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Gupta A, Dutt V, Sharma N, Kajale S, Bhatt A, Shafi S, Azhar E, Zumla A, Sharma A. Examining the microbial composition of natural springs in Bhaderwah, Jammu and Kashmir, India. Environ Monit Assess 2023; 195:949. [PMID: 37450062 DOI: 10.1007/s10661-023-11507-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/10/2023] [Indexed: 07/18/2023]
Abstract
Natural springs are the main source of water supply for domestic and agricultural use for humans living in the mountainous regions of Asia. Increasing anthropogenic activities with associated waste load, coupled with inadequate sanitation, and contamination of natural water resources and the environment are emerging as important public health issues. We performed a prospective microbiological and physicochemical investigation of water samples from seven distinct natural springs situated at an altitude of 1615 m in the Bhaderwah region of Jammu and Kashmir, India. Bacterial groups belonging to opportunistic pathogens such as members of Moraxellaceae (Acinetobacter), Arcobacteraceae (Pseudoarcobacter), Pseudomonadaceae (Pseudomonas), Oxalobacteraceae (Massilia), and Flavobacteriaceae (Flavobacterium) were observed. The total coliform test indicated an intermediate level of risk of fecal contamination of the springs, except for one site. Through a questionnaire-based survey of the local population, we discovered that around 40% of participants had suffered from waterborne diseases including typhoid (~14%) and diarrhea (~11%). Our data suggests that increased surveillance of fecal contamination and heterotrophic opportunistic pathogens is needed to enhance water quality and reduce health risks for people living in mountainous regions.
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Affiliation(s)
- Abhishek Gupta
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Vandana Dutt
- Institute of Mountain Environment, University of Jammu, Bhaderwah Campus, Jammu and Kashmir, India
| | - Neeraj Sharma
- Institute of Mountain Environment, University of Jammu, Bhaderwah Campus, Jammu and Kashmir, India.
| | - Swapnil Kajale
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Arun Bhatt
- GB Pant Institute of Engineering and Technology, Garhwal, Uttarakhand, India
| | - Shuja Shafi
- Mass Gatherings and Global Health Network, London, UK
| | - Esam Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, and Medical Laboratory Sciences Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Alimuddin Zumla
- Division of Infection and Immunity, NIHR Biomedical Research Centre, UCL Hospitals NHS Foundation Trust, University College London, London, UK
| | - Avinash Sharma
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India.
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Brown G, Hoedt EC, Keely S, Shah A, Walker MM, Holtmann G, Talley NJ. Role of the duodenal microbiota in functional dyspepsia. Neurogastroenterol Motil 2022; 34:e14372. [PMID: 35403776 PMCID: PMC9786680 DOI: 10.1111/nmo.14372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/04/2022] [Accepted: 03/14/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Functional dyspepsia (FD) is a common and debilitating gastrointestinal disorder attributed to altered gut-brain interactions. While the etiology of FD remains unknown, emerging research suggests the mechanisms are likely multifactorial and heterogenous among patient subgroups. Small bowel motor disturbances, visceral hypersensitivity, chronic microinflammation, and increased intestinal tract permeability have all been linked to the pathogenesis of FD. Recently, alterations to the gut microbiome have also been implicated to play an important role in the disease. Changes to the duodenal microbiota may either trigger or be a consequence of immune and neuronal disturbances observed in the disease, but the mechanisms of influence of small intestinal flora on gastrointestinal function and symptomatology are unknown. PURPOSE This review summarizes and synthesizes the literature on the link between the microbiota, low-grade inflammatory changes in the duodenum and FD. This review is not intended to provide a complete overview of FD or the small intestinal microbiota, but instead outline some of the key conceptual advances in understanding the interactions between altered gastrointestinal bacterial communities; dietary factors; host immune activation; and stimulation of the gut-brain axes in patients with FD versus controls. Current and emerging treatment approaches such as dietary interventions and antibiotic or probiotic use that have demonstrated symptom benefits for patients are reviewed, and their role in modulating the host-microbiota is discussed. Finally, suggested opportunities for diagnostic and therapeutic improvements for patients with this condition are presented.
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Affiliation(s)
- Georgia Brown
- School of Medicine and Public HealthUniversity of NewcastleNewcastleNew South WalesAustralia,AGIRA (Australian Gastrointestinal Research Alliance)NewcastleNew South WalesAustralia,NHMRC Centre of Research Excellence in Digestive HealthNewcastleNew South WalesAustralia
| | - Emily C. Hoedt
- AGIRA (Australian Gastrointestinal Research Alliance)NewcastleNew South WalesAustralia,NHMRC Centre of Research Excellence in Digestive HealthNewcastleNew South WalesAustralia,School of Biomedical Sciences and PharmacyUniversity of NewcastleNewcastleNew South WalesAustralia,Hunter Medical Research InstituteNew Lambton HeightsNewcastleNew South WalesAustralia
| | - Simon Keely
- AGIRA (Australian Gastrointestinal Research Alliance)NewcastleNew South WalesAustralia,NHMRC Centre of Research Excellence in Digestive HealthNewcastleNew South WalesAustralia,School of Biomedical Sciences and PharmacyUniversity of NewcastleNewcastleNew South WalesAustralia,Hunter Medical Research InstituteNew Lambton HeightsNewcastleNew South WalesAustralia
| | - Ayesha Shah
- AGIRA (Australian Gastrointestinal Research Alliance)NewcastleNew South WalesAustralia,NHMRC Centre of Research Excellence in Digestive HealthNewcastleNew South WalesAustralia,Faculty of Medicine and Faculty of Health and Behavioural SciencesThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Marjorie M. Walker
- School of Medicine and Public HealthUniversity of NewcastleNewcastleNew South WalesAustralia,AGIRA (Australian Gastrointestinal Research Alliance)NewcastleNew South WalesAustralia,NHMRC Centre of Research Excellence in Digestive HealthNewcastleNew South WalesAustralia
