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Lalitha N, Katneni VK, Jangam AK, Suganya PN, Sukumaran S, Muralidhar M. Insight into the bacterial communities in the sediment-water interface across different salinities of Pacific White shrimp, Penaeus vannamei, by metabarcoding. Lett Appl Microbiol 2025; 78:ovaf020. [PMID: 39929187 DOI: 10.1093/lambio/ovaf020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Revised: 01/01/2025] [Accepted: 02/09/2025] [Indexed: 02/26/2025]
Abstract
Microbes play an important role in the food chain by metabolizing organic matter, cycling nutrients, and maintaining a dynamic equilibrium among organisms in water and sediment. The objective is to study the fluctuating taxonomic microbial diversity profile in the sediment-water interface at different days of culture (DOC) of Penaeus vannamei in varying salinities using the Illumina MiSeq platform. Sediment samples were collected in Tamil Nadu, India, from low-saline, brackish water, and high-saline ponds at 30, 60, and 90 DOC. Bacterial richness and diversity in species were high in low-saline ponds. Beta-diversity variation indicated more differences in bacterial composition in high- and low-saline ponds. The predominant phyla observed were Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Firmicutes, and Cyanobacteria. High-saline ponds accounted for more nitrification bacterial communities, sulfur-reducing bacterial communities, sulfur-oxidizing bacterial communities, and high redox potential, whereas denitrification bacterial communities were high in brackish water ponds.
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Affiliation(s)
- Natarajan Lalitha
- ICAR-Central Institute of Brackishwater Aquaculture, Chennai 600 028, India
| | | | - Ashok Kumar Jangam
- ICAR-Central Institute of Brackishwater Aquaculture, Chennai 600 028, India
| | | | - Suvana Sukumaran
- ICAR-Central Research Institute for Dryland Agriculture, Hyderabad 500 059, India
| | - Moturi Muralidhar
- ICAR-Central Institute of Brackishwater Aquaculture, Chennai 600 028, India
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Kim MK, Lim BS, Lee CS, Srinivasan S. Bacterial Diversity in the Different Ecological Niches Related to the Yonghwasil Pond (Republic of Korea). Microorganisms 2024; 12:2547. [PMID: 39770750 PMCID: PMC11677111 DOI: 10.3390/microorganisms12122547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2024] [Revised: 11/23/2024] [Accepted: 11/28/2024] [Indexed: 01/11/2025] Open
Abstract
The bacteriome profile was studied in freshwater ecosystems within the Yonghwasil pond, situated at the National Institute of Ecology, Seocheon-gun, Chungcheongnam-do, central western Korea. Six samples from water, mud, and soil niches were assessed, specifically from lake water, bottom mud (sediment), and root-soil samples of Bulrush, wild rice, Reed, and Korean Willow. Notably, the phylum Actinobacteria exhibited an upward trend moving from water to mud to soil samples, whereas Chloroflexi showed a contrasting decrease. Across the board, Proteobacteria emerged as the reigning phylum, and subsequent dominance was attributed to Firmicutes and Actinobacteria. The water samples were characterized by an enriched presence of Cyanobacteria and Bacteroidetes, whereas the mud samples distinctly housed a higher concentration of Chloroflexi. Assessing biodiversity through OTU and ACE indices revealed a subdued species richness in the water samples. On the contrary, mud samples stood out with the highest OTU and ACE metrics, signifying a microbially diverse habitat. Bulrush, wild rice, Reed, and Willow samples showed intermediate microbial diversity. The Shannon index further corroborated the pronounced microbial diversity in mud and Bulrush habitats with others. This research elucidates the microbial intricacies across different habitats within Yonghwasil Pond, emphasizing the pivotal role of environmental matrices in shaping bacterial communities.
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Affiliation(s)
| | | | - Chang Seok Lee
- Department of Bio and Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 01797, Republic of Korea
| | - Sathiyaraj Srinivasan
- Department of Bio and Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 01797, Republic of Korea
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Singh AK, Abedin MM, Das S, Najar IN, Lepcha YD, Mishra PK, Amit A, Tiwari HK, Rai AK. Unraveling microbial landscapes: high-throughput amplicon sequencing reveals distinct bacterial communities and potential health risks in potable springs of the Indian Himalayas. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-35577-9. [PMID: 39570527 DOI: 10.1007/s11356-024-35577-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 11/13/2024] [Indexed: 11/22/2024]
Abstract
Spring water is a vital drinking resource for residents in the Eastern Himalayas' Sikkim, India. While our initial investigations into spring water quality highlighted concerning levels of fecal coliform bacteria, the bacterial community composition (BCC) of these springs remains largely unexplored. This study sought to elucidate the BCC of Himalayan spring water, exploring its effects on water quality and delving into the unique bacterial ecology of these high-altitude springs. Bacterial diversity was assessed using 16S rRNA gene amplicon (V3-V4) library sequencing. The Greengenes reference database facilitated the classification of de-novo assembled operational taxonomic units (OTUs). The findings of this study revealed Proteobacteria (39.78%), Planctomycetes (35.76%), Verrucomicrobia (32.65%), and Bacteroidetes (37.04%) as predominant phyla across the four major districts: East, West, South, and North. Additionally, distinct genera emerged as dominant in each district: Emticicia in the East, Prosthecobacter in the South, and Planctomyces in the North and West. Of potential health concern, pathogenic bacteria like Corynebacterium, Acinetobacter, Legionella, Mycobacterium, and Clostridium were detected, albeit in low abundance. Their presence, even in minor quantities, might indicate potential future health risks for the communities relying on these springs. However, a substantial portion of the bacterial sequence remained unidentified (> = 40.0%), showcasing no sequence similarity with the reference database. This intriguing "dark matter" in bacterial DNA hints at a potential treasure trove of yet-to-be-identified species. Future taxonomic profiling of these novel sequences may offer a deeper understanding of Himalayan springs' microbial makeup. Furthermore, these novel bacterial sequences will be instrumental in enhancing our global understanding of bacterial community structures and their ecological adaptations in high-altitude, low-temperature environments.
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Affiliation(s)
- Ashish Kumar Singh
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, Sikkim, India
| | - Md Minhajul Abedin
- Institute of Bioresources and Sustainable Development, Regional Centre, Tadong, Sikkim, India
- National Agri-Food Biotechnology Institute (DBT-NABI), Mohali, Punjab, India
| | - Saurav Das
- Department of Agronomy & Horticulture, University of Nebraska, Lincoln, NE, USA
| | - Ishfaq Nabi Najar
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, Sikkim, India
| | - Yangchen D Lepcha
- Government of Sikkim, State Institute of Rural Development, Gangtok, Sikkim, India
| | | | - Abhishek Amit
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, Sikkim, India
| | - Hare Krishna Tiwari
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, Sikkim, India
| | - Amit Kumar Rai
- Institute of Bioresources and Sustainable Development, Regional Centre, Tadong, Sikkim, India.
- National Agri-Food Biotechnology Institute (DBT-NABI), Mohali, Punjab, India.
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Hossein Najdegerami E, Manaffar R. Using a combination of phospholipid fatty acids profiles and DNA-based sequencing analyses to detect shifts in the biofloc microbial community in different carbon sources and carbon/nitrogen ratios. VETERINARY RESEARCH FORUM : AN INTERNATIONAL QUARTERLY JOURNAL 2024; 15:425-434. [PMID: 39280855 PMCID: PMC11401133 DOI: 10.30466/vrf.2024.2015189.4060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 03/04/2024] [Indexed: 09/18/2024]
Abstract
A 35-day study investigated the impact of carbon sources and carbon/nitrogen (C/N) ratios on the microbial community of biofloc. For this purpose, we utilized a combination of phospho-lipid fatty acids (PLFAs) profiles and DNA-based sequencing methods to investigate changes in the microbial community composition and structure. The experiment involved three carbon sources including Dextrin (DEX), corn starch (CS) and wheat bran (WB) at two C/N ratios (19 and 30). The results indicated that WB and CS were found to decrease nitrogen metabolite concentration while increasing total suspended solids and bacterial density compared to DEX. The treatments exhibited variations in microbial communities and the use of polymerase chain reaction/ denaturing gradient gel electrophoresis analysis revealed distinct dominant bacterial species linked to carbon sources and C/N ratios. Furthermore, the highest levels of bacteria and protozoa PLFAs biomarkers were observed in the C/N30 ratio and WB treatment while the ratio for poly-β-hydroxybutyrate/PLFAs and fungi biomarkers displayed a decrease. Also, by incorporating the results of PLFAs profile and conducting a principal component analysis, the treatments were categorized into distinct groups based on both the carbon source and C/N ratios. Overall, both methods yield consistent results. PLFAs offered additional insights into the microbial composition beyond bacterial structure while DNA-based analysis provided finer taxonomic resolution.
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Affiliation(s)
| | - Ramin Manaffar
- Department of Fisheries, Faculty of Natural Resources, Urmia University, Urmia, Iran
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Raza B, Zheng Z, Zhu J, Yang W. A Review: Microbes and Their Effect on Growth Performance of Litopenaeus vannamei (White Leg Shrimps) during Culture in Biofloc Technology System. Microorganisms 2024; 12:1013. [PMID: 38792842 PMCID: PMC11123971 DOI: 10.3390/microorganisms12051013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
In the modern era of Aquaculture, biofloc technology (BFT) systems have attained crucial attention. This technology is used to reduce water renewal with the removal of nitrogen and to provide additional feed. In BFT, microorganisms play a crucial role due to their complex metabolic properties. Pathogens can be controlled through multiple mechanisms using probiotics, which can promote host development and enhance the quality of the culture environment. During culturing in a biofloc technology system, the supplementation of microalgae and its accompanying bacteria plays a beneficial role in reducing nitrogenous compounds. This enhances water quality and creates favorable environmental conditions for specific bacterial groups, while simultaneously reducing the dependency on carbon sources with higher content. The fluctuations in the bacterial communities of the intestine are closely associated with the severity of diseases related to shrimp and are used to evaluate the health status of shrimp. Overall, we will review the microbes associated with shrimp culture in BFT and their effects on shrimp growth. We will also examine the microbial impacts on the growth performance of L. vannamei in BFT, as well as the close relationship between probiotics and the intestinal microbes of L. vannamei.
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Affiliation(s)
| | | | | | - Wen Yang
- School of Marine Sciences, Ningbo University, Ningbo 315832, China; (B.R.); (Z.Z.); (J.Z.)
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Hou Y, Yu Z, Jia R, Li B, Zhu J. Integrated rice-yellow catfish farming resulting in variations in the agricultural environment, rice growth performance, and soil bacterial communities. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:28967-28981. [PMID: 38564129 DOI: 10.1007/s11356-024-33108-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/23/2024] [Indexed: 04/04/2024]
Abstract
Different rice production patterns exert varying comprehensive impacts on the agricultural environment. Integrated rice-fish farming, an advanced and rapidly developing agricultural production pattern, aims to improve resource utilization efficiency and enhance food productivity. To unravel the responses and internal interactions of the agricultural ecological environment to integrated rice-fish farming, we assessed and compared environmental factor, rice growth performance, and soil microbiome in both integrated rice-yellow catfish farming (IRYF) and rice monoculture (RM) systems. Our results revealed significant increases in the total nitrogen and ammonia concentrations in the paddy water and soil induced by the IRYF. Rice growth performance in the IRYF group surpassed that in the RM group. IRYF obviously impacted almost all dominant bacterial phyla, genera, and functional groups (top ten most abundant), enhancing the ability of bacteria to degrade and utilize organic matter. Additionally, IRYF led to noticeable reductions in the Shannon, Simpson, Chao 1, and Pielou_J indices. IRYF strengthened the interconnections between various taxonomic units in bacterial co-occurrence network, resulting in increased complexity, stability, and disturbance resistance in the soil bacterial community. IRYF notably facilitated the transition from a community assembly dominated by stochastic processes to one dominated by deterministic processes for the soil bacterial community. The deterministic process driving this transition was variable selection. All the environmental factors, except for soil nitrate, demonstrated relatively high contributions to alterations in soil bacterial communities, with environmental variables significantly positively correlated with the soil bacterial community in the IRYF group. Alterations in functionality, composition, and diversity of the soil bacterial community were clearly associated with most environmental variables and rice growth performance indices. Our research contributed to understanding the comprehensive impacts of integrated rice-fish farming on agricultural ecosystems and provide theoretical support for achieving the sustainable agricultural production and optimizing the rice production patterns.
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Affiliation(s)
- Yiran Hou
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Zhaoxiong Yu
- Fisheries Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 611731, China
| | - Rui Jia
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Bing Li
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Jian Zhu
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China.
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Hou Y, Jia R, Sun W, Li B, Zhu J. Influences of the Integrated Rice-Crayfish Farming System with Different Stocking Densities on the Paddy Soil Microbiomes. Int J Mol Sci 2024; 25:3786. [PMID: 38612595 PMCID: PMC11011395 DOI: 10.3390/ijms25073786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Integrated rice-fish farming has emerged as a novel agricultural production pattern to address global food security challenges. Aiming to determine the optimal, scientifically sound, and sustainable stocking density of red claw crayfish (Cherax quadricarinatus) in an integrated rice-crayfish farming system, we employed Illumina high-throughput 16S rRNA gene sequencing to evaluate the impact of different stocking densities of red claw crayfish on the composition, diversity, function, and co-occurrence network patterns of soil bacterial communities. The high stocking density of red claw crayfish reduced the diversity and evenness of the soil bacterial community during the mid-culture stage. Proteobacteria, Actinobacteria, and Chloroflexi emerged as the most prevalent phyla throughout the experimental period. Low stocking densities initially boosted the relative abundance of Actinobacteria in the paddy soil, while high densities did so during the middle and final stages. There were 90 distinct functional groups identified across all the paddy soil samples, with chemoheterotrophy and aerobic chemoheterotrophy being the most abundant. Low stocking densities initially favored these functional groups, whereas high densities enhanced their relative abundances in the later stages of cultivation. Medium stocking density of red claw crayfish led to a more complex bacterial community during the mid- and final culture stages. The experimental period showed significant correlations with soil bacterial communities, with total nitrogen (TN) and total phosphorus (TP) concentrations emerging as primary factors contributing to the alterations in soil bacterial communities. In summary, our findings demonstrated that integrated rice-crayfish farming significantly impacted the soil microbiomes and environmental factors at varying stocking densities. Our study contributed to theoretical insights into the profound impact of integrated rice-crayfish farming with various stocking densities on bacterial communities in paddy soils.
