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Applications and Prospects of CRISPR/Cas9-Mediated Base Editing in Plant Breeding. Curr Issues Mol Biol 2023; 45:918-935. [PMID: 36826004 PMCID: PMC9955079 DOI: 10.3390/cimb45020059] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/10/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 system (Cas9) has been used at length to optimize multiple aspects of germplasm resources. However, large-scale genomic research has indicated that novel variations in crop plants are attributed to single-nucleotide polymorphisms (SNPs). Therefore, substituting single bases into a plant genome may produce desirable traits. Gene editing by CRISPR/Cas9 techniques frequently results in insertions-deletions (indels). Base editing allows precise single-nucleotide changes in the genome in the absence of double-strand breaks (DSBs) and donor repair templates (DRTs). Therefore, BEs have provided a new way of thinking about genome editing, and base editing techniques are currently being utilized to edit the genomes of many different organisms. As traditional breeding techniques and modern molecular breeding technologies complement each other, various genome editing technologies have emerged. How to realize the greater potential of BE applications is the question we need to consider. Here, we explain various base editings such as CBEs, ABEs, and CGBEs. In addition, the latest applications of base editing technologies in agriculture are summarized, including crop yield, quality, disease, and herbicide resistance. Finally, the challenges and future prospects of base editing technologies are presented. The aim is to provide a comprehensive overview of the application of BE in crop breeding to further improve BE and make the most of its value.
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Wang P, Liu J, Han S, Wang Y, Duan Y, Liu T, Hou L, Zhang Z, Li L, Lin Y. Polyethylene mulching film degrading bacteria within the plastisphere: Co-culture of plastic degrading strains screened by bacterial community succession. JOURNAL OF HAZARDOUS MATERIALS 2023; 442:130045. [PMID: 36162306 DOI: 10.1016/j.jhazmat.2022.130045] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
As an ecological niche close to the polymer, microorganisms in the plastisphere possess the advantage of degrading plastics. This study aims to investigate the bacterial community succession and obtain degrading bacteria in the plastisphere, as well as identify the most efficient degradation combination by co-culture of multiple strains. The findings demonstrate the alpha-diversity indices of the plastisphere bacterial community are significantly lower, and the community structure is regularly and significantly altered. With the time of culture, the plastisphere community composition alters regularly, and the hydrocarbon-degrading genera become the core members. Functional prediction of community reveals the potential for Xenobiotics Biodegradation and Metabolism of plastisphere, and the apparent variations detections of polyethylene mulching film (PMF) indicating the PMF degrading ability of plastisphere. Besides, three PMF-degrading bacterial strains, Rhodopseudomonas sp. P1 (P), Rhodanobacter sp. Rs (R) and Microbacterium sp. M1 (M), are screened for co-culture with PMF degrading strain Bacillus aryabhattai 5-3 (B). By considering bacterial growth, biofilm adhesion, and apparent degradation of different samples, RB (R. sp. Rs + B. aryabhattai 5-3) is ultimately selected as the best PMF degradation combination. This study provides a new possibility for plastisphere-related research from the perspective of mitigating plastic pollution on agricultural land.
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Affiliation(s)
- Peiyuan Wang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Jiaxi Liu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Siqi Han
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Yufan Wang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Yifan Duan
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Tingting Liu
- College of Science, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Lijun Hou
- Department of Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, Quebec H9X 3V9, Canada
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Yanbing Lin
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, PR China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China.
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153
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Ji Y, Yue L, Cao X, Chen F, Li J, Zhang J, Wang C, Wang Z, Xing B. Carbon dots promoted soybean photosynthesis and amino acid biosynthesis under drought stress: Reactive oxygen species scavenging and nitrogen metabolism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159125. [PMID: 36181808 DOI: 10.1016/j.scitotenv.2022.159125] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/23/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023]
Abstract
With global warming and water scarcity, improving the drought tolerance and quality of crops is critical for food security and human health. Here, foliar application of carbon dots (CDs, 5 mg·L-1) could scavenge reactive oxygen species accumulation in soybean leaves under drought stress, thereby enhancing photosynthesis and carbohydrate transport. Moreover, CDs stimulated root secretion (e.g., amino acids, organic acids, and auxins) and recruited beneficial microorganisms (e.g., Actinobacteria, Ascomycota, Acidobacteria and Glomeromycota), which facilitate nitrogen (N) activation in the soil. Meanwhile, the expression of GmNRT, GmAMT, and GmAQP genes were up-regulated, indicating enhanced N and water uptake. The results demonstrated that CDs could promote nitrogen metabolism and enhance amino acid biosynthesis. Particularly, the N content in soybean shoots and roots increased significantly by 13.2 % and 30.5 %, respectively. The amino acids content in soybean shoots and roots increased by 257.5 % and 57.5 %, respectively. Consequently, soybean yields increased significantly by 21.5 %, and the protein content in soybean kernels improved by 3.7 %. Therefore, foliar application of CDs can support sustainable nano-enabled agriculture to combat climate change.
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Affiliation(s)
- Yahui Ji
- Institute of Environmental Processes and Pollution Control, School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Le Yue
- Institute of Environmental Processes and Pollution Control, School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xuesong Cao
- Institute of Environmental Processes and Pollution Control, School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Feiran Chen
- Institute of Environmental Processes and Pollution Control, School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jing Li
- Institute of Environmental Processes and Pollution Control, School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jiangshan Zhang
- Institute of Environmental Processes and Pollution Control, School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Chuanxi Wang
- Institute of Environmental Processes and Pollution Control, School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, USA
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154
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Functional Endophytes Regulating Plant Secondary Metabolism: Current Status, Prospects and Applications. Int J Mol Sci 2023; 24:ijms24021153. [PMID: 36674663 PMCID: PMC9867233 DOI: 10.3390/ijms24021153] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 01/11/2023] Open
Abstract
Endophytes, which are widely found in host plants and have no harmful effects, are a vital biological resource. Plant endophytes promote plant growth and enhance plants' resistance to diseases, pests, and environmental stresses. In addition, they enhance the synthesis of important secondary metabolites in plants and improve the potential applicability of plants in agriculture, medicine, food, and horticulture. In this review, we summarize the recent progress in understanding the interaction between endophytes and plants and summarize the construction of synthetic microbial communities (SynComs) and metaomics analysis of the interaction between endophytes and plants. The application and development prospects of endophytes in agriculture, medicine, and other industries are also discussed to provide a reference for further study of the interaction between endophytes and plants and further development and utilization of endophytes.
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155
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Hu B, Wang W, Chen J, Liu Y, Chu C. Genetic improvement toward nitrogen-use efficiency in rice: Lessons and perspectives. MOLECULAR PLANT 2023; 16:64-74. [PMID: 36380584 DOI: 10.1016/j.molp.2022.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/08/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
The indispensable role of nitrogen fertilizer in ensuring world food security together with the severe threats it poses to the ecosystem makes the usage of nitrogen fertilizer a major challenge for sustainable agriculture. Genetic improvement of crops with high nitrogen-use efficiency (NUE) is one of the most feasible solutions for tackling this challenge. In the last two decades, extensive efforts toward dissecting the variation of NUE-related traits and the underlying genetic basis in different germplasms have been made, and a series of achievements have been obtained in crops, especially in rice. Here, we summarize the approaches used for genetic dissection of NUE and the functions of the causal genes in modulating NUE as well as their applications in NUE improvement in rice. Strategies for exploring the variants controlling NUE and breeding future crops with "less-input-more-output" for sustainable agriculture are also proposed.
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Affiliation(s)
- Bin Hu
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, 510642, Guangzhou, China.
| | - Wei Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, 510642, Guangzhou, China
| | - Jiajun Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Yongqiang Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengcai Chu
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, 510642, Guangzhou, China.
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156
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Zhang S, Sun C, Liu X, Liang Y. Enriching the endophytic bacterial microbiota of Ginkgo roots. Front Microbiol 2023; 14:1163488. [PMID: 37138610 PMCID: PMC10150934 DOI: 10.3389/fmicb.2023.1163488] [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: 02/10/2023] [Accepted: 03/20/2023] [Indexed: 05/05/2023] Open
Abstract
Bacterial endophytes of Ginkgo roots take part in the secondary metabolic processes of the fossil tree and contribute to plant growth, nutrient uptake, and systemic resistance. However, the diversity of bacterial endophytes in Ginkgo roots is highly underestimated due to the lack of successful isolates and enrichment collections. The resulting culture collection contains 455 unique bacterial isolates representing 8 classes, 20 orders, 42 families, and 67 genera from five phyla: Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Deinococcus-Thermus, using simply modified media (a mixed medium without any additional carbon sources [MM)] and two other mixed media with separately added starch [GM] and supplemented glucose [MSM]). A series of plant growth-promoting endophytes had multiple representatives within the culture collection. Moreover, we investigated the impact of refilling carbon sources on enrichment outcomes. Approximately 77% of the natural community of root-associated endophytes were predicted to have successfully cultivated the possibility based on a comparison of the 16S rRNA gene sequences between the enrichment collections and the Ginkgo root endophyte community. The rare or recalcitrant taxa in the root endosphere were mainly associated with Actinobacteria, Alphaproteobacteria, Blastocatellia, and Ktedonobacteria. By contrast, more operational taxonomic units (OTUs) (0.6% in the root endosphere) became significantly enriched in MM than in GM and MSM. We further found that the bacterial taxa of the root endosphere had strong metabolisms with the representative of aerobic chemoheterotrophy, while the functions of the enrichment collections were represented by the sulfur metabolism. In addition, the co-occurrence network analysis suggested that the substrate supplement could significantly impact bacterial interactions within the enrichment collections. Our results support the fact that it is better to use the enrichment to assess the cultivable potential and the interspecies interaction as well as to increase the detection/isolation of certain bacterial taxa. Taken together, this study will deepen our knowledge of the indoor endophytic culture and provide important insights into the substrate-driven enrichment.
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Affiliation(s)
- Shuangfei Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, Hunan, China
| | - Chongran Sun
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, Hunan, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, Hunan, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, Hunan, China
- *Correspondence: Yili Liang
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157
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Shen Q, Fu W, Chen B, Zhang X, Xing S, Ji C, Zhang X. Community response of soil microorganisms to combined contamination of polycyclic aromatic hydrocarbons and potentially toxic elements in a typical coking plant. Front Microbiol 2023; 14:1143742. [PMID: 36950156 PMCID: PMC10025358 DOI: 10.3389/fmicb.2023.1143742] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/07/2023] [Indexed: 03/08/2023] Open
Abstract
Both polycyclic aromatic hydrocarbons (PAHs) and potentially toxic elements (PTEs) of coking industries impose negative effects on the stability of soil ecosystem. Soil microbes are regarded as an essential moderator of biochemical processes and soil remediation, while their responses to PAHs-PTEs combined contamination are largely unknown. In the present study, soil microbial diversity and community composition in the typical coking plant under the chronic co-exposure of PAHs and PTEs were investigated and microbial interaction networks were built to reveal microbial co-occurrence patterns. The results indicated that the concentrations of PAHs in the soil inside the coking plant were significantly higher than those outside the plant. The mean concentration of ∑16PAHs was 2894.4 ng·g-1, which is 5.58 times higher than that outside the plant. The average Hg concentration inside the coking plant was 22 times higher than the background value of Hebei province. The soil fungal community inside the coking plant showed lower richness compared with that of outside community, and there are significant difference in the bacterial and fungal community composition between inside and outside of coking plant (p < 0.01). Predicted contribution of different environmental factors to each dominant species based on random forest identified 20 and 25 biomarkers in bacteria and fungi, respectively, that were highly sensitive to coking plant soil in operation, such as Betaproteobacteria,Sordariomycetes and Dothideomycetes. Bacterial and fungal communities were shaped by the soil chemical properties (pH), PTEs (Hg), and PAHs together in the coking plant soils. Furthermore, the bacterial and fungal interaction patterns were investigated separately or jointly by intradomain and interdomain networks. Competition is the main strategy based on the co-exclusion pattern in fungal community, and the competitive relationship inside the coking plant is more complex than that outside the plant. In contrast, cooperation is the dominant strategy in bacterial networks based on the co-occurrence pattern. The present study provided insights into microbial response strategies and the interactions between bacteria and fungi under long-term combined contamination.
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Affiliation(s)
- Qihui Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Fu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Shuping Xing
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chuning Ji
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Xin Zhang,
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158
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Abstract
The concept of one health highlights that human health is not isolated but connected to the health of animals, plants and environments. In this Review, we demonstrate that soils are a cornerstone of one health and serve as a source and reservoir of pathogens, beneficial microorganisms and the overall microbial diversity in a wide range of organisms and ecosystems. We list more than 40 soil microbiome functions that either directly or indirectly contribute to soil, plant, animal and human health. We identify microorganisms that are shared between different one health compartments and show that soil, plant and human microbiomes are perhaps more interconnected than previously thought. Our Review further evaluates soil microbial contributions to one health in the light of dysbiosis and global change and demonstrates that microbial diversity is generally positively associated with one health. Finally, we present future challenges in one health research and formulate recommendations for practice and evaluation.
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Affiliation(s)
- Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA.
| | - Marcel G A van der Heijden
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland. .,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.
