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Ma C, Xu C, Zhang T, Mu Q, Lv J, Xing Q, Yang Z, Xu Z, Guan Y, Chen C, Ni K, Dai X, Ding W, Hu J, Bao Z, Wang S, Liu P. Tracking the hologenome dynamics in aquatic invertebrates by the holo-2bRAD approach. Commun Biol 2024; 7:827. [PMID: 38972908 PMCID: PMC11228047 DOI: 10.1038/s42003-024-06509-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 06/26/2024] [Indexed: 07/09/2024] Open
Abstract
The "hologenome" concept is an increasingly popular way of thinking about microbiome-host for marine organisms. However, it is challenging to track hologenome dynamics because of the large amount of material, with tracking itself usually resulting in damage or death of the research object. Here we show the simple and efficient holo-2bRAD approach for the tracking of hologenome dynamics in marine invertebrates (i.e., scallop and shrimp) from one holo-2bRAD library. The stable performance of our approach was shown with high genotyping accuracy of 99.91% and a high correlation of r > 0.99 for the species-level profiling of microorganisms. To explore the host-microbe association underlying mass mortality events of bivalve larvae, core microbial species changed with the stages were found, and two potentially associated host SNPs were identified. Overall, our research provides a powerful tool with various advantages (e.g., cost-effective, simple, and applicable for challenging samples) in genetic, ecological, and evolutionary studies.
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Affiliation(s)
- Cen Ma
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, China
| | - Chang Xu
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Tianqi Zhang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qianqian Mu
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Jia Lv
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
| | - Qiang Xing
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, China
| | - Zhihui Yang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Zhenyuan Xu
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Yalin Guan
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Chengqin Chen
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Kuo Ni
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoting Dai
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Institute of Gerontology, Geriatrics Center, University of Michigan, Ann Arbor, MI, USA
| | - Wei Ding
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jingjie Hu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Zhenmin Bao
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Shi Wang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Pingping Liu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China.
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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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Yang J, Zhou S, Fu Z, Xiao B, Li M, Yu G, Ma Z, Zong H. Fermented Astragalus membranaceus could promote the liver and intestinal health of juvenile tiger grouper ( Epinephelus fuscoguttatus). Front Physiol 2023; 14:1264208. [PMID: 37781230 PMCID: PMC10534042 DOI: 10.3389/fphys.2023.1264208] [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] [Received: 07/20/2023] [Accepted: 09/01/2023] [Indexed: 10/03/2023] Open
Abstract
In order to understand the effects of fermented Astragalus membranaceus (FAM) on the liver and intestinal health of tiger grouper (Epinephelus fuscoguttatus), this study was conducted. This study evaluates the effects of different levels of FAM on liver and intestinal tissue structure, serum biochemical parameters, intestinal digestive enzyme, and microbiota structure of tiger grouper. Fish were fed with diets (crude protein ≥ 48.0%, crude fat ≥ 10.0%) with five levels of FAM (L1:0.25%, L2: 0.5%, L3: 1%, L4: 2% and L5: 4%) in the experimental groups and a regular diet was used as the control (L0: 0%) for 8 weeks. Compared with AM, the protein content of FAM was significantly changed by 34.70%, indicating that a large amount of bacterial protein was produced after AM fermentation, and its nutritional value was improved. FAM had significant effects on the growth performance of tiger grouper (p < 0.05). The high-density lipoprotein cholesterol (HDL-C) was highest in L4 group, being significantly different from L0 group. The area and diameter of hepatocytes were lowest in L3 and L4, and the density of hepatocyte was highest in L4 group and relatively decreased in L5 group. The mucosal height and muscular thickness were highest in L3 group. The intestinal microbiota structure of tiger grouper was changed under the intervention of FAM. The lower abundance of potential pathogenic bacteria and higher abundance of probiotics colonization in the L4 group showed that the dose of FAM had the best effect on improving the health of intestinal microbiota. This study indicates that the addition of FAM in the feed contributes to liver health, improves intestinal morphology, and regulates the intestinal microbiota of tiger grouper. The addition ratio of 1%-2% is better for intestinal and liver health, and a high addition ratio will cause liver damage. Our work will provide a reference for the addition and management of FAM in the aquaculture industry.
