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Jiang X, Peng Z, Zhang J. Starting with screening strains to construct synthetic microbial communities (SynComs) for traditional food fermentation. Food Res Int 2024; 190:114557. [PMID: 38945561 DOI: 10.1016/j.foodres.2024.114557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/16/2024] [Accepted: 05/26/2024] [Indexed: 07/02/2024]
Abstract
With the elucidation of community structures and assembly mechanisms in various fermented foods, core communities that significantly influence or guide fermentation have been pinpointed and used for exogenous restructuring into synthetic microbial communities (SynComs). These SynComs simulate ecological systems or function as adjuncts or substitutes in starters, and their efficacy has been widely verified. However, screening and assembly are still the main limiting factors for implementing theoretic SynComs, as desired strains cannot be effectively obtained and integrated. To expand strain screening methods suitable for SynComs in food fermentation, this review summarizes the recent research trends in using SynComs to study community evolution or interaction and improve the quality of food fermentation, as well as the specific process of constructing synthetic communities. The potential for novel screening modalities based on genes, enzymes and metabolites in food microbial screening is discussed, along with the emphasis on strategies to optimize assembly for facilitating the development of synthetic communities.
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Affiliation(s)
- Xinyi Jiang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zheng Peng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Juan Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China.
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Wang Y, Wang Y, Zhou K, Zhang H, Cheng M, Wang B, Yan X. Isolation of a facultative methanotroph Methylocystis iwaonis SD4 from rice rhizosphere and establishment of rapid genetic tools for it. Biotechnol Lett 2024; 46:713-724. [PMID: 38733438 DOI: 10.1007/s10529-024-03495-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/10/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024]
Abstract
Methanotrophs of the genus Methylocystis are frequently found in rice paddies. Although more than ten facultative methanotrophs have been reported since 2005, none of these strains was isolated from paddy soil. Here, a facultative methane-oxidizing bacterium, Methylocystis iwaonis SD4, was isolated and characterized from rhizosphere samples of rice plants in Nanjing, China. This strain grew well on methane or methanol but was able to grow slowly using acetate or ethanol. Moreover, strain SD4 showed sustained growth at low concentrations of methane (100 and 500 ppmv). M. iwaonis SD4 could utilize diverse nitrogen sources, including nitrate, urea, ammonium as well as dinitrogen. Strain SD4 possessed genes encoding both the particulate methane monooxygenase and the soluble methane monooxygenase. Simple and rapid genetic manipulation methods were established for this strain, enabling vector transformation and unmarked genetic manipulation. Fast growth rate and efficient genetic tools make M. iwaonis SD4 an ideal model to study facultative methanotrophs, and the ability to grow on low concentration of methane implies its potential in methane removal.
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Affiliation(s)
- Yinghui Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Yuying Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Keyu Zhou
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Haili Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Minggen Cheng
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Baozhan Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Xin Yan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China.
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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Zhang B, Nasar J, Dong S, Zhou X, Gao Q. Differential regulation of belowground rhizospheric ecosystem by biological and chemical nitrogen supplies: implications for maize yield enhancement mechanisms. PLANT BIOLOGY (STUTTGART, GERMANY) 2024. [PMID: 38985647 DOI: 10.1111/plb.13689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 06/04/2024] [Indexed: 07/12/2024]
Abstract
Nitrogen (N) content affects aboveground maize growth and nutrient absorption by altering the belowground rhizospheric ecosystem, impacting both yield and quality. However, the mechanisms through which different N supply methods (chemical and biological N supplies) regulate the belowground rhizospheric ecosystem to enhance maize yield remain unclear. To address this issue, we conducted a field experiment in northeast China, comprising three treatments: maize monocropping without N fertilizer application (MM), maize/alfalfa intercropping without N fertilizer application (BNF), and maize monocropping with N fertilizer application (CNS). The MM treatment represents the control, while the BNF treatment represents the biological N supply form, and CNS treatment represents the chemical N supply form. In the autumn of 2019, samples of maize and rhizospheric soil were collected to assess parameters including yield, rhizospheric soil characteristics, and microbial indicators. Both BNF and MM significantly increased maize yield and different yield components compared with MM, with no statistically significant difference in total yield between BNF and CNS. Furthermore, BNF significantly improved N by 12.61% and available N (AN) by 13.20% compared with MM. Furthermore, BNF treatment also significantly increased the Shannon index by 1.90%, while the CNS treatment significantly increased the Chao1 index by 28.1% and ACE index by 29.49%, with no significant difference between CNS and BNF. However, CNS had a more pronounced impact on structure of the rhizosphere soil bacterial community compared to BNF, inducing more significant fluctuations within the microbial network (modularity index and negative cohesion index). Regarding N transformation pathways predicted by bacterial functions, BNF significantly increased the N fixation pathway, while CNS significantly increased assimilatory nitrate reduction. In CNS, AN, NO3-N, NH4-N, assimilatory nitrate reduction, and community structure contributed significantly to maize yield, whereas in BNF, N fixation, community structure, community stability, NO3-N, and NH4-N played significant roles in enhancing maize yield. While CNS and BNF can achieve comparable maize yields in practical agricultural production, they have significantly different impacts on the belowground rhizosphere ecosystem, leading to different mechanisms of yield enhancement.
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Affiliation(s)
- B Zhang
- College of Resources and Environmental Sciences/Key Laboratory of Sustainable Utilization of Soil Resources in the Commodity Grain Bases in Jilin Province, Jilin Agricultural University, Changchun, China
| | - J Nasar
- College of Resources and Environmental Sciences/Key Laboratory of Sustainable Utilization of Soil Resources in the Commodity Grain Bases in Jilin Province, Jilin Agricultural University, Changchun, China
| | - S Dong
- College of Resources and Environmental Sciences/Key Laboratory of Sustainable Utilization of Soil Resources in the Commodity Grain Bases in Jilin Province, Jilin Agricultural University, Changchun, China
| | - X Zhou
- College of Resources and Environmental Sciences/Key Laboratory of Sustainable Utilization of Soil Resources in the Commodity Grain Bases in Jilin Province, Jilin Agricultural University, Changchun, China
| | - Q Gao
- College of Resources and Environmental Sciences/Key Laboratory of Sustainable Utilization of Soil Resources in the Commodity Grain Bases in Jilin Province, Jilin Agricultural University, Changchun, China
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Wang D, He X, Baer M, Lami K, Yu B, Tassinari A, Salvi S, Schaaf G, Hochholdinger F, Yu P. Lateral root enriched Massilia associated with plant flowering in maize. MICROBIOME 2024; 12:124. [PMID: 38982519 PMCID: PMC11234754 DOI: 10.1186/s40168-024-01839-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 05/16/2024] [Indexed: 07/11/2024]
Abstract
BACKGROUND Beneficial associations between plants and soil microorganisms are critical for crop fitness and resilience. However, it remains obscure how microorganisms are assembled across different root compartments and to what extent such recruited microbiomes determine crop performance. Here, we surveyed the root transcriptome and the root and rhizosphere microbiome via RNA sequencing and full-length (V1-V9) 16S rRNA gene sequencing from genetically distinct monogenic root mutants of maize (Zea mays L.) under different nutrient-limiting conditions. RESULTS Overall transcriptome and microbiome display a clear assembly pattern across the compartments, i.e., from the soil through the rhizosphere to the root tissues. Co-variation analysis identified that genotype dominated the effect on the microbial community and gene expression over the nutrient stress conditions. Integrated transcriptomic and microbial analyses demonstrated that mutations affecting lateral root development had the largest effect on host gene expression and microbiome assembly, as compared to mutations affecting other root types. Cooccurrence and trans-kingdom network association analysis demonstrated that the keystone bacterial taxon Massilia (Oxalobacteraceae) is associated with root functional genes involved in flowering time and overall plant biomass. We further observed that the developmental stage drives the differentiation of the rhizosphere microbial assembly, especially the associations of the keystone bacteria Massilia with functional genes in reproduction. Taking advantage of microbial inoculation experiments using a maize early flowering mutant, we confirmed that Massilia-driven maize growth promotion indeed depends on flowering time. CONCLUSION We conclude that specific microbiota supporting lateral root formation could enhance crop performance by mediating functional gene expression underlying plant flowering time in maize. Video Abstract.
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Affiliation(s)
- Danning Wang
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
| | - Xiaoming He
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
| | - Marcel Baer
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
| | - Klea Lami
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
- Plant Nutrition, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
| | - Baogang Yu
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
| | - Alberto Tassinari
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, 40127, Italy
| | - Silvio Salvi
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, 40127, Italy
| | - Gabriel Schaaf
- Plant Nutrition, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
| | - Frank Hochholdinger
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
| | - Peng Yu
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany.
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany.
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Huang H, Li M, Guo Q, Zhang R, Zhang Y, Luo K, Chen Y. Influence of Drought Stress on the Rhizosphere Bacterial Community Structure of Cassava ( Manihot esculenta Crantz). Int J Mol Sci 2024; 25:7326. [PMID: 39000433 PMCID: PMC11242396 DOI: 10.3390/ijms25137326] [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: 05/29/2024] [Revised: 06/26/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024] Open
Abstract
Drought presents a significant abiotic stress that threatens crop productivity worldwide. Rhizosphere bacteria play pivotal roles in modulating plant growth and resilience to environmental stresses. Despite this, the extent to which rhizosphere bacteria are instrumental in plant responses to drought, and whether distinct cassava (Manihot esculenta Crantz) varieties harbor specific rhizosphere bacterial assemblages, remains unclear. In this study, we measured the growth and physiological characteristics, as well as the physical and chemical properties of the rhizosphere soil of drought-tolerant (SC124) and drought-sensitive (SC8) cassava varieties under conditions of both well-watered and drought stress. Employing 16S rDNA high-throughput sequencing, we analyzed the composition and dynamics of the rhizosphere bacterial community. Under drought stress, biomass, plant height, stem diameter, quantum efficiency of photosystem II (Fv/Fm), and soluble sugar of cassava decreased for both SC8 and SC124. The two varieties' rhizosphere bacterial communities' overall taxonomic structure was highly similar, but there were slight differences in relative abundance. SC124 mainly relied on Gamma-proteobacteria and Acidobacteriae in response to drought stress, and the abundance of this class was positively correlated with soil acid phosphatase. SC8 mainly relied on Actinobacteria in response to drought stress, and the abundance of this class was positively correlated with soil urease and soil saccharase. Overall, this study confirmed the key role of drought-induced rhizosphere bacteria in improving the adaptation of cassava to drought stress and clarified that this process is significantly related to variety.
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Affiliation(s)
- Huling Huang
- School of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (H.H.); (M.L.); (Q.G.); (R.Z.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Mingchao Li
- School of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (H.H.); (M.L.); (Q.G.); (R.Z.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Qiying Guo
- School of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (H.H.); (M.L.); (Q.G.); (R.Z.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Rui Zhang
- School of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (H.H.); (M.L.); (Q.G.); (R.Z.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Yindong Zhang
- Key Laboratory of Plant Disease and Pest Control of Hainan Province, Institute of Plant Protection, Hainan Academy of Agricultural Sciences, Haikou 571100, China;
| | - Kai Luo
- School of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (H.H.); (M.L.); (Q.G.); (R.Z.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Yinhua Chen
- School of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (H.H.); (M.L.); (Q.G.); (R.Z.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
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Jyoti SD, Singh G, Pradhan AK, Tarpley L, Septiningsih EM, Talukder SK. Rice breeding for low input agriculture. FRONTIERS IN PLANT SCIENCE 2024; 15:1408356. [PMID: 38974981 PMCID: PMC11224470 DOI: 10.3389/fpls.2024.1408356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/24/2024] [Indexed: 07/09/2024]
Abstract
A low-input-based farming system can reduce the adverse effects of modern agriculture through proper utilization of natural resources. Modern varieties often need to improve in low-input settings since they are not adapted to these systems. In addition, rice is one of the most widely cultivated crops worldwide. Enhancing rice performance under a low input system will significantly reduce the environmental concerns related to rice cultivation. Traits that help rice to maintain yield performance under minimum inputs like seedling vigor, appropriate root architecture for nutrient use efficiency should be incorporated into varieties for low input systems through integrated breeding approaches. Genes or QTLs controlling nutrient uptake, nutrient assimilation, nutrient remobilization, and root morphology need to be properly incorporated into the rice breeding pipeline. Also, genes/QTLs controlling suitable rice cultivars for sustainable farming. Since several variables influence performance under low input conditions, conventional breeding techniques make it challenging to work on many traits. However, recent advances in omics technologies have created enormous opportunities for rapidly improving multiple characteristics. This review highlights current research on features pertinent to low-input agriculture and provides an overview of alternative genomics-based breeding strategies for enhancing genetic gain in rice suitable for low-input farming practices.
