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Lian Y, Zhen L, Chen X, Li Y, Li X. Microbial biomarkers as indication of dynamic and heterogeneous urban water environments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:107304-107316. [PMID: 36460885 DOI: 10.1007/s11356-022-24539-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Water samples for the 16S rRNA gene and water quality analyses were collected from around 155 km of river segments surrounding the urban areas in Xi'an, China. Multiple statistical analyses showed that the dynamic shifts of microbial communities in the Chan, Ba, and Feng Rivers from the spring to the summer seasons were apparent but little in the Zao River. The heterogeneity of microbial distributions was more due to the influence of hydrologic conditions and various sources of inflows in the rivers. The LEfSe analysis showed that the Chan and Zao Rivers, both more impacted by the sewage effluents, were more differentially abundant with bacteria related to polluted water, but the Ba and Feng Rivers, both on the outer side of the city, were more abundant with microbial communities in soil and freshwater environments in the summer. Multiple statistical analyses indicated that environmental variables had significant impacts on microbial communities. The geographical information system-based spatial analysis showed heterogeneity of microbial community distributions along the rivers. This study showed that the high-throughput sequencing analysis could identify some pathogenic bacteria that would significantly threaten public health and eco-environments in urban rivers.
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Affiliation(s)
- Yanqing Lian
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, Jiangsu, China.
- Yangtze Institute for Conservation and Development, Hohai University, Nanjing, 210098, Jiangsu, China.
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, 97 Yanxiang Road, Xi'an , 710061, Shaanxi, China.
| | - Lisha Zhen
- Microbiology Institute of Shaanxi, Shaanxi Academy of Sciences, 76 Xiying Road, Xi'an, 710043, Shaanxi, China
| | - Xi Chen
- School of Urban Planning and Municipal Engineering, Xi'an Polytechnic University, 19 South Jinhua Road, Xi'an, 710048, Shaanxi, China
| | - Yang Li
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, 97 Yanxiang Road, Xi'an , 710061, Shaanxi, China
| | - Xiaona Li
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, 97 Yanxiang Road, Xi'an , 710061, Shaanxi, China
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Engloner AI, Vargha M, Kós P, Borsodi AK. Planktonic and epilithic prokaryota community compositions in a large temperate river reflect climate change related seasonal shifts. PLoS One 2023; 18:e0292057. [PMID: 37733803 PMCID: PMC10513243 DOI: 10.1371/journal.pone.0292057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 09/12/2023] [Indexed: 09/23/2023] Open
Abstract
In freshwaters, microbial communities are of outstanding importance both from ecological and public health perspectives, however, they are threatened by the impact of global warming. To reveal how different prokaryotic communities in a large temperate river respond to environment conditions related to climate change, the present study provides the first detailed insight into the composition and spatial and year-round temporal variations of planktonic and epilithic prokaryotic community. Microbial diversity was studied using high-throughput next generation amplicon sequencing. Sampling was carried out monthly in the midstream and the littoral zone of the Danube, upstream and downstream from a large urban area. Result demonstrated that river habitats predominantly determine the taxonomic composition of the microbiota; diverse and well-differentiated microbial communities developed in water and epilithon, with higher variance in the latter. The composition of bacterioplankton clearly followed the prolongation of the summer resulting from climate change, while the epilithon community was less responsive. Rising water temperatures was associated with increased abundances of many taxa (such as phylum Actinobacteria, class Gammaproteobacteria and orders Synechococcales, Alteromonadales, Chitinophagales, Pseudomonadales, Rhizobiales and Xanthomonadales), and the composition of the microbiota also reflected changes of several further environmental factors (such as turbidity, TOC, electric conductivity, pH and the concentration of phosphate, sulphate, nitrate, total nitrogen and the dissolved oxygen). The results indicate that shift in microbial community responding to changing environment may be of crucial importance in the decomposition of organic compounds (including pollutants and xenobiotics), the transformation and accumulation of heavy metals and the occurrence of pathogens or antimicrobial resistant organisms.