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159
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Ding JYM, Ho LS, Ibrahim J, Teh CK, Goh KM. Impact of sterilization and chemical fertilizer on the microbiota of oil palm seedlings. Front Microbiol 2023; 14:1091755. [PMID: 37180248 PMCID: PMC10172575 DOI: 10.3389/fmicb.2023.1091755] [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: 11/07/2022] [Accepted: 04/11/2023] [Indexed: 05/16/2023] Open
Abstract
Soil nutrients and microbiota are known as essential components for healthy plant growth and crop productivity. However, limited studies have been conducted on the importance of soil microbiota in the early growth of oil palm seedlings (Elaeis guineensis Jacq.) under the influence of nitrogen, phosphorus and potassium (NPK) compound fertilizer (nitrogen, phosphorus, and potassium). In this study, we analyzed the root microbial community associated with seedlings grown under normal and sterilized soil conditions to ascertain the microbial strains potentially associated with soil, plant health and chemical fertilizer efficiency. Oil palm seedlings were grown under four treatments: (i) fertilized normal soil (+FN), (ii) unfertilized normal soil (-FN), (iii) fertilized sterilized soil (+FS) and (iv) unfertilized sterilized soil (-FS). Our findings revealed that chemical fertilizer promoted the growth of the copiotrophs Pseudomonadota and Bacteroidota in the control +FN, which are known to degrade complex polysaccharides. After autoclaving, the soil macronutrient content did not change, but soil sterilization reduced microbial diversity in the +FS and -FS treatments and altered the soil microbiota composition. Sterilized soil with a depleted microbial population adversely affected crop growth, which was exacerbated by fertilizer use. In the rhizosphere and rhizoplane compartments, a total of 412 and 868 amplicon sequence variances (ASVs) were found depleted in the +FS and -FS treatments, respectively. Several genera were identified in the ASVs with diminished abundance, including Humibacter, Microbacterium, Mycobacterium, 1921-2, HSB OF53-F07, Mucilaginibacter, Bacillus, Paenibacillus, and several unclassified genera, suggesting their possible roles in promoting the plant growth of oil palm seedlings. Soil sterilization might remove these beneficial microbes from the bulk soil pool, affecting the colonization ability in the rhizocompartments as well as their role in nutrient transformation. Therefore, this study provides useful insights concerning the benefits of a soil microbiome survey before making fertilizer recommendations.
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Affiliation(s)
- Joyce Yoon Mei Ding
- Biotechnology & Breeding Department, Sime Darby Plantation Technology Centre Sdn. Bhd., Serdang, Selangor, Malaysia
- *Correspondence: Joyce Yoon Mei Ding,
| | - Li Sim Ho
- Biotechnology & Breeding Department, Sime Darby Plantation Technology Centre Sdn. Bhd., Serdang, Selangor, Malaysia
| | - Julia Ibrahim
- Biotechnology & Breeding Department, Sime Darby Plantation Technology Centre Sdn. Bhd., Serdang, Selangor, Malaysia
| | - Chee Keng Teh
- Biotechnology & Breeding Department, Sime Darby Plantation Technology Centre Sdn. Bhd., Serdang, Selangor, Malaysia
| | - Kian Mau Goh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
- Kian Mau Goh,
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160
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Fan W, Tang F, Wang J, Dong J, Xing J, Shi F. Drought-induced recruitment of specific root-associated bacteria enhances adaptation of alfalfa to drought stress. Front Microbiol 2023; 14:1114400. [PMID: 36910228 PMCID: PMC9995459 DOI: 10.3389/fmicb.2023.1114400] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023] Open
Abstract
Drought is a major abiotic stress that threatens crop production. Soil microbiomes are thought to play a role in enhancing plant adaptation to various stresses. However, it remains unclear whether soil microbiomes play a key role when plants are challenged by drought and whether different varieties are enriched with specific bacteria at the rhizosphere. In this study, we measured changes in growth phenotypes, physiological and biochemical characteristics of drought-tolerant alfalfa (AH) and drought-sensitive (QS) under sterilized and unsterilized soil conditions with adequate watering and with drought stress, and analyzed the rhizosphere bacterial community composition and changes using 16S rRNA high-throughput sequencing. We observed that the unsterilized treatment significantly improved the growth, and physiological and biochemical characteristics of alfalfa seedlings under drought stress compared to the sterilized treatment. Under drought stress, the fresh and dry weight of seedlings increased by 35.24, 29.04, and 11.64%, 2.74% for unsterilized AH and QS, respectively, compared to sterilized treatments. The improvement was greater for AH than for QS. AH and QS recruited different rhizosphere bacteria when challenged by drought. Interestingly, under well-watered conditions, the AH rhizosphere was already rich in drought-tolerant bacterial communities, mainly Proteobacteria and Bacteroidetes, whereas these bacteria started to increase only when QS was subjected to drought. When drought stress was applied, AH was enriched with more drought-tolerant bacteria, mainly Acidobacteria, while the enrichment was weaker in QS rhizosphere. Therefore, the increase in drought tolerance of the drought-tolerant variety AH was greater than that of the drought-sensitive variety QS. Overall, this study confirmed the key role of drought-induced rhizosphere bacteria in improving the adaptation of alfalfa to drought stress, and clarified that this process is significantly related to the variety (genotype). The results of this study provide a basis for improving drought tolerance in alfalfa by regulating the rhizosphere microbiome.
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Affiliation(s)
- Wenqiang Fan
- Key Laboratory of Grassland Resources of the Ministry of Education and Key Laboratory of Forage Cultivation, Processing and High-Efficiency Utilization of the Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Fang Tang
- Key Laboratory of Grassland Resources of the Ministry of Education and Key Laboratory of Forage Cultivation, Processing and High-Efficiency Utilization of the Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Jiani Wang
- Key Laboratory of Grassland Resources of the Ministry of Education and Key Laboratory of Forage Cultivation, Processing and High-Efficiency Utilization of the Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Jiaqi Dong
- Key Laboratory of Grassland Resources of the Ministry of Education and Key Laboratory of Forage Cultivation, Processing and High-Efficiency Utilization of the Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Jing Xing
- Key Laboratory of Grassland Resources of the Ministry of Education and Key Laboratory of Forage Cultivation, Processing and High-Efficiency Utilization of the Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Fengling Shi
- Key Laboratory of Grassland Resources of the Ministry of Education and Key Laboratory of Forage Cultivation, Processing and High-Efficiency Utilization of the Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
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161
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Sun Y, Zhao H, Chen Z, Chen H, Li B, Wang C, Lin X, Cai Y, Zhou D, Ouyang L, Zhu C, He H, Peng X. Comparison of the Phenotypic Performance, Molecular Diversity, and Proteomics in Transgenic Rice. PLANTS (BASEL, SWITZERLAND) 2022; 12:156. [PMID: 36616286 PMCID: PMC9824520 DOI: 10.3390/plants12010156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
The extent of molecular diversity and differentially expressed proteins (DEPs) in transgenic lines provide valuable information to understand the phenotypic performance of transgenic crops compared with their parents. Here, we compared the differences in the phenotypic variation of twelve agronomic and end-use quality traits, the extent of microsatellite diversity, and DEPs of a recurrent parent line with three transgenic rice restorer lines carrying either CRY1C gene on chromosome 11 or CRY2A gene on chromosome 12 or both genes. The three transgenic lines had significantly smaller stem borer infestation than the recurrent parent without showing significant differences among most agronomic traits, yield components, and end-use quality traits. Using 512 microsatellite markers, the three transgenic lines inherited 2.9-4.3% of the Minghui 63 donor genome and 96.3-97.1% of the CH891 recurrent parent genome. As compared with the recurrent parent, the number of upregulated and down-regulated proteins in the three transgenic lines varied from 169 to 239 and from 131 to 199, respectively. Most DEPs were associated with the secondary metabolites biosynthesis transport and catabolism, carbohydrate transport and metabolism, post-translational modification, and signal transduction mechanisms. Although several differentially expressed proteins were observed between transgenic rice and its recurrent parent, the differences may not have been associated with grain yield and most other phenotypic traits in transgenic rice.
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Affiliation(s)
- Yue Sun
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Huan Zhao
- Jiangxi Biotech Vocational College, JAU, Nanchang 330200, China
| | - Zhongkai Chen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Huizhen Chen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Bai Li
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Chunlei Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Xiaoli Lin
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Yicong Cai
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Dahu Zhou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Linjuan Ouyang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Changlan Zhu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Xiaosong Peng
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
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162
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Tao S, Yin H, Fang Y, Zhang Y, Zhang N, Qu L. Elevated O 3 concentrations alter the compartment-specific microbial communities inhabiting rust-infected poplars. Environ Microbiol 2022; 25:990-1006. [PMID: 36582119 DOI: 10.1111/1462-2920.16332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/29/2022] [Indexed: 12/31/2022]
Abstract
Elevated ozone (O3 ) can affect the susceptivity of plants to rust pathogens. However, the collective role of microbiomes involved in such interaction remains largely elusive. We exposed two cultivated poplar clones exhibiting differential O3 sensitivities, to non-filtered ambient air (NF), NF + 40 ppb or NF + 60 ppb O3 -enriched air in field open-top chambers and then inoculated Melampsora larici-populina urediniospores to study their response to rust infection and to investigate how microbiomes inhabiting four compartments (phyllosphere, rhizosphere, root endosphere, bulk soil) are involved in this response. We found that hosts with higher O3 sensitivity had significantly lower rust severity than hosts with lower sensitivity. Furthermore, the effect of increased O3 on the diversity and composition of microbial communities was highly dependent on poplar compartments, with the microbial network complexity patterns being completely opposite between the two clones. Notably, microbial source analysis estimated that phyllosphere fungal communities predominately derived from root endosphere and vice versa, suggesting a potential transmission mechanism between plant above- and below-ground systems. These promising results suggest that further investigations are needed to better understand the interactions of abiotic and biotic stresses on plant performance and the role of the microbiome in driving these changes.
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Affiliation(s)
- Siqi Tao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, China.,Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People's Republic of China
| | - Haiyue Yin
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Yue Fang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Yunxia Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Naili Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, China.,Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People's Republic of China
| | - Laiye Qu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Science, Beijing, China
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163
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Kasemsap P, Bloom AJ. Breeding for Higher Yields of Wheat and Rice through Modifying Nitrogen Metabolism. PLANTS (BASEL, SWITZERLAND) 2022; 12:85. [PMID: 36616214 PMCID: PMC9823454 DOI: 10.3390/plants12010085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Wheat and rice produce nutritious grains that provide 32% of the protein in the human diet globally. Here, we examine how genetic modifications to improve assimilation of the inorganic nitrogen forms ammonium and nitrate into protein influence grain yield of these crops. Successful breeding for modified nitrogen metabolism has focused on genes that coordinate nitrogen and carbon metabolism, including those that regulate tillering, heading date, and ammonium assimilation. Gaps in our current understanding include (1) species differences among candidate genes in nitrogen metabolism pathways, (2) the extent to which relative abundance of these nitrogen forms across natural soil environments shape crop responses, and (3) natural variation and genetic architecture of nitrogen-mediated yield improvement. Despite extensive research on the genetics of nitrogen metabolism since the rise of synthetic fertilizers, only a few projects targeting nitrogen pathways have resulted in development of cultivars with higher yields. To continue improving grain yield and quality, breeding strategies need to focus concurrently on both carbon and nitrogen assimilation and consider manipulating genes with smaller effects or that underlie regulatory networks as well as genes directly associated with nitrogen metabolism.
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164
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Zhou X, Wang J, Liu F, Liang J, Zhao P, Tsui CKM, Cai L. Cross-kingdom synthetic microbiota supports tomato suppression of Fusarium wilt disease. Nat Commun 2022; 13:7890. [PMID: 36550095 PMCID: PMC9780251 DOI: 10.1038/s41467-022-35452-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
The role of rhizosphere microbiota in the resistance of tomato plant against soil-borne Fusarium wilt disease (FWD) remains unclear. Here, we showed that the FWD incidence was significantly negatively correlated with the diversity of both rhizosphere bacterial and fungal communities. Using the microbiological culturomic approach, we selected 205 unique strains to construct different synthetic communities (SynComs), which were inoculated into germ-free tomato seedlings, and their roles in suppressing FWD were monitored using omics approach. Cross-kingdom (fungi and bacteria) SynComs were most effective in suppressing FWD than those of Fungal or Bacterial SynComs alone. This effect was underpinned by a combination of molecular mechanisms related to plant immunity and microbial interactions contributed by the bacterial and fungal communities. This study provides new insight into the dynamics of microbiota in pathogen suppression and host immunity interactions. Also, the formulation and manipulation of SynComs for functional complementation constitute a beneficial strategy in controlling soil-borne disease.
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Affiliation(s)
- Xin Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
- University of Chinese Academy of Sciences, 100101, Beijing, P. R. China
| | - Jinting Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
- University of Chinese Academy of Sciences, 100101, Beijing, P. R. China
| | - Fang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Junmin Liang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Peng Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Clement K M Tsui
- Faculty of Medicine, University of British Columbia, Vancouver, Canada
- National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Pathology, Sidra Medicine, Doha, Qatar
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China.
- University of Chinese Academy of Sciences, 100101, Beijing, P. R. China.
