhimurium. The majority of acetylated lysine residues of r-proteins were found to be regulated by both acetyltransferase Pat and metabolic intermediate acetyl phosphate. Our results show that acetylation plays a critical role in the assembly of the mature 70S ribosome complex by modulating r-proteins binding to rRNA. Moreover, appropriate acetylation is important for the interactions between elongation factors and polysomes, as well as regulating ribosome translation efficiency and fidelity. Dysregulation of acetylation could alter bacterial sensitivity to ribosome-targeting antibiotics. Collectively, our data suggest that the acetylation homeostasis of ribosomes is crucial for their assembly and function. Furthermore, this mechanism may represent a universal response to environmental signals across different cell types.

Diversity and Co-Occurrence Patterns of Soil Bacterial and Fungal Communities of Chinese Cordyceps Habitats at Shergyla Mountain, Tibet: Implications for the Occurrence

Chinese Cordyceps is a well-known medicinal larva-fungus symbiote distributed in the Qinghai-Tibetan Plateau and adjacent areas. Previous studies have involved its artificial cultivation but commercial cultivation is difficult to perform because the crucial factors triggering the occurrence of Chinese Cordyceps are not quite clear. The occurrence of Chinese Cordyceps is greatly affected by the soil environment, including the soil’s physicochemical and microecological properties. In this study, the effects of these soil properties on the occurrence of Chinese Cordyceps were investigated. The results show that the physicochemical properties, including easily oxidizable organic carbon (EOC), soil organic carbon (SOC), humic acid carbon (HAC), humin carbon (HMC), and pH, might be negatively related to the occurrence of Chinese Cordyceps, and soil water content (SWC) might be positively related. Several soil physicochemical parameters (pH, SOC, HMC, HAC, available potassium (APO), available phosphorus (APH), microbial biomass carbon (MBC), and the ratio of NH₄⁺ to NO₃⁻ (NH₄⁺/NO₃⁻)) and microbial properties interact and mix together, which might affect the occurrence of Chinese Cordyceps. Soil microbial community structure was also a possible factor, and a low level of bacterial and fungal diversity was suitable for the occurrence of Chinese Cordyceps. The intra-kingdom network revealed that a closer correlation of the bacterial community might help the occurrence of Chinese Cordyceps, while a closer correlation of the fungal community might suppress it. The inter-kingdom network revealed that the occurrence rate of Chinese Cordyceps might be negatively correlated with the stability of the correlation state of the soil habitat. In conclusion, this study shows that soil physicochemical properties and microbial communities could be greatly related with the occurrence of Chinese Cordyceps. In addition, soil physicochemical properties, the level of bacterial and fungal diversity, and correlations of bacterial and fungal communities should be controlled to a certain level to increase the production of Chinese Cordyceps in artificial cultivation.

Variation of Diatoms and Silicon in a Tributary of the Three Gorges Reservoir: Evidence of Interaction

To gain insight into the variation of diatoms and silicon and their interaction in a tributary of the Three Gorges Reservoir (TGR), the Xiangxi River was chosen as a representative tributary, and dissolved silicon (DSi) and biogenic silicon (BSi) were investigated monthly from February 2015 to December 2016, accompanied by diatom species composition and cell density analyses. The results showed that the diatom population and its relationship with silicon concentration were significantly different between the lacustrine zone and riverine zone (P < 0.05). The cell density in the lacustrine zone (6.20 × 105 ~ 9.97 × 107 cells/L) was significantly higher than that in the riverine zone (7.90 × 104 ~ 1.81 × 107 cells/L) (P < 0.01). Water velocity was a key factor in determining the diatom species composition. Centric diatoms were the dominant species in the lacustrine zone, and pennate diatoms were the primary species in the riverine zone, which indicated that centric diatoms outcompete pennate diatoms under the influence of the TGR’s operation. BSi showed a significant linear relationship with the cell density. DSi had a significant negative relationship with the cell density in the lacustrine zone, while no significant relationship was found in the riverine zone. This meant that the main contributor to BSi was diatoms, but DSi was primarily affected by water discharge, not diatom uptake. It could be deduced that the spatiotemporal heterogeneity of diatom communities was influenced by the TGR’s operation. Silicon cycling in the tributary was significantly affected by diatoms, and the current concentration of DSi was sufficient for diatom growth and showed no significant effects on the diatom community.

