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Liao M, Xu M, Hu R, Xu Z, Bonvillain C, Li Y, Li X, Luo X, Wang J, Wang J, Zhao S, Gu Z. The chromosome-level genome assembly of the red swamp crayfish Procambarus clarkii. Sci Data 2024; 11:885. [PMID: 39143139 PMCID: PMC11325019 DOI: 10.1038/s41597-024-03718-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 07/31/2024] [Indexed: 08/16/2024] Open
Abstract
Red swamp crayfish, Procambarus clarkii, is the most cultured freshwater crayfish species. It attracts significant research attention due to its considerable economic importance. However, the limited availability of genome information has impeded further genetic studies and breeding programs. By utilizing Illumina, PacBio, and Hi-C sequencing technologies, we present a more comprehensive and continuous chromosome-level assembly for P. clarkii than the published one. The final genome size is 4.03 Gb, consisting of 2,358 scaffolds with a N50 of 42.87 Mb. Notably, 3.68 Gb, corresponding to 91.42% of the genome, was anchored to 94 chromosomes. The assembly comprises 70.64% repetitive sequences, including 5.21% tandem repeats and 65.40% transposable elements. Additionally, a total of 4,456 non-coding RNAs and 28,852 protein-coding genes were predicted in the P. clarkii genome, with 96.26% of the genes were annotated. This high-quality genome assembly not only represents a significant improvement for the genome of P. clarkii and provides insights into the unique genome evolution, but also offers valuable information for developing freshwater aquaculture and accelerating genetic breeding.
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Affiliation(s)
- Mingcong Liao
- College of Fisheries and Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan laboratory, Wuhan, 430070, China
| | - Meng Xu
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, 510632, China
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Ruixue Hu
- College of Fisheries and Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan laboratory, Wuhan, 430070, China
| | - Zhiwei Xu
- College of Fisheries and Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan laboratory, Wuhan, 430070, China
| | - Christopher Bonvillain
- Department of Biological Sciences, Nicholls State University, P.O. Box 2021, Thibodaux, Louisiana, 70310, USA
| | - Ying Li
- College of Fisheries and Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan laboratory, Wuhan, 430070, China
| | - Xu Li
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Xiaohong Luo
- College of Fisheries and Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan laboratory, Wuhan, 430070, China
| | - Jianghua Wang
- College of Fisheries and Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Wang
- Genetic engineering research center, School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Shancen Zhao
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Zemao Gu
- College of Fisheries and Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Hongshan laboratory, Wuhan, 430070, China.
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Ma Y, Yu A, Zhang L, Zheng R. Effects of Rice-Frog Co-Cropping on the Soil Microbial Community Structure in Reclaimed Paddy Fields. BIOLOGY 2024; 13:396. [PMID: 38927276 PMCID: PMC11200385 DOI: 10.3390/biology13060396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 05/20/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024]
Abstract
Utilizing and improving the productivity of reclaimed land are highly significant for alleviating the problem of food production shortage in China, and the integrated rice-frog farming model can improve soil fertility. However, there are few studies on the use of integrated rice-frog farming technology to improve the fertility of reclaimed land and increase its efficiency in food production. Therefore, this study was conducted to evaluate the effects of the rice-frog co-cropping mode on the soil fertility and microbial diversity of reclaimed land. A rice monoculture group (SF), low-density rice-frog co-cropping group (SD, 5000 frogs/mu, corresponds to 8 frogs/m2), and high-density rice-frog co-cropping group (SG, 10,000 frogs/mu, corresponds to 15 frogs/m2) were established and tested. The contents of total nitrogen, soil organic matter, available potassium, and available phosphorus of the soil in the SG group were significantly higher than those in the SF group (p < 0.05) in the mature stage of rice. Compared with the SF group, the SD and SG groups improved the soil microbial diversity and changed the structure of the microbial community. This study indicates that compared with the rice monoculture mode, the rice-frog co-cropping pattern can improve the soil fertility, as well as microbial diversity, of reclaimed land.