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165
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Wang Z, Yang T, Mei X, Wang N, Li X, Yang Q, Dong C, Jiang G, Lin J, Xu Y, Shen Q, Jousset A, Banerjee S. Bio-Organic Fertilizer Promotes Pear Yield by Shaping the Rhizosphere Microbiome Composition and Functions. Microbiol Spectr 2022; 10:e0357222. [PMID: 36453930 PMCID: PMC9769518 DOI: 10.1128/spectrum.03572-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022] Open
Abstract
Bio-organic fertilizers (BOF) containing both organic amendments and beneficial microorganisms have been consistently shown to improve soils fertility and yield. However, the exact mechanisms which link amendments and yields remain disputed, and the complexity of bio-organic fertilizers may work in parallel in several ways. BOF may directly improve yield by replenishing soil nutrients or introducing beneficial microbial genes or indirectly by altering the soil microbiome to enrich native beneficial microorganisms. In this work, we aim to disentangle the relative contributions of direct and indirect effects on pear yield. We treated pear trees with either chemical fertilizer or organic fertilizer with/without the plant-beneficial bacterium Bacillus velezensis SQR9. We then assessed, in detail, soil physicochemical and biological properties (metagenome sequencing) as well as pear yield. We then evaluated the relative importance of direct and indirect effects of soil amendments on pear yield. Both organic treatments increased plant yield by up to 20%, with the addition of bacteria tripling the increase driven by organic fertilizer alone. This increase could be linked to alterations in soil physicochemical properties, bacterial community function, and metabolism. Supplementation of organic fertilizer SQR9 increased rhizosphere microbiome richness and functional diversity. Fertilizer-sensitive microbes and functions responded as whole guilds. Pear yield was most positively associated with the Mitsuaria- and Actinoplanes-dominated ecological clusters and with gene clusters involved in ion transport and secondary metabolite biosynthesis. Together, these results suggested that bio-organic fertilizers mainly act indirectly on plant yield by creating soil chemical properties which promote a plant-beneficial microbiome. IMPORTANCE Bio-organic fertilization is a widely used, eco-friendly, sustainable approach to increasing plant productivity in the agriculture and fruit industries. However, it remains unclear whether the promotion of fruit productivity is related to specific changes in microbial inoculants, the resident microbiome, and/or the physicochemical properties of rhizosphere soils. We found that bio-organic fertilizers alter soil chemical properties, thus manipulating specific microbial taxa and functions within the rhizosphere microbiome of pear plants to promote yield. Our work unveils the ecological mechanisms which underlie the beneficial impacts of bio-organic fertilizers on yield promotion in fruit orchards, which may help in the design of more efficient biofertilizers to promote sustainable fruit production.
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Affiliation(s)
- Zhonghua Wang
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Key Laboratory of Plant immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - Tianjie Yang
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Key Laboratory of Plant immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Xinlan Mei
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Key Laboratory of Plant immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Ningqi Wang
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Key Laboratory of Plant immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Xiaogang Li
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - Qingsong Yang
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - Caixia Dong
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Key Laboratory of Plant immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Gaofei Jiang
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Key Laboratory of Plant immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Jing Lin
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - Yangchun Xu
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Key Laboratory of Plant immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Qirong Shen
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Key Laboratory of Plant immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Alexandre Jousset
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Key Laboratory of Plant immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, North Dakota, USA
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166
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Defining Composition and Function of the Rhizosphere Microbiota of Barley Genotypes Exposed to Growth-Limiting Nitrogen Supplies. mSystems 2022; 7:e0093422. [PMID: 36342125 PMCID: PMC9765016 DOI: 10.1128/msystems.00934-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The microbiota populating the rhizosphere, the interface between roots and soil, can modulate plant growth, development, and health. These microbial communities are not stochastically assembled from the surrounding soil, but their composition and putative function are controlled, at least partially, by the host plant. Here, we use the staple cereal barley as a model to gain novel insights into the impact of differential applications of nitrogen, a rate-limiting step for global crop production, on the host genetic control of the rhizosphere microbiota. Using a high-throughput amplicon sequencing survey, we determined that nitrogen availability for plant uptake is a factor promoting the selective enrichment of individual taxa in the rhizosphere of wild and domesticated barley genotypes. Shotgun sequencing and metagenome-assembled genomes revealed that this taxonomic diversification is mirrored by a functional specialization, manifested by the differential enrichment of multiple Gene Ontology terms, of the microbiota of plants exposed to nitrogen conditions limiting barley growth. Finally, a plant soil feedback experiment revealed that host control of the barley microbiota underpins the assembly of a phylogenetically diverse group of bacteria putatively required to sustain plant performance under nitrogen-limiting supplies. Taken together, our observations indicate that under nitrogen conditions limiting plant growth, host-microbe and microbe-microbe interactions fine-tune the host genetic selection of the barley microbiota at both taxonomic and functional levels. The disruption of these recruitment cues negatively impacts plant growth. IMPORTANCE The microbiota inhabiting the rhizosphere, the thin layer of soil surrounding plant roots, can promote the growth, development, and health of their host plants. Previous research indicated that differences in the genetic composition of the host plant coincide with variations in the composition of the rhizosphere microbiota. This is particularly evident when looking at the microbiota associated with input-demanding modern cultivated varieties and their wild relatives, which have evolved under marginal conditions. However, the functional significance of these differences remains to be fully elucidated. We investigated the rhizosphere microbiota of wild and cultivated genotypes of the global crop barley and determined that nutrient conditions limiting plant growth amplify the host control on microbes at the root-soil interface. This is reflected in a plant- and genotype-dependent functional specialization of the rhizosphere microbiota, which appears to be required for optimal plant growth. These findings provide novel insights into the significance of the rhizosphere microbiota for plant growth and sustainable agriculture.
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167
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Li X, Liu Y, Wang Z, Yang C, Zhang R, Luo Y, Ma Y, Deng Y. Microbiome analysis and biocontrol bacteria isolation from rhizosphere soils associated with different sugarcane root rot severity. Front Bioeng Biotechnol 2022; 10:1062351. [PMID: 36588942 PMCID: PMC9802638 DOI: 10.3389/fbioe.2022.1062351] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
To explore the causal pathogen and the correlated rhizosphere soil microecology of sugarcane root rot, we sampled the sugarcane root materials displaying different disease severity, and the corresponding rhizosphere soil, for systematic root phenotype and microbial population analyses. We found that with increased level of disease severity reflected by above-ground parts of sugarcane, the total root length, total root surface area and total volume were significantly reduced, accompanied with changes in the microbial population diversity and structure in rhizosphere soil. Fungal community richness was significantly lower in the rhizosphere soil samples from mildly diseased plant than that from either healthy plant, or severely diseased plant. Particularly, we noticed that a peculiar decrease of potential pathogenic fungi in rhizosphere soil, including genera Fusarium, Talaromyces and Neocosmospora, with increased level of disease severity. As for bacterial community, Firmicutes was found to be of the highest level, while Acidobacteria and Chloroflexi of the lowest level, in rhizosphere soil from healthy plant compared to that from diseased plant of different severity. FUNGuild prediction showed that the proportion of saprophytic fungi was higher in the rhizosphere soil of healthy plants, while the proportion of pathogenic fungi was higher in the rhizosphere soil of diseased plants. By co-occurrence network analysis we demonstrated the Bacillus and Burkholderia were in a strong interaction with Fusarium pathogen(s). Consistently, the biocontrol and/or growth-promoting bacteria isolated from the rhizosphere soil were mostly (6 out of 7) belonging to Bacillus and Burkholderia species. By confrontation culture and pot experiments, we verified the biocontrol and/or growth-promoting property of the isolated bacterial strains. Overall, we demonstrated a clear correlation between sugarcane root rot severity and rhizosphere soil microbiome composition and function, and identified several promising biocontrol bacteria strains with strong disease suppression effect and growth-promoting properties.
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Affiliation(s)
- Xinyang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Yue Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Laboratory of Crop Physiology and Field Ecology, Northwest A&F University, Yangling, China
| | - Ziting Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Chenglong Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Runzhi Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Yibao Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Yuming Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Yizhen Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China,*Correspondence: Yizhen Deng,
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168
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Villar-Moreno R, Tienda S, Gutiérrez-Barranquero JA, Carrión VJ, de Vicente A, Cazorla FM, Arrebola E. Interplay between rhizospheric Pseudomonas chlororaphis strains lays the basis for beneficial bacterial consortia. FRONTIERS IN PLANT SCIENCE 2022; 13:1063182. [PMID: 36589057 PMCID: PMC9797978 DOI: 10.3389/fpls.2022.1063182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Pseudomonas chlororaphis (Pc) representatives are found as part of the rhizosphere-associated microbiome, and different rhizospheric Pc strains frequently perform beneficial activities for the plant. In this study we described the interactions between the rhizospheric Pc strains PCL1601, PCL1606 and PCL1607 with a focus on their effects on root performance. Differences among the three rhizospheric Pc strains selected were first observed in phylogenetic studies and confirmed by genome analysis, which showed variation in the presence of genes related to antifungal compounds or siderophore production, among others. Observation of the interactions among these strains under lab conditions revealed that PCL1606 has a better adaptation to environments rich in nutrients, and forms biofilms. Interaction experiments on plant roots confirmed the role of the different phenotypes in their lifestyle. The PCL1606 strain was the best adapted to the habitat of avocado roots, and PCL1607 was the least, and disappeared from the plant root scenario after a few days of interaction. These results confirm that 2 out 3 rhizospheric Pc strains were fully compatible (PCL1601 and PCL1606), efficiently colonizing avocado roots and showing biocontrol activity against the fungal pathogen Rosellinia necatrix. The third strain (PCL1607) has colonizing abilities when it is alone on the root but displayed difficulties under the competition scenario, and did not cause deleterious effects on the other Pc competitors when they were present. These results suggest that strains PCL1601 and PCL1606 are very well adapted to the avocado root environment and could constitute a basis for constructing a more complex beneficial microbial synthetic community associated with avocado plant roots.
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Affiliation(s)
- Rafael Villar-Moreno
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Sandra Tienda
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Jose A. Gutiérrez-Barranquero
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Víctor J. Carrión
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Antonio de Vicente
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Francisco M. Cazorla
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Eva Arrebola
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
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169
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Wang Z, Liu X, Zhou W, Sinclair F, Shi L, Xu J, Gui H. Land use intensification in a dry-hot valley reduced the constraints of water content on soil microbial diversity and multifunctionality but increased CO 2 production. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 852:158397. [PMID: 36055510 DOI: 10.1016/j.scitotenv.2022.158397] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 08/21/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Conversion of abandoned land (mainly savanna) into cropland generally occurs in fragile ecosystems such as dry-hot valleys (DHVs) in southwest China, with the intent of increasing land productivity and conducting ecological restoration. However, the effects of conversion on soil microbial communities and carbon turnover of savanna ecosystems remain unclear, since savannas could be a vital but overlooked carbon sink. To illustrate the ecological consequences of land-use change (LUC) for savanna ecosystems, a 1-year field experiment was conducted in DHVs of southwest China. The soil properties, microbial respiration, and metagenomics from two different land-use types (grassland and mango plantation) were examined to reveal the effects of regional LUC on soil C turnover and microbial traits. Conversion from degraded grassland into cropland increased the contribution of soil microclimate to the microbial community composition, reduced the constraints of soil water content (SWC), and further decreased nutrient availability. LUC reshaped the composition and structure of soil bacterial communities. Specifically, soil dominant microbes that belonged to Actinobacteria and Proteobacteria were significantly enriched by conversion, while rare microbes that belonged to a wider range of phyla were generally depleted, leading to an overall decrease in community diversity. In addition, LUC-induced changes in soil characteristics and microbial communities further decreased soil multifunctionality as well as the carbon use efficiency of microbes. Intensified microbial respiration and a significant increase in the soil CO2 efflux were observed following LUC, which could drive changes in soil microbial community composition and functions (such as growth and regeneration). In summary, through simultaneously reducing constraints on SWC and decreasing nutrient availability, conversion from degraded grassland to cropland in a DHV decreased soil microbial diversity and multifunctionality, and increased microbial respiration and soil CO2 efflux. Our study provides new insights for understanding the role and mechanisms of LUC in soil carbon turnover in ecologically fragile areas such as DHVs.
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Affiliation(s)
- Zhenghong Wang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiang Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology, Lanzhou University, Lanzhou 730000, China
| | - Wenjun Zhou
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
| | - Fergus Sinclair
- World Agroforestry Centre (ICRAF), United Nations Avenue, Gigiri, P.O. Box 30677-00100, Nairobi, Kenya
| | - Lingling Shi
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jianchu Xu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Heng Gui
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Cheng J, Tan H, Shan M, Duan M, Ye L, Yang Y, He L, Shen H, Yang Z, Wang X. Genome-wide identification and characterization of the NPF genes provide new insight into low nitrogen tolerance in Setaria. FRONTIERS IN PLANT SCIENCE 2022; 13:1043832. [PMID: 36589108 PMCID: PMC9795848 DOI: 10.3389/fpls.2022.1043832] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
Introduction Nitrogen (N) is essential for plant growth and yield production and can be taken up from soil in the form of nitrate or peptides. The NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family (NPF) genes play important roles in the uptake and transportation of these two forms of N. Methods Bioinformatic analysis was used to identify and characterize the NPF genes in Setaria. RNA-seq was employed to analyze time-series low nitrate stress response of the SiNPF genes. Yeast and Arabidopsis mutant complementation were used to test the nitrate transport ability of SiNRT1.1B1 and SiNRT1.1B2. Results We identified 92 and 88 putative NPF genes from foxtail millet (Setaria italica L.) and its wild ancestor green foxtail (Setaria viridis L.), respectively. These NPF genes were divided into eight groups according to their sequence characteristics and phylogenetic relationship, with similar intron-exon structure and motifs in the same subfamily. Twenty-six tandem duplication and 13 segmental duplication events promoted the expansion of SiNPF gene family. Interestingly, we found that the tandem duplication of the SiNRT1.1B gene might contribute to low nitrogen tolerance of foxtail millet. The gene expression atlas showed that the SiNPFs were divided into two major clusters, which were mainly expressed in root and the above ground tissues, respectively. Time series transcriptomic analysis further revealed the response of these SiNPF genes to short- and long- time low nitrate stress. To provide natural variation of gene information, we carried out a haplotype analysis of these SiNPFs and identified 2,924 SNPs and 400 InDels based on the re-sequence data of 398 foxtail millet accessions. We also predicted the three-dimensional structure of the 92 SiNPFs and found that the conserved proline 492 residues were not in the substrate binding pocket. The interactions of SiNPF proteins withNO 3 - were analyzed using molecular docking and the pockets were then identified. We found that the SiNPFs-NO 3 - binding energy ranged from -3.8 to -2.7 kcal/mol. Discussion Taken together, our study provides a comprehensive understanding of the NPF gene family in Setaria and will contribute to function dissection of these genes for crop breeding aimed at improving high nitrogen use efficiency.