Responses of spatial-temporal dynamics of bacterioplankton community to large-scale reservoir operation: a case study in the Three Gorges Reservoir, China

Large rivers are commonly regulated by damming, yet the effects of such disruption on bacterioplankton community structures have not been adequately studied. The aim of this study was to explore the biogeographical patterns present under dam regulation and to uncover the major drivers structuring bacterioplankton communities. Bacterioplankton assemblages in the Three Gorges Reservoir (TGR) were analyzed using Illumina Miseq sequencing by comparing seven sites located within the TGR before and after impoundment. This approach revealed ecological and spatial-temporal variations in bacterioplankton community composition along the longitudinal axis. The community was dynamic and dominated by Proteobacteria and Actinobacteria phyla, encompassing 39.26% and 37.14% of all sequences, respectively, followed by Bacteroidetes (8.67%) and Cyanobacteria (3.90%). The Shannon-Wiener index of the bacterioplankton community in the flood season (August) was generally higher than that in the impoundment season (November). Principal Component Analysis of the bacterioplankton community compositions showed separation between different seasons and sampling sites. Results of the relationship between bacterioplankton community compositions and environmental variables highlighted that ecological processes of element cycling and large dam disturbances are of prime importance in driving the assemblages of riverine bacterioplankton communities.

Profiling of Sediment Microbial Community in Dongting Lake before and after Impoundment of the Three Gorges Dam

The sediment microbial community in downstream-linked lakes can be affected by the operation of large-scale water conservancy projects. The present study determined Illumina reads (16S rRNA gene amplicons) to analyze and compare the bacterial communities from sediments in Dongting Lake (China) before and after impoundment of the Three Gorges Dam (TGD), the largest hydroelectric project in the world. Bacterial communities in sediment samples in Dongting Lake before impoundment of the TGD (the high water period) had a higher diversity than after impoundment of the TGD (the low water period). The most abundant phylum in the sediment samples was Proteobacteria (36.4%–51.5%), and this result was due to the significant abundance of Betaproteobacteria and Deltaproteobacteria in the sediment samples before impoundment of the TGD and the abundance of Gammaproteobacteria in the sediment samples after impoundment of the TGD. In addition, bacterial sequences of the sediment samples are also affiliated with Acidobacteria (11.0% on average), Chloroflexi (10.9% on average), Bacteroidetes (6.7% on average), and Nitrospirae (5.1% on average). Variations in the composition of the bacterial community within some sediment samples from the river estuary into Dongting Lake were related to the pH values. The bacterial community in the samples from the three lake districts of Dongting Lake before and after impoundment of the TGD was linked to the nutrient concentration.

Temporal Patterns in Bacterioplankton Community Composition in Three Reservoirs of Similar Trophic Status in Shenzhen, China

The bacterioplankton community composition's (BCC) spatial and temporal variation patterns in three reservoirs (Shiyan, Xikeng, and LuoTian Reservoir) of similar trophic status in Bao'an District, Shenzhen (China), were investigated using PCR amplification of the 16S rDNA gene and the denaturing gradient gel electrophoresis (DGGE) techniques. Water samples were collected monthly in each reservoir during 12 consecutive months. Distinct differences were detected in band number, pattern, and density of DGGE at different sampling sites and time points. Analysis of the DGGE fingerprints showed that changes in the bacterial community structure mainly varied with seasons, and the patterns of change indicated that seasonal forces might have a more significant impact on the BCC than eutrophic status in the reservoirs, despite the similar Shannon-Weiner index among the three reservoirs. The sequences obtained from excised bands were affiliated with Cyanobacteria, Firmicutes, Bacteriodetes, Acidobacteria, Actinobacteria, Planctomycetes, and Proteobacteria.

