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Zhao J, Liu X, Hou L, Xu G, Guan F, Zhang W, Luo H, Wu N, Yao B, Zhang C, Delaplace P, Tian J. The seed endophytic microbe Microbacterium testaceum M15 enhances the cold tolerance and growth of rice (Oryza sativa L.). Microbiol Res 2024; 289:127908. [PMID: 39321593 DOI: 10.1016/j.micres.2024.127908] [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: 07/15/2024] [Revised: 09/01/2024] [Accepted: 09/12/2024] [Indexed: 09/27/2024]
Abstract
The potential of seed endophytic microbes to enhance plant growth and resilience is well recognized, yet their role in alleviating cold stress in rice remains underexplored due to the complexity of these microbial communities. In this study, we investigated the diversity of seed endophytic microbes in two rice varieties, the cold-sensitive CB9 and the cold-tolerant JG117. Our results revealed significant differences in the abundance of Microbacteriaceae, with JG117 exhibiting a higher abundance under both cold stress and room temperature conditions compared to CB9. Further analysis led to the identification of a specific cold-tolerant microbe, Microbacterium testaceum M15, in JG117 seeds. M15-inoculated CB9 plants showed enhanced growth and cold tolerance, with a germination rate increase from 40 % to 56.67 % at 14℃ and a survival rate under cold stress (4℃) doubling from 22.67 % to 66.67 %. Additionally, M15 significantly boosted chlorophyll content by over 30 %, increased total protein by 16.31 %, reduced malondialdehyde (MDA) levels by 37.76 %, and increased catalase activity by 26.15 %. Overall, our study highlights the potential of beneficial endophytic microbes like M. testaceum M15 in improving cold tolerance in rice, which could have implications for sustainable agricultural practices and increased crop productivity in cold-prone regions.
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Affiliation(s)
- Jintong Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Gembloux Agro-Bio Tech, University of Liege, TERRA - Teaching & Research Center, Plant Sciences, Gembloux 5030, Belgium; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoqing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ligang Hou
- Rice Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, Jilin 136100, China
| | - Guoshun Xu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Feifei Guan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huiying Luo
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ningfeng Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Bin Yao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya 572000, China
| | - Pierre Delaplace
- Gembloux Agro-Bio Tech, University of Liege, TERRA - Teaching & Research Center, Plant Sciences, Gembloux 5030, Belgium
| | - Jian Tian
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Tyagi A, Ali S, Mir RA, Sharma S, Arpita K, Almalki MA, Mir ZA. Uncovering the effect of waterlogging stress on plant microbiome and disease development: current knowledge and future perspectives. FRONTIERS IN PLANT SCIENCE 2024; 15:1407789. [PMID: 38903424 PMCID: PMC11187287 DOI: 10.3389/fpls.2024.1407789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/16/2024] [Indexed: 06/22/2024]
Abstract
Waterlogging is a constant threat to crop productivity and ecological biodiversity. Plants face multiple challenges during waterlogging stress like metabolic reprogramming, hypoxia, nutritional depletion, reduction in gaseous exchange, pH modifications, microbiome alterations and disease promotion all of which threaten plants survival. Due to global warming and climatic change, the occurrence, frequency and severity of flooding has dramatically increased posing a severe threat to food security. Thus, developing innovative crop management technologies is critical for ensuring food security under changing climatic conditions. At present, the top priority among scientists is to find nature-based solutions to tackle abiotic or biotic stressors in sustainable agriculture in order to reduce climate change hazards to the environment. In this regard, utilizing plant beneficial microbiome is one of the viable nature based remedial tool for mitigating abiotic stressors like waterlogging. Beneficial microbiota provides plants multifaceted benefits which improves their growth and stress resilience. Plants recruit unique microbial communities to shield themselves against the deleterious effects of biotic and abiotic stress. In comparison to other stressors, there has been limited studies on how waterlogging stress affects plant microbiome structure and their functional traits. Therefore, it is important to understand and explore how waterlogging alters plant microbiome structure and its implications on plant survival. Here, we discussed the effect of waterlogging stress in plants and its microbiome. We also highlighted how waterlogging stress promotes pathogen occurrence and disease development in plants. Finally, we highlight the knowledge gaps and areas for future research directions on unwiring how waterlogging affects plant microbiome and its functional traits. This will pave the way for identifying resilient microbiota that can be engineered to promote their positive interactions with plants during waterlogging stress.