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Affiliation(s)
- Jinjin Cheng
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Helin Tan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Meng Shan
- College of Life Sciences, Shanxi Agricultural University, Taigu, China
| | - Mengmeng Duan
- College of Life Sciences, Shanxi Agricultural University, Taigu, China
| | - Ling Ye
- College of Life Sciences, Shanxi Agricultural University, Taigu, China
| | - Yulu Yang
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Lu He
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Huimin Shen
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Zhirong Yang
- Department of Basic Sciences, Shanxi Agricultural University, Taigu, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, Taigu, China
| | - Xingchun Wang
- College of Life Sciences, Shanxi Agricultural University, Taigu, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, Taigu, China
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171
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Zhang X, Ma YN, Wang X, Liao K, He S, Zhao X, Guo H, Zhao D, Wei HL. Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes. MICROBIOME 2022; 10:216. [PMID: 36482381 PMCID: PMC9733015 DOI: 10.1186/s40168-022-01422-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Plants and their associated microbiota constitute an assemblage of species known as holobionts. The plant seed microbiome plays an important role in nutrient uptake and stress attenuation. However, the core vertically transmitted endophytes remain largely unexplored. RESULTS To gain valuable insights into the vertical transmission of rice seed core endophytes, we conducted a large-scale analysis of the microbiomes of two generations of six different rice varieties from five microhabitats (bulk soil, rhizosphere, root, stem, and seed) from four geographic locations. We showed that the microhabitat rather than the geographic location and rice variety was the primary driver of the rice microbiome assemblage. The diversity and network complexity of the rice-associated microbiome decreased steadily from far to near the roots, rice exterior to interior, and from belowground to aboveground niches. Remarkably, the microbiomes of the roots, stems, and seeds of the rice interior compartments were not greatly influenced by the external environment. The core bacterial endophytes of rice were primarily comprised of 14 amplicon sequence variants (ASVs), 10 of which, especially ASV_2 (Pantoea) and ASV_48 (Xanthomonas), were identified as potentially vertically transmitted taxa because they existed across generations, were rarely present in exterior rice microhabitats, and were frequently isolated from rice seeds. The genome sequences of Pantoea and Xanthomonas isolated from the parental and offspring seeds showed a high degree of average nucleotide and core protein identity, indicating vertical transmission of seed endophytes across generations. In silico prediction indicated that the seed endophytes Pantoea and Xanthomonas possessed streamlined genomes with short lengths, low-complexity metabolism, and various plant growth-promoting traits. We also found that all strains of Pantoea and Xanthomonas exhibited cellulase activity and produced indole-3-acetic acid. However, most strains exhibited insignificant antagonism to the major pathogens of rice, such as Magnaporthe oryzae and X. oryzae pv. oryzae. CONCLUSION Overall, our study revealed that microhabitats, rather than site-specific environmental factors or host varieties, shape the rice microbiome. We discovered the vertically transmitted profiles and keystone taxa of the rice microbiome, which led to the isolation of culturable seed endophytes and investigation of their potential roles in plant-microbiome interactions. Our results provide insights on vertically transmitted microbiota and suggest new avenues for improving plant fitness via the manipulation of seed-associated microbiomes. Video Abstract.
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Affiliation(s)
- Xiaoxia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yi-Nan Ma
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xing Wang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Kaiji Liao
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Shanwen He
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xia Zhao
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Hebao Guo
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Dongfang Zhao
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Hai-Lei Wei
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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Microbiome-based biotechnology for reducing food loss post harvest. Curr Opin Biotechnol 2022; 78:102808. [PMID: 36183451 DOI: 10.1016/j.copbio.2022.102808] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 08/21/2022] [Accepted: 08/29/2022] [Indexed: 12/14/2022]
Abstract
Microbiomes have an immense potential to enhance plant resilience to various biotic and abiotic stresses. However, intrinsic microbial communities respond to changes in their host's physiology and environment during plant's life cycle. The potential of the inherent plant microbiome has been neglected for a long time, especially for the postharvest period. Currently, close to 50% of all produced fruits and vegetables are lost either during production or storage. Biological control of spoilage and storage diseases is still lacking sufficiency. Today, novel multiomics technologies allow us to study the microbiome and its responses on a community level, which will help to advance current classic approaches and develop more effective and robust microbiome-based solutions for fruit and vegetable storability, quality, and safety.
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173
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Gao YQ, Chao DY. Localization and circulation: vesicle trafficking in regulating plant nutrient homeostasis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1350-1363. [PMID: 36321185 DOI: 10.1111/tpj.16020] [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: 07/23/2022] [Revised: 10/11/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
Nutrient homeostasis is essential for plant growth and reproduction. Plants, therefore, have evolved tightly regulated mechanisms for the uptake, translocation, distribution, and storage of mineral nutrients. Considering that inorganic nutrient transport relies on membrane-based transporters and channels, vesicle trafficking, one of the fundamental cell biological processes, has become a hotspot of plant nutrition studies. In this review, we summarize recent advances in the study of how vesicle trafficking regulates nutrient homeostasis to contribute to the adaptation of plants to heterogeneous environments. We also discuss new perspectives on future studies, which may inspire researchers to investigate new approaches to improve the human diet and health by changing the nutrient quality of crops.
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Affiliation(s)
- Yi-Qun Gao
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Dai-Yin Chao
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
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Sarkar S, Kamke A, Ward K, Hartung E, Ran Q, Feehan B, Galliart M, Jumpponen A, Johnson L, Lee ST. Pseudomonas cultivated from Andropogon gerardii rhizosphere show functional potential for promoting plant host growth and drought resilience. BMC Genomics 2022; 23:784. [PMID: 36451103 PMCID: PMC9710129 DOI: 10.1186/s12864-022-09019-0] [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: 06/21/2022] [Accepted: 11/16/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Climate change will result in more frequent droughts that can impact soil-inhabiting microbiomes (rhizobiomes) in the agriculturally vital North American perennial grasslands. Rhizobiomes have contributed to enhancing drought resilience and stress resistance properties in plant hosts. In the predicted events of more future droughts, how the changing rhizobiome under environmental stress can impact the plant host resilience needs to be deciphered. There is also an urgent need to identify and recover candidate microorganisms along with their functions, involved in enhancing plant resilience, enabling the successful development of synthetic communities. RESULTS In this study, we used the combination of cultivation and high-resolution genomic sequencing of bacterial communities recovered from the rhizosphere of a tallgrass prairie foundation grass, Andropogon gerardii. We cultivated the plant host-associated microbes under artificial drought-induced conditions and identified the microbe(s) that might play a significant role in the rhizobiome of Andropogon gerardii under drought conditions. Phylogenetic analysis of the non-redundant metagenome-assembled genomes (MAGs) identified a bacterial genome of interest - MAG-Pseudomonas. Further metabolic pathway and pangenome analyses recovered genes and pathways related to stress responses including ACC deaminase; nitrogen transformation including assimilatory nitrate reductase in MAG-Pseudomonas, which might be associated with enhanced drought tolerance and growth for Andropogon gerardii. CONCLUSIONS Our data indicated that the metagenome-assembled MAG-Pseudomonas has the functional potential to contribute to the plant host's growth during stressful conditions. Our study also suggested the nitrogen transformation potential of MAG-Pseudomonas that could impact Andropogon gerardii growth in a positive way. The cultivation of MAG-Pseudomonas sets the foundation to construct a successful synthetic community for Andropogon gerardii. To conclude, stress resilience mediated through genes ACC deaminase, nitrogen transformation potential through assimilatory nitrate reductase in MAG-Pseudomonas could place this microorganism as an important candidate of the rhizobiome aiding the plant host resilience under environmental stress. This study, therefore, provided insights into the MAG-Pseudomonas and its potential to optimize plant productivity under ever-changing climatic patterns, especially in frequent drought conditions.
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Affiliation(s)
- Soumyadev Sarkar
- grid.36567.310000 0001 0737 1259Division of Biology, Kansas State University, Manhattan, KS USA
| | - Abigail Kamke
- grid.36567.310000 0001 0737 1259Division of Biology, Kansas State University, Manhattan, KS USA
| | - Kaitlyn Ward
- grid.36567.310000 0001 0737 1259Division of Biology, Kansas State University, Manhattan, KS USA
| | - Eli Hartung
- grid.36567.310000 0001 0737 1259Division of Biology, Kansas State University, Manhattan, KS USA
| | - Qinghong Ran
- grid.36567.310000 0001 0737 1259Division of Biology, Kansas State University, Manhattan, KS USA
| | - Brandi Feehan
- grid.36567.310000 0001 0737 1259Division of Biology, Kansas State University, Manhattan, KS USA
| | - Matthew Galliart
- grid.256032.00000 0001 2285 6924Department of Biological Sciences, Fort Hays State University, Hays, KS USA
| | - Ari Jumpponen
- grid.36567.310000 0001 0737 1259Division of Biology, Kansas State University, Manhattan, KS USA
| | - Loretta Johnson
- grid.36567.310000 0001 0737 1259Division of Biology, Kansas State University, Manhattan, KS USA
| | - Sonny T.M. Lee
- grid.36567.310000 0001 0737 1259Division of Biology, Kansas State University, Manhattan, KS USA
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Feng H, Guo C, Li Z, Gao Y, Zhang Q, Geng Z, Wang J, Chen G, Liu K, Li H, Yang W. Machine learning assisted dynamic phenotypes and genomic variants help understand the ecotype divergence in rapeseed. FRONTIERS IN PLANT SCIENCE 2022; 13:1028779. [PMID: 36457523 PMCID: PMC9705987 DOI: 10.3389/fpls.2022.1028779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/14/2022] [Indexed: 06/17/2023]
Abstract
Three ecotypes of rapeseed, winter, spring, and semi-winter, have been formed to enable the plant to adapt to different geographic areas. Although several major loci had been found to contribute to the flowering divergence, the genomic footprints and associated dynamic plant architecture in the vegetative growth stage underlying the ecotype divergence remain largely unknown in rapeseed. Here, a set of 41 dynamic i-traits and 30 growth-related traits were obtained by high-throughput phenotyping of 171 diverse rapeseed accessions. Large phenotypic variation and high broad-sense heritability were observed for these i-traits across all developmental stages. Of these, 19 i-traits were identified to contribute to the divergence of three ecotypes using random forest model of machine learning approach, and could serve as biomarkers to predict the ecotype. Furthermore, we analyzed genomic variations of the population, QTL information of all dynamic i-traits, and genomic basis of the ecotype differentiation. It was found that 213, 237, and 184 QTLs responsible for the differentiated i-traits overlapped with the signals of ecotype divergence between winter and spring, winter and semi-winter, and spring and semi-winter, respectively. Of which, there were four common divergent regions between winter and spring/semi-winter and the strongest divergent regions between spring and semi-winter were found to overlap with the dynamic QTLs responsible for the differentiated i-traits at multiple growth stages. Our study provides important insights into the divergence of plant architecture in the vegetative growth stage among the three ecotypes, which was contributed to by the genetic differentiation, and might contribute to environmental adaption and yield improvement.
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Affiliation(s)
- Hui Feng
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Chaocheng Guo
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zongyi Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yuan Gao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zedong Geng
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jing Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Guoxing Chen
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Haitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, School of Life Sciences, Hubei University, Wuhan, China
| | - Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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Singh A, Kumar M, Chakdar H, Pandiyan K, Kumar SC, Zeyad MT, Singh BN, Ravikiran KT, Mahto A, Srivastava AK, Saxena AK. Influence of host genotype in establishing root associated microbiome of indica rice cultivars for plant growth promotion. Front Microbiol 2022; 13:1033158. [PMID: 36452918 PMCID: PMC9702084 DOI: 10.3389/fmicb.2022.1033158] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/20/2022] [Indexed: 08/29/2023] Open
Abstract
Rice plants display a unique root ecosystem comprising oxic-anoxic zones, harboring a plethora of metabolic interactions mediated by its root microbiome. Since agricultural land is limited, an increase in rice production will rely on novel methods of yield enhancement. The nascent concept of tailoring plant phenotype through the intervention of synthetic microbial communities (SynComs) is inspired by the genetics and ecology of core rhizobiome. In this direction, we have studied structural and functional variations in the root microbiome of 10 indica rice varieties. The studies on α and β-diversity indices of rhizospheric root microbiome with the host genotypes revealed variations in the structuring of root microbiome as well as a strong association with the host genotypes. Biomarker discovery, using machine learning, highlighted members of class Anaerolineae, α-Proteobacteria, and bacterial genera like Desulfobacteria, Ca. Entotheonella, Algoriphagus, etc. as the most important features of indica rice microbiota having a role in improving the plant's fitness. Metabolically, rice rhizobiomes showed an abundance of genes related to sulfur oxidation and reduction, biofilm production, nitrogen fixation, denitrification, and phosphorus metabolism. This comparative study of rhizobiomes has outlined the taxonomic composition and functional diversification of rice rhizobiome, laying the foundation for the development of next-generation microbiome-based technologies for yield enhancement in rice and other crops.
