Microbial community structure and metabolic potential in the coastal sediments around the Yellow River Estuary

Vertical distribution characteristics and influencing factors of bacterial communities in a sediment profile of Bohai Sea

Research on the diversity of bacterial communities and their influencing factors in the sediments of the Bohai Sea remains limited. This study used high-throughput sequencing technology to explore the vertical distribution characteristics and influencing factors (depth, heavy metals, and nutrients) of bacterial communities in sediment core B18 from the Bohai Sea. Our results indicated that the dominant phyla were Proteobacteria, Desulfobacterota, Acidobacteriota, Chloroflexi, Bacteroidota, and Actinobacteriota, with Alphaproteobacteria, Gammaproteobacteria, Bacteroidia, Anaerolineae, Thermoanaerobaculia, and Desulfobulbia as the dominant classes. Depth exerted a pronounced influence on bacterial community diversities, with bacterial communities (excluding Proteobacteria, Bacteroidota, and Verrucomicrobiota) displaying a positive correlation with depth. Anaerobic bacteria like Desulfobacterota and Chloroflexi were more prevalent in the deeper sediment layers. In contrast, most bacterial communities exhibited a negative relationship with heavy metal concentrations. Notably, As, Pb, and Cd contents exhibited relatively high levels of pollution and had a considerably negative effect on bacterial diversity. Bacterial communities with adaptability to heavy metals (such as Proteobacteria, Bacteroidota, Verrucomicrobiota) demonstrated a competitive advantage in the Bohai Sea sediment bacterial community compositions. Meanwhile, bacterial communities related to nitrogen, phosphorus, and sulfur cycling (Proteobacteria, Bacteroidota, Verrucomicrobiota) were relatively abundant. This study offers valuable insights into the diversity and compositions of bacterial communities in the Bohai Sea sediment profile by elucidating the vertical distribution and influencing factors of sediment bacterial communities.

Ecological niche and environmental adaptability of denitrifiers in the yellow river estuary

Our study explores the ecological niche and environmental adaptability of nirS- and nirK-type denitrifying microbial in the Yellow River estuary. Our findings indicate that anthropogenic nitrogen loading has precipitated substantial ecological challenges within these ecosystems. By assessing the biogeographical distribution and community assembly mechanisms of denitrifying microbial, we identified salinity as a pivotal factor influencing their diversity and prevalence, with increased salinity levels positively associated with enhanced microbial populations. Additionally, our research suggests that stochastic processes predominantly govern the assembly of nirS-type communities, whereas deterministic processes are more influential for nirK-type communities. Network analysis further revealed that denitrifying microbial communities in low-salinity areas exhibit greater complexity and modularity. Integrating microbial ecological and phylogenetic analysis with structural equation modeling, we established a link between microbial community characteristics and denitrification rates, underscoring the significance of microbial community understanding for effective ecosystem management.

Bacterial community composition and metabolic characteristics of three representative marine areas in northern China

Bacteria are essential components of ecosystems, participating in nutrient cycling and biogeochemical processes, and playing a crucial role in maintaining the stability of marine ecosystems. However, the biogeographic distribution patterns of bacterial diversity and metabolic functions in the estuarine and coastal areas of northern China remain unclear. Here, we used metagenomic sequencing to investigate the bacterial community composition and metabolic functions in sediments from the adjacent waters of the Yellow River Estuary, the Yellow Sea Cold Water Mass, and the adjacent waters of the Yangtze River Estuary. Among the 9164 species that were found, the most dominant microbial communities are Pseudomonadota, Actinomycetota, Bacteroidota, and Bacillota, but there are significant differences in the species composition in these three typical habitats. Amino acid metabolism and carbohydrate metabolic pathways were highly enriched. Glycoside hydrolases (GHs) predominate in carbon metabolism across all samples. In nitrogen metabolic pathway, genes related to organic degradation and synthesis are more abundant in the Yellow River Estuary than the other two habitats. In sulfur metabolic pathway, genes involved in assimilatory sulfate reduction are significantly enriched. Assimilatory sulfate reduction might be crucial for sulfur metabolism in coastal regions, with a full assimilatory nitrate reduction pathway found in Desulfobacterota. This research offers insights into the compositional diversity, metabolic functions, and biogeographic distribution patterns of bacterial communities in sediments from typical marine areas of northern China.

