Impact of pollution and seasonal changes on microbial community structure in surface water

Mlejnková, Hana; Sovová, Kateřina

doi:10.2166/wst.2010.080

Cited by 15 publications

(7 citation statements)

References 22 publications

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“…Proteobacteria was the most prevalent phylum in all the wastewater samples tested, followed by Actinobacteria and Firmicutes (Figure 2). Our results are in accordance with previous studies that showed that these phyla are dominant in wastewaters (Mlejnkova and Sovova, 2010;Bengtsson-Palme et al 2014). The microbial community structure is significantly dependent on the level of water pollution, and abundance of Proteobacteria or Bacteroidetes is reported to be a consequence of water pollution by human activities (Mlejnkova and Sovova, 2010;Suriya et al 2017).…”

Section: Microbial Composition Population Structure and Functional Classificationsupporting

confidence: 94%

Wastewater used for urban agriculture in West Africa as a reservoir for antibacterial resistance dissemination

Bougnom

Zongo²,

McNally

et al. 2019

Environmental Research

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State of art metagenomics were used to investigate the microbial population, antibiotic resistance genes and plasmids of medical interest in wastewater used for urban agriculture in Ouagadougou (Burkina Faso). Wastewater samples were collected from three canals near agricultural fields in three neighbourhoods. Assessment of microbial population diversity revealed different microbial patterns among the different samples. Sequencing reads from the wastewaters revealed different functional specializations of microbial communities, with the predominance of carbohydrates and proteins metabolism functions. Eleven pathogen-specific and 56 orthologous virulence factor genes were detected in the wastewater samples. These virulence factors are usually found in human pathogens that cause gastroenteritis and/or diarrhoea. A wide range of antibiotic resistance genes was identified; 81 are transmissible by mobile genetic elements. These included seven different extended spectrum β-lactamase genes encoding synthesis of four enzyme families, including two metallo-β-lactamases (bla and bla). Ten different incompatibility groups of Enterobacteriaceae plasmid replicons (ColE, FIB, FIC, FII, P, Q, R, U, Y, and A/C), and 30 plasmid replicon types from Gram-positive bacteria. All are implicated in the wide distribution of antibiotic resistance genes. We conclude that wastewater used for urban agriculture in the city represents a high risk for spreading bacteria and antimicrobial resistance among humans and animals.

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Section: Microbial Composition Population Structure and Functional Classificationsupporting

confidence: 94%

Wastewater used for urban agriculture in West Africa as a reservoir for antibacterial resistance dissemination

Bougnom

Zongo²,

McNally

et al. 2019

Environmental Research

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“…This is potentially a major limitation in identifying biomarkers of an urban biome as when climate, weather and season are considered large intra-city variations in the microbiome may be observed. Research on microbial communities in the environment has found changes associated with seasons [22, 23]. Human contact has been shown to contribute to the microbial sequences observed in MetaSUB and so seasonal differences in clothing may also shape these communities [8].…”

Section: Discussionmentioning

confidence: 99%

Application of machine learning techniques for creating urban microbial fingerprints

Ryan

2019

Biol Direct

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Background Research has found that human associated microbial communities play a role in homeostasis and the disruption of these communities may be important in an array of medical conditions. However outside of the human body many of these communities remain poorly studied. The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is characterizing the microbiomes of urban environments with the aim to improve design of mass transit systems. As part of the CAMDA 2018 MetaSUB Forensics Challenge 311 city microbiome samples were provided to create urban microbial fingerprints, as well as a further 3 mystery datasets for validation. Results MetaSUB samples were clustered using t-SNE in an unsupervised fashion to almost discrete groups, which upon inspection represented city of origin. Based on this clustering, geographically close metropolitan areas appear to display similar microbial profiles such as those of Auckland and Hamilton. Mystery unlabeled samples were provided part of the challenge. A random forest classifier built on the initial dataset of 311 samples was capable of correctly classifying 83.3% of the mystery samples to their city of origin. Random Forest analyses also identified features with the highest discriminatory power, ranking bacterial species such as Campylobacter jejuni and Staphylococcus argenteus as highly predictive of city of origin. The surface from which the sample was collected displayed little detectable impact on the microbial profiles in the data generated here. The proportion of reads classified per sample varied greatly and so de-novo assembly was applied to recover genomic fragments representing organisms not captured in reference databases. Conclusions Current methods can differentiate urban microbiome profiles from each other with relative ease. De-novo assembly indicated that the MetaSUB metagenomic data contains adequate depth to recover metagenomic assembled genomes and that current databases are not sufficient to fully characterize urban microbiomes. Profiles found here indicate there may be a relationship between geographical distance between areas and the urban microbiome composition although this will need further research. The impact of these different profiles on public health is currently unknown but the MetaSUB consortium is uniquely suited to evaluate these and provide a roadmap for the inclusion of urban microbiome information for city planning and public health policy. Reviewers This article was reviewed by Dimitar Vassilev, Eran Elhaik and Chengsheng Zhu. Electronic supplementary material The online version of this article (10.1186/s13062-019-0245-x) contains supplementary material, which is available to authorized users.

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“…Bacteria are considered to be highly sensitive to their surrounding environments owing to their rapid reproductive ability and simple structure [106]. Different populations of bacteria may emerge in different environmental conditions, depending on their abilities to metabolize certain compounds and nutrients [107]. For instance, in an anoxic environment, the composition of the strictly aerobic microbial community in the river water may be affected [73].…”

Section: Reliability Of Bacterial Community In Waterways Biomonitoringmentioning

confidence: 99%

A Review of Current and Emerging Approaches for Water Pollution Monitoring

Zolkefli

Sharuddin

Yusoff

et al. 2020

Water

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The aquatic ecosystem is continuously threatened by the infiltration and discharge of anthropogenic wastewaters. This issue requires the unending improvement of monitoring systems to become more comprehensive and specific to targeted pollutants. This review intended to elucidate the overall aspects explored by researchers in developing better water pollution monitoring tools in recent years. The discussion is encircled around three main elements that have been extensively used as the basis for the development of monitoring methods, namely the dissolved compounds, bacterial indicator, and nucleic acids. The latest technologies applied in wastewater and surface water mapped from these key players were reviewed and categorized into physicochemical and compound characterizations, biomonitoring, and molecular approaches in taxonomical and functional analyses. Overall, researchers are continuously rallying to enhance the detection of causal source for water pollution through either conventional or mostly advanced approaches focusing on spectrometry, high-throughput sequencing, and flow cytometry technology among others. From this review’s perspective, each pollution evaluation technology has its own advantages and it would be beneficial for several aspects of pollutants assessments to be combined and established as a complementary package for better aquatic environmental management in the long run.

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Impact of pollution and seasonal changes on microbial community structure in surface water

Cited by 15 publications

References 22 publications

Wastewater used for urban agriculture in West Africa as a reservoir for antibacterial resistance dissemination

Wastewater used for urban agriculture in West Africa as a reservoir for antibacterial resistance dissemination

Application of machine learning techniques for creating urban microbial fingerprints

A Review of Current and Emerging Approaches for Water Pollution Monitoring

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