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Affiliation(s)
- Yunshuang Ma
- Provincial Key Laboratory of Wildlife Biotechnology and Conservation and Utilization, Zhejiang Normal University, Jinhua 321004, China; (Y.M.); (A.Y.)
| | - Anran Yu
- Provincial Key Laboratory of Wildlife Biotechnology and Conservation and Utilization, Zhejiang Normal University, Jinhua 321004, China; (Y.M.); (A.Y.)
| | - Liangliang Zhang
- Xingzhi College, Zhejiang Normal University, Jinhua 321004, China;
| | - Rongquan Zheng
- Provincial Key Laboratory of Wildlife Biotechnology and Conservation and Utilization, Zhejiang Normal University, Jinhua 321004, China; (Y.M.); (A.Y.)
- Xingzhi College, Zhejiang Normal University, Jinhua 321004, China;
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Liu S, Wang Z, Wang Z, Wu Q, Zhou J, Wang R, Han J, Su X. Comparison of the gut microbiota and metabolism in different regions of Red Swamp Crayfish ( Procambarus clarkii). Front Microbiol 2023; 14:1289634. [PMID: 38188569 PMCID: PMC10770849 DOI: 10.3389/fmicb.2023.1289634] [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: 09/07/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
Background The gut microbiota is very important for maintaining the homeostasis and health of crustaceans. Many factors affect the gut microbiota of crustaceans, one of which is temperature. However, it is currently unclear how temperature affects the gut microbiota and metabolites of Procambarus clarkii. Methods Using metagenomic sequencing and gas chromatography-mass spectrometry (GC-MS) techniques, the gut microbiota and metabolites of P. clarkii from Hubei (HB), Jiangsu (JS), Shandong (SD), and Zhejiang (ZJ) in China were investigated. Results Under the impact of temperature, the gut microbiota and metabolites of P. clarkii exhibit a specific trend of change. The primary pathogenic bacteria affecting P. clarkii are Citrobacter, Enterobacterium, and Aeromonas, which are affected by temperature. Two metabolites, namely, sugars and amino acids, are regulated by temperature. Implication This study demonstrated that the gut microbiota and gut metabolites of P. clarkii were considerably affected by temperature. It provides a theoretical basis for the systematic study of P. clarkii and provides a basis for a healthy culture of P. clarkii.
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Affiliation(s)
- Songyi Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Ziyan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Ze Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Qiaoli Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Jun Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Rixin Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Jiaojiao Han
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Xiurong Su
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
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Vigil K, Aw TG. Comparison of de novo assembly using long-read shotgun metagenomic sequencing of viruses in fecal and serum samples from marine mammals. Front Microbiol 2023; 14:1248323. [PMID: 37808316 PMCID: PMC10556685 DOI: 10.3389/fmicb.2023.1248323] [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: 06/27/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction Viral diseases of marine mammals are difficult to study, and this has led to a limited knowledge on emerging known and unknown viruses which are ongoing threats to animal health. Viruses are the leading cause of infectious disease-induced mass mortality events among marine mammals. Methods In this study, we performed viral metagenomics in stool and serum samples from California sea lions (Zalophus californianus) and bottlenose dolphins (Tursiops truncates) using long-read nanopore sequencing. Two widely used long-read de novo assemblers, Canu and Metaflye, were evaluated to assemble viral metagenomic sequencing reads from marine mammals. Results Both Metaflye and Canu assembled similar viral contigs of vertebrates, such as Parvoviridae, and Poxviridae. Metaflye assembled viral contigs that aligned with one viral family that was not reproduced by Canu, while Canu assembled viral contigs that aligned with seven viral families that was not reproduced by Metaflye. Only Canu assembled viral contigs from dolphin and sea lion fecal samples that matched both protein and nucleotide RefSeq viral databases using BLASTx and BLASTn for Anelloviridae, Parvoviridae and Circoviridae families. Viral contigs assembled with Canu aligned with torque teno viruses and anelloviruses from vertebrate hosts. Viruses associated with invertebrate hosts including densoviruses, Ambidensovirus, and various Circoviridae isolates were also aligned. Some of the invertebrate and vertebrate viruses reported here are known to potentially cause mortality events and/or disease in different seals, sea stars, fish, and bivalve species. Discussion Canu performed better by producing the most viral contigs as compared to Metaflye with assemblies aligning to both protein and nucleotide databases. This study suggests that marine mammals can be used as important sentinels to surveil marine viruses that can potentially cause diseases in vertebrate and invertebrate hosts.
