Sedimentary bacterial communities in subtropical Beibu Gulf: Assembly process and functional profile

Distribution heterogeneity of sediment bacterial community in the river-lake system impacted by nonferrous metal mines: Diversity, composition and co-occurrence patterns

Although aquaculture provides a stable and high-quality source of food, the environmental effects related to large-scale industrial aquacultural activities have raised concern. To identify the influence of aquacultural activities on sedimentary bacterial communities, we collected surface and deeper sediments from a series of sites subjected to varying intensities of aquacultural activities within Eastern Lake Taihu, China. The associated physicochemical properties were measured, and 16S rRNA gene sequencing was applied to determine the related bacterial communities in sediment. The diversity and composition of bacterial communities within the surface sediments differed significantly from those of the deeper sediment samples. Marked differences were also found between the surface sediments of the aquaculture-influenced and non-aquaculturally influenced sites. More importantly, phylogenetic structure analysis indicated that stochastic processes dominated the assembly of the bacterial communities; yet, the relative contribution of deterministic processes to bacterial community assembly was greater in the aquacultural zones than in the non-aquacultural zones. Furthermore, we identified total phosphorus (TP) as the most important factor driving the assembly of bacterial communities influenced by aquaculture in sediment. These findings provide useful information for ecological assessments and remediation strategies for aquaculture-influenced ecosystems.

Immobilization of phosphorus in sediment-water system by hydrous iron oxide and hydrous iron oxide/calcite mixture under feed input condition

Although wetlands are one of the major ecosystems on the earth, information about the bacterial communities in different types of wetlands, especially in northeast China, has not yet been fully described. The aim of this study was to compare bacterial community compositions between sediment and water in different types of wetlands of northeast China. In this study, sediment and water samples were synchronously collected from different types of wetlands in northeast China. The bacterial communities were analyzed with Illumina MiSeq sequencing targeting the 16S rRNA gene. The results showed that the dominant phyla (relative abundance > 5%) across all sediment samples were Proteobacteria and Chloroflexi, while those across all water samples were Proteobacteria, Actinobacteria, and Bacteroidetes. Bacterial community composition was distinctly different among wetlands at the phylum and genus levels, and the indicator species for different sediment and water samples also varied greatly. The alpha diversity of bacterial community was higher in sediment samples than in water samples, and the lowest alpha diversity was detected in two coastal wetlands, both in sediment and in water samples. A heatmap analysis at the genus level and principal coordinate analysis revealed that all bacterial communities in sediment or in water samples were separated into distinct groups according to wetland type, and the communities in two coastal wetlands were highly similar to each other both in sediment and water samples, respectively. Bacterial communities in sediment were mainly affected by the available K content, followed by total C and total N, soil pH, etc., while in water, the communities were mainly affected by total P, total K, etc. The results revealed that bacterial community compositions between sediment and water samples were significantly different, and the communities in two coastal wetlands were more similar than those in other wetlands. The wetland sediment samples demonstrated higher community alpha diversity than the water samples, and alpha diversity was lowest in both the sediment and water of two coastal wetlands. Moreover, bacterial communities in sediment and water were driven by different environmental factors.

Microbes play central roles in ocean food webs and global biogeochemical processes. Yet, the information available regarding the highly diverse bacterial communities in these systems is not comprehensive. Here we investigated the diversity, assembly process, and species coexistence frequency of bacterial communities in seawater and sediment across ∼600 km of the eastern Chinese marginal seas using 16S rRNA gene amplicon sequencing. Our analyses showed that compared with seawater, bacterial communities in sediment possessed higher diversity and experienced tight phylogenetic distribution. Neutral model analysis showed that the relative contribution of stochastic processes to the assembly process of bacterial communities in sediment was lower than that in seawater. Functional prediction results showed that sulfate-reducing bacteria (SRB) were enriched in the core bacterial sub-communities. The bacterial diversities of both sediment and seawater were positively associated with the relative abundance of SRB. Co-occurrence analysis showed that bacteria in seawater exhibited a more complex interaction network and closer co-occurrence relationships than those in sediment. The SRB of seawater were centrally located in the network and played an essential role in sustaining the complex network. In addition, further analysis indicated that the SRB of seawater helped maintain the high stability of the bacterial network. Overall, this study provided further comprehensive information regarding the characteristics of bacterial communities in the ocean, and provides new insights into keystone taxa and their roles in sustaining microbial diversity and stability in ocean.