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Affiliation(s)
- Subroto Das Jyoti
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Gurjeet Singh
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | | | - Lee Tarpley
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Shyamal K. Talukder
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
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Xu S, Hong L, Wu T, Liu X, Ding Z, Liu L, Shao Q, Zheng Y, Xing B. Insight into saffron associated microbiota from different origins and explore the endophytes for enhancement of bioactive compounds. Food Chem 2024; 456:140006. [PMID: 38870814 DOI: 10.1016/j.foodchem.2024.140006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/31/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
Crocus sativus L. is a perennial crop for its valuable active compounds. Plant-associated microbes impact on the quality and efficacy of medicinal herbs by promoting bioactive components accumulation. However, how microbes influence the accumulation of bioactive components in saffron have not been well studied. Here, the microbiome in C. sativus derived from 3 core production areas were deciphered by 16S rDNA sequencing and the relationship between endophytes and bioactive ingredients were further investigated. The main results are as follows: (1) Both Comamonadaceae and Burkholderiaceae were positively correlated with the content of bioactive components in the stigmas. (2) The synthesis of crocin was positively correlated with Xanthomonadaceae, negatively correlated with Lachnospiraceae and Prevotellaceae. Therefore, further investigation is required to determine whether Xanthomonadaceae plays an unknown function in the synthesis of crocin. These findings provide guidelines for disentangling the function of endophytes in the production of bioactive ingredients and thus for microbe-mediated breeding.
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Affiliation(s)
- Sirui Xu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China; Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A & F University, Hangzhou 311300, China
| | - Liang Hong
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China; Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A & F University, Hangzhou 311300, China
| | - Tong Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China; Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A & F University, Hangzhou 311300, China
| | - Xinting Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China; Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A & F University, Hangzhou 311300, China
| | - Zihan Ding
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China; Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A & F University, Hangzhou 311300, China
| | - Li Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China; Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A & F University, Hangzhou 311300, China
| | - Qingsong Shao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China; Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A & F University, Hangzhou 311300, China
| | - Ying Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China; Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A & F University, Hangzhou 311300, China.
| | - Bingcong Xing
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China; Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A & F University, Hangzhou 311300, China.
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Zhou X, Chen X, Yang K, Guo X, Liu G, Zhuang G, Zheng G, Fortin D, Ma A. Vegetation restoration in an alpine meadow: Insights from soil microbial communities and resource limitation across soil depth. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 360:121129. [PMID: 38749128 DOI: 10.1016/j.jenvman.2024.121129] [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: 03/30/2024] [Revised: 05/01/2024] [Accepted: 05/08/2024] [Indexed: 06/05/2024]
Abstract
Aboveground vegetation restoration shapes the soil microbial community structure and affects microbial resource acquisition. However, the changes in soil microbial resource limitation in subsoil during vegetation restoration are still unclear. In this study, the microbial community structure and resource limitation in an alpine meadow soil profile that had undergone natural restoration for short-term (4-year) and long-term (10-year) restoration in response to vegetation restoration were explored through high-throughput sequencing analysis and extracellular enzyme stoichiometry (EES). There was no significant difference in microbial composition and α diversity between short- and long-term restoration soils. Soil microorganisms in this alpine meadow were mainly limited by phosphorus. Carbon limitation of soil microorganisms was significantly decreased in each layer (0-15, 15-30, 30-45, 45-60, and 60-80 cm corresponding to L1, L2, L3, L4, and L5, respectively) of long-term restoration soils when compared to that of the short-term restoration soil layers, while phosphorus limitation of microorganisms in subsoil (60-80 cm) was significantly increased by 17.38%. Soil nutrients, pH, moisture content, and microbial composition are the main drivers of microbial resource limitation in restoration, and their effects on microbial resource limitation were different in short- and long-term restoration. Meanwhile, key microbial taxa have a significant impact on microbial resource limitation, especially in short-term restoration soils. This study suggested that vegetation restoration significantly affected soil microbial resource limitation, and could alleviate microbial resource limitations by adding nutrients, thus accelerating the process of vegetation restoration in alpine ecosystems.
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Affiliation(s)
- Xiaorong Zhou
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianke Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 101400, China; Sino-Danish Center for Education and Research, Beijing, 101400, China
| | - Kang Yang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaowei Guo
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Guohua Liu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guoqiang Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guodong Zheng
- School of Environmental Studies, China University of Geosciences, Wuhan, 430078, China
| | | | - Anzhou Ma
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
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9
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Xun W, Liu Y, Ma A, Yan H, Miao Y, Shao J, Zhang N, Xu Z, Shen Q, Zhang R. Dissection of rhizosphere microbiome and exploiting strategies for sustainable agriculture. THE NEW PHYTOLOGIST 2024; 242:2401-2410. [PMID: 38494698 DOI: 10.1111/nph.19697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 03/07/2024] [Indexed: 03/19/2024]
Abstract
The rhizosphere microbiome plays critical roles in plant growth and provides promising solutions for sustainable agriculture. While the rhizosphere microbiome frequently fluctuates with the soil environment, recent studies have demonstrated that a small proportion of the microbiome is consistently assembled in the rhizosphere of a specific plant genotype regardless of the soil condition, which is determined by host genetics. Based on these breakthroughs, which involved exploiting the plant-beneficial function of the rhizosphere microbiome, we propose to divide the rhizosphere microbiome into environment-dominated and plant genetic-dominated components based on their different assembly mechanisms. Subsequently, two strategies to explore the different rhizosphere microbiome components for agricultural production are suggested, that is, the precise management of the environment-dominated rhizosphere microbiome by agronomic practices, and the elucidation of the plant genetic basis of the plant genetic-dominated rhizosphere microbiome for breeding microbiome-assisted crop varieties. We finally present the major challenges that need to be overcome to implement strategies for modulating these two components of the rhizosphere microbiome.
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Affiliation(s)
- Weibing Xun
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunpeng Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Aiyuan Ma
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - He Yan
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Youzhi Miao
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiahui Shao
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Nan Zhang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhihui Xu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruifu Zhang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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10
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Yang M, Chen T, Liu Y, Huang L. Visualizing set relationships: EVenn's comprehensive approach to Venn diagrams. IMETA 2024; 3:e184. [PMID: 38898979 PMCID: PMC11183158 DOI: 10.1002/imt2.184] [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: 02/04/2024] [Revised: 02/24/2024] [Accepted: 03/01/2024] [Indexed: 06/21/2024]
Abstract
Venn diagrams serve as invaluable tools for visualizing set relationships due to their ease of interpretation. Widely applied across diverse disciplines such as metabolomics, genomics, transcriptomics, and proteomics, their utility is undeniable. However, the operational complexity has been compounded by the absence of standardized data formats and the need to switch between various platforms for generating different Venn diagrams. To address these challenges, we introduce the EVenn platform, a versatile tool offering a unified interface for efficient data exploration and visualization of diverse Venn diagrams. EVenn (http://www.ehbio.com/test/venn) streamlines the data upload process with a standardized format, enhancing the capabilities for multimodule analysis. This comprehensive protocol outlines various applications of EVenn, featuring representative results of multiple Venn diagrams, data uploads in the centralized data center, and step-by-step case demonstrations. Through these functionalities, EVenn emerges as a valuable and user-friendly tool for the in-depth exploration of multiomics data.
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Affiliation(s)
- Mei Yang
- Institute of Traditional Chinese MedicineTianjin University of Traditional Chinese MedicineTianjinChina
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao‐di Herbs, National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Tong Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao‐di Herbs, National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Yong‐Xin Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Luqi Huang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao‐di Herbs, National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
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11
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Gao Y, Yang Q, Chen Q, He Y, He W, Geng J, Zhang Y, Zhou Y, Zhu ZR. Plants attacked above-ground by leaf-mining flies change below-ground microbiota to enhance plant defense. HORTICULTURE RESEARCH 2024; 11:uhae121. [PMID: 38919561 PMCID: PMC11197306 DOI: 10.1093/hr/uhae121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 04/14/2024] [Indexed: 06/27/2024]
Abstract
Root-associated microbiomes play a crucial role in plant responses to biotic and abiotic stresses. Plants can enrich beneficial microbes to increase their stress-relieving ability. Above-ground insect herbivory is among the most detrimental stresses for plants, especially to crop production. However, few studies have explored how root-associated microbiomes respond to herbivores and influence plant-defense functions under herbivory stress. We investigate the changes and functional role of root-associated microbial communities under herbivory stress using leafminer (Liriomyza trifolii) and cowpea (Vigna unguiculata) as a focal system. We did this by using a combination of 16S ribosomal RNA gene profiling and metagenomic sequencing to test for differences in co-occurrence networks and functions between cowpea plants infested and noninfested with leafminers. The results demonstrated that leafminer infestation caused a shift in the rhizosphere microbiome, which was characterized by a significant variation in microbiome community structure and composition, the selection of hub microbes involved in nitrogen (N) metabolism, and functional enrichment related to N metabolism. Notably, nitrogen-fixing bacteria Bradyrhizobium species were actively enriched and selected to be hubs in the rhizosphere. Inoculation with Bradyrhizobium enhanced cowpea performance under leafminer stress and increased protease inhibitor levels to decrease leafminer fitness. Overall, our study characterized the changes of root-associated microbiota between leafminer-infested and noninfested cowpea plants and revealed the mechanisms underlying the rhizosphere microbiome shift that enhance plant performance and defense against herbivory. Our findings provide further support for the notion that plants enrich rhizosphere microbes to counteract aboveground insect herbivores.
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Affiliation(s)
- Yang Gao
- Hainan Institute, Zhejiang University, Sanya, 572025, China
- State Key Laboratory of Rice Biology, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qiong Yang
- School of BioSciences, Bio21 Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Qiulin Chen
- Hainan Institute, Zhejiang University, Sanya, 572025, China
- State Key Laboratory of Rice Biology, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yunchuan He
- Hainan Institute, Zhejiang University, Sanya, 572025, China
- State Key Laboratory of Rice Biology, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wei He
- Hainan Institute, Zhejiang University, Sanya, 572025, China
- State Key Laboratory of Rice Biology, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jiamei Geng
- Hainan Institute, Zhejiang University, Sanya, 572025, China
- State Key Laboratory of Rice Biology, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yunzeng Zhang
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Ying Zhou
- Hainan Institute, Zhejiang University, Sanya, 572025, China
| | - Zeng-Rong Zhu
- Hainan Institute, Zhejiang University, Sanya, 572025, China
- State Key Laboratory of Rice Biology, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
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12
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Wang Z, Dai Q, Su D, Zhang Z, Tian Y, Tong J, Chen S, Yan C, Yang J, Cui X. Comparative analysis of the microbiomes of strawberry wild species Fragaria nilgerrensis and cultivated variety Akihime using amplicon-based next-generation sequencing. Front Microbiol 2024; 15:1377782. [PMID: 38873161 PMCID: PMC11169695 DOI: 10.3389/fmicb.2024.1377782] [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: 01/28/2024] [Accepted: 05/07/2024] [Indexed: 06/15/2024] Open
Abstract
Fragaria nilgerrensis is a wild strawberry species widely distributed in southwest China and has strong ecological adaptability. Akihime (F. × ananassa Duch. cv. Akihime) is one of the main cultivated strawberry varieties in China and is prone to infection with a variety of diseases. In this study, high-throughput sequencing was used to analyze and compare the soil and root microbiomes of F. nilgerrensis and Akihime. Results indicate that the wild species F. nilgerrensis showed higher microbial diversity in nonrhizosphere soil and rhizosphere soil and possessed a more complex microbial network structure compared with the cultivated variety Akihime. Genera such as Bradyrhizobium and Anaeromyxobacter, which are associated with nitrogen fixation and ammonification, and Conexibacter, which is associated with ecological toxicity resistance, exhibited higher relative abundances in the rhizosphere and nonrhizosphere soil samples of F. nilgerrensis compared with those of Akihime. Meanwhile, the ammonia-oxidizing archaea Candidatus Nitrososphaera and Candidatus Nitrocosmicus showed the opposite tendencies. We also found that the relative abundances of potential pathogenic genera and biocontrol bacteria in the Akihime samples were higher than those in the F. nilgerrensis samples. The relative abundances of Blastococcus, Nocardioides, Solirubrobacter, and Gemmatimonas, which are related to pesticide degradation, and genus Variovorax, which is associated with root growth regulation, were also significantly higher in the Akihime samples than in the F. nilgerrensis samples. Moreover, the root endophytic microbiomes of both strawberry species, especially the wild F. nilgerrensis, were mainly composed of potential biocontrol and beneficial bacteria, making them important sources for the isolation of these bacteria. This study is the first to compare the differences in nonrhizosphere and rhizosphere soils and root endogenous microorganisms between wild and cultivated strawberries. The findings have great value for the research of microbiomes, disease control, and germplasm innovation of strawberry.