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Affiliation(s)
| | - Tiong Gim Aw
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
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Liu Y, Wang G, Li Y, Zhang Z, Pang S, He X, Song J. Spray losses study of two pesticides by UASS in integrated rice-crayfish farming system and acute toxicity evaluation on Procambarus clarkii. FRONTIERS IN PLANT SCIENCE 2023; 14:1212818. [PMID: 37767301 PMCID: PMC10519795 DOI: 10.3389/fpls.2023.1212818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023]
Abstract
Introduction While the integrated rice-crayfish (Procambarus clarkii) farming system (IRCFS) is widely developing in China, the widespread use of Unmanned Aerial Spraying Systems (UASS) to protect rice from pests has led to potential pesticide risk for the crayfish in IRCFS. Therefore, it is crucial to examine UASS's spray deposition and drift in IRCFS. Method In this study, we used the oligonucleotide sequence-tracking / dot-blotting (OSTDB) method to trace pesticide spraying. We collected detailed data not only on spray loss in the paddy fields, but also on spray drift in the breeding ditches caused by upwind and downwind spray areas. Additionally, pesticide residues in the breeding ditches were measured using LC-MS/MS by collecting water samples after pesticide application. Results The data analysis indicated that the spray loss in the paddy field was significantly greater than that in the breeding ditches. The spray drift in the breeding ditches, caused by the upwind spray area, was seven times higher than that originating from the downwind spray area. Furthermore, the results also revealed that the bulk flow between the paddy fields and the breeding ditches contributed a substantial amount of pesticide residue to the water body in the breeding ditches. In addition, we investigated the acute toxicities of common insecticides using in paddy fields, including thiamethoxam (THI), chlorantraniliprole (CHI), THI·CHI-Mix and THI·CHI-WG. Discussion The results demonstrated that the spray losses and spray drift from UASS spray applications of these pesticides in IRCFS would not cause acute toxicity or death in crayfish. These findings provide important materials for establishing pesticide application standards and guiding the field testing of droplet deposition and drift in IRCFS.
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Affiliation(s)
- Yang Liu
- College of Science, China Agricultural University, Beijing, China
- College of Agricultural Unmanned Systems, China Agricultural University, Beijing, China
| | - Guangyu Wang
- College of Science, China Agricultural University, Beijing, China
| | - Yuanyuan Li
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhenhua Zhang
- College of Science, China Agricultural University, Beijing, China
- College of Agricultural Unmanned Systems, China Agricultural University, Beijing, China
| | - Sen Pang
- College of Science, China Agricultural University, Beijing, China
| | - Xiongkui He
- College of Science, China Agricultural University, Beijing, China
- College of Agricultural Unmanned Systems, China Agricultural University, Beijing, China
| | - Jianli Song
- College of Science, China Agricultural University, Beijing, China
- College of Agricultural Unmanned Systems, China Agricultural University, Beijing, China
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Zhu X, Yang P, Xiong G, Wei H, Zhang L, Wang Z, Ning K. Microbial biogeochemical cycling reveals the sustainability of the rice-crayfish co-culture model. iScience 2023; 26:106769. [PMID: 37234090 PMCID: PMC10206492 DOI: 10.1016/j.isci.2023.106769] [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: 09/29/2022] [Revised: 02/08/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
Aquaculture has great potential in nourishing the global growing population, while such staggering yields are coupled with environmental pollution. Rice-crayfish co-culture models (RCFP) have been widely adopted in China due to their eco-friendliness. However, little is known about RCFP's microbiome pattern, which hinders our understanding of its sustainability. This study has conducted metagenomic analysis across aquaculture models and habitats, which revealed aquaculture model-specific biogeochemical cycling pattern (e.g., nitrogen (N), sulfur (S), and carbon (C)): RCFP is advantageous in N-assimilation, N-contamination, and S-pollutants removal, while non-RCFP features N denitrification process and higher S metabolism ability, producing several hazardous pollutants in non-RCFP (e.g., nitric oxide, nitrogen monoxide, and sulfide). Moreover, RCFP has greater capacity for carbohydrate enzyme metabolism compared with non-RCFP in environmental habitats, but not in crayfish gut. Collectively, RCFP plays an indispensable role in balancing aquaculture productivity and environmental protection, which might be applied to the blue transformation of aquaculture.