Responses of bacterial communities in seagrass sediments to polycyclic aromatic hydrocarbon-induced stress

The seagrass meadows represent one of the highest productive marine ecosystems, and have the great ecological and economic values. Bacteria play important roles in energy flow, nutrient biogeochemical cycle and organic matter turnover in marine ecosystems. The seagrass meadows are experiencing a world-wide decline, and the pollution is one of the main reasons. Polycyclic aromatic hydrocarbons (PAHs) are thought be the most common. Bacterial communities in the seagrass Enhalus acoroides sediments were analyzed for their responses to PAHs induced stress. Dynamics of the composition and abundance of bacterial communities during the incubation period were explored by polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative PCR assay, respectively. Both the incubation time and the PAHs concentration played significant roles in determining the microbial diversity, as reflected by the detected DGGE bands. Analysis of sequencing results showed that the Gammaproteobacteria were dominant in the seagrass sediments, accounting for 61.29 % of all sequenced bands. As PAHs could be used as carbon source for microbes, the species and diversity of the PAH-added groups (group 1 and 2) presented higher Shannon Wiener index than the group CK, with the group 1 showing the highest values almost through the same incubation stage. Patterns of changes in abundance of the three groups over the experiment time were quite different. The bacterial abundance of the group CK and group 2 decreased sharply from 4.15 × 10(11) and 6.37 × 10(11) to 1.17 × 10(10) and 1.07 × 10(10) copies/g from day 2 to 35, respectively while bacterial abundance of group 1 increased significantly from 1.59 × 10(11) copies/g at day 2 to 8.80 × 10(11) copies/g at day 7, and then dropped from day 14 till the end of the incubation. Statistical analysis (UMPGA and PCA) results suggested that the bacterial community were more likely to be affected by the incubation time than the concentration of the PAHs. This study provided the important information about dynamics of bacterial community under the PAHs stress and revealed the high bacterial diversity in sediments of E. acoroides. Investigation results also indicated that microbial community structure in the seagrass sediment were sensible to the PAHs induced stress, and may be used as potential indicators for the PAHs contamination.

Impacts of the Three Gorges Dam on microbial structure and potential function

The Three Gorges Dam has significantly altered ecological and environmental conditions within the reservoir region, but how these changes affect bacterioplankton structure and function is unknown. Here, three widely accepted metagenomic tools were employed to study the impact of damming on the bacterioplankton community in the Xiangxi River. Our results indicated that bacterioplankton communities were both taxonomically and functionally different between backwater and riverine sites, which represent communities with and without direct dam effects, respectively. There were many more nitrogen cycling Betaproteobacteria (e.g., Limnohabitans), and a higher abundance of functional genes and KEGG orthology (KO) groups involved in nitrogen cycling in the riverine sites, suggesting a higher level of bacterial activity involved in generating more nitrogenous nutrients for the growth of phytoplankton. Additionally, the KO categories involved in carbon and sulfur metabolism, as well as most of the detected functional genes also showed clear backwater and riverine patterns. As expected, these diversity patterns all significantly correlated with environmental characteristics, confirming that the bacterioplankton communities in the Xiangxi River were really affected by environmental changes from the Three Gorges Dam. This study provides a first comparative metagenomic insight for evaluating the impacts of the large dam on microbial function.

