Sediment Bacterial Communities Research Articles

Wastewater treatment plant effluent discharge decreases bacterial community diversity and network complexity in urbanized coastal sediment

The wastewater treatment plant (WWTP) effluent discharge affects the microorganisms in the receiving water bodies. Despite the ecological significance of microbial communities in pollutant degradation and element cycling, how the community diversity is affected by effluent remains obscure. Here, we compared the sediment bacterial communities exposed to different intensities of WWTP effluent discharge in Hangzhou Bay, China: i) a severely polluted area that receives effluent from an industrial WWTP, ii) a moderately polluted area that receives effluent from a municipal WWTP, and iii) less affected area that inner the bay. We found that the sediment bacterial diversity decreased dramatically with pollution levels of inorganic nutrients, heavy metals, and organic halogens. Microbial community assembly model analysis revealed increased environmental selection and decreased species migration rate in the severely polluted area, resulting in high phylogenetic clustering of the bacterial communities. The ecological networks were less complex in the two WWTP effluent receiving areas than in the inner bay area, as suggested by the smaller network size and lower modularity. Fewer negative network associations were detected in the severely (6.7%) and moderately (8.3%) polluted areas than in the less affected area (16.7%), indicating more collaborative inter-species behaviors are required under stressful environmental conditions. Overall, our results reveal the fundamental impacts of WWTP effluents on the ecological processes shaping coastal microbial communities and point to the potential adverse effects of diversity loss on ecosystem functions.

Sediment bacterial and fungal communities exhibit distinct responses to microplastic types and sizes in Taihu lake

Microplastics (MPs) are emerging contaminants in aquatic environments, yet their impact on sediment microbiota and biogeochemical processes were not well reported. Herein, microcosm experiments were performed to investigate the effects of MPs (Polystyrene, PS and Polyethylene, PE) with three size classes (ranging from 100 nm to 150–200 μm) on sediment bacterial and fungal communities over 60-day incubation from Taihu Lake. High-throughput sequencing revealed the alpha diversities of bacterial and fungal communities were reduced by MPs, dependent on MPs’ size and type. Bacterial community structures were significantly altered under all MPs treatments, with clustering for the same size class for PS and PE. Fungal community structures were significantly affected for all MPs, with PS and PE exhibiting different effects. Co-occurrence network analysis suggested MPs changed bacterial and fungal network complexities. Proteobacteria and Ascomycota formed strong associations with other phyla and demonstrated tolerance to MPs exposure. Actinobacteria, Firmicutes, and Chytridiomycota were the main respondents to MPs. The enzyme concentrations were stimulated by MPs, indicating carbon and nitrogen uptakes might be increased. Therefore, PS and PE had similar impacts on the microbial community (particularly bacteria), and sizes of MPs were the main influencing factors. MPs shifted community structure and network with distinct responses from bacteria and fungi, likely leading to the alteration of microbial-involved carbon and nitrogen cycling.

Nutrient enrichment drives the sediment microbial communities in Chinese mitten crab Eriocheir sinensis culture

Microbial communities play a critical role in aquaculture ecosystems. To identify the influence of sediment nutrient levels on microbial communities, sediment and water samples were collected from Chinese mitten crab Eriocheir sinensis culture ponds with different nutrient enrichment levels. Relevant physicochemical properties were measured, and 16 S rRNA gene sequencing was applied to identify relevant bacterial communities in the sediments. The results showed that the diversity and composition of microbial communities in sediments with different levels of nutrient enrichment varied considerably. Proteobacteria was the most abundant phylum in all samples, followed by Bacteroidetes, and Desulfobacterota with relative abundances of 23.5–40.9%, 9.8–21.5%, and 9.6–18.1%, respectively. Notably, total nitrogen (TN), organic matter (OM), and pH were important factors driving sediment bacterial community aggregation, the TN concentration explaining 61.5% of the microbial community variation. This study highlights that long-term culture activities alter the degree of sediment nutrient enrichment, which in turn affects microbial community composition and may ultimately have an impact on culture efficiency.