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Affiliation(s)
- Jingru Yang
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Shengjie Zhou
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Zhengyi Fu
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Bo Xiao
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Minghao Li
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Gang Yu
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Zhenhua Ma
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Humin Zong
- National Marine Environmental Center, Dalian, China
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Wen Z, Xu X, Xiang D, Xu J, Yang Q, Wang X, Liu J, Luo M, Wei W. Effects of Lipopolysaccharide and Deoxynivalenol on the Survival, Antioxidant and Immune Response, and Histopathology of Crayfish ( Procambarus clarkii). Toxins (Basel) 2023; 15:479. [PMID: 37624236 PMCID: PMC10467083 DOI: 10.3390/toxins15080479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/11/2023] [Accepted: 07/21/2023] [Indexed: 08/26/2023] Open
Abstract
Bacterial lipopolysaccharide (LPS) in the aquatic environment has been reported to cause diseases in red swamp crayfish (Procambarus clarkii). In addition, deoxynivalenol (DON) is one of the primary mycotoxins found in aquaculture. However, the potential synergistic toxic effects of LPS and DON on crayfish are yet to be fully elucidated. In this study, crayfish were exposed to LPS (1 mg kg-1), DON (3 mg kg-1), and their combination (1 mg kg-1 LPS + 3 mg kg-1 DON, L+D) for a duration of six days. Co-exposure to LPS and DON exhibited the lowest survival rate compared to the control or individual treatments with LPS or DON alone. In the initial stage of the experiment, the combined treatment of LPS and DON showed a more pronounced up-regulation of antioxidant and immune-related enzymes in the sera compared to the other treatment groups, with a fold change ranging from 1.3 to 15. In addition, the (L+D) treatment group showed a down-regulation of immune-related genes, as well as Toll pathway-related genes in the hepatopancreas compared to LPS or DON. Moreover, the (L+D) treatment group demonstrated a 100% incidence of histopathological changes in the hepatopancreas, which were significantly more severe compared to the other three groups. In conclusion, our study provides physiological and histopathological evidence that the co-exposure to LPS and DON exerted synergistic toxic effects on crayfish. The observed effects could potentially hinder the development of the crayfish aquaculture industry in China.
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Affiliation(s)
- Zhengrong Wen
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, College of Animal Science, Yangtze University, Jingzhou 434025, China; (Z.W.); (D.X.); (Q.Y.)
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.X.); (J.X.); (X.W.)
| | - Xiaoli Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.X.); (J.X.); (X.W.)
| | - Dan Xiang
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, College of Animal Science, Yangtze University, Jingzhou 434025, China; (Z.W.); (D.X.); (Q.Y.)
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.X.); (J.X.); (X.W.)
| | - Junfeng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.X.); (J.X.); (X.W.)
| | - Qiufeng Yang
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, College of Animal Science, Yangtze University, Jingzhou 434025, China; (Z.W.); (D.X.); (Q.Y.)
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.X.); (J.X.); (X.W.)
| | - Xiaofu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.X.); (J.X.); (X.W.)
| | - Jiashou Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China;
| | - Mingzhong Luo
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, College of Animal Science, Yangtze University, Jingzhou 434025, China; (Z.W.); (D.X.); (Q.Y.)
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China;
| | - Wei Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.X.); (J.X.); (X.W.)
