Prevalence of Antibiotic Resistance Genes and Bacterial Community Composition in a River Influenced by a Wastewater Treatment Plant

Antibiotic resistance represents a global health problem, requiring better understanding of the ecology of antibiotic resistance genes (ARGs), their selection and their spread in the environment. Antibiotics are constantly released to the environment through wastewater treatment plant (WWTP) effluents. We investigated, therefore, the effect of these discharges on the prevalence of ARGs and bacterial community composition in biofilm and sediment samples of a receiving river. We used culture-independent approaches such as quantitative PCR to determine the prevalence of eleven ARGs and 16S rRNA gene-based pyrosequencing to examine the composition of bacterial communities. Concentration of antibiotics in WWTP influent and effluent were also determined. ARGs such as qnrS, bla _TEM, bla _CTX-M, bla _SHV, erm(B), sul(I), sul(II), tet(O) and tet(W) were detected in all biofilm and sediment samples analyzed. Moreover, we observed a significant increase in the relative abundance of ARGs in biofilm samples collected downstream of the WWTP discharge. We also found significant differences with respect to community structure and composition between upstream and downstream samples. Therefore, our results indicate that WWTP discharges may contribute to the spread of ARGs into the environment and may also impact on the bacterial communities of the receiving river.     

Diversity,abundance, and spatial distribution of riverine microbial communities response to effluents from swine farm versus farmhouse restaurant

The 454 pyrosequencing technique was applied to evaluate microbial community composition in sediment and water samples collected from the river receiving effluents from a swine farm and a farmhouse restaurant, respectively. For each sample, 4,600 effective sequences were selected and used to do the bacterial diversity and abundance analysis, respectively. Bacterial phylotype richness in the river sediment sample without effluent input was higher than the other samples, and the river water sample with addition of effluent from the swine farm had the least richness. Effluents from both the swine farm and the farmhouse restaurant have the potential to decrease the bacterial diversity and abundance in the river sediment and water, especially it is more significant in the river sediment. Effect of effluent from the swine farm on riverine bacterial communities was more significant than that from the farmhouse restaurant. Characterization of bacterial community composition in sediments from two tributaries of the downstream river showed that various effluents from the swine farm and the farmhouse restaurant have the similar potential to reduce the natural variability in riverine ecosystems, and contribute to the biotic homogenization in the river sediment.     

Characterization of Bacterial Communities in Sediments Receiving Various Wastewater Effluents with High-Throughput Sequencing Analysis

454 Pyrosequencing was applied to examine bacterial communities in sediment samples collected from a river receiving effluent discharge from rural domestic sewage (RDS) and various factories, including a tannery (TNS), clothing plant (CTS), and button factory (BTS), respectively. For each sample, 4,510 effective sequences were selected and utilized to do the bacterial diversity and abundance analysis, respectively. In total, 1,288, 2,036, 1,800, and 2,150 operational taxonomic units were obtained at 3 % distance cutoff in TNS, CTS, BTS, and RDS, respectively. Bacterial phylotype richness in RDS was higher than the other samples, and TNS had the least richness. The most predominant class in the TNS, CTS, and BTS samples is Betaproteobacteria. Cyanobacteria (no_rank) is the most predominant one in the RDS sample. Circa 31 % sequences in TNS were affiliated with the Rhodocyclales order. In the four samples, Aeromonas, Arcobacter, Clostridium, Legionella, Leptospira, Mycobacterium, Pseudomonas, and Treponema genera containing pathogenic bacteria were detected. Characterization of bacterial communities in sediments from various downstream branches indicated that distinct wastewater effluents have similar potential to reduce the natural variability in river ecosystems and contribute to the river biotic homogenization.     