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Affiliation(s)
- Zongneng Wang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Qingzhong Dai
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Daifa Su
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | | | - Yunxia Tian
- Kunming Academy of Agricultural Science, Kunming, China
| | - Jiangyun Tong
- Kunming Academy of Agricultural Science, Kunming, China
| | - Shanyan Chen
- Kunming Academy of Agricultural Science, Kunming, China
| | - Congwen Yan
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Junyu Yang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
- Yunnan International Joint Laboratory of Virology and Immunology, Kunming, China
| | - Xiaolong Cui
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
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13
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Wang T, Gao M, Shao W, Wang L, Yang C, Wang X, Yao S, Zhang B. Dissecting the role of soybean rhizosphere-enriched bacterial taxa in modulating nitrogen-cycling functions. Appl Microbiol Biotechnol 2024; 108:347. [PMID: 38805033 PMCID: PMC11133221 DOI: 10.1007/s00253-024-13184-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/30/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024]
Abstract
Crop roots selectively recruit certain microbial taxa that are essential for supporting their growth. Within the recruited microbes, some taxa are consistently enriched in the rhizosphere across various locations and crop genotypes, while others are unique to specific planting sites or genotypes. Whether these differentially enriched taxa are different in community composition and how they interact with nutrient cycling need further investigation. Here, we sampled bulk soil and the rhizosphere soil of five soybean varieties grown in Shijiazhuang and Xuzhou, categorized the rhizosphere-enriched microbes into shared, site-specific, and variety-specific taxa, and analyzed their correlation with the diazotrophic communities and microbial genes involved in nitrogen (N) cycling. The shared taxa were dominated by Actinobacteria and Thaumarchaeota, the site-specific taxa were dominated by Actinobacteria in Shijiazhuang and by Nitrospirae in Xuzhou, while the variety-specific taxa were more evenly distributed in several phyla and contained many rare operational taxonomic units (OTUs). The rhizosphere-enriched taxa correlated with most diazotroph orders negatively but with eight orders including Rhizobiales positively. Each group within the shared, site-specific, and variety-specific taxa negatively correlated with bacterial amoA and narG in Shijiazhuang and positively correlated with archaeal amoA in Xuzhou. These results revealed that the shared, site-specific, and variety-specific taxa are distinct in community compositions but similar in associations with rhizosphere N-cycling functions. They exhibited potential in regulating the soybean roots' selection for high-efficiency diazotrophs and the ammonia-oxidizing and denitrification processes. This study provides new insights into soybean rhizosphere-enriched microbes and their association with N cycling. KEY POINTS: • Soybean rhizosphere affected diazotroph community and enriched nifH, amoA, and nosZ. • Shared and site- and variety-specific taxa were dominated by different phyla. • Rhizosphere-enriched taxa were similarly associated with N-cycle functions.
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Affiliation(s)
- Tianshu Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Miao Gao
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weiwei Shao
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Li Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chunyan Yang
- The Key Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050031, China
| | - Xing Wang
- Jiangsu Xuhuai Regional Institute of Agricultural Sciences, Xuzhou, 221131, China
| | - Shuihong Yao
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Bin Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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14
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Griffin C, Oz MT, Demirer GS. Engineering plant-microbe communication for plant nutrient use efficiency. Curr Opin Biotechnol 2024; 88:103150. [PMID: 38810302 DOI: 10.1016/j.copbio.2024.103150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024]
Abstract
Nutrient availability and efficient use are critical for crop productivity. Current agricultural practices rely on excessive chemical fertilizers, contributing to greenhouse gas emissions and environmental pollution. Rhizosphere microbes facilitate plant nutrient acquisition and contribute to nutrient use efficiency. Thus, engineering plant-microbe communication within the rhizosphere emerges as a promising and sustainable strategy to enhance agricultural productivity. Recent advances in plant engineering have enabled the development of plants capable of selectively enriching beneficial microbes through root exudates. At the same time, synthetic biology techniques have produced microbes capable of improving nutrient availability and uptake by plants. By engineering plant-microbe communication, researchers aim to harness beneficial soil microbes, thereby offering a targeted and efficient approach to optimizing plant nutrient use efficiency.
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Affiliation(s)
- Catherine Griffin
- Department of Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - M Tufan Oz
- Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Gozde S Demirer
- Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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15
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Chi Z, Li Y, Zhang J, Hu M, Wu Y, Fan X, Li Z, Miao Q, Li W. Effects of nitrogen application on ammonium assimilation and microenvironment in the rhizosphere of drip-irrigated sunflower under plastic mulch. Front Microbiol 2024; 15:1390331. [PMID: 38841064 PMCID: PMC11150556 DOI: 10.3389/fmicb.2024.1390331] [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: 02/23/2024] [Accepted: 05/07/2024] [Indexed: 06/07/2024] Open
Abstract
This study investigated the effect of nitrogen application on the rhizosphere soil microenvironment of sunflower and clarified the relationship between ammonium assimilation and the microenvironment. In a field experiment high (HN, 190 kg/hm2), medium (MN, 120 kg/hm2) and low nitrogen (CK, 50 kg/hm2) treatments were made to replicate plots of sunflowers using drip irrigation. Metagenomic sequencing was used to analyze the community structure and functional genes involved in the ammonium assimilation pathway in rhizosphere soil. The findings indicated that glnA and gltB played a crucial role in the ammonium assimilation pathway in sunflower rhizosphere soil, with Actinobacteria and Proteobacteria being the primary contributors. Compared with CK treatment, the relative abundance of Actinobacteria increased by 15.57% under MN treatment, while the relative abundance decreased at flowering and maturation stages. Conversely, the relative abundance of Proteobacteria was 28.57 and 61.26% higher in the MN treatment during anthesis and maturation period, respectively, compared with the CK. Furthermore, during the bud stage and anthesis, the abundance of Actinobacteria, Proteobacteria, and their dominant species were influenced mainly by rhizosphere soil EC, ammonium nitrogen (NH 4 + -N), and nitrate nitrogen (NO 3 - -N), whereas, at maturity, soil pH and NO 3 - -N played a more significant role in shaping the community of ammonium-assimilating microorganisms. The MN treatment increased the root length density, surface area density, and root volume density of sunflower at the bud, flowering, and maturity stages compared to the CK. Moreover, root exudates such as oxalate and malate were positively correlated with the dominant species of Actinobacteria and Proteobacteria during anthesis and the maturation period. Under drip irrigation, applying 120 kg/hm2 of nitrogen to sunflowers effectively promoted the community structure of ammonium-assimilating microorganisms in rhizosphere soil and had a positive influence on the rhizosphere soil microenvironment and sunflower root growth.
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Affiliation(s)
- Zhaonan Chi
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Yuxin Li
- Inner Mongolia Key Lab of Molecular Biology, Inner Mongolia Medical University, Hohhot, China
| | - Jiapeng Zhang
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Min Hu
- Vocational and Technical College of Inner Mongolia Agricultural University, Baotou, China
| | - Yixuan Wu
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Xueqin Fan
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhen Li
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Qingfeng Miao
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Weiping Li
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, China
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16
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Guo JW, Mohamad OAA, Wang X, Egamberdieva D, Tian B. Editorial: Microbiome associated with plant pathogens, pathogenesis, and their applications in developing sustainable agriculture. Front Microbiol 2024; 15:1423961. [PMID: 38841068 PMCID: PMC11152044 DOI: 10.3389/fmicb.2024.1423961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 05/09/2024] [Indexed: 06/07/2024] Open
Affiliation(s)
- Jian-Wei Guo
- College of Agronomy and Life Sciences, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Osama Abdalla Abdelshafy Mohamad
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Department of Environmental Science, Institute of Environmental Studies, Arish University, El-Arish, Egypt
| | - Xiaolin Wang
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Dilfuza Egamberdieva
- Faculty of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
- Institute of Fundamental and Applied Research, National Research University TIIAME, Tashkent, Uzbekistan
| | - Baoyu Tian
- Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, China
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17
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Wang S, Zheng X, Ye J, Sun Z, Chen Z, Cao G, Zhang Y, Shen F, Gao CX, Qian H. Impact of climate zones and seasons on indoor airborne microbial communities: Insights from a comprehensive analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171879. [PMID: 38521271 DOI: 10.1016/j.scitotenv.2024.171879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/18/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024]
Abstract
Bacteria and fungi are ubiquitous throughout built environments and are suspended in the air, potentially affecting human health. However, the impacts of climate zones on the diversity, structure, and stochastic assembly of indoor airborne microbes remain unknown. This study comprehensively analyzed indoor airborne microbes across five climate zones in China during the summer and winter using high-throughput sequencing. The diversity and structure of indoor airborne communities vary across climatic zones. A random forest model was used to identify biomarkers in different climate zones. The results showed no relationship between the biomarkers and their rankings in mean relative abundance. The Sloan neutral model fitting results indicated that the impact of climate zones on the stochastic process in the assembly of indoor airborne microbes was considerably more important than that of seasons. Additionally, the influence of seasons on the diversity, structure, and stochastic assembly process of indoor airborne microbes differed among different climate zones. The diversity, structure, and stochastic assembly processes of bacteria present distinctive outcomes in climate zones and seasons compared with those of fungi. Overall, these findings indicate that customized strategies are necessary to manage indoor airborne microbial communities in each climate zone, season, and for specific microbial species.
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Affiliation(s)
- Shengqi Wang
- School of Energy and Environment, Southeast University, Nanjing 210096, China; Centre for Youth Mental Health, The University of Melbourne, Parkville, VIC, Australia; Orygen, 35 Poplar Road, Parkville, VIC, Australia
| | - Xiaohong Zheng
- School of Energy and Environment, Southeast University, Nanjing 210096, China
| | - Jin Ye
- School of Energy and Power, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Zongke Sun
- Department of Environmental Microbiology, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
| | - Ziguang Chen
- Institute of Building Environmental and Energy Efficiency, China Academy of Building Research, Beijing 100013, China
| | - Guoqing Cao
- Institute of Building Environmental and Energy Efficiency, China Academy of Building Research, Beijing 100013, China
| | - Yin Zhang
- School of Space and Environment, Beihang University, Beijing 100191, China
| | - Fangxia Shen
- School of Space and Environment, Beihang University, Beijing 100191, China
| | - Caroline X Gao
- Centre for Youth Mental Health, The University of Melbourne, Parkville, VIC, Australia; Orygen, 35 Poplar Road, Parkville, VIC, Australia; School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Hua Qian
- School of Energy and Environment, Southeast University, Nanjing 210096, China.
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18
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Zhang S, Xu L, Zheng Q, Hu J, Jiang D, Dai T, Tian Z. The tetraploid wheat (Triticum dicoccum (Schrank) Schuebl.) improves nitrogen uptake and assimilation adaptation to nitrogen-deficit stress. PLANTA 2024; 259:151. [PMID: 38733553 DOI: 10.1007/s00425-024-04432-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/04/2024] [Indexed: 05/13/2024]
Abstract
MAIN CONCLUSION The genetic diversity in tetraploid wheat provides a genetic pool for improving wheat productivity and environmental resilience. The tetraploid wheat had strong N uptake, translocation, and assimilation capacity under N deficit stress, thus alleviating growth inhibition and plant N loss to maintain healthy development and adapt to environments with low N inputs. Tetraploid wheat with a rich genetic variability provides an indispensable genetic pool for improving wheat yield. Mining the physiological mechanisms of tetraploid wheat in response to nitrogen (N) deficit stress is important for low-N-tolerant wheat breeding. In this study, we selected emmer wheat (Kronos, tetraploid), Yangmai 25 (YM25, hexaploid), and Chinese spring (CS, hexaploid) as materials. We investigated the differences in the response of root morphology, leaf and root N accumulation, N uptake, translocation, and assimilation-related enzymes and gene expression in wheat seedlings of different ploidy under N deficit stress through hydroponic experiments. The tetraploid wheat (Kronos) had stronger adaptability to N deficit stress than the hexaploid wheats (YM25, CS). Kronos had better root growth under low N stress, expanding the N uptake area and enhancing N uptake to maintain higher NO3- and soluble protein contents. Kronos exhibited high TaNRT1.1, TaNRT2.1, and TaNRT2.2 expression in roots, which promoted NO3- uptake, and high TaNRT1.5 and TaNRT1.8 expression in roots and leaves enhanced NO3- translocation to the aboveground. NR and GS activity in roots and leaves of Kronos was higher by increasing the expression of TANIA2, TAGS1, and TAGS2, which enhanced the reduction and assimilation of NO3- as well as the re-assimilation of photorespiratory-released NH4+. Overall, Kronos had strong N uptake, translocation, and assimilation capacity under N deficit stress, alleviating growth inhibition and plant N loss and thus maintaining a healthy development. This study reveals the physiological mechanisms of tetraploid wheat that improve nitrogen uptake and assimilation adaptation under low N stress, which will provide indispensable germplasm resources for elite low-N-tolerant wheat improvement and breeding.
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Affiliation(s)
- Siqi Zhang
- Key Laboratory of Crop Physiology Ecology and Production Management of Ministry of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Libing Xu
- Key Laboratory of Crop Physiology Ecology and Production Management of Ministry of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Qiaomei Zheng
- Key Laboratory of Crop Physiology Ecology and Production Management of Ministry of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Jinling Hu
- Key Laboratory of Crop Physiology Ecology and Production Management of Ministry of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Dong Jiang
- Key Laboratory of Crop Physiology Ecology and Production Management of Ministry of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Tingbo Dai
- Key Laboratory of Crop Physiology Ecology and Production Management of Ministry of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Zhongwei Tian
- Key Laboratory of Crop Physiology Ecology and Production Management of Ministry of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, Jiangsu, People's Republic of China.