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Alvanou MV, Feidantsis K, Staikou A, Apostolidis AP, Michaelidis B, Giantsis IA. Probiotics, Prebiotics, and Synbiotics Utilization in Crayfish Aquaculture and Factors Affecting Gut Microbiota. Microorganisms 2023; 11:1232. [PMID: 37317206 DOI: 10.3390/microorganisms11051232] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 06/16/2023] Open
Abstract
Aquaculture is affected by numerous factors that may cause various health threats that have to be controlled by the most environmentally friendly approaches. In this context, prebiotics, probiotics, and synbiotics are frequently incorporated into organisms' feeding rations to ameliorate the health status of the host's intestine, enhancing its functionality and physiological performance, and to confront increasing antimicrobial resistance. The first step in this direction is the understanding of the complex microbiome system of the organism in order to administer the optimal supplement, in the best concentration, and in the correct way. In the present review, pre-, pro-, and synbiotics as aquaculture additives, together with the factors affecting gut microbiome in crayfish, are discussed, combined with their future prospective outcomes. Probiotics constitute non-pathogenic bacteria, mainly focused on organisms' energy production and efficient immune response; prebiotics constitute fiber indigestible by the host organism, which promote the preferred gastrointestinal tract microorganisms' growth and activity towards the optimum balance between the gastrointestinal and immune system's microbiota; whereas synbiotics constitute their combination as a blend. Among pro-, pre-, and synbiotics' multiple benefits are boosted immunity, increased resistance towards pathogens, and overall welfare promotion. Furthermore, we reviewed the intestinal microbiota abundance and composition, which are found to be influenced by a plethora of factors, including the organism's developmental stage, infection by pathogens, diet, environmental conditions, culture methods, and exposure to toxins. Intestinal microbial communities in crayfish exhibit high plasticity, with infections leading to reduced diversity and abundance. The addition of synbiotic supplementation seems to provide better results than probiotics and prebiotics separately; however, there are still conflicting results regarding the optimal concentration.
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Affiliation(s)
- Maria V Alvanou
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100 Florina, Greece
| | - Konstantinos Feidantsis
- Laboratory of Animal Physiology, Department of Zoology, Faculty of Science, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Alexandra Staikou
- Laboratory of Marine and Terrestrial Animal Diversity, Department of Zoology, Facultyof Science, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki,Greece
| | - Apostolos P Apostolidis
- Laboratory of Ichthyology & Fisheries, Department of Animal Production, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Basile Michaelidis
- Laboratory of Animal Physiology, Department of Zoology, Faculty of Science, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Ioannis A Giantsis
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100 Florina, Greece
- Laboratory of Ichthyology & Fisheries, Department of Animal Production, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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Zhang L, Xu Z, Sun Y, Gao Y, Zhu L. Coal Mining Activities Driving the Changes in Microbial Community and Hydrochemical Characteristics of Underground Mine Water. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:13359. [PMID: 36293941 PMCID: PMC9603172 DOI: 10.3390/ijerph192013359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/09/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Coal mining can cause groundwater pollution, and microorganism may reflect/affect its hydrochemical characteristics, yet little is known about the microorganism's distribution characteristics and its influence on the formation and evolution of mine water quality in underground coal mines. Here, we investigated the hydrochemical characteristics and microbial communities of six typical zones in a typical North China coalfield. The results showed that hydrochemical compositions and microbial communities of the water samples displayed apparent zone-specific patterns. The microbial community diversity of the six zones followed the order of surface waters > coal roadways > water sumps ≈ rock roadways ≈ goafs > groundwater aquifers. The microbial communities corresponded to the redox sensitive indices' levels. Coal roadways and goafs were the critical zones of groundwater pollution prevention and control. During tunneling in the panel, pyrite was oxidized by sulfur-oxidizing bacteria leading to SO42- increase. With the closure of the panel and formation of the goaf, SO42- increased rapidly for a short period. However, with the time since goaf closure, sulfate-reducing bacteria (e.g., c_Thermodesulfovibrionia, Desulfobacterium_catecholicum, etc.) proportion increased significantly, leading to SO42- concentration's decrease by 42% over 12 years, indicating the long-term closed goafs had a certain self-purification ability. These findings would benefit mine water pollution prevention and control by district.