| | - Gerald Holtmann
- AGIRA (Australian Gastrointestinal Research Alliance)NewcastleNew South WalesAustralia,NHMRC Centre of Research Excellence in Digestive HealthNewcastleNew South WalesAustralia,Faculty of Medicine and Faculty of Health and Behavioural SciencesThe University of QueenslandSt. LuciaQueenslandAustralia,Department of Gastroenterology & HepatologyPrincess Alexandra HospitalWoolloongabbaQueenslandAustralia
| | - Nicholas J. Talley
- School of Medicine and Public HealthUniversity of NewcastleNewcastleNew South WalesAustralia,AGIRA (Australian Gastrointestinal Research Alliance)NewcastleNew South WalesAustralia,NHMRC Centre of Research Excellence in Digestive HealthNewcastleNew South WalesAustralia,Hunter Medical Research InstituteNew Lambton HeightsNewcastleNew South WalesAustralia
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Li Y, Khan FH, Wu J, Zhang Y, Jiang Y, Chen X, Yao Y, Pan Y, Han X. Drivers of Spatiotemporal Eukaryote Plankton Distribution in a Trans-Basin Water Transfer Canal in China. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.899993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Planktonic eukaryotes are important components of aquatic ecosystems, and analyses of the whole eukaryotic planktonic community composition and function have far-reaching significance for water resource management. We aimed to understand the spatiotemporal variation and drivers of eukaryotic plankton distribution in the Middle Route Project of the South-to-North Water Diversion in Henan Province, China. Specifically, we examined planktonic assemblages and water quality at five stations along the canal and another one located before the dam in March, June, September, and December 2019. High-throughput sequencing revealed that the eukaryotic plankton community was primarily composed of 53 phyla, 200 genera, and 277 species, with Cryptophyta, Ciliophora, and norank_k_Cryptophyta being the dominant phyla. Redundancy analysis of the eukaryotic community and environmental factors showed that five vital factors affecting eukaryotic plankton distribution were oxidation-reduction potential, nitrate nitrogen, pH, total phosphorus, and water flow velocity. Furthermore, the geographical distribution of eukaryotic communities was consistent with the distance decay model. Importantly, environmental selection dominantly shaped the geographical distribution of the eukaryotic community. In summary, our study elucidates the ecological response of planktonic eukaryotes by identifying the diversity and ecological distribution of planktonic eukaryotes in trans-basin diversion channels.
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Wang N, Feng BN, Hu B, Cheng YL, Guo YH, Qian H. Neuroprotection of chicoric acid in a mouse model of Parkinson's disease involves gut microbiota and TLR4 signaling pathway. Food Funct 2022; 13:2019-2032. [PMID: 35103734 DOI: 10.1039/d1fo02216d] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Chicoric acid (CA), a polyphenolic acid obtained from chicory and purple coneflower (Echinacea purpurea), has been regarded as a nutraceutical to combat inflammation, viruses and obesity. Parkinson's disease (PD) is a common neurodegenerative disorder, and the microbiota-gut-brain axis might be the potential mechanism in the pathogenesis and development of PD. The results obtained in this study demonstrated that oral pretreatments of CA significantly prevented the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced motor dysfunctions and death of nigrostriatal dopaminergic neurons along with the inhibition of glial hyperactivation and the increment in striatal neurotrophins. 16S rRNA sequence results showed that CA significantly reduced MPTP-induced microbial dysbiosis and partially restored the composition of the gut microbiota to normal, including decreased phylum Bacteroidetes and genera Parabacteroide, as well as increased phylum Firmicutes, genera Lactobacillus and Ruminiclostridium. Besides, CA promoted colonic epithelial integrity and restored normal SCFA production. We also observed that proinflammatory cytokines such as TNF-α and IL-1β in the serum, striatum and colon were reduced by CA, indicating that CA prevented neuroinflammation and gut inflammation, in which the suppression of the TLR4/MyD88/NF-κB signaling pathway might be the underlying molecular mechanism. These findings demonstrated that CA had neuroprotective effects on MPTP-induced PD mice possibly via modulating the gut microbiota and inhibiting inflammation throughout the brain-gut axis.
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Affiliation(s)
- Ning Wang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Bai-Nian Feng
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, China
| | - Bin Hu
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yu-Liang Cheng
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Ya-Hui Guo
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - He Qian
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
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Zlatković S, Medić O, Predojević D, Nikolić I, Subakov-simić G, Onjia A, Berić T, Stanković S. Spatio-Temporal Dynamics in Physico-Chemical Properties, Phytoplankton and Bacterial Diversity as an Indication of the Bovan Reservoir Water Quality. Water 2022; 14:391. [DOI: 10.3390/w14030391] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The study aimed to investigate the physico-chemical properties as well as phytoplankton and bacterial community diversity of Bovan Lake reservoir in Serbia to gain insight into the seasonal dynamic of water quality. All analyses were performed at three localities and water depths in spring, summer, autumn, and winter 2019. Seven phytoplankton phyla comprising 139 taxa were detected at all three localities (Chlorophyta 58%, Bacillariophyta 14%, Cyanobacteria 9%, Chrysophyta 5%, Dinophyta 5%, Euglenophyta 5%, and Cryptophyta 4%). Winter 2019 was characterized by the presence of 36 unique species in all phyla except Euglenophyta. Bacterial diversity analyses showed that Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, and Verrucomicrobia dominated the water intake locality at all three water depths (0.5, 10, and 20 m below the surface). In general, the physico-chemical parameters, phytoplankton, and bacterial community composition depended on the season and the water depth and showed that Bovan Lake was of satisfactory ecological status and water quality at all localities, and meets the needs for all intended purposes.