Community dynamics of prokaryotic and eukaryotic microbes in an estuary reservoir

This study demonstrates both prokaryotic and eukaryotic community structures and dominant taxonomies in different positions of the greatest estuary reservoir for drinking water source in the world in four seasons of one year using 454 pyrosequencing method with total of 312,949 16S rRNA and 374,752 18S rRNA gene fragments, including 1,652 bacteria OTUs and 1,182 fungus OTUs. During winter and spring, the community composition at the phylum level showed that microorganisms had similar structures but their quantities were different. Similarly, obvious changes at the genus level were observed among the samples taken in winter and spring between summer and fall. Microorganisms located the reservoir inlet were founded to be different from those in rear at both phylum and genus level. Air temperature had a stronger effect than sampling location on the microbial community structure. Total nitrogen and dissolved oxygen were algae-monitoring indicators during the whole year. Moreover, Bacillus was an efficient indicator during summer and autumn for bacteria OTUs.

Estimating cyanobacteria community dynamics and its relationship with environmental factors

The cyanobacteria community dynamics in two eutrophic freshwater bodies (Tiegang Reservoir and Shiyan Reservoir) was studied with both a traditional microscopic counting method and a PCR-DGGE genotyping method. Results showed that cyanobacterium Phormidium tenue was the predominant species; twenty-six cyanobacteria species were identified in water samples collected from the two reservoirs, among which fourteen were identified with the morphological method and sixteen with the PCR-DGGE method. The cyanobacteria community composition analysis showed a seasonal fluctuation from July to December. The cyanobacteria population peaked in August in both reservoirs, with cell abundances of 3.78 × 10⁸ cells L^-1 and 1.92 × 10⁸ cells L^-1 in the Tiegang and Shiyan reservoirs, respectively. Canonical Correspondence Analysis (CCA) was applied to further investigate the correlation between cyanobacteria community dynamics and environmental factors. The result indicated that the cyanobacteria community dynamics was mostly correlated with pH, temperature and total nitrogen. This study demonstrated that data obtained from PCR-DGGE combined with a traditional morphological method could reflect cyanobacteria community dynamics and its correlation with environmental factors in eutrophic freshwater bodies.

Linking fluorescence spectroscopy to diffuse soil source for dissolved humic substances in the Daning River, China

Dissolved organic matter collected in Daning River (China) in July 2009 was investigated with parallel factor analysis (PARAFAC) and fluorescence spectroscopy with the aim of identifying the origin of dissolved humic substance (HS) components. Two HS-like fluorescence components (peak M and C) with excitation/emission (ex/em) maxima at 305/406 nm and 360/464 nm showed relatively uniform distribution in the vertical direction for each sampling site but a trend of accumulation down the river, independent of the highly heterogeneous water environment as implicated by water quality parameters (i.e., water temperature, algae density, chlorophyll a, dissolved oxygen, dissolved organic carbon, pH, conductivity and turbidity), while an amino acid/protein-like component (peak T; ex/em = 280/334 nm) was quite variable in its spatial distribution, implying strong influence from point sources (e.g. sewage discharge) and local microbial activities. The fluorescence intensity (F max in Raman units) at these ex/em wavelength pairs fell in the range of 0.031-0.358, 0.051-0.224 and 0.026-0.115 for peak T, M and C, respectively. In addition, the F max values of peak C covaried with M (i.e. C = 0.503 ×M, p < 0.01, R (2) = 0.973). Taken together, these results indicate that peak M and C originated primarily and directly from the same soil sources that were diffusive in the catchment, but peak T was more influenced by local point sources (e.g. wastewater discharge) and in situ microbial activities. This study presents new insights into the currently controversial origin of some HS components (e.g."peak M", as commonly referred to in the literature). This study highlights that natural water samples should be collected at various depths in addition to along a river/stream flow path so as to better evaluate the origin of HS fluorescence components.

