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Article: [High-throughput qPCR and Amplicon Sequencing as Complementary Methods for Profiling Antibiotic Resistance Genes in Urban Wetland Parks].

Huang, Fu-Yi / Zhou, Shu-Yi-Dan / Pan, Ting / Zhou, Xin-Yuan / Su, Jian-Qiang / Zhang, Xian

Huan jing ke xue= Huanjing kexue

2024 Volume 45, Issue 1, Page(s) 576–583

Abstract: Urban wetland parks are an important practice for urban wetland protection and utilization due to the vast ecosystem service value. As emerging contaminants, antibiotic resistance genes (ARGs) are great attractions for environmental research and public ... ...

Abstract	Urban wetland parks are an important practice for urban wetland protection and utilization due to the vast ecosystem service value. As emerging contaminants, antibiotic resistance genes (ARGs) are great attractions for environmental research and public concerns. Based on high-throughput qPCR and high-throughput amplicon sequencing techniques, we investigated the occurrence, abundance, and distribution profiles of antibiotic resistance genes in the aquatic environment of Xiamen urban wetland parks (five sites). The influencing factors and driving mechanisms of antibiotic resistance genes were deciphered on the basis of microbial community structure and water quality. Diverse and abundant ARGs were observed and coexisted in urban wet parks. A total of 217 ARGs were detected in the water body of urban wetland parks, with an abundance up to 6.48×10
MeSH term(s)	Humans ; Genes, Bacterial/genetics ; Wetlands ; Anti-Bacterial Agents/analysis ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Microbiota
Chemical Substances	Anti-Bacterial Agents
Language	Chinese
Publishing date	2024-01-12
Publishing country	China
Document type	English Abstract ; Journal Article
ISSN	0250-3301
ISSN	0250-3301
DOI	10.13227/j.hjkx.202302194
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Article ; Online: Mapping the profiles and underlying driving mechanisms of the antibiotic resistome and microbiome within a subtropical complex river watershed.

Zhou, Xin-Yuan / Zhou, Shu-Yi-Dan / Huang, Fu-Yi / Zhu, Longji / Su, Jian-Qiang

Journal of hazardous materials

2023 Volume 465, Page(s) 133392

Abstract: Antibiotic resistance is an escalating global concern, leading to millions of annual deaths worldwide. Human activities can impact antibiotic resistance gene (ARG) prevalence in aquatic ecosystems, but the intricate interplay between anthropogenic ... ...

Abstract	Antibiotic resistance is an escalating global concern, leading to millions of annual deaths worldwide. Human activities can impact antibiotic resistance gene (ARG) prevalence in aquatic ecosystems, but the intricate interplay between anthropogenic disturbances and river system resilience, and their respective contributions to the dynamics of different river segments, remains poorly understood. In this study, we investigate the antibiotic resistome and microbiome in water and sediment samples from two distinct sub-watersheds within a specific watershed. Results show a decrease in the number of core ARGs downstream in water, while sediments near densely populated areas exhibit an increase. PCoA ordination reveals clear geographic clustering of resistome and microbiome among samples from strong anthropogenic disturbed areas, reservoir areas, and estuary area. Co-occurrence networks highlight a higher connectivity of mobile genetic elements (MGEs) in disturbed areas compared to reservoir areas, presenting a threat to densely populated areas. Water quality parameters and antibiotics concentration were the key factors shaping the ARG profiles in sediment samples from urban regions. Overall, our study reveals distinct patterns of ARGs in sediment and water samples, emphasizing the importance of considering both anthropogenic and natural factors in comprehending and managing ARG distribution in river systems.
MeSH term(s)	Humans ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Microbiota ; Rivers
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2023-12-29
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1491302-1
ISSN	1873-3336 ; 0304-3894
ISSN (online)	1873-3336
ISSN	0304-3894
DOI	10.1016/j.jhazmat.2023.133392
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Article: [Microplastic-Induced Alterations to Antibiotic Resistance Genes in Seawater].

