Profiling microbial communities in a watershed undergoing intensive anthropogenic activities

Effects of microplastics on microbial community dynamics in sediments from the Volturno River ecosystem, Italy

In this study, the sources, abundance, and ecological implications of microplastic (MP) pollution in Volturno, one of the main rivers in southern Italy, were explored by investigating the MP concentration levels in sediments collected along the watercourse. The samples were sieved through 5- and 2-mm sieves and treated with selective organic solvents. The polymer classes polystyrene (PS), polyethylene (PE), polypropylene (PP), polyethylene terephthalate (PET), polycarbonate (PC), nylon 6 (PA6), and nylon 6,6 (PA66) were quantified using pyrolysis-gas chromatography-mass spectrometry (Py-GC/MS) and high-performance liquid chromatography (HPLC). Furthermore, a 16S rRNA metagenomic analysis was performed using next-generation sequencing in Ion Torrent™ to explore the bacterial taxonomy and ecological dynamics of sediment samples. The MPs were detected in all samples collected from the study area. PP and PET were the most abundant and frequently detected polymer types in the analysed samples. The total MP concentration ranged from 1.05 to 14.55 ppm (parts per million), identifying two distinct data populations: high- and low-MP-contaminated sediments. According to the Polymer Hazard Index (PHI), MP pollution was categorised as hazard levels III and IV (corresponding to the danger category). Metagenomic data revealed that the presence of MPs significantly affected the abundance of bacterial taxa; Flavobacteraceae and Nocardiaceae, which are known to degrade polymeric substances, were present in high-MP-contaminated sediments. This study provides new insights into the ecological relevance of MP pollution and suggests that microorganisms may serve as biomarkers of MP pollution.

Temporal and Spatial Variation Characteristics and Influencing Factors of Bacterial Community in Urban Landscape Lakes

Urban landscape lakes are closely related to human activity, but there are limited studies on their bacterial community characteristics and risks to human health. In this study, four different types of urban landscape lakes in Xi'an were selected, and the bacterial community structures in different seasons were analyzed by Illumina Nova high-throughput sequencing technology. Seasonal variations in bacterial communities were analyzed by linear discriminant analysis, STAMP difference analysis, and nonmetric multidimensional scaling. Redundancy analysis was used to investigate the influencing factors. Furthermore, the metabolic functions of bacterial communities were predicted by Tax4Fun. There were clear seasonal differences in the α-diversity of bacteria, with bacterial diversity being higher in winter than in summer in the four urban landscape lakes, and the diversity of different water sources was different; the distributions of Proteobacteria, Actinobacteria, Chloroflexi, and Verrucomicrobia had significant seasonal differences; and the dominant bacteria at the genus level had obvious temporal and spatial differences. Furthermore, a variety of environmental factors had an impact on bacterial communities, and temperature, DO, and nitrogen were the primary factors affecting the seasonal variation in bacteria. There are also significant seasonal differences in the metabolic functions of bacterial communities. These results are helpful for understanding the current status of bacteria in the aquatic environments of such urban landscape lakes.

Characterization of microbial communities in seven wetlands with different anthropogenic burden using Next Generation Sequencing in Bogotá, Colombia

Wetlands represent key ecosystems due to their remarkable biodiversity, ecological functions and multiple ecosystem services provided. In Colombia, there are 31,702 wetlands, 13 of which are in Bogotá, capital of the country. Despite the fundamental socioecological support of these aquatic ecosystems, a tremendous loss and degradation of these ecosystems has been observed due to anthropogenic perturbations. Therefore, the aim of this study was to describe the status of seven Bogotá wetlands with variable anthropogenic interventions by measuring organoleptic, physicochemical, and microbiological parameters, using commercial kits, highly sensitive equipment, and next-generation sequencing of the 16S- and 18S-rRNA genes. Our findings describe the status of seven wetlands with different anthropogenic burden in Bogotá-Colombia where physicochemical and microbiology signals of contamination were observed. Additionally, some profiles in the composition of the microbial communities, together with certain physicochemical characteristics, may represent an insight into the environmental dynamics, where Beta Proteobacteria such as Malikia represent a potential keystone in aquatic ecosystems impacted by wastewater effluent discharges; the presence of nitrates and phosphates explain the abundance of bacteria capable of oxidizing these compounds, such as Polynucleobacter. Moreover, the presence of specific prokaryotic and eukaryotic organisms, such as Clostridium, Cryptococcus, Candida, and Naegleria, reported in one or more of the wetlands assessed here, could represent a possible pathogenic risk for human and animal health. This study performed a complete evaluation of seven Bogotá wetlands with different anthropogenic impacts for the first time, and our findings emphasize the importance of maintaining continuous monitoring of these water bodies given their remarkable ecological importance and potential spill-over of several pathogens to humans and animals.

The microbiome of the marine flatworm Macrostomum lignano provides fitness advantages and exhibits circadian rhythmicity

The close association between animals and their associated microbiota is usually beneficial for both partners. Here, we used a simple marine model invertebrate, the flatworm Macrostomum lignano, to characterize the host-microbiota interaction in detail. This analysis revealed that the different developmental stages each harbor a specific microbiota. Studies with gnotobiotic animals clarified the physiological significance of the microbiota. While no fitness benefits were mediated by the microbiota when food was freely available, animals with microbiota showed significantly increased fitness with a reduced food supply. The microbiota of M. lignano shows circadian rhythmicity, affecting both the total bacterial load and the behavior of specific taxa. Moreover, the presence of the worm influences the composition of the bacterial consortia in the environment. In summary, the Macrostomum-microbiota system described here can serve as a general model for host-microbe interactions in marine invertebrates.

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.

Microbial community structural response to variations in physicochemical features of different aquifers

Introduction

The community structure of groundwater microorganisms has a significant impact on groundwater quality. However, the relationships between the microbial communities and environmental variables in groundwater of different recharge and disturbance types are not fully understood.

Methods

In this study, measurements of groundwater physicochemical parameters and 16S rDNA high-throughput sequencing technology were used to assess the interactions between hydrogeochemical conditions and microbial diversity in Longkou coastal aquifer (LK), Cele arid zone aquifer (CL), and Wuhan riverside hyporheic zone aquifer (WH). Redundancy analysis indicated that the primary chemical parameters affecting the microbial community composition were NO3 -, Cl-, and HCO3 -.