Effects of Farmhouse Hotel and Paper Mill Effluents on Bacterial Community Structures in Sediment and Surface Water of Nanxi River,China

The pyrosequencing technique was used to evaluate bacterial community structures in sediment and surface water samples taken from Nanxi River receiving effluents from a paper mill and a farmhouse hotel, respectively. For each sample, 4,610 effective bacterial sequences were selected and used to do the analysis of diversity and abundance, respectively. Bacterial phylotype richness in the sediment sample without effluent input was higher than the other samples, and the surface water sample with addition of effluent from the paper mill contained the least richness. Effluents from both the paper mill and farmhouse hotel have a potential to reduce the bacterial diversity and abundance in the sediment and surface water, especially it is more significant in the sediment. The effect of the paper mill effluent on the sediment and surface water bacterial communities was more serious than that of the farmhouse hotel effluent. Characterization of microbial community structures in the sediment and surface water from two tributaries of the downstream river indicated that various effluents from the paper mill and farmhouse hotel have the similar potential to decrease the natural variability in riverine microbial ecosystems.     

Metagenomic Profiling of Microbial Composition and Antibiotic Resistance Determinants in Puget Sound

Human-health relevant impacts on marine ecosystems are increasing on both spatial and temporal scales. Traditional indicators for environmental health monitoring and microbial risk assessment have relied primarily on single species analyses and have provided only limited spatial and temporal information. More high-throughput, broad-scale approaches to evaluate these impacts are therefore needed to provide a platform for informing public health. This study uses shotgun metagenomics to survey the taxonomic composition and antibiotic resistance determinant content of surface water bacterial communities in the Puget Sound estuary. Metagenomic DNA was collected at six sites in Puget Sound in addition to one wastewater treatment plant (WWTP) that discharges into the Sound and pyrosequenced. A total of ∼550 Mbp (1.4 million reads) were obtained, 22 Mbp of which could be assembled into contigs. While the taxonomic and resistance determinant profiles across the open Sound samples were similar, unique signatures were identified when comparing these profiles across the open Sound, a nearshore marina and WWTP effluent. The open Sound was dominated by α-Proteobacteria (in particular Rhodobacterales sp.), γ-Proteobacteria and Bacteroidetes while the marina and effluent had increased abundances of Actinobacteria, β-Proteobacteria and Firmicutes. There was a significant increase in the antibiotic resistance gene signal from the open Sound to marina to WWTP effluent, suggestive of a potential link to human impacts. Mobile genetic elements associated with environmental and pathogenic bacteria were also differentially abundant across the samples. This study is the first comparative metagenomic survey of Puget Sound and provides baseline data for further assessments of community composition and antibiotic resistance determinants in the environment using next generation sequencing technologies. In addition, these genomic signals of potential human impact can be used to guide initial public health monitoring as well as more targeted and functionally-based investigations.     

Bacterial Community Composition in Central European Running Waters Examined by Temperature Gradient Gel Electrophoresis and Sequence Analysis of 16S rRNA Genes

The bacterial community composition in small streams and a river in central Germany was examined by temperature gradient gel electrophoresis (TGGE) with PCR products of 16S rRNA gene fragments and sequence analysis. Complex TGGE band patterns suggested high levels of diversity of bacterial species in all habitats of these environments. Cluster analyses demonstrated distinct differences among the communities in stream and spring water, sandy sediments, biofilms on stones, degrading leaves, and soil. The differences between stream water and sediment were more significant than those between sites within the same habitat along the stretch from the stream source to the mouth. TGGE data from an entire stream course suggest that, in the upper reach of the stream, a special suspended bacterial community is already established and changes only slightly downstream. The bacterial communities in water and sediment in an acidic headwater with a pH below 5 were highly similar to each other but deviated distinctly from the communities at the other sites. As ascertained by nucleotide sequence analysis, stream water communities were dominated by Betaproteobacteria (one-third of the total bacteria), whereas sediment communities were composed mainly of Betaproteobacteria and members of the Fibrobacteres/Acidobacteria group (each accounting for about 25% of bacteria). Sequences obtained from bacteria from water samples indicated the presence of typical cosmopolitan freshwater organisms. TGGE bands shared between stream and soil samples, as well as sequences found in bacteria from stream samples that were related to those of soil bacteria, demonstrated the occurrence of some species in both stream and soil habitats. Changes in bacterial community composition were correlated with geographic distance along a stream, but in comparisons of different streams and rivers, community composition was correlated only with environmental conditions.     