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Affiliation(s)
- Li Zhang
- School of Resources and Geosciences, China University of Mining and Technology, Xuzhou 221116, China
| | - Zhimin Xu
- School of Resources and Geosciences, China University of Mining and Technology, Xuzhou 221116, China
- Fundamental Research Laboratory for Mine Water Hazards Prevention and Controlling Technology, Xuzhou 221006, China
| | - Yajun Sun
- School of Resources and Geosciences, China University of Mining and Technology, Xuzhou 221116, China
- Fundamental Research Laboratory for Mine Water Hazards Prevention and Controlling Technology, Xuzhou 221006, China
| | - Yating Gao
- School of Resources and Geosciences, China University of Mining and Technology, Xuzhou 221116, China
| | - Lulu Zhu
- School of Resources and Geosciences, China University of Mining and Technology, Xuzhou 221116, China
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Huang X, Li M, Huang Y, Yang H, Geng Y, Ouyang P, Chen D, Yin L, Yang S, Jiang J, Luo W, He Z. Microbiome analysis reveals microecological advantages of emerging ditchless rice-crayfish co-culture mode. Front Microbiol 2022; 13:892026. [PMID: 35935240 PMCID: PMC9355531 DOI: 10.3389/fmicb.2022.892026] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Ditchless rice-crayfish co-culture is an emerging model of rice-crayfish farming that circumvents the potential hazards of digging ditches in traditional rice-crayfish farming. However, due to the complex interactions among crayfish, ambient microbiota, and environmental variables, it is necessary to assess the differences in bacterial structure between ditchless and traditional rice-crayfish culture. In this study, the crayfish culture area in the Sichuan basin was selected as the study area, and the bacterial communities of two rice-crayfish culture systems were compared by high-throughput sequencing of 16S rDNA. The results showed that the ditchless system had lower water depth, higher dissolved oxygen, lower total ammonia nitrogen and lower morbidity. There are intuitive differences in the composition of environmental bacterial communities due to environmental changes, even if they are similar in composition at the phylum level. Microbiota in sediments from ditchless systems appear to produce less ammonia nitrogen. The abundance of the pathogens colonizing the intestine of ditchless crayfish was lower than ditched one, and the composition was similar to water. Ditch-farmed crayfish appear to be more susceptible to environmental microbes and have a more fragile intestinal structure. Water depth and dissolved oxygen are the main environmental factors that determine the distribution of microbiota. This study is the first to investigate the bacterial ecology of a ditchless rice- crayfish farming system. The results show that the ditchless rice-crayfish culture model has a more superior bacterial system than the traditional rice-crayfish culture.
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Affiliation(s)
- Xiaoli Huang
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Minghao Li
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ya Huang
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hai Yang
- Haide Aquatic Technology Co., Ltd, Yibin, China
| | - Yi Geng
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Yi Geng,
| | - Ping Ouyang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Defang Chen
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Lizi Yin
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shiyong Yang
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jun Jiang
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wei Luo
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhi He
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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Yang Q, Ai X, Dong J, Yang Y, Zhou S, Liu Y, Xu N. Elimination of Pendimethalin in Integrated Rice and Procambarus clarkii Breeding Models and Dietary Risk Assessments. Foods 2022; 11:foods11091300. [PMID: 35564023 PMCID: PMC9105123 DOI: 10.3390/foods11091300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022] Open
Abstract
This study investigated elimination of the herbicide pendimethalin using an integrated rice and Procambarus clarkii breeding model of indoor and outdoor (pond culture) exposure tests. The pendimethalin levels in 484 samples from the primary rice and P. clarkii integrated breeding areas in Hubei province were monitored, and dietary risk assessments of pendimethalin were calculated. Pendimethalin was quantified using high-performance liquid chromatography tandem mass spectrometry, and detection levels were linear in the range of 1.0 to 10.0 μg/L, and peak areas were positively correlated with concentration, with a correlation coefficient of 0.9996. Recoveries ranged from 86.9 to 103.5%, and the limit of quantitation was 2.5 × 10−4 μg/L in water, and 1 × 10−2 μg/kg in tissues, sediments, and waterweeds. The dissipation rate of pendimethalin in tissues and water followed first-order kinetics, with half-lives of 0.51–5.64 d. In 484 samples taken from aquaculture farms, pendimethalin was detected in 8.67% of the samples at levels in the range of 1.95 to 8.26 μg/kg in Hubei province from 2018 to 2020. The maximum residue limit of pendimethalin in P. clarkii has not been established in China, but our dietary risk assessments indicated that consumption of P. clarkii from integrated rice farms was acceptable.