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Affiliation(s)
- Yiran Hou
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (Y.H.); (R.J.); (W.S.)
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Rui Jia
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (Y.H.); (R.J.); (W.S.)
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Wei Sun
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (Y.H.); (R.J.); (W.S.)
| | - Bing Li
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (Y.H.); (R.J.); (W.S.)
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Jian Zhu
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (Y.H.); (R.J.); (W.S.)
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
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Stocker MD, Smith JE, Pachepsky YA, Blaustein RA. Fine-scale spatiotemporal variations in bacterial community diversity in agricultural pond water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:170143. [PMID: 38242477 DOI: 10.1016/j.scitotenv.2024.170143] [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: 10/17/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 01/21/2024]
Abstract
Microbial communities in surface waters are affected by environmental conditions and can influence changes in water quality. To explore the hypothesis that the microbiome in agricultural waters associates with spatiotemporal variations in overall water quality and, in turn, has implications for resource monitoring and management, we characterized the relationships between the microbiota and physicochemical properties in a model irrigation pond as a factor of sampling time (i.e., 9:00, 12:00, 15:00) and location within the pond (i.e., bank vs. interior sites and cross-sectional depths at 0, 1, and 2 m). The microbial communities, which were defined by 16S rRNA gene sequencing analysis, significantly varied based on all sampling factors (PERMANOVA P < 0.05 for each). While the relative abundances of dominant phyla (e.g., Proteobacteria and Bacteroidetes) were relatively stable throughout the pond, subtle yet significant increases in α-diversity were observed as the day progressed (ANOVA P < 0.001). Key water quality properties that also increased between the morning and afternoon (i.e., pH, dissolved oxygen, and temperature) positively associated with relative abundances of Cyanobacteria, though were inversely proportional to Verrucomicrobia. These properties, among additional parameters such as bioavailable nutrients (e.g., NH3, NO3, PO4), chlorophyll, phycocyanin, conductivity, and colored dissolved organic matter, exhibited significant relationships with relative abundances of various bacterial genera as well. Further investigation of the microbiota in underlying sediments revealed significant differences between the bank and interior sites of the pond (P < 0.05 for α- and β-diversity). Overall, our findings emphasize the importance of accounting for time of day and water sampling location and depth when surveying the microbiomes of irrigation ponds and other small freshwater sources.
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Affiliation(s)
- M D Stocker
- United States Department of Agriculture, Agricultural Research Services, Environmental Microbial and Food Safety Laboratory, Beltsville, MD 20705, USA.
| | - J E Smith
- United States Department of Agriculture, Agricultural Research Services, Environmental Microbial and Food Safety Laboratory, Beltsville, MD 20705, USA; Oak Ridge Institute of Science and Education, Oak Ridge, TN 37830, USA
| | - Y A Pachepsky
- United States Department of Agriculture, Agricultural Research Services, Environmental Microbial and Food Safety Laboratory, Beltsville, MD 20705, USA
| | - R A Blaustein
- University of Maryland, Department of Nutrition and Food Science, College Park, MD 20742, USA
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Miron RJ, Zhang Y. Understanding exosomes: Part 1-Characterization, quantification and isolation techniques. Periodontol 2000 2024; 94:231-256. [PMID: 37740431 DOI: 10.1111/prd.12520] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 09/24/2023]
Abstract
Exosomes are the smallest subset of extracellular signaling vesicles secreted by most cells with a diameter in the range of 30-150 nm. Their use has gained great momentum recently due to their ability to be utilized as diagnostic tools with a vast array of therapeutic applications. Over 5000 publications are currently being published yearly on this topic, and this number is only expected to dramatically increase as novel therapeutic strategies continue to be investigated. This review article first focuses on understanding exosomes, including their cellular origin, biogenesis, function, and characterization. Thereafter, overviews of the quantification methods and isolation techniques are given with discussion over their potential use as novel therapeutics in regenerative medicine.
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Affiliation(s)
- Richard J Miron
- Department of Periodontology, University of Bern, Bern, Switzerland
| | - Yufeng Zhang
- Department of Oral Implantology, University of Wuhan, Wuhan, China
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Yoo SS, Lee DW, Ham HJ, Yeo IJ, Chang JY, Yun J, Son DJ, Han S, Hong JT. Presenilin-2 knock-In mice show severe depressive behavior via DVL3 downregulation. CNS Neurosci Ther 2024; 30:e14370. [PMID: 37501340 PMCID: PMC10848049 DOI: 10.1111/cns.14370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/07/2022] [Accepted: 06/17/2023] [Indexed: 07/29/2023] Open
Abstract
INTRODUCTION Alzheimer's disease (AD) is the most common form of dementia. Depression is one of the most critical psychiatric complications of AD, and 20%-30% of patients with AD experience symptoms of depression. Phospho-glycogen synthase kinase-3 beta (GSK3β) is known to be associated with AD and depression. Furthermore, the role of disheveled (DVL) is known to regulate GSK3β. Moreover, presenilin-2 (PS2) and DVL have cross-talk with each other. Also, it is widely hypothesized that stress leads to hypersecretion of cortisol and is thus associated with depression. Dickkopf WNT signaling pathway inhibitor-1 (DKK-1) is a crucial factor regulating depression and both amyloid beta (Aβ) and phosphorylation of tau are widely known as a biomarker of AD. METHODS To investigate the relationship between AD and depression, and possible pathways connecting the two diseases, we examined memory function and depression-related behavior test results in PS2 knock-in AD mice (PS2 MT). Next, we confirmed that there are relationships between DVL, depression, and cognitive disease through the comparative toxicogenomics database (https://ctdbase.org) and STRING (https://string-db.org) database. RESULTS PS2 knock-in mice showed much more severe memory impairment and depression than PS2 wild-type mice (PS2 WT). In AD-related behavioral experiments, PS2 MT mice showed more memory dysfunction compared with PS2 WT group mice. Moreover, Aβ and phosphorylation of tau showed higher expression in PS2 MT mice than in PS2 WT mice. Depression-related behavioral tests showed that PS2 MT mice exhibited more depressive behaviors than PS2 WT mice. Furthermore, both higher cortisol levels and higher expression of DKK-1 were found in PS2 MT mice relative to PS2 WT mice. The results indicated that there is a relationship between DVL and the release of AD-related mediators and expression of the depression-related glucocorticoid receptor and DKK-1. In the PS2 knock-in group, DVL was significantly decreased compared with the PS2 WT group. CONCLUSION Depression increases the risk of developing AD and other forms of dementia. Recent evidence indicates that depression symptoms could trigger changes in memory and thinking over time. However, it is recognized that there are no drugs to facilitate a full recovery for both AD and depression. However, our results suggest that AD and depression could be associated, and DVL could be a significant target for the association between AD and depression.
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Affiliation(s)
- Seung Sik Yoo
- College of Pharmacy and Medical Research CenterChungbuk National UniversityCheongjuSouth Korea
| | - Dong Won Lee
- Ministry of Food and Drug Safety (MFDS)CheongjuSouth Korea
- Korea Health Industry Development InstituteCheongjuSouth Korea
| | - Hyeon Joo Ham
- College of Pharmacy and Medical Research CenterChungbuk National UniversityCheongjuSouth Korea
| | - In Jun Yeo
- College of Pharmacy and Medical Research CenterChungbuk National UniversityCheongjuSouth Korea
| | - Ju Young Chang
- College of Pharmacy and Medical Research CenterChungbuk National UniversityCheongjuSouth Korea
| | - Jaesuk Yun
- College of Pharmacy and Medical Research CenterChungbuk National UniversityCheongjuSouth Korea
| | - Dong Ju Son
- College of Pharmacy and Medical Research CenterChungbuk National UniversityCheongjuSouth Korea
| | - Sang‐Bae Han
- College of Pharmacy and Medical Research CenterChungbuk National UniversityCheongjuSouth Korea
| | - Jin Tae Hong
- College of Pharmacy and Medical Research CenterChungbuk National UniversityCheongjuSouth Korea
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Exploring the Interspecific Interactions and the Metabolome of the Soil Isolate Hylemonella gracilis. mSystems 2023; 8:e0057422. [PMID: 36537799 PMCID: PMC9948732 DOI: 10.1128/msystems.00574-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Microbial community analysis of aquatic environments showed that an important component of its microbial diversity consists of bacteria with cell sizes of ~0.1 μm. Such small bacteria can show genomic reductions and metabolic dependencies with other bacteria. However, so far, no study has investigated if such bacteria exist in terrestrial environments like soil. Here, we isolated soil bacteria that passed through a 0.1-μm filter. The complete genome of one of the isolates was sequenced and the bacterium was identified as Hylemonella gracilis. A set of coculture assays with phylogenetically distant soil bacteria with different cell and genome sizes was performed. The coculture assays revealed that H. gracilis grows better when interacting with other soil bacteria like Paenibacillus sp. AD87 and Serratia plymuthica. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct cell-cell contact. Our study indicates that in soil there are bacteria that can pass through a 0.1-μm filter. These bacteria may have been overlooked in previous research on soil microbial communities. Such small bacteria, exemplified here by H. gracilis, can induce transcriptional and metabolomic changes in other bacteria upon their interactions in soil. In vitro, the studied interspecific interactions allowed utilization of growth substrates that could not be utilized by monocultures, suggesting that biochemical interactions between substantially different sized soil bacteria may contribute to the symbiosis of soil bacterial communities. IMPORTANCE Analysis of aquatic microbial communities revealed that parts of its diversity consist of bacteria with cell sizes of ~0.1 μm. Such bacteria can show genomic reductions and metabolic dependencies with other bacteria. So far, no study investigated if such bacteria exist in terrestrial environments such as soil. Here, we show that such bacteria also exist in soil. The isolated bacteria were identified as Hylemonella gracilis. Coculture assays with phylogenetically different soil bacteria revealed that H. gracilis grows better when cocultured with other soil bacteria. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct contact. Our study revealed that bacteria are present in soil that can pass through 0.1-μm filters. Such bacteria may have been overlooked in previous research on soil microbial communities and may contribute to the symbiosis of soil bacterial communities.
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Zhang Y, Feng S, Gao F, Wen H, Zhu L, Li M, Xi Y, Xiang X. The Relationship between Brachionus calyciflorus-Associated Bacterial and Bacterioplankton Communities in a Subtropical Freshwater Lake. Animals (Basel) 2022; 12:ani12223201. [PMID: 36428428 PMCID: PMC9686566 DOI: 10.3390/ani12223201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
Zooplankton bodies are organic-rich micro-environments that support fast bacterial growth. Therefore, the abundance of zooplankton-associated bacteria is much higher than that of free-living bacteria, which has profound effects on the nutrient cycling of freshwater ecosystems. However, a detailed analysis of associated bacteria is still less known, especially the relationship between those bacteria and bacterioplankton. In this study, we analyzed the relationships between Brachionus calyciflorus-associated bacterial and bacterioplankton communities in freshwater using high-throughput sequencing. The results indicated that there were significant differences between the two bacterial communities, with only 29.47% sharing OTUs. The alpha diversity of the bacterioplankton community was significantly higher than that of B. calyciflorus-associated bacteria. PCoA analysis showed that the bacterioplankton community gathered deeply, while the B. calyciflorus-associated bacterial community was far away from the whole bacterioplankton community, and the distribution was relatively discrete. CCA analysis suggested that many environmental factors (T, DO, pH, TP, PO43-, NH4+, and NO3-) regulated the community composition of B. calyciflorus-associated bacteria, but the explanatory degree of variability was only 37.80%. High-throughput sequencing revealed that Raoultella and Delftia in Proteobacteria were the dominant genus in the B. calyciflorus-associated bacterial community, and closely related to the biodegradation function. Moreover, several abundant bacterial members participating in carbon and nitrogen cycles were found in the associated bacterial community by network analysis. Predictive results from FAPROTAX showed that the predominant biogeochemical cycle functions of the B. calyciflorus-associated bacterial community were plastic degradation, chemoheterotrophy, and aerobic chemoheterotrophy. Overall, our study expands the current understanding of zooplankton-bacteria interaction and promotes the combination of two different research fields.