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Affiliation(s)
- Anshika Tyagi
- Department of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
| | - Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
| | - Rakeeb Ahmad Mir
- Department of Biotechnology, School of Life Sciences, Central University of Kashmir, Ganderbal, Jammu and Kashmir, India
| | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Kumari Arpita
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Mohammed A. Almalki
- Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Zahoor Ahmad Mir
- Department of Plant Science and Agriculture, University of Manitoba, Winnipeg, MB, Canada
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Zhao J, Yu X, Zhang C, Hou L, Wu N, Zhang W, Wang Y, Yao B, Delaplace P, Tian J. Harnessing microbial interactions with rice: Strategies for abiotic stress alleviation in the face of environmental challenges and climate change. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168847. [PMID: 38036127 DOI: 10.1016/j.scitotenv.2023.168847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Abstract
Rice, which feeds more than half of the world's population, confronts significant challenges due to environmental and climatic changes. Abiotic stressors such as extreme temperatures, drought, heavy metals, organic pollutants, and salinity disrupt its cellular balance, impair photosynthetic efficiency, and degrade grain quality. Beneficial microorganisms from rice and soil microbiomes have emerged as crucial in enhancing rice's tolerance to these stresses. This review delves into the multifaceted impacts of these abiotic stressors on rice growth, exploring the origins of the interacting microorganisms and the intricate dynamics between rice-associated and soil microbiomes. We highlight their synergistic roles in mitigating rice's abiotic stresses and outline rice's strategies for recruiting these microorganisms under various environmental conditions, including the development of techniques to maximize their benefits. Through an in-depth analysis, we shed light on the multifarious mechanisms through which microorganisms fortify rice resilience, such as modulation of antioxidant enzymes, enhanced nutrient uptake, plant hormone adjustments, exopolysaccharide secretion, and strategic gene expression regulation, emphasizing the objective of leveraging microorganisms to boost rice's stress tolerance. The review also recognizes the growing prominence of microbial inoculants in modern rice cultivation for their eco-friendliness and sustainability. We discuss ongoing efforts to optimize these inoculants, providing insights into the rigorous processes involved in their formulation and strategic deployment. In conclusion, this review emphasizes the importance of microbial interventions in bolstering rice agriculture and ensuring its resilience in the face of rising environmental challenges.
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Affiliation(s)
- Jintong Zhao
- Gembloux Agro-Bio Tech, University of Liege, TERRA - Teaching & Research Center, Plant Sciences, 5030 Gembloux, Belgium; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoxia Yu
- School of Water Resources & Environmental Engineering, East China University of Technology, Nanchang, Jiangxi 330000, China
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Sanya Institute, Hainan, Academy of Agricultural Sciences, Sanya 572000, China
| | - Ligang Hou
- Rice Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, Jilin 136100, China
| | - Ningfeng Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuan Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Pierre Delaplace
- Gembloux Agro-Bio Tech, University of Liege, TERRA - Teaching & Research Center, Plant Sciences, 5030 Gembloux, Belgium
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Han B, Yang F, Shen S, Mu M, Zhang K. Effects of soil habitat changes on antibiotic resistance genes and related microbiomes in paddy fields. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 895:165109. [PMID: 37385504 DOI: 10.1016/j.scitotenv.2023.165109] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/22/2023] [Accepted: 06/22/2023] [Indexed: 07/01/2023]
Abstract
The changes of paddy soil habitat profoundly affect the structure and function of soil microorganisms, but how this process drives the growth and spread of manure- derived antibiotic resistance genes (ARGs) after entering the soil is unclear. Herein, this study explored the environmental fate and behavior of various ARGs in the paddy soil during rice growth period. Results showed that most ARG abundances in flooded soil was lower than that in non-flooded soil during rice growth (decreased by 33.4 %). And soil dry-wet alternation altered microbial community structure in paddy field (P < 0.05), showing that Actinobacteria and Firmicutes increased in proportion under non-flooded conditions, and Chloroflexi, Proteobacteria and Acidobacteria evolved into the dominant groups in flooded soil. Meanwhile, the correlation between ARGs and bacterial communities was stronger than that with mobile genetic elements (MGEs) in both flooded and non-flooded paddy soils. Furthermore, soil properties, especially oxidation reduction potential (ORP), were proved to be an essential factor in regulating the variability of ARGs in the whole rice growth stage by structural equation model, with a direct influence (λ = 0.38, P < 0.05), following by similar effects of bacterial communities and MGEs (λ = 0.36, P < 0.05; λ = 0.29, P < 0.05). This study demonstrated that soil dry-wet alternation effectively reduced the proliferation and dissemination of most ARGs in paddy fields, providing a novel agronomic measure for pollution control of antibiotic resistance in farmland ecosystem.