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19
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Zhuang Y, Wang H, Tan F, Wu B, Liu L, Qin H, Yang Z, He M. Rhizosphere metabolic cross-talk from plant-soil-microbe tapping into agricultural sustainability: Current advance and perspectives. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108619. [PMID: 38604013 DOI: 10.1016/j.plaphy.2024.108619] [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: 12/06/2023] [Revised: 03/21/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
Rhizosphere interactions from plant-soil-microbiome occur dynamically all the time in the "black microzone" underground, where we can't see intuitively. Rhizosphere metabolites including root exudates and microbial metabolites act as various chemical signalings involving in rhizosphere interactions, and play vital roles on plant growth, development, disease suppression and resistance to stress conditions as well as proper soil health. Although rhizosphere metabolites are a mixture from plant roots and soil microbes, they often are discussed alone. As a rapid appearance of various omics platforms and analytical methods, it offers possibilities and opportunities for exploring rhizosphere interactions in unprecedented breadth and depth. However, our comprehensive understanding about the fine-tuning mechanisms of rhizosphere interactions mediated by these chemical compounds still remain clear. Thus, this review summarizes recent advances systemically including the features of rhizosphere metabolites and their effects on rhizosphere ecosystem, and looks forward to the future research perspectives, which contributes to facilitating better understanding of biochemical communications belowground and helping identify novel rhizosphere metabolites. We also address challenges for promoting the understanding about the roles of rhizosphere metabolites in different environmental stresses.
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Affiliation(s)
- Yong Zhuang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China.
| | - Hao Wang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Furong Tan
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Bo Wu
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Linpei Liu
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Han Qin
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - ZhiJuan Yang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Mingxiong He
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China.
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20
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Wang X, Zhang J, Lu X, Bai Y, Wang G. Two diversities meet in the rhizosphere: root specialized metabolites and microbiome. J Genet Genomics 2024; 51:467-478. [PMID: 37879496 DOI: 10.1016/j.jgg.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 10/15/2023] [Accepted: 10/15/2023] [Indexed: 10/27/2023]
Abstract
Plants serve as rich repositories of diverse chemical compounds collectively referred to as specialized metabolites. These compounds are of importance for adaptive processes, including interactions with various microbes both beneficial and harmful. Considering microbes as bioreactors, the chemical diversity undergoes dynamic changes when root-derived specialized metabolites (RSMs) and microbes encounter each other in the rhizosphere. Recent advancements in sequencing techniques and molecular biology tools have not only accelerated the elucidation of biosynthetic pathways of RSMs but also unveiled the significance of RSMs in plant-microbe interactions. In this review, we provide a comprehensive description of the effects of RSMs on microbe assembly in the rhizosphere and the influence of corresponding microbial changes on plant health, incorporating the most up-to-date information available. Additionally, we highlight open questions that remain for a deeper understanding of and harnessing the potential of RSM-microbe interactions to enhance plant adaptation to the environment. Finally, we propose a pipeline for investigating the intricate associations between root exometabolites and the rhizomicrobiome.
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Affiliation(s)
- Xiaochen Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jingying Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China
| | - Xinjun Lu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China.
| | - Guodong Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China.
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21
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Juliyanti V, Itakura R, Kotani K, Lim SY, Suzuki G, Chong CW, Song BK, Rahman S. Comparative analysis of root associated microbes in tropical cultivated and weedy rice (Oryza spp.) and temperate cultivated rice. Sci Rep 2024; 14:9656. [PMID: 38671238 PMCID: PMC11053024 DOI: 10.1038/s41598-024-60384-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 04/22/2024] [Indexed: 04/28/2024] Open
Abstract
Weedy rice is a major problem in paddy fields around the world. It is well known that weedy rice appears to grow faster and mature earlier than cultivated rice. It is possible that differences in the root microbial genetics are correlated with this characteristic. This study incorporated 16S rRNA amplicon sequencing to study the microbial composition in the rhizosphere and endosphere of rice root. No significant difference was found between the microbiota associated with weedy and cultivated rice lines grown in the same field. It was found that the endosphere had less microbial diversity compared to the rhizosphere. The major groups of bacteria found in the endosphere are from the phylum Proteobacteria, Myxococcota, Chloroflexota, and Actinobacteria. In addition, by analyzing the microbiome of japonica rice grown in the field in a temperate climate, we found that despite differences in genotype and location, some bacterial taxa were found to be common and these members of the putative rice core microbiome can also be detected by in situ hybridization. The delineation of a core microbiome in the endosphere of rice suggests that these bacterial taxa might be important in the life cycle of a wide range of rice types.
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Affiliation(s)
- Vani Juliyanti
- School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Ryota Itakura
- Division of Natural Science, Osaka Kyoiku University, Kashiwara, 582-8582, Japan
| | - Kanta Kotani
- Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Shu Yong Lim
- Genomics Facility, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Go Suzuki
- Division of Natural Science, Osaka Kyoiku University, Kashiwara, 582-8582, Japan
| | - Chun Wie Chong
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Beng Kah Song
- School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Sadequr Rahman
- School of Science, Monash University Malaysia, Bandar Sunway, Malaysia.
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Bandar Sunway, Malaysia.
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22
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Liu S, Liu R, Zhang S, Shen Q, Chen J, Ma H, Ge C, Hao L, Zhang J, Shi S, Pang C. The Contributions of Sub-Communities to the Assembly Process and Ecological Mechanisms of Bacterial Communities along the Cotton Soil-Root Continuum Niche Gradient. Microorganisms 2024; 12:869. [PMID: 38792699 PMCID: PMC11123189 DOI: 10.3390/microorganisms12050869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 05/26/2024] Open
Abstract
Soil microbes are crucial in shaping the root-associated microbial communities. In this study, we analyzed the effect of the soil-root niche gradient on the diversity, composition, and assembly of the bacterial community and co-occurrence network of two cotton varieties. The results revealed that the bacterial communities in cotton soil-root compartment niches exhibited a skewed species abundance distribution, dominated by abundant taxa showing a strong spatial specificity. The assembly processes of the rhizosphere bacterial communities were mainly driven by stochastic processes, dominated by the enrichment pattern and supplemented by the depletion pattern to recruit bacteria from the bulk soil, resulting in a more stable bacterial community. The assembly processes of the endosphere bacterial communities were determined by processes dominated by the depletion pattern and supplemented by the enrichment pattern to recruit species from the rhizosphere, resulting in a decrease in the stability and complexity of the community co-occurrence network. The compartment niche shaped the diversity of the bacterial communities, and the cotton variety genotype was an important source of diversity in bacterial communities within the compartment niche. We suggest that the moderate taxa contribute to significantly more changes in the diversity of the bacterial community than the rare and abundant taxa during the succession of bacterial communities in the cotton root-soil continuum.
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Affiliation(s)
- Shaodong Liu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Ruihua Liu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Siping Zhang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Qian Shen
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Jing Chen
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Huijuan Ma
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Changwei Ge
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Lidong Hao
- Postdoctoral Mobile Station, Lanzhou University, Lanzhou 730000, China
| | - Jinshan Zhang
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Shubing Shi
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Chaoyou Pang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
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23
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Tan W, Nian H, Tran LSP, Jin J, Lian T. Small peptides: novel targets for modulating plant-rhizosphere microbe interactions. Trends Microbiol 2024:S0966-842X(24)00085-4. [PMID: 38670883 DOI: 10.1016/j.tim.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024]
Abstract
The crucial role of rhizosphere microbes in plant growth and their resilience to environmental stresses underscores the intricate communication between microbes and plants. Plants are equipped with a diverse set of signaling molecules that facilitate communication across different biological kingdoms, although our comprehension of these mechanisms is still evolving. Small peptides produced by plants (SPPs) and microbes (SPMs) play a pivotal role in intracellular signaling and are essential in orchestrating various plant development stages. In this review, we posit that SPPs and SPMs serve as crucial signaling agents for the bidirectional cross-kingdom communication between plants and rhizosphere microbes. We explore several potential mechanistic pathways through which this communication occurs. Additionally, we propose that leveraging small peptides, inspired by plant-rhizosphere microbe interactions, represents an innovative approach in the field of holobiont engineering.
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Affiliation(s)
- Weiyi Tan
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA.
| | - Jing Jin
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China.
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China.
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24
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Yu X, Zhu H. Nutrient stress-primed microbial communities improve plant resilience. Sci Bull (Beijing) 2024:S2095-9273(24)00291-3. [PMID: 38704355 DOI: 10.1016/j.scib.2024.04.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2024]
Affiliation(s)
- Xiaocheng Yu
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA
| | - Hongyan Zhu
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA.
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25
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Ju Y, Jia Y, Cheng B, Wang D, Gu D, Jing W, Zhang H, Chen X, Li G. NRT1.1B mediates rice plant growth and soil microbial diversity under different nitrogen conditions. AMB Express 2024; 14:39. [PMID: 38647736 PMCID: PMC11035536 DOI: 10.1186/s13568-024-01683-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/25/2024] [Indexed: 04/25/2024] Open
Abstract
Interactions between microorganisms and plants can stimulate plant growth and promote nitrogen cycling. Nitrogen fertilizers are routinely used in agriculture to improve crop growth and yield; however, poor use efficiency impairs the optimal utilization of such fertilizers. Differences in the microbial diversity and plant growth of rice soil under different nitrogen application conditions and the expression of nitrogen-use efficiency-related genes have not been previously investigated. Therefore, this study investigates how nitrogen application and nitrogen-use efficiency-related gene NRT1.1B expression affect the soil microbial diversity and growth indices of two rice varieties, Huaidao 5 and Xinhuai 5. In total, 103,463 and 98,427 operational taxonomic units were detected in the soils of the Huaidao 5 and Xinhuai 5 rice varieties, respectively. The Shannon and Simpson indices initially increased and then decreased, whereas the Chao and abundance-based coverage estimator indices decreased after the application of nitrogen fertilizer. Nitrogen fertilization also reduced soil bacterial diversity and richness, as indicated by the reduced abundances of Azotobacter recorded in the soils of both rice varieties. Nitrogen application initially increased and then decreased the grain number per panicle, yield per plant, root, stem, and leaf nitrogen, total nitrogen content, glutamine synthetase, nitrate reductase, urease, and root activities of both varieties. Plant height showed positive linear trends in response to nitrogen application, whereas thousand-grain weights showed a negative trend. Our findings may be used to optimize nitrogen fertilizer use for rice cultivation and develop crop-variety-specific strategies for nitrogen fertilizer application.
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Affiliation(s)
- Yawen Ju
- Huai'an Key Laboratory of Agricultural Biotechnology, Huaiyin Institute of Agricultural Science in Xuhuai Region of Jiangsu, Huai'an, 223001, China
| | - Yanyan Jia
- Huai'an Key Laboratory of Agricultural Biotechnology, Huaiyin Institute of Agricultural Science in Xuhuai Region of Jiangsu, Huai'an, 223001, China
| | - Baoshan Cheng
- Huai'an Key Laboratory of Agricultural Biotechnology, Huaiyin Institute of Agricultural Science in Xuhuai Region of Jiangsu, Huai'an, 223001, China
| | - Di Wang
- Huai'an Key Laboratory of Agricultural Biotechnology, Huaiyin Institute of Agricultural Science in Xuhuai Region of Jiangsu, Huai'an, 223001, China
| | - Dalu Gu
- Huai'an Key Laboratory of Agricultural Biotechnology, Huaiyin Institute of Agricultural Science in Xuhuai Region of Jiangsu, Huai'an, 223001, China
| | - Wenjiang Jing
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Key Laboratory of Crop Cultivation and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Hao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Key Laboratory of Crop Cultivation and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
| | - Xinhong Chen
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223001, China.
| | - Gang Li
- Huai'an Key Laboratory of Agricultural Biotechnology, Huaiyin Institute of Agricultural Science in Xuhuai Region of Jiangsu, Huai'an, 223001, China.
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26
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Wang M, Lin M, Liu Q, Li C, Pang X. Fungal, but not bacterial, diversity and network complexity promote network stability during roadside slope restoration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 922:171007. [PMID: 38401731 DOI: 10.1016/j.scitotenv.2024.171007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 02/10/2024] [Accepted: 02/13/2024] [Indexed: 02/26/2024]
Abstract
To restore degraded roadside ecosystems, conventional methods such as revegetation and soil amendment are frequently employed. However, our understanding of the long-term effects of these restoration approaches on soil microbial diversity and network complexity across different vegetation types remains poor, which contributes to poor restoration outcomes. In this study, we explored the effects of roadside slope restoration on microbial communities across different vegetation types at varying stages of restoration. We found that restoration time had a more pronounced impact on microbial diversity than specific vegetation type. As restoration progressed, microbial network complexity and fungal diversity increased, but bacterial diversity declined, suggesting that keystone taxa may contribute to network complexity. Interestingly, bacterial network complexity increased concomitant with decreasing network modularity and robustness, which may compromise system stability. Distinct vegetation types were associated with restoration-sensitive microbial communities at different restoration stages. Leguminouse and nitrogen-fixing plants, such as Albiziak alkora, Ginkgo biloba, Rhus chinensis, Rhapis excels, and Rubia cordifolia exhibited such associations after five years of restoration. These keystone taxa included Proteobacteria, Actinobacteria, Chloroflexi, Gemmatimonadota, and Myxococcota. We also found that bacterial alpha diversity was significantly correlated with restoration time, soil pH, moisture, available phosphate, nitrate nitrogen, and plant height, while fungal diversity was primarily shaped by restoration time. Together, our findings suggest that soil properties, environmental factors, vegetation type, and dominant species can be manipulated to guide the trajectory of ecological recovery by regulating the abundance of certain microbial taxa.