The Soil Bacterial Communities of South African Fynbos Riparian Ecosystems Invaded by Australian Acacia Species

Riparian ecosystem along rivers and streams are characterised by lateral and longitudinal ecological gradients and, as a result, harbour unique biodiversity. Riparian ecosystems in the fynbos of the Western Cape, South Africa, are characterised by seasonal dynamics, with summer droughts followed by high flows during winter. The unique hydrology and geomorphology of riparian ecosystems play an important role in shaping these ecosystems. The riparian vegetation in the Western Cape has, however, largely been degraded due to the invasion of non-indigenous plants, in particular Acacia mearnsii, A. saligna and A. dealbata. This study investigated the effect of hydrology and invasion on the bacterial communities associated with fynbos riparian ecosystems. Bacterial communities were characterised with automated ribosomal intergenic spacer analysis (ARISA) and 454 16S rDNA pyrosequencing. Chemical and physical properties of soil within sites were also determined and correlated with community data. Sectioning across the lateral zones revealed significant differences in community composition, and the specific bacterial taxa influenced. Results also showed that the bacterial community structure could be linked to Acacia invasion. The presence of invasive Acacia was correlated with specific bacterial phyla. However, high similarity between cleared and pristine sites suggests that the effect of Acacia on the soil bacterial community structure may not be permanent. This study demonstrates how soil bacterial communities are influenced by hydrological gradients associated with riparian ecosystems and the impact of Acacia invasion on these communities.     

Distribution of sediment bacterial and archaeal communities in plateau freshwater lakes

Both Bacteria and Archaea might be involved in various biogeochemical processes in lacustrine sediment ecosystems. However, the factors governing the intra-lake distribution of sediment bacterial and archaeal communities in various freshwater lakes remain unclear. The present study investigated the sediment bacterial and archaeal communities in 13 freshwater lakes on the Yunnan Plateau. Quantitative PCR assay showed a large variation in bacterial and archaeal abundances. Illumina MiSeq sequencing illustrated high bacterial and archaeal diversities. Bacterial abundance was regulated by sediment total organic carbon and total nitrogen, and water depth, while nitrate nitrogen was an important determinant of bacterial diversity. Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, and Verrucomicrobia were the major components of sediment bacterial communities. Proteobacteria was the largest phylum, but its major classes and their proportions varied greatly among different lakes, affected by sediment nitrate nitrogen. In addition, both Euryarchaeota and Crenarchaeota were important members in sediment archaeal communities, while unclassified Archaea usually showed the dominance.     

城镇化背景下深圳典型流域鱼类群落特征及驱动因子

理解城镇的快速发展对河流鱼类群落结构的影响,是城镇河流科学管理和生物多样性保护的关键基础。本研究于2019年丰水期（8月）和枯水期（11月）,选取我国城镇化典型城市-深圳域内两个处于不同城镇化程度的代表性流域,应用多重统计方法比较分析了流域间鱼类群落结构的差异,并探讨了驱动鱼类群落变异的关键环境要素。结果发现,城镇化程度高的观澜河流域其鱼类种类组成、优势类群、生物多样性指数与城镇化程度低的坪山河流域有明显差别。 具体表现为：城镇化程度高的流域土著敏感种类如异鱲、吸鳅等几近消失,优势类群为外来入侵耐受种类,其物种多样性显著低于城镇化程度低的流域（P<0.05）。同时,外来鱼类在城镇河段其数量占比平均达92.5%,广泛分布于深圳城镇河流中。在环境因素方面,城镇化程度高的观澜河流域水体理化指标总氮、总磷、氨氮、化学需氧量、生化需氧量、高锰酸盐指数均显著性高于城镇化程度低的坪山河流域（P<0.05）。基于Bray-Curtis距离的冗余分析显示：城镇用地占比和总氮是影响观澜河和坪山河流域鱼类群落差异的主要因素。城镇化进程中河流生境的改变已影响到土著鱼类的生物多样性。因此,推动以恢复土著鱼类生物多样性的河流生态治理与保护是今后水生态目标管理的重要方向。     