Bosten Lake is a typical inland lake in the arid and semiarid region of northwestern China. However, the influence of the dissolved organic matter (DOM) source composition on the bacterial community structure and diversity across various functional zones, as well as the role of the bacterial community structure in regulating DOM composition, remains unclear. In this study, we combined excitation-emission matrix (EEM) fluorescence spectroscopy with the parallel factor analysis (PARAFAC) method to investigate the characteristics and source distribution of the DOM fluorescence components in the water of Bosten Lake. The bacterial community characteristics in both water and sediment samples were analysed through high-throughput sequencing. The relationships among bacterial communities, DOM fluorescence components, and environmental factors were elucidated through principal component analysis and redundancy analysis. The results revealed that (1) the DOM of Bosten Lake contained three humus-like fractions and one protein-like fraction, with endogenous proteins being the primary source of DOM, complemented by exogenous humus inputs. (2) The richness and diversity of bacterial communities in sediments are significantly higher than those in water bodies, among which Proteobacteria dominate the composition of bacterial communities. (3) Ammonia nitrogen (NH4 +–N) significantly influenced the bacterial community composition, with microorganisms associated with the nitrogen cycle dominating the bacterial community in both water and sediment. Total dissolved solids (TDS) is a key factor influencing the composition of bacterial communities in water bodies. Across all sampling sites in Bosten Lake, the mean TDS concentration was 900 mg/L, with high levels causing structural damage to microbial enzymes (4) The DOM fluorescence component explained 64.9% of the variation in the bacterial community composition, indicating a strong response relationship between bacterial communities and DOM components. Overall, these results provide a scientific basis for the protection of the ecological environment of Bosten Lake.

Effects of polypropylene films and leached dissolved organic matters on bacterial community structure in mangrove sediments

In river-lake systems, sediment and water column are two distinct habitats harboring different bacterial communities which play a crucial role in biogeochemical processes. In this study, we employed Phylogenetic Investigation of Communities by Reconstruction of Unobserved States to assess the potential functions and functional redundancy of the bacterial communities in sediment and water in a eutrophic river-lake ecosystem, Poyang Lake in China. Bacterial communities in sediment and water had distinct potential functions of carbon, nitrogen, and sulfur metabolisms as well as phosphorus cycle, while the differences between rivers and the lake were inconspicuous. Bacterial communities in sediment had a higher relative abundance of genes associated with carbohydrate metabolism, carbon fixation pathways in prokaryotes, methane metabolism, anammox, nitrogen fixation, and dissimilatory sulfate reduction than that of water column. Bacterial communities in water column were higher in lipid metabolism, assimilatory nitrate reduction, dissimilatory nitrate reduction, phosphonate degradation, and assimilatory sulfate reduction than that of sediment bacterial communities. Furthermore, the variations in functional composition were closely associated to the variations in taxonomic composition in both habitats. In general, the bacterial communities in water column had a lower functional redundancy than in sediment. Moreover, comparing to the overall functions, bacterial communities had a lower functional redundancy of nitrogen metabolism and phosphorus cycle in water column and lower functional redundancy of nitrogen metabolism in sediment. Distance-based redundancy analysis and mantel test revealed close correlations between nutrient factors and functional compositions. The results suggested that bacterial communities in this eutrophic river-lake system of Poyang Lake were vulnerable to nutrient perturbations, especially the bacterial communities in water column. The results enriched our understanding of the bacterial communities and major biogeochemical processes in the eutrophic river-lake ecosystems.