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Affiliation(s)
- Xue Zhu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Guangzhou Xiong
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Huimin Wei
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Zhang
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi Wang
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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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: 3] [Impact Index Per Article: 3.0] [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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Ge L, Sun Y, Li Y, Wang L, Guo G, Song L, Wang C, Wu G, Zang X, Cai X, Li S, Li P. Ecosystem sustainability of rice and aquatic animal co-culture systems and a synthesis of its underlying mechanisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 880:163314. [PMID: 37030380 DOI: 10.1016/j.scitotenv.2023.163314] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/20/2023] [Accepted: 04/01/2023] [Indexed: 04/14/2023]
Abstract
Integrated planting and breeding of rice and aquatic animals, including traditional rice-fish co-culture (RF), has been conducted for over 1200 years. It is one of the primary modes of modern ecologically sustainable agriculture. Rice and aquatic animal (RA) co-culture systems reduce risks of environmental pollution, reduce greenhouse gas emissions, maintain soil fertility, stabilize grain incomes, and preserve paddy field biodiversity. Nevertheless, the mechanisms that underlie the ecological sustainability of these systems remain controversial and poorly understood, restricting their practice at a larger scale. Here, the latest advance in understanding the evolution and extension of RA systems is synthesized, in addition to a discussion of the underlying ecological mechanisms of taxonomic interactions, complementary nutrient use, and microbially-driven elemental cycling. Specifically, the aim of this review is to provide a theoretical framework for the design of sustainable agricultural systems by integrating traditional knowledge and modern technologies.
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Affiliation(s)
- Lei Ge
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Yu Sun
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Yujie Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Luyao Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Guanqing Guo
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Lili Song
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Cui Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Guogan Wu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Xiaoyun Zang
- Shanghai Co-Elite Agricultural Sci-Tech (Group) Co., Ltd., Shanghai 201106, China
| | - Xiaomei Cai
- Shanghai Co-Elite Agricultural Sci-Tech (Group) Co., Ltd., Shanghai 201106, China
| | - Shuangxi Li
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
| | - Peng Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; Shanghai Co-Elite Agricultural Sci-Tech (Group) Co., Ltd., Shanghai 201106, China.
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Arunrat N, Sereenonchai S, Sansupa C, Kongsurakan P, Hatano R. Effect of Rice Straw and Stubble Burning on Soil Physicochemical Properties and Bacterial Communities in Central Thailand. BIOLOGY 2023; 12:biology12040501. [PMID: 37106702 PMCID: PMC10135879 DOI: 10.3390/biology12040501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023]
Abstract
Rice straw and stubble burning is widely practiced to clear fields for new crops. However, questions remain about the effects of fire on soil bacterial communities and soil properties in paddy fields. Here, five adjacent farmed fields were investigated in central Thailand to assess changes in soil bacterial communities and soil properties after burning. Samples of soil prior to burning, immediately after burning, and 1 year after burning were obtained from depths of 0 to 5 cm. The results showed that the pH, electrical conductivity, NH4-N, total nitrogen, and soil nutrients (available P, K, Ca, and Mg) significantly increased immediately after burning due to an increased ash content in the soil, whereas NO3-N decreased significantly. However, these values returned to the initial values. Chloroflexi were the dominant bacteria, followed by Actinobacteria and Proteobacteria. At 1 year after burning, Chloroflexi abundance decreased remarkably, whereas Actinobacteria, Proteobacteria, Verrucomicrobia, and Gemmatimonadetes abundances significantly increased. Bacillus, HSB OF53-F07, Conexibacter, and Acidothermus abundances increased immediately after burning, but were lower 1 year after burning. These bacteria may be highly resistant to heat, but grow slowly. Anaeromyxobacter and Candidatus Udaeobacter dominated 1 year after burning, most likely because of their rapid growth and the fact that they occupy areas with increased soil nutrient levels after fires. Amidase, cellulase, and chitinase levels increased with increased organic matter levels, whereas β-glucosidase, chitinase, and urease levels positively correlated with the soil total nitrogen level. Although clay and soil moisture strongly correlated with the soil bacterial community’s composition, negative correlations were found for β-glucosidase, chitinase, and urease. In this study, rice straw and standing stubble were burnt under high soil moisture and within a very short time, suggesting that the fire was not severe enough to raise the soil temperature and change the soil microbial community immediately after burning. However, changes in soil properties due to ash significantly increased the diversity indices, which was noticeable 1 year after burning.