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Affiliation(s)
- Qiuhong Yang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (Q.Y.); (J.D.); (Y.Y.); (S.Z.); (Y.L.); (N.X.)
| | - Xiaohui Ai
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (Q.Y.); (J.D.); (Y.Y.); (S.Z.); (Y.L.); (N.X.)
- Key Laboratory of Control of Quality and Safety for Aquatic Products, Ministry of Agriculture and Rural Affairs, Beijing 100141, China
- Correspondence:
| | - Jing Dong
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (Q.Y.); (J.D.); (Y.Y.); (S.Z.); (Y.L.); (N.X.)
| | - Yibin Yang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (Q.Y.); (J.D.); (Y.Y.); (S.Z.); (Y.L.); (N.X.)
| | - Shun Zhou
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (Q.Y.); (J.D.); (Y.Y.); (S.Z.); (Y.L.); (N.X.)
| | - Yongtao Liu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (Q.Y.); (J.D.); (Y.Y.); (S.Z.); (Y.L.); (N.X.)
- Key Laboratory of Control of Quality and Safety for Aquatic Products, Ministry of Agriculture and Rural Affairs, Beijing 100141, China
| | - Ning Xu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (Q.Y.); (J.D.); (Y.Y.); (S.Z.); (Y.L.); (N.X.)
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9
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The Microbiome Structure of a Rice-Crayfish Integrated Breeding Model and Its Association with Crayfish Growth and Water Quality. Microbiol Spectr 2022; 10:e0220421. [PMID: 35384719 PMCID: PMC9045173 DOI: 10.1128/spectrum.02204-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The rice-crayfish (RC) integrated breeding model is an important and special agricultural ecosystem that provides a unique ecological environment for exploring the microbial diversity, composition, and functional capacity. To date, little is known about the effect of the breeding model on microbiome assembly and breeding model-specific microbiome composition and the association of the microbiome with water quality and crayfish growth. In the present study, we assessed the taxonomic shifts in gut and water microbiomes and their associations with water quality and crayfish growth in the RC and crayfish monoculture (CM) breeding models across six time points of rice growth, including seedling (a), tillering and jointing (b), blooming (c), filling (d), fruiting (e), and rotting of rice residues (f). Dominant bacterial phyla, such as Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes, were detected in both gut and water microbiomes across breeding models. Notably, the diversity and structure of the gut and water microbiomes significantly (P < 0.001) differed between the RC and CM models, with higher microbial diversity being noted in the RC model than in the CM model. The taxa enriched in the RC model included Bacillus sp., Streptomyces sp., Lactobacillus sp., Prevotella sp., Rhodobacter sp., Bifidobacterium sp., Akkermansia sp., and Lactococcus sp., some of which are potentially beneficial to animals. However, opportunistic pathogens, such as Citrobacter sp. and Aeromonas sp., were depleted in the RC model. Furthermore, in the RC model, the enriched taxa that formed complex cooccurrence networks showed a significant positive correlation with water quality and crayfish growth, whereas the depleted taxa showed a significant negative correlation with water quality and crayfish growth. These results suggest that the RC model has a better microbiome composition and that RC model-specific microbes could play important roles in improving crayfish growth and water quality. IMPORTANCE The present study comprehensively compared two different breeding models in terms of their microbiome composition and the associations of the microbiomes with crayfish growth and water quality. RC model-specific microbiome composition was identified; these microbes were found to have a positive association with water quality and crayfish growth. These results provide valuable information for guiding microbial isolation and culture and for potentially harnessing the power of the microbiome to improve crayfish production and health and water quality.