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Tyagi I, Tyagi K, Bhutiani R, Chandra K, Kumar V. Bacterial diversity assessment of world's largest sewage-fed fish farms with special reference to water quality: a Ramsar site. Environ Sci Pollut Res Int 2021; 28:42372-42386. [PMID: 33813698 DOI: 10.1007/s11356-021-13756-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
Bacterial community structure is one of the essential components of aquaculture dynamics and plays an important role in maintaining wetland health. The present work is an effort to study the structure of bacterial communities in the world's largest sewage-fed fish farms, the East Kolkata Wetlands (EKWs), along with their predicted functional metabolic pathways and correlation with environmental variables. Sequencing data analysis revealed the abundance of genera such as Arcobacter (0-50%), Pseudomonas (0-15%), Sulfurospirillum (0-9%), Cloacibacterium (0-6%), hgcI clade (7-29%), C39 (0-9%), V6 (3-36%), Fluiivicola (1-6%) and Cyanobium (3-8%) in the EKWs. Further, water quality analysis of three treatment groups, i.e. Sewage, Sewage F-1 and Sewage F-2, revealed that dissolved oxygen (DO), biochemical oxygen demand (BOD) and chemical oxygen demand (COD) differed significantly and violated the standard prescribed norms (Central Pollution Control Board, CPCB, New Delhi) for fishery propagation and irrigation in India. Further, the correlation matrix analysis between the abundance of bacterial genera and environmental variables indicated that DO, BOD and COD were mainly responsible for bacterial community structure and their proliferation in the EKWs. Our results indicated that the abundance of genera such as Arcobacter, Pseudomonas, Sulfurospirillum and Cloacibacterium has an inverse relationship with BOD and COD. Our observations based on the bacterial community structure and deteriorated water quality indicate the ineffective functioning and poor management of this man-made constructed wetland.
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Affiliation(s)
- Inderjeet Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 700053, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 700053, India
| | - Rakesh Bhutiani
- Department of Environmental Sciences, Gurukul Kangri Vishwavidyalaya, Haridwar, 249404, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 700053, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 700053, India.
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Zhu C, Zhang J, Wang X, Yang Y, Chen N, Lu Z, Ge Q, Jiang R, Zhang X, Yang Y, Chen T. Responses of cyanobacterial aggregate microbial communities to algal blooms. Water Res 2021; 196:117014. [PMID: 33751971 DOI: 10.1016/j.watres.2021.117014] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 02/11/2021] [Accepted: 03/04/2021] [Indexed: 06/12/2023]
Abstract
Freshwater lakes are threatened by harmful cyanobacterial blooms, whose basic unit is Cyanobacterial Aggregate (CA). CA-attached bacteria play a significant role through different blooming stages with substantial variation of their taxonomic structure. However, little is known about their functional variations and functional links with cyanobacteria due to the lack of reference genomes. In this longitudinal study, we collected 16 CA samples from Lake Taihu, one of China's largest freshwater lakes, from April 2015 to February 2016, and sequenced their V4 region of 16S rRNA genes, full metagenomes (MG), and metatranscriptomes (MT). The analysis of these data revealed the dynamics of microbial taxonomic and functional structure in CAs, influenced by both external environmental factors and internal metabolism. 55 OTUs, 456 genes, and 37 transcripts showed significantly differential abundance across the early, middle, and late blooming stages (ANOVA test, P < 0.05). Total nitrogen and total phosphorus were proved to be the most important environmental drivers of microbial taxonomic and functional variations in CAs (Mantel's r > 0.25, P < 0.05). We constructed 161 high-quality metagenome-assembled genomes (MAGs), out of which 22 were cyanobacterial strains with diverse energy pathways, transporters and prokaryotic defense systems. Based on these MAGs, we constructed a cyanobacteria-bacteria co-nitrogen-pathway and a cyanobacteria-bacteria co-phosphorus-pathway, by which we demonstrated how nitrogen and phosphorus influence the dynamics of the microbial structure to a certain extent by affecting these co-pathways. Overall, these results characterized the taxonomic, functional, and transcriptional variations of microbes in CAs through different blooming stages. Genome assembly and metabolic analysis of cyanobacteria and their attached bacteria suggested that the material exchange and signal transduction do, indeed, exist among them. Our understanding of the underlying molecular pathways for cyanobacterial blooms could lead to the control of blooms by interventional strategies to disrupt critical microbes' expression.
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Affiliation(s)
- Congmin Zhu
- Institute for Artificial Intelligence and Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China
| | - Junyi Zhang
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China; Wuxi Environmental Monitoring Centre, Wuxi, China
| | - Xin Wang
- Department of Ultrasound, Peking Union Medical College Hospital, Beijing 100005, China
| | | | - Ning Chen
- Institute for Artificial Intelligence and Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China
| | - Zuhong Lu
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Qinyu Ge
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Rui Jiang
- Bioinformatics Division and Center for Synthetic & Systems Biology, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xuegong Zhang
- Bioinformatics Division and Center for Synthetic & Systems Biology, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Ting Chen
- Institute for Artificial Intelligence and Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China; Tsinghua-Fuzhou Institute for Data Technology, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing 100084, China.
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Yang Y, Ashworth AJ, Durso LM, Savin M, DeBruyn JM, Cook K, Moore PA, Owens PR. Do Long-Term Conservation Pasture Management Practices Influence Microbial Diversity and Antimicrobial Resistant Genes in Runoff? Front Microbiol 2021; 12:617066. [PMID: 33897633 PMCID: PMC8060697 DOI: 10.3389/fmicb.2021.617066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 03/15/2021] [Indexed: 12/02/2022] Open
Abstract
Runoff from land-applied manure and poultry litter is one mechanism by which manure-borne bacteria are transported over large distances in the environment. There is a global concern that antimicrobial resistant (AMR) genes may be transmitted through the food chain from animal manures to soil to surface water. However, details are lacking on the ecology of AMR genes in water runoff as well as how conservation management practices may affect the runoff microbiome or minimize the movement of AMR genes. The aim of this study was to identify microbial community structure and diversity in water runoff following 14-years of poultry litter and cattle manure deposition and to evaluate the amount of AMR genes under five conventional and conservation pasture management strategies. Since 2004, all watersheds received annual poultry litter at a rate of 5.6 Mg ha−1 and were consistently managed. Surface runoff samples were collected from each watershed from 2018 to 2019, characterized using Illumina 16S rRNA gene amplicon sequencing and enumerated for four AMR-associated genes (ermB, sulI, intlI, and blactx-m-32) using quantitative PCR. Overall, long-term pasture management influenced water microbial community structure, with effects differing by year (p < 0.05). Bacterial richness (Chao1 index) was influenced by pasture management, with the lowest richness occurring in the control (nearby non-agricultural water source) and the greatest under fields that were hayed (no cattle presence). Runoff bacterial richness in watersheds increased following poultry litter applications, indicating poultry litter is a possible source of bacteria and altered runoff community structure. The blactx-m-32 gene was not detected in any surface water sample. The remaining three AMR genes were absent in the non-agricultural control, but present in agricultural samples. However, there was no impact (p > 0.05) from pasture management on the abundance of these genes, indicating both conventional and conservation practices have similar ecologies for these targets; however, there was a greater detection of sulI genes from runoff in continuously grazed systems in 2019, with hay being lowest in 2019. Results illustrate that the edge of field buffer strips may increase bacterial richness in water runoff, but these changes in richness do not greatly impact target AMR genes in the United States largest land-use category.