Results

The species and quantity of microorganisms in the river-groundwater interaction area were considerably higher than those in areas with high salinity [Shannon: WH (6.28) > LK (4.11) > CL (3.96); Chao1: WH (4,868) > CL (1510) > LK (1,222)]. Molecular ecological network analysis demonstrated that the change in microbial interactions caused by evaporation was less than that caused by seawater invasion under high-salinity conditions [(nodes, links): LK (71,192) > CL (51,198)], whereas the scale and nodes of the microbial network were greatly expanded under low-salinity conditions [(nodes, links): WH (279,694)]. Microbial community analysis revealed that distinct differences existed in the classification levels of the different dominant microorganism species in the three aquifers.

Discussion

Environmental physical and chemical conditions selected the dominant species according to microbial functions. Gallionellaceae, which is associated with iron oxidation, dominated in the arid zones, while Rhodocyclaceae, which is related to denitrification, led in the coastal zones, and Desulfurivibrio, which is related to sulfur conversion, prevailed in the hyporheic zones. Therefore, dominant local bacterial communities can be used as indicators of local environmental conditions.

Spatial and temporal dynamics of microbial community composition and factors influencing the surface water and sediments of urban rivers

The temporal and spatial characteristics of urban river bacterial communities help us understand the feedback mechanism of bacteria to changes in the aquatic environment. The Fuhe River plays an important role in determining the water ecological environment of Baiyangdian Lake. 16S rRNA gene sequencing was used to study the microbial distribution characteristics in the Fuhe River in different seasons. The results showed that some environmental factors of the surface water (ammonia nitrogen (NH₃-N), total nitrogen (TN), and total phosphorus (TP)) were different on the spatial and temporal scales. Moreover, there were no seasonal differences in the contents of TN, TP, total organic carbon (TOC), or heavy metals in the sediments. The distributions of Cyanobacteria, Actinomycetes and Firmicutes in the water and Actinomycetes and Planctomycetes in the sediments differed significantly among seasons (P < 0.05). There were significant spatial differences in bacteria in the surface water, with the highest abundance of Proteobacteria recorded in the river along with the highest nutrient concentration, while the abundance of Bacteroidetes was higher in the upstream than the downstream. Microbial communities in the water were most sensitive to temperature (T) and the TP concentration (P < 0.01). Moreover, differences in the bacterial community were better explained by the content of heavy metals in the sediments than by the chemical characteristics. A PICRUSt metabolic inference analysis showed that the effect of high summer temperatures on the enzyme action led to an increase in the abundances of the metabolic-related genes of the river microorganisms.

Metagenomics reveals biogeochemical processes carried out by sediment microbial communities in a shallow eutrophic freshwater lake

Introduction

As the largest shallow freshwater lake in the North China Plain, Baiyangdian lake is essential for maintaining ecosystem functioning in this highly populated region. Sediments are considered to record the impacts of human activities.

Methods

The abundance, diversity and metabolic pathways of microbial communities in sediments were studied by metagenomic approach to reveal patterns and mechanism of C, N, P and S cycling under the threat of lake eutrophication.

Results

Many genera, with plural genes encoding key enzymes involved in genes, belonging to Proteobacteria and Actinobacteria which were the most main phylum in bacterial community of Baiyangdian sediment were involved in C, N, S, P cycling processes, such as Nocardioides (Actinobacteria), Thiobacillus, Nitrosomonas, Rhodoplanes and Sulfuricaulis (Proteobacteria).For instance, the abundance of Nocardioides were positively correlated to TN, EC, SOC and N/P ratio in pathways of phytase, regulation of phosphate starvation, dissimilatory sulfate reduction and oxidation, assimilatory sulfate reduction, assimilatory nitrate reduction and reductive tricarboxylic acid (rTCA) cycle. Many key genes in C, N, P, S cycling were closely related to the reductive citrate cycle. A complete while weaker sulfur cycle between SO₄ ^2- and HS^- might occur in Baiyangdian lake sediments compared to C fixation and N cycling. In addition, dissimilatory nitrate reduction to ammonia was determined to co-occur with denitrification. Methanogenesis was the main pathway of methane metabolism and the reductive citrate cycle was accounted for the highest proportion of C fixation processes. The abundance of pathways of assimilatory nitrate reduction, denitrification and dissimilatory nitrate reduction of nitrogen cycling in sediments with higher TN content was higher than those with lower TN content. Besides, Nocardioides with plural genes encoding key enzymes involved in nasAB and nirBD gene were involved in these pathways.

Discussion

Nocardioides involved in the processes of assimilatory nitrate reduction, denitrification and dissimilatory nitrate reduction of nitrogen cycling may have important effects on nitrogen transformation.

Factors driving the halophyte rhizosphere bacterial communities in coastal salt marshes

Introduction

Root-associated microorganisms promote plant growth and provide protection from stresses. Halophytes are the fundamental components maintaining ecosystem functions of coastal salt marshes; however, it is not clear how their microbiome are structured across large spatial scales. Here, we investigated the rhizosphere bacterial communities of typical coastal halophyte species (Phragmites australis and Suaeda salsa) in temperate and subtropical salt marshes across 1,100 km in eastern China.

Methods

The sampling sites were located from 30.33 to 40.90°N and 119.24 to 121.79°E across east China. A total of 36 plots were investigated in the Liaohe River Estuary, the Yellow River Estuary, Yancheng, and Hangzhou Bay in August 2020. We collected shoot, root, and rhizosphere soil samples. the number of pakchoi leaves, total fresh and dry weight of the seedlings was counted. The soil properties, plant functional traits, the genome sequencing, and metabolomics assay were detected.

Results

The results showed that soil nutrients (total organic carbon, dissolved organic carbon, total nitrogen, soluble sugars, and organic acids) are high in the temperate marsh, while root exudates (measured by metabolite expressions) are significantly higher in the subtropical marsh. We observed higher bacterial alpha diversity, more complex network structure, and more negative connections in the temperate salt marsh, which suggested intense competition among bacterial groups. Variation partitioning analysis showed that climatic, edaphic, and root exudates had the greatest effects on the bacteria in the salt marsh, especially for abundant and moderate subcommunities. Random forest modeling further confirmed this but showed that plant species had a limited effect.