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10
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Chen X, Fan L, Qiu L, Dong X, Wang Q, Hu G, Meng S, Li D, Chen J. Metagenomics Analysis Reveals Compositional and Functional Differences in the Gut Microbiota of Red Swamp Crayfish, Procambarus clarkii, Grown on Two Different Culture Environments. Front Microbiol 2021; 12:735190. [PMID: 34733252 PMCID: PMC8558459 DOI: 10.3389/fmicb.2021.735190] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/21/2021] [Indexed: 11/13/2022] Open
Abstract
The structure and function of intestinal microorganisms are closely related to host metabolism, development, physiology, and health. The red swamp crayfish, Procambarus clarkii, is an important farmed aquatic species in China, which is grown in aquaculture ponds and rice paddy fields. Since these are two distinct cultivation environments with important differences in nutrient input and ecological community composition, we hypothesized that they may have different effects on the gut microbiota of the crayfish. Here, we sought to examine this hypothesis. To that aim, metagenomics analyses were applied to unveil the taxonomic composition and functional diversity of the microbiota in the intestines of red swamp crayfish grown in aquaculture ponds and rice-crayfish cultivation environments. The results showed that Firmicutes and Proteobacteria were the two most abundant microbial components. In addition, the relative abundance of bacterial and archaeal communities, but not that of fungal and viral communities, significantly differed between the two environments. The abundance of genes involved in pathways related to genetic information processing and human diseases was lower in the guts of red swamp crayfish grown in rice-crayfish cultivation environments. In particular, the abundance of two gene sets, K13730 and K08303, which are related to epithelial cell invasion by Listeria monocytogenes and Helicobacter pylori, respectively, decreased in this culture environment. In addition, the samples from rice-crayfish cultivation environments tended to have lower relative abundance of glycosyltransferases (GTs), which were the most abundant carbohydrate-active enzymes in the samples from both groups, higher abundance of glycoside hydrolases, and lower abundance of GT2.
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Affiliation(s)
- Xi Chen
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Limin Fan
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Liping Qiu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi, China
| | - Xinxu Dong
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Qing Wang
- Wuxi COFCO Engineering & Technology Co., Ltd., Wuxi, China
| | - Gengdong Hu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi, China
| | - Shunlong Meng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi, China
| | - Dandan Li
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi, China
| | - Jiazhang Chen
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
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11
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Ding Y, Song X, Cao X, He L, Liu S, Yu Z. Healthier Communities of Phytoplankton and Bacteria Achieved via the Application of Modified Clay in Shrimp Aquaculture Ponds. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182111569. [PMID: 34770083 PMCID: PMC8583407 DOI: 10.3390/ijerph182111569] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 11/25/2022]
Abstract
The composition and stability of microbial communities in aquaculture water are crucial for the healthy growth of shrimp and present considerable risk to aquatic ecosystems. The modified clay (MC) method has been proposed as an efficient and safe solution for the mitigation of harmful algal blooms (HABs). Currently, the effects of MC on microbial communities in aquaculture water remain unknown. Here, we adopted the MC method to regulate shrimp-culture water quality and evaluated the effects of MC on the composition and stability of phytoplankton together with bacteria communities through high-throughput sequencing. On the one hand, a prominent change in the composition of microbial community was observed, with green algae becoming the most abundant genera and pathogens being infrequent in the MC-treated pond, which was more conducive to the growth of shrimp than that in the control pond. Moreover, MC could increase the diversity and stability of the microbial community structure in the water column, which had a higher anti-interference ability, as demonstrated by the analysis of the diversity and molecular ecological network. Taken together, MC could reduce the possibility for the occurrence of HABs and maintain a stable microbial community, which is beneficial for the health and high yield of shrimp.
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Affiliation(s)
- Yu Ding
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.D.); (X.C.); (L.H.); (S.L.); (Z.Y.)
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Chinese Academy of Sciences, Beijing 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Xiuxian Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.D.); (X.C.); (L.H.); (S.L.); (Z.Y.)
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Chinese Academy of Sciences, Beijing 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Correspondence: ; Tel.: +86-532-82898587
| | - Xihua Cao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.D.); (X.C.); (L.H.); (S.L.); (Z.Y.)
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Liyan He
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.D.); (X.C.); (L.H.); (S.L.); (Z.Y.)
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Shanshan Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.D.); (X.C.); (L.H.); (S.L.); (Z.Y.)
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Chinese Academy of Sciences, Beijing 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhiming Yu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.D.); (X.C.); (L.H.); (S.L.); (Z.Y.)
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Chinese Academy of Sciences, Beijing 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
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