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Affiliation(s)
- Yongzhi Zhang
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China
| | - Sen Feng
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China
| | - Fan Gao
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China
| | - Hao Wen
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China
| | - Lingyun Zhu
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China
| | - Meng Li
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China
| | - Yilong Xi
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Founded by Anhui Province and Ministry of Education, Wuhu 241002, China
| | - Xianling Xiang
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Founded by Anhui Province and Ministry of Education, Wuhu 241002, China
- Correspondence: author:
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Bianco K, de Farias BO, Gonçalves-Brito AS, Alves do Nascimento AP, Magaldi M, Montenegro K, Flores C, Oliveira S, Monteiro MA, Spisso BF, Pereira MU, Ferreira RG, Albano RM, Cardoso AM, Clementino MM. Mobile resistome of microbial communities and antimicrobial residues from drinking water supply systems in Rio de Janeiro, Brazil. Sci Rep 2022; 12:19050. [PMID: 36351942 PMCID: PMC9646821 DOI: 10.1038/s41598-022-21040-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 09/22/2022] [Indexed: 11/10/2022] Open
Abstract
Antibiotic resistance genes (ARGs) are widespread in the environment due to the overuse of antibiotics and other pollutants, posing a threat to human and animal health. In this study, we evaluated antimicrobial residues, bacterial diversity and ARGs in two important watersheds, Guandu and São João, that supply drinking water to Rio de Janeiro city, Brazil. In addition, tap water samples were collected from three different cities in Rio de Janeiro State, including the metropolitan area of Rio de Janeiro city. Clarithromycin, sulfamethoxazole and azithromycin were found in untreated water and drinking water in all samples. A greater abundance of Proteobacteria was observed in Guandu and São João watersheds, with most of the sequences belonging to the Gammaproteobacteria class. A plasmidome-focused metagenomics approach revealed 4881 (Guandu), 3705 (São João) and 3385 (drinking water) ARGs mainly associated with efflux systems. The genes encoding metallo-β-lactamase enzymes (blaAIM, blaGIM, blaIMP, and blaVIM) were detected in the two watersheds and in drinking water samples. Moreover, we demonstrated the presence of the colistin resistance genes mcr-3 and mcr-4 (both watersheds) and mcr-9 (drinking water and Guandu) for the first time in Brazil. Our data emphasize the importance of introducing measures to reduce the disposal of antibiotics and other pollutants capable of promoting the occurrence and spread of the microbial resistome on aquatic environments and predicting possible negative impacts on human health.
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Affiliation(s)
- Kayo Bianco
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil.
| | - Beatriz Oliveira de Farias
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil
| | - Andressa Silva Gonçalves-Brito
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil
| | - Ana Paula Alves do Nascimento
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil
| | - Mariana Magaldi
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil
| | - Kaylanne Montenegro
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil
| | - Claudia Flores
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil
| | - Samara Oliveira
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil
| | - Mychelle Alves Monteiro
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil
| | - Bernardete Ferraz Spisso
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil
| | - Mararlene Ulberg Pereira
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil
| | - Rosana Gomes Ferreira
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil
| | | | | | - Maysa Mandetta Clementino
- Instituto Nacional de Controle de Qualidade Em Saúde INCQS/FIOCRUZ, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 4365, Brazil
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Spilsbury F, Foysal MJ, Tay A, Gagnon MM. Gut Microbiome as a Potential Biomarker in Fish: Dietary Exposure to Petroleum Hydrocarbons and Metals, Metabolic Functions and Cytokine Expression in Juvenile Lates calcarifer. Front Microbiol 2022; 13:827371. [PMID: 35942316 PMCID: PMC9356228 DOI: 10.3389/fmicb.2022.827371] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 06/13/2022] [Indexed: 11/23/2022] Open
Abstract
The gut microbiome of fish contains core taxa whose relative abundances are modulated in response to diet, environmental factors, and exposure to toxicogenic chemicals, influencing the health of the host fish. Recent advances in genomics and metabolomics have suggested the potential of microbiome analysis as a biomarker for exposure to toxicogenic compounds. In this 35-day laboratory study, 16S RNA sequencing and multivariate analysis were used to explore changes in the gut microbiome of juvenile Lates calcarifer exposed to dietary sub-lethal doses of three metals: vanadium (20 mg/kg), nickel (480 mg/kg), and iron (470 mg/kg), and to two oils: bunker C heavy fuel oil (HFO) (1% w/w) and Montara, a typical Australian medium crude oil (ACO) (1% w/w). Diversity of the gut microbiome was significantly reduced compared to negative controls in fish exposed to metals, but not petroleum hydrocarbons. The core taxa in the microbiome of negative control fish comprised phyla Proteobacteria (62%), Firmicutes (7%), Planctomycetes (3%), Actinobacteria (2%), Bacteroidetes (1%), and others (25%). Differences in the relative abundances of bacterial phyla of metal-exposed fish were pronounced, with the microbiome of Ni-, V-, and Fe-exposed fish dominated by Proteobacteria (81%), Firmicutes (68%), and Bacteroidetes (48%), respectively. The genus Photobacterium was enriched proportionally to the concentration of polycyclic aromatic hydrocarbons (PAHs) in oil-exposed fish. The probiotic lactic acid bacterium Lactobacillus was significantly reduced in the microbiota of fish exposed to metals. Transcription of cytokines IL-1, IL-10, and TNF-a was significantly upregulated in fish exposed to metals but unchanged in oil-exposed fish compared to negative controls. However, IL-7 was significantly downregulated in fish exposed to V, Ni, Fe, and HFOs. Fish gut microbiome exhibits distinctive changes in response to specific toxicants and shows potential for use as biomarkers of exposure to V, Ni, Fe, and to PAHs present in crude oil.
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Affiliation(s)
- Francis Spilsbury
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Alfred Tay
- Helicobacter Research Laboratory, The Marshall Centre, School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia
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Functional and Seasonal Changes in the Structure of Microbiome Inhabiting Bottom Sediments of a Pond Intended for Ecological King Carp Farming. BIOLOGY 2022; 11:biology11060913. [PMID: 35741434 PMCID: PMC9220171 DOI: 10.3390/biology11060913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/09/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Bottom sediments are usually classified as extreme habitats for microorganisms. They are defined as matter deposited on the bottom of water bodies through the sedimentation process. The quality of sediments is extremely important for the good environmental status of water, because they are an integral part of the surface water environment. Microorganisms living in sediments are involved in biogeochemical transformations and play a fundamental role in maintaining water purity, decomposition of organic matter, and primary production. As a rule, studies on bottom sediments focus on monitoring their chemistry and pollution, while little is known about the structure of bacterial communities inhabiting this extreme environment. In this study, Next-Generation Sequencing (NGS) was combined with the Community-Level Physiological Profiling (CLPP) technique to obtain a holistic picture of bacterial biodiversity in the bottom sediments from Cardinal Pond intended for ecological king carp farming. It was evident that the bottom sediments of the studied pond were characterized by a rich microbiota composition, whose structure and activity depended on the season, and the most extensive modifications of the biodiversity and functionality of microorganisms were noted in summer. Abstract The main goal of the study was to determine changes in the bacterial structure in bottom sediments occurring over the seasons of the year and to estimate microbial metabolic activity. Bottom sediments were collected four times in the year (spring, summer, autumn, and winter) from 10 different measurement points in Cardinal Pond (Ślesin, NW Poland). The Next-Generation Sequencing (MiSeq Illumina) and Community-Level Physiological Profiling techniques were used for identification of the bacterial diversity structure and bacterial metabolic and functional activities over the four seasons. It was evident that Proteobacteria, Acidobacteria, and Bacteroidetes were the dominant phyla, while representatives of Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria predominated at the class level in the bottom sediments. An impact of the season on biodiversity and metabolic activity was revealed with the emphasis that the environmental conditions in summer modified the studied parameters most strongly. Carboxylic and acetic acids and carbohydrates were metabolized most frequently, whereas aerobic respiration I with the use of cytochrome C was the main pathway used by the microbiome of the studied bottom sediments.
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16
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Monitoring Bacterial Community Dynamics in Abalone (Haliotis discus hannai) and the Correlations Associated with Aquatic Diseases. WATER 2022. [DOI: 10.3390/w14111769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Bacteria are an integral component of their host. However, information about the microbiota living in and around many aquatic animals is lacking. In this study, multiplex bar-coded pyrosequencing of the 16S ribosomal RNA gene was used to monitor the dynamics of abalone, Haliotis discus hannai, bacterial communities in the intestine, water from cement culture ponds, and surrounding sea areas. Correlations between the bacterial communities and common aquaculture diseases were also evaluated. A total of 329,798 valid sequences and 15,277 operational taxonomic units (OTUs) from 32 samples were obtained by 454 tag amplicon pyrosequencing. The Shannon indices of the seawater samples ranged from 2.84 to 5.6 and the Shannon indices of the abalone intestine samples ranged from 1.2 to 5.12, which were much lower than those of seawater. The dominant phyla in seawater samples were Proteobacteria, Bacteroidetes, Fusobacteria, Cyanobacteria, etc. The dominant phyla in the abalone intestine varied greatly in different months. The dominant genera in the seawater of the cement culture ponds changed in different months, mainly Psychrilyobacter and Pseudoalteromonas. The dominant genera in seawater from the open sea vary considerably between months. The dominant genus of bacteria in the abalone intestine during the months when abalones are susceptible to disease is mainly Mycoplasma spp. Canonical correspondence analysis revealed that bacterial communities in seawater and the intestine responded differently to environmental variables, with similar microbiota in the same area. pH, dissolved oxygen concentration, and temperature were closely related to the samples from the sea area. Oxidation-reduction potential, salinity, phosphate, nitrate, and ammonia nitrogen concentrations were closely related to the water samples from the artificial pools. These findings may add significantly to our understanding of the complex interactions between microbiota and environmental variables in the abalone intestine as well as in the surrounding seawater.
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Wei YL, Long ZJ, Ren MX. Microbial community and functional prediction during the processing of salt production in a 1000-year-old marine solar saltern of South China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 819:152014. [PMID: 34852250 DOI: 10.1016/j.scitotenv.2021.152014] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/15/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
In Hainan Island, South China, a 1000-year-old marine saltern has been identified as an intangible cultural heritage due to its historical complicated salt-making techniques, whereas the knowledge about this saltern is extremely limited. Herein, DNA sequencing and biochemical technologies were applied to determine bacterial and fungal communities of this saltern and their possible functions during four stages of salt-making, i.e. seawater storage, mud solarization, brine concentrating, and solar crystallization. The results showed that both of bacterial and fungal communities were suffered from significant changes during processing of salt-making in Danzhou Ancient Saltern, whereas the richness and diversity of bacterial community dominated by Proteobacteria, Bacteroidota and Cyanobacteria was considerably greater than that of fungal community dominated by Ascomycota, Basidiomycota and Mortierellomycota. Additionally, the succession of bacterial community was closely associated with both of salt physicochemical properties (Na+, Cl-, total phosphorus, total nitrogen, Ca2+ and Mg2+) and bacteria themselves, whereas fungal community was more closely associated with physicochemical properties than fungi themselves. Importantly, Cyanobium_PCC-6307, Synechococcus_CC9902, Marinobacter, Prevotella and Halomonas as dominant bacterial genera respectively related to the metabolisms of amino acid, carbohydrate, terpenoids/polyketides, lipid and nucleotide were correlated with salt flavors. Saprophytic and saprotroph-symbiotroph fungi dominated by Aspergillus, Mortierella, Amanita, Neocucurbitaria and Tausonia also played core roles in the formation of salt flavors including umami and sweet smells. These findings revealed the highly specified microbiome community in this 1000-year-old saltern that mainly selected by brine solarization on basalt platforms, which is helpful to explore the underlying mechanisms of traditional salt-making techniques and to explore the useful microbes for nowadays food, medicine and chemical industries.
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Affiliation(s)
- Ya-Li Wei
- Ministry of Education Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Hainan University, Haikou 570228, PR China; Center for Terrestrial Biodiversity of the South China Sea, Hainan University, Haikou 570228, PR China
| | - Zi-Jie Long
- Ministry of Education Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Hainan University, Haikou 570228, PR China; Center for Terrestrial Biodiversity of the South China Sea, Hainan University, Haikou 570228, PR China
| | - Ming-Xun Ren
- Ministry of Education Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Hainan University, Haikou 570228, PR China; Center for Terrestrial Biodiversity of the South China Sea, Hainan University, Haikou 570228, PR China.
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18
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Basha AK, Kuttanapilly LV, Vaiyapuri M, Rathore G, Tripathi G, Prasad KP, Badireddy MR, Joseph TC. Microbial diversity and composition in acidic sediments of freshwater finfish culture ponds fed with two types of feed - A metagenomic approach. Lett Appl Microbiol 2022; 75:171-181. [PMID: 35419857 DOI: 10.1111/lam.13720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/26/2022] [Accepted: 04/01/2022] [Indexed: 11/27/2022]
Abstract
Microbial community profile associated with acidic pond sediments (APS) (pH=3.0-4.5) of freshwater finfish aquaculture ponds (n=8) was investigated. Sediment DNA extracted from the eight APS were subjected to high-throughput sequencing of V3 and V4 regions which yielded 7236 operational taxonomic units (OTUs) at a similarity of 97%. Overall results showed higher proportion of bacterial OTUs than archaeal OTUs in all the APS. Euryarchaeota (23%), Proteobacteria (19%), Chloroflexi (17%) Crenarchaeota (5.3%), Bacteroidetes (4.8%), Nitrospirae (3.2%), Nanoarchaeaeota (3%) which together constituted 75% of the microbial diversity. At the genus level, there was high preponderance of methanogens namely Methanolinea (5.4%), Methanosaeta (4.5%) and methanotrops, Bathyarchaeota (5%) in APS. Moreover, the abundant phyla in the APS were not drastically affected by the administration of chicken slaughter waste (R-group ponds) and commercial fish feed (C-group ponds), since 67% of the OTUs generated remained common in the APS of both the groups of ponds. There was a minimal difference of 24-26% of OTUs between C-group and R-group ponds suggesting the existence of a core microbial community in these ponds driven by acidic pH over the years. This study concludes that microbial diversity in pond sediment was influenced to a lesser extent by the addition of chicken slaughter waste but was majorly driven by acidic nature of the pond.