Zhou, Shu-Yi-Dan / Zhu, Yong-Guan / Huang, Fu-Yi

Huan jing ke xue= Huanjing kexue

2021 Volume 42, Issue 8, Page(s) 3785–3790

Abstract: The increasing and combined pollution of microplastics (MPs) and antibiotic resistance genes (ARGs) in aquatic environments is a great ecological and health concern. However, MP-induced alterations to ARGs in seawater is poorly understood, impeding risk ... ...

Abstract	The increasing and combined pollution of microplastics (MPs) and antibiotic resistance genes (ARGs) in aquatic environments is a great ecological and health concern. However, MP-induced alterations to ARGs in seawater is poorly understood, impeding risk assessment of plastics. We profiled the diversity and abundance of ARGs and mobile genetic elements (MGEs) in seawater after the addition of three different MPs (PE, PVC, and PVA) and 49-day aerated incubation.A total of 20, 35, 42, and 64 ARGs were detected in BLK, PE, PVC, and PVA, with 2, 4, 2, and 3 MGEs, respectively. The absolute abundance of ARGs in the seawater aerated with MPs ranged from 4.01×10
Language	Chinese
Publishing date	2021-07-26
Publishing country	China
Document type	English Abstract ; Journal Article
ISSN	0250-3301
ISSN	0250-3301
DOI	10.13227/j.hjkx.202101009
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Article ; Online: Antibiotic resistome in groundwater and its association with mountain springs and river.

Huang, Fu-Yi / Zhao, Yi / Neilson, Roy / Zhou, Xin-Yuan / Li, Hu / Ding, Lei / Zhou, Shu-Yi-Dan / Su, Jian-Qiang

Ecotoxicology and environmental safety

2023 Volume 252, Page(s) 114603

Abstract: The distribution of antibiotic resistance genes (ARGs) in water sources potentially threatens drinking water safety. However, the sources of antibiotic resistome in groundwater are still under-investigated. Here, we evaluated the profiles of antibiotic ... ...

Abstract	The distribution of antibiotic resistance genes (ARGs) in water sources potentially threatens drinking water safety. However, the sources of antibiotic resistome in groundwater are still under-investigated. Here, we evaluated the profiles of antibiotic resistome in peri-urban groundwater and its associated water sources (river and mountain spring) to characterize the antibiotic resistome from natural water sources on groundwater resistome. A total of 261 antibiotic resistome were detected in groundwater, mountain spring, and river samples. The relative abundances of ARGs and mobile genetic elements (MGEs) were significantly higher in the river samples than in spring water and groundwater samples. The resistome profiles were similar between groundwater and spring water but differed from the river samples. According to source tracking results, the groundwater resistome was likely to be derived from springs (28.0%-50.0%) and rivers (28.6%-48.6%), which share the same trend for the source tracking of bacterial communities. Bacterial α-diversity, bacterial β-diversity, and MGEs directly or indirectly affected the ARGs in groundwater samples. Although the abundance of groundwater resistome was not elevated by river and spring water, groundwater resistomes were diverse and may be derived from both river and spring water. We highlight the importance of groundwater resistome and its association with potential water sources, providing a better understanding and basis for the effective control of the ARG proliferation and dissemination in groundwater from exogenous water bodies in the future.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Rivers/microbiology ; Bacteria/genetics ; Water ; Groundwater
Chemical Substances	Anti-Bacterial Agents ; Water (059QF0KO0R)
Language	English
Publishing date	2023-02-02
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	436536-7
ISSN	1090-2414 ; 0147-6513
ISSN (online)	1090-2414
ISSN	0147-6513
DOI	10.1016/j.ecoenv.2023.114603
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Zs.A 1418: Show issues

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Article ; Online: Skin microbiota interact with microbes on office surfaces

Hu Li / Shu-Yi-Dan Zhou / Roy Neilson / Xin-Li An / Jian-Qiang Su

Environment International, Vol 168, Iss , Pp 107493- (2022)

2022

Abstract: The indoor environment is recognized as a potential contributor to human health impacts through resident microbiomes. Indoor surface microbial communities are formed from several sources, environmental and anthropogenic. In this study, we characterized ... ...