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Affiliation(s)
- Yichao Yang
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Amanda J Ashworth
- USDA-ARS, Poultry Production and Product Safety Research Unit, Fayetteville, AR, United States
| | - Lisa M Durso
- USDA-ARS, Agroecosystem Management Research Unit, Lincoln, NE, United States
| | - Mary Savin
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Jennifer M DeBruyn
- Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Kimberly Cook
- USDA-ARS, Nutrition, Food Safety/Quality, Office of National Programs, Beltsville, MD, United States
| | - Philip A Moore
- USDA-ARS, Poultry Production and Product Safety Research Unit, Fayetteville, AR, United States
| | - Phillip R Owens
- USDA-ARS, Dale Bumpers Small Farms Research Center, Booneville, AR, United States
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Acharya K, Halla FF, Massawa SM, Mgana SM, Komar T, Davenport RJ, Werner D. Chlorination effects on DNA based characterization of water microbiomes and implications for the interpretation of data from disinfected systems. J Environ Manage 2020; 276:111319. [PMID: 32889498 DOI: 10.1016/j.jenvman.2020.111319] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
Quantitative PCR (qPCR) and next generation sequencing (NGS) are nucleic acid based microbiology techniques that provide new insights into drinking water quality, but considerable uncertainty remains around their correct interpretation. We noticed the presence of bacterial DNA from various putative pathogens, including from faecal indicator bacteria (FIB), in disinfected water, when culturable FIB were absent. To understand these observations better we studied the effect of chlorination on conventional and DNA based microbial water quality assessments. Surface water chlorination reduced plate counts for various FIB by up to >6 log units, intact cell counts by flow cytometry by 3.3 log units, and 16S rRNA gene copies by qPCR by 1.5 and 1.6 log units for total bacteria and total coliforms, respectively. Nanopore sequencing of 16S rRNA amplicons with the portable MinION device revealed the DNA from several families containing putative pathogens appeared to be more resistant than that of other bacteria to degradation by chlorine disinfection. For instance, 16S rRNA genes assigned to the Enterobacteriaceae family, members of which are mostly the target of coliform tests, increased in relative abundance from 0.001 ± 0.0002% to 0.0036 ± 0.003% after chlorine treatment. Hence, metagenomic drinking water data needs to be interpreted with caution. Plate counts and flow cytometry in combination with DNA based analysis provide more robust insight than NGS or qPCR alone.
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Affiliation(s)
- Kishor Acharya
- School of Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, United Kingdom.
| | - Franella Francos Halla
- Department of Environmental Engineering, School of Environmental Science and Technology, Ardhi University, Dar Es Salaam, Tanzania
| | - Said Maneno Massawa
- Department of Environmental Engineering, School of Environmental Science and Technology, Ardhi University, Dar Es Salaam, Tanzania
| | - Shaaban Mrisho Mgana
- Department of Environmental Engineering, School of Environmental Science and Technology, Ardhi University, Dar Es Salaam, Tanzania
| | - Tom Komar
- School of Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, United Kingdom
| | - Russell J Davenport
- School of Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, United Kingdom
| | - David Werner
- School of Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, United Kingdom
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Chang W, Sun J, Pang Y, Zhang S, Gong L, Lu J, Feng B, Xu R. Effects of different habitats on the bacterial community composition in the water and sediments of Lake Taihu, China. Environ Sci Pollut Res Int 2020; 27:44983-44994. [PMID: 32772287 DOI: 10.1007/s11356-020-10376-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
Bacterial communities are sensitive to environmental fluctuations, and a better understanding of the relationships between bacterial community distribution and complex environmental conditions is important for the remediation of lake ecosystems. In this study, bacterial communities from 7 water and 7 sediment samples in 3 different regions (east, the hydrophyte-dominated region; north, the transitional region; west, the highly polluted region) of Lake Taihu were investigated via high-throughput sequencing. The physicochemical characterization showed that there were obvious differences in the trophic statuses of the three lake regions, which were mainly due to the differences in pollutant concentration and hydrophyte coverage. The Shannon and Simpson values indicated that the diversity of bacterial communities in water was the highest in the eastern region, followed by the northern and western regions, while there was no significant difference in the bacterial community characteristics in sediments among lake regions. We found that the western lake region had the highest Cyanobacteria concentration (34.71%), suggesting that Cyanobacteria may have competitive advantages over the other bacterioplankton in water columns without plants. The abundances of Chlorobi detected in the water samples in the east (2.69%) and north (6.66%) were higher than those in the west because the high turbidity in the western lake region was unsuitable for the growth of Chlorobi. Nitrospirae (average 6.36%) and Chloroflexi (average 11.62%) were more common in the sediments than in the water of Lake Taihu, suggesting that the nutrient level of Lake Taihu sediment was higher than that of water bodies. Welch's t test revealed that there were significant differences in species abundance (such as Microcystis, Synechococcus, Flavobacterium, and hgcI_clade) among the different regions, except that the east was relatively similar to the north. Canonical correspondence analysis demonstrated that TN, TP, and DO showed significant effects on the relative abundance of the dominant bacterial genera in water, while TOC, TP, and TN were positively correlated with TOC, TP and TN. This study provides useful information for understanding the variation in the diversity of bacterial communities in different habitats of Lake Taihu.