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Affiliation(s)
- Ahamed Kusunur Basha
- ICAR-Central Institute of Fisheries Technology, Visakhapatnam Research Centre, Visakhapatnam, 530 003, Andhra Pradesh, India
| | | | - Murugadas Vaiyapuri
- ICAR-Central Institute of Fisheries Technology, Cochin, 682 029, Kerala, India
| | - Gaurav Rathore
- ICAR-National Bureau of Fish Genetic Resources, Lucknow, 226 002, Uttar Pradesh, India
| | - Gayatri Tripathi
- ICAR-Central Institute of Fisheries Education, Versova, Mumbai, 400 061, Maharashtra, India
| | - Kurcheti Pani Prasad
- ICAR-Central Institute of Fisheries Education, Versova, Mumbai, 400 061, Maharashtra, India
| | - Madhusudana Rao Badireddy
- ICAR-Central Institute of Fisheries Technology, Visakhapatnam Research Centre, Visakhapatnam, 530 003, Andhra Pradesh, India
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Hajiali F, Jin T, Yang G, Santos M, Lam E, Moores A. Mechanochemical Transformations of Biomass into Functional Materials. CHEMSUSCHEM 2022; 15:e202102535. [PMID: 35137539 DOI: 10.1002/cssc.202102535] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Biomass is one of the promising alternatives to petroleum-derived materials and plays a major role in our fight against climate change by providing renewable sources of chemicals and materials. Owing to its chemical and structural complexity, the transformation of biomass into value-added products requires a profound understanding of its composition at different scales and innovative methods such as combining physical and chemical processes. In this context, the use of mechanochemistry in biomass valorization is currently growing owing to its potentials as an efficient, sustainable, and environmentally friendly approach. This review highlights the latest advances in the transformation of biomass (i. e., chitin, cellulose, hemicellulose, lignin, and starch) to functional materials using mechanochemical-assisted methods. We focused here on the methodology of biomass processing, influencing factors, and resulting properties with an emphasis on achieving functional materials rather than breaking down the biopolymer chains into smaller molecules. Opportunities and limitations associated this methodology were discussed accordingly for future directions.
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Affiliation(s)
- Faezeh Hajiali
- Centre in Green Chemistry and Catalysis, Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Quebec, H3A 0B8, Canada
| | - Tony Jin
- Centre in Green Chemistry and Catalysis, Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Quebec, H3A 0B8, Canada
| | - Galen Yang
- Centre in Green Chemistry and Catalysis, Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Quebec, H3A 0B8, Canada
| | - Madison Santos
- Department of Bioengineering, McGill University, 3480 University St., Montreal, Quebec, H3A 0E9, Canada
| | - Edmond Lam
- Centre in Green Chemistry and Catalysis, Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Quebec, H3A 0B8, Canada
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, 6100 Royalmount Avenue, Montreal, Quebec, H4P 2R2, Canada
| | - Audrey Moores
- Centre in Green Chemistry and Catalysis, Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Quebec, H3A 0B8, Canada
- Department of Materials Engineering, McGill University, 3610 University Street, Montreal, Quebec, H3A 0 C5, Canada
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Shi J, Zhang B, Liu J, Fang Y, Wang A. Spatiotemporal dynamics in microbial communities mediating biogeochemical cycling of nutrients across the Xiaowan Reservoir in Lancang River. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:151862. [PMID: 34826492 DOI: 10.1016/j.scitotenv.2021.151862] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/27/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
Microbes drive biogeochemical cycles of nutrients controlling water quality in freshwater ecosystems, yet little is known regarding how spatiotemporal variation in the microbial community affects this ecosystem-level functional processes to resist perturbations. Here we examined spatiotemporal dynamics of microbial communities in paired stratified water columns and sediments collected from the Xiaowan Reservoir of Lancang-Mekong River over a year long period. Results highlighted distinctive spatiotemporal patterns of microbial communities in water columns mainly driven by sulfate, dissolved oxygen, nitrate and temperature, whilst sediment communities only showed a seasonal variation pattern governed by pH, reduced inorganic sulfur, sulfate, organic matter and total nitrogen. Microbial co-occurrence networks revealed the succession of keystone taxa in both water columns and sediments, reflecting core ecological functions in response to altered environmental conditions. Specifically, in shallow water, keystone nitrogen fixers and denitrifiers were responsible for providing nitrogen nutrients in summer, while recalcitrant substance degraders likely supplied microbially available organic matters to maintain ecosystem stability in winter. But in deep water, methane oxidation was the critical process linked to microbial-mediated cycle of carbon, nitrogen and sulfur. In addition, carbon metabolism and mercury methylation mediated by sulfate reducers, denitrifiers and nitrogen fixers were core functioning features of sediments in summer and winter, respectively. This work expands our knowledge of the importance of keystone taxa in maintaining stability of reservoir ecosystems under changing environments, providing new perspectives for water resource conservation and management.
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Affiliation(s)
- Jiaxin Shi
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, China
| | - Baogang Zhang
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, China
| | - Jun Liu
- State Key Laboratory of Agricultural Microbiology, State Environmental Protection Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yun Fang
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Aijie Wang
- State Key Laboratory of Urban Water Resources and Environments, Harbin Institute of Technology, Harbin 150090, China
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21
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Kumar M, Gupta G, Varghese T, Srivastava PP, Gupta S. Preparation and characterization of glucose-conjugated super-paramagnetic iron oxide nanoparticles (G-SPIONs) for removal of Edwardsiella tarda and Aeromonas hydrophila from water. Microsc Res Tech 2022; 85:1768-1783. [PMID: 35038205 DOI: 10.1002/jemt.24037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 11/09/2022]
Abstract
The present research was conducted to prepare efficient G-SPIONs by co-precipitation to remove Edwardsiella tarda and Aeromonas hydrophila from the aqueous solution. The synthesized G-SPIONs were characterized by UV-Vis spectrophotometer, DLS, FEG-TEM, FT-IR, XRD, and VSM analysis. The results showed that the synthesized G-SPIONs had super-paramagnetic properties (58.31 emu/g) and spherical shape (16 ± 3 nm). The antibacterial activity was assessed in sterilized distilled water at different G-SPIONs concentrations viz. 0, 1.5, 3, 6, 12, 24, 48, 120, and 240 mg/L against E. tarda and A. hydrophila with various bacterial loads viz. 1 × 103 , 1 × 104 , 1 × 105 , 1 × 106 , and 1 × 107 CFU/ml at different time intervals 15, 30, 45, and 60 min. At a lower bacterial load of E. tarda and A. hydrophila 1 × 103 -1 × 104 CFU/ml, 100% bacterial load was removed by 15 min exposure with NPs concentration 6-48 mg/L and 1.5-6 mg/L, respectively. Cent percent bacterial removal was observed in both the bacterial species even at higher bacterial load (1 × 105 -1 × 107 CFU/ml) by increasing exposure time (15-60 min) and nanoparticle concentration as well (24-240 mg/L). At an initial bacterial load of E. tarda and A. hydrophila (1 × 103 -1 × 107 CFU/ml), the EC50 ranged between 0.01-6.51 mg/L and 0.02-3.84 mg/L, respectively, after 15-60 min exposure. Thus, it is concluded that the antibacterial effect of G-SPIONs depends on concentration and exposure time. Hence, G-SPIONs can be used as an antibacterial/biocidal agent to treat Edwardsiellosis and Aeromonosis disease in aquaculture.
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Affiliation(s)
- Munish Kumar
- Fish Nutrition, Biochemistry and Physiology Division, ICAR-Central Institute of Fisheries Education, Mumbai, India
| | - Gyandeep Gupta
- Fish Nutrition, Biochemistry and Physiology Division, ICAR-Central Institute of Fisheries Education, Mumbai, India
| | - Tincy Varghese
- Fish Nutrition, Biochemistry and Physiology Division, ICAR-Central Institute of Fisheries Education, Mumbai, India
| | | | - Subodh Gupta
- Fish Nutrition, Biochemistry and Physiology Division, ICAR-Central Institute of Fisheries Education, Mumbai, India
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22
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Elsheshtawy A, Clokie BGJ, Albalat A, Beveridge A, Hamza A, Ibrahim A, MacKenzie S. Characterization of External Mucosal Microbiomes of Nile Tilapia and Grey Mullet Co-cultured in Semi-Intensive Pond Systems. Front Microbiol 2021; 12:773860. [PMID: 34966368 PMCID: PMC8710667 DOI: 10.3389/fmicb.2021.773860] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/10/2021] [Indexed: 11/13/2022] Open
Abstract
The external mucosal surfaces of the fish harbor complex microbial communities, which may play pivotal roles in the physiological, metabolic, and immunological status of the host. Currently, little is known about the composition and role of these communities, whether they are species and/or tissue specific and whether they reflect their surrounding environment. Co-culture of fish, a common practice in semi-intensive aquaculture, where different fish species cohabit in the same contained environment, is an easily accessible and informative model toward understanding such interactions. This study provides the first in-depth characterization of gill and skin microbiomes in co-cultured Nile tilapia (Oreochromis niloticus) and grey mullet (Mugil capito) in semi-intensive pond systems in Egypt using 16S rRNA gene-based amplicon sequencing. Results showed that the microbiome composition of the external surfaces of both species and pond water was dominated by the following bacterial phyla: Proteobacteria, Fusobacteriota, Firmicutes, Planctomycetota, Verrucomicrobiota, Bacteroidota, and Actinobacteriota. However, water microbial communities had the highest abundance and richness and significantly diverged from the external microbiome of both species; thus, the external autochthonous communities are not a passive reflection of their allochthonous communities. The autochthonous bacterial communities of the skin were distinct from those of the gill in both species, indicating that the external microbiome is likely organ specific. However, gill autochthonous communities were clearly species specific, whereas skin communities showed higher commonalities between both species. Core microbiome analysis identified the presence of shared core taxa between both species and pond water in addition to organ-specific taxa within and between the core community of each species. These core taxa included possibly beneficial genera such as Uncultured Pirellulaceae, Exiguobacterium, and Cetobacterium and opportunistic potential pathogens such as Aeromonas, Plesiomonas, and Vibrio. This study provides the first in-depth mapping of bacterial communities in this semi-intensive system that in turn provides a foundation for further studies toward enhancing the health and welfare of these cultured fish and ensuring sustainability.
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Affiliation(s)
- Ahmed Elsheshtawy
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom.,Faculty of Aquatic and Fisheries Sciences, Kafrelsheikh University, Kafr El Sheikh, Egypt
| | | | - Amaya Albalat
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Allan Beveridge
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Ahmad Hamza
- AQUAVET for Fish Nutrition and Health Solutions, Kafr El Sheikh, Egypt
| | | | - Simon MacKenzie
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
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23
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Li K, Zhao S, Guan W, Li KJ. Planktonic bacteria in white shrimp (Litopenaeus vannamei) and channel catfish (Letalurus punetaus) aquaculture ponds in a salt-alkaline region. Lett Appl Microbiol 2021; 74:212-219. [PMID: 34778977 DOI: 10.1111/lam.13600] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/01/2021] [Accepted: 10/26/2021] [Indexed: 01/01/2023]
Abstract
Aquaculture in salt-alkaline regions is encouraged in China, and culture of many aquatic species has been introduced into these areas. In this study, we cultured two species, white shrimp (Litopenaeus vannamei) and channel catfish (Letalurus punetaus) separately in aquaculture ponds in a salt-alkaline region in northwest China and assessed the impacts of the aquaculture operations on the planktonic bacterial community in the culture ponds. Culture of both species decreased the planktonic bacterial diversity and altered the bacterial community structure in the aquaculture ponds compared with the source water. Among the 10 dominant bacterial phyla, 8 were significantly correlated with environmental parameters; the exception was Actinobacteriota, the most dominant phylum, and Firmicutes. Proteobacteria and Bacteroidota abundances showed significant positive correlations with alkalinity, whereas Patescibacteria, Cyanobacteria, Planctomycetota, and Verrucomicrobiota abundance were positively correlated with salinity. Linear regression analysis showed that alkalinity was positively correlated with bacterial beta diversity and salinity was negatively correlated with that. In addition, white shrimp aquaculture significantly lowered the alkalinity, which suggests that culture of this species in inland salt-alkaline regions is a potential dealkalization solution.
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Affiliation(s)
- K Li
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - S Zhao
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - W Guan
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - K J Li
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
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24
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Lukassen MB, Menanteau-Ledouble S, de Jonge N, Schram E, Nielsen JL. Impact of water quality parameters on geosmin levels and geosmin producers in European recirculating aquaculture systems. J Appl Microbiol 2021; 132:2475-2487. [PMID: 34773307 DOI: 10.1111/jam.15358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/03/2021] [Accepted: 11/07/2021] [Indexed: 11/28/2022]
Abstract
AIMS Geosmin is associated with off-flavour problems in recirculating aquaculture systems (RAS) and represents an economic problem for the aquaculture industry. This study aims at investigating factors influencing the composition of the bacterial microbiota, in particular the presence of geosmin producers and the environmental and farming factors favouring geosmin accumulation. METHODS AND RESULTS Several water quality parameters were correlated to the composition of the microbiota with special emphasis on the presence of geosmin producers within 26 different RAS from four European countries. Three novel groups of geosmin-producing bacteria were quantified to identify potential correlations with geosmin concentration. CONCLUSIONS The microbiome differed significantly between systems. However, phosphate levels, calcium levels and redox potential correlated to geosmin concentration in the water and the presence of the Actinomycetales geosmin-producers but not with the presence of other groups of geosmin-producing bacteria. Oxygen levels and conductivity were found to negatively correlate with geosmin concentration. A large proportion of the detected geosmin producers represented novel taxonomic groups not previously linked with this activity. SIGNIFICANCE AND IMPACT OF THE STUDY These results improve our understanding of the diversity of microbiota in RAS and the water quality parameters favouring the populations of geosmin-producing bacteria and the production of geosmin.