Bacterial community shift revealed Chromatiaceae and Alcaligenaceae as potential bioindicators in the receiving river due to palm oil mill effluent final discharge

A thorough outlook on the effect of palm oil mill effluent (POME) final discharge towards bacterial community dynamics in the receiving river is provided in this study by using a high-throughput MiSeq. The shift of bacterial composition could be used to determine the potential bacterial indicators to indicate contamination caused by POME. This study showed that the POME final discharge did not only alter the natural physicochemical properties of the river water but also caused the reduction of bacterial diversity in the receiving river. The Chromatiaceae and Alcaligenaceae which were not detected in the upstream but were detected in the downstream part of the river are proposed as the indicator bacteria to indicate the river water contamination caused by POME final discharge. The emergence of either one or both bacteria in the downstream part of the river were shown to be carried over by the effluent. Therefore, an accurate pollution monitoring approach using bacterial indicator is expected to complement the conventional POME pollution assessment method which is currently dependent on the physicochemical properties of the final discharge. This is the first study that reported on the potential indicator bacteria for the assessment of river water contamination caused by POME final discharge.     

Temporal dynamics of sediment bacterial communities in monospecific stands of Juncus maritimus and Spartina maritima

In the present study, we used 16S rRNA barcoded pyrosequencing to investigate to what extent monospecific stands of different salt marsh plant species (Juncus maritimus and Spartina maritima), sampling site and temporal variation affect sediment bacterial communities. We also used a bioinformatics tool, PICRUSt, to predict metagenome gene functional content. Our results showed that bacterial community composition from monospecific stands of both plant species varied temporally, but both host plant species maintained compositionally distinct communities of bacteria. Juncus sediment was characterised by higher abundances of Alphaproteobacteria, Myxococcales, Rhodospirillales, NB1–j and Ignavibacteriales, while Spartina sediment was characterised by higher abundances of Anaerolineae, Synechococcophycidae, Desulfobacterales, SHA–20 and Rhodobacterales. The differences in composition and higher taxon abundance between the sediment bacterial communities of stands of both plant species may be expected to affect overall metabolic diversity. In line with this expectation, there were also differences in the predicted enrichment of selected metabolic pathways. In particular, bacterial communities of Juncus sediment were predicted to be enriched for pathways related to the degradation of various (xenobiotic) compounds. Bacterial communities of Spartina sediment in turn were predicted to be enriched for pathways related to the biosynthesis of various bioactive compounds. Our study highlights the differences in composition and predicted functions of sediment‐associated bacterial communities from two different salt marsh plant species. Loss of salt marsh habitat may thus be expected to both adversely affect microbial diversity and ecosystem functioning and have consequences for environmental processes such as nutrient cycling and pollutant remediation.     

Comparative metagenomic,phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients

Terrestrial ecosystems are receiving elevated inputs of nitrogen (N) from anthropogenic sources and understanding how these increases in N availability affect soil microbial communities is critical for predicting the associated effects on belowground ecosystems. We used a suite of approaches to analyze the structure and functional characteristics of soil microbial communities from replicated plots in two long-term N fertilization experiments located in contrasting systems. Pyrosequencing-based analyses of 16S rRNA genes revealed no significant effects of N fertilization on bacterial diversity, but significant effects on community composition at both sites; copiotrophic taxa (including members of the Proteobacteria and Bacteroidetes phyla) typically increased in relative abundance in the high N plots, with oligotrophic taxa (mainly Acidobacteria) exhibiting the opposite pattern. Consistent with the phylogenetic shifts under N fertilization, shotgun metagenomic sequencing revealed increases in the relative abundances of genes associated with DNA/RNA replication, electron transport and protein metabolism, increases that could be resolved even with the shallow shotgun metagenomic sequencing conducted here (average of 75 000 reads per sample). We also observed shifts in the catabolic capabilities of the communities across the N gradients that were significantly correlated with the phylogenetic and metagenomic responses, indicating possible linkages between the structure and functioning of soil microbial communities. Overall, our results suggest that N fertilization may, directly or indirectly, induce a shift in the predominant microbial life-history strategies, favoring a more active, copiotrophic microbial community, a pattern that parallels the often observed replacement of K-selected with r-selected plant species with elevated N.     