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Affiliation(s)
- Wenjie Chang
- College of Environment, Hohai University, Nanjing, 210098, China
- Jiangsu Provincial Academy of Environmental Science, Nanjing, 210036, China
| | - Jieli Sun
- College of Environment, Hohai University, Nanjing, 210098, China
| | - Yong Pang
- College of Environment, Hohai University, Nanjing, 210098, China.
| | - Songhe Zhang
- College of Environment, Hohai University, Nanjing, 210098, China
| | - Lixue Gong
- Jiangsu Provincial Academy of Environmental Science, Nanjing, 210036, China
| | - Jiaang Lu
- Jiangsu Provincial Academy of Environmental Science, Nanjing, 210036, China
| | - Bin Feng
- Jiangsu Provincial Academy of Environmental Science, Nanjing, 210036, China
| | - Ruichen Xu
- College of Environment, Hohai University, Nanjing, 210098, China
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Zhao M, Ma YT, He SY, Mou X, Wu L. Dynamics of bacterioplankton community structure in response to seasonal hydrological disturbances in Poyang Lake, the largest wetland in China. FEMS Microbiol Ecol 2020; 96:5863183. [DOI: 10.1093/femsec/fiaa064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 06/25/2020] [Indexed: 11/14/2022] Open
Abstract
ABSTRACT
Bacterioplankton communities play a critical role in biogeochemical cycling in freshwater environments, but how the hydrological regime impacts the assembly of bacterioplankton communities remains unclear. This study examined differences in bacterioplankton community structures between wet (July and September) and dry (October and November) seasons in two consecutive years (2016 and 2017) in Poyang Lake, the largest seasonal freshwater lake in China. Our results revealed no overall difference in bacterioplankton compositions and their predicted functions among spatially separated sites. However, bacterioplankton communities did show significant temporal shifts, mainly between samples in November and other months. Transitions from the dry to the wet season were observed in October in both sampling years. Meanwhile, insignificant spatial but significant temporal differences were also found for physicochemical variables. Moreover, redundancy analysis indicates that compared with water depth, water temperature was found to better explain changes in the bacterioplankton community. These findings consistently indicate that the bacterioplankton community in Poyang Lake is relatively less sensitive to annual hydrology shifts than water temperature and nutrient conditions.
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Affiliation(s)
- Man Zhao
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China
| | - Yan-tian Ma
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China
| | - Shi-yao He
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China
| | - Xiaozhen Mou
- Department of Biological Sciences, Kent State University, OH 44242, USA
| | - Lan Wu
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China
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12
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Liu TT, Yang H. Comparative analysis of the total and active bacterial communities in the surface sediment of Lake Taihu. FEMS Microbiol Ecol 2020; 96:5815072. [PMID: 32239216 DOI: 10.1093/femsec/fiaa059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/29/2020] [Indexed: 11/13/2022] Open
Abstract
Bacterial communities play crucial roles in the biogeochemical cycle of the surface sediments of freshwater lakes, but previous studies on bacterial community changes in this habitat have mostly been based on the total bacterial community (DNA level), while an exploration of the active microbiota at the RNA level has been lacking. Herein, we analysed the bacterial communities in the surface sediments of Lake Taihu at the DNA and RNA levels. Using MiSeq sequencing and real-time quantification, we found that the sequencing and quantitative results obtained at the RNA level compared with the DNA level were more accurate in responding to the spatiotemporal dynamic changes of the bacterial community. Although both sequencing methods indicated that Proteobacteria, Chloroflexi, Acidobacteria, Nitrospirae, Bacteroidetes and Actinobacteria were the dominant phyla, the co-occurrence network at the RNA level could better reflect the close relationship between microorganisms in the surface sediment. Additionally, further analysis showed that Prochlorococcus and Microcystis were the most relevant and dominant genera of Cyanobacteria in the total and active bacterial communities, respectively; our results also demonstrated that the analysis of Cyanobacteria-related groups at the RNA level was more 'informative'.
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Affiliation(s)
- Tong-Tong Liu
- State Key Laboratory of Microbial metabolism, and School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Hong Yang
- State Key Laboratory of Microbial metabolism, and School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
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Akter N, Wahiduzzaman M, Yeasmin A, Islam K, Luo J. Spatial Modelling of Bacterial Diversity over the Selected Regions in Bangladesh by Next-Generation Sequencing: Role of Water Temperature. Applied Sciences 2020; 10:2537. [DOI: 10.3390/app10072537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In this study, a spatial model has been developed to investigate the role of water temperature to the distribution of bacteria over the selected regions in the Bay of Bengal, located in the southern region of Bangladesh using next-generation sequencing. Bacterial concentration, quantitative polymerase chain reactions, and sequencing were performed on water samples and identified Acidobacteria, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Firmicutes, Nitrospirae, Planctomycetes, Proteobacteria, and Verrucomicrobia. The spatial model tessellated the parts of the Bay of Bengal with hexagons and analyzed the relationship between the distribution of bacteria and water temperature. A geographically weighted regression was used to observe whether water temperature contributed strongly or weakly to the distribution of bacteria. The residuals were examined to assess the model’s fitness. The spatial model has the potential to predict the bacterial diversity in the selected regions of Bangladesh.
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Pineda-Mendoza RM, Briones-Roblero CI, Gonzalez-Escobedo R, Rivera-Orduña FN, Martínez-Jerónimo F, Zúñiga G. Seasonal changes in the bacterial community structure of three eutrophicated urban lakes in Mexico city, with emphasis on Microcystis spp. Toxicon 2020; 179:8-20. [PMID: 32142716 DOI: 10.1016/j.toxicon.2020.02.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 02/08/2020] [Accepted: 02/26/2020] [Indexed: 10/24/2022]
Abstract
Artificial urban lakes commonly have physicochemical conditions that contribute to rapid anthropogenic eutrophication and development of cyanobacterial blooms. Microcystis is the dominat genus in most freshwater bodies and is one of the main producter of microcystins. Using 454-pyrosequencing we characterized the bacterial community, with special emphasis on Microcystis, in three recreational urban lakes from Mexico City in both wet and dry seasons. We also evaluated some physicochemical parameters that might influence the presence of Microcystis blooms, and we associated the relative abundance of heterotrophic and autotrophic bacterial communities with their possible metabolic capacities. A total of 14 phyla, 18 classes, 39 orders, 53 families and 48 bacterial genera were identified in both seasons in the three urban lakes. Cyanobacteria had the highest relative abundance followed by Proteobacteria and Actinobacteria. Microcystis was the dominant taxon followed by Arthrospira, Planktothrix and Synechococcus. We also found heterotrophic bacteria associated with the blooms, such as Rhodobacter, Pseudomonas, Sphingomonas and, Porphyrobacter. The highest richness, diversity and dominance were registered in the bacterial community of the Virgilio Uribe Olympic Rowing-Canoeing Track in both seasons, and the lowest values were found in the Chapultepec Lake. The canonical correspondence analysis showed that dissolved oxygen and NO3-N concentrations might explain the presence of Microcystis blooms. The metabolic prediction indicated that these communities are involved in photosynthesis, oxidative phosphorylation, methane metabolism, carbon fixation, and nitrogen and sulfur metabolism. The lakes studied had a high prevalence of Microcystis, but average values of microcystins did not exceed the maximum permissible level established by the United States Environmental Protection Agency for recreational and cultural activities. The presence of cyanobacteria and microcystins at low to moderate concentrations in the three lakes could result in ecosystem disruption and increase animal and human health risks.