Impact of microplastics on lead-contaminated riverine sediments: Based on the enzyme activities, DOM fractions, and bacterial community structure

Microplastics (MPs) are able to interact with diverse contaminants in sediments. However, the impacts of MPs on sediment properties and bacterial community structure in heavy metal-contaminated sediments remain unclear. In this study, we investigated the adsorption of Pb(II) by sediment-MPs mixtures and the effects of different concentration MPs on sediment enzyme activities, DOM fractions, and Pb bioavailability in riverine sediments, and further explored the response of sediment microbial community to Pb in the presence of MPs. The results indicated that the addition of MPs significantly decreased the adsorption amount of Pb(II) by sediments, especially decreased by 12.6% at 10% MPs treatment. Besides, the changes in enzyme activities, DOM fractions exhibited dose-dependent effects of MPs. The higher level of MPs (5% and 10%) tends to transform Pb into more bioavailable fractions in sediments. Also, MPs amendment was observed to alter sediment bacterial community structures, and community differences were evident in the uncontaminated and lead-contaminated sediments. Therein, significant increase of Bacteroidota, Proteobacteria and decrease of Firmicutes abundance in Pb-contaminated sediment at the phylum level were observed. These findings are expected to provide comprehensive information for assessing the combined ecological risks of heavy metals and MPs in riverine sediments.

Distribution of heavy metals (arsenic, cobalt, copper and zinc) composition and bacterial communities in sediments along tropical river east coast Malaysia

Distribution of heavy metals (arsenic, cobalt, copper and zinc) composition and bacterial communities in sediments along tropical river east coast Malaysia

Reclaimed water use improved polluted water's self-purification capacity --Evidenced by water quality factors and bacterial community structure

Reclaimed water is increasingly adopted around the world to relieve water resource crisis induced by accelerated urbanization process. Compared with natural water bodies, aquatic ecosystems replenished with reclaimed water are usually enriched with organic matter, total nitrogen (TN) and phosphorus (TP). However, whether and how nutrient stoichiometric characteristic can impact receiving waters' self-purification remains poorly addressed. Here, we evaluated the effects of reclaimed water use on water's self-purification capacity in terms of water quality, sedimentary bacterial diversity, bacterial community structure and function. Results showed that reclaimed water use has improved water quality of domestic polluted urban rivers and increased bacterial genus-level abundance, but failed to directly affect bacterial biodiversity indexes and evenness of receiving waters. Water organic matter input from reclaimed water was the decisive factor in shaping sedimentary bacterial community structure rather than temperature. Meanwhile, compared with non-reclaimed water, reclaimed water replenishment enhanced polluted waters' carbon (C)-, N- and P-removing functions, suggesting an improvement of self-purification capacity. Our findings could improve the understanding of the ecological impact of reclaimed water on urban aquatic ecosystem, and inform the rational use of reclaimed water in urban rivers.

Potential of sediment bacterial communities from Manila Bay (Philippines) to degrade low-density polyethylene (LDPE).

The persistence of plastics and its effects in different environments where they accumulate, particularly in coastal areas, is of serious concern. These plastics exhibit signs of degradation, possibly mediated by microorganisms. In this study, we investigated the potential of sediment microbial communities from Manila Bay, Philippines, which has a severe plastics problem, to degrade low-density polyethylene (LDPE). Plastics in selected sites were quantified and sediment samples from sites with the lowest and highest plastic accumulation were collected. These sediments were then introduced and incubated with LDPE in vitro for a period of 91days. Fourier transform infrared spectroscopy detected the appearance of carbonyl and vinyl products on the plastic surface, indicating structural surface modifications attributed to polymer degradation. Communities attached to the plastics were profiled using high-throughput sequencing of the V4-V5 region of the 16S rRNA gene. Members of the phylum Proteobacteria dominated the plastic surface throughout the experiment. Several bacterial taxa associated with hydrocarbon degradation were also enriched, with some taxa positively correlating with the biodegradation indices, suggesting potential active roles in the partial biodegradation of plastics. Other taxa were also present, which might be consuming by-products or providing nourishment for other groups, indicating synergy in utilizing the plastic as the main carbon source and creation of a microenvironment within the plastics biofilm. This study showed that sediment microbes from Manila Bay may have naturally occurring microbial groups potentially capable of partially degrading plastics, supporting previous studies that the biodegradation potential for plastics is ubiquitously present in marine microbial assemblages.