Abstract	The indoor environment is recognized as a potential contributor to human health impacts through resident microbiomes. Indoor surface microbial communities are formed from several sources, environmental and anthropogenic. In this study, we characterized the bacterial and fungal communities from various sources typical of a working office environment including dust, fingers, and computer keyboards and mice. The composition of the dust bacterial community was significantly different from the other tested surfaces (P < 0.05), whereas the dust fungal community was only significantly different from fingers (P < 0.05). Bacterial and fungal communities were both shaped by deterministic processes, and bacterial communities had a higher migration rate. Results of a network analysis showed that the microbial community interactions of keyboards and mice were mainly competitive. Fast expectation–maximization microbial source tracking (FEAST) identified the sources of > 70 % of the keyboard and mouse microbial communities. Biomarkers for each sample types were identified by LDA Effect Size (LEfSE) analysis, some of which were soil-derived and potential anthropogenic pathogens, indicating the potential for exchange of microbes among outdoor, human and indoor surfaces. The current study shows that the source of microorganisms at the office interface is highly traceable and that their migration is linked to human activity. The migration of potentially pathogenic microbes were identified, emphasising the importance of personal hygiene.
Keywords	Skin microbiome ; Indoor environment ; Source tracking ; Indoor microbiome ; Pathogen ; Environmental sciences ; GE1-350
Language	English
Publishing date	2022-10-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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Article ; Online: HiLi-chip: A high-throughput library construction chip for comprehensive profiling of environmental microbial communities.

Lin, Chenshuo / Huang, Fu-Yi / Zhou, Shu-Yi-Dan / Li, Hu / Zhang, Xian / Su, Jian-Qiang

Environmental research

2022 Volume 213, Page(s) 113650

Abstract: Investigating the contribution and associations of environmental microbes to ecological health and human well-being is in great demand with the goal of One Health proposed. To achieve the goal, there is an urgent need for accurate approaches to obtaining ...

Abstract	Investigating the contribution and associations of environmental microbes to ecological health and human well-being is in great demand with the goal of One Health proposed. To achieve the goal, there is an urgent need for accurate approaches to obtaining a large amount of high-resolution molecular information from various microbes. In this study, we developed a high-throughput library construction chip (HiLi-Chip) for profiling environmental microbial communities and evaluated its performance. The HiLi-Chip showed high conformity with the conventional Pacbio method in terms of α-diversity, community composition of abundant bacteria (>83%), as well as rare taxa (>84%) and human pathogens detection (>67%), indicating its advantages of accuracy, high-throughput, cost-efficiency, and broad practicability. It is suggested that the optimal strategy of the HiLi-Chip was a 2.4 μL PCR mixture per sample (∼2.4 ng DNA) with a 216-sample × 24-replicate format. We have successfully applied the HiLi-Chip to the Jiulongjiang River and identified 51 potential human bacterial pathogens with a total relative abundance of 0.22%. Additionally, under limited nutrients and similar upstream environments, bacteria tended to impose competitive pressures, resulting in a more connected network at the downstream river confluence (RC). Whereas narrow niche breadth of bacteria and upstream environmental heterogeneity probably promoted niche complementary and environment selection leading to fewer links at RC in the midsection of the river. Core bacteria might represent the entire bacterial community and enhance network stability through synergistic interactions with other core bacteria. Collectively, our results demonstrate that the HiLi-Chip is a robust tool for rapid comprehensive profiling of microbial communities in environmental samples and has significant implications for a profound understanding of environmental microbial interactions.
MeSH term(s)	Bacteria/genetics ; Humans ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Rivers
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2022-06-08
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	205699-9
ISSN	1096-0953 ; 0013-9351
ISSN (online)	1096-0953
ISSN	0013-9351
DOI	10.1016/j.envres.2022.113650
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Zs.A 726: Show issues

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Article ; Online: City-scale distribution of airborne antibiotic resistance genes.