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Affiliation(s)
- Attila I. Engloner
- Centre for Ecological Research, Eötvös Loránd Research Network, Budapest, Hungary
| | - Márta Vargha
- Department of Public Health Laboratories, National Public Health Centre, Budapest, Hungary
| | - Péter Kós
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
- Department of Biotechnology, Faculty of Science and Informatics, Szeged University, Szeged, Hungary
| | - Andrea K. Borsodi
- Centre for Ecological Research, Eötvös Loránd Research Network, Budapest, Hungary
- Department of Microbiology, ELTE Eötvös Loránd University, Budapest, Hungary
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Wei X, Huang Z, Jiang L, Li Y, Zhang X, Leng Y, Jiang C. Charting the landscape of the environmental exposome. IMETA 2022; 1:e50. [PMID: 38867899 PMCID: PMC10989948 DOI: 10.1002/imt2.50] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/13/2022] [Accepted: 07/30/2022] [Indexed: 06/14/2024]
Abstract
The exposome depicts the total exposures in the lifetime of an organism. Human exposome comprises exposures from environmental and humanistic sources. Biological, chemical, and physical environmental exposures pose potential health threats, especially to susceptible populations. Although still in its nascent stage, we are beginning to recognize the vast and dynamic nature of the exposome. In this review, we systematically summarize the biological and chemical environmental exposomes in three broad environmental matrices-air, soil, and water; each contains several distinct subcategories, along with a brief introduction to the physical exposome. Disease-related environmental exposures are highlighted, and humans are also a major source of disease-related biological exposures. We further discuss the interactions between biological, chemical, and physical exposomes. Finally, we propose a list of outstanding challenges under the exposome research framework that need to be addressed to move the field forward. Taken together, we present a detailed landscape of environmental exposome to prime researchers to join this exciting new field.
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Affiliation(s)
- Xin Wei
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouZhejiangChina
| | - Zinuo Huang
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouZhejiangChina
| | - Liuyiqi Jiang
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouZhejiangChina
| | - Yueer Li
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouZhejiangChina
| | - Xinyue Zhang
- Department of GeneticsStanford UniversityStanfordCaliforniaUSA
| | - Yuxin Leng
- Department of Intensive Care UnitPeking University Third HospitalBeijingChina
| | - Chao Jiang
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouZhejiangChina
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
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Biodegradation, Decolorization, and Detoxification of Di-Azo Dye Direct Red 81 by Halotolerant, Alkali-Thermo-Tolerant Bacterial Mixed Cultures. Microorganisms 2022; 10:microorganisms10050994. [PMID: 35630437 PMCID: PMC9147255 DOI: 10.3390/microorganisms10050994] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/01/2022] [Accepted: 05/04/2022] [Indexed: 01/27/2023] Open
Abstract
Azo dyes impact the environment and deserve attention due to their widespread use in textile and tanning industries and challenging degradation. The high temperature, pH, and salinity used in these industries render industrial effluent decolorization and detoxification a challenging process. An enrichment technique was employed to screen for cost-effective biodegraders of Direct Red 81 (DR81) as a model for diazo dye recalcitrant to degradation. Our results showed that three mixed bacterial cultures achieved ≥80% decolorization within 8 h of 40 mg/L dye in a minimal salt medium with 0.1% yeast extract (MSM-Y) and real wastewater. Moreover, these mixed cultures showed ≥70% decolorization within 24 h when challenged with dye up to 600 mg/L in real wastewater and tolerated temperatures up to 60 °C, pH 10, and 5% salinity in MSM-Y. Azoreductase was the main contributor to DR81 decolorization based on crude oxidative and reductive enzymatic activity of cell-free supernatants and was stable at a wide range of pH and temperatures. Molecular identification of azoreductase genes suggested multiple AzoR genes per mixed culture with a possible novel azoreductase gene. Metabolite analysis using hyphenated techniques suggested two reductive pathways for DR81 biodegradation involving symmetric and asymmetric azo-bond cleavage. The DR81 metabolites were non-toxic to Artemia salina nauplii and Lepidium sativum seeds. This study provided evidence for DR81 degradation using robust stress-tolerant mixed cultures with potential use in azo dye wastewater treatment.
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Paruch L. Molecular Diagnostic Tools Applied for Assessing Microbial Water Quality. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:5128. [PMID: 35564522 PMCID: PMC9105083 DOI: 10.3390/ijerph19095128] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 11/16/2022]
Abstract
Microbial water quality is of vital importance for human, animal, and environmental health. Notably, pathogenically contaminated water can result in serious health problems, such as waterborne outbreaks, which have caused huge economic and social losses. In this context, the prompt detection of microbial contamination becomes essential to enable early warning and timely reaction with proper interventions. Recently, molecular diagnostics have been increasingly employed for the rapid and robust assessment of microbial water quality implicated by various microbial pollutants, e.g., waterborne pathogens and antibiotic-resistance genes (ARGs), imposing the most critical health threats to humans and the environment. Continuous technological advances have led to constant improvements and expansions of molecular methods, such as conventional end-point PCR, DNA microarray, real-time quantitative PCR (qPCR), multiplex qPCR (mqPCR), loop-mediated isothermal amplification (LAMP), digital droplet PCR (ddPCR), and high-throughput next-generation DNA sequencing (HT-NGS). These state-of-the-art molecular approaches largely facilitate the surveillance of microbial water quality in diverse aquatic systems and wastewater. This review provides an up-to-date overview of the advancement of the key molecular tools frequently employed for microbial water quality assessment, with future perspectives on their applications.