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Affiliation(s)
- Bingjun Han
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China
| | - Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China.
| | - Shizhou Shen
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China; Dali, Yunnan, Agro-Ecosystem, National Observation and Research Station, Dali, China
| | - Meirui Mu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China
| | - Keqiang Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China; Dali, Yunnan, Agro-Ecosystem, National Observation and Research Station, Dali, China.
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Michl K, Berg G, Cernava T. The microbiome of cereal plants: The current state of knowledge and the potential for future applications. ENVIRONMENTAL MICROBIOME 2023; 18:28. [PMID: 37004087 PMCID: PMC10064690 DOI: 10.1186/s40793-023-00484-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
The plant microbiota fulfils various crucial functions related to host health, fitness, and productivity. Over the past years, the number of plant microbiome studies continued to steadily increase. Technological advancements not only allow us to produce constantly increasing datasets, but also to extract more information from them in order to advance our understanding of plant-microbe interactions. The growing knowledge base has an enormous potential to improve microbiome-based, sustainable agricultural practices, which are currently poorly understood and have yet to be further developed. Cereal plants are staple foods for a large proportion of the world's population and are therefore often implemented in microbiome studies. In the present review, we conducted extensive literature research to reflect the current state of knowledge in terms of the microbiome of the four most commonly cultivated cereal plants. We found that currently the majority of available studies are targeting the wheat microbiome, which is closely followed by studies on maize and rice. There is a substantial gap, in terms of published studies, addressing the barley microbiome. Overall, the focus of most microbiome studies on cereal plants is on the below-ground microbial communities, and there is more research on bacteria than on fungi and archaea. A meta-analysis conducted in the frame of this review highlights microbiome similarities across different cereal plants. Our review also provides an outlook on how the plant microbiota could be harnessed to improve sustainability of cereal crop production.
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Affiliation(s)
- Kristina Michl
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010 Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010 Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469 Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Golm, OT Germany
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010 Austria
- School of Biological Sciences, Faculty of Environmental and Life Sciences, Southampton, SO17 1BJ UK
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Martínez‐Arias C, Witzell J, Solla A, Martin JA, Rodríguez‐Calcerrada J. Beneficial and pathogenic plant-microbe interactions during flooding stress. PLANT, CELL & ENVIRONMENT 2022; 45:2875-2897. [PMID: 35864739 PMCID: PMC9543564 DOI: 10.1111/pce.14403] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 05/29/2023]
Abstract
The number and intensity of flood events will likely increase in the future, raising the risk of flooding stress in terrestrial plants. Understanding flood effects on plant physiology and plant-associated microbes is key to alleviate flooding stress in sensitive species and ecosystems. Reduced oxygen supply is the main constrain to the plant and its associated microbiome. Hypoxic conditions hamper root aerobic respiration and, consequently, hydraulic conductance, nutrient uptake, and plant growth and development. Hypoxia favours the presence of anaerobic microbes in the rhizosphere and roots with potential negative effects to the plant due to their pathogenic behaviour or their soil denitrification ability. Moreover, plant physiological and metabolic changes induced by flooding stress may also cause dysbiotic changes in endosphere and rhizosphere microbial composition. The negative effects of flooding stress on the holobiont (i.e., the host plant and its associated microbiome) can be mitigated once the plant displays adaptive responses to increase oxygen uptake. Stress relief could also arise from the positive effect of certain beneficial microbes, such as mycorrhiza or dark septate endophytes. More research is needed to explore the spiralling, feedback flood responses of plant and microbes if we want to promote plant flood tolerance from a holobiont perspective.