Conclutions

Taken together, the results of this study revealed soil properties (chemical properties) and root exudates (metabolites) had the greatest influence on the bacterial community of salt marsh, especially for abundant and moderate taxa. Our results provided novel insights into the biogeography of halophyte microbiome in coastal wetlands and can be beneficial for policymakers in decision-making on the management of coastal wetlands.

Anthropogenic impact accelerates antibiotic resistome diversity in the mangrove sediment of Indian Sundarban

Mangroves are situated in convergence zones between fresh and marine water and are prone to pollution and deforestation. This study explored the microbiome structure, function and antibiotic resistome of Indian Sundarban. The taxonomic Chao1 estimated diversity was highest in uninhabited Kalash (1204.64 ± 12.72) and lowest in Godkhali, which experiences considerable human activities (1158.76 ± 11.18). The alpha diversity showed negative correlation (p < 0.05) with PAH such as Acenaphthene (r = -0.56), Acenaphthylene (r = -0.62), Fluoranthene (r = -0.59), Fluorene (r = -0.55), Phenanthrene (r = -0.57), while the biochemical parameters phosphate (r = 0.58) and salinity (r = 0.58) had a significant (p < 0.05) positive correlation. The data suggest the importance of physicochemical parameters in maintaining the mangrove microbiome. The taxonomic composition was dominated by Proteobacteria (54.12 ± 0.37). All sites were dominated by ARGs such as rpoB2, cpxR, ompR, camP, and bacA. Comparing the Sundarban mangrove sediment resistome with mangrove from other sites in India (Kerala) and China (Guangxi, Hainan, and Shenzhen) suggested that resistome from Indian mangrove has a significantly (p < 0.05) higher ARG diversity compared to Chinese mangroves. Yet, the abundance of the ARG was significantly (p < 0.05) lower in the Indian mangroves posing a much greater risk if enriched. The study suggests that anthropogenic activities and pollution degrade the microbiome diversity, disturb the microbiome functions, and enrich ARGs.

Distribution of sediment microbial communities and their relationship with surrounding environmental factors in a typical rural river, Southwest China

With rapid urbanization and industrialization, rural rivers in China are facing deterioration in water quality and ecosystem health. Microorganisms living in river sediments are involved in biogeochemical processes, mineralization, and degradation of pollutants. Understanding bacterial community distribution in rural rivers could help evaluate the response of river ecosystems to environmental pollution and understand the river self-purification mechanism. In this study, the relationship between characteristics of sediment microbial communities and the surrounding environmental factors in a typical rural river was analyzed using 16S rRNA gene sequencing technology. The results showed that the dominant bacterial groups in the river sediment were Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, and Firmicutes, accounting for 83.61% of the total microbial load. Different areas have different sources of pollution which give rise to specific dominant bacteria. The upstream part of the river flows through an agricultural cultivation area where the dominant bacteria were norank_f_Gemmatimonadaceae, Haliangium, and Pseudolabrys, possessing obvious nitrogen- and phosphorus-metabolizing activities. The midstream section flows through an urban area where the dominant bacteria were Marmoricola, Nocardioides, Gaiella, Sphingomonas, norank_f_67-14, Subgroup_10, Agromyces, and Lysobacter, with strong metabolizing activity for toxic pollutants. The dominant bacteria in the downstream part were Clostridium_sensu_stricto_1, norank_f__Bacteroidetes_vadinHA17, Candidatus_Competibacter, and Methylocystis. Redundancy analysis and correlation heatmap analysis showed that environmental factors: ammonia nitrogen (NH₄⁺-N) and total nitrogen (TN) in the sediment, and pH, temperature, TN, electrical conductivity (EC), and total dissolved solids (TDS) in the water, significantly affected the bacterial community in the sediment. The PICRUSt2 functional prediction analysis identified that the main function of bacteria in the sediment was metabolism (77.3%), specifically carbohydrate, amino acid, and energy metabolism. These activities are important for degrading organic matter and removing pollutants from the sediments. The study revealed the influence of organic pollutants derived from human activities on the bacterial community composition in the river sediments. It gave a new insight into the relationship between environmental factors and bacterial community distribution in rural watershed ecosystems, providing a theoretical basis for self-purification and bioremediation of rural rivers.

Bacterial community response to chronic heavy metal contamination in marine sediments of the East China Sea

Marine sediments act as a sink for various heavy metals, which may have profound impact on sedimentary microbiota. However, our knowledge about the collaborative response of bacterial community to chronic heavy metal contamination remains little. In this study, concentrations of seven heavy metals (As, Cd, Cr, Cu, Hg, Pb, and Zn) in sediments collected from the East China Sea were analyzed and Illumina Miseq 16 S rRNA sequencing was applied to characterize the structure of bacterial community. Microbiota inhabiting sediments in the East China Sea polluted with heavy metals showed different community composition from relatively pristine sites. The response of bacterial community to heavy metal stress was further interrogated with weighted correlation network analysis (WGCNA). WGCNA revealed ten bacterial modules exhibiting distinct co-occurrence patterns and among them, five modules were related to heavy metal pollution. Three of them were positively correlated with an increase in at least one heavy metal concentration, hubs (more influential bacterial taxa) of which were previously reported to be involved in the geochemical cycling of heavy metals or possess tolerance to heavy metals, while another two modules showed opposite patterns. Our research suggested that ecological functional transition might have occurred in East China Sea sediments by shifts of community composition with sensitive modules majorly involved in the meaningful global biogeochemical cycling of carbon, sulfur, and nitrogen replaced by more tolerant groups of bacteria due to long-term exposure to low-concentration heavy metals. Hubs may serve as indicators of perturbations of benthic bacterial community caused by heavy metal pollution and support monitoring remediation of polluted sites in marine environments.