Zhou, Xin-Yuan / Li, Hu / Zhou, Shu-Yi-Dan / Zhang, Yu-Sen / Su, Jian-Qiang

The Science of the total environment

2022 Volume 856, Issue Pt 2, Page(s) 159176

Abstract: Concerns around urban air quality have been increasing worldwide due to large-scale urbanization. A large volume of work has been focused on the chemical pollutants in the air and their impacts on human health. However, the profile of airborne microbial ... ...

Abstract	Concerns around urban air quality have been increasing worldwide due to large-scale urbanization. A large volume of work has been focused on the chemical pollutants in the air and their impacts on human health. However, the profile of airborne microbial contaminants, especially antibiotic resistance genes (ARGs), is largely understudied. Here, high-throughput quantitative PCR (HT-qPCR) was employed to explore the temporal and spatial distribution of airborne ARGs from 11 sites with various functional zones and different urbanization levels within Xiamen, China. A total of 104 unique ARGs and 23 mobile genetic elements (MGEs) were detected across all samples. Temporal shift was observed in the distribution of ARG profiles, with significantly higher relative abundance of ARGs detected in summer than that in spring. Temperature is the key predictor of the total relative abundance of ARGs and MGEs in summer, while PM
MeSH term(s)	Humans ; Anti-Bacterial Agents ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Cities ; Urbanization
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2022-10-01
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2022.159176
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Zs.A 949: Show issues

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Article ; Online: Manure and biochar have limited effect on lettuce leaf endophyte resistome.

Wang, Yan-Zi / Zhou, Shu-Yi-Dan / Zhou, Xin-Yuan / An, Xin-Li / Su, Jian-Qiang

The Science of the total environment

2022 Volume 860, Page(s) 160515

Abstract: Soil amendment with manure compost and biochar is widely adopted to improve soil fertility and promote plant growth, and their effects on soil microbial communities and resistome have been well documented. However, there is sparse information regarding ... ...

Abstract	Soil amendment with manure compost and biochar is widely adopted to improve soil fertility and promote plant growth, and their effects on soil microbial communities and resistome have been well documented. However, there is sparse information regarding their effects on vegetable endophytes, which represent a major source of human exposure to pathogens and antibiotic resistance genes (ARGs) when eaten raw. Here, we investigated the impacts of manure compost or biochar addition on the bacterial community compositions and ARGs in the soil-lettuce continuum including soil, seed, leaf, and root samples. A total of 137 ARGs and 31 mobile genetic elements (MGEs) were detected in all the samples after 60 days of cultivation. The relative abundance of ARGs and the diversity of bacteria communities presented a consistent decreasing trend from soil to root endophytes, then leaf endophytes. Manure compost addition increased the diversity and abundance of ARGs in soil, while significant changes in the ARG profiles and bacterial communities were not observed in leaf endophytes after manure compost or biochar addition, or both. Bipartite networks analysis suggested that seed microbiome was one of the major sources of plant endophytes and ARGs. Twenty potential human pathogens were isolated from lettuce, indicating potential exposure risk to pathogens via the consumption of raw lettuce. These results suggest limited impacts of manure compost and biochar addition on lettuce endophytes and highlight the contribution of seed microbiome to endophyte ARG profiles.
MeSH term(s)	Humans ; Genes, Bacterial ; Endophytes ; Lactuca/genetics ; Manure/analysis ; Soil Microbiology ; Bacteria/genetics ; Soil ; Anti-Bacterial Agents ; Plant Leaves/chemistry
Chemical Substances	Manure ; biochar ; Soil ; Anti-Bacterial Agents
Language	English
Publishing date	2022-11-25
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2022.160515
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Zs.A 949: Show issues

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Article ; Online: Effects of alpine meadows with different degradation gradients on the stability of the soil micro-foodweb in the Tibetan Plateau

Lili Nian / Xiaoning Zhang / Liangliang Li / Shu-Yi-Dan Zhou / Xingyu Liu / Xiaodan Li / Xiaoyu Liu / Qiqi Zhao / Yingying Wu / Fasih Ullah Haider / Xuelu Liu / Yingbo Yang

Ecological Indicators, Vol 158, Iss , Pp 111390- (2024)

1481

Abstract: Resource-transfer connections among bacteria, fungi, and microbivorous nematodes play an integral role in the decomposition pathways of soil micro-foodweb. Exploring the response of soil bacteria, fungi, and nematodes to grassland degradation is crucial ... ...