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Affiliation(s)
- Clara Martínez‐Arias
- Departamento de Sistemas y Recursos Naturales, Escuela Técnica Superior de Ingeniería de Montes, Forestal y del Medio NaturalUniversidad Politécnica de MadridMadridSpain
| | - Johanna Witzell
- Department of Forestry and Wood TechnologyLinnaeus UniversityVäxjöSweden
| | - Alejandro Solla
- Faculty of Forestry, Institute for Dehesa Research (INDEHESA)Universidad de ExtremaduraPlasenciaSpain
| | - Juan Antonio Martin
- Departamento de Sistemas y Recursos Naturales, Escuela Técnica Superior de Ingeniería de Montes, Forestal y del Medio NaturalUniversidad Politécnica de MadridMadridSpain
| | - Jesús Rodríguez‐Calcerrada
- Departamento de Sistemas y Recursos Naturales, Escuela Técnica Superior de Ingeniería de Montes, Forestal y del Medio NaturalUniversidad Politécnica de MadridMadridSpain
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Wang Q, Liu Y, Su Y, Cheng C, Shang B, Agathokleous E, Feng Z. Effects of elevated ozone on bacterial communities inhabiting the phyllo- and endo-spheres of rice plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154705. [PMID: 35318051 DOI: 10.1016/j.scitotenv.2022.154705] [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: 01/08/2022] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
To explore the effects of elevated ozone (O3) on microbial communities inhabiting phyllo- and endo-spheres of Japonica rice leaves, cultivars Nangeng 5055 (NG5055) and Wuyujing 27 (WYJ27) were grown in either charcoal-filtered air (CF) or elevated O3 (ambient O3 + 40 ppb, E-O3) in field open-top chambers (OTCs) during a growing season. E-O3 increased the values of the Shannon (43-80%) and Simpson (34-51%) indexes of the phyllo-and endo-spheric bacterial communities in NG5055. E-O3 also increased the values of the phyllosphere Simpson index by 58% and the endosphere Shannon index by 54% in WYJ27. Both diversity indexes positively correlated with the contents of nitrogen, phosphorus, magnesium, and soluble sugar, and negatively correlated with the contents of starch and condensed tannins. The leaf-associated bacterial community composition significantly changed in both rice cultivars under E-O3. Moreover, the leaf-associated bacterial communities in NG5055 were more sensitive to E-O3 than those in WYJ27. The chemical properties explained 70% and 98% of variations in the phyllosphere and endosphere bacterial communities, respectively, suggesting a predominant role of chemical status for the endospheric bacterial community. Most variation (57.3%) in the endosphere bacterial community assembly was explained by phosphorus. Gammaproteobacteria and Pantoea were found to be the most abundant class (63-76%) and genus (38-48%) in the phyllosphere and endosphere, respectively. E-O3 significantly increased the relative abundance of Bacteroidetes in the phyllosphere bacterial community and decreased the relative abundance of Gammaproteobacteria in the endophytic community. In conclusion, elevated O3 increased the diversity of bacterial communities of leaf phyllosphere and endosphere, and leaf chemical properties had a more pronounced effect on the endosphere bacterial community.
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Affiliation(s)
- Qi Wang
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Yuanyuan Liu
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Yi Su
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Cheng Cheng
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Bo Shang
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Evgenios Agathokleous
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Zhaozhong Feng
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China.
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Wang Y, Li X, Chi Y, Song W, Yan Q, Huang J. Changes of the Freshwater Microbial Community Structure and Assembly Processes during Different Sample Storage Conditions. Microorganisms 2022; 10:1176. [PMID: 35744694 PMCID: PMC9229623 DOI: 10.3390/microorganisms10061176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/02/2022] [Accepted: 06/06/2022] [Indexed: 12/04/2022] Open
Abstract
A long-standing dilemma for microbial analyses is how to handle and store samples, as it is widely assumed that the microbial diversity and community patterns would be affected by sample storage conditions. However, it is quite challenging to maintain consistency in field sampling, especially for water sample collection and storage. To obtain a comprehensive understanding of how sample storage conditions impact microbial community analyses and the magnitude of the potential storage effects, freshwater samples were collected and stored in bottles with lid closed and without lid at room temperature for up to 6 days. We revealed the dynamics of prokaryotic and eukaryotic microbial communities under different storage conditions over time. The eukaryotic microbial communities changed at a faster rate than the prokaryotic microbial communities during storage. The alpha diversity of the eukaryotic microbial communities was not substantially influenced by container status or storage time for up to 12 h, but the beta diversity differed significantly between the control and all treatment samples. By contrast, no significant changes of either the alpha or beta diversity of the prokaryotic microbial communities were observed within 12 h of room-temperature storage, regardless of the container status. The potential interactions between microbial taxa were more complex when samples were stored in sealed bottles, and the deterministic processes played an increasingly important role in shaping the freshwater microbial communities with storage time. Our results suggest that water samples collected and stored without refrigeration for no more than 12 h may still be useful for downstream analyses of prokaryotic microbial communities. If the eukaryotic microbial communities are desired, storage of water samples should be limited to 3 h at room temperature.