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Affiliation(s)
- Arjun Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
- ICAR-Central Soil Salinity Research Institute, RRS, Lucknow, India
| | - Murugan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Kuppusamy Pandiyan
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
- Ginning Training Center, ICAR-Central Institute for Research on Cotton Technology, Nagpur, India
| | - Shiv Charan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | | | | | - K. T. Ravikiran
- ICAR-Central Soil Salinity Research Institute, RRS, Lucknow, India
| | - Arunima Mahto
- National Institute of Plant Genome Research, New Delhi, India
| | | | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
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Guo H, He X, Zhang H, Tan R, Yang J, Xu F, Wang S, Yang C, Ding G. Physiological Responses of Cigar Tobacco Crop to Nitrogen Deficiency and Genome-Wide Characterization of the NtNPF Family Genes. PLANTS (BASEL, SWITZERLAND) 2022; 11:3064. [PMID: 36432793 PMCID: PMC9697317 DOI: 10.3390/plants11223064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/02/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
Tobacco prefers nitrate as a nitrogen (N) source. However, little is known about the molecular components responsible for nitrate uptake and the physiological responses of cigar tobacco to N deficiency. In this study, a total of 117 nitrate transporter 1 (NRT1) and peptide transporter (PTR) family (NPF) genes were comprehensively identified and systematically characterized in the whole tobacco genome. The NtNPF members showed significant genetic diversity within and across subfamilies but showed conservation between subfamilies. The NtNPF genes are dispersed unevenly across the chromosomes. The phylogenetic analysis revealed that eight subfamilies of NtNPF genes are tightly grouped with their orthologues in Arabidopsis. The promoter regions of the NtNPF genes had extensive cis-regulatory elements. Twelve core NtNPF genes, which were strongly induced by N limitation, were identified based on the RNA-seq data. Furthermore, N deprivation severely impaired plant growth of two cigar tobaccos, and CX26 may be more sensitive to N deficiency than CX14. Moreover, 12 hub genes respond differently to N deficiency between the two cultivars, indicating the vital roles in regulating N uptake and transport in cigar tobacco. The findings here contribute towards a better knowledge of the NtNPF genes and lay the foundation for further functional analysis of cigar tobacco.
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Affiliation(s)
- Hao Guo
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuyou He
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Zhang
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Ronglei Tan
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinpeng Yang
- Tobacco Research Institute of Hubei Province, Wuhan 430030, China
| | - Fangsen Xu
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Sheliang Wang
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunlei Yang
- Tobacco Research Institute of Hubei Province, Wuhan 430030, China
| | - Guangda Ding
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
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Kumaishi K, Usui E, Suzuki K, Kobori S, Sato T, Toda Y, Takanashi H, Shinozaki S, Noda M, Takakura A, Matsumoto K, Yamasaki Y, Tsujimoto H, Iwata H, Ichihashi Y. High throughput method of 16S rRNA gene sequencing library preparation for plant root microbial community profiling. Sci Rep 2022; 12:19289. [PMID: 36369356 PMCID: PMC9652414 DOI: 10.1038/s41598-022-23943-x] [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: 05/26/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022] Open
Abstract
Microbiota are a major component of agroecosystems. Root microbiota, which inhabit the inside and surface of plant roots, play a significant role in plant growth and health. As next-generation sequencing technology allows the capture of microbial profiles without culturing the microbes, profiling of plant microbiota has become a staple tool in plant science and agriculture. Here, we have increased sample handling efficiency in a two-step PCR amplification protocol for 16S rRNA gene sequencing of plant root microbiota, improving DNA extraction using AMPure XP magnetic beads and PCR purification using exonuclease. These modifications reduce sample handling and capture microbial diversity comparable to that obtained by the manual method. We found a buffer with AMPure XP magnetic beads enabled efficient extraction of microbial DNA directly from plant roots. We also demonstrated that purification using exonuclease before the second PCR step enabled the capture of higher degrees of microbial diversity, thus allowing for the detection of minor bacteria compared with the purification using magnetic beads in this step. In addition, our method generated comparable microbiome profile data in plant roots and soils to that of using common commercially available DNA extraction kits, such as DNeasy PowerSoil Pro Kit and FastDNA SPIN Kit for Soil. Our method offers a simple and high-throughput option for maintaining the quality of plant root microbial community profiling.
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Affiliation(s)
- Kie Kumaishi
- grid.509462.cRIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074 Japan
| | - Erika Usui
- grid.509462.cRIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074 Japan
| | - Kenta Suzuki
- grid.509462.cRIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074 Japan
| | - Shungo Kobori
- grid.509462.cRIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074 Japan
| | - Takumi Sato
- grid.509462.cRIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074 Japan
| | - Yusuke Toda
- grid.26999.3d0000 0001 2151 536XGraduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-8657 Japan
| | - Hideki Takanashi
- grid.26999.3d0000 0001 2151 536XGraduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-8657 Japan
| | - Satoshi Shinozaki
- MAYEKAWA Research Institute Co., LTD, Koto-Ku, Tokyo, 135-8482 Japan
| | - Munehiro Noda
- MAYEKAWA Research Institute Co., LTD, Koto-Ku, Tokyo, 135-8482 Japan
| | - Akiko Takakura
- MAYEKAWA Research Institute Co., LTD, Koto-Ku, Tokyo, 135-8482 Japan
| | - Kayoko Matsumoto
- MAYEKAWA Research Institute Co., LTD, Koto-Ku, Tokyo, 135-8482 Japan
| | - Yuji Yamasaki
- grid.265107.70000 0001 0663 5064Arid Land Research Center, Tottori University, Tottori, 680-0001 Japan
| | - Hisashi Tsujimoto
- grid.265107.70000 0001 0663 5064Arid Land Research Center, Tottori University, Tottori, 680-0001 Japan
| | - Hiroyoshi Iwata
- grid.26999.3d0000 0001 2151 536XGraduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-8657 Japan
| | - Yasunori Ichihashi
- grid.509462.cRIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074 Japan
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179
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Chao S, Wang H, Zhang S, Chen G, Mao C, Hu Y, Yu F, Wang S, Lv L, Chen L, Feng G. Novel RNA Viruses Discovered in Weeds in Rice Fields. Viruses 2022; 14:2489. [PMID: 36366587 PMCID: PMC9717734 DOI: 10.3390/v14112489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/03/2022] [Accepted: 11/06/2022] [Indexed: 11/12/2022] Open
Abstract
Weeds often grow alongside crop plants. In addition to competing with crops for nutrients, water and space, weeds host insect vectors or act as reservoirs for viral diversity. However, little is known about viruses infecting rice weeds. In this work, we used metatranscriptomic deep sequencing to identify RNA viruses from 29 weed samples representing 23 weed species. A total of 224 RNA viruses were identified: 39 newly identified viruses are sufficiently divergent to comprise new families and genera. The newly identified RNA viruses clustered within 18 viral families. Of the identified viruses, 196 are positive-sense single-stranded RNA viruses, 24 are negative-sense single-stranded RNA viruses and 4 are double-stranded RNA viruses. We found that some novel RNA viruses clustered within the families or genera of several plant virus species and have the potential to infect plants. Collectively, these results expand our understanding of viral diversity in rice weeds. Our work will contribute to developing effective strategies with which to manage the spread and epidemiology of plant viruses.
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Affiliation(s)
- Shufen Chao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311400, China
| | - Haoran Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311400, China
| | - Shu Zhang
- Institute of Plant Protection & Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430000, China
| | - Guoqing Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311400, China
| | - Chonghui Mao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311400, China
| | - Yang Hu
- Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang 550000, China
| | - Fengquan Yu
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang 110000, China
| | - Shuo Wang
- Sanya Agricultural Technology Extension and Service Centre, Sanya 572000, China
| | - Liang Lv
- Institute of Plant Protection & Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430000, China
| | - Long Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311400, China
| | - Guozhong Feng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311400, China
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180
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Cuartero J, Pascual JA, Vivo JM, Özbolat O, Sánchez-Navarro V, Weiss J, Zornoza R, Martínez-Mena M, García E, Ros M. Melon/cowpea intercropping pattern influenced the N and C soil cycling and the abundance of soil rare bacterial taxa. Front Microbiol 2022; 13:1004593. [PMID: 36419434 PMCID: PMC9676475 DOI: 10.3389/fmicb.2022.1004593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2022] Open
Abstract
The high use of pesticides, herbicides, and unsustainable farming practices resulted in losses of soil quality. Sustainable farming practices such as intercropping could be a good alternative to traditional monocrop, especially using legumes such as cowpea (Vigna unguiculata L. Walp). In this study, different melon and cowpea intercropping patterns (melon mixed with cowpea in the same row (MC1); alternating one melon row and one cowpea row (MC2); alternating two melon rows and one cowpea row (MC3)) were assayed to study the intercropping effect on soil bacterial community through 16S rRNA region in a 3-year experiment. The results indicated that intercropping showed high content of total organic carbon, total nitrogen and ammonium, melon yield, and bacterial diversity as well as higher levels of beneficial soil microorganisms such a Pseudomonas, Aeromicrobium, Niastella, or Sphingomonas which can promote plant growth and plant defense against pathogens. Furthermore, intercropping showed a higher rare taxa diversity in two (MC1 and MC2) out of the three intercropping systems. In addition, N-cycling genes such as nirB, nosZ, and amoA were more abundant in MC1 and MC2 whereas the narG predicted gene was far more abundant in the intercropping systems than in the monocrop at the end of the 3-year experiment. This research fills a gap in knowledge about the importance of soil bacteria in an intercropping melon/cowpea pattern, showing the benefits to yield and soil quality with a decrease in N fertilization.
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Affiliation(s)
- Jessica Cuartero
- Centre of Edaphology and Applied Biology of the Segura (CSIC), University Campus of Espinardo, Murcia, Spain
| | - Jose Antonio Pascual
- Centre of Edaphology and Applied Biology of the Segura (CSIC), University Campus of Espinardo, Murcia, Spain
| | - Juana-María Vivo
- Department of Statistics and Operations Research, CMN & IMIB-Arrixaca, University of Murcia, Murcia, Spain
| | - Onurcan Özbolat
- Institute of Plant Biotechnology, Plaza del Hospital s/n, Technical University of Cartagena, Cartagena, Spain
| | - Virginia Sánchez-Navarro
- Institute of Plant Biotechnology, Plaza del Hospital s/n, Technical University of Cartagena, Cartagena, Spain
| | - Julia Weiss
- Institute of Plant Biotechnology, Plaza del Hospital s/n, Technical University of Cartagena, Cartagena, Spain
| | - Raúl Zornoza
- Institute of Plant Biotechnology, Plaza del Hospital s/n, Technical University of Cartagena, Cartagena, Spain
- Department of Agricultural Science, Polytechnic University of Cartagena, Cartagena, Spain
| | - María Martínez-Mena
- Centre of Edaphology and Applied Biology of the Segura (CSIC), University Campus of Espinardo, Murcia, Spain
| | - Eloisa García
- Centre of Edaphology and Applied Biology of the Segura (CSIC), University Campus of Espinardo, Murcia, Spain
| | - Margarita Ros
- Centre of Edaphology and Applied Biology of the Segura (CSIC), University Campus of Espinardo, Murcia, Spain
- *Correspondence: Margarita Ros
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181
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Zhou N, Mei CM, Zhu XY, Zhao JJ, Ma MG, Li WD. Research progress of rhizosphere microorganisms in Fritillaria L. medicinal plants. Front Bioeng Biotechnol 2022; 10:1054757. [PMID: 36420438 PMCID: PMC9676442 DOI: 10.3389/fbioe.2022.1054757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/25/2022] [Indexed: 12/01/2023] Open
Abstract
The soil's rhizosphere is a highly active place where the exchange of substances and information occurs among plants, soils, and microorganisms. The microorganisms involved are crucial to the activities of plant growth and development, metabolism, and reproduction. Fritillaria L. medicinal plants are unique Chinese medicinal ingredients, but the continuous cropping obstacles formed in the artificial planting process is severely harmful to the growth and development of these medicinal plants. In this review, we summarized the current species and distribution of Fritillaria L. in China, and analyzed the changes in microbial diversity (mainly among bacteria and fungi) in the rhizosphere of these plants under long-term continuous cropping. The fungi showed an increasing trend in the soil rhizosphere, resulting in the transition of the soil from the high-fertility "bacterial type" to the low-fertility "fungal type" as planting years increased. Furthermore, the interaction between Fritillaria L. medicinal plants and the rhizosphere microorganisms was reviewed, and promising applications for the rhizosphere microbiome in the cultivation of Fritillaria L. medicinal plants were suggested. It is expected that this review will facilitate the in-depth understanding of rhizosphere microorganisms in the growth, accumulation of active ingredients, and disease control of Fritillaria L.