Streambed microbial communities in the transition zone between groundwater and a first-order stream as impacted by bidirectional water exchange

The input of nitrate and other agricultural pollutants in higher-order streams largely derives from first-order streams. The streambed as the transition zone between groundwater and stream water has a decisive impact on the attenuation of such pollutants. This reactivity is not yet well understood for lower-order agricultural streams, which are often anthropogenically altered and lack the streambed complexity allowing for extensive hyporheic exchange. Reactive hot spots in such streambeds have been hypothesized as a function of hydrology, which controls the local gaining (groundwater exfiltration) or losing (infiltration) of stream water. However, streambed microbial communities and activities associated with such reactive zones remain mostly uncharted. In this study, sediments of a first-order agriculturally impacted stream in southern Germany were investigated. Along with a hydraulic dissection of distinct gaining and losing reaches of the stream, community composition and the abundance of bacterial communities in the streambed were investigated using PacBio long-read sequencing of bacterial 16S rRNA gene amplicons, and qPCR of bacterial 16S rRNA and denitrification genes (nirK and nirS). We show that bidirectional water exchange between groundwater and the stream represents an important control for sediment microbiota, especially for nitrate-reducing populations. Typical heterotrophic denitrifiers were most abundant in a midstream net losing section, while up- and downstream net gaining sections were associated with an enrichment of sulfur-oxidizing potential nitrate reducers affiliated with Sulfuricurvum and Thiobacillus spp. Dispersal-based community assembly was found to dominate such spots of groundwater exfiltration. Our results indicate a coupling of N- and S-cycling processes in the streambed of an agricultural first-order stream, and a prominent control of microbiology by hydrology and hydrochemistry in situ. Such detailed local heterogeneities in exchange fluxes and streambed microbiomes have not been reported to date, but seem relevant for understanding the reactivity of lower-order streams.

Bacterial communities in peat swamps reflect changes associated with catchment urbanisation

Like many peat wetlands around the world, Temperate Highland Peat Swamps on Sandstone (THPSS), located in the Sydney Basin, Australia, have been impacted by urban development. In this paper, we used Illumina 16S rRNA DNA amplicon sequencing to characterise and compare the bacterial communities of surface (top 0–2 cm) and deep (50 cm) sediments in peat swamps that occur in both urbanised and non-urbanised catchments. Proteobacteria (32.2% of reads), Acidobacteria (23.6%) and Chloroflexi (10.7%) were the most common phyla of the dataset. There were significant differences in the bacterial community structure between catchment types and depths apparent at the phyla level. Proteobacteria, Bacteroidetes, Actinobacteria and Verrucomicrobia made up a greater proportion of the reads in the surface sediments than the deeper sediments, while Chloroflexi and Nitrospirae were relatively more common in the deeper than the surface sediment. By catchment type, Acidobacteria were more common in swamps occurring in non-urbanised catchments, while Nitrospirae, Bacteroidetes and Actinobacteria were more common in those in urbanised catchments. Microbial community structure was significantly correlated with sediment pH, as was the relative abundance of several phyla, including Acidobacteria (negative correlation) and Bacteroidetes (positive correlation). As an indicator of trophic shift from oligotrophic to copiotrophic conditions associated with urbanised catchment, we found significant differences ratios of β-Proteobacteria to Acidobacteria and Bacteriodetes to Acidobacteria between the catchment types. Based on SIMPER results we suggest the relative abundance of Nitrosomonadaceae family as a potential indicator of urban degradation. As the first study to analyse the bacterial community structure of THPSS using sequencing of 16S rDNA, we reveal the utility of such analyses and show that urbanisation in the Blue Mountains is impacting the microbial ecology of these important peatland ecosystems.

Response mechanism of microbial community to seasonal hypoxia in marine ranching

Seasonal hypoxia, as an increasingly recognized environmental issue, frequently occurred in marine ranching from northern Yellow Sea, China. Although microorganisms play an important ecological role in marine ecosystems, but little is known on the response mechanism of microbial community to seasonal hypoxia in marine ranching. A total of 132 seawater samples and 47 sediment samples were collected from the marine ranching, both in the death disaster zone of sea cucumbers and the non-disaster zone, and in different months. 16S rRNA gene high-throughput sequencing was used to explore the microbial community and its influencing factors. The results showed that the stratification in community composition and dissolved oxygen content appeared in August. The Alpha diversity in seawater was higher in summer than in winter, and significant differences in Beta diversity appeared between the death disaster zone of sea cucumbers and the non-disaster zone in sediments. In addition, environmental effects explained more of the variation in bacterial community composition in seawater as compared with spatial effects did, whereas, sedimentary bacterial communities were more closely related to spatial effects. The present results could provide fundamental data for understanding the response mechanism of the microbial community to seasonal hypoxia in marine ranching and are of great significance for the management and protection of marine ranching.

Identification of groundwater microbial communities and their connection to the hydrochemical environment in southern Laizhou Bay, China

The microbial community plays an important role in the biogeochemical cycle in coastal groundwater ecosystems. However, the composition and controlling factors of the microbial community in coastal closed groundwater systems (CCGSs) with high salinity have rarely been studied. Here, we investigated and analyzed the hydrochemical characteristics and microbial community composition of seven brine samples with high total dissolved solid (TDS) values ranging from 74.5 to 132.3 g/L within and across three coastal saltworks (Yangkou, Hanting, and Changyi) in southern Laizhou Bay (SLB). The bacterial diversity was independent of salinity. Compared with those of low-salinity groundwater, the diversity of the microbial community in brine was lower, but the richness was slightly higher. There was a significant correlation between the microbial community diversity and groundwater sources, which indicated that the microbial communities were affected by groundwater sources. A comparison of the microbial community compositions of the three saltworks showed that the Hanting and Changyi saltworks had similar microbial communities due to their similar sampling depths. In addition, the main force shaping the differences in the microbial communities in both coastal open groundwater systems (COGSs) and CCGSs was identified as the hydraulic connection with the seawater controlled by hydrogeological conditions formed throughout geological history. This study can help to elucidate the biogeochemical processes in coastal aquifers.

Sediment-associated microbial community profiling: sample pre-processing through sequential membrane filtration for 16S rRNA amplicon sequencing

BACKGROUND

Sequential membrane filtration as a pre-processing step for capturing sediment-associated microorganisms could provide good quality and integrity DNA that can be preserved and kept at ambient temperatures before community profiling through culture-independent molecular techniques. However, the effects of sample pre-processing via filtration on DNA-based profiling of sediment-associated microbial community diversity and composition are poorly understood. Specifically, the influences of pre-processing on the quality and quantity of extracted DNA, high-throughput DNA sequencing reads, and detected microbial taxa need further evaluation.