Synchronous control of nitrogen and phosphorus release from sediments in shallow lakes under wind disturbance by modified zeolite and Ca/Al-based sludge combination

To inhibit eutrophication caused by endogenous pollutants release, the experiment explored the efficiency and mechanism of the synchronous control of nitrogen (N) and phosphorus (P) release from sediments in shallow lakes under wind disturbance by modified Ca/Al-based sludge (MS) and modified zeolite (MZ). High-temperature calcination and NaCl impregnation increased the pore volume of MS and Na+ content of MZ, and the adsorption capacity of MS for PO43--P and MZ for NH4+-N was as high as 42.01 and 20.28 mg g-1. The results of a 90-day incubation experiment showed that the addition of MS and MZ increased the abundance of Thauera, Nitrospira, Denitratisoma, and Clostridium, while decreasing the proportion of Proteus Hauser and Saccharimonadales, thereby reducing the active N and P contents in sediments through microbial transformation. At the same time, the efficient adsorption performance of the MS and MZ resulted in a significant decrease in pollutants in the interstitial water and sediments. In addition, sediment resuspension caused by wind disturbance increased the contact between sediments and remediation agents, resulting in the action depth of covering materials exceeding 100 mm. Compared to adding MS or MZ alone, the combination of the two (MSZG) could synchronously, efficiently, and stably inhibit N and P release. Under the coupling effects of physical interception, physicochemical adsorption, and biotransformation, the average TN, NH4+-N, TP, and PO43--P in the overlying water of the MSZG decreased by 72.13%, 88.92%, 69.28%, and 81.26%, respectively, compared to Control, which satisfying the Class III standard for surface water. Therefore, this study could provide reference for controlling endogenous release, improving eutrophication in shallow lakes under wind disturbance, and recycling residual sludge from sewage plants.

Ions and nanoparticles of Ag and/or Cd metals in a model aquatic microcosm: Effects on the abundance, diversity and functionality of the sediment bacteriome

Metals can be adsorbed on particulate matter, settle in sediments and cause alterations in aquatic environments. This study assesses the effect of Ag and/or Cd, both in ionic and nanoparticle (NP) forms, on the microbiome of sediments. For that purpose, aquatic controlled-microcosm experiments were exposed to an environmentally relevant and at tenfold higher doses of each form of the metals. Changes in the bacteriome were inferred by 16S rDNA sequencing. Ionic Ag caused a significant decrease of several bacterial families, whereas the effect was opposite when mixed with Cd, e.g., Desulfuromonadaceae family; in both cases, the bacteriome functionalities were greatly affected, particularly the nitrogen and sulfur metabolism. Compared to ionic forms, metallic NPs produced hardly any change in the abundance of microbial families, although the α-biodiversity of the bacteriome was reduced, and the functionality altered, when exposed to the NPs´ mixture. Our goal is to understand how metals, in different forms and combinations, released into the environment may endanger the health of aquatic ecosystems. This work may help to understand how aquatic metal pollution alters the structure and functionality of the microbiome and biogeochemical cycles, and how these changes can be addressed.

Response of microbial communities to exogenous nitrate nitrogen input in black and odorous sediment

Since nitrate nitrogen (NO3--N) input has proved an effective approach for the treatment of black and odorous river waterbody, it was controversial whether the total nitrogen concentration standard should be raised when the effluent from the sewage treatment plant is discharged into the polluted river. To reveal the effect of exogenous nitrate (NO3--N) on black odorous waterbody, sediments with different features from contaminated rivers were collected, and the changes of physical and chemical characteristics and microbial community structure in sediments before and after the addition of exogenous NO3--N were investigated. The results showed that after the input of NO3--N, reducing substances such as acid volatile sulfide (AVS) in the sediment decreased by 80 % on average, ferrous (Fe2+) decreased by 50 %, yet the changing trend of ammonia nitrogen (NH4+-N) in some sediment samples increased while others decreased. High-throughput sequencing results showed that the abundance of Thiobacillus at most sites increased significantly, becoming the dominant genus in the sediment, and the abundance of functional genes in the metabolome increased, such as soxA, soxX, soxY, soxZ. Network analysis showed that sediment microorganisms evolved from a single sulfur oxidation ecological function to diverse ecological functions, such as nitrogen cycle nirB, nirD, nirK, nosZ, and aerobic decomposition. In summary, inputting an appropriate amount of exogenous NO3--N is beneficial for restoring and maintaining the oxidation states of river sediment ecosystems.

Marine sediments are identified as an environmental reservoir for Escherichia coli: comparing signature-based and novel amplicon sequencing approaches for microbial source tracking

Viable Escherichia coli were detected in sediments near a point of wastewater discharge in a marine coastal environment in Sweden. Since high concentrations were found in the sediments nearest the pipe, this suggested that treated wastewater effluent was the source of the microbes. In order to examine this hypothesis, different bioinformatics approaches were applied using 16S rRNA gene V3-V4 amplicon sequences from the sediments. Both signature-based source tracking using sequence libraries describing known sources of fecal water pollution (SourceTracker); and, a curated source tracking method, indicated that sediments were contaminated with wastewater. The results from the curated approach were independently confirmed using differential abundance analysis (DESeq2). A number of taxa originating from wastewater were identified which can be used to describe contamination of the sediments, and examine the spread of these specific taxa, even at low relative abundance, along the urban coast. Sequences of phylum Bacteroidetes (such as Bacteroides and Prevotella) and Firmicutes (such as Romboutsia) increased in sediments with higher concentrations of E. coli. In addition, sequences from Trichococcus are proposed as an indicator for treated wastewater. All three source tracking approaches, and the detection of viable E. coli, suggest that urban sediments can be a reservoir for indicator bacteria.