Contribution of pollution gradient to the sediment microbiome and potential pathogens in urban streams draining into Lake Victoria (Kenya).

In sub-Saharan Africa (SSA), urban rivers/streams have long been subjected to anthropogenic pollution caused by urbanization, resulting in significantly altered chemical and biological properties of surface water and sediments. However, little is known about the diversity and structure of river microbial community composition and pathogens, as well as how they respond to anthropogenic inputs. High-throughput 16S rRNA amplicon sequencing and PICRUSt predictive function profiling were used in this study to conduct a comprehensive analysis of the spatial bacterial distribution and metabolic functions in sediment of two urban streams (Kisat and Auji) flowing through Kisumu City, Kenya. Results revealed that sediment samples from the highly urbanized mid and lower stream catchment zones of both streams had significantly higher levels of total organic carbon (TOC), total nitrogen (TN), total phosphorous (TP) than the less urbanized upper catchment zone, and were severely polluted with toxic heavy metals lead (Pb), cadmium (Cd), and copper (Cu). Differential distribution of Actinobacteria, Proteobacteria, Chloroflexi, and Verrucomicrobia in sediment bacterial composition was detected along stream catchment zones. The polluted mid and lower catchment zones were rich in Actinobacteria and Proteobacteria, as well as a variety of potential pathogenic taxa such as Corynebacterium, Staphylococcus, Cutibacterium, Turicella, Acinetobacter, and Micrococcus, as well as enteric bacteria such as Faecalibacterium, Shewanella, Escherichia, Klebsiella, Enterococcus, Prevotella, Legionella, Vibrio and Salmonella. Furthermore, PICRUSt metabolic inference analysis revealed an increasing enrichment in the sediments of genes associated with carbon and nitrogen metabolism, disease pathogenesis, and virulence. Environmental factors (TOC, Pb, Cd, TN, pH) and geographical distance as significant drivers of sediment bacterial community assembly, with the environmental selection to play a dominant role. In polluted river catchment zone sediment samples, Pb content was the most influential sediment property, followed by TOC and Cd content. Given the predicted increase in urbanization in SSA, further alteration of surface water and sediment microbiome due to urban river pollution is unavoidable, with potential long-term effects on ecosystem function and potential health hazards. As a result, this study provides valuable information for ecological risk assessment and management of urban rivers impacted by diffuse and point source anthropogenic inputs, which is critical for future proactive and sustainable urban waste management, monitoring, and water pollution control in low-income countries.

Characterization of the Sediment Bacterial Community Structure and Composition in Najafgarh Lake and Adjoining Dhansa Barrage.

This study was undertaken to assess the changes in the community structure, diversity, and composition of sediment bacteria in a shallow lake, Najafgarh Lake (NL), that receives untreated sewage effluent through drains connected to it. These changes were analyzed by comparing the sediment bacterial community structure of NL to the sediment bacterial community structure of Dhansa Barrage (DB), which receives no such effluents. 16S rRNA amplicon was used for bacterial community analysis. Water and sediment samples were also analyzed and compared revealing high conductivity, ammonia, nitrite content, and low dissolved oxygen in NL. The organic matter content is also higher in the sediments of NL. Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria are the predominant phyla in both sites and account for 91% of total bacterial abundance in DB and only 77% in the case of NL. Proteobacteria have the highest relative abundance, accounting for around 42% of the total bacterial population in the case of DB and Firmicutes has the highest relative abundance in Najafgarh at 30%. The diversity analysis found significant differences in the community structure at the two sites. The variation in the bacterial communities in the two wetlands is significantly associated with two water parameters (conductivity and temperature) and two sediment parameters (Sediment Nitrogen and Sediment Organic Matter). Correlation Analysis showed that high ammonia, nitrite, and conductance in NL resulted in bacterial communities shifting towards phyla abundant in degraded ecosystems like Acidobacteria, Choloroflexi, Caldiserica, Aminicenantes, Thaumarchaeota, and Planctomycetes.

