Diversity and abundance of antibiotic resistance genes and their relationship with nutrients and land use of the inflow rivers of Taihu Lake

Fernanda, Prilli Arista; Liu, Shuang; Yuan, Tianma; Ramalingam, Bharathi; Lu, Jing; Sekar, Raju

doi:10.3389/fmicb.2022.1009297

Cited by 7 publications

(5 citation statements)

References 71 publications

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“…Water physicochemical and microbiological characteristics at the selected sampling locations in the summer and winter of 2020 are shown in Supplementary Figure S3. Results for the spring and summer of 2019 have been reported previously (Fernanda et al, 2022). Two-way ANOVA showed that all parameters except water temperature (WT) showed spatial differences between rivers, while all parameters except chlorophyll a showed significant seasonal variation (Supplementary Table S2).…”

Section: Water Quality Analysessupporting

confidence: 72%

“…The filters were kept at −20 °C until they were used for DNA extraction using the PowerSoil DNA Isolation Kit (MoBio Inc., Carlsbad, CA) according to the manufacturer's instructions. This kit and procedure were used in our previous studies (Vadde et al, 2019b;Fernanda et al, 2022). At least three DNA extracts were prepared for each location and season.…”

Section: Dna Extractionmentioning

confidence: 99%

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Industrial and agricultural land uses affected the water quality and shaped the bacterial communities in the inflow rivers of Taihu Lake

Liu,

Lu,

Adriaenssens

et al. 2024

Front. Environ. Sci.

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Taihu Lake is the third-largest freshwater lake in China and is vital as a drinking water source, as well as for irrigation water, flood control, and other functions. Taihu Lake is connected to many inflow rivers, which contribute to the water resource but also to its pollution. Investigating the correlation between water quality, bacterial community structure, and land-use types is essential for pollution control. Yet, few studies have been conducted on all the major inflow rivers of Taihu Lake. This study aimed to assess the bacterial community composition of major inflow rivers of the lake and determine the relationship between the bacterial community, water quality, and land-use. Water samples were collected from ten inflow rivers across four seasons in 2019–2020. DNA extracted from the samples was used for 16S rRNA gene-targeted next-generation sequencing to determine the bacterial community structures. Thirteen physicochemical and microbiological parameters were used to assess the water quality, and the land-use pattern surrounding each sampling location was also profiled. The bacterial community composition demonstrated significant seasonal variation. In summer, the community variation was correlated with chlorophyll a, pH, and phosphate-P, and electric conductivity, nitrate-N, and ammonium-N in winter. Rivers in the northwest were more nutrient-rich than those in the southwest. The industrial, residential, and agricultural land-use categories correlated strongly with the bacterial community composition and water nutrient parameters. Accordingly, farmland drainage, untreated domestic wastewater, and industrial pollution were identified as the major objectives for more effective water quality management in the region.

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Section: Water Quality Analysessupporting

confidence: 72%

Section: Dna Extractionmentioning

confidence: 99%

Industrial and agricultural land uses affected the water quality and shaped the bacterial communities in the inflow rivers of Taihu Lake

Liu,

Lu,

Adriaenssens

et al. 2024

Front. Environ. Sci.

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“…To survey a broad range of genes, we also used a second method, which is a relative quantification method on a HT-qPCR platform. This method has recently been used by numerous studies (Muurinen et al, 2021;Fernanda et al, 2022;Flater et al, 2022;Kasuga et al, 2022;Mware et al, 2022;Samanta et al, 2022) because it allows for simultaneous presence/absence detection of numerous genes (Stedfeld). HT-qPCR is also limiting in the volume of each reaction (6.7 x 10 -3 mL vs 2 mL in conventional qPCR), which directly influences its detection limits.…”

Section: Discussionmentioning

confidence: 99%

Comparison of antibiotic resistance genes in swine manure storage pits of Iowa, USA

Neher¹,

Soupir²,

Andersen³

et al. 2023

Front. Antibiot.