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Wang E, Zhou Y, Liang Y, Ling F, Xue X, He X, Zhai X, Xue Y, Zhou C, Tang G, Wang G. Rice flowering improves the muscle nutrient, intestinal microbiota diversity, and liver metabolism profiles of tilapia (Oreochromis niloticus) in rice-fish symbiosis. MICROBIOME 2022; 10:231. [PMID: 36527140 PMCID: PMC9756501 DOI: 10.1186/s40168-022-01433-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/21/2022] [Indexed: 05/28/2023]
Abstract
BACKGROUND Rice-fish symbiosis, as an ecological and green aquaculture model, is an effective measure to relieve the environmental stress from intensive aquaculture. Compared with traditional aquaculture, the altered rearing pattern and environment will make differences in muscle nutrient and quality, intestinal microbiota, body metabolism, and even disease resistance in fish. RESULTS To investigate this, we explored the differences between rice-tilapia (aRT and bRT) and tank-tilapia (aTT and bTT) models at the periods before and after rice flowering using 16S rRNA sequencing and untargeted metabolomics. The results showed that compared with tilapia reared in the tank model, the fish body length and weight, the muscle total umami amino acid, and monounsaturated fatty acid content were obviously higher in the rice-fish model, especially after rice flowering. Compared with other groups, the intestinal microbiota diversity of fish in the bRT group was significantly higher; the dominant microbiota was Bacteroidetes and Firmicutes at the phylum level, Bacteroides and Turicibacter at the genus level, and the relative abundances of Gram-negative, potentially pathogenic, and stress-tolerant bacteria were the highest, lowest, and highest, respectively. Besides, the differential metabolite analysis indicated that rice-fish symbiosis improved the metabolic profiles and modulated the metabolic pathways in tilapia. Moreover, the correlation analysis of 16S sequencing and metabolomics showed that Bacteroides showed a positive correlation with many metabolites related to amino acid, fatty acid, and lipid metabolism. Video Abstract CONCLUSIONS: In summary, rice flowering improves the tilapia muscle nutrient, intestinal microbiota diversity, and disease resistance and modulates the host metabolism to acclimatize the comprehensive environment in rice-fish symbiosis. Specifically, rice flowering alters the microbiota abundance involved in amino acid, fatty acid, and lipid metabolism, resulting in improving the muscle nutrient and quality through the crosstalk of gut microbial and host metabolism. Our study will provide not only new insight into the gut microbiota-metabolism-phenotype axis, but also strong support for the promotion and application of rice-fish symbiosis in aquaculture.