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Affiliation(s)
- Yunfeng Wang
- Institute of Evolution & Marine Biodiversity, College of Fisheries, Ocean University of China, Qingdao 266003, China; (Y.W.); (Y.C.); (W.S.)
- Donghu Experimental Station of Lake Ecosystems, Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xinghao Li
- Key Laboratory of Regional Development and Environmental Response, Hubei Engineering Research Center for Rural Drinking Water Security, Hubei University, Wuhan 430062, China;
| | - Yong Chi
- Institute of Evolution & Marine Biodiversity, College of Fisheries, Ocean University of China, Qingdao 266003, China; (Y.W.); (Y.C.); (W.S.)
- Donghu Experimental Station of Lake Ecosystems, Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Weibo Song
- Institute of Evolution & Marine Biodiversity, College of Fisheries, Ocean University of China, Qingdao 266003, China; (Y.W.); (Y.C.); (W.S.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China;
| | - Jie Huang
- Donghu Experimental Station of Lake Ecosystems, Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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Hernández I, Taulé C, Pérez-Pérez R, Battistoni F, Fabiano E, Rivero D, Nápoles MC. Endophytic rhizobia promote the growth of Cuban rice cultivar. Symbiosis 2021. [DOI: 10.1007/s13199-021-00803-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Chialva M, Ghignone S, Cozzi P, Lazzari B, Bonfante P, Abbruscato P, Lumini E. Water management and phenology influence the root-associated rice field microbiota. FEMS Microbiol Ecol 2020; 96:5877241. [DOI: 10.1093/femsec/fiaa146] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 07/21/2020] [Indexed: 12/14/2022] Open
Abstract
ABSTRACTMicrobial communities associated with plants are greatly influenced by water availability in soil. In flooded crops, such as rice, the impact of water management on microbial dynamics is not fully understood. Here, we present a comprehensive study of the rice microbiota investigated in an experimental field located in one of the most productive areas of northern Italy. The microbiota associated with paddy soil and root was investigated using 454 pyrosequencing of 16S, ITS and 18S rRNA gene amplicons under two different water managements, upland (non-flooded, aerobic) and lowland (traditional flooding, anaerobic), at three plant development stages. Results highlighted a major role of the soil water status in shaping microbial communities, while phenological stage had low impacts. Compositional shifts in prokaryotic and fungal communities upon water management consisted in significant abundance changes of Firmicutes, Methanobacteria, Chloroflexi, Sordariomycetes, Dothideomycetes and Glomeromycotina. A vicariance in plant beneficial microbes and between saprotrophs and pathotrophs was observed between lowland and upland. Moreover, through network analysis, we demonstrated different co-abundance dynamics between lowland and upland conditions with a major impact on microbial hubs (strongly interconnected microbes) that fully shifted to aerobic microbes in the absence of flooding.
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Affiliation(s)
- Matteo Chialva
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, I-10125 Torino, Italy
| | - Stefano Ghignone
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Viale P.A. Mattioli 25, I-10125 Torino, Italy
| | - Paolo Cozzi
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Via E. Bassini 15/Via A. Corti 12, I-20133 Milano, Italy
| | - Barbara Lazzari
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Via E. Bassini 15/Via A. Corti 12, I-20133 Milano, Italy
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, I-10125 Torino, Italy
| | - Pamela Abbruscato
- Rice Genomics Unit, PTP Science Park, Via Einstein Loc. Cascina Codazza, I-26900 Lodi, Italy
| | - Erica Lumini
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Viale P.A. Mattioli 25, I-10125 Torino, Italy
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