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Affiliation(s)
- Rosa María Pineda-Mendoza
- Departamento de Zoología. Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Ciudad de México, Mexico
| | - Carlos Iván Briones-Roblero
- Departamento de Zoología. Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Ciudad de México, Mexico
| | - Roman Gonzalez-Escobedo
- Departamento de Zoología. Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Ciudad de México, Mexico
| | - Flor N Rivera-Orduña
- Departamento de Microbiología. Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Ciudad de México, Mexico
| | - Fernando Martínez-Jerónimo
- Departamento de Zoología. Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Ciudad de México, Mexico
| | - Gerardo Zúñiga
- Departamento de Zoología. Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Ciudad de México, Mexico.
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Zhu CM, Zhang JY, Guan R, Hale L, Chen N, Li M, Lu ZH, Ge QY, Yang YF, Zhou JZ, Chen T. Alternate succession of aggregate-forming cyanobacterial genera correlated with their attached bacteria by co-pathways. Sci Total Environ 2019; 688:867-879. [PMID: 31255824 DOI: 10.1016/j.scitotenv.2019.06.150] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 06/10/2019] [Indexed: 06/09/2023]
Abstract
Freshwater lakes are threatened by harmful blooms characterized by Cyanobacterial Aggregates (CAs) that are normally aggregated with extracellular polysaccharides released by cyanobacteria to form a phycosphere. It is possible that mutualistic relationships exist between bacteria and cyanobacteria in these CAs wherein bacterial products supplement cyanobacterial growth, and cyanobacterial exudates, in turn, serve as substrates for bacteria, thus augmenting the stability of each constituent. However, little is known about the exact interaction between cyanobacteria and their attached bacteria in CAs. Therefore, in this study, we collected 26 CA samples from Lake Taihu, a large freshwater lake in China from March of 2015 to February of 2016. We then sequenced both the V4 regions of 16S rRNA genes and full metagenomes, resulting in 610 Mb of 16S rRNA gene data and 198.98 Gb of high-quality metagenomic data. We observed that two cyanobacteria genera (Microcystis and Dolichospermum) alternately dominated CAs along the sampling time and specific bacterial genera attached to different cyanobacteria genera dominated CAs. More specifically, Dolichospermum dominates CAs when water temperature is low and total nitrogen is high, while Microcystis dominates CAs when water temperature is high and total nitrogen is low. Moreover, we found specific bacterial genera attached to different cyanobacteria genera dominated CAs. The cyanobacteria-bacteria related pairs Dolichospermum-Burkholderia and Microcystis-Hyphomonas were detected by ecological networks construction. Bacterial communities in CAs were found to be more correlated with the cyanobacterial community (Mantel's r = 0.76, P = 0.001) than with environmental factors (Mantel's r = 0.27, P = 0.017). A potential codependent nitrogen-cycling pathway between cyanobacteria and their attached bacteria was constructed, indicating their functional link. Overall, these results demonstrated that mutualistic relationships do, indeed, exist between cyanobacteria and bacteria in CAs at both taxonomic and gene levels, providing biological clues potentially leading to the control of blooms by interventional strategies to disrupt bacteria-cyanobacteria relationships and co-pathways.
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Affiliation(s)
- Cong-Min Zhu
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division, Center for Synthetic & Systems Biology, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Jun-Yi Zhang
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China; Wuxi Environmental Monitoring Centre, Wuxi, China
| | - Rui Guan
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Lauren Hale
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Ning Chen
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division, Center for Synthetic & Systems Biology, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Ming Li
- College of Resources and Environment, Northwest A & F University, Yangling, People's Republic of China
| | - Zu-Hong Lu
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Qin-Yu Ge
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Yun-Feng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Ji-Zhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China; School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ting Chen
- Institute for Artificial Intelligence, Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China; Tsinghua-Fuzhou Institute for Data Technology, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing 100084, China.
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Zhang W, Zhou Y, Jeppesen E, Wang L, Tan H, Zhang J. Linking heterotrophic bacterioplankton community composition to the optical dynamics of dissolved organic matter in a large eutrophic Chinese lake. Sci Total Environ 2019; 679:136-147. [PMID: 31082588 DOI: 10.1016/j.scitotenv.2019.05.055] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 05/04/2019] [Accepted: 05/05/2019] [Indexed: 06/09/2023]
Abstract
Elucidation of the linkages between the bacterial community composition and chromophoric dissolved organic matter (CDOM) in lake ecosystems is critical for the understanding of the inland water carbon cycling. Despite substantial research into the relationship between the bacteria community and the bulk DOM pool, knowledge of the specific relationship between the optical dynamics of DOM and the bacterioplankton community in lake ecosystems is still poor. We investigated the linkages between the optical dynamics of DOM and bacteria composition in shallow eutrophic Lake Taihu, China. Redundancy Analysis (RDA) indicated that besides water temperature and phytoplankton biomass, also CDOM was an important factor determining the composition of the bacterial community. Generalized Additive Models (GAM) showed that terrestrial humic-like C1 and tyrosine-like C4 were the key factors explaining the abundance of the main bacterial clades. C1 was closely correlated with Verrucomicrobia, Actinobacteria, Alphaproteobacteria, Betaproteobacteria and Planctomycetes, and C4 was closely related to the latter two and to Bacteroidetes. At family level, the dominant families - Pelagibacteraceae (Alphaproteobacteria) and Gemmataceae (Planctomycetes) - were related to both allochthonous and autochthonous CDOM fluorophores but responded differently to the various CDOM components. Tryptophan-like C2 was significantly and positively correlated with Gemmataceae and Ellin6075 (Acidobacteria). Additionally, we found that the biomasses of Cyanophyta, terrestrial humic-like C1, tryptophan-like C4 and C5 were significantly related to the richness of heterotrophic bacterioplankton. Our results provide new insight into the relationship between bacteria and DOM optical dynamics although the mechanisms leading to these relationships need further experimental investigations.