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Affiliation(s)
- Min Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, China; School of Ecology and Environment, Hainan University, China
| | - Mao Lin
- College of Geography and Resources, Sichuan Normal University, Chengdu 610101, China
| | - Qinghua Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, China
| | - Cheng Li
- School of Ecology and Environment, Hainan University, China
| | - Xueyong Pang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, China.
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27
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Chen M, Feng S, Lv H, Wang Z, Zeng Y, Shao C, Lin W, Zhang Z. OsCIPK2 mediated rice root microorganisms and metabolites to improve plant nitrogen uptake. BMC PLANT BIOLOGY 2024; 24:285. [PMID: 38627617 PMCID: PMC11020999 DOI: 10.1186/s12870-024-04982-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/03/2024] [Indexed: 04/19/2024]
Abstract
Crop roots are colonized by large numbers of microorganisms, collectively known as the root-microbiome, which modulate plant growth, development and contribute to elemental nutrient uptake. In conditions of nitrogen limitation, the over-expressed Calcineurin B-like interacting protein kinase 2 (OsCIPK2) gene with root-specific promoter (RC) has been shown to enhance growth and nitrogen uptake in rice. Analysis of root-associated bacteria through high-throughput sequencing revealed that OsCIPK2 has a significant impact on the diversity of the root microbial community under low nitrogen stress. The quantification of nifH gene expression demonstrated a significant enhancement in nitrogen-fixing capabilities in the roots of RC transgenetic rice. Synthetic microbial communities (SynCom) consisting of six nitrogen-fixing bacterial strains were observed to be enriched in the roots of RC, leading to a substantial improvement in rice growth and nitrogen uptake in nitrogen-deficient soils. Forty and twenty-three metabolites exhibiting differential abundance were identified in the roots and rhizosphere soils of RC transgenic rice compared to wild-type (WT) rice. These findings suggest that OSCIPK2 plays a role in restructuring the microbial community in the roots through the regulation of metabolite synthesis and secretion. Further experiments involving the exogenous addition of citric acid revealed that an optimal concentration of this compound facilitated the growth of nitrogen-fixing bacteria and substantially augmented their population in the soil, highlighting the importance of citric acid in promoting nitrogen fixation under conditions of low nitrogen availability. These findings suggest that OsCIPK2 plays a role in enhancing nitrogen uptake by rice plants from the soil by influencing the assembly of root microbial communities, thereby offering valuable insights for enhancing nitrogen utilization in rice cultivation.
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Affiliation(s)
- Mengying Chen
- College of JunCao Science and Ecology, Fujian Agricultural and Forestry University, Fuzhou, Fujian, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Shizhong Feng
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - He Lv
- College of JunCao Science and Ecology, Fujian Agricultural and Forestry University, Fuzhou, Fujian, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Zewen Wang
- College of JunCao Science and Ecology, Fujian Agricultural and Forestry University, Fuzhou, Fujian, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Yuhang Zeng
- College of JunCao Science and Ecology, Fujian Agricultural and Forestry University, Fuzhou, Fujian, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Caihong Shao
- Soil and Fertilizer & Resources and Environment Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Wenxiong Lin
- College of JunCao Science and Ecology, Fujian Agricultural and Forestry University, Fuzhou, Fujian, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhixing Zhang
- College of JunCao Science and Ecology, Fujian Agricultural and Forestry University, Fuzhou, Fujian, 350002, China.
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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28
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Zhao C, Onyino J, Gao X. Current Advances in the Functional Diversity and Mechanisms Underlying Endophyte-Plant Interactions. Microorganisms 2024; 12:779. [PMID: 38674723 PMCID: PMC11052469 DOI: 10.3390/microorganisms12040779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/06/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Plant phenotype is a complex entity largely controlled by the genotype and various environmental factors. Importantly, co-evolution has allowed plants to coexist with the biotic factors in their surroundings. Recently, plant endophytes as an external plant phenotype, forming part of the complex plethora of the plant microbial assemblage, have gained immense attention from plant scientists. Functionally, endophytes impact the plant in many ways, including increasing nutrient availability, enhancing the ability of plants to cope with both abiotic and biotic stress, and enhancing the accumulation of important plant secondary metabolites. The current state of research has been devoted to evaluating the phenotypic impacts of endophytes on host plants, including their direct influence on plant metabolite accumulation and stress response. However, there is a knowledge gap in how genetic factors influence the interaction of endophytes with host plants, pathogens, and other plant microbial communities, eventually controlling the extended microbial plant phenotype. This review will summarize how host genetic factors can impact the abundance and functional diversity of the endophytic microbial community, how endophytes influence host gene expression, and the host-endophyte-pathogen disease triangle. This information will provide novel insights into how breeders could specifically target the plant-endophyte extended phenotype for crop improvement.
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Affiliation(s)
- Caihong Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Johnmark Onyino
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiquan Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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Bamba M, Akyol TY, Azuma Y, Quilbe J, Andersen SU, Sato S. Synergistic effects of plant genotype and soil microbiome on growth in Lotus japonicus. FEMS Microbiol Ecol 2024; 100:fiae056. [PMID: 38678008 PMCID: PMC11068475 DOI: 10.1093/femsec/fiae056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 03/25/2024] [Accepted: 04/10/2024] [Indexed: 04/29/2024] Open
Abstract
The biological interactions between plants and their root microbiomes are essential for plant growth, and even though plant genotype (G), soil microbiome (M), and growth conditions (environment; E) are the core factors shaping root microbiome, their relationships remain unclear. In this study, we investigated the effects of G, M, and E and their interactions on the Lotus root microbiome and plant growth using an in vitro cross-inoculation approach, which reconstructed the interactions between nine Lotus accessions and four soil microbiomes under two different environmental conditions. Results suggested that a large proportion of the root microbiome composition is determined by M and E, while G-related (G, G × M, and G × E) effects were significant but small. In contrast, the interaction between G and M had a more pronounced effect on plant shoot growth than M alone. Our findings also indicated that most microbiome variations controlled by M have little effect on plant phenotypes, whereas G × M interactions have more significant effects. Plant genotype-dependent interactions with soil microbes warrant more attention to optimize crop yield and resilience.
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Affiliation(s)
- Masaru Bamba
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai 980-8577, Japan
| | - Turgut Yigit Akyol
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Yusuke Azuma
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai 980-8577, Japan
| | - Johan Quilbe
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Stig Uggerhøj Andersen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai 980-8577, Japan
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30
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Liu Y, Liu R, Feng Z, Hu R, Zhao F, Wang J. Regulation of wheat growth by soil multifunctionality and metagenomic-based microbial functional profiles under mulching treatments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:170881. [PMID: 38360319 DOI: 10.1016/j.scitotenv.2024.170881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/07/2024] [Accepted: 02/08/2024] [Indexed: 02/17/2024]
Abstract
Soil microbial functional genes play key roles in biogeochemical processes that are closely related to crop development. However, the regulation of crop growth by the composition and potential interactions of metagenomic-based functional genes is poorly understood. Therefore, in a long-term mulching experiment, the regulation of wheat growth by soil multifunctionality, microbial functional profiles driven by soil properties and microbial activity was studied. Soil properties and microbial activity were significantly separated into distinct mulching treatments, and were significantly declined by plastic film mulching treatment, similar to soil multifunctionality. Only carbon (C) and phosphorus (P) cycling gene compositions were divided significantly into distinct mulching treatments to varying degrees. Similarly, intra- and inter-connected sub-networks associated with C and P cycling genes were more complex and stable than the sub-networks containing nitrogen cycling genes. Despite core functional genes being located in the middle of each network, they were rarely observed in the metagenomic assembly genomes. Subsequently, the dominant soil properties and microbial activity had greater effects on C cycling gene composition and network, which played essential roles in wheat growth regulation. Overall, wheat yield and biomass were affected differently by straw and plastic film mulching treatments, and were mainly regulated by C cycling gene network and soil multifunctionality, respectively. The results of the present study provide novel insights into wheat growth regulation by soil microbial functional profiles, with potential implications for sustainable crop production in mulching conservation agroecosystems.
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Affiliation(s)
- Yang Liu
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Science, Northwest University, Xi'an 710127, China; Shaanxi Key Laboratory for Carbon Neutral Technology, Northwest University, Xi'an 710127, China
| | - Rui Liu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling 712100, China
| | - Zhen Feng
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Science, Northwest University, Xi'an 710127, China
| | - Rong Hu
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Science, Northwest University, Xi'an 710127, China
| | - Fazhu Zhao
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Science, Northwest University, Xi'an 710127, China; Shaanxi Key Laboratory for Carbon Neutral Technology, Northwest University, Xi'an 710127, China
| | - Jun Wang
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Science, Northwest University, Xi'an 710127, China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling 712100, China; Shaanxi Key Laboratory for Carbon Neutral Technology, Northwest University, Xi'an 710127, China.
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31
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Li X, Zheng X, Yadav N, Saha S, Salama ES, Li X, Wang L, Jeon BH. Rational management of the plant microbiome for the Second Green Revolution. PLANT COMMUNICATIONS 2024; 5:100812. [PMID: 38213028 PMCID: PMC11009158 DOI: 10.1016/j.xplc.2024.100812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/06/2023] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
The Green Revolution of the mid-20th century transformed agriculture worldwide and has resulted in environmental challenges. A new approach, the Second Green Revolution, seeks to enhance agricultural productivity while minimizing negative environmental impacts. Plant microbiomes play critical roles in plant growth and stress responses, and understanding plant-microbiome interactions is essential for developing sustainable agricultural practices that meet food security and safety challenges, which are among the United Nations Sustainable Development Goals. This review provides a comprehensive exploration of key deterministic processes crucial for developing microbiome management strategies, including the host effect, the facilitator effect, and microbe-microbe interactions. A hierarchical framework for plant microbiome modulation is proposed to bridge the gap between basic research and agricultural applications. This framework emphasizes three levels of modulation: single-strain, synthetic community, and in situ microbiome modulation. Overall, rational management of plant microbiomes has wide-ranging applications in agriculture and can potentially be a core technology for the Second Green Revolution.
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Affiliation(s)
- Xiaofang Li
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Xin Zheng
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Nikita Yadav
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, South Korea
| | - Shouvik Saha
- Natural Resources Research Institute, University of Minnesota Duluth, Hermantown, MN 55811, USA; Department of Biotechnology, Brainware University, Barasat, Kolkata 700125, West Bengal, India
| | - El-Sayed Salama
- Department of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Likun Wang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China.
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, South Korea.
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Jiang Y, Zhang Y, Liu Y, Zhang J, Jiang M, Nong C, Chen J, Hou K, Chen Y, Wu W. Plant Growth-Promoting Rhizobacteria Are Key to Promoting the Growth and Furanocoumarin Synthesis of Angelica dahurica var. formosana under Low-Nitrogen Conditions. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:6964-6978. [PMID: 38525888 DOI: 10.1021/acs.jafc.3c09655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Microbiomes are the most important members involved in the regulation of soil nitrogen metabolism. Beneficial interactions between plants and microbiomes contribute to improving the nitrogen utilization efficiency. In this study, we investigated the Apiaceae medicinal plant Angelica dahurica var. formosana. We found that under a low-nitrogen treatment, the abundance of carbon metabolites in the rhizosphere secretions of A. dahurica var. formosana significantly increased, thereby promoting the ratio of C to N in rhizosphere and nonrhizosphere soils, increasing carbon sequestration, and shaping the microbial community composition, thus promoting a higher yield and furanocoumarin synthesis. Confirmation through the construction of a synthetic microbial community and feedback experiments indicated that beneficial plant growth-promoting rhizobacteria play a crucial role in improving nitrogen utilization efficiency and selectively regulating the synthesis of target furanocoumarins under low nitrogen conditions. These findings may contribute additional theoretical evidence for understanding the mechanisms of interaction between medicinal plants and rhizosphere microorganisms.