Abstract	Resource-transfer connections among bacteria, fungi, and microbivorous nematodes play an integral role in the decomposition pathways of soil micro-foodweb. Exploring the response of soil bacteria, fungi, and nematodes to grassland degradation is crucial for predicting the direction and trajectory of degradation. However, the knowledge about soil bacteria-fungi-nematode interactions in ecosystem function and nutrient cycling must be highlighted properly, especially in the Qinghai-Tibet Plateau. Therefore, this study focuses on four alpine meadows at different degenerate gradients (non-degraded grassland, slightly degraded grassland, moderately degraded grassland, and severely degraded grassland) on the Qinghai-Tibet Plateau. The investigation of soil bacteria-fungi-nematode interactions uses high-throughput sequencing and correlation network analysis. The results demonstrate significant variations in the composition of soil nematode genera, and bacterial and fungal phyla, across different degradation stages. Moreover, the diversity of nematodes, bacteria and fungi declined as grassland degradation worsened. Principal component analysis (PCA) revealed that alpine meadows with varying degradation gradients significantly influenced the community structure of bacteria, fungi, and nematodes. Mantel analysis indicated that soil water content (P < 0.05), total phosphorus (P < 0.05), and total nitrogen (P < 0.05) were the primary soil properties affecting the soil bacterial community. Similarly, available soil potassium (P < 0.05), microbial biomass carbon (P < 0.05), and microbial biomass nitrogen (P < 0.05) were the main soil factors influencing the soil fungal community. In contrast, the correlation between individual soil characteristics and soil nematodes did not reach a significant level, suggesting that a blend of physical and chemical properties regulates the soil nematode community. As grassland degradation intensified, the number of links in the interaction network of bacteria, fungi, and ...
Keywords	Degraded alpine meadow ; Nematode metabolic footprint ; Related ecological network ; Soil micro-foodweb ; Qinghai-Tibet Plateau ; Ecology ; QH540-549.5
Subject code	630
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Skin microbiota interact with microbes on office surfaces

Li, Hu / Zhou, Shu-Yi-Dan / Neilson, Roy / An, Xin-Li / Su, Jian-Qiang

Environment international. 2022 Aug. 27,

2022

Abstract	The indoor environment is recognized as a potential contributor to human health impacts through resident microbiomes. Indoor surface microbial communities are formed from several sources, environmental and anthropogenic. In this study, we characterized the bacterial and fungal communities from various sources typical of a working office environment including dust, fingers, and computer keyboards and mice. The composition of the dust bacterial community was significantly different from the other tested surfaces (P < 0.05), whereas the dust fungal community was only significantly different from fingers (P < 0.05). Bacterial and fungal communities were both shaped by deterministic processes, and bacterial communities had a higher migration rate. Results of a network analysis showed that the microbial community interactions of keyboards and mice were mainly competitive. Fast expectation-maximization microbial source tracking (FEAST) identified the sources of > 70% of the keyboard and mouse microbial communities. Biomarkers for each sample types were identified by LDA Effect Size (LEfSE) analysis, some of which were soil-derived and potential anthropogenic pathogens, indicating the potential for exchange of microbes among outdoor, human and indoor surfaces. The current study shows that the source of microorganisms at the office interface is highly traceable and that their migration is linked to human activity. The migration of potentially pathogenic microbes were identified, emphasising the importance of personal hygiene.
Keywords	bacterial communities ; biomarkers ; computers ; dust ; environment ; fungal communities ; fungi ; good hygiene practices ; human health ; humans ; microbiome ; working conditions
Language	English
Dates of publication	2022-0827
Publishing place	Elsevier Ltd
Document type	Article
Note	Pre-press version
ZDB-ID	554791-x
ISSN	1873-6750 ; 0160-4120
ISSN (online)	1873-6750
ISSN	0160-4120
DOI	10.1016/j.envint.2022.107493
Database	NAL-Catalogue (AGRICOLA)

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