RESULTS

We assessed the impact of pre-processing freshwater sediment samples by sequential membrane filtration (from 10, 5 to 0.22 μm pore size) for 16S rRNA-based community profiling of sediment-associated microorganisms. Specifically, we examined if there would be method-driven differences between non- and pre-processed sediment samples regarding the quality and quantity of extracted DNA, PCR amplicon, resulting high-throughput sequencing reads, microbial diversity, and community composition. We found no significant difference in the qualities and quantities of extracted DNA and PCR amplicons, and the read abundance after bioinformatics processing (i.e., denoising and chimeric-read filtering steps) between the two methods. Although the non- and pre-processed sediment samples had more unique than shared amplicon sequence variants (ASVs), we report that their shared ASVs accounted for 74% of both methods' absolute read abundance. More so, at the genus level, the final collection filter identified most of the genera (95% of the reads) captured from the non-processed samples, with a total of 51 false-negative (2%) and 59 false-positive genera (3%). We demonstrate that while there were differences in shared and unique taxa, both methods revealed comparable microbial diversity and community composition.

CONCLUSIONS

Our observations highlight the feasibility of pre-processing sediment samples for community analysis and the need to further assess sampling strategies to help conceptualize appropriate study designs for sediment-associated microbial community profiling.

Microbial diversity in intensively farmed lake sediment contaminated by heavy metals and identification of microbial taxa bioindicators of environmental quality

The cumulative effects of anthropogenic stress on freshwater ecosystems are becoming increasingly evident and worrisome. In lake sediments contaminated by heavy metals, the composition and structure of microbial communities can change and affect nutrient transformation and biogeochemical cycling of sediments. In this study, bacterial and archaeal communities of lake sediments under fish pressure contaminated with heavy metals were investigated by the Illumina MiSeq platform. Despite the similar content of most of the heavy metals in the lagoon sediments, we found that their microbial communities were different in diversity and composition. This difference would be determined by the resilience or tolerance of the microbial communities to the heavy metal enrichment gradient. Thirty-two different phyla and 66 different microbial classes were identified in sediment from the three lagoons studied. The highest percentages of contribution in the differentiation of microbial communities were presented by the classes Alphaproteobacteria (19.08%), Cyanophyceae (14.96%), Betaproteobacteria (9.01%) y Actinobacteria (7.55%). The bacteria that predominated in sediments with high levels of Cd and As were Deltaproteobacteria, Actinobacteria, Coriobacteriia, Nitrososphaeria and Acidobacteria (Pomacocha), Alphaproteobacteria, Chitinophagia, Nitrospira and Clostridia (Tipicocha) and Betaproteobacteria (Tranca Grande). Finally, the results allow us to expand the current knowledge of microbial diversity in lake sediments contaminated with heavy metals and to identify bioindicators taxa of environmental quality that can be used in the monitoring and control of heavy metal contamination.

The interaction of acidophiles driving community functional responses to the re-inoculated chalcopyrite bioleaching process

Re-inoculation was an effective way to improve bioleaching efficiency by enhancing the synergetic effects of biogenic Fe³⁺ coupling with S⁰ oxidation. However, the complex microbial interactions after re-inoculation have received far less attention, which was crucial to the bioleaching performances. Herein, the enriched ferrous oxidizers (FeO) or sulfur oxidizers (SO) were inoculated to chalcopyrite microcosm, then they were crossly re-inoculated again to characterize the interspecific interaction patterns. The results showed that the dominant species in Fe groups were Acidithiobacillus ferrooxidans, while A. thiooxidans predominated in S groups. Introducing FeO resulted in a great disturbance by shifting the community diversity and evenness significantly (p < 0.05). In comparison, the communities intensified by SO maintained the original composition and structures. Microbial networks were constructed positively and modularly. The networks intensified by FeO were less connected and complex with less nodes and edges, but showed faster responses to the re-inoculation disturbance reflected by shorter average path length. Interestingly, the genus Leptospirillum were identified as keystones in S groups, playing critical roles in iron-oxidizing with lots of sulfur oxidizers. The introduced sulfur oxidizers enhanced microbial cooperation, formed robust community with strong bio-dissolution capability, and harbored the highest bioleaching efficiency. These findings improved our understanding about the acidophiles interactions, which drive community functional responses to the re-inoculated bioleaching process.

Effects of chronic exposure of antibiotics on microbial community structure and functions in hyporheic zone sediments

Microbial communities in hyporheic zones (HZ) provide vital biogeochemical functions such as contaminant degradation for river ecosystems. Antibiotics are contaminants that have been increasingly detected in HZ sediments. In this study, sediments from different HZ locations in a contaminated river, Maozhou river, China were sampled and analyzed using qPCR and high-throughput sequencing to investigate the effect of antibiotic contamination on microbial community structures and functions in HZ sediments. Results indicated that types and concentrations of antibiotics in HZ sediments were heterogeneously distributed that were largely consistent with the distribution of antibiotic sources. Sediments near animal farm and hospital contained higher antibiotic concentrations compared with those from mainstream. The distribution of ARGs was well correlated with antibiotics. Bacterial indicator genera indicating differences between mainstream area and other sampling areas were positively correlated with antibiotics, suggesting the influences of antibiotics on reshaping microbial community structures. PICRUSt revealed positive relationships between antibiotics and predicted functional genes involved in defense, signal transduction, and recombination and repair. This imply the defensive response of microbial communities on antibiotic attack. These results indicated that antibiotic contamination in the watershed posed a potential risk on HZ microbial community structures and functions, which may further threaten river ecosystem functions.

Global Trends of Benthic Bacterial Diversity and Community Composition Along Organic Enrichment Gradients of Salmon Farms

The analysis of benthic bacterial community structure has emerged as a powerful alternative to traditional microscopy-based taxonomic approaches to monitor aquaculture disturbance in coastal environments. However, local bacterial diversity and community composition vary with season, biogeographic region, hydrology, sediment texture, and aquafarm-specific parameters. Therefore, without an understanding of the inherent variation contained within community complexes, bacterial diversity surveys conducted at individual farms, countries, or specific seasons may not be able to infer global universal pictures of bacterial community diversity and composition at different degrees of aquaculture disturbance. We have analyzed environmental DNA (eDNA) metabarcodes (V3-V4 region of the hypervariable SSU rRNA gene) of 138 samples of different farms located in different major salmon-producing countries. For these samples, we identified universal bacterial core taxa that indicate high, moderate, and low aquaculture impact, regardless of sampling season, sampled country, seafloor substrate type, or local farming and environmental conditions. We also discuss bacterial taxon groups that are specific for individual local conditions. We then link the metabolic properties of the identified bacterial taxon groups to benthic processes, which provides a better understanding of universal benthic ecosystem function(ing) of coastal aquaculture sites. Our results may further guide the continuing development of a practical and generic bacterial eDNA-based environmental monitoring approach.