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Affiliation(s)
- Lisa Paruch
- Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research-NIBIO Oluf Thesens vei 43, 1433 Aas, Norway
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Eraqi WA, ElRakaiby MT, Megahed SA, Yousef NH, Elshahed MS, Yassin AS. Spatiotemporal Analysis of the Water and Sediment Nile Microbial Community Along an Urban Metropolis. MICROBIAL ECOLOGY 2021; 82:288-298. [PMID: 33420624 DOI: 10.1007/s00248-020-01674-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/28/2020] [Indexed: 06/12/2023]
Abstract
Assessing microbial identity, diversity, and community structure could be a valuable tool for monitoring the impact of xenobiotics and anthropogenic inputs in rivers, especially in urban and industrial settings. Here, we characterize the Nile River microbial community in water and sediments in summer and winter at five locations that span its natural flow through the Cairo metropolis. 16S rRNA gene datasets were analyzed to identify the role played by sample type (sediment versus water), season, and location in shaping the community, as well as to predict functional potential of the Nile River microbiome. Microbial communities were mostly influenced by sampling type (sediments versus water), while seasonal effects were only observed in water samples. Spatial differences did not represent a significant factor in shaping the community in either summer or winter seasons. Proteobacteria was the most abundant phylum in both water and sediment samples, with the order Betaproteobacteriales being the abundant one. Chloroflexi and Bacteroidetes were also prevalent in sediment samples, while Cyanobacteria and Actinobacteria were abundant in water samples. The linear discriminative analysis effect size (LEfSe) identified the cyanobacterial genus Cyanobium PCC-6307 as the main variable between summer and winter water. Sequences representing human and animal potential pathogens, as well as toxin-producing Cyanobacteria, were identified in low abundance within the Nile microbiome. Functionally predicted metabolic pathways predicted the presence of antibiotic biosynthesis, as well as aerobic xenobiotic degradation pathways in the river microbiome.
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Affiliation(s)
- Walaa A Eraqi
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Kasr-Eleini St, Cairo, 11562, Egypt
| | - Marwa T ElRakaiby
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Kasr-Eleini St, Cairo, 11562, Egypt
| | - Salwa A Megahed
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Kasr-Eleini St, Cairo, 11562, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), 6th of October, Giza, 12585, Egypt
| | - Noha H Yousef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74074, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74074, USA
| | - Aymen S Yassin
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Kasr-Eleini St, Cairo, 11562, Egypt.
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Filling the Gaps in the Cyanobacterial Tree of Life-Metagenome Analysis of Stigonema ocellatum DSM 106950, Chlorogloea purpurea SAG 13.99 and Gomphosphaeria aponina DSM 107014. Genes (Basel) 2021; 12:genes12030389. [PMID: 33803228 PMCID: PMC8001431 DOI: 10.3390/genes12030389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/18/2021] [Accepted: 03/03/2021] [Indexed: 12/26/2022] Open
Abstract
Cyanobacteria represent one of the most important and diverse lineages of prokaryotes with an unparalleled morphological diversity ranging from unicellular cocci and characteristic colony-formers to multicellular filamentous strains with different cell types. Sequencing of more than 1200 available reference genomes was mainly driven by their ecological relevance (Prochlorococcus, Synechococcus), toxicity (Microcystis) and the availability of axenic strains. In the current study three slowly growing non-axenic cyanobacteria with a distant phylogenetic positioning were selected for metagenome sequencing in order to (i) investigate their genomes and to (ii) uncover the diversity of associated heterotrophs. High-throughput Illumina sequencing, metagenomic assembly and binning allowed us to establish nearly complete high-quality draft genomes of all three cyanobacteria and to determine their phylogenetic position. The cyanosphere of the limnic isolates comprises up to 40 heterotrophic bacteria that likely coexisted for several decades, and it is dominated by Alphaproteobacteria and Bacteriodetes. The diagnostic marker protein RpoB ensured in combination with our novel taxonomic assessment via BLASTN-dependent text-mining a reliable classification of the metagenome assembled genomes (MAGs). The detection of one new family and more than a dozen genera of uncultivated heterotrophic bacteria illustrates that non-axenic cyanobacteria are treasure troves of hidden microbial diversity.