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Affiliation(s)
- Mie Bech Lukassen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg East, Denmark
| | | | - Nadieh de Jonge
- Department of Chemistry and Bioscience, Aalborg University, Aalborg East, Denmark
| | - Edward Schram
- Wageningen Marine Research, IJmuiden, The Netherlands
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg East, Denmark
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25
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Nadella RK, Panda SK, Madhusudana Rao B, Pani Prasad K, Raman RP, Mothadaka MP. Antibiotic resistance of culturable heterotrophic bacteria isolated from shrimp (Penaeus vannamei) aquaculture ponds. MARINE POLLUTION BULLETIN 2021; 172:112887. [PMID: 34450408 DOI: 10.1016/j.marpolbul.2021.112887] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 08/15/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
Shrimp aquaculture is one of the fastest growing food-producing avenues, where antibiotics usage has become an issue of great concern due to the development of antimicrobial resistance in bacteria. A total of 2304 bacterial isolates from 192 samples (sediment, water, shrimp, and source water) from Andhra Pradesh, India were screened. Antibiotic resistance of bacterial isolates was highest for oxytetracycline (23.4%) followed by erythromycin (12.7%), co-trimoxazole (10%) ciprofloxacin (9.6%), and chloramphenicol (6%), of which 11.9% isolates were multi-drug resistant. Bacterial isolates from shrimp (26.7%), water (23.9%), and sediment (19.6%) samples exhibited more resistance (p ≤ 0.05) towards oxytetracycline. Higher antibacterial resistance was observed from samples of southern Andhra Pradesh (locations L6 and L7). Gram negative bacteria were more prevalent (64%) and showed significantly (p ≤ 0.01) higher resistance. This study indicated the wider distribution of antibiotic-resistant bacteria in shrimp aquaculture ponds with potential risk to humans and the environment.
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Affiliation(s)
- Ranjit Kumar Nadella
- MFB Division, ICAR-Central Institute of Fisheries Technology, Willingdon Island, Matsyapuri P.O., Cochin 682029, Kerala, India
| | - Satyen Kumar Panda
- QAM Division, ICAR-Central Institute of Fisheries Technology, Willingdon Island, Matsyapuri P.O., Cochin 682029, Kerala, India
| | - B Madhusudana Rao
- ICAR-Central Institute of Fisheries Technology, Visakhapatnam Research Centre, Visakhapatnam 530003, Andhra Pradesh, India
| | - K Pani Prasad
- Aquatic Environment and Health Management Division, ICAR-Central Institute of Fisheries Education, Versova, Mumbai 400061, Maharashtra, India
| | - R P Raman
- Aquatic Environment and Health Management Division, ICAR-Central Institute of Fisheries Education, Versova, Mumbai 400061, Maharashtra, India
| | - Mukteswar Prasad Mothadaka
- MFB Division, ICAR-Central Institute of Fisheries Technology, Willingdon Island, Matsyapuri P.O., Cochin 682029, Kerala, India.
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26
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Biodiversity and Sediment Contamination in Wet Stormwater Ponds Depending on Design and Catchment Characteristics. SUSTAINABILITY 2021. [DOI: 10.3390/su132111809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Stormwater ponds are a common way to handle stormwater and are used to retain pollutants through sedimentation. The ponds resemble small natural lakes and will be colonized by flora and fauna. How design with respect to age, ratio between wet volume and reduced catchment area and land use influences the retention and how biodiversity is affected was examined. Age and ratio were determined in 135 and 59 ponds, respectively, and 12 of these ponds were selected for studies of dry weight (DW), organic matter (OM), total phosphorus (TP) and aluminum (Al), zinc (Zn), copper (Cu), chromium (Cr), cadmium (Cd) and lead (Pb) in the sediment. Invertebrate biodiversity was determined by Shannon–Wiener index (H’) and Pielou Evenness (J). DW, OM, TP and metals in the sediment close to the outlet of the ponds were influenced by pond age and the volume/area ratio whereas the sediment in the inlet area was more affected by the catchment type. Biodiversity increased with increasing ratio, while age had no effect on the sediment biodiversity but some effect on the water phase biodiversity. Biodiversity decreased with higher OM and TP and tend to decrease with increasing metal content. Higher volume/area ratio results in less sediment accumulation which improves the biodiversity. More pollutants are accumulating with age, which negatively affects the biodiversity. In conclusion, pond ratio, catchment type and, to some extent, age effect the load of contaminants in the sediment and the pond biodiversity. Proper design and management are recommended as a mitigating measure.
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27
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Lv J, Yuan R, Wang S. Water diversion induces more changes in bacterial and archaeal communities of river sediments than seasonality. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 293:112876. [PMID: 34098351 DOI: 10.1016/j.jenvman.2021.112876] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/01/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Previous studies have demonstrated that seasonal variation is often the most important factor affecting aquatic bacterial assemblages. Whether anthropogenic activities can dominate community dynamics remains unknown. Based on 16S rRNA high-throughput sequencing technology, this study revealed and compared the relative influence of water diversions and seasonality on bacterial and archaeal communities in river sediments from a region with obvious seasonality. The results indicate that the influence of water diversion on bacteria and archaea in water-receiving river sediments exceeded the influence of seasonal variation. Water diversion affected microbes by increasing EC, salinity, water flow rate, and organic matter carbon and nitrogen contents. Seasonal variations affected microbes by altering water temperature. Diversion responders but no season responders were classified by statistical methods in the microbial community. Diversion responder numbers were related to nitrogen concentrations, complex organic carbon contents and EC values, which were mainly affected by water diversion. With the joint impact of water diversion and seasonality, the correlations of bacterial and archaeal numbers with environmental factors were obviously weakened due to the increases in the ecological niche breadths of microorganisms. Natural seasonal changes in bacterial and archaeal communities were totally altered by changes in salinity, nutrients, and hydrological conditions induced by anthropogenic water diversions. These results highlight that human activity may be a stronger driver than natural seasonality in the alteration of bacterial and archaeal communities.
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Affiliation(s)
- Jiali Lv
- College of Environmental and Resource Sciences, Shanxi University, Taiyuan, 030006, China; Shanxi Laboratory for Yellow River, Taiyuan, 030006, China; Key Laboratory of Agricultural Water Resources Research, Innovation Academy for Seed Design, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China; Sino-Danish College of University of Chinese Academy of Sciences, Beijing, 101408, China; Sino-Danish Centre for Education and Research, Beijing, 101408, China
| | - Ruiqiang Yuan
- College of Environmental and Resource Sciences, Shanxi University, Taiyuan, 030006, China; Shanxi Laboratory for Yellow River, Taiyuan, 030006, China.
| | - Shiqin Wang
- Key Laboratory of Agricultural Water Resources Research, Innovation Academy for Seed Design, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
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28
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Nguyen TTT, Foysal MJ, Fotedar R, Gupta SK, Siddik MAB, Tay CY. The Effect of Two Dietary Protein Sources on Water Quality and the Aquatic Microbial Communities in Marron (Cherax cainii) Culture. MICROBIAL ECOLOGY 2021; 82:299-308. [PMID: 33432372 DOI: 10.1007/s00248-021-01681-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
Feeding freshwater crayfish species with different diets not only affects the water quality but also induces the abundance of various microbial communities in their digestive tracts. In this context, very limited research has been undertaken to understand the impacts of various protein incorporated aqua-diets on the characteristics of water and its microbial communities. In this study, we have critically analysed the water quality parameters including pH, dissolved oxygen, nitrate, nitrite, ammonia and phosphorus, as well as bacterial communities under marron (Cherax cainii) aquaculture, fed fishmeal (FM) and poultry by-product meal (PBM)-based diets for 60 days. The results unveiled that over the time, feeding has significant impacts on organic waste accumulation, especially ammonia, nitrate, nitrite and phosphate, while no effects were observed on pH and dissolved oxygen. Analysis of 16S rRNA sequence data of water sample indicated significant (P < 0.05) shift of microbial abundance in post-fed FM and PBM water with the evidence of microbial transmission from the gut of marron. Post-fed marron resulted in a significant correlation of Hafnia, Enterobacter, Candidatus Bacilloplasma and Aquitella with the quality and microbial population of water. The results of this study generated valuable knowledge database of microbes-water relationship for better health management practices and production of marron aquaculture fed with FM and PBM diets in under restricted feeding regime with the feeding ratios provided.
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Affiliation(s)
- Thi Thu Thuy Nguyen
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
- Department of Experimental Biology, Research Institute for Aquaculture No.2, Cần Thơ, Vietnam
| | - Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh.
| | - Ravi Fotedar
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Sanjay Kumar Gupta
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India.
| | - Muhammad A B Siddik
- Department of Fisheries Biology and Genetics, Patuakhali Science and Technology University, Patuakhali, Bangladesh
| | - Chin-Yen Tay
- Helicobacter Research Laboratory, Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
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29
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Zhou A, Xie S, Zhang Y, Chuan J, Tang H, Li X, Zhang L, Xu G, Zou J. Interaction of environmental eukaryotic microorganisms and fungi in the pond-cultured carps: new insights into the potential pathogenic fungi in the freshwater aquaculture. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:38839-38854. [PMID: 33745047 DOI: 10.1007/s11356-021-13231-y] [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: 11/26/2020] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
The quality and safety of the aquatic products have gradually become the focus of global attention. In this study, the environmental eukaryotic and fungi communities in pond-cultured grass carp (Ctenopharyngodon idellus) and the koi carp (Cyprinus carpio L.) were investigated. For comparative analysis, the alpha diversity shows that the environmental microbial abundance in the koi carp groups were higher than that in the grass carp groups, while beta diversity reveals that the differences of the microbial community composition and structures in the grass carp groups were significantly higher than those in the koi carp groups. Meanwhile, the environmental microbial diversity of grass carp groups was higher than that of koi carp groups at phylum level, but showed no significant difference at genus level. Additionally, the dominant total phyla were Opisthokonta, Stramenopiles plusAlveolates plusRhizaria, Archaeplastida, Cryptophyceae, and Centrohelida for the 18S rRNA gene and Ciliophora, Chlorophyta, and Ascomycota for the ITS2 rRNA gene in both of the two carp groups. Additionally, annotation analysis showed that the biomarkers in the grass carp groups are significantly higher than those of the koi carp groups. Furthermore, the functional prediction of Funguild showed significant difference in outputs, while similarity in trophic modes and guild types between the two carp groups. Meanwhile, the total relative abundances of animal pathogen, fungal parasite, and plant pathogen were extremely similar between the two carp groups. Surprisingly, one pathogenic fungus of genus Fusarium was identified in both the environments of two carp groups based on filtered operational taxonomic unit tables. Overall, this is the first robust report to understand the characteristics of environmental eukaryotic microorganisms and fungi in the edible and ornamental carps. Our results also provide the basic data for the prevention of fungal diseases and the healthy culture of the carps.
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Affiliation(s)
- Aiguo Zhou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A 5 T1, Canada
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Shaolin Xie
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Yue Zhang
- Departments of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Jiacheng Chuan
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A 5 T1, Canada
| | - Huijuan Tang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Xiang Li
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A 5 T1, Canada
| | - Li Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Guohuan Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
| | - Jixing Zou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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30
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Lastauskienė E, Valskys V, Stankevičiūtė J, Kalcienė V, Gėgžna V, Kavoliūnas J, Ružauskas M, Armalytė J. The Impact of Intensive Fish Farming on Pond Sediment Microbiome and Antibiotic Resistance Gene Composition. Front Vet Sci 2021; 8:673756. [PMID: 34113676 PMCID: PMC8186532 DOI: 10.3389/fvets.2021.673756] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/16/2021] [Indexed: 01/04/2023] Open
Abstract
Aquaculture is a fast-growing animal food sector, and freshwater fish farming is particularly common in Central and Eastern Europe. As the biodiversity of fishery ponds is changed toward fulfilling the industrial needs, precautions should be taken to keep the system sustainable and protect the adjacent environment from possible damage. Due to risk of infectious diseases, antibiotics are used in aquaculture production systems. The constant exposure to antimicrobials can contribute to the rise of antibiotic resistance in aquaculture products and the adjacent ecosystems, with possibility of dissemination to the wider environment as well as between animals and humans. Even though previous studies have found antibiotic resistance genes in the sediments and water of farming ponds, the tendency and direction of spreading is not clear yet. The objective of this project was to evaluate the influence of intensive fish farming on the condition of water bodies used for the aquaculture and the environment, concentrating on the impact of the aquaculture on the surrounding water ecosystems as well as the possibility of transferring the pollutants and antibiotic resistance genes to both environment and the human hosts. Combined measurement of antibiotic and heavy metal contamination, toxicity assessment, microorganism diversity, and the detection of common antibiotic resistance genes was performed in the sediments of one fishery farm ponds as well as sampling points upstream and downstream. All the tested sediment samples did not show significantly elevated heavy metal concentrations and no substantial veterinary antibiotic pollution. From the antibiotic resistance genes tested, the presence of aminoglycoside and β-lactam resistance determinants as well as the presence of integrons could be of concern for the possibility of transfer to humans. However, despite the lack of heavy metal and antibiotic pollution, the sediments showed toxicity, the cause of which should be explored more.
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Affiliation(s)
- Eglė Lastauskienė
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Vaidotas Valskys
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Jonita Stankevičiūtė
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Virginija Kalcienė
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Vilmantas Gėgžna
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Justinas Kavoliūnas
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Modestas Ružauskas
- Institute of Microbiology and Virology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Julija Armalytė
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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31
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Abate TA, Desta AF, Love NG. Evaluating tannery wastewater treatment performance based on physicochemical and microbiological characteristics: An Ethiopian case study. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2021; 93:658-669. [PMID: 32474980 PMCID: PMC8246915 DOI: 10.1002/wer.1364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
Tanneries are an important industrial sector in Ethiopia; consequently, gaps in wastewater treatment process performance need to be identified as the country increases its emphasis on compliance. A case study was conducted to evaluate physicochemical and microbial water quality at a tannery near Addis Ababa. The treatment process was designed for the following: sulfide oxidation; biological oxygen demand reduction; and chromium removal. While some of Ethiopia's standards for industrial wastewater treatment were met through treatment, effluent COD, sulfide, total nitrogen, and total chromium guidelines were not. 16S rRNA gene analysis was used to evaluate the microbial community composition across the treatment train. The results show that common ruminant phyla were dominant throughout, with Firmicutes and Bacteroidetes comprising 77% to 82% relative abundance. The Firmicutes Clostridium increased consistently in relative abundance with treatment, comprising 39% to 61% of the total bacterial community in the effluent. Improved treatment is needed to meet environmental and public health goals. PRACTITIONER POINTS: Case Study of tannery wastewater treatment in Ethiopia shows ineffective treatment of chemical pollutants. Microbiological pollutants from tannery wastewater systems can introduce agents of importance to public health The microbiological composition of tannery influent, mixed liquor and effluent contains mostly four bacterial phyla lead by Firmicutes. Most pathogenic bacterial genera found in the tannery wastewater treatment system became a decreasing percentage of the total population. Clostridium comprises up to 61% of the effluent bacterial population and deserves further evaluation to better understand the consequences of its dominance.