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Affiliation(s)
- Nong Zhou
- College of Pharmacy, Engineering Center of State Ministry of Education for Standardization of Chinese Medicine Processing, Nanjing University of Chinese Medicine, Nanjing, China
- Chongqing Engineering Laboratory of Green Planting and Deep Processing of Famous-region Drug in the Three Gorges Reservoir Region, College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
| | - Chun-Mei Mei
- College of Pharmacy, Engineering Center of State Ministry of Education for Standardization of Chinese Medicine Processing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xing-Yu Zhu
- College of Pharmacy, Engineering Center of State Ministry of Education for Standardization of Chinese Medicine Processing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jing-Jing Zhao
- Chongqing Engineering Laboratory of Green Planting and Deep Processing of Famous-region Drug in the Three Gorges Reservoir Region, College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
| | - Ming-Guo Ma
- Chongqing Engineering Laboratory of Green Planting and Deep Processing of Famous-region Drug in the Three Gorges Reservoir Region, College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
- Research Center of Biomass Clean Utilization, Beijing Key Laboratory of Lignocellulosic Chemistry, College of Materials Science and Technology, Beijing Forestry University, Beijing, China
| | - Wei-Dong Li
- College of Pharmacy, Engineering Center of State Ministry of Education for Standardization of Chinese Medicine Processing, Nanjing University of Chinese Medicine, Nanjing, China
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182
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Aoki W, Kogawa M, Matsuda S, Matsubara K, Hirata S, Nishikawa Y, Hosokawa M, Takeyama H, Matoh T, Ueda M. Massively parallel single-cell genomics of microbiomes in rice paddies. Front Microbiol 2022; 13:1024640. [PMID: 36406415 PMCID: PMC9669790 DOI: 10.3389/fmicb.2022.1024640] [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: 08/22/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Plant growth-promoting microbes (PGPMs) have attracted increasing attention because they may be useful in increasing crop yield in a low-input and sustainable manner to ensure food security. Previous studies have attempted to understand the principles underlying the rhizosphere ecology and interactions between plants and PGPMs using ribosomal RNA sequencing, metagenomic sequencing, and genome-resolved metagenomics; however, these approaches do not provide comprehensive genomic information for individual species and do not facilitate detailed analyses of plant-microbe interactions. In the present study, we developed a pipeline to analyze the genomic diversity of the rice rhizosphere microbiome at single-cell resolution. We isolated microbial cells from paddy soil and determined their genomic sequences by using massively parallel whole-genome amplification in microfluidic-generated gel capsules. We successfully obtained 3,237 single-amplified genomes in a single experiment, and these genomic sequences provided insights into microbial functions in the paddy ecosystem. Our approach offers a promising platform for gaining novel insights into the roles of microbes in the rice rhizomicrobiome and to develop microbial technologies for improved and sustainable rice production.
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Affiliation(s)
- Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan,*Correspondence: Wataru Aoki,
| | - Masato Kogawa
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | | | | | | | - Yohei Nishikawa
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan,Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Masahito Hosokawa
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan,Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan,Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan,Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Tokyo, Japan
| | - Haruko Takeyama
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan,Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan,Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan,Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Tokyo, Japan,Haruko Takeyama,
| | - Toru Matoh
- Kyoto Agriculture Research Institute KARI, Kyoto, Japan,Toru Matoh,
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan,Mitsuyoshi Ueda,
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183
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Liu W, Qiu K, Xie Y, Wang R, Li H, Meng W, Yang Y, Huang Y, Li Y, He Y. Years of sand fixation with Caragana korshinskii drive the enrichment of its rhizosphere functional microbes by accumulating soil N. PeerJ 2022; 10:e14271. [PMID: 36340191 PMCID: PMC9635361 DOI: 10.7717/peerj.14271] [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: 06/06/2022] [Accepted: 09/28/2022] [Indexed: 11/05/2022] Open
Abstract
C. korshinskii is one of the most widely-planted sand-fixing legumes in northwest China and exploring its rhizosphere microbiome is of great ecological importance. However, the effect of long-term sand fixation on the composition, diversity, and underlying functions of microbes in the C. korshinskii rhizosphere in dryland ecosystems remain unclear. Here, we performed high-throughput sequencing using a 16S rRNA (absolute quantification) and bacterial functional annotation of prokaryotic taxa (FAPROTAX) analysis and an ITS (relative quantification) and fungal functional guild (FUNGuild) analysis to investigate the C. korshinskii rhizosphere microbiome and metabolic functional groups at different sand-fixing ages (six years, CK6; twelve years, CK12; and eighteen years, CK18) and determined the physicochemical properties of the rhizosphere soil. Results showed that the key bacterial taxa of the rhizosphere were significantly more abundant in CK18 than in CK12 and CK6 at the phylum-class-genus level, and that fungal Glomeromycota was also significantly more abundant in the CK18 rhizosphere compared to CK12 and CK6. Among these bacterial taxa, the enrichment effect of key, functional, genus-level species of bacteria was the most obvious, including Rhizobium, Ensifer, Neorhizobium, Mesorhizobium, Streptomyces, Sphingomonas, and Flavobacterium, which are N-fixing and/or phosphate-solubilizing groups. The significant improvement seen in the physicochemical properties of the CK18 rhizosphere soil, including the higher total nitrogen (TN), available nitrogen (AN), pH, electrical conductivity (EC), higher N:P ratio, and lower C:N ratio, all demonstrated the relationship between the rhizosphere microbes and soil carbon (C) and nitrogen (N) cycling. A redundancy analysis (RDA) of different taxonomic levels indicated a close positive relationship between rhizosphere microbes and AN. In addition, the functional groups of the C. korshinskii rhizosphere bacteria were closely related to soil AN and were mainly composed of chemoheterotrophy and aerobic chemoheterotrophy. A Spearman correlation analysis revealed that these functional groups were mainly identified from bacterial Actinobacteria, Proteobacteria, Verrucomicrobia, Bacteroidetes, and fungal Glomeromycota. Our study provides evidence that the rhizosphere microbes of C. korshinskii are closely related to the accumulation of N in the restoration of desert ecosystems, and that the ecological functional processes they are involved in mainly involve C and N cycles, which play an important role in desertification reversal.
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Affiliation(s)
- Wangsuo Liu
- School of Agriculture, Ningxia University, Yinchuan, China,Department of Desertification Prevention, Ningxia Grape Wine and Desertification Prevention Technical College, Yinchuan, Ningxia, China
| | - Kaiyang Qiu
- School of Agriculture, Ningxia University, Yinchuan, China,Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China,Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China
| | - Yingzhong Xie
- School of Agriculture, Ningxia University, Yinchuan, China,Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China,Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China
| | - Ruixia Wang
- Ningxia Administration of Baijitan National Nature Reserve, Yinchuan, China
| | - Haichao Li
- Ningxia Administration of Baijitan National Nature Reserve, Yinchuan, China
| | - Wenfen Meng
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yi Yang
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yeyun Huang
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yayuan Li
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yi He
- School of Agriculture, Ningxia University, Yinchuan, China
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184
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Wang P, Liu T, Liu J, Duan Y, Han S, Zhang Z, Li L, Lin Y. Effects of different colored polyethylene mulching films on bacterial communities from soil during enrichment incubation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 246:114160. [PMID: 36215881 DOI: 10.1016/j.ecoenv.2022.114160] [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: 07/07/2022] [Revised: 09/27/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Studies have shown that mulching agricultural fields with plastic residues can influence microbial communities in the environment, but few studies have investigated the differences in the soil microbial communities in distinct areas under mulching with different colored plastic products. Thus, in this study, we explored how different colored polyethylene mulching films (PMFs) might affect soil bacterial communities during enrichment incubation. We found significant differences in the bacterial communities under different colored PMFs after incubation. Treatment with the same colored PMF obtained more similar bacterial community compositions. For instance, at the class level, Gammaproteobacteria and Bacteroidia were most abundant with black PMF, whereas Actinobacteria and Bacteroidia were most abundant with white PMF. The most abundant genera were Acinetobacter and Chryseobacterium with black PMF but Rhodanobacter and Paenarthrobacter with white PMF. Polyethylene- and hydrocarbon-degrading bacteria were the core members detected under both treatments, and the bacterial communities were predicted to have the potential for the biodegradation and metabolism of xenobiotics after enrichment culture according to the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) tool. In addition, the bacterial communities in soil from Xinjiang treated with white PMF and in soil from Yangling treated with black PMF were strongly correlated and stable. Our results suggest that the color of the PMF applied affected the soil bacterial communities, where plastics with the same color may have recruited similar species of microorganisms, although the origins of these microorganisms were not the same.
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Affiliation(s)
- Peiyuan Wang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tingting Liu
- College of Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiaxi Liu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yifan Duan
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Siqi Han
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Yanbing Lin
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China.
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185
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Tan X, Xie H, Yu J, Wang Y, Xu J, Xu P, Ma B. Host genetic determinants drive compartment-specific assembly of tea plant microbiomes. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2174-2186. [PMID: 35876474 PMCID: PMC9616527 DOI: 10.1111/pbi.13897] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/17/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Diverse host factors drive microbial variation in plant-associated environments, whereas their genetic mechanisms remain largely unexplored. To address this, we coupled the analyses of plant genetics and microbiomes in this study. Using 100 tea plant (Camellia sinensis) cultivars, the microbiomes of rhizosphere, root endosphere and phyllosphere showed clear compartment-specific assembly, whereas the subpopulation differentiation of tea cultivars exhibited small effects on microbial variation in each compartment. Through microbiome genome-wide association studies, we examined the interactions between tea genetic loci and microbial variation. Notably, genes related to the cell wall and carbon catabolism were heavily linked to root endosphere microbial composition, whereas genes related to the metabolism of metal ions and small organic molecules were overrepresented in association with rhizosphere microbial composition. Moreover, a set of tea genetic variants, including the cytoskeleton-related formin homology interacting protein 1 gene, were strongly associated with the β-diversity of phyllosphere microbiomes, implying their interactions with the overall structure of microbial communities. Our results create a catalogue of tea genetic determinants interacting with microbiomes and reveal the compartment-specific microbiome assembly driven by host genetics.
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Affiliation(s)
- Xiangfeng Tan
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource SciencesZhejiang UniversityHangzhouChina
- Zhejiang Provincial Key Laboratory of Agricultural, Resources and EnvironmentZhejiang UniversityHangzhouChina
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhouChina
| | - Hengtong Xie
- Institution of Tea ScienceZhejiang UniversityHangzhouChina
| | - Jingwen Yu
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhouChina
| | - Yuefei Wang
- Institution of Tea ScienceZhejiang UniversityHangzhouChina
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource SciencesZhejiang UniversityHangzhouChina
- Zhejiang Provincial Key Laboratory of Agricultural, Resources and EnvironmentZhejiang UniversityHangzhouChina
| | - Ping Xu
- Institution of Tea ScienceZhejiang UniversityHangzhouChina
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource SciencesZhejiang UniversityHangzhouChina
- Zhejiang Provincial Key Laboratory of Agricultural, Resources and EnvironmentZhejiang UniversityHangzhouChina
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhouChina
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186
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Jiang MZ, Zhu HZ, Zhou N, Liu C, Jiang CY, Wang Y, Liu SJ. Droplet microfluidics-based high-throughput bacterial cultivation for validation of taxon pairs in microbial co-occurrence networks. Sci Rep 2022; 12:18145. [PMID: 36307549 PMCID: PMC9616874 DOI: 10.1038/s41598-022-23000-7] [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: 05/26/2022] [Accepted: 10/21/2022] [Indexed: 12/31/2022] Open
Abstract
Co-occurrence networks inferred from the abundance data of microbial communities are widely applied to predict microbial interactions. However, the high workloads of bacterial isolation and the complexity of the networks themselves constrained experimental demonstrations of the predicted microbial associations and interactions. Here, we integrate droplet microfluidics and bar-coding logistics for high-throughput bacterial isolation and cultivation from environmental samples, and experimentally investigate the relationships between taxon pairs inferred from microbial co-occurrence networks. We collected Potamogeton perfoliatus plants (including roots) and associated sediments from Beijing Olympic Park wetland. Droplets of series diluted homogenates of wetland samples were inoculated into 126 96-well plates containing R2A and TSB media. After 10 days of cultivation, 65 plates with > 30% wells showed microbial growth were selected for the inference of microbial co-occurrence networks. We cultivated 129 bacterial isolates belonging to 15 species that could represent the zero-level OTUs (Zotus) in the inferred co-occurrence networks. The co-cultivations of bacterial isolates corresponding to the prevalent Zotus pairs in networks were performed on agar plates and in broth. Results suggested that positively associated Zotu pairs in the co-occurrence network implied complicated relations including neutralism, competition, and mutualism, depending on bacterial isolate combination and cultivation time.
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Affiliation(s)
- Min-Zhi Jiang
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000 People’s Republic of China
| | - Hai-Zhen Zhu
- grid.9227.e0000000119573309State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 People’s Republic of China
| | - Nan Zhou
- grid.9227.e0000000119573309State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 People’s Republic of China
| | - Chang Liu
- grid.9227.e0000000119573309State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 People’s Republic of China
| | - Cheng-Ying Jiang
- grid.9227.e0000000119573309State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 People’s Republic of China
| | - Yulin Wang
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000 People’s Republic of China
| | - Shuang-Jiang Liu
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000 People’s Republic of China ,grid.9227.e0000000119573309State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 People’s Republic of China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
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187
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Chai X, Wang X, Pi Y, Wu T, Zhang X, Xu X, Han Z, Wang Y. Nitrate transporter MdNRT2.4 interacts with rhizosphere bacteria to enhance nitrate uptake in apple rootstocks. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6490-6504. [PMID: 35792505 DOI: 10.1093/jxb/erac301] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Plants have developed complex mechanisms to adapt to changing nitrate (NO3-) concentrations and can recruit microbes to boost nitrogen absorption. However, little is known about the relationship between functional genes and the rhizosphere microbiome in NO3- uptake of apple rootstocks. Here, we found that variation in Malus domestica NO3- transporter (MdNRT2.4) expression contributes to nitrate uptake divergence between two apple rootstocks. Overexpression of MdNRT2.4 in apple seedlings significantly improved tolerance to low nitrogen via increasing net NO3- influx at the root surface. However, inhibiting the root plasma membrane H+-ATPase activity abolished NO3- uptake and led to NO3- release, suggesting that MdNRT2.4 encodes an H+-coupled nitrate transporter. Surprisingly, the nitrogen concentration of MdNRT2.4-overexpressing apple seedlings in unsterilized nitrogen-poor soil was higher than that in sterilized nitrogen-poor soil. Using 16S ribosomal RNA gene profiling to characterize the rhizosphere microbiota, we found that MdNRT2.4-overexpressing apple seedlings recruited more bacterial taxa with nitrogen metabolic functions, especially Rhizobiaceae. We isolated a bacterial isolate ARR11 from the apple rhizosphere soil and identified it as Rhizobium. Inoculation with ARR11 improved apple seedling growth in nitrogen-poor soils, compared with uninoculated seedlings. Together, our results highlight the interaction of host plant genes with the rhizosphere microbiota for host plant nutrient uptake.