The response of microbial community structure and sediment properties to anthropogenic activities in Caohai wetland sediments

This study aimed to investigate the response of sediment microbial communities (including bacteria and archaeal groups) in Caohai Lake to anthropogenic activities. The sediment samples were collected from the regions with high anthropogenic interference and low anthropogenic interference. Their physicochemical properties and enzyme activities were analyzed, and the bacterial and archaeal communities were investigated using high-throughput sequencing technology. The results showed that the physicochemical characters changed by anthropogenic activities were the important factors that influenced enzyme activities, alpha diversity, key functional taxa, and community structure. And the impact of anthropogenic activities on microbial communities might follow a non-linear pattern. Furthermore, few significant differences of alpha indices between the high and low disturbed areas, but clear differences of microbial community composition analysis and beta-diversity analysis were observed. The hypothesis was proved that the intensity of anthropogenic impacts in Caohai had not reached the potential thresholds. The best distinguish biomarkers between the two areas and the most related key nodes among the network did not always have a high microbial abundance. The anthropogenic activities might influence the microbial community by affecting a small number of the key taxon in the ecological network. These findings provided a valuable understanding of how sediment microorganisms respond to anthropogenic activities in Caohai Lake.

Microplastic pollution and its relationship with the bacterial community in coastal sediments near Guangdong Province, South China

The ecological stress caused by microplastic (MP) pollution in marine environments has attracted global attention. However, few studies have investigated the relationship between MP pollution and the microbial community in natural sediments. This study was the first to systematically characterize MP pollution (i.e., its abundance, shape, size and color) and investigate its relationship with the bacterial community in coastal sediments from Guangdong, South China, by microscopic observation and Illumina sequencing. The results of this study indicated that the abundance of microplastics (MPs), which was 344 ± 24 items/kg in 33 coastal sediments from 11 sites from South China, represented a relatively high level of MP pollution. MPs with sizes of <0.5 m, 0.5-1.0 mm and 1-2 mm accounted for the highest proportion (75%) in the sediments. Fiber/film (82%) and white/blue (91%) were the dominant shapes and colors, respectively, in all MP samples. Furthermore, the abundances, three shapes (fiber, film and fragment), three sizes (<0.5 mm, 0.5-1.0 mm and 1-2 mm), and two colors (blue and white) of MPs displayed positive correlations with some potential pathogens, including Vibrio, Pseudomonas, Bacillus and Streptococcus, but exhibited negative correlations with an environmentally friendly bacterial genus, Sphingomonas (which degrades various hazardous organic compounds), indicating that MPs might increase the potential ecological risks of coastal sediments. Our results may help to elucidate the relationship between MP pollution and the microbial community in coastal sediments.

Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring

Bioindication has become an indispensable part of water quality monitoring in most countries of the world, with the presence and abundance of bioindicator taxa, mostly multicellular eukaryotes, used for biotic indices. In contrast, microbes (bacteria, archaea and protists) are seldom used as bioindicators in routine assessments, although they have been recognized for their importance in environmental processes. Recently, the use of molecular methods has revealed unexpected diversity within known functional groups and novel metabolic pathways that are particularly important in energy and nutrient cycling. In various habitats, microbial communities respond to eutrophication, metals, and natural or anthropogenic organic pollutants through changes in diversity and function. In this review, we evaluated the common trends in these changes, documenting that they have value as bioindicators and can be used not only for monitoring but also for improving our understanding of the major processes in lotic and lentic environments. Current knowledge provides a solid foundation for exploiting microbial taxa, community structures and diversity, as well as functional genes, in novel monitoring programs. These microbial community measures can also be combined into biotic indices, improving the resolution of individual bioindicators. Here, we assess particular molecular approaches complemented by advanced bioinformatic analysis, as these are the most promising with respect to detailed bioindication value. We conclude that microbial community dynamics are a missing link important for our understanding of rapid changes in the structure and function of aquatic ecosystems, and should be addressed in the future environmental monitoring of freshwater ecosystems.

Microbial community compositions and sulfate-reducing bacterial profiles in malodorous urban canal sediments

Anthropogenically impacted urban canals represent distinct freshwater ecosystems that could shape microbial communities in underlying sediments; however, knowledge of the relationships between environmental factors and microbial community compositions and their functions in such an environment is limited. This study characterized the microbial community compositions of malodorous canal sediments at six locations along the Saen Saep Canal in Thailand. 16S rRNA gene amplicon sequencing (MiSeq, Illumina) revealed dominant genera classified as fermentative bacteria, methanogens, and sulfate-reducing bacteria (SRB), all of which emphasized anaerobic environments. SRB, as the primary producers of malodorous hydrogen sulfide, accounted for 8.2-30.4% of the total sequences. dsrB gene clone libraries further identified the SRB species. A constrained correspondence analysis demonstrated a spatial pattern of SRB that correlated with physicochemical parameters in which nitrate and sulfate in sediments were the most influencing factors. Overall, a better understanding of the SRB and other related microorganisms in canal sediments can assist in the future implementation of appropriate olfactory abatement and management methodologies in urban canals.

Critical evaluation of biodegradation studies on synthetic plastics through a systematic literature review

Increasing amounts of plastic waste in the environment and their fragmentation into smaller particles known as microplastics (particles, <5mm) have raised global concerns due to their persistency in the environment and their potential to act as vectors for harmful substances or pathogenic microorganisms. One possible solution to this problem is biodegradation of plastics by microorganisms. However, the scientific information on plastic-degrading microorganisms is scattered across different scientific publications. We conducted a systematic literature review (SLR) with predefined criteria using the online databases of Scopus and Web of Science to find papers on bacterial biodegradation of synthetic petroleum-based polymers. The aims of this SLR were to provide an updated list of all of the currently known bacteria claimed to biodegrade synthetic plastics, to determine and define the best methods to assess biodegradation, to critically evaluate the existing studies, and to propose directions for future research on polymer biodegradation in support of more rapid development of biodegradation technologies. Most of the bacteria identified here from the 145 reviewed papers belong to the phyla Proteobacteria, Firmicutes and Actinobacteria, and most were isolated from contaminated sites, such as landfill sites. Just under a half of the studies (44%) investigated the biodegradability of polyethylenes and derivates, particularly low-density polyethylenes. The methods used to monitor the biodegradation were mainly scanning electron microscopy and Fourier-transform infrared spectroscopy. We propose that: (1) future research should focus on biodegradation of microplastics arising from the most common pollutants (e.g. polyethylenes); (2) bacteria should be isolated from environments that are permanently contaminated with plastics; and (3) a combination of different observational methods should be used to confirm bacterial biodegradation of these plastics. Finally, when reporting, researchers need to follow standard protocols and include all essential information needed for repetition of the experiments by other research groups.