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Affiliation(s)
- Yijie Jiang
- College of Agronomy, Sichuan Agricultural University, Cheng, Du 611130, China
| | - Yunxin Zhang
- College of Agronomy, Sichuan Agricultural University, Cheng, Du 611130, China
| | - Yanan Liu
- College of Agronomy, Sichuan Agricultural University, Cheng, Du 611130, China
| | - Jiaheng Zhang
- College of Agronomy, Sichuan Agricultural University, Cheng, Du 611130, China
| | - Meiyan Jiang
- College of Agronomy, Sichuan Agricultural University, Cheng, Du 611130, China
| | - Changguo Nong
- College of Agronomy, Sichuan Agricultural University, Cheng, Du 611130, China
| | - Jinsong Chen
- College of Agronomy, Sichuan Agricultural University, Cheng, Du 611130, China
| | - Kai Hou
- College of Agronomy, Sichuan Agricultural University, Cheng, Du 611130, China
| | - Yinyin Chen
- College of Agronomy, Sichuan Agricultural University, Cheng, Du 611130, China
| | - Wei Wu
- College of Agronomy, Sichuan Agricultural University, Cheng, Du 611130, China
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Jiang L, Ke D, Sun B, Zhang J, Lyu S, Yu H, Chen P, Mao X, Liu Q, Chen W, Fan Z, Huang L, Yin S, Deng Y, Li C. Root microbiota analysis of Oryza rufipogon and Oryza sativa reveals an orientation selection during the domestication process. Microbiol Spectr 2024; 12:e0333023. [PMID: 38470483 PMCID: PMC10986595 DOI: 10.1128/spectrum.03330-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 02/15/2024] [Indexed: 03/13/2024] Open
Abstract
The root-associated microbiota has a close relation to the life activities of plants, and its composition is affected by the rhizospheric environment and plant genotypes. Rice (Oryza sativa) was domesticated from the ancestor species Oryza rufipogon. Many important agricultural traits and adversity resistance of rice have changed during a long time of natural domestication and artificial selection. However, the influence of rice genotypes on root microbiota in important agricultural traits remains to be explained. In this study, we performed 16S rRNA and internal transcribed spacer (ITS) gene amplicon sequencing to generate bacterial and fungal community profiles of O. rufipogon and O. sativa, both of which were planted in a farm in Guangzhou and had reached the reproductive stage. We compared their root microbiota in detail by alpha diversity, beta diversity, different species, core microbiota, and correlation analyses. We found that the relative abundance of bacteria was significantly higher in the cultivated rice than in the common wild rice, while the relative abundance of fungi was the opposite. Significant differences in agricultural traits between O. rufipogon and O. sativa showed a high correlation with core microorganisms in the two Oryza species, which only existed in either or had obviously different abundance in both two species, indicating that rice genotype/phenotype had a strong influence on recruiting specific microorganisms. Our study provides a theoretical basis for the in-depth understanding of rice root microbiota and the improvement of rice breeding from the perspective of the interaction between root microorganisms and plants.IMPORTANCEPlant root microorganisms play a vital role not only in plant growth and development but also in responding the biotic and abiotic stresses. Oryza sativa is domesticated from Oryza rufipogon which has many excellent agricultural traits especially containing resistance to biotic and abiotic stresses. To improve the yield and resistance of cultivated rice, it is particularly important to deeply research on differences between O. sativa and O. rufipogon and find beneficial microorganisms to remodel the root microbiome of O. sativa.
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Affiliation(s)
- Liqun Jiang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Da Ke
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Bingrui Sun
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Jing Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Shuwei Lyu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Hang Yu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Pingli Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Xingxue Mao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Qing Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Wenfeng Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Zhilan Fan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Li Huang
- Healthtimegene Institute, Shenzhen, China
| | - Sanjun Yin
- Healthtimegene Institute, Shenzhen, 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
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
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Zhang H, Nie M, Du X, Chen S, Liu H, Wu C, Tang Y, Lei Z, Shi G, Zhao X. Selenium and Bacillus proteolyticus SES increased Cu-Cd-Cr uptake by ryegrass: highlighting the significance of key taxa and soil enzyme activity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:29113-29131. [PMID: 38568308 DOI: 10.1007/s11356-024-32959-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/13/2024] [Indexed: 04/24/2024]
Abstract
Many studies have focused their attention on strategies to improve soil phytoremediation efficiency. In this study, a pot experiment was carried out to investigate whether Se and Bacillus proteolyticus SES promote Cu-Cd-Cr uptake by ryegrass. To explore the effect mechanism of Se and Bacillus proteolyticus SES, rhizosphere soil physiochemical properties and rhizosphere soil bacterial properties were determined further. The findings showed that Se and Bacillus proteolyticus SES reduced 23.04% Cu, 36.85% Cd, and 9.85% Cr from the rhizosphere soil of ryegrass. Further analysis revealed that soil pH, organic matter, soil enzyme activities, and soil microbial properties were changed with Se and Bacillus proteolyticus SES application. Notably, rhizosphere key taxa (Bacteroidetes, Actinobacteria, Firmicutes, Patescibacteria, Verrucomicrobia, Chloroflexi, etc.) were significantly enriched in rhizosphere soil of ryegrass, and those taxa abundance were positively correlated with soil heavy metal contents (P < 0.01). Our study also demonstrated that in terms of explaining variations of soil Cu-Cd-Cr content under Se and Bacillus proteolyticus SES treatment, soil enzyme activities (catalase and acid phosphatase) and soil microbe properties showed 42.5% and 12.2% contributions value, respectively. Overall, our study provided solid evidence again that Se and Bacillus proteolyticus SES facilitated phytoextraction of soil Cu-Cd-Cr, and elucidated the effect of soil key microorganism and chemical factor.
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Affiliation(s)
- Huan Zhang
- College of Resources and Environment, Huazhong Agricultural University / Research Center of Trace Elements, Wuhan, 430070, China
- Key Laboratory of Se-Enriched Products Development and Quality Control, Ministry of Agriculture and Rural Affairs/ National-Local Joint Engineering Laboratory of Se-Enriched Food Development, Ankang, 725000, China
| | - Min Nie
- College of Resources and Environment, Huazhong Agricultural University / Research Center of Trace Elements, Wuhan, 430070, China
| | - Xiaoping Du
- Key Laboratory of Se-Enriched Products Development and Quality Control, Ministry of Agriculture and Rural Affairs/ National-Local Joint Engineering Laboratory of Se-Enriched Food Development, Ankang, 725000, China
| | - Suhua Chen
- National-Local Joint Engineering Research Center of Heavy Metals Pollutants Control and Resource Utilization (Nanchang Hangkong University), Nanchang, 330063, China
| | - Hanliang Liu
- Key Laboratory of Geochemical Exploration, Institute of Geophysical and Geochemical Exploration, CAGS, Langfang, 065000, Hebei, China
| | - Chihhung Wu
- Fujian Provincial Key Laboratory of Resources and Environment Monitoring & Sustainable Management and Utilization, Sanming University, Sanming, 365004, China
| | - Yanni Tang
- College of Resources and Environment, Huazhong Agricultural University / Research Center of Trace Elements, Wuhan, 430070, China
| | - Zheng Lei
- College of Resources and Environment, Huazhong Agricultural University / Research Center of Trace Elements, Wuhan, 430070, China
| | - Guangyu Shi
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Xiaohu Zhao
- College of Resources and Environment, Huazhong Agricultural University / Research Center of Trace Elements, Wuhan, 430070, China.
- Key Laboratory of Se-Enriched Products Development and Quality Control, Ministry of Agriculture and Rural Affairs/ National-Local Joint Engineering Laboratory of Se-Enriched Food Development, Ankang, 725000, China.
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Li Y, Pan Z, Liao J, Dai R, Lin JG, Ling J, Xu Y. Micro-aeration and low influent C/N are key environmental factors for achieving ANAMMOX in livestock farming wastewater treatment plants. WATER RESEARCH 2024; 253:120141. [PMID: 38377919 DOI: 10.1016/j.watres.2023.120141] [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: 02/03/2023] [Revised: 05/24/2023] [Accepted: 05/27/2023] [Indexed: 02/22/2024]
Abstract
Anaerobic ammonium oxidation (ANAMMOX)-mediated system is a cost-effective green nitrogen removal process. However, there are few examples of successful application of this advanced wastewater denitrification process in wastewater treatment plants, and the understanding of how to implement anaerobic ammonia oxidation process in full-scale is still limited. In this study, it was found that the abundance of anaerobic ammonia-oxidizing bacteria (AnAOB) in the two livestock wastewater plants named J1 and J2, respectively, showed diametrically opposed trends of waxing and waning with time. The microbial communities of the activated sludge in the two plants at different time were sampled and analyzed by high-throughput sequencing of 16S rRNA genes. Structural equation models (SEMs) were used to reveal the key factors affecting the realization of the ANAMMOX. Changes in the concentration of dissolved oxygen and C/N had a significant effect on the relative abundance of anaerobic ammonia oxidation bacteria (AnAOB). The low concentration of DO (0.2∼0.5 mg/L) could inhibit the activity of nitrifying bacteria (NOB) to achieve partial oxidation of ammonia nitrogen and provide sufficient substrate for the growth of AnAOB, similar to the CANON (Completely Autotrophic Nitrogen removal Over Nitrite). Unlike CANON, heterotrophic denitrification is also a particularly critical part of the livestock wastewater treatment, and a suitable C/N of about 0.6 could reduce the competition risk of heterotrophic microorganisms to AnAOB and ensure a good ecological niche for AnAOB. Based on the results of 16S rRNA and microbial co-occurrence networks, it was discovered that microorganisms in the sludge not only had a richer network interaction, but also achieved a mutually beneficial symbiotic interaction network among denitrifying bacteria (Pseudomonas sp., Terrimonas sp., Dokdonella sp.), AnAOB (Candidatus Brocadia sp.) at DO of 0.2∼0.5 mg/L and C/N of 0.6. Among the top 20 in abundance of genus level, AnAOB had a high relative abundance of 27.66%, followed by denitrifying bacteria of 3.67%, AOB of 0.64% and NOB of 0.26%, which is an essential indicator for the emergence of an AnAOB-dominated nitrogen removal cycle. In conclusion, this study highlights the importance of dissolved oxygen and C/N regulation by analyzing the mechanism of ANAMMOX sludge extinction and growth in two plants under anthropogenic regulation of AnAOB in full-scale wastewater treatment systems.
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Affiliation(s)
- Yuxin Li
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Zhenzhong Pan
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Jingsong Liao
- Yikangsheng Environmental Science and Technology Limited Company of Guangdong, Yunfu, 527400, China
| | - Ruizhi Dai
- Yikangsheng Environmental Science and Technology Limited Company of Guangdong, Yunfu, 527400, China
| | - Jih-Gaw Lin
- Institute of Environmental Engineering, National Chiao Tung University, 1001 University Road, Hsinchu City, 30010, Taiwan
| | - Jiayin Ling
- School of Environmental and Chemical Engineering, Zhaoqing University, Zhaoqing, 526061, China
| | - Yanbin Xu
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China.
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Shen J, Wang M, Wang E. Exploitation of the microbiome for crop breeding. NATURE PLANTS 2024; 10:533-534. [PMID: 38514786 DOI: 10.1038/s41477-024-01657-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Affiliation(s)
- Jiayong Shen
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Mingxing Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Ertao Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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37
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Yu Z, Wang Z, Liu L. Electrophysiological techniques in marine microalgae study: A new perspective for harmful algal bloom (HAB) research. HARMFUL ALGAE 2024; 134:102629. [PMID: 38705615 DOI: 10.1016/j.hal.2024.102629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 05/07/2024]
Abstract
Electrophysiological techniques, by measuring bioelectrical signals and ion channel activities in tissues and cells, are now widely utilized to study ion channel-related physiological functions and their underlying mechanisms. Electrophysiological techniques have been extensively employed in the investigation of animals, plants, and microorganisms; however, their application in marine algae lags behind that in other organisms. In this paper, we present an overview of current electrophysiological techniques applicable to algae while reviewing the historical usage of such techniques in this field. Furthermore, we explore the potential specific applications of electrophysiological technology in harmful algal bloom (HAB) research. The application prospects in the studies of stress tolerance, competitive advantage, nutrient absorption, toxin synthesis and secretion by HAB microalgae are discussed and anticipated herein with the aim of providing novel perspectives on HAB investigations.
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Affiliation(s)
- Zhiming Yu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory of Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Zhongshi Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory of Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Lidong Liu
- The Djavad Mowafaghian Centre for Brian Health and Department of Medicine, University of British Columbia, Vancouver, BC, Canada
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38
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Noman M, Ahmed T, Wang J, White JC. Micronutrient-microbiome interplay: a critical regulator of soil-plant health. Trends Microbiol 2024; 32:319-320. [PMID: 38395702 DOI: 10.1016/j.tim.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 02/13/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024]
Abstract
The delicate balance between soil micronutrients and the phytobeneficial microbiome is crucial for maintaining soil-plant health. Recently, Dai et al. established a correlation between elemental micronutrients and the soil microbiome that regulates plant quality and productivity, offering innovative and sustainable solutions to increase agricultural production in a changing climate.
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Affiliation(s)
- Muhammad Noman
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Temoor Ahmed
- Xianghu Laboratory, Hangzhou 311231, China; Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; MEU Research Unit, Middle East University, Amman, Jordan.
| | - Jiaoyu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Jason C White
- The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA.