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Affiliation(s)
- Xiaofen Chai
- College of Horticulture, China Agricultural University, Beijing, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), the Ministry of Agriculture and Rural Affairs, Beijing, P. R. China
| | - Xiaona Wang
- College of Horticulture, China Agricultural University, Beijing, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), the Ministry of Agriculture and Rural Affairs, Beijing, P. R. China
| | - Ying Pi
- College of Horticulture, China Agricultural University, Beijing, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), the Ministry of Agriculture and Rural Affairs, Beijing, P. R. China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), the Ministry of Agriculture and Rural Affairs, Beijing, P. R. China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), the Ministry of Agriculture and Rural Affairs, Beijing, P. R. China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), the Ministry of Agriculture and Rural Affairs, Beijing, P. R. China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), the Ministry of Agriculture and Rural Affairs, Beijing, P. R. China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), the Ministry of Agriculture and Rural Affairs, Beijing, P. R. China
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GWAS, MWAS and mGWAS provide insights into precision agriculture based on genotype-dependent microbial effects in foxtail millet. Nat Commun 2022; 13:5913. [PMID: 36207301 PMCID: PMC9546826 DOI: 10.1038/s41467-022-33238-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 09/09/2022] [Indexed: 11/09/2022] Open
Abstract
Genetic and environmental factors collectively determine plant growth and yield. In the past 20 years, genome-wide association studies (GWAS) have been conducted on crops to decipher genetic loci that contribute to growth and yield, however, plant genotype appears to be insufficient to explain the trait variations. Here, we unravel the associations between genotypic, phenotypic, and rhizoplane microbiota variables of 827 foxtail millet cultivars by an integrated GWAS, microbiome-wide association studies (MWAS) and microbiome genome-wide association studies (mGWAS) method. We identify 257 rhizoplane microbial biomarkers associated with six key agronomic traits and validated the microbial-mediated growth effects on foxtail millet using marker strains isolated from the field. The rhizoplane microbiota composition is mainly driven by variations in plant genes related to immunity, metabolites, hormone signaling and nutrient uptake. Among these, the host immune gene FLS2 and transcription factor bHLH35 are widely associated with the microbial taxa of the rhizoplane. We further uncover a plant genotype-microbiota interaction network that contributes to phenotype plasticity. The microbial-mediated growth effects on foxtail millet are dependent on the host genotype, suggesting that precision microbiome management could be used to engineer high-yielding cultivars in agriculture systems.
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Khanna K, Kohli SK, Sharma N, Kour J, Devi K, Bhardwaj T, Dhiman S, Singh AD, Sharma N, Sharma A, Ohri P, Bhardwaj R, Ahmad P, Alam P, Albalawi TH. Phytomicrobiome communications: Novel implications for stress resistance in plants. Front Microbiol 2022; 13:912701. [PMID: 36274695 PMCID: PMC9583171 DOI: 10.3389/fmicb.2022.912701] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
The agricultural sector is a foremost contributing factor in supplying food at the global scale. There are plethora of biotic as well as abiotic stressors that act as major constraints for the agricultural sector in terms of global food demand, quality, and security. Stresses affect rhizosphere and their communities, root growth, plant health, and productivity. They also alter numerous plant physiological and metabolic processes. Moreover, they impact transcriptomic and metabolomic changes, causing alteration in root exudates and affecting microbial communities. Since the evolution of hazardous pesticides and fertilizers, productivity has experienced elevation but at the cost of impeding soil fertility thereby causing environmental pollution. Therefore, it is crucial to develop sustainable and safe means for crop production. The emergence of various pieces of evidence depicting the alterations and abundance of microbes under stressed conditions proved to be beneficial and outstanding for maintaining plant legacy and stimulating their survival. Beneficial microbes offer a great potential for plant growth during stresses in an economical manner. Moreover, they promote plant growth with regulating phytohormones, nutrient acquisition, siderophore synthesis, and induce antioxidant system. Besides, acquired or induced systemic resistance also counteracts biotic stresses. The phytomicrobiome exploration is crucial to determine the growth-promoting traits, colonization, and protection of plants from adversities caused by stresses. Further, the intercommunications among rhizosphere through a direct/indirect manner facilitate growth and form complex network. The phytomicrobiome communications are essential for promoting sustainable agriculture where microbes act as ecological engineers for environment. In this review, we have reviewed our building knowledge about the role of microbes in plant defense and stress-mediated alterations within the phytomicrobiomes. We have depicted the defense biome concept that infers the design of phytomicrobiome communities and their fundamental knowledge about plant-microbe interactions for developing plant probiotics.
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Affiliation(s)
- Kanika Khanna
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, India
- Department of Microbiology, DAV University, Jalandhar, India
| | - Sukhmeen Kaur Kohli
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, India
| | - Nandni Sharma
- Department of Zoology, Guru Nanak Dev University, Amritsar, India
| | - Jaspreet Kour
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, India
| | - Kamini Devi
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, India
| | - Tamanna Bhardwaj
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, India
| | - Shalini Dhiman
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, India
| | - Arun Dev Singh
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, India
| | - Neerja Sharma
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, India
| | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Puja Ohri
- Department of Zoology, Guru Nanak Dev University, Amritsar, India
| | - Renu Bhardwaj
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, India
| | - Parvaiz Ahmad
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Botany, S.P. College Srinagar, Jammu and Kashmir, India
| | - Pravej Alam
- Department of Biology, College of Science and Humanities, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Thamer H. Albalawi
- Department of Biology, College of Science and Humanities, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
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Wu Y, Sun J, Yu P, Zhang W, Lin Y, Ma D. The rhizosphere bacterial community contributes to the nutritional competitive advantage of weedy rice over cultivated rice in paddy soil. BMC Microbiol 2022; 22:232. [PMID: 36180838 PMCID: PMC9523940 DOI: 10.1186/s12866-022-02648-1] [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: 05/31/2022] [Accepted: 09/22/2022] [Indexed: 11/18/2022] Open
Abstract
Background Weedy rice competes for nutrients and living space with cultivated rice, which results in serious reductions in rice production. The rhizosphere bacterial community plays an important role in nutrient competition between species. It is therefore important to clarify the differences in the diversities of the inter rhizosphere bacterial community between cultivated rice and weedy rice. The differences in compositions and co-occurrence networks of the rhizosphere bacterial community of cultivated rice and weedy rice are largely unknown and thus the aim of our study. Results In our study, the different rhizosphere bacterial community structures in weedy rice (AW), cultivated rice (AY) and cultivated rice surrounded by weedy rice (WY) were determined based on 16S rRNA gene sequencing. The majority of the WY rhizosphere was enriched with unique types of microorganisms belonging to Burkholderia. The rhizosphere bacterial community showed differences in relative abundance among the three groups. Network analysis revealed a more complex co-occurrence network structure in the rhizosphere bacterial community of AW than in those of AY and WY due to a higher degree of Microbacteriaceae and Micrococcaceae in the network. Both network analysis and functional predictions reveal that weedy rice contamination dramatically impacts the iron respiration of the rhizosphere bacterial community of cultivated rice. Conclusions Our study shows that there are many differences in the rhizosphere bacterial community of weedy rice and cultivated rice. When cultivated rice was disturbed by weedy rice, the rhizosphere bacterial community and co-occurrence network also changed. The above differences tend to lead to a nutritional competitive advantage for weedy rice in paddy soils. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02648-1.
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Affiliation(s)
- Yue Wu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Jian Sun
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Pengcheng Yu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Weiliang Zhang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Youze Lin
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Dianrong Ma
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China.
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191
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Wen Z, Yao W, Han M, Xu X, Wu F, Yang M, Fazal A, Yin T, Qi J, Lu G, Yang R, Song X, Yang Y. Differential assembly of root-associated bacterial and fungal communities of a dual transgenic insect-resistant maize line at different host niches and different growth stages. Front Microbiol 2022; 13:1023971. [PMID: 36246225 PMCID: PMC9557180 DOI: 10.3389/fmicb.2022.1023971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
Transgenic technology has been widely applied to crop development, with genetically modified (GM) maize being the world’s second-largest GM crop. Despite the fact that rhizosphere bacterial and fungal populations are critical regulators of plant performance, few studies have evaluated the influence of GM maize on these communities. Plant materials used in this study included the control maize line B73 and the mcry1Ab and mcry2Ab dual transgenic insect-resistant maize line 2A-7. The plants and soils samples were sampled at three growth stages (jointing, flowering, and maturing stages), and the sampling compartments from the outside to the inside of the root are surrounding soil (SS), rhizospheric soil (RS), and intact root (RT), respectively. In this study, the results of alpha diversity revealed that from the outside to the inside of the root, the community richness and diversity declined while community coverage increased. Morever, the different host niches of maize rhizosphere and maize development stages influenced beta diversity according to statistical analysis. The GM maize line 2A-7 had no significant influence on the composition of microbial communities when compared to B73. Compared to RS and SS, the host niche RT tended to deplete Chloroflexi, Gemmatimonadetes and Mortierellomycota at phylum level. Nitrogen-fixation bacteria Pseudomonas, Herbaspirillum huttiense, Rhizobium leguminosarum, and Sphingomonas azotifigens were found to be enriched in the niche RT in comparison to RS and SS, whilst Bacillus was found to be increased and Stenotrophomonas was found to be decreased at the maturing stage as compared to jointing and flowering stages. The nitrogen fixation protein FixH (clusters of orthologous groups, COG5456), was found to be abundant in RT. Furthermore, the pathogen fungus that causes maize stalk rot, Gaeumannomyces radicicola, was found to be abundant in RT, while the beneficial fungus Mortierella hyalina was found to be depleted in RT. Lastly, the abundance of G. radicicola gradually increased during the development of maize. In conclusion, the host niches throughout the soil-plant continuum rather than the Bt insect-resistant gene or Bt protein secretion were primarily responsible for the differential assembly of root-associated microbial communities in GM maize, which provides the theoretical basis for ecological agriculture.
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Affiliation(s)
- Zhongling Wen
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, China
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Weixuan Yao
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Mi Han
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xinhong Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Fengci Wu
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Agro-Biotechnology Research Institute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Minkai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, China
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Aliya Fazal
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Tongming Yin
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Jinliang Qi
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, China
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Guihua Lu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, China
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- School of Life Sciences, Huaiyin Normal University, Huaian, China
| | - Rongwu Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, China
- *Correspondence: Rongwu Yang,
| | - Xinyuan Song
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Agro-Biotechnology Research Institute, Jilin Academy of Agricultural Sciences, Changchun, China
- Xinyuan Song,
| | - Yonghua Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, China
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Yonghua Yang,
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Hui J, An X, Li Z, Neuhäuser B, Ludewig U, Wu X, Schulze WX, Chen F, Feng G, Lambers H, Zhang F, Yuan L. The mycorrhiza-specific ammonium transporter ZmAMT3;1 mediates mycorrhiza-dependent nitrogen uptake in maize roots. THE PLANT CELL 2022; 34:4066-4087. [PMID: 35880836 PMCID: PMC9516061 DOI: 10.1093/plcell/koac225] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/18/2022] [Indexed: 06/15/2023]
Abstract
Most plant species can form symbioses with arbuscular mycorrhizal fungi (AMFs), which may enhance the host plant's acquisition of soil nutrients. In contrast to phosphorus nutrition, the molecular mechanism of mycorrhizal nitrogen (N) uptake remains largely unknown, and its physiological relevance is unclear. Here, we identified a gene encoding an AMF-inducible ammonium transporter, ZmAMT3;1, in maize (Zea mays) roots. ZmAMT3;1 was specifically expressed in arbuscule-containing cortical cells and the encoded protein was localized at the peri-arbuscular membrane. Functional analysis in yeast and Xenopus oocytes indicated that ZmAMT3;1 mediated high-affinity ammonium transport, with the substrate NH4+ being accessed, but likely translocating uncharged NH3. Phosphorylation of ZmAMT3;1 at the C-terminus suppressed transport activity. Using ZmAMT3;1-RNAi transgenic maize lines grown in compartmented pot experiments, we demonstrated that substantial quantities of N were transferred from AMF to plants, and 68%-74% of this capacity was conferred by ZmAMT3;1. Under field conditions, the ZmAMT3;1-dependent mycorrhizal N pathway contributed >30% of postsilking N uptake. Furthermore, AMFs downregulated ZmAMT1;1a and ZmAMT1;3 protein abundance and transport activities expressed in the root epidermis, suggesting a trade-off between mycorrhizal and direct root N-uptake pathways. Taken together, our results provide a comprehensive understanding of mycorrhiza-dependent N uptake in maize and present a promising approach to improve N-acquisition efficiency via plant-microbe interactions.