Profiling multiple heavy metal contamination and bacterial communities surrounding an iron tailing pond in Northwest China

Northwest China is abundant in iron ore reserves and has become one of the important iron ore mining bases in China. However, the contamination and microbial community structure of iron tailing ponds in Northwest China have not been extensively investigated. In the present study, we characterized the main physicochemical properties, the multiple heavy metal contamination, and the bacterial community structure of the soils surrounding an iron tailing pond in Linze County, Zhangye city, Gansu Province. The tailing-associated soils were barren, exhibiting alkaline pH and low organic matter (OM), total nitrogen (TN) and total potassium (TK) compared with the control areas. There was considerable multiple heavy metal pollution in the iron tailing pond, mainly including lead (Pb), manganese (Mn), arsenic (As), cadmium (Cd), zinc (Zn), iron (Fe) and copper (Cu). Among the 303 identified core operational taxonomic units (OTUs), Actinobacteria, Proteobacteria and Deinococcus-Thermus were predominant at the phylum level, and Blastococcus, Arthrobacter, Marmoricola, Kocuria, Truepera, and Sphingomonadaceae were prevalent at a finer taxonomic level. The bacterial richness and diversity of the tailing samples were significantly lower than those of the reference samples. RDA, VPA and Spearman correlation analyses showed that the soil pH, CEC, OM, TP, TK, Cd, Pb, Ni, Zn, As and Mn had significant effects on the bacterial community composition and distribution. This work profiles the basic features of the soil physicochemical properties, the multiple heavy metal contamination and the bacterial community structure in an iron tailing pond in Northwest China, thereby providing a foundation for the future ecological remediation of the iron tailing environment in the area.

Contaminated aquatic sediments

The remediation of contaminated aquatic sediments requires a range of expertise from assessment (investigation, risk evaluations, modeling, and remedy selection) to design and construction. Research in 2019 has added to knowledge on optimizing the use of passive samplers for assessing chemical concentrations in sediment porewater. The porewater and black carbon appear to be better predictors of contaminant bioaccumulation than total organic carbon alone. This has led to better characterization of potential risk at sediment sites. Tools to identify and model sources of chemicals have been developed and used particularly for some metals, polynuclear aromatic hydrocarbons and polychlorinated biphenyls. There is great emphasis on beneficially using dredged sediment, treating it as a resource rather than a waste. Amendments used in sediment caps continue to be refined including the use of activated carbon within the caps and by itself. A technique involving 16S rRNA has been established as a means of identifying microbiological composition that naturally degrade contaminants. © 2020 Water Environment Federation PRACTITIONER POINTS: Sediment capping technology continues to advance Sampling and testing methods continue to be refined Natural processes such as biodegradation are being better understood Beneficial use of dredged sediment continue to be emphasized.

Characteristics of spatial and seasonal bacterial community structures in a river under anthropogenic disturbances

In this study, the seasonal characteristics of microbial community compositions at different sites in a river under anthropogenic disturbances (Maozhou River) were analyzed using Illumina HiSeq sequencing. Taxonomic analysis revealed that Proteobacteria was the most abundant phylum in all sites, followed by Actinobacteria, Bacteroidetes, Chloroflexi, Acidobacteria and Firmicutes. The variations of the community diversities and compositions between the seasons were not significant. However, significant differences between sites as well as water and sediment samples were observed. These results indicated that sites under different levels of anthropogenic disturbances have selected distinct bacterial communities. pH, dissolved oxygen (DO), concentrations of total nitrogen (TN) and heavy metals were the main factors that influence the diversity and the composition of bacterial community. Specifically, the relative abundance of Proteobacteria was negatively correlated with pH and DO and positively correlated with TN, while Actinobacteria and Verrucomicrobia showed the opposite pattern. Moreover, positive correlations between the relative abundances of Firmicutes and Bacteroidetes and the concentration of heavy metals were also found. Results of functional prediction analysis showed no significant differences of the carbon, nitrogen and phosphorus metabolism across the sites and seasons. Potential pathogens such as Vibrio, Arcobacter, Acinetobacter and Pseudomonas were found in these samples, which may pose potential risks for environment and human health. This study reveals the effect of anthropogenic activities on the riverine bacterial community compositions and provides new insights into the relationships between the environmental factors and the bacterial community distributions in a freshwater ecosystem under anthropogenic disturbances.

Characterizing a riverine microbiome impacted by extreme disturbance caused by a mining sludge tsunami

Studies on disturbance events in riverine systems caused by environmental disasters and their effects on microbial diversity are scarce. Here, we evaluated the impact of the collapse of an iron ore dam holding approximately 50 million cubic meters of waste on both water and sediment microbiomes by deeply sequencing the 16S rRNA gene. Samples were taken from two impacted rivers and one reference river 7, 30 and 150 days postdisturbance. The impacted community structure changed greatly over spatiotemporal scales, being less diverse and more uneven, particularly on day 7 for the do Carmo River (the closest to the dam). However, the reference community structure remained similar between sampling events. Moreover, the impacted sediments were positively correlated with metals. The taxa abundance varied greatly over spatiotemporal scales, allowing for the identification of several potential bioindicators, e.g., Comamonadaceae, Novosphingobium, Sediminibacterium and Bacteriovorax. Our results showed that the impacted communities consisted mostly of Fe(II) oxidizers and Fe(III) reducers, aromatic compound degraders and predator bacteria. Network analysis showed a highly interconnected microbiome whose interactions switched from positive to negative or vice versa between the impacted and reference communities. This work revealed potential molecular signatures associated with the rivers heavily impacted by metals that might be useful sentinels for predicting riverine health.