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He X, Wang D, Jiang Y, Li M, Delgado-Baquerizo M, McLaughlin C, Marcon C, Guo L, Baer M, Moya YAT, von Wirén N, Deichmann M, Schaaf G, Piepho HP, Yang Z, Yang J, Yim B, Smalla K, Goormachtig S, de Vries FT, Hüging H, Baer M, Sawers RJH, Reif JC, Hochholdinger F, Chen X, Yu P. Heritable microbiome variation is correlated with source environment in locally adapted maize varieties. NATURE PLANTS 2024; 10:598-617. [PMID: 38514787 DOI: 10.1038/s41477-024-01654-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 02/15/2024] [Indexed: 03/23/2024]
Abstract
Beneficial interactions with microorganisms are pivotal for crop performance and resilience. However, it remains unclear how heritable the microbiome is with respect to the host plant genotype and to what extent host genetic mechanisms can modulate plant-microbiota interactions in the face of environmental stresses. Here we surveyed 3,168 root and rhizosphere microbiome samples from 129 accessions of locally adapted Zea, sourced from diverse habitats and grown under control and different stress conditions. We quantified stress treatment and host genotype effects on the microbiome. Plant genotype and source environment were predictive of microbiome abundance. Genome-wide association analysis identified host genetic variants linked to both rhizosphere microbiome abundance and source environment. We identified transposon insertions in a candidate gene linked to both the abundance of a keystone bacterium Massilia in our controlled experiments and total soil nitrogen in the source environment. Isolation and controlled inoculation of Massilia alone can contribute to root development, whole-plant biomass production and adaptation to low nitrogen availability. We conclude that locally adapted maize varieties exert patterns of genetic control on their root and rhizosphere microbiomes that follow variation in their home environments, consistent with a role in tolerance to prevailing stress.
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Affiliation(s)
- Xiaoming He
- College of Resources and Environment, and Academy of Agricultural Sciences, Southwest University (SWU), Chongqing, People's Republic of China
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Danning Wang
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Yong Jiang
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Meng Li
- Department of Plant Science, Pennsylvania State University, State College, PA, USA
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Chloee McLaughlin
- Department of Plant Science, Pennsylvania State University, State College, PA, USA
| | - Caroline Marcon
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Li Guo
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Marcel Baer
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Yudelsy A T Moya
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Nicolaus von Wirén
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Marion Deichmann
- Plant Nutrition, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Gabriel Schaaf
- Plant Nutrition, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | | | - Zhikai Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Bunlong Yim
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Germany
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Franciska T de Vries
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Hubert Hüging
- Crop Science Group, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Mareike Baer
- Institute of Nutrition and Food Sciences, Department of Food Microbiology and Hygiene, University of Bonn, Bonn, Germany
| | - Ruairidh J H Sawers
- Department of Plant Science, Pennsylvania State University, State College, PA, USA.
| | - Jochen C Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
| | - Frank Hochholdinger
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany.
| | - Xinping Chen
- College of Resources and Environment, and Academy of Agricultural Sciences, Southwest University (SWU), Chongqing, People's Republic of China.
| | - Peng Yu
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany.
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany.
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Yao Y, Liu C, Zhang Y, Lin Y, Chen T, Xie J, Chang H, Fu Y, Cheng J, Li B, Yu X, Lyu X, Feng Y, Bian X, Jiang D. The Dynamic Changes of Brassica napus Seed Microbiota across the Entire Seed Life in the Field. PLANTS (BASEL, SWITZERLAND) 2024; 13:912. [PMID: 38592934 PMCID: PMC10975644 DOI: 10.3390/plants13060912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
The seed microbiota is an important component given by nature to plants, protecting seeds from damage by other organisms and abiotic stress. However, little is known about the dynamic changes and potential functions of the seed microbiota during seed development. In this study, we investigated the composition and potential functions of the seed microbiota of rapeseed (Brassica napus). A total of 2496 amplicon sequence variants (ASVs) belonging to 504 genera in 25 phyla were identified, and the seed microbiota of all sampling stages were divided into three groups. The microbiota of flower buds, young pods, and seeds at 20 days after flowering (daf) formed the first group; that of seeds at 30 daf, 40 daf and 50 daf formed the second group; that of mature seeds and parental seeds were clustered into the third group. The functions of seed microbiota were identified by using PICRUSt2, and it was found that the substance metabolism of seed microbiota was correlated with those of the seeds. Finally, sixty-one core ASVs, including several potential human pathogens, were identified, and a member of the seed core microbiota, Sphingomonas endophytica, was isolated from seeds and found to promote seedling growth and enhance resistance against Sclerotinia sclerotiorum, a major pathogen in rapeseed. Our findings provide a novel perspective for understanding the composition and functions of microbiota during seed development and may enhance the efficiency of mining beneficial seed microbes.
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Affiliation(s)
- Yao Yao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Changxing Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yu Zhang
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Yang Lin
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Tao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Haibin Chang
- Huanggang Academy of Agricultural Science, Huanggang 438000, China;
| | - Yanping Fu
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiao Yu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xueliang Lyu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yanbo Feng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xuefeng Bian
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
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Xian WD, Chen J, Zheng Z, Ding J, Xi Y, Zhang Y, Qu W, Tang C, Li C, Liu X, Li W, Wang J. Water masses influence the variation of microbial communities in the Yangtze River Estuary and its adjacent waters. Front Microbiol 2024; 15:1367062. [PMID: 38572235 PMCID: PMC10987813 DOI: 10.3389/fmicb.2024.1367062] [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: 01/08/2024] [Accepted: 02/28/2024] [Indexed: 04/05/2024] Open
Abstract
The Yangtze River estuary (YRE) are strongly influenced by the Kuroshio and terrigenous input from rivers, leading to the formation of distinct water masses, however, there remains a limited understanding of the full extent of this influence. Here the variation of water masses and bacterial communities of 58 seawater samples from the YRE and its adjacent waters were investigated. Our findings suggested that there were 5 water masses in the studied area: Black stream (BS), coastal water in the East China Sea (CW), nearshore mixed water (NM), mixed water in the middle and deep layers of the East China Sea (MM), and deep water blocks in the middle of the East China Sea (DM). The CW mass harbors the highest alpha diversity across all layers, whereas the NM mass exhibits higher diversity in the surface layer but lower in the middle layers. Proteobacteria was the most abundant taxa in all water masses, apart from that, in the surface layer masses, Cyanobacterium, Bacteroidota, and Actinobacteriota were the highest proportion in CW, while Bacteroidota and Actinobacteriota were the highest proportion in NM and BS; in the middle layer, Bacteroidota and Actinobacteriota were dominant phylum in CW and BS masses, but Cyanobacterium was main phylum in NM mass; in the bottom layer, Bacteroidota and Actinobacteriota were the dominant phylum in CW, while Marininimicrobia was the dominated phylum in DM and MM masses. Network analysis suggests water masses have obvious influence on community topological characteristics, moreover, community assembly across masses also differ greatly. Taken together, these results emphasized the significant impact of water masses on the bacterial composition, topological characteristics and assembly process, which may provide a theoretical foundation for predicting alterations in microbial communities within estuarine ecosystems under the influence of water masses.
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Affiliation(s)
- Wen-Dong Xian
- Marine Microorganism Ecological & Application Lab, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Jinhui Chen
- Marine Microorganism Ecological & Application Lab, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Zheng Zheng
- Marine Microorganism Ecological & Application Lab, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Junjie Ding
- Marine Microorganism Ecological & Application Lab, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Yinli Xi
- Marine Microorganism Ecological & Application Lab, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Yiying Zhang
- Marine Microorganism Ecological & Application Lab, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Wu Qu
- Marine Microorganism Ecological & Application Lab, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Chunyu Tang
- Marine Microorganism Ecological & Application Lab, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Changlin Li
- Marine Microorganism Ecological & Application Lab, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Xuezhu Liu
- Marine Microorganism Ecological & Application Lab, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Wei Li
- College of Science, Shantou University, Shantou, China
| | - Jianxin Wang
- Marine Microorganism Ecological & Application Lab, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
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Sena L, Mica E, Valè G, Vaccino P, Pecchioni N. Exploring the potential of endophyte-plant interactions for improving crop sustainable yields in a changing climate. FRONTIERS IN PLANT SCIENCE 2024; 15:1349401. [PMID: 38571718 PMCID: PMC10988515 DOI: 10.3389/fpls.2024.1349401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/05/2024] [Indexed: 04/05/2024]
Abstract
Climate change poses a major threat to global food security, significantly reducing crop yields as cause of abiotic stresses, and for boosting the spread of new and old pathogens and pests. Sustainable crop management as a route to mitigation poses the challenge of recruiting an array of solutions and tools for the new aims. Among these, the deployment of positive interactions between the micro-biotic components of agroecosystems and plants can play a highly significant role, as part of the agro-ecological revolution. Endophytic microorganisms have emerged as a promising solution to tackle this challenge. Among these, Arbuscular Mycorrhizal Fungi (AMF) and endophytic bacteria and fungi have demonstrated their potential to alleviate abiotic stresses such as drought and heat stress, as well as the impacts of biotic stresses. They can enhance crop yields in a sustainable way also by other mechanisms, such as improving the nutrient uptake, or by direct effects on plant physiology. In this review we summarize and update on the main types of endophytes, we highlight several studies that demonstrate their efficacy in improving sustainable yields and explore possible avenues for implementing crop-microbiota interactions. The mechanisms underlying these interactions are highly complex and require a comprehensive understanding. For this reason, omic technologies such as genomics, transcriptomics, proteomics, and metabolomics have been employed to unravel, by a higher level of information, the complex network of interactions between plants and microorganisms. Therefore, we also discuss the various omic approaches and techniques that have been used so far to study plant-endophyte interactions.
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Affiliation(s)
- Lorenzo Sena
- Dipartimento di Scienze della Vita, Sede Agraria, UNIMORE - Università di Modena e Reggio Emilia, Reggio Emilia, Italy
- Centro di Ricerca Cerealicoltura e Colture Industriali, CREA – Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Vercelli, Italy
| | - Erica Mica
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica, UPO – Università del Piemonte Orientale, Complesso San Giuseppe, Vercelli, Italy
| | - Giampiero Valè
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica, UPO – Università del Piemonte Orientale, Complesso San Giuseppe, Vercelli, Italy
| | - Patrizia Vaccino
- Centro di Ricerca Cerealicoltura e Colture Industriali, CREA – Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Vercelli, Italy
| | - Nicola Pecchioni
- Dipartimento di Scienze della Vita, Sede Agraria, UNIMORE - Università di Modena e Reggio Emilia, Reggio Emilia, Italy
- Centro di Ricerca Cerealicoltura e Colture Industriali, CREA – Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Vercelli, Italy
- Centro di Ricerca Cerealicoltura e Colture Industriali, CREA – Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Foggia, Italy
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Guo L, Liu S, Zhang P, Hakeem A, Song H, Yu M, Wang F. Effects of Different Mulching Practices on Soil Environment and Fruit Quality in Peach Orchards. PLANTS (BASEL, SWITZERLAND) 2024; 13:827. [PMID: 38592801 PMCID: PMC10975533 DOI: 10.3390/plants13060827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 04/11/2024]
Abstract
Mulching practices have been used to improve peach growth and production across the globe. However, the impact of mulching on the physiochemical properties and soil characteristics of orchards remains largely unknown. This study aimed to decipher the impacts of various mulching patterns on the soil environment and the quality of Prunus persica fruit in "Zijinhuangcui". Three treatments were set up, which included black ground fabric mulch (BF) and two living grass mulch treatments (HV: hairy vetch and RG: ryegrass). The results showed that different mulching treatments have different effects on soil, plant growth, and fruit quality. Living grass mulch treatments, especially the HV treatment, significantly improved soil nutrients by enhancing nitrogen-related indicators. Of note, the BF treatment had higher total phosphorus and available phosphorus contents than the HV and RG treatments. The HV treatment had the highest relative abundance of Proteobacteria (33.49%), which is associated with symbiotic nitrogen fixation, followed by RG (25.62%), and BF (22.38%) at the young fruit stage. Similarly, the abundance of Terrimonas, which has a unique nitrogen fixation system at the genus level, was significantly higher in the living grass mulch (HV, 1.30-3.13% and RG, 2.27-4.24%) than in the BF treatment. Living grass mulch also promoted tree growth, increased fruit sugar content, sugar-related components, and sugar-acid ratio, and reduced the acid content. Collectively, the findings of this study show that living grass mulch can promote tree growth and improve fruit quality by improving soil fertility, bacterial diversity, and richness.