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Affiliation(s)
| | - Adey F. Desta
- Molecular, Cellular and Microbial BiologyAddis Ababa UniversityAddis AbabaEthiopia
| | - Nancy G. Love
- Department of Civil and Environmental EngineeringUniversity of MichiganAnn ArborMIUSA
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32
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SYBR Green real-time qPCR method: Diagnose drowning more rapidly and accurately. Forensic Sci Int 2021; 321:110720. [PMID: 33639416 DOI: 10.1016/j.forsciint.2021.110720] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 02/06/2021] [Indexed: 12/17/2022]
Abstract
In the field of drowning research, the method of diatom morphology has been most applied to determine whether the cause of death is drowning. However, the characteristics of complex operation, high level of professional knowledge drive us to propose a new method. Here, based on the common phytoplankton in water(such as diatoms and Aeromonas), aiming at the rbcL, 23 S, NIES, rPOD, Hly and preprotoxin aerolysin gene, we designed 6 pairs of specific primers and applied SYBR Green real-time qPCR(RT-qPCR) method to detect phytoplankton in the Pearl River Basin of Guangdong Province, China, so as to achieve the purpose of diagnosing drowning. After the experimental verification of the corresponding algae species and the standard strains of bacteria, as well as the verification of tissue samples (lung, liver and kidney) of 56 cases( 40 drowning cases and 16 non-drowning cases), we found that these primers were of great accuracy and tedious laboratory work of diatom test was reduced. Based on the advantages of high throughput, short period and high sensitivity, this RT-qPCR method is expected to diagnose drowning more rapidly and accurately.
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33
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Sabu EA, Gonsalves MJ, Sreepada RA, Shivaramu MS, Ramaiah N. Evaluation of the Physiological Bacterial Groups in a Tropical Biosecured, Zero-Exchange System Growing Whiteleg Shrimp, Litopenaeus vannamei. MICROBIAL ECOLOGY 2021; 81:335-346. [PMID: 32880700 DOI: 10.1007/s00248-020-01575-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 08/10/2020] [Indexed: 06/11/2023]
Abstract
To elucidate the individual and multiple roles of physiological bacterial groups involved in biogeochemical cycles of carbon, nitrogen, phosphorus and sulfur, the changes in the abundance of aerobic bacteria (heterotrophs, methane oxidizers, ammonia oxidizers, sulfur oxidizers, phosphate solubilizers, phosphate accumulators) and anaerobic bacteria (total anaerobes, nitrate reducers, denitrifiers and sulfate reducers) were investigated in a biosecured, zero-exchange system stocked with whiteleg shrimp, Litopenaeus vannamei for one production cycle. Key water quality parameters during the 96-day production cycle fell within the normal range for L. vannamei culture. Results of Spearman's correlation matrix revealed that different sets of variables correlated at varying levels of significance of the interrelationships between bacterial abundances and water quality parameters. The three nitrogenous species (ammonia, nitrite and nitrate) strongly influenced the physiological bacterial groups' abundance. The strong relationship of bacterial groups with phytoplankton biomass and abundance clearly showed the trophic interconnections in nutrient exchange/recycling. Canonical correspondence analysis performed to assess the total variation revealed that the three dissolved nitrogen species followed by salinity, temperature, phytoplankton biomass and pH collectively accounted for as much as 82% of the total variation. In conclusion, the results of the study revealed that the major drivers that interweaved biogeochemical cycles are the three dissolved nitrogen species, which microbially mediated various aerobic-anaerobic assimilation/dissimilation processes in the pond ecosystem. Considering the pond microbial ecology becoming an important management tool where applied research could improve the economic and environmental sustainability of the aquaculture industry, the findings of the present study are practically relevant.
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Affiliation(s)
- Elaine A Sabu
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403 004, India
- School of Earth, Ocean and Atmospheric Sciences, Goa University, Taleigao Plateau, Goa, 403 206, India
| | - Maria Judith Gonsalves
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403 004, India.
| | - R A Sreepada
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403 004, India
| | - Mamatha S Shivaramu
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403 004, India
- Department of Food Protectants & Infestation Control, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka, 570 020, India
| | - N Ramaiah
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403 004, India
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Huang Y, Miyamoto D, Hidaka M, Adachi T, Gu WL, Eguchi S. Regenerative medicine for the hepatobiliary system: A review. JOURNAL OF HEPATO-BILIARY-PANCREATIC SCIENCES 2020; 28:913-930. [PMID: 33314713 DOI: 10.1002/jhbp.882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/05/2020] [Accepted: 11/20/2020] [Indexed: 12/16/2022]
Abstract
Liver transplantation, the only proven treatment for end-stage liver disease and acute liver failure, is hampered by the scarcity of donors. Regenerative medicine provides an alternative therapeutic approach. Tremendous efforts dedicated to liver regenerative medicine include the delivery of transplantable cells, microtissues, and bioengineered whole livers via tissue engineering and the maintenance of partial liver function via extracorporeal support. This brief review summarizes the current status of regenerative medicine for the hepatobiliary system. For liver regenerative medicine, the focus is on strategies for expansion of transplantable hepatocytes, generation of hepatocyte-like cells, and therapeutic potential of engineered tissues in liver disease models. For biliary regenerative medicine, the discussion concentrates on the methods for generation of cholangiocyte-like cells and strategies in the treatment of biliary disease. Significant advances have been made in large-scale and long-term expansion of liver cells. The development of tissue engineering and stem cell induction technology holds great promise for the future treatment of hepatobiliary diseases. The application of regenerative medicine in liver still lacks extensive animal experiments. Therefore, a large number of preclinical studies are necessary to provide sufficient evidence for their therapeutic effectiveness. Much remains to be done for the treatment of hepatobiliary diseases with regenerative medicine.
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Affiliation(s)
- Yu Huang
- Department of Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.,Department of Surgery, School of Medicine, Guangzhou First People's Hospital, South China University of Technology, Guangdong, China
| | - Daisuke Miyamoto
- Department of Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Masaaki Hidaka
- Department of Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Tomohiko Adachi
- Department of Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Wei-Li Gu
- Department of Surgery, School of Medicine, Guangzhou First People's Hospital, South China University of Technology, Guangdong, China
| | - Susumu Eguchi
- Department of Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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Chopyk J, Nasko DJ, Allard S, Bui A, Pop M, Mongodin EF, Sapkota AR. Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond. ENVIRONMENTAL MICROBIOME 2020; 15:18. [PMID: 33902740 PMCID: PMC8067656 DOI: 10.1186/s40793-020-00365-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/29/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUND Ponds are important freshwater habitats that support both human and environmental activities. However, relative to their larger counterparts (e.g. rivers, lakes), ponds are understudied, especially with regard to their microbial communities. Our study aimed to fill this knowledge gap by using culture-independent, high-throughput sequencing to assess the dynamics, taxonomy, and functionality of bacterial and viral communities in a freshwater agricultural pond. RESULTS Water samples (n = 14) were collected from a Mid-Atlantic agricultural pond between June 2017 and May 2018 and filtered sequentially through 1 and 0.2 μm filter membranes. Total DNA was then extracted from each filter, pooled, and subjected to 16S rRNA gene and shotgun sequencing on the Illumina HiSeq 2500 platform. Additionally, on eight occasions water filtrates were processed for viral metagenomes (viromes) using chemical concentration and then shotgun sequenced. A ubiquitous freshwater phylum, Proteobacteria was abundant at all sampling dates throughout the year. However, environmental characteristics appeared to drive the structure of the community. For instance, the abundance of Cyanobacteria (e.g. Nostoc) increased with rising water temperatures, while a storm event appeared to trigger an increase in overall bacterial diversity, as well as the relative abundance of Bacteroidetes. This event was also associated with an increase in the number of antibiotic resistance genes. The viral fractions were dominated by dsDNA of the order Caudovirales, namely Siphoviridae and Myovirdae. CONCLUSIONS Overall, this study provides one of the largest datasets on pond water microbial ecology to date, revealing seasonal trends in the microbial taxonomic composition and functional potential.
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Affiliation(s)
- Jessica Chopyk
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, USA.
- Department of Pathology University of California San Diego, La Jolla, California, USA.
| | - Daniel J Nasko
- Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Sciences, University of Maryland, College Park, MD, USA
| | - Sarah Allard
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, USA
| | - Anthony Bui
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, USA
| | - Mihai Pop
- Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Sciences, University of Maryland, College Park, MD, USA
| | - Emmanuel F Mongodin
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Amy R Sapkota
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, USA
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Malayil L, Ramachandran P, Chattopadhyay S, Cagle R, Hittle L, Ottesen A, Mongodin EF, Sapkota AR. Metabolically-active bacteria in reclaimed water and ponds revealed using bromodeoxyuridine DNA labeling coupled with 16S rRNA and shotgun sequencing. WATER RESEARCH 2020; 184:116185. [PMID: 32726735 DOI: 10.1016/j.watres.2020.116185] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 07/09/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
Understanding the complex microbiota of agricultural irrigation water is vital to multiple sectors of sustainable agriculture and public health. To date, microbiome characterization methods have provided comprehensive profiles of aquatic microbiotas, but have not described which taxa are likely metabolically-active. Here, we combined 5‑bromo‑2'-deoxyuridine (BrdU) labeling with 16S rRNA and shotgun sequencing to identify metabolically-active bacteria in reclaimed and agricultural pond water samples (n = 28) recovered from the Mid-Atlantic United States between March 2017 and January 2018. BrdU-treated samples were significantly less diverse (alpha diversity) compared to non-BrdU-treated samples. The most abundant taxa in the metabolically-active fraction of water samples (BrdU-treated samples) were unclassified Actinobacteria, Flavobacterium spp., Pseudomonas spp. and Aeromonas spp. Interestingly, we also observed that antimicrobial resistance and virulence gene profiles seemed to be more diverse and more abundant in non-BrdU-treated water samples compared to BrdU-treated samples. These findings raise the possibility that these genes may be associated more with relic (inactive) DNA present in the tested water types rather than viable, metabolically-active microorganisms. Our study demonstrates that the coupled use of BrdU labeling and sequencing can enhance understanding of the metabolically-active fraction of bacterial communities in alternative irrigation water sources. Agricultural pond and reclaimed waters are vital to the future of sustainable agriculture, and thus, the full understanding of the pathogenic potential of these waters is important to guide mitigation strategies that ensure appropriate water quality for intended purposes.
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Affiliation(s)
- Leena Malayil
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, United States
| | - Padmini Ramachandran
- Food and Drug Administration, Office of Regulatory Science, Division of Microbiology, HFS-712, 5001 Campus Drive, College Park, MD20740, United States
| | - Suhana Chattopadhyay
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, United States
| | - Robin Cagle
- Food and Drug Administration, Office of Regulatory Science, Division of Microbiology, HFS-712, 5001 Campus Drive, College Park, MD20740, United States
| | - Lauren Hittle
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201United States
| | - Andrea Ottesen
- Food and Drug Administration, Office of Regulatory Science, Division of Microbiology, HFS-712, 5001 Campus Drive, College Park, MD20740, United States
| | - Emmanuel F Mongodin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201United States
| | - Amy R Sapkota
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, United States.
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Zou S, Gong L, Khan TA, Pan L, Yan L, Li D, Cao L, Li Y, Ding X, Yi G, Sun Y, Hu S, Xia L. Comparative analysis and gut bacterial community assemblages of grass carp and crucian carp in new lineages from the Dongting Lake area. Microbiologyopen 2020; 9:e996. [PMID: 32175674 PMCID: PMC7221430 DOI: 10.1002/mbo3.996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/31/2019] [Accepted: 12/31/2019] [Indexed: 12/17/2022] Open
Abstract
Gut microbiota are known to play an important role in health and nutrition of the host and have been attracting an increasing attention. Farming of new lineages of grass carp and crucian carp has been developed rapidly as these species were found to outperform indigenous ones in terms of growth rate and susceptibility to diseases. Despite this rapid development, no studies have addressed the characteristics of their gut microbiota as a potential factor responsible for the improved characteristics. To reveal whether microbiomes of the new lineages are different from indigenous ones, and therefore could be responsible for improved growth features, intestinal microbiota from the new lineages were subjected to high-throughput sequencing. While the phyla Firmicutes, Fusobacteria and Proteobacteria were representing the core bacterial communities that comprised more than 75% in all fish intestinal samples, significant differences were found in the microbial community composition of the new linages versus indigenous fish populations, suggesting the possibility that results in the advantages of enhanced disease resistance and rapid growth for the new fish lineages. Bacterial composition was similar between herbivorous and omnivorous fish. The relative abundance of Bacteroidetes and Actinobacteria was significantly higher in omnivores compared to that of herbivores, whereas Cetobacterium_sp. was abundant in herbivores. We also found that the gut microbiota of freshwater fish in the Dongting lake area was distinct from those of other areas. Network graphs showed the reduced overall connectivity of gut bacteria in indigenous fish, whereas the bacteria of the new fish lineage groups showed hubs with more node degree. A phylogenetic investigation of communities by reconstruction of unobserved states inferred function profile showed several metabolic processes were more active in the new lineages compared to indigenous fish. Our findings suggest that differences in gut bacterial community composition may be an important factor contributing to the rapid growth and high disease resistance of the new fish lineages.