Antibiotic-resistance profile in environmental bacteria isolated from penicillin production wastewater treatment plant and the receiving river

The antibiotic‐resistance characteristics of bacterial strains in antibiotic production wastewater treatment plants (WWTP) that contain high concentrations of antibiotics are unknown, as are the environmental effects of the discharge of wastewater from such facilities. In this study, 417 strains were individually isolated from the effluent of a WWTP that treated penicillin G production wastewater, as well as from downstream and upstream areas of the receiving river. The minimum inhibition concentrations (MICs) of 18 antibiotics representing seven classes were then determined for each of these strains. Relatively high similarity in the bacterial composition existed between the wastewater and downstream river samples when compared with the upstream sample. High resistance ratios and MIC values were observed for almost all antibiotics in wastewater isolates, followed by strains from downstream river, of which the resistance ratios and levels were still significantly higher than those of upstream strains. The resistance ratios and levels also significantly differed among strains belonged to different species in the penicillin production wastewater effluent and downstream river. In both samples, the resistances to β‐lactam antibiotics were more frequent, with much higher levels, than the other class antibiotics. Then five clinically important resistant genes mainly coding for extended‐spectrum β‐lactamases (ESBLs) were determined for all strains, only bla_TEM‐1 which did not belong to ESBL was detected in 17.3% and 11.0% of strains isolated from wastewater and downstream river respectively. Class I integrons were detected in 14% of wastewater isolates and 9.1% of downstream isolates, and primarily contained gene cassettes conferring resistance to aminoglycoside antibiotics. The unexpectedly high levels of multiple antibiotic resistance in strains from wastewater and downstream river were speculated to be mainly due to multidrug efflux systems.     

Phosphorus chemistry and bacterial community composition interact in brackish sediments receiving agricultural discharges

Background

External nutrient discharges have caused eutrophication in many estuaries and coastal seas such as the Baltic Sea. The sedimented nutrients can affect bacterial communities which, in turn, are widely believed to contribute to release of nutrients such as phosphorus from the sediment.

Methods

We investigated relationships between bacterial communities and chemical forms of phosphorus as well as elements involved in its cycling in brackish sediments using up-to-date multivariate statistical methods. Bacterial community composition was determined by terminal restriction fragment length polymorphism and cloning of the 16S rRNA gene.

Results and Conclusions

The bacterial community composition differed along gradients of nutrients, especially of different phosphorus forms, from the estuary receiving agricultural phosphorus loading to the open sea. This suggests that the chemical composition of sediment phosphorus, which has been affected by riverine phosphorus loading, influenced on bacterial communities. Chemical and spatial parameters explained 25% and 11% of the variation in bacterial communities. Deltaproteobacteria, presumptively sulphate and sulphur/iron reducing, were strongly associated to chemical parameters, also when spatial autocorrelation was taken into account. Sulphate reducers correlated positively with labile organic phosphorus and total nitrogen in the open sea sediments. Sulphur/iron reducers and sulphate reducers linked to iron reduction correlated positively with aluminium- and iron-bound phosphorus, and total iron in the estuary. The sulphate and sulphur/iron reducing bacteria can thus have an important role both in the mineralization and mobilization of nutrients from sediment.

Significance

Novelty in our study is that relationships between bacterial community composition and different phosphorus forms, instead of total phosphorus, were investigated. Total phosphorus does not necessarily bring out interactions between bacteria and phosphorus chemistry since proportions of easily usable mobile (reactive) phosphorus and immobile phosphorus forms in different sediments can vary. Our study suggested possible feedbacks between different forms of phosphorus and bacterial community composition.     

Mixed effects of effluents from a wastewater treatment plant on river ecosystem metabolism: subsidy or stress?