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Affiliation(s)
- Lei Guo
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China;
| | - Siyu Liu
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Research Center of Jiangsu Province, Nanjing 210095, China
| | - Peizhi Zhang
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Research Center of Jiangsu Province, Nanjing 210095, China
| | - Abdul Hakeem
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Research Center of Jiangsu Province, Nanjing 210095, China
| | - Hongfeng Song
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China (M.Y.)
| | - Mingliang Yu
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China (M.Y.)
| | - Falin Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China;
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Fang T, Han X, Yue Y. Disease-resistant varieties of Chinese cabbage ( Brassica rapa L. ssp. pekinensis) inhibit Plasmodiophora brassicae infestation by stabilising root flora structure. FRONTIERS IN PLANT SCIENCE 2024; 15:1328845. [PMID: 38504895 PMCID: PMC10950205 DOI: 10.3389/fpls.2024.1328845] [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: 10/30/2023] [Accepted: 01/31/2024] [Indexed: 03/21/2024]
Abstract
The application of disease-resistant varieties is the most cost-effective method for solving the problem of clubroot. "Shangpin," a disease-resistant variety of Chinese cabbage with broad-spectrum immunity to Plasmodiophora brassicae (P. brassicae), was screened in a previous study. Based on 16S rRNA sequencing technology, we annotated the compositional differences between the rhizosphere, rhizoplane, and endosphere bacterial communities of "Shangpin" and "83-1" under P. brassicae stress. Alpha diversity analysis showed that the abundance of microorganisms in the root system of "83-1" changed more than that of "Shangpin" after P. brassicae infestation, and Beta diversity analysis indicated that Flavobacterium and Sphingomonas may mediate clubroot resistance, while Nitrospira, Nitrosospira, and Pseudomonas may mediate P. brassicae infestation among the bacteria in the Top 10 abundances. Microbial functional analyses showed that the root microorganisms of "83-1" were metabolically weakened after P. brassicae inoculation and were inhibited in competition with pathogenic bacteria. Conversely, the root microorganisms of "Shangpin" maintained the strength of their metabolic capacity, which took a favorable position in competition with the pathogen and inhibited the growth and development of the pathogen, thus showing resistance. Root secretions of "Shangpin" significantly inhibited the incidence and disease index of clubroot, which indicated that under clubroot stress, resistant varieties maintain root microbial diversity and microbial community functions through specific root exudates, enriching the genera Flavobacterium and Sphingomonas, thus showing resistance. The results of this study reveal the resistance mechanism of resistant varieties to clubroot and provide new insights into the prevention and control of clubroot in Chinese cabbage.
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Affiliation(s)
| | | | - Yanling Yue
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
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Zhang S, Wang Z, Yi L, Ye X, Suo F, Chen X, Lu X. Bacterial response to the combined pollution of benzo[a]pyrene and decabromodiphenyl ether in soil under flooding anaerobic condition. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133137. [PMID: 38056265 DOI: 10.1016/j.jhazmat.2023.133137] [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: 09/04/2023] [Revised: 11/26/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
Abstract
This study investigated the interaction between the co-pollutants of Benzo[a]pyrene (BaP) and decabromodiphenyl ether (BDE-209) and the bacterial community in soil under flooding anaerobic condition. Three levels of combined pollution (at nominal concentrations of 1, 5, and 25 mg/kg, respectively, for each pollutant), their corresponding sterilized controls, and a blank control (CK) were set up. During the incubation time of 270 days, BaP attenuated more easily than BDE-209. The second-order rate constant of BaP attenuation was negatively correlated with the Ln value of initial BaP concentration. Maximal difference in bacterial community occurred between the CK soil and the highly polluted soil. Desulfomonilaceae, Parcubacteria and Rhodanobacter were probably involved in BaP and BDE-209 degradation, while Nitrosomonadaceae, Phenylobacterium and Mitochondria were significantly suppressed by BaP and BDE-209 or their degrading products. Genes narI, bcrC, fadJ, had, dmpC, narG and CfrA were involved in the degradation of BaP and BDE-209. Impacts of BaP and BDE-209 on metabolisms of carbon, nitrogen and sulfur were not significant. The results provide guidance for the management and remediation of the contaminated soil.
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Affiliation(s)
- Shuai Zhang
- Ministry of Education Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, PR China
| | - Zhaoyang Wang
- Ministry of Education Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, PR China
| | - Lijin Yi
- Ministry of Education Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, PR China
| | - Xiangyu Ye
- Ministry of Education Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, PR China
| | - Fanyu Suo
- Ministry of Education Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, PR China
| | - Xuexia Chen
- Ministry of Education Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, PR China
| | - Xiaoxia Lu
- Ministry of Education Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, PR China.
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46
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Hou M, Zhu Y, Chen H, Wen Y. Chiral herbicide imazethapy influences plant-soil feedback on nitrogen metabolism by shaping rhizosphere microorganisms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:18625-18635. [PMID: 38351351 DOI: 10.1007/s11356-024-32393-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/05/2024] [Indexed: 03/09/2024]
Abstract
Herbicides are known to affect the soil nitrogen cycle by shaping soil microorganisms. However, it is not clear how herbicides regulate diverse transformation processes of soil nitrogen cycling by altering rhizosphere microorganisms, subsequently influencing the feedback to plant nitrogen metabolism. Here, we investigated how imazethapyr (IM) enantiomers drive plant-soil feedback on nitrogen metabolism by altering the rhizosphere microorganisms. The results indicated that (R)- and (S)-IM significantly changed the composition and structure rhizosphere microbiome with enantioselectivity and functional changes in microbial communities were associated with soil nitrogen circulation. The determination of nitrogen-cycling functional genes further supported the above findings. The results revealed that (R)- and (S)-IM could change the abundance of nitrogen-cycling functional genes by changing specific bacteria abundances, such as Bacteroidetes, Proteobacteria, and Acidobacteria, thus resulting in diverse nitrogen transformation processes. The alternation of nitrogen transformation processes indicated (R)-IM exhibited a more notable tendency to form a nitrogen cycling pattern with lower energy cost and higher nitrogen retention than (S)-IM. Sterilization experiments demonstrated changes in soil nitrogen cycling drive plant nitrogen metabolism and rhizosphere microorganisms are responsible for the above process of plant-soil feedback for nitrogen metabolism. Under IM enantiomer treatments, rhizosphere microorganisms might stimulate glutamate synthesis by promoting NH4+ uptake and glutamine-glutamate synthesis cycling in roots, thus contributing to positive feedback, with (R)-IM treatments showing more pronounced positive feedback on nitrogen metabolism than (S)-IM treatments. Our results provide theoretical support for determining the mechanism by which IM enantiomers drive plant-soil nitrogen metabolism by changing the rhizosphere microbial communities.
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Affiliation(s)
- Mengchun Hou
- MOE Key Laboratory of Environmental Remediation & Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Youfeng Zhu
- MOE Key Laboratory of Environmental Remediation & Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hui Chen
- Ningbo Key Laboratory of Agricultural Germplasm Resources Mining and Environmental Regulation, College of Science and Technology, Ningbo University, Cixi, 315300, China
| | - Yuezhong Wen
- MOE Key Laboratory of Environmental Remediation & Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
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47
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Zhan C, Wang M. Disease resistance through M genes. NATURE PLANTS 2024; 10:352-353. [PMID: 38409293 DOI: 10.1038/s41477-024-01644-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Affiliation(s)
- Chengfang Zhan
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
- State Key Laboratory of Rice Biology & Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Mengcen Wang
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China.
- State Key Laboratory of Rice Biology & Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Global Education Program for AgriScience Frontiers, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan.
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48
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Xin W, Zhang J, Yu Y, Tian Y, Li H, Chen X, Li W, Liu Y, Lu T, He B, Xiong Y, Yang Z, Xu T, Tang W. Root microbiota of tea plants regulate nitrogen homeostasis and theanine synthesis to influence tea quality. Curr Biol 2024; 34:868-880.e6. [PMID: 38366595 DOI: 10.1016/j.cub.2024.01.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 11/26/2023] [Accepted: 01/16/2024] [Indexed: 02/18/2024]
Abstract
The flavor profile of tea is influenced not only by different tea varieties but also by the surrounding soil environment. Recent studies have indicated the regulatory role of soil microbes residing in plant roots in nutrient uptake and metabolism. However, the impact of this regulatory mechanism on tea quality remains unclear. In this study, we showed that a consortium of microbes isolated from tea roots enhanced ammonia uptake and facilitated the synthesis of theanine, a key determinant of tea taste. Variations were observed in the composition of microbial populations colonizing tea roots and the rhizosphere across different seasons and tea varieties. By comparing the root microorganisms of the high-theanine tea variety Rougui with the low-theanine variety Maoxie, we identified a specific group of microbes that potentially modulate nitrogen metabolism, subsequently influencing the theanine levels in tea. Furthermore, we constructed a synthetic microbial community (SynCom) mirroring the microbe population composition found in Rougui roots. Remarkably, applying SynCom resulted in a significant increase in the theanine content of tea plants and imparted greater tolerance to nitrogen deficiency in Arabidopsis. Our study provides compelling evidence supporting the use of root microorganisms as functional microbial fertilizers to enhance tea quality.
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Affiliation(s)
- Wei Xin
- College of Horticulture, School of Future Technology, and Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; College of Ecology and Resources Engineering, Wuyi University, Wuyishan 354300, Fujian, China
| | - Jianming Zhang
- College of Ecology and Resources Engineering, Wuyi University, Wuyishan 354300, Fujian, China
| | - Yongdong Yu
- College of Horticulture, School of Future Technology, and Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Yunhe Tian
- College of Horticulture, School of Future Technology, and Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Hao Li
- College of Horticulture, School of Future Technology, and Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Xiaolu Chen
- College of Horticulture, School of Future Technology, and Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Wei Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanlin Liu
- College of Horticulture, School of Future Technology, and Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Ting Lu
- College of Horticulture, School of Future Technology, and Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Biyun He
- College of Horticulture, School of Future Technology, and Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Yan Xiong
- College of Horticulture, School of Future Technology, and Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Zhenbiao Yang
- College of Horticulture, School of Future Technology, and Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, Guangdong 518055, P.R. China; Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, P.R. China.
| | - Tongda Xu
- College of Horticulture, School of Future Technology, and Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
| | - Wenxin Tang
- College of Horticulture, School of Future Technology, and Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
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Zhang W, Gao R, Tian L, Xu Z. Integrated microbiome and metabolomics analysis reveal the relationship between plant-specialized metabolites and microbial community in Phellodendron amurense. FRONTIERS IN PLANT SCIENCE 2024; 15:1363063. [PMID: 38450408 PMCID: PMC10915045 DOI: 10.3389/fpls.2024.1363063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 01/29/2024] [Indexed: 03/08/2024]
Abstract
Phellodendron amurense is the essential source of bisbenzylisoquinoline alkaloids (BIAs), making it a highly valued raw material in traditional Chinese medicine. The plant's root secondary metabolism is intricately linked to the microbial communities that surround it. However, the root-associated microbiomes of P. amurense, as well as the potential correlation between its bioactive compounds and these microbiomes, remain poorly understood. Here, the metabolic profiles of root, rhizosphere, and bulk soils of P. amurense revealed the dramatic differences in the relative content of plant-specialized metabolites. A total of 31, 21, and 0 specialized metabolites in P. amurense were identified in the root, rhizosphere soil, and bulk soil, respectively, with higher content of the seven major BIAs observed in the rhizosphere compared with that in the bulk soils. The composition of the bulk and rhizosphere microbiomes was noticeably distinct from that of the endospheric microbiome. The phylum Cyanobacteria accounted for over 60% of the root endosphere communities, and the α-diversity in root was the lowest. Targeted seven BIAs, namely, berberine, palmatine, magnocurarine, phellodendrine, jatrorrhizine, tetrahydropalmatine, and magnoflorine, were significantly positively correlated with Nectriaceae and Sphingobacteriaceae. This study has illuminated the intricate interaction networks between P. amurense root-associated microorganisms and their key chemical compounds, providing the theoretical foundation for discovering biological fertilizers and laying the groundwork for cultivating high-quality medicinal plants.
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Affiliation(s)
- Wanran Zhang
- School of Pharmaceutical Sciences, Guizhou University, Guiyang, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Ranran Gao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lixia Tian
- School of Pharmaceutical Sciences, Guizhou University, Guiyang, China
| | - Zhichao Xu
- College of Life Science, Northeast Forestry University, Harbin, China
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50
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Zhao J, Yu X, Zhang C, Hou L, Wu N, Zhang W, Wang Y, Yao B, Delaplace P, Tian J. Harnessing microbial interactions with rice: Strategies for abiotic stress alleviation in the face of environmental challenges and climate change. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168847. [PMID: 38036127 DOI: 10.1016/j.scitotenv.2023.168847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Abstract
Rice, which feeds more than half of the world's population, confronts significant challenges due to environmental and climatic changes. Abiotic stressors such as extreme temperatures, drought, heavy metals, organic pollutants, and salinity disrupt its cellular balance, impair photosynthetic efficiency, and degrade grain quality. Beneficial microorganisms from rice and soil microbiomes have emerged as crucial in enhancing rice's tolerance to these stresses. This review delves into the multifaceted impacts of these abiotic stressors on rice growth, exploring the origins of the interacting microorganisms and the intricate dynamics between rice-associated and soil microbiomes. We highlight their synergistic roles in mitigating rice's abiotic stresses and outline rice's strategies for recruiting these microorganisms under various environmental conditions, including the development of techniques to maximize their benefits. Through an in-depth analysis, we shed light on the multifarious mechanisms through which microorganisms fortify rice resilience, such as modulation of antioxidant enzymes, enhanced nutrient uptake, plant hormone adjustments, exopolysaccharide secretion, and strategic gene expression regulation, emphasizing the objective of leveraging microorganisms to boost rice