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Affiliation(s)
- Sheng Zou
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Liang Gong
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Tahir Ali Khan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Lifei Pan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Liang Yan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Dongjie Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Lina Cao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Yanping Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Xuezhi Ding
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Ganfeng Yi
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Yunjun Sun
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Shengbiao Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Liqiu Xia
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
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Manikkam R, Imchen M, Kaari M, Angamuthu V, Venugopal G, Thangavel S, Joseph J, Ramasamy B, Kumavath R. Metagenomic insights unveil the dominance of undescribed Actinobacteria in pond ecosystem of an Indian shrine. Meta Gene 2020. [DOI: 10.1016/j.mgene.2019.100639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Hou L, Mulla SI, Niño-Garcia JP, Ning D, Rashid A, Hu A, Yu CP. Deterministic and stochastic processes driving the shift in the prokaryotic community composition in wastewater treatment plants of a coastal Chinese city. Appl Microbiol Biotechnol 2019; 103:9155-9168. [DOI: 10.1007/s00253-019-10177-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/12/2019] [Accepted: 10/07/2019] [Indexed: 12/20/2022]
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40
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Gao T, Cui B, Kong X, Bai Z, Zhuang X, Qian Z. Investigation of bacterial diversity and pathogen abundances in gibel carp (Carassius auratus gibelio) ponds during a cyprinid herpesvirus 2 outbreak. Microbiologyopen 2019; 8:e907. [PMID: 31432609 PMCID: PMC6813457 DOI: 10.1002/mbo3.907] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 06/12/2019] [Accepted: 06/28/2019] [Indexed: 12/28/2022] Open
Abstract
Cyprinid herpesvirus 2 (CyHV-2) infection is detrimental to gibel carp health and may result in severe economic loss in freshwater aquaculture. However, information regarding the interaction of this pathogen with the aquatic environment is scarce. In this study, quantitative polymerase chain reaction (qPCR) and high-throughput sequencing were used to determine the abundances of pathogens and bacterial community compositions in two aquaculture ponds in Jiangsu Province, China. The results indicate that the concentrations of six selected pathogens were higher in the water than in the sediment and that these concentrations peaked during disease outbreak. In total, 8,326 and 18,244 operational taxonomic units were identified from water and sediment samples, respectively. The dominant phyla were Proteobacteria, Actinobacteria, Cyanobacteria, Bacteroidetes, and Chlorobi in water samples and Proteobacteria, Firmicutes, Actinobacteria, Chloroflexi, and Bacteroidetes in sediment samples. Bacterial communities were similar at the phylum level in different ponds, although significant differences were observed at the genus level. In addition, bacterial diversity was associated with environmental factors (temperature, chemical oxygen demand, NO2- -N, NO3- -N, and NH4+ -N) in the pond where the outbreak occurred. Additionally, CyHV-2 abundance was positively correlated with dissolved oxygen levels and Aeromonas spp. abundance in pond water (p < .01). This study provides comprehensive insight into the mechanisms of interaction between potential pathogens and the freshwater environment of aquaculture ponds during CyHV-2 disease outbreaks. Furthermore, the results from this study can contribute to improvement of the aquatic environment and establishment of disease prevention and control measures.
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Affiliation(s)
- Tianming Gao
- College of Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijingChina
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
| | - Bingjian Cui
- College of Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijingChina
- Farmland Irrigation Research InstituteChinese Academy of Agricultural SciencesXinxiangChina
| | - Xiao Kong
- College of Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijingChina
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
| | - Zhihui Bai
- College of Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijingChina
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
| | - Xuliang Zhuang
- College of Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijingChina
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
| | - Zhi Qian
- College of Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijingChina
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Daae HL, Heldal KK, Madsen AM, Olsen R, Skaugset NP, Graff P. Occupational exposure during treatment of offshore drilling waste and characterization of microbiological diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 681:533-540. [PMID: 31121403 DOI: 10.1016/j.scitotenv.2019.05.131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
The exposure for workers handling and recycling offshore drilling waste are previously not described, and given the potential for exposure to hazardous components, there is a need for characterizing this occupational exposure. In this study five plants recycling offshore drilling waste with different techniques were included. Measurements were conducted in both winter and summer to include seasonal exposure variations. Altogether >200 personal air-exposure measurements for oil mist, oil vapor, volatile organic compounds (VOC), hydrogen sulfide (H2S) and solvents were carried out respectively. Microorganisms related to drilling waste were identified in bulk samples and in stationary air measurements from two of the plants. The exposure to oil mist and oil vapor were below 10% of the current Norwegian occupational exposure limits (OEL) for all measured components. The plants using the Resoil or TCC method had a statistically significant higher exposure to oil vapor than the plant using complete combustion (p-value <0.05). No statistically significant difference was found between the different treatment methods for oil mist. The exposure to solvents was generally low (additive factor < 0.03). Endotoxin measurements done during winter showed a median concentration of 5.4 endotoxin units (EU)/m3. Levels of H2S above the odor threshold of 0.1 ppm were measured at four plants. Both drill mud and slop water contained a high number and diversity of bacteria (2-4 × 104 colony forming unit (CFU)/mL), where a large fraction was Gram-negative species. Some of the identified microorganisms are classified as potentially infectious pathogens for humans and thus might be a hazard to workers.
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Affiliation(s)
- Hanne Line Daae
- National Institute of Occupational Health, Pb 5330 Majorstuen, N-0304 Oslo, Norway
| | - Kari Kulvik Heldal
- National Institute of Occupational Health, Pb 5330 Majorstuen, N-0304 Oslo, Norway
| | - Anne Mette Madsen
- The National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100 Copenhagen Ø, Denmark
| | - Raymond Olsen
- National Institute of Occupational Health, Pb 5330 Majorstuen, N-0304 Oslo, Norway
| | - Nils Petter Skaugset
- National Institute of Occupational Health, Pb 5330 Majorstuen, N-0304 Oslo, Norway
| | - Pål Graff
- National Institute of Occupational Health, Pb 5330 Majorstuen, N-0304 Oslo, Norway.
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Wu K, Zhao W, Wang Q, Yang X, Zhu L, Shen J, Cheng X, Wang J. The Relative Abundance of Benthic Bacterial Phyla Along a Water-Depth Gradient in a Plateau Lake: Physical, Chemical, and Biotic Drivers. Front Microbiol 2019; 10:1521. [PMID: 31354648 PMCID: PMC6635551 DOI: 10.3389/fmicb.2019.01521] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/18/2019] [Indexed: 02/01/2023] Open
Abstract
Water-depth biodiversity gradient, one of the typical biogeographical patterns on Earth, is understudied for bacteria in freshwater ecosystems, and thus left the underlying mechanisms poorly understood especially for benthic bacteria. Here, we investigated the water-depth distribution of surface sediment bacterial phyla and their driving factors in Lake Lugu, a plateau lake in Southwest China. Our results revealed that the relative abundance of 11 dominant bacterial phyla showed various water-depth patterns, such as increasing, decreasing, hump-shaped, and U-shaped patterns. These patterns across phyla were consistent with their different niche positions of water depth, while the occupancy-abundance relationships were not dependent on phylum attributes. Consistently, phylum abundance was best explained by water depth; other physical and chemical factors, such as metal ion concentrations, SiO2, and pH, can also explain the variations in some bacterial phyla. Chemical variables were the main drivers of the dominant bacterial phyla. However, biotic variables also showed substantial importance for some phyla, such as Planctomycetes, Actinobacteria, and WS3. This work could provide new insights into the general water-depth patterns and underlying mechanisms of the relative abundance of bacterial phyla in freshwater ecosystems.
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Affiliation(s)
- Kaiyuan Wu
- School of Environment and Civil Engineering, Jiangnan University, Wuxi, China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Wenqian Zhao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.,School of Biological Sciences, Nanjing Normal University, Nanjing, China
| | - Qian Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Xiangdong Yang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Lifeng Zhu
- School of Biological Sciences, Nanjing Normal University, Nanjing, China
| | - Ji Shen
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Xiaoying Cheng
- School of Environment and Civil Engineering, Jiangnan University, Wuxi, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
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The Role of Pseudomonas in Heterotrophic Nitrification: A Case Study on Shrimp Ponds ( Litopenaeus vannamei) in Soc Trang Province. Microorganisms 2019; 7:microorganisms7060155. [PMID: 31146455 PMCID: PMC6616971 DOI: 10.3390/microorganisms7060155] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/22/2019] [Accepted: 05/28/2019] [Indexed: 01/08/2023] Open
Abstract
Based on a total of 6,295,650 sequences from the V3 and V4 regions (16S ribosomal RNA), the composition of the microorganism communities in the water of three Litopenaeus vannamei (Decapoda, Whiteleg shrimp; Soc Trang, Vietnam) ponds were identified. Pseudomonas (10–20.29%), Methylophilus (13.26–24.28%), and Flavobacterium (2.6–19.29%) were the most abundant genera. The total ammonia (TAN) concentration (p = 0.025) and temperature (p = 0.015) were significantly correlated with the relative abundance of Pseudomonas in two bacterial communities (ST1, ST4), whereas the predictive functions of microorganism communities based on 16S rRNA gene data was estimated using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUST), which showed that nitrogen metabolism was significantly negatively correlated (p = 0.049) with TAN concentration. The abundance of Pseudomonas and nitrogen metabolism increased with a decrease in TAN concentration. The correlation between TAN concentration and the abundance of Pseudomonas was followed by the isolation, and heterotrophic nitrifying performance analysis was used to confirm our findings. Six Pseudomonas strains capable of heterotrophic nitrification were isolated from the three water samples and showed a complete reduction of 100 mg/L NH4Cl during a 96-h cultivation. These results indicate the potential of applying Pseudomonas in shrimp ponds for water treatment.
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Foysal M, Fotedar R, Gupta S, Chaklader M. Biological ball filters regulate bacterial communities in marron (
Cherax cainii
) culture system. Lett Appl Microbiol 2019; 68:455-463. [DOI: 10.1111/lam.13125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/29/2019] [Accepted: 01/30/2019] [Indexed: 11/28/2022]
Affiliation(s)
- M.J. Foysal
- School of Molecular and Life Sciences Curtin University Bentley WA Australia
- Department of Genetic Engineering and Biotechnology Shahjalal University of Science and Technology Sylhet Bangladesh
| | - R. Fotedar
- School of Molecular and Life Sciences Curtin University Bentley WA Australia
| | - S.K. Gupta
- School of Molecular and Life Sciences Curtin University Bentley WA Australia
- ICAR‐Indian Institute of Agricultural Biotechnology Ranchi India
| | - M.R. Chaklader
- School of Molecular and Life Sciences Curtin University Bentley WA Australia
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Abstract
Organisms display astonishing levels of cell and molecular diversity, including genome size, shape, and architecture. In this chapter, we review how the genome can be viewed as both a structural and an informational unit of biological diversity and explicitly define our intended meaning of genetic information. A brief overview of the characteristic features of bacterial, archaeal, and eukaryotic cell types and viruses sets the stage for a review of the differences in organization, size, and packaging strategies of their genomes. We include a detailed review of genetic elements found outside the primary chromosomal structures, as these provide insights into how genomes are sometimes viewed as incomplete informational entities. Lastly, we reassess the definition of the genome in light of recent advancements in our understanding of the diversity of genomic structures and the mechanisms by which genetic information is expressed within the cell. Collectively, these topics comprise a good introduction to genome biology for the newcomer to the field and provide a valuable reference for those developing new statistical or computation methods in genomics. This review also prepares the reader for anticipated transformations in thinking as the field of genome biology progresses.
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Alfiansah YR, Hassenrück C, Kunzmann A, Taslihan A, Harder J, Gärdes A. Bacterial Abundance and Community Composition in Pond Water From Shrimp Aquaculture Systems With Different Stocking Densities. Front Microbiol 2018; 9:2457. [PMID: 30405548 PMCID: PMC6200860 DOI: 10.3389/fmicb.2018.02457] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/25/2018] [Indexed: 12/14/2022] Open
Abstract
In shrimp aquaculture, farming systems are carefully managed to avoid rearing failure due to stress, disease, or mass mortality, and to achieve optimum shrimp production. However, little is known about how shrimp farming systems affect biogeochemical parameters and bacterial communities in rearing water, whether high stocking densities (intensive system) will increase the abundance of pathogenic bacteria. In this study, we characterized bacterial communities in shrimp ponds with different population densities. Water quality, such as physical parameters, inorganic nutrient concentrations, and cultivable heterotrophic bacterial abundances, including potential pathogenic Vibrio, were determined in moderate density/semi-intensive (40 post-larvae m-3) and high density/intensive shrimp ponds (90 post-larvae m-3), over the shrimp cultivation time. Free-living and particle-attached bacterial communities were characterized by amplicon sequencing of the 16S rRNA gene. Suspended particulate matter (SPM), salinity, chlorophyll a, pH, and dissolved oxygen differed significantly between semi-intensive and intensive systems. These variations contrasted with the equal abundance of cultivable heterotrophic bacteria and inorganic nutrient concentrations. Bacterial communities were dominated by Gammaproteobacteria, Alphaproteobacteria, Flavobacteriia, Bacilli, and Actinobacteria. Halomonas and Psychrobacter were the most dominant genera in the particle-attached fractions, while Salegentibacter, Sulfitobacter, and Halomonas were found in the free-living fractions of both systems. Redundancy analysis indicated that among the observed environmental parameters, salinity was best suited to explain patterns in the composition of both free-living and particle-attached bacterial communities (R2: 15.32 and 12.81%, respectively), although a large fraction remained unexplained. Based on 16S rRNA gene sequences, aggregated particles from intensive ponds loaded a higher proportion of Vibrio than particles from semi-intensive ponds. In individual ponds, sequence proportions of Vibrio and Halomonas displayed an inverse relationship that coincided with changes in pH. Our observations suggest that high pH-values may suppress Vibrio populations and eventually pathogenic Vibrio. Our study showed that high-density shrimp ponds had a higher prevalence of Vibrio, increased amounts of SPM, and higher phytoplankton abundances. To avoid rearing failure, these parameters have to be managed carefully, for example by providing adequate feed, maintaining pH level, and removing organic matter deposits regularly.