Impacts of high-quality coal mine drainage recycling for replenishment of aquatic ecosystems in arid regions of China: Bacterial community responses

Coal mine water is usually recycled as supplementary water for aquatic ecosystems in arid and semiarid mining regions of China. To ensure ecosystem health, the coal mine water is rigorously treated using several processes, including reverse osmosis, to meet surface water quality standards. However, the potential environmental impacts of this management pattern on the ecological function of receiving water bodies are unclear. In this study, we built several microcosm water ecosystems to simulate the receiving water bodies. High-quality treated coal mine drainage was mixed into the model water bodies at different concentrations, and the sediment bacterial community response and functional changes were systematically investigated. The results showed that the high-quality coal mine drainage could still shape bacterial taxonomic diversity, community composition and structure, with a concentration threshold of approximately 50%. Moreover, both the Mantel test and the structural equation model indicated that the salinity fluctuation caused by the receiving of coal mine drainage was the primary factor shaping the bacterial communities. 10 core taxa in the molecular ecological network influenced by coal mine drainage were identified, with the most critical taxa being patescibacteria and g_Geothermobacter. Furthermore, the pathway of carbohydrate metabolism as well as signaling molecules and interactions was up-regulated, whereas amino acid metabolism showed the opposite trend. All results suggested that the complex physical-chemical and biochemical processes in water ecosystems may be affected by the coal mine drainage. The bacterial community response and underlying functional changes may accelerate internal nutrient cycling, which may have a potential impact on algal bloom outbreaks.

Temporal and Spatial Variations of the Bacterial Diversity in a Deep Alkaline Lake

This study aimed to investigate the effects of thermal stratification and complete mixing conditions on the bacterial diversity of a deep alkaline lake. For this purpose, the water and sediment samples were collected during the winter turnover and stratification periods, and bacterial communities were assessed by metabarcoding. The results showed that temperature shaped the bacterial community patterns in the lake. While the bacterial communities of the water samples showed high similarity during the mixing period, communities had distinctive patterns in the epilimnion and hypolimnion during stratification. The diversity and evenness of the bacterial communities increased with depth, whereas the bacterial communities of sediments were more even and diverse than in water. Proteobacteria members dominated the sediment communities representing 41% to 62% of the total reads in the samples. Particularly, Gammaproteobacteria was the major class found in the sediment; higher abundances were recorded in the mixing period representing 33–51%. Additionally, Actinobacteria species were more abundant in the water samples representing 22–52% of all reads during the stratification period. Due to the complete mixing conditions in the lake, a homogenized bacterial community structure was observed in the lake with minor spatial changes, and a clear divergence was observed between epilimnion and hypolimnion. On the other hand, the sediment bacterial community showed a more stable profile.

Nitrogen occurrence forms and bacterial community in sediment influenced by Bellamya purificata bioturbation