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Affiliation(s)
- Erlong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- Northwest A&F University Shenzhen Research Institute, Shenzhen, 518000, Guangdong, China.
| | - Ya Zhou
- Chongqing Three Gorges Vocational College, Chongqing, 404155, China.
| | - Yue Liang
- Department of Chemical Engineering, Auburn University, Auburn, AL, 36849, USA
| | - Fei Ling
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaoshu Xue
- Chongqing Three Gorges Vocational College, Chongqing, 404155, China
| | - Xianlin He
- Chongqing Three Gorges Vocational College, Chongqing, 404155, China
| | - Xuliang Zhai
- Chongqing Fisheries Technical Extension Center, Chongqing, 401121, China
| | - Yang Xue
- Chongqing Fisheries Technical Extension Center, Chongqing, 401121, China
| | - Chunlong Zhou
- Chongqing Fisheries Technical Extension Center, Chongqing, 401121, China
| | - Guo Tang
- Chongqing Three Gorges Vocational College, Chongqing, 404155, China
| | - Gaoxue Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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11
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Arunrat N, Sansupa C, Kongsurakan P, Sereenonchai S, Hatano R. Soil Microbial Diversity and Community Composition in Rice-Fish Co-Culture and Rice Monoculture Farming System. BIOLOGY 2022; 11:biology11081242. [PMID: 36009869 PMCID: PMC9404718 DOI: 10.3390/biology11081242] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 12/20/2022]
Abstract
Simple Summary The integration of fish in rice fields can influence the diversity and structural composition of soil microbial communities. Therefore, soil microorganisms between rice–fish co-culture (RF) and rice monoculture (MC) were compared. The key findings revealed that Actinobacteria, Chloroflexi, Proteobacteria, Acidobacteria, and Planctomycetes were the most dominant taxa across both paddy fields. The most abundant genus in MC belonged to Anaeromyxobacter, whereas that in RF was Bacillus. Nitrogen fixation, aromatic compound degradation, and hydrocarbon degradation were more abundant in RF. Phosphatase, β-glucosidase, cellulase, and urease enzymes were detected in both paddy fields. However, a 2-year conversion from organic rice to rice–fish co-culture may not be long enough to significantly alter alpha diversity indices. Abstract Soil microorganisms play an important role in determining nutrient cycling. The integration of fish into rice fields can influence the diversity and structural composition of soil microbial communities. However, regarding the rice–fish co-culture (RF) farming system in Thailand, the study of the diversity and composition of soil microbes is still limited. Here, we aim to compare the microbial diversity, community composition, and functional structure of the bacterial communities between RF and rice monoculture (MC) farming systems and identify the environmental factors shaping bacterial community composition. Bacterial taxonomy was observed using 16s rRNA gene amplicon sequencing, and the functional structures of the bacterial communities were predicted based on their taxonomy and sequences. The results showed that soil organic carbon, total nitrogen (TN), organic matter, available phosphorous, and clay content were significantly higher in RF than in MC. The most dominant taxa across both paddy rice fields belonged to Actinobacteria, Chloroflexi, Proteobacteria, Acidobacteria, and Planctomycetes. The taxa Nitrosporae, Rokubacteria, GAL15, and Elusimicrobia were significantly different between both rice fields. At the genus level, Bacillus, Anaeromyxobacter, and HSB OF53-F07 were the predominant genera in both rice fields. The most abundant genus in MC was Anaeromyxobacter, whereas RF belonged to Bacillus. The community composition in MC was positively correlated with magnesium and sand content, while in RF was positively correlated with pH, TN, and clay content. Nitrogen fixation, aromatic compound degradation, and hydrocarbon degradation were more abundant in RF, while cellulolysis, nitrification, ureolysis, and phototrophy functional groups were more abundant in MC. The enzymes involved in paddy soil ecosystems included phosphatase, β-glucosidase, cellulase, and urease. These results provide novel insights into integrated fish in the paddy field as an efficient agricultural development strategy for enhancing soil microorganisms that increase soil fertility.
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Affiliation(s)
- Noppol Arunrat
- Faculty of Environment and Resource Studies, Mahidol University, Nakhon Pathom 73170, Thailand
- Correspondence:
| | - Chakriya Sansupa
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Praeploy Kongsurakan
- Graduate School of Fisheries Science and Environmental Studies, Nagasaki University, 1–14 Bunkyo-machi, Nagasaki 852–8521, Japan
| | - Sukanya Sereenonchai
- Faculty of Environment and Resource Studies, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Ryusuke Hatano
- Laboratory of Soil Science, Research Faculty of Agriculture, Hokkaido University, Sapporo 060–8589, Japan
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