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Affiliation(s)
- Wei Zhang
- Centre for Research on Environmental Ecology and Fish Nutrition (Ministry of Agriculture, China), Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education, China), National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, PR China
| | - Yongqiang Zhou
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Erik Jeppesen
- Department of Bioscience, Aarhus University, Silkeborg DK-8600, Denmark; Sino-Danish Centre for Education and Research (SDC), Beijing 100049, PR China
| | - Liqing Wang
- Centre for Research on Environmental Ecology and Fish Nutrition (Ministry of Agriculture, China), Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education, China), National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, PR China
| | - Hongxin Tan
- Centre for Research on Environmental Ecology and Fish Nutrition (Ministry of Agriculture, China), Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education, China), National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, PR China.
| | - Junyi Zhang
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210008, PR China; Wuxi Environmental Monitoring Centre, Wuxi 214023, PR China.
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Zhu C, Zhang J, Nawaz MZ, Mahboob S, Al-Ghanim KA, Khan IA, Lu Z, Chen T. Seasonal succession and spatial distribution of bacterial community structure in a eutrophic freshwater Lake, Lake Taihu. Sci Total Environ 2019; 669:29-40. [PMID: 30877958 DOI: 10.1016/j.scitotenv.2019.03.087] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 03/04/2019] [Accepted: 03/06/2019] [Indexed: 06/09/2023]
Abstract
In aquatic ecosystems, both phytoplankton and bacteria play pivotal roles. Based on 16S rRNA gene sequencing, considerable research focused on phytoplankton colony attached and free-living bacteria has revealed the close relationship between them, and indicated that the entire bacterial community mediates crucial biogeochemical processes in aquatic ecosystems. However, our understanding of their distribution patterns and response to environmental factors remains poor. Besides, picocyanobacteria, which were omitted from attached bacteria analysis, were reported to be important in cyanobacterial blooms. To explore the spatiotemporal variation of the entire bacterial community with their driving environmental factors and detect the relationships among them, we collected 61 water samples spanning one year and the entire Lake Taihu regions for surveying the entire bacterial community. Our results indicated: 1) seasonal variation of the bacterial community composition was stronger than spatial variation due to the clearly seasonal variation of Microcystis, Synechococcus (pico-cyanobacteria) and other bacteria (Actinomycetales, Pirellulaceae and Sphingobacteriaceae); 2) the spatial distribution of the bacterial community showed that different phyla were dominant in different regions; 3) the bacterial co-occurrence networks varied seasonally and were dominated by Microcystis, ACK-M1, Chthoniobacteraceae, Synechococcus, Pirellulaceae and Pelagibacteraceae; 4) phytoplankton density, chlorophyll a, water temperature and total nitrogen were the major factors that drove the spatiotemporal variation of bacterial community composition. This study revealed the seasonal succession and spatial distribution of the entire bacterial community in Lake Taihu, providing new insights into the relationship between water bloom-forming cyanobacterial species and other bacteria, and their response to environmental factors in eutrophic freshwater ecosystem.
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Affiliation(s)
- Congmin Zhu
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, Beijing; National Research Center for Information Science and Technnology, Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Artificial Intelligence, State Key Lab of Intelligent Technology and Systems, Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China
| | - Junyi Zhang
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; Wuxi Environmental Monitoring Centre, Wuxi 214121, China
| | - Muhammad Zohaib Nawaz
- Department of Computer Science, University of Agriculture, Faisalabad 38040, Pakistan; Center for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad 38040, Pakistan; Wuxi Metagene Science & Technology Co., Ltd, Wuxi, People's Republic of China
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Khalid A Al-Ghanim
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Iqrar Ahmad Khan
- Center for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad 38040, Pakistan
| | - Zuhong Lu
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Ting Chen
- Institute for Artificial Intelligence, State Key Lab of Intelligent Technology and Systems, Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China; Tsinghua-Fuzhou Institute of Digital Technology, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing 100084, China.
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18
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Brandt J, Albertsen M. Investigation of Detection Limits and the Influence of DNA Extraction and Primer Choice on the Observed Microbial Communities in Drinking Water Samples Using 16S rRNA Gene Amplicon Sequencing. Front Microbiol 2018; 9:2140. [PMID: 30245681 PMCID: PMC6137089 DOI: 10.3389/fmicb.2018.02140] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/21/2018] [Indexed: 01/02/2023] Open
Abstract
In recent years, 16S rRNA gene amplicon sequencing has been widely adopted for analyzing the microbial communities in drinking water (DW). However, no comprehensive attempts have been made to illuminate the inherent method biases specifically relating to DW communities. In this study, we investigated the impact of DNA extraction and primer choice on the observed microbial community, and furthermore estimated the detection limit of the 16S rRNA gene amplicon sequencing in these experimental settings. Of the two DNA extraction kits investigated, the PowerWater DNA Isolation Kit resulted in higher yield, better reproducibility and more OTUs identified compared to the FastDNA SPIN Kit for Soil, which is also commonly used within DW microbiome research. The use of three separate primer-sets targeting the V1-3, V3-4, and V4 region of the 16S rRNA gene revealed large differences in OTU abundances, with some of the primers unable to detect entire phyla. Estimations of the detection limit were based on bacteria-free water samples (1 L) spiked with Escherichia coli cells in different concentrations [101–106 cells/ml]. E.coli could be detected in all samples, however, samples with ∼101 cells/ml had several contaminating OTUs constituting approximately 8% of the read abundances. Based on our findings, we recommend using the PowerWater DNA Isolation Kit for DNA extraction in combination with PCR amplification of the V3-4 or V4 region for DW samples if a broad overview of the microbial community is to be obtained.