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Affiliation(s)
- Jing Hui
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, MOE, China Agricultural University, Beijing, 100193, China
| | - Xia An
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, MOE, China Agricultural University, Beijing, 100193, China
| | - Zhibo Li
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, MOE, China Agricultural University, Beijing, 100193, China
| | - Benjamin Neuhäuser
- Department of Nutritional Crop Physiology, Institute of Crop Science, University of Hohenheim, Stuttgart, 70593, Germany
| | - Uwe Ludewig
- Department of Nutritional Crop Physiology, Institute of Crop Science, University of Hohenheim, Stuttgart, 70593, Germany
| | - Xuna Wu
- Department of Plant Systems Biology, Institute for Physiology and Biotechnology of Plants, University of Hohenheim, Stuttgart, 70593, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, Institute for Physiology and Biotechnology of Plants, University of Hohenheim, Stuttgart, 70593, Germany
| | - Fanjun Chen
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, MOE, China Agricultural University, Beijing, 100193, China
| | - Gu Feng
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, MOE, China Agricultural University, Beijing, 100193, China
| | - Hans Lambers
- School of Biological Science and Institute of Agriculture, University of Western Australia, Perth, WA6009, Australia
| | - Fusuo Zhang
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, MOE, China Agricultural University, Beijing, 100193, China
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Afridi MS, Javed MA, Ali S, De Medeiros FHV, Ali B, Salam A, Sumaira, Marc RA, Alkhalifah DHM, Selim S, Santoyo G. New opportunities in plant microbiome engineering for increasing agricultural sustainability under stressful conditions. FRONTIERS IN PLANT SCIENCE 2022; 13:899464. [PMID: 36186071 PMCID: PMC9524194 DOI: 10.3389/fpls.2022.899464] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/08/2022] [Indexed: 07/30/2023]
Abstract
Plant microbiome (or phytomicrobiome) engineering (PME) is an anticipated untapped alternative strategy that could be exploited for plant growth, health and productivity under different environmental conditions. It has been proven that the phytomicrobiome has crucial contributions to plant health, pathogen control and tolerance under drastic environmental (a)biotic constraints. Consistent with plant health and safety, in this article we address the fundamental role of plant microbiome and its insights in plant health and productivity. We also explore the potential of plant microbiome under environmental restrictions and the proposition of improving microbial functions that can be supportive for better plant growth and production. Understanding the crucial role of plant associated microbial communities, we propose how the associated microbial actions could be enhanced to improve plant growth-promoting mechanisms, with a particular emphasis on plant beneficial fungi. Additionally, we suggest the possible plant strategies to adapt to a harsh environment by manipulating plant microbiomes. However, our current understanding of the microbiome is still in its infancy, and the major perturbations, such as anthropocentric actions, are not fully understood. Therefore, this work highlights the importance of manipulating the beneficial plant microbiome to create more sustainable agriculture, particularly under different environmental stressors.
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Affiliation(s)
| | - Muhammad Ammar Javed
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
| | - Sher Ali
- Department of Food Engineering, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), São Paulo, Brazil
| | | | - Baber Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Abdul Salam
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sumaira
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Romina Alina Marc
- Food Engineering Department, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Cluj-Napoca, Romania
| | - Dalal Hussien M. Alkhalifah
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
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Chen C, Yang B, Gao A, Yu Y, Zhao FJ. Transformation of arsenic species by diverse endophytic bacteria of rice roots. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 309:119825. [PMID: 35870529 DOI: 10.1016/j.envpol.2022.119825] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/17/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Rice growing in flooded paddy soil often accumulates considerable levels of inorganic and organic arsenic (As) species, which may cause toxicity to plants and/or pose a risk to human health. The bioavailability and toxicity of As in soil depends on its chemical species, which undergo multiple transformations driven primarily by soil microbes. However, the role of endophytes inside rice roots in As species transformation remains largely unknown. We quantified the abundances of microbial functional genes involved in As transformation in the endosphere and rhizosphere of rice roots growing in three paddy soils in a pot experiment. We also isolated 46 different bacterial endophytes and tested their abilities to transform various As species. The absolute abundances of the arsenate reductase gene arsC and the dissimilatory arsenate reductase gene arrA in the endosphere were comparable to those in the rhizosphere, whereas the absolute abundances of the arsenite methylation gene arsM and arsenite oxidation gene aioA in the endosphere were lower. After normalization based on the bacterial 16S rRNA gene, all four As transformation genes showed higher relative abundances in the endosphere than in the rhizosphere. Consistent with the functional gene data, all of the 30 aerobic endophytic isolates were able to reduce arsenate, but only 3 strains could oxidize arsenite. Among the 16 anaerobic endophytic isolates, 4 strains belonging to Desulfovibrio, Terrisporobacter or Clostridium could methylate arsenite and/or methylarsenite. Six strains of aerobic endophytes could demethylate methylarsenite, among which three strains also could reduce and demethylate methylarsenate. None of the isolates could demethylate dimethylarsenate. These results suggest that diverse endophytes living inside rice roots could participate in As species transformation and affect As accumulation and species distribution in rice plants.
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Affiliation(s)
- Chuan Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Baoyun Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Axiang Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yu Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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195
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A Wild Rice Rhizobacterium Burkholderia cepacia BRDJ Enhances Nitrogen Use Efficiency in Rice. Int J Mol Sci 2022; 23:ijms231810769. [PMID: 36142689 PMCID: PMC9503923 DOI: 10.3390/ijms231810769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022] Open
Abstract
Rice domestication has dramatically improved its agronomic traits, albeit with unavoidable significantly reduced genetic diversity. Dongxiang common wild rice, the wild rice species distributed in northernmost China, exhibits excellent resistance against stress and diseases and provides a rich genetic resource for rice breeding. Most of the studies focus on the function of the plant genes, often disregarding the role of the root microbes associated with the plants. In this work, we isolated a Burkholderia strain from the root of Dongxiang wild rice, which we identified as Burkholderia cepacia BRDJ, based on a phylogenetic analysis. This strain promoted the rice growth under greenhouse conditions. The grain yield was higher in a rice line containing a small genomic fragment derived from the Dongxiang wild rice, compared to the indica rice cultivar Zhongzao 35. This new strain also increased the plant biomass under limiting nitrogen conditions. Interestingly, this strain had a differential effect on indica and japonica rice varieties under full nitrogen supply conditions. By genome sequencing and comparison with another two B. cepacia strains, we observed enriched genes related with nitrogen fixation and phytohormone and volatiles biosynthesis that may account for the growth-promoting effects of the BRDJ. BRDJ has the potential to be used as a biofertilizer in promoting nitrogen use efficiency and overall growth in rice.
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Seasonal Succession and Temperature Response Pattern of a Microbial Community in the Yellow Sea Cold Water Mass. Appl Environ Microbiol 2022; 88:e0116922. [PMID: 36000863 PMCID: PMC9469719 DOI: 10.1128/aem.01169-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Explaining the temporal dynamics of marine microorganisms is critical for predicting their changing pattern under environmental disturbances. Although the effect of temperature on microbial seasonality has been widely studied, the phylogenetic structure of the temperature response pattern and the extent to which temperature shift leads to disruptive community changes are still unclear. Here, we explored the microbial seasonal dynamics in the Yellow Sea Cold Water Mass (YSCWM) that occurs in summer and disappears in winter and tested the temperature thresholds and phylogenetic coherence in response to temperature change. The existence of YSCWM generates strong temperature gradients in summer and confers little temperature change during seasonal transition, thus representing a unique intermediate state. The microbial community of YSCWM is more similar to that in the previous YSCWM in winter than that outside YSCWM. Temperature alone explains >50% of the community variation, suggesting that a temperature shift can induce a nearly seasonality-level community variance in summer. Persistence of most previous winter YSCWM inhabitants in YSCWM leads to conservation in predicted functional potentials and cooccurrence patterns, indicating a decisive role of temperature in maintaining functionality. Evaluation of the temperature threshold reveals that a small temperature change can lead to significant community turnover, with most taxa negatively responding to an elevation in temperature. The temperature response pattern is phylogenetically structured, and closely related taxa show an incohesive response. Our study provides novel insights into microbial seasonality and into how marine microorganisms respond to temperature fluctuations. IMPORTANCE Microbial seasonality is driven by a set of covarying factors including temperature. There is still a lack of understanding of the details of the phylogenetic structure and susceptibility of microbial communities in response to temperature variation. Through examination of the microbial community in a seasonally occurring summer cold water mass, which experiences little temperature change during seasonal transition, we show here that the cold water mass leads to nearly seasonality-level variations in community composition and predicted functional profile in summer. Moreover, massive community turnover occurs within a small temperature shift, with most taxa decreasing in abundance in response to increased temperature, and contrasting response patterns are observed between phylogenetically closely related taxa. These results suggest temperature as the fundamental factor over other covarying factors in structuring microbial seasonality, providing important insights into the variation mode of the microbial community under temperature disturbances.
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197
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Gao Y, Qi S, Wang Y. Nitrate signaling and use efficiency in crops. PLANT COMMUNICATIONS 2022; 3:100353. [PMID: 35754172 PMCID: PMC9483113 DOI: 10.1016/j.xplc.2022.100353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/06/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Nitrate (NO3-) is not only an essential nutrient but also an important signaling molecule for plant growth. Low nitrogen use efficiency (NUE) of crops is causing increasingly serious environmental and ecological problems. Understanding the molecular mechanisms of NO3- regulation in crops is crucial for NUE improvement in agriculture. During the last several years, significant progress has been made in understanding the regulation of NO3- signaling in crops, and some key NO3- signaling factors have been shown to play important roles in NO3- utilization. However, no detailed reviews have yet summarized these advances. Here, we focus mainly on recent advances in crop NO3- signaling, including short-term signaling, long-term signaling, and the impact of environmental factors. We also review the regulation of crop NUE by crucial genes involved in NO3- signaling. This review provides useful information for further research on NO3- signaling in crops and a theoretical basis for breeding new crop varieties with high NUE, which has great significance for sustainable agriculture.
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Affiliation(s)
- Yangyang Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Shengdong Qi
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China.
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Zhou X, Zhang HL, Lu XW, Zhao P, Liu F, Qi ZH, Tang F, Duan WJ, Cai L. Applying meta-data of soybean grain in origin trace and quarantine inspection. Food Res Int 2022; 162:111998. [DOI: 10.1016/j.foodres.2022.111998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/20/2022] [Accepted: 09/26/2022] [Indexed: 11/04/2022]
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199
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Zhang Z, Xiao YS, Zhan Y, Zhang Z, Liu Y, Wei Y, Xu T, Li J. Tomato microbiome under long-term organic and conventional farming. IMETA 2022; 1:e48. [PMID: 38868718 PMCID: PMC10989780 DOI: 10.1002/imt2.48] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/30/2022] [Accepted: 07/25/2022] [Indexed: 06/14/2024]
Abstract
The compartment niche is the main reason behind the shifts in endophytic bacterial communities. Long-term organic greenhouse exerted limited influence on the variations of endophytic bacterial communities. Organic greenhouse and root had more complex co-occurrence networks than conventional greenhouse and stem, respectively. Cultivable method results found that Protecbacteria, Bacteriodes, and Actinobacteria are the dominant phyla in the endophytes.
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Affiliation(s)
- Zeyu Zhang
- College of Resources and Environmental ScienceChina Agricultural UniversityBeijingChina
| | - Yang Sean Xiao
- College of Water Resources and Civil EngineeringChina Agricultural UniversityBeijingChina
| | - Yabin Zhan
- College of Resources and Environmental ScienceChina Agricultural UniversityBeijingChina
| | - Zengqiang Zhang
- College of Resources and Environmental ScienceNorthwest A&F UniversityYanglinChina
| | - Youzhou Liu
- Institute of Plant ProtectionJiangsu Academy of Agricultural SciencesNanjingChina
| | - Yuquan Wei
- College of Resources and Environmental ScienceChina Agricultural UniversityBeijingChina
| | - Ting Xu
- College of Resources and Environmental ScienceChina Agricultural UniversityBeijingChina
| | - Ji Li
- College of Resources and Environmental ScienceChina Agricultural UniversityBeijingChina
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Santos-Medellín C, Edwards J, Nguyen B, Sundaresan V. Acquisition of a complex root microbiome reshapes the transcriptomes of rice plants. THE NEW PHYTOLOGIST 2022; 235:2008-2021. [PMID: 35590484 DOI: 10.1111/nph.18261] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Soil microorganisms can colonize plant roots and assemble in communities engaged in symbiotic relationships with their host. Though the compositional dynamics of root-associated microbiomes have been extensively studied, the host transcriptional response to these communities is poorly understood. Here, we developed an experimental system by which rice plants grown under axenic conditions can acquire a defined endosphere microbiome. Using this setup, we performed a cross-sectional characterization of plant transcriptomes in the presence or absence of a complex microbial community. To account for compositional variation, plants were inoculated with soil-derived microbiomes harvested from three distinct agricultural sites. Soil microbiomes triggered a major shift in the transcriptional profiles of rice plants that included the downregulation of one-third to one-fourth of the families of leucine-rich repeat receptor-like kinases and nucleotide-binding leucine-rich repeat receptors expressed in roots. Though the expression of several genes was consistent across all soil sources, a large fraction of this response was differentially impacted by soil type. These results demonstrate the role of root microbiomes in sculpting the transcriptomes of host plants and highlight the potential involvement of the two main receptor families of the plant immune system in the recruitment and maintenance of an endosphere microbiome.
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Affiliation(s)
| | - Joseph Edwards
- Department of Plant Biology, University of California, Davis, Davis, CA, 95616, USA
| | - Bao Nguyen
- Department of Plant Biology, University of California, Davis, Davis, CA, 95616, USA
| | - Venkatesan Sundaresan
- Department of Plant Biology, University of California, Davis, Davis, CA, 95616, USA
- Department of Plant Sciences, University of California, Davis, Davis, CA, 95616, USA
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