Effects of microplastics on the structure and function of bacterial communities in sediments of a freshwater lake

STUDY OF BACTERIAL DIVERSITY IN MARINE SEDIMENTS IN TRUONG SA ARCHIPELAGO, VIET NAM BY TRADITIONAL CULTURE-DEPENDENT METHODS IN COMBINATION WITH DENATURING GRADIENT GEL ELECTROPHORESIS (DGGE)The denaturing gradient gel electrophoresis (DGGE) is an effective culture-independent technique for assessing diversity of microbial communities. In this study, the PCR-DGGE technique was applied for analyzing the diversity of bacterial communities in marine sediment in the Truong Sa archipelago (Spratly Islands), Vietnam, and a comparison with cultivable bacterial fraction was performed. Three sediment samples taken from different depths were used in the study. A total of 17 bacterial strains were isolated and divided into 6 groups based on their colony and cell morphologies. Comparative analyses of nearly full-length 16S rDNA sequences retrieved from six representative strains of these morphologically distinguished groups indicated that they were most closely related to Bacillus amyloliquefaciens, Bacillus filamentosus, Bacillus endophyticus, Bacillus licheniformis, Pseudomonas balearica, and Raoultella ornithinolytica. The PCR-DGGE analyses carried out with the three sediment samples showed relatively diverse bacterial communities with 9 distinct bands, 6 of which were related to the isolated representatives, whereas the other three were identified as Vibrio proteolyticus, Priestia filamentosa, and Clostridium halophilum. Thus, by applying the PCR-DGGE technique, more thorough information on bacterial communities in the sediment of Truong Sa archipelago could be elucidated, providing useful information for further studies on the conservation and utilization of microbial resources in this ecosystem.

Microbial communities in sediment are an important indicator linking to environmental pollution in urban river systems. However, how the diversity and structure of bacterial communities in sediments from an urban river network respond to different environmental factors has not been well studied. The goal of this study was to understand the patterns of bacterial communities in sediments from a highly dense urbanized river network in the lower Yangtze River Delta by Illumina MiSeq sequencing. The correlations between bacterial communities, the environmental gradient and geographical distance were analyzed by redundancy analysis (RDA) and network methods. The diversity and richness of bacterial community in sediments increased from upstream to downstream consistently with the accumulation of nutrient in the urban river network. Bacterial community composition and structure showed obvious spatial changes, leading to two distinct groups, which were significantly related to the characteristics of nutrient and heavy metal in sediments. Humic substance, available nitrogen, available phosphorus, Zn, Cu, Hg and As were selected as the key environmental factors shaping the bacterial community in sediments based on RDA. The co-occurrence patterns of bacterial networks showed that positive interaction between bacterial communities increased but the connectivity among bacterial genera and stability of sediment ecosystem reduced under a higher content of nutrient and heavy metal in average. The sensitive and ubiquitous taxa with an overproportional response to key environmental factors were detected as indicator species, which provided a novel method for the prediction of the pollution risk of sediment in an urban river network.

Urban rivers play a critical role in maintaining ecological functions and ensuring water security, yet their microbial communities remain vulnerable to seasonal and anthropogenic disturbances. In this study, we employed 16S rRNA gene sequencing along with multivariate statistical methods to systematically investigate the characteristics of bacterial community composition and assembly mechanisms in river water and sediment of the Yellow River (Zhengzhou Section) across different seasons. Based on high-throughput sequencing and canonical correspondence analysis, bacterial community diversity in river water was found to be significantly higher during the wet season than in the dry season, primarily driven by water temperature, nutrient concentrations, and electrical conductivity. Conversely, bacterial community in sediment remained more stable, though pollution-tolerant bacteria became dominant in sediment with elevated pollutant concentrations during the dry season. Analyses of community assembly mechanisms showed that bacterial community in river water and sediment during wet season were mainly influenced by environmental selective pressures, including stochastic dispersal and physic-chemical barriers. Meanwhile, bacterial community in river water and sediment during dry season were more dominated by deterministic processes. Principal Coordinate Analysis and PERMANOVA further validated the significant impact of seasonal variation on bacterial community structure in both river water and sediment. These findings offer practical guidance for river ecosystem management and support the optimization of water use and environmental protection strategies in the Yellow River.

The spatial and seasonal variations of bacterial community structure and influencing factors in river sediments

Recovery trajectories of the bacterial community at distances in the receiving river under wastewater treatment plant discharge

Effect of salinity and algae biomass on mercury cycling genes and bacterial communities in sediments under mercury contamination: Implications of the mercury cycle in arid regions.