Endogenous water pollution and excessive nitrogen in ponds have always been prominent problems threatening aquaculture. To solve this problem, a 70-day indoor simulation experiment was conducted. The snail Bellamya purificata was stocked at four different densities: 0, 15, 30, and 60 individuals/tank, represented as CON (control), LD (low density), MD (medium density), and HD (high density), respectively, to investigate the effects of B. purificata on the nitrogen occurrence forms and bacterial communities in the sediment. At the end of the experiment, the nitrate concentration was significantly higher, while the total nitrogen content was significantly lower in the MD group than in the other three groups. Ammonia monooxygenase activity was significantly lower in the CON group than in the other three groups, and hydroxylamine oxidase activity was significantly higher in the HD group than in the other three groups. The CON and MD groups showed the highest and lowest values in nitrate reductase activity, respectively. The hydroxylamine reductase activity decreased significantly with increasing density. Through 16S ribosomal RNA (rRNA) high-throughput sequencing, significantly affected bacterial communities by B. purificata were found. Alpha diversity results showed that, a significantly lower Shannon index was observed in the MD group than in the other three groups. The LD and MD groups showed the highest and lowest Chao1 index values, respectively. Phyla Nitrospinae and family Nitrosomonadaceae were significantly enriched in the HD and MD groups, respectively. Redundancy analysis (RDA) indicated a significant correlation between differential bacterial taxa and TN content. Predicted functional analysis based on FAPROTAX (Functional annotation of prokaryotic taxa) database showed that functional groups aerobic ammonia oxidation and aerobic nitrite oxidation were significantly enriched in the MD group. Overall, B. purificata significantly altered the bacterial community composition, increased hydroxylamine oxidase and ammonia monooxygenase activities, enhanced the bacterial nitrification process, and promoted the transformation of total nitrogen to nitrate. Moreover, B. purificata stocked at 30 and 60 individuals/tank appeared to have a significant promotion effect on the bacterial community and nitrogen occurrence forms in the sediment. Hence, co-culturing B. purificata may be a feasible and effective ecological restoration method to alleviate excess nitrogen and reduce water eutrophication.

Homogenisation of water and sediment bacterial communities in a shallow lake (lake Balihe, China)

Abstract Planktonic and benthic bacterial communities hold central roles in the functioning of freshwater ecosystems and mediate key ecosystem services such as primary production and nutrient remineralisation. Although it is clear that such communities vary in composition both within and between lakes, the environmental factors and processes shaping the diversity and composition of freshwater bacteria are still not fully understood. In order to assess seasonal and spatial variability in lake bacterial communities and identify environmental factors underpinning biogeographical patterns, we performed a large‐scale sampling campaign with paired water and sediment sample collection at 18 locations during four seasons in Lake Balihe, a subtropical shallow fish‐farming lake in mid‐eastern China. Pelagic and benthic bacterial communities were distinctly different in terms of diversity, taxonomic composition and community structure, with Actinobacteria, Bacteroidetes, Cyanobacteria and Alphaproteobacteria dominating lake water, and Acidobacteria, Bacteroidetes, Chloroflexi, Gammaproteobacteria and Deltaproteobacteria dominating sediment. Nevertheless, these two communities had stronger spatial concordance and overlap in taxa during spring and autumn seasons. Together, the main drivers of both the spatial and temporal variations in Lake Balihe bacterial communities were identified as water temperature, turbidity, nitrogen and phosphorus availability, and thermal stratification controlled by wind‐mixing and activity of the dense farmed fish populations. Notably, populations affiliated with Firmicutes, known to be abundant in fish gut microbiome, were especially abundant in the summer season and locations where high fish biomass was found, suggesting a potential link between fish gut microbiome and the pelagic bacterial communities. Our findings demonstrated seasonal homogenisation of pelagic and benthic bacterial communities linked to marked shifts in a set of seasonally‐driven environmental variables including water temperature and nutrient availability.

Human access and deterministic processes play a major role in structuring planktonic and sedimentary bacterial and eukaryotic communities in lakes.

Lakes provide habitat for a diverse array of species and offer a wide range of ecosystem services for humanity. However, they are highly vulnerable as they are not only impacted by adverse actions directly affecting them, but also those on the surrounding environment. Improving knowledge on the processes responsible for community assembly in different biotic components will aid in the protection and restoration of lakes. Studies to date suggested a combination of deterministic (where biotic/abiotic factors act on fitness differences amongst taxa) and stochastic (where dispersal plays a larger factor in community assembly) processes are responsible for structuring biotic communities, but there is no consensus on the relative roles these processes play, and data is lacking for lakes. In the present study, we sampled different biotic components in 34 lakes located on the South Island of New Zealand. To obtain a holistic view of assembly processes in lakes we used metabarcoding to investigate bacteria in the sediment and surface waters, and eukaryotes in the sediment and two different size fractions of the water column. Physicochemical parameters were collected in parallel. Results showed that deterministic processes dominated the assembly of lake communities although the relative importance of variable and homogeneous selection differed among the biotic components. Variable selection was more important in the sediment (SSbact and SSeuks) and for the bacterioplankton (Pbact) while the assembly of the eukaryotic plankton (SPeuks, LPeuks) was driven more by homogeneous selection. The ease of human access to the lakes had a significant effect on lake communities. In particular, clade III of SAR11 and Daphnia pulex were only present in lakes with public access. This study provides insights into the distribution patterns of different biotic components and highlights the value in understanding the drivers of different biological communities within lakes.

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

Microbes in rivers are an important part of the biogeochemical cycle in aquatic ecosystems, and understanding the major factors that influence the composition of microbial communities has an important role in assessing and improving ecosystem functioning. A high-throughput 16 S rRNA gene sequencing technique was employed to sequence bacterial communities in 21 sediment samples and 21 water samples from an urban river WWTP (wastewater treatment plant) discharge. A systematic study of changes in bacterial community composition in downstream river sediment and water was conducted. The study found that compared with the bacterial diversity in the natural upstream area of the wastewater outfall, the bacterial diversity in the sediment lower reaches decreased significantly, while the bacterial abundance and diversity in the water increased significantly. The Mantel test and redundancy analysis showed that the downstream distance and physicochemical properties were significantly related to the succession of bacterial communities in the sediment downstream of the WWTP discharge. Among them, TOC (total organic carbon) was the most important factor affecting the change in the bacterial community in the downstream sediment. The physicochemical properties were significantly correlated with the succession of bacterial communities in the water downstream of the WWTP discharge. Among them, TN (total nitrogen), PO43--P (phosphorus phosphate) and TP (total phosphorus) were the main factors that affected the change in the bacterial community in the downstream water. Key taxa in the co-occurrence network at different distances downstream reflected the depth of the effect of the WWTP effluent on the bacterial community. The bacterial community in the lower reaches of the river sediment showed a strong recovery ability under the influence of pollutants, while the bacterial community in the lower reaches of the river water was difficult to recover under the influence of pollutants. In general, pollutants contained in effluent are the key to changing the composition of bacterial communities in the lower reaches of the river, but exogenous bacteria in effluent are not. This study provides a basis for further improving the effluent discharge standards of WWTPs in the future.

The Effect of the Artificial Reef on the Structure and Function of Sediment Bacterial Community

The bacterial community in sediment is sensitive to artificial disturbance, and they respond differently to human disturbance, such as changing the nutrient cycling and energy flow in marine ecosystems. However, little is known about the dynamics and distribution of bacterial community structures in marine sediments and potential biogeochemical functions during the long-time succession in marine ranching. In the present study, we compared the dynamics of the bacterial composition and potential biogeochemical functions of sediment to ten years (TR) and one-year new artificial reef (NR) areas using metagenomic next-generation sequencing technology. Results revealed that NR reduces the Pielou’s evenness and Shannon index. Similarly, nonmetric multidimensional scaling showed that the beta diversity of sediment bacterial communities in NR significantly differed between TR and non-artificial reef areas. Previously, TR biomarkers were frequently associated with organic matter decomposing and assimilating in the organically enriched sediments (i.e., Acinetobacter). The soluble reactive phosphate (SRP) and total phosphorus (TP) concentrations were thought to be the primary driving forces in shaping the microbial community in sediment. Pseudomonas, Lactobacillus, and Ralstonia have a significant positive correlation with SRP, TP, nitrate, and TN, but a negative association with pH, Salinity, Hg, and depth. NR was found to have more negative correlation nodes, indicating that taxa face more competition or predation press. Vibrio served as the module-hubs in the network in all areas. In addition, chemoheterotrophy, aerobic chemoheterotrophy, and fermentation were the three most prominent functions of the three areas, accounting for 59.96% of the relative abundance of the functional annotation. Different bacteria in sediments may change the amount of biogeochemical cycle in the marine ranching ecosystem. These findings can increase our understanding of the succession of the microecosystem for the marine ranching sedimentary environment by revealing how artificial reefs affect the indigenous sediment bacterial community and their responses to environmental variation.