Response of microbial community to different media in start-up period of Annan constructed wetland in Beijing of China

Microbial community, as the decomposers of constructed wetland (CW), plays crucial role in biodegradation and biotransformation of pollutants, nutrient cycling and the maintenance of ecosystem balance. In this study, 9 water samples, 6 sediment samples, and 8 plant samples were collected in Annan CW, which has the functions of water treatment and wetland culture park. The characteristics of microbial community structure in different media were illustrated by using of high-throughput sequencing-based metagenomics approach and statistical analysis. Meanwhile, this study identified and classified human pathogens in CW to avoid potential risks to human health. The results showed that dominant bacteria phyla in CW include Proteobacteria, Bacteroides, Actinobacteria, Firmicutes and Verrucomicrobia. The distribution of microorganisms in three media is different, but not significant. And the pH and DO profoundly affected microbe abundance, followed by water temperature. The microbial diversity in sediments is the highest, which is similar with the detection of human pathogens in sediments. Moreover, compared with Calamus, Lythrum salicaria and Reed, Scirpus tabernaemontani has fewer pathogenic microorganisms. The distribution of microorganisms in the CW is complex, and a variety of human pathogens are detected, which is more prone to create potential risks to human health and should receive additional attention.

Unexpected enrichment of antibiotic resistance genes and organic remediation genes in high-altitude lakes at Eastern Tibetan Plateau

Elevation has a strong effect on aquatic microbiome. However, we know little about the effects of elevation on functional genes, especially antibiotic resistance genes (ARGs) and organic remediation genes (ORGs) in freshwater ecosystems. In this study, we analyzed five classes of functional genes including ARGs, metal resistance genes (MRGs), ORGs, bacteriophages, and virulence genes between two high-altitude lakes (HALs) and two low-altitude lakes (LALs) in Mountain Siguniang at Eastern Tibetan Plateau by means of GeoChip 5.0. No differences (Student's t-test, p > 0.05) of gene richness including ARGs, MRGs, ORGs, bacteriophages, and virulence genes in HALs and LALs were found. The abundance of most ARGs and ORGs was higher in HALs than in LALs. For MRGs, the abundance of macro metal resistance genes of potassium, calcium, and aluminum was higher in HALs than in LALs (Student's t-test, p < 0.05; all Cohen's d > 0.8). The abundance of some heavy metal resistance genes of lead and mercury was lower in HALs than in LALs (Student's t-test, p < 0.05; all Cohen's d < -0.8). The composition of these functional genes in HALs differed significantly from in LALs. The functional gene network in HALs was also more complex than that in LALs. We speculate that enrichment of ARGs and ORGs in HALs is related to different microbial communities, exogenous ARGs, and enriched persistent organic pollutants through long-range atmospheric transport driven by the Indian monsoon. This study highlights the unexpected enrichment of ARGs, MRGs, and ORGs in remote lakes at high elevations.

Contrasting archaeal and bacterial community assembly processes and the importance of rare taxa along a depth gradient in shallow coastal sediments

Marine microbial communities assemble along a sediment depth gradient and are responsible for processing organic matter. Composition of the microbial community along the depth is affected by various biotic and abiotic factors, e.g., the change of redox gradient, the availability of organic matter, and the interactions of different taxa. The community structure is also subjected to some random changes caused by stochastic processes of birth, death, immigration and emigration. However, the high-resolution shifts of microbial community and mechanisms of the vertical assembly processes in marine sediments remain poorly described. Archaeal and bacterial communities were analyzed based on 16S rRNA gene amplicon sequencing and metagenomes in the Bohai Sea sediment samples. The archaeal community was dominated by Thaumarchaeota with increased alpha diversity along depth. Proteobacteria was the dominant bacterial group with decreased alpha diversity as depth increased. Sampling sites and depths collectively affected the beta-diversity for both archaeal and bacterial communities. The dominant mechanism determining archaeal community assembly was determinism, which was mostly contributed by homogeneous selection, i.e., consistent selection pressures in different locations or depths. In contrast, bacterial community assembly was dominated by stochasticity. Co-occurrence networks among different taxa and key functional genes revealed a tight community with low modularity in the bottom sediment, and disproportionately more interactions among low abundant ASVs. This suggests a significant contribution to community stabilization by rare taxa, and suggests that the bottom layer, rather than surface sediments may represent a hotspot for benthic microbial interactions.