Effects of wet and dry seasons on the aquatic bacterial community structure of the Three Gorges Reservoir

This study investigated effects of wet and dry seasons on the bacterial community structure of the Three Gorges Reservoir by using denaturing gradient gel electrophoresis analysis of the PCR-amplified bacterial 16S rRNA gene. Bacterial diversity, as determined by the Shannon index, the Simpson's index, and the Richness, dramatically changed in between the dry and wet seasons. The changes in the diversity and relative abundance of microbial populations among the five sites during the wet season have become more marked than those observed during the dry season. Furthermore, cluster analysis also showed these changes. The phylogenetic analysis indicated that Betaproteobacteria is the dominant population, followed by Actinobacterium, in both the wet season and dry season. The water quality parameters were quite stable at all five sites during the same season but noticeably varied from season to season. Canonical correspondence analysis also indicated that the changes in the bacterial community composition were primarily correlated with the variations in temperature, transparency, and the concentrations of NH4 (+)-N. Slight changes in bacterial community composition among the five sites during the dry season were correlated with different environments. However, during the wet season, major changes were correlated not only with environments, but also it may be associated with the bacterial populations from the surrounding areas and tributaries of the Three Gorges Reservoir.

Spatial variation of bacterial community structure of the Northern South China Sea in relation to water chemistry

Spatial distribution, diversity and composition of bacterial communities of the northern South China Sea (SCS) surface water and the relationship with the in situ environmental chemistry were investigated. Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) was used to investigate the bacterial community structure. The DGGE gel showed that each sample harbored a distinct bacterial community structure and spatial variations of bacterial community composition among all samples were obviously. A total of 17 intensive bands were excised and the sequence analysis of these DGGE bands revealed that Proteobacteria were the dominant bacterial group of surface water in the north part of SCS. Results of the taxonomic analysis showed that the communities consisted of Proteobacteria (α-subdivision, β-subdivision, γ-subdivision), Actinobacteria, Cyanobacteria, Bacteroidetes and Firmicutes. Unweighted pair group method with arithmetic averages clustering of the sampling stations indicated that all stations were classified mainly based on geographical proximity. Canonical correspondence analysis (CCA) was employed to further investigate the relationships between DGGE band pattern and the environmental variables and the first two CCA ordination axes suggested that the structure of the bacterial community was significantly correlated with the variables of nitrate (F = 1.24, P < 0.05).

Seasonal variation of Microcystis in Lake Taihu and its relationships with environmental factors

In order to monitor the changes of Microcystis along with temporal and spatial variations, seasonal variation of Microcystis in Lake Taihu was investigated by 16S-23S rRNA internal transcribed spacer denaturing gradient gel electrophoresis (16S-23S rRNA-ITS DGGE) and microscopic evaluation. Samples were collected quarterly at four sites (River Mouth, Meiliang Bay, Cross Area, and Lake Center) from August 2006 to April 2007. Results showed that Microcystis dominated total phytoplankton abundance at the four sites in all seasons except winter. The average annual abundance of Microcystis was relatively high at River Mouth and Meiliang Bay, reaching 81.22 x 10(6) and 61.32 x 10(6) cells/L, respectively. For temporal variations, Shannon-Wiener diversity index (H') according to DGGE profile revealed the richness of Microcystis in summer (H' = 1.375 +/- 0.034) and winter (H' = 1.650 +/- 0.032) was lower than that in spring (H' = 2.078 +/- 0.031) and autumn (H' = 2.365 +/- 0.032) (P <0.05). While for spatial variations, the richness of Microcystis at River Mouth (H' = 2.015 +/- 0.074) was higher than at other sites during four seasons (P < 0.01). Very few differences of Microcystis diversity in the same season were observed among the other three sites (P > 0.05). Canonical correspondence analysis (CCA) was performed to elucidate the relationships between Microcystis operational taxonomic units (OTUs) composition and the environmental factors. Results of CCA revealed that temperature was strongly positively correlated with the first axis (r = 0.963), while TSS was negative correlated with the second axis (r = -0.716). Phylogenetic tree based on the sequencing results of target bands on DGGE gel indicated that samples collected in summer and winter constituted two separated clusters.