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Özdemir V, Arga KY, Aziz RK, Bayram M, Conley SN, Dandara C, Endrenyi L, Fisher E, Garvey CK, Hekim N, Kunej T, Şardaş S, Von Schomberg R, Yassin AS, Yılmaz G, Wang W. Digging Deeper into Precision/Personalized Medicine: Cracking the Sugar Code, the Third Alphabet of Life, and Sociomateriality of the Cell. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 24:62-80. [PMID: 32027574 DOI: 10.1089/omi.2019.0220] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Precision/personalized medicine is a hot topic in health care. Often presented with the motto "the right drug, for the right patient, at the right dose, and the right time," precision medicine is a theory for rational therapeutics as well as practice to individualize health interventions (e.g., drugs, food, vaccines, medical devices, and exercise programs) using biomarkers. Yet, an alien visitor to planet Earth reading the contemporary textbooks on diagnostics might think precision medicine requires only two biomolecules omnipresent in the literature: nucleic acids (e.g., DNA) and proteins, known as the first and second alphabet of biology, respectively. However, the precision/personalized medicine community has tended to underappreciate the third alphabet of life, the "sugar code" (i.e., the information stored in glycans, glycoproteins, and glycolipids). This article brings together experts in precision/personalized medicine science, pharmacoglycomics, emerging technology governance, cultural studies, contemporary art, and responsible innovation to critically comment on the sociomateriality of the three alphabets of life together. First, the current transformation of targeted therapies with personalized glycomedicine and glycan biomarkers is examined. Next, we discuss the reasons as to why unraveling of the sugar code might have lagged behind the DNA and protein codes. While social scientists have historically noted the importance of constructivism (e.g., how people interpret technology and build their values, hopes, and expectations into emerging technologies), life scientists relied on the material properties of technologies in explaining why some innovations emerge rapidly and are more popular than others. The concept of sociomateriality integrates these two explanations by highlighting the inherent entanglement of the social and the material contributions to knowledge and what is presented to us as reality from everyday laboratory life. Hence, we present a hypothesis based on a sociomaterial conceptual lens: because materiality and synthesis of glycans are not directly driven by a template, and thus more complex and open ended than sequencing of a finite length genome, social construction of expectations from unraveling of the sugar code versus the DNA code might have evolved differently, as being future-uncertain versus future-proof, respectively, thus potentially explaining the "sugar lag" in precision/personalized medicine diagnostics over the past decades. We conclude by introducing systems scientists, physicians, and biotechnology industry to the concept, practice, and value of responsible innovation, while glycomedicine and other emerging biomarker technologies (e.g., metagenomics and pharmacomicrobiomics) transition to applications in health care, ecology, pharmaceutical/diagnostic industries, agriculture, food, and bioengineering, among others.
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Affiliation(s)
- Vural Özdemir
- OMICS: A Journal of Integrative Biology, New Rochelle, New York.,Senior Advisor and Writer, Emerging Technology Governance and Responsible Innovation, Toronto, Ontario, Canada
| | - K Yalçın Arga
- Health Institutes of Turkey, Istanbul, Turkey.,Department of Bioengineering, Faculty of Engineering, Marmara University, İstanbul, Turkey
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt.,The Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt
| | - Mustafa Bayram
- Department of Food Engineering, Faculty of Engineering, Gaziantep University, Gaziantep, Turkey
| | - Shannon N Conley
- STS Futures Lab, School of Integrated Sciences, James Madison University, Harrisonburg, Virginia
| | - Collet Dandara
- Division of Human Genetics, Department of Pathology and Institute for Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Laszlo Endrenyi
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Erik Fisher
- School for the Future of Innovation in Society and the Consortium for Science, Policy and Outcomes, Arizona State University, Tempe, Arizona
| | - Colin K Garvey
- Stanford Institute for Human-Centered Artificial Intelligence, Stanford University, Palo Alto, California
| | - Nezih Hekim
- Department of Biochemistry, Faculty of Medicine, İstanbul Medipol University, İstanbul, Turkey
| | - Tanja Kunej
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Domzale, Slovenia
| | - Semra Şardaş
- Faculty of Pharmacy, İstinye University, İstanbul, Turkey
| | - Rene Von Schomberg
- Directorate General for Research and Innovation, European Commission, Brussel, Belgium.,Technical University Darmstadt, Darmstadt, Germany
| | - Aymen S Yassin
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt.,The Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt
| | - Gürçim Yılmaz
- Writer and Editor, Cultural Studies, and Curator of Contemporary Arts, İstanbul, Turkey
| | - Wei Wang
- Key Municipal Laboratory of Clinical Epidemiology, Capital Medical University, Beijing, China.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
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