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Free-Living and Particle-Associated Bacterioplankton in Large Rivers of the Mississippi River Basin Demonstrate Biogeographic Patterns

The different drainage basins of large rivers such as the Mississippi River represent interesting systems in which to study patterns in freshwater microbial biogeography. Spatial variability in bacterioplankton communities in six major rivers (the Upper Mississippi, Missouri, Illinois, Ohio, Tennessee, and Arkansas) of the Mississippi River Basin was characterized using Ion Torrent 16S rRNA amplicon sequencing. When all systems were combined, particle-associated (>3 μm) bacterial assemblages were found to be different from free-living bacterioplankton in terms of overall community structure, partly because of differences in the proportional abundance of sequences affiliated with major bacterial lineages (Alphaproteobacteria, Cyanobacteria, and Planctomycetes). Both particle-associated and free-living communities ordinated by river system, a pattern that was apparent even after rare sequences or those affiliated with Cyanobacteria were removed from the analyses. Ordination of samples by river system correlated with environmental characteristics of each river, such as nutrient status and turbidity. Communities in the Upper Mississippi and the Missouri and in the Ohio and the Tennessee, pairs of rivers that join each other, contained similar taxa in terms of presence-absence data but differed in the proportional abundance of major lineages. The most common sequence types detected in particle-associated communities were picocyanobacteria in the Synechococcus/Prochlorococcus/Cyanobium (Syn/Pro) clade, while free-living communities also contained a high proportion of LD12 (SAR11/Pelagibacter)-like Alphaproteobacteria. This research shows that while different tributaries of large river systems such as the Mississippi River harbor distinct bacterioplankton communities, there is also microhabitat variation such as that between free-living and particle-associated assemblages.     

Cross-habitat impacts of species decline: response of estuarine sediment communities to changing detrital resources

Food webs of many ecosystems are sustained by organic matter from other habitats. Human activities and climatic change are increasingly modifying the quality and supply of these resources, yet for most ecosystems it is unknown how the taxonomic composition of organic matter influences community composition. Along the coastline of Sydney, Australia, the once abundant habitat-forming macroalga, Phyllospora comosa, is now locally extinct. Shallow reefs are now primarily occupied by Sargassum sp. and, to a lesser extent, the kelp Ecklonia radiata. We experimentally manipulated the supply of P. comosa, Sargassum sp. and E. radiata to estuarine sediments to assess responses by macroinvertebrate communities to: (1) changing the identity of the dominant detrital resource; and (2) varying the ratio of input of different macrophytes. Estuarine sediments dosed with P. comosa supported greater abundances of macroinvertebrates than sediments receiving Sargassum sp. or the kelp E. radiata. Whereas plots receiving Sargassum sp. or E. radiata had fewer macroinvertebrates than controls, plots receiving a moderate (120 g dry weight per m²) loading of P. comosa had more. Mixtures of detritus dominated by P. comosa supported similar macroinvertebrate communities to monocultures of the alga. Communities in sediments receiving detritus comprised of less than one-third P. comosa were, however, distinctly different. Our study provides evidence that the ecological ramifications of species decline can extend to spatially removed ecosystems, subsidised by allochthonous materials. Even prior to extinction of detrital sources, small changes in their provision of organic matter may alter the structure of subsidised communities.     

Invasion of Spartina alterniflora on Zostera japonica enhances the abundances of bacteria by absolute quantification sequencing analysis

Plant invasion can alter soil organic matter composition and indirectly impact estuary ecology; therefore, it is paramount to understand how plant invasion influences the bacterial community. Here, we present an absolute quantification 16S rRNA gene sequencing to investigate the bacterial communities that were collected from Zostera japonica and Spartina alterniflora covered areas and Z. japonica degradation areas in the Yellow River Estuary. Our data revealed that the absolute quantity of bacteria in the surface layer was significantly (p < .05) higher than that in the bottom and degradation areas. Following the invasion of S. alterniflora, the abundances of Bacteroidia, Acidimicrobiaceae, and Dehalococcoidaceaewere enriched in the S. alterniflora sediment. In addition, variations in the composition of sediment bacterial communities at the phylum level were the most intimately related to total organic carbon (TOC), and the content of heavy metals could reduce the abundance of bacteria. This study provided some information to understand the effects of S. alterniflora invasion on Z. japonica from the perspective of microbiome level.     

Influence of hyporheic zone characteristics on the structure and activity of microbial assemblages

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