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Affiliation(s)
- Jakob Brandt
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
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Sun MF, Zhu YL, Zhou ZL, Jia XB, Xu YD, Yang Q, Cui C, Shen YQ. Neuroprotective effects of fecal microbiota transplantation on MPTP-induced Parkinson's disease mice: Gut microbiota, glial reaction and TLR4/TNF-α signaling pathway. Brain Behav Immun 2018; 70:48-60. [PMID: 29471030 DOI: 10.1016/j.bbi.2018.02.005] [Citation(s) in RCA: 379] [Impact Index Per Article: 63.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 01/14/2018] [Accepted: 02/12/2018] [Indexed: 12/11/2022] Open
Abstract
Parkinson's disease (PD) patients display alterations in gut microbiota composition. However, mechanism between gut microbial dysbiosis and pathogenesis of PD remains unexplored, and no recognized therapies are available to halt or slow progression of PD. Here we identified that gut microbiota from PD mice induced motor impairment and striatal neurotransmitter decrease on normal mice. Sequencing of 16S rRNA revealed that phylum Firmicutes and order Clostridiales decreased, while phylum Proteobacteria, order Turicibacterales and Enterobacteriales increased in fecal samples of PD mice, along with increased fecal short-chain fatty acids (SCFAs). Remarkably, fecal microbiota transplantation (FMT) reduced gut microbial dysbiosis, decreased fecal SCFAs, alleviated physical impairment, and increased striatal DA and 5-HT content of PD mice. Further, FMT reduced the activation of microglia and astrocytes in the substantia nigra, and reduced expression of TLR4/TNF-α signaling pathway components in gut and brain. Our study demonstrates that gut microbial dysbiosis is involved in PD pathogenesis, and FMT can protect PD mice by suppressing neuroinflammation and reducing TLR4/TNF-α signaling.
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Affiliation(s)
- Meng-Fei Sun
- Wuxi Medical School, Jiangnan University, Wuxi 214122, China
| | - Ying-Li Zhu
- Wuxi Medical School, Jiangnan University, Wuxi 214122, China
| | - Zhi-Lan Zhou
- Wuxi Medical School, Jiangnan University, Wuxi 214122, China
| | - Xue-Bing Jia
- Wuxi Medical School, Jiangnan University, Wuxi 214122, China
| | - Yi-Da Xu
- Wuxi Medical School, Jiangnan University, Wuxi 214122, China
| | - Qin Yang
- Wuxi Medical School, Jiangnan University, Wuxi 214122, China
| | - Chun Cui
- Wuxi Medical School, Jiangnan University, Wuxi 214122, China
| | - Yan-Qin Shen
- Wuxi Medical School, Jiangnan University, Wuxi 214122, China.
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20
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Zhang J, Ding X, Guan R, Zhu C, Xu C, Zhu B, Zhang H, Xiong Z, Xue Y, Tu J, Lu Z. Evaluation of different 16S rRNA gene V regions for exploring bacterial diversity in a eutrophic freshwater lake. Sci Total Environ 2018; 618:1254-1267. [PMID: 29089134 DOI: 10.1016/j.scitotenv.2017.09.228] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Revised: 09/08/2017] [Accepted: 09/21/2017] [Indexed: 05/26/2023]
Abstract
Massive partial sequencing of 16S rRNA genes has become the predominant tool used for studying microbial ecology. However, determining which hypervariable regions and primer sets should be used for screening microbial communities requires extensive investigation if controversial results are to be avoided. Here, the performances of different variable regions of the 16S rRNA gene on bacterial diversity studies were evaluated in silico with respect to the SILVA non-redundant reference database (SILVA SSU Ref 123NR), and subsequently verified using samples from Lake Taihu in China, a eutrophic lake. We found that the bacterial community composition results were strongly impacted by the different V regions. The results show that V1-V2 and V1-V3 regions were the most reliable regions in the full-length 16S rRNA sequences, while most V3 to V6 regions (including V3, V4, V3-V4, V5, V4-V5, V6, V3-V6, V4-V6, and V5-V6) were more closely aligned with the SILVA SSU Ref 123NR database. Overall, V4 was the most prominent V region for achieving good domain specificity, higher coverage and a broader spectrum in the Bacteria domain, as confirmed by the validation experiments. S-D-Bact-0564-a-S-15/S-D-Bact-0785-b-A-18 is, therefore, a promising primer set for surveying bacterial diversity in eutrophic lakes.
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Affiliation(s)
- Junyi Zhang
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; Wuxi Environmental Monitoring Centre, Wuxi 214121, China
| | - Xiao Ding
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Rui Guan
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Congmin Zhu
- MOE Key Lab of Bioinformatics, Bioinformatics Division/Center for Synthetic and Systems Biology, TNLIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Chao Xu
- Wuxi Environmental Monitoring Centre, Wuxi 214121, China
| | - Bingchuan Zhu
- Wuxi Environmental Monitoring Centre, Wuxi 214121, China
| | - Hu Zhang
- Wuxi Environmental Monitoring Centre, Wuxi 214121, China
| | - Zhipeng Xiong
- Lake Taihu Cyanobacterial Blooms Research Institute, Wuxi Metagene Science & Technology Co., Ltd, Wuxi 214135, China
| | - Yingang Xue
- Key Laboratory of Environmental Protection of Water Environment Biological Monitoring of Jiangsu Province, Changzhou Environmental Monitoring Center, Changzhou 213001, China
| | - Jing Tu
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zuhong Lu
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.
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Gao W, Chen Z, Li Y, Pan Y, Zhu J, Guo S, Hu L, Huang J. Bioassessment of a Drinking Water Reservoir Using Plankton: High Throughput Sequencing vs. Traditional Morphological Method. Water 2018; 10:82. [DOI: 10.3390/w10010082] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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