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Antimicrobial resistance (AMR) can develop in deep-pit swine manure storage when bacteria are selectively pressured by unmetabolized antibiotics. Subsequent manure application on row crops is then a source of AMR into soil and downstream runoff water. Therefore, understanding the patterns of diverse antibiotic resistance genes (ARGs) in manure among different farms is important for both interpreting the results of the detection of these genes from previous studies and for the use of these genes as bioindicators of manure borne antibiotic resistance in the environment. Previous studies of manure-associated ARGs are based on limited samples of manures. To better understand the distribution of ARGs between manures, we characterized manures from 48 geographically independent swine farms across Iowa. The objectives of this study were to characterize the distribution of ARGs among these manures and to evaluate what factors in manure management may influence the presence of ARGs in manures. Our analysis included quantification of two commonly found ARGs in swine manure, ermB and tetM. Additionally, we characterized a broader suite of 31 ARGs which allowed for simultaneous assays of the presence or absence of multiple genes. We found the company integrator had a significant effect on both ermB (P=0.0007) and tetM gene concentrations (P=0.0425). Our broad analysis on ARG profiles found that the tet(36) gene was broadly present in swine manures, followed by the detection of tetT, tetM, erm(35), ermF, ermB, str, aadD, and intl3 in samples from 14 farms. Finally, we provide a comparison of methods to detect ARGs in manures, specifically comparing conventional and high-throughput qPCR and discuss their role in ARG environmental monitoring efforts. Results of this study provide insight into commonalities of ARG presence in manure holding pits and provide supporting evidence that company integrator decisions may impact ARG concentrations.

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“…A format for amplification of 384 ARGs in 5184 qPCR assays, including MGEs, were developed in 2012 [ 18 ]. The high throughput (HT) qPCR method has been widely used for a comprehensive profiling of ARGs in aquatic environments [ 19 - 23 ]. With newly discovered ARGs such as variants of mcr , a new primer set was published in 2018 [ 24 ], covering most of the classes of ARGs and MGEs.…”

Section: Advancement Of Methodologies For Args Detectionmentioning

confidence: 99%

Resistome Study in Aquatic Environments

Shin

Han

Hur

2022

J. Microbiol. Biotechnol.

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Since the first discovery of antibiotics, introduction of new antibiotics has been coupled with the occurrence of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Rapid dissemination of ARB and ARGs in the aquatic environments has become a global concern. ARB and ARGs have been already disseminated in the aquatic environments via various routes. Main hosts of most of ARGs were found to belong to Gammaproteobacteria class, including clinically important potential pathogens. Transmission of ARGs also occurs by horizontal gene transfer (HGT) mechanisms between bacterial strains in the aquatic environments, resulting in ubiquity of ARGs. Thus, a few of ARGs and MGEs ( e.g. , strA , sul1 , int1 ) have been suggested as indicators for global comparability of contamination level in the aquatic environments. With ARB and ARGs contamination, the occurrence of critical pathogens has been globally issued due to their widespread in the aquatic environments. Thus, active surveillance systems have been launched worldwide. In this review, we described advancement of methodologies for ARGs detection, and occurrence of ARB and ARGs and their dissemination in the aquatic environments. Even though numerous studies have been conducted for ARB and ARGs, there is still no clear strategy to tackle antibiotic resistance (AR) in the aquatic environments. At least, for consistent surveillance, a strict framework should be established for further research in the aquatic environments.

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Diversity and abundance of antibiotic resistance genes and their relationship with nutrients and land use of the inflow rivers of Taihu Lake

Cited by 7 publications

References 71 publications

Industrial and agricultural land uses affected the water quality and shaped the bacterial communities in the inflow rivers of Taihu Lake

Industrial and agricultural land uses affected the water quality and shaped the bacterial communities in the inflow rivers of Taihu Lake

Comparison of antibiotic resistance genes in swine manure storage pits of Iowa, USA

Resistome Study in Aquatic Environments

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