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Affiliation(s)
- Yustian Rovi Alfiansah
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany.,Laboratory of Marine Microbiology, Research Center for Oceanography, Indonesian Institute of Sciences, Jakarta, Indonesia
| | | | - Andreas Kunzmann
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
| | - Arief Taslihan
- Balai Besar Pengembangan Budidaya Air Payau, Jepara, Indonesia
| | - Jens Harder
- Department of Microbiology, Max Planck Institute for Marine Microbiology (MPI), Bremen, Germany
| | - Astrid Gärdes
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
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Huang F, Pan L, Song M, Tian C, Gao S. Microbiota assemblages of water, sediment, and intestine and their associations with environmental factors and shrimp physiological health. Appl Microbiol Biotechnol 2018; 102:8585-8598. [PMID: 30039332 DOI: 10.1007/s00253-018-9229-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 12/14/2022]
Abstract
Microorganisms play crucial roles in nutrient cycling, water quality maintenance, and farmed animal health. Increasing evidences have revealed a close association between unstable microbial environments and disease occurrences in aquaculture. Thereupon, we used high-throughput sequencing technology to comprehensively compare the bacterial communities of water, sediment, and intestine in mariculture ponds at the middle and late stages of Litopenaeus vannamei farming and analyzed whether changes of their microbiota assemblages were associated with environmental factors and shrimp physiological health. Results showed that bacterial community structures were significantly distinct among water, sediment, and intestine; meanwhile, the relative abundances of intestinal dominant taxa were significantly changed between different rearing stages. Compared with intestine and water, shrimp intestine and sediment had a similar profile of the dominant bacterial genera by cluster analysis, and the observed species, diversity indexes, and shared OTUs of bacterial communities in intestine and sediment were simultaneously increased after shrimp were farmed for 90 days. These results reflected a closer relationship between microbiotas in sediment and intestine, which was further proved by nonmetric multidimensional scaling analysis. However, bacterial communities in water, sediment, and intestine responded differently to environmental variables by redundancy and correlation analysis. More importantly, shrimp physiological parameters were closely associated with bacterial variations in the gut and/or ambient, especially the gut microbiota owning significantly high levels of predicted functional pathways involved in disease emergence. These findings may greatly add to our understanding of the microbiota characteristics of the shrimp pond ecosystem and the complex interactions among shrimp, ambient microflora, and environmental variables.
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Affiliation(s)
- Fei Huang
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, Shandong, China
| | - Luqing Pan
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, Shandong, China. .,Fisheries College, Ocean University of China, Yushan Road 5, Qingdao, 266003, China.
| | - Mengsi Song
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, Shandong, China
| | - Changcheng Tian
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, Shandong, China
| | - Shuo Gao
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, Shandong, China
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Truchado P, Gil MI, Suslow T, Allende A. Impact of chlorine dioxide disinfection of irrigation water on the epiphytic bacterial community of baby spinach and underlying soil. PLoS One 2018; 13:e0199291. [PMID: 30020939 PMCID: PMC6051574 DOI: 10.1371/journal.pone.0199291] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 06/05/2018] [Indexed: 12/13/2022] Open
Abstract
The contamination of pathogenic bacteria through irrigation water is a recognized risk factor for fresh produce. Irrigation water disinfection is an intervention strategy that could be applied to reduce the probability of microbiological contamination of crops. Disinfection treatments should be applied ensuring minimum effective doses, which are efficient in inhibiting the microbial contamination while avoiding formation and accumulation of chemical residues. Among disinfection technologies available for growers, chlorine dioxide (ClO2) represents, after sodium hypochlorite, an alternative disinfection treatment, which is commercially applied by growers in the USA and Spain. However, in most of the cases, the suitability of this treatment has been tested against pathogenic bacteria and low attention have been given to the impact of chemical residues on the bacterial community of the vegetable tissue. The aim of this study was to (i) to evaluate the continual application of chlorine dioxide (ClO2) as a water disinfection treatment of irrigation water during baby spinach growth in commercial production open fields, and (ii) to determine the subsequent impact of these treatments on the bacterial communities in water, soil, and baby spinach. To gain insight into the changes in the bacterial community elicited by ClO2, samples of treated and untreated irrigation water as well as the irrigated soil and baby spinach were analyzed using Miseq® Illumina sequencing platform. Next generation sequencing and multivariate statistical analysis revealed that ClO2 treatment of irrigation water did not affect the diversity of the bacterial community of water, soil and crop, but significant differences were observed in the relative abundance of specific bacterial genera. This demonstrates the different susceptibility of the bacteria genera to the ClO2 treatment. Based on the obtained results it can be concluded that the phyllosphere bacterial community of baby spinach was more influenced by the soil bacteria community rather than that of irrigation water. In the case of baby spinach, the use of low residual ClO2 concentrations (approx. 0.25 mg/L) to treat irrigation water decreased the relative abundance of Pseudomonaceae (2.28-fold) and Enterobacteriaceae (2.5-fold) when comparing treated versus untreated baby spinach. Members of these two bacterial families are responsible for food spoilage and foodborne illnesses. Therefore, a reduction of these bacterial families might be beneficial for the crop and for food safety. In general it can be concluded that the constant application of ClO2 as a disinfection treatment for irrigation water only caused changes in two bacterial families of the baby spinach and soil microbiota, without affecting the major phyla and classes. The significance of these changes in the bacterial community should be further evaluated.
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Affiliation(s)
- Pilar Truchado
- Research Group on Quality, Safety and Bioactivity of Plant Foods, CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
| | - María Isabel Gil
- Research Group on Quality, Safety and Bioactivity of Plant Foods, CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
| | - Trevor Suslow
- Department of Plant Science, University of California, One Shields Avenue, Mann Laboratory, Davis, CA, United States of America
| | - Ana Allende
- Research Group on Quality, Safety and Bioactivity of Plant Foods, CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
- * E-mail:
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Zhang H, Zhao Z, Chen S, Wang Y, Feng J, Jia J, Kang P, Li S. Geographical patterns of denitrifying bacterial communities associated with different urban lakes. RSC Adv 2018; 8:17079-17090. [PMID: 35539271 PMCID: PMC9080392 DOI: 10.1039/c8ra01295d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 04/30/2018] [Indexed: 11/21/2022] Open
Abstract
The geographical variation of denitrifying bacterial communities and water quality parameters in urban lakes distributed across nine provinces in China were determined. The Illumina sequencing data of the denitrifying encoding gene nirS was examined in the samples collected from nine localities (pairwise geographical distance: 200–2600 km). The results showed that fundamental differences in water quality were observed among different urban lakes. The highest nitrate (2.02 mg L−1) and total nitrogen (3.82 mg L−1) concentrations were observed in Pingzhuang (P < 0.01). The algal cell concentration ranged from 1.29 × 108 to 3.0 × 109 cell per L. The sequencing data generated a total of 421058 high quality nirS gene reads that resulted in 6369 OTUs (97% cutoff), with Proteobacteria and Firmicutes being the dominant taxa. A co-occurrence network analysis indicated that the top five genera identified as keystone taxa were Dechlorospirillum sp., Alicycliphilus sp., Dechloromonas sp., Pseudogulbenkiania sp., and Paracoccus sp. A redundancy analysis (RDA) further revealed that distinct denitrifying bacterial communities inhabited the different urban lakes, and influenced by urban lake water ammonia nitrogen, manganese and algal cell concentrations. A variance partitioning analysis (VPA) also showed that geographic location was more important than water quality factors in structuring the denitrifying bacterial communities. Together, these results provide new insight into understanding of denitrifying bacterial communities associated with geographically distributed urban lakes on a larger scale, and these results also expand our exploration of aquatic microbial ecology in freshwater bodies. The geographical variation of denitrifying bacterial communities and water quality parameters in urban lakes distributed across nine provinces in China were determined.![]()
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Affiliation(s)
- Haihan Zhang
- Key Laboratory of Northwest Resource
- Environment and Ecology
- MOE
- Xi'an University of Architecture and Technology
- Xi'an 710055
| | - Zhenfang Zhao
- Key Laboratory of Northwest Resource
- Environment and Ecology
- MOE
- Xi'an University of Architecture and Technology
- Xi'an 710055
| | - Shengnan Chen
- Key Laboratory of Northwest Resource
- Environment and Ecology
- MOE
- Xi'an University of Architecture and Technology
- Xi'an 710055
| | - Yue Wang
- Key Laboratory of Northwest Resource
- Environment and Ecology
- MOE
- Xi'an University of Architecture and Technology
- Xi'an 710055
| | - Ji Feng
- Key Laboratory of Northwest Resource
- Environment and Ecology
- MOE
- Xi'an University of Architecture and Technology
- Xi'an 710055
| | - Jingyu Jia
- Key Laboratory of Northwest Resource
- Environment and Ecology
- MOE
- Xi'an University of Architecture and Technology
- Xi'an 710055
| | - Pengliang Kang
- Key Laboratory of Northwest Resource
- Environment and Ecology
- MOE
- Xi'an University of Architecture and Technology
- Xi'an 710055
| | - Sulin Li
- Key Laboratory of Northwest Resource
- Environment and Ecology
- MOE
- Xi'an University of Architecture and Technology
- Xi'an 710055
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50
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Nakayama T, Tuyet Hoa TT, Harada K, Warisaya M, Asayama M, Hinenoya A, Lee JW, Phu TM, Ueda S, Sumimura Y, Hirata K, Phuong NT, Yamamoto Y. Water metagenomic analysis reveals low bacterial diversity and the presence of antimicrobial residues and resistance genes in a river containing wastewater from backyard aquacultures in the Mekong Delta, Vietnam. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 222:294-306. [PMID: 28062224 DOI: 10.1016/j.envpol.2016.12.041] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 12/12/2016] [Accepted: 12/17/2016] [Indexed: 06/06/2023]
Abstract
The environmental pathways for the dissemination of antibiotic resistance have recently received increased attention. Aquatic environments act as reservoirs or sources of antimicrobial-resistant bacteria, antimicrobial residues, and antimicrobial resistance genes (ARGs). Therefore, it is imperative to identify the role of polluted water in the dissemination of antimicrobial resistance. The aim of this study was to evaluate the antimicrobial residues, ARGs, and microbiota in the freshwater systems of the Mekong Delta. We selected 12 freshwater sites from aquacultures and rivers in Can Tho, Vietnam and analyzed them for 45 antimicrobial residues and 8 ARGs by LC/MS/MS and real-time PCR, respectively. A 16S rDNA-based metagenomic analysis was conducted to characterize the water microbiota. Residues of sulfamethoxazole (10/12) and sulfadimidine (7/12) were widely detected, together with the sulfa-resistance genes sul1 (11/12) and sul2 (9/12). Additionally, sulfamethoxazole residues and the β-lactamase-resistance gene blaCTX-M-1 were detected in eight freshwater systems (8/12), suggesting that these freshwater systems may have been polluted by human activity. The metagenomic analysis showed that all the tested freshwater systems contained the phyla Proteobacteria, Actinobacteria, and Bacteroidetes, representing 64% of the total microbiota. Moreover, the Cai Rang River site (Ri-E), which is located at the merge point of wastewaters from backyard-based aquacultures, contained the genera Polynucleobacter, Variovorax, and Limnohabitans, representing more than 78.4% of the total microbiota. Bacterial diversity analysis showed that the Ri-E exhibited the lowest diversity compared with other regions. Principal coordinate analysis showed that the differences among water microbiotas in backyard-based aquacultures could be explained by the farmers' aquaculture techniques. In conclusion, this study demonstrated a collapse of bacterial diversity at the merge point of wastewaters from backyard-based aquacultures in the Mekong Delta.
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Affiliation(s)
- Tatsuya Nakayama
- Global Collaboration Center, Osaka University, 2-7, Yamadaoka, Suita, Osaka, 565-0871, Japan; Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58, Rinku Ourai Kita, Izumisano, Osaka, 598-8531, Japan; Graduate School of Pharmaceutical Science, Osaka University, 1-6, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tran Thi Tuyet Hoa
- College of Aquaculture and Fisheries, Can Tho University, Campus II, 3/2 Street, Ninh Kieu, Can Tho, Viet Nam
| | - Kazuo Harada
- Global Collaboration Center, Osaka University, 2-7, Yamadaoka, Suita, Osaka, 565-0871, Japan; Graduate School of Pharmaceutical Science, Osaka University, 1-6, Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Minae Warisaya
- Graduate School of Pharmaceutical Science, Osaka University, 1-6, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Megumi Asayama
- Graduate School of Pharmaceutical Science, Osaka University, 1-6, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Atsushi Hinenoya
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58, Rinku Ourai Kita, Izumisano, Osaka, 598-8531, Japan
| | - Joon Won Lee
- Global Collaboration Center, Osaka University, 2-7, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tran Minh Phu
- College of Aquaculture and Fisheries, Can Tho University, Campus II, 3/2 Street, Ninh Kieu, Can Tho, Viet Nam
| | - Shuhei Ueda
- Global Collaboration Center, Osaka University, 2-7, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoshinori Sumimura
- Global Collaboration Center, Osaka University, 2-7, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kazumasa Hirata
- Global Collaboration Center, Osaka University, 2-7, Yamadaoka, Suita, Osaka, 565-0871, Japan; Graduate School of Pharmaceutical Science, Osaka University, 1-6, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Nguyen Thanh Phuong
- College of Aquaculture and Fisheries, Can Tho University, Campus II, 3/2 Street, Ninh Kieu, Can Tho, Viet Nam
| | - Yoshimasa Yamamoto
- Global Collaboration Center, Osaka University, 2-7, Yamadaoka, Suita, Osaka, 565-0871, Japan; Osaka Prefectural Institute of Public Health, 1-3-69, Nakamichi, Higashinari-ku, Osaka, 537-0025, Japan
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