Geographic patterns and determinants of antibiotic resistomes in coastal sediments across complex ecological gradients.

Coastal areas are highly influenced by terrestrial runoffs and anthropogenic disturbances, commonly leading to ecological gradients from bay, nearshore, to offshore areas. Although the occurrence and distribution of sediment antibiotic resistome are explored in various coastal environments, little information is available regarding geographic patterns and determinants of coastal sediment antibiotic resistomes across ecological gradients at the regional scale. Here, using high-throughput quantitative PCR, we investigated the geographic patterns of 285 antibiotic resistance genes (ARGs) in coastal sediments across a ~ 200 km scale in the East China Sea. Sediment bacterial communities and physicochemical properties were characterized to identify the determinants of sediments antibiotic resistome. Higher richness and abundance of ARGs were detected in the bay samples compared with those in nearshore and offshore samples, and significant negative correlations between the richness and/or abundance of ARGs and the distance to coastline (DTC) were identified, whereas different types of ARGs showed inconsistency in their relationships with DTC. The composition of antibiotic resistome showed significant correlations with nutrition-related variables (including NH4 +-N, NO3 --N, and total phosphorus) and metals/metalloid (including As, Cu, Ni, and Zn), suggesting that terrestrial disturbances largely shape the antibiotic resistome. The Bipartite network showed strong associations between ARGs and mobile genetic elements (MGEs), and Partial Least Squares Path Modeling further revealed that terrestrial disturbance strength (as indicated by DTC) directly affected abiotic environmental conditions and bacterial community composition, and indirectly affected antibiotic resistome via MGEs. These findings provide insights into regional variability of sediment antibiotic resistome and its shaping path across complex ecological gradients, highlighting terrestrial disturbances as determinative forces in shaping coastal sediment antibiotic resistomes.

Sediment sulfate content determines assembly processes and network stability of bacteria communities of coastal land-based shrimp aquaculture ponds

Sediment bacteria communities in shrimp pond are intricately linked to ecosystem function and the provision of services, such as nutrient cycling and excess nutrient metabolism in sediment. However, little is known about the main factor (assembly processes) governing abundant and rare bacterial diversity in land-based shrimp ponds. This study quantified the composition, spatial distribution, and assembly mechanisms of bacterial communities sampled from the sediment of 78 land-based shrimp ponds distributed along approximately 1700 km of the southeastern coastal zone of China. This was done using 16S rRNA gene amplicon sequencing. The bacterial community similarities decreased with spatial distance. Variation of bacterial community was mostly attributed to deterministic (environmental filtering) processes. Sediment sulfate concentrations regulated the balance between stochastic and deterministic bacterial community assembly processes, as indicated by the negative relationship between the stochasticity ratio, and network analysis highlighted increasingly sparse interconnections and less frequent co-occurrences among bacterial communities under greater sulfate concentrations. Our results demonstrate the negative impacts of sulfates associated with coastal aquaculture on sediment bacterial community dynamics, community assembly, and ecosystem function.

Structural Diversity of Bacterial Communities and Its Relation to Environmental Factors in the Surface Sediments from Main Stream of Qingshui River

This paper aims to preliminarily understand the structure and diversity of the bacterial community in the sediments of the Qingshui River, and analyze the differences of dominant bacteria in different river reaches, and identify the influence degree of environmental factors. In this study, surface sediments of the main stream of the Qingshui River were selected to analyze both bacterial community composition and a diversity index using the high-throughput sequencing analysis of bacterial 16S rDNA, further exploring their relationships with environmental factors. Results showed that 16,855 OTUs in the surface sediments belonged to 66 phyla, 164 classes, 274 orders, 317 families, and 501 genera of bacteria, while carbon/nitrogen-fixing bacteria were dominant at the class and genus level. There was a significant (p < 0.05) spatial difference between bacterial species composition and the diversity index in surface sediments. Proteobacteria was the most abundant phylum in the sediments of the main stream of the Qingshui River, with an average abundance of 48.15%, followed by Bacteroidetes (21.74%) and Firmicutes (5.71%). The abundance of Alphaproteobacteria in Proteobacteria was the highest (15.38%) and followed by Flavobacteriia in Bacteroidetes (11.57%). The most dominant bacteria genera were different at different areas. The most dominant genera were Phyllobacterium in Kaicheng, Qiying, Liwang, Tongxin and Changshantou, with relative abundances of 4.27%, 4.67%, 5.88%, 4.15% and 6.22%, respectively. Flavobacterium was the most dominant genus in both Dongjiao and Sanying, with a relative abundance of 5.03% and 5.84%, respectively. Rhodobacter was the most dominant genus in Hexi, with a relative abundance of 8.29%. Gillisia was the most dominant genus in Quanyanshan, with a relative abundance of 5.51%. Pearson correlation analysis further indicated that NH4+, pH, and Cr were the main factors affecting the bacterial community structure and diversity in surface sediments. Therefore, our findings suggest that both nutrient elements (i.e., N) and toxic heavy metalloids affect the abundance and diversity of bacteria in surface sediments from the main stream of the Qingshui River. Areas of the river sampled in this study provide the biggest microbial sampling coverage to date. The results provide a preliminary understanding of bacterial communities in sediments of different reaches of the Qingshui River, and provide a reference for further research on the application of functional bacteria in pollution control of the Qingshui River.

Organic matter degradation and bacterial communities in surface sediment influenced by Procambarus clarkia.

To alleviate excessive organic matter (OM) accumulation in sediments and reduce the risk of endogenous water pollution and eutrophication in aquaculture ponds, an 84-day experiment investigated the effect of the red swamp crayfish Procambarus clarkii on the OM degradation and bacterial communities in sediments. The experiment established two groups, P. clarkia treatment and control (represented as PG and CG, respectively), with three replicates for each group. At the end of experiment, the total, light fraction, and heavy fraction organic matter concentrations in the sediment of the PG group were significantly lower than those of the CG group. Significantly higher oxidation-reduction potential (ORP) and more extensively degraded OM, indicated by fatty acids, were observed in the PG group. Compared to the CG group, the average OM removal efficiency induced by crayfish in the PG group was 15.24%. Using 16S ribosomal RNA (rRNA) high-throughput sequencing, we investigated the differences in benthic bacterial communities between the PG and CG groups. Linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed that Nitrospirae, Nitrospira, Alphaproteobacteria, OLB14, Nitrospirales, Rhodobacterales, Rhizobiales, Micrococcales, Nitrospiraceae, Rhodobacteraceae, Nitrospira, Rhodobacter, Thermomonas, and Denitratisoma were significantly enriched in the PG group. Four significantly different functional groups related to OM degradation were determined between the PG and CG groups according to the functional annotation of procaryotic taxa (FAPROTAX) analysis. These four functional groups, aerobic chemoheterotrophy, manganese oxidation, dark iron oxidation, and dark sulfide oxidation, showed significantly higher relative abundances in the PG group. Overall, P. clarkia effectively increased the ORP values of sediments to provide favorable conditions for OM degradation and changed the composition and function of bacterial communities to improve bacterial abilities for OM decomposition, thereby promoting OM degradation in the sediment.