Spatial-temporal distribution of microplastics in surface water and sediments of Maozhou River within Guangdong-Hong Kong-Macao Greater Bay Area

Concerns over the negative impacts of microplastics on human health have led to growing attention on the occurrence of microplastics in aquatic environment. Recent studies have extended their focus from marine to inland waters, especially on the spatial-temporal distribution of the microplastics in urban rivers. In this study, Maozhou River, the largest river in Shenzhen, a tributary of the Pearl River, was selected as a representative inland waterway of Guangdong-Hong Kong-Macao Greater Bay Area. The spatial-temporal investigation was performed on microplastics in the surface water and sediments of 17 sites along the mainstream of the Maozhou River. Results show that microplastics were widely and unevenly distributed along the river and reached the high abundances on the site most intensively surrounded by industries as well as the sites downstream. The abundances in dry season ranged from 4.0 ± 1.0 to 25.5 ± 3.5 items·L^-1 in water and 35 ± 15 to 560 ± 70 item·kg^-1 in sediments, which were relatively higher than those observed in the wet season (water: 3.5 ± 1.0 to 10.5 ± 2.5 items·L^-1; sediments: 25 ± 5 to 360 ± 90 item·kg^-1; p value < 0.05). The dominant types of the microplastics were identified as: PE Polyethylene (PE, water: 45.0%, sediments: 42.0%), polypropylene (PP, water and sediments: 12.5%), polystyrene (PS, water: 34.5%; sediments 14.5%) and polyvinyl chloride (PVC, water: 2.0%; sediments: 15%). Moreover, metals like Al, Si, Ca were discovered on the rough surface of the microplastics, indicating the interactions between the microplastics and the aquatic environment. Through a comprehensive comparison with other major inland waters in China, this work provides valuable data on the microplastics pollution of a representative inland water in the Greater Bay Area, and will further contribute to a better understanding on the land-based input of microplastics from the intensively affected inland waters.

Dissolved Metal(loid) Concentrations and Their Relations with Chromophoric and Fluorescent Dissolved Organic Matter in an Urban River in Shenzhen, South China

Urbanization is often accompanied by aquatic metal(loid) pollution, which is regulated by dissolved organic matter (DOM). However, the relationships between dissolved metal(loid) concentration and the bulk, chromophoric, and fluorescent DOM in black and odorous urban rivers are still poorly understood. Here, we investigated the dissolved metal(loid) concentrations of Zn, Cu, Cr, As, Pb, and Cd and their correlations with DOM-related parameters in water samples from a polluted urbanized watershed in Shenzhen, China. The results showed that the Zn and Cu concentrations in the mainstream and tributary exceeded the national standards, and the wastewater treatment plant (WWTP) was an important source, as indicated by the abrupt concentration increases downstream of the WWTP. The dissolved metal(loid) concentrations were not always significantly correlated with the dissolved organic carbon (DOC) concentration or the ultraviolet absorbance at 254 nm (UV254); however, they were more likely to be correlated with the maximum fluorescence intensity (Fmax) of protein-like fluorescent DOM components. A strong correlation between the Cu/DOC ratio and specific UV254 (SUVA254) previously reported did not exist in the present study. Instead, the Cu/DOC ratio was positively correlated with the Fmax/DOC ratios for protein-like fluorescent DOM components. Our study highlights that protein-like fluorescent DOM may be more important than humic-like fluorescence DOM and chromophoric DOM in terms of interacting with dissolved metal(loid)s in black and odorous urban rivers.

Dynamics of bacterial community in Tonle Sap Lake, a large tropical flood-pulse system in Southeast Asia

Tonle Sap Lake, the largest freshwater body in Southeast Asia, plays an important role in lives and environment. The lake is reportedly under anthropogenic pressure and suffers from eutrophication. The floating villagers suffer from waterborne diseases. However, the shift in bacterial community due to human activities in this great lake has not yet been reported. We aimed to determine the dynamics of the bacterial community and their concentration in the lake using 67 surface waters, 53 sub-layer waters and 59 sediment samples by Next Generation Sequencing (NGS). The bacterial communities in the surface water and sub-layer water were similar but they differed from the sediment; however, their abundance showed spatiotemporal variations. The bacterial diversity reached the highest value in the dry season but lowest value in the rainy season in the surface water and sediment. Their diversity in the sub-layer water was highest in the transition from dry to rainy season. The total 16S rRNA gene copy number in the sediment were >100 times higher than that measured in the water. The Cyanobacteria, Actinobacteria, and Proteobacteria concentrations in the lake water increased in the dry season and reached a peak in the transition from dry to rainy season. The concentrations of Proteobacteria and Firmicutes elevated in the lake water and sediment, respectively, in the floating villages which were >10 times higher than the places with non-point sources. The bacterial concentration and its diversity in the Tonle Sap Lake changed based on the lake water volume between rainy and dry season. The bacterial concentration in the Tonle Sap Lake diluted with the water inflow from Mekong River and its tributaries in the rainy season. As influenced by the fecal waste, the bacterial community in the floating villages differed from the places with non-point source.

Occurrence of antibiotics in the main rivers of Shenzhen, China: Association with antibiotic resistance genes and microbial community

The occurrence and distribution of antibiotics were investigated in surface water and sediment collected from the main rivers of Shenzhen, China. Total concentrations of 20 selected antibiotics ranged from 36.510 to 1075.687 ng L^-1 (mean 244.992 ng L^-1) in 31 water samples and from 28.124 to 2728.810 ng g^-1 (mean 680.169 ng g^-1) in 31 sediment samples. Notably, STZ and SDZ were the dominant antibiotics in both water and sediment as their higher concentrations compared with the other compounds. Furthermore, comprehensive profiling of antibiotic resistance genes (ARGs) and microbial community was performed to gain an understanding of the evolution and dissemination of ARGs in microbial communities caused by the occurrence of antibiotics in sediment samples from Maozhou River. As a result, the sul1 gene was found to be the most abundant ARG and Proteobacteria was the most abundant microorganism in all the samples (37.4-51.7%), followed by Bacteroidetes (15.3-18.4%). Statistical analysis figured out the relations among antibiotics, ARGs and microbial community. A specific conclusion could be drawn from the positive correlations among the bla_d gene, Fusobacteria, and sulfamethoxazole. It suggests that antibiotics may be positively linked to the expression of ARGs in certain bacteria, and thus high reproduction would occur within the bacterial community. Overall, the widespread distribution of ARGs underscores the need for further research on the mechanism of antibiotics influence as emerging contaminants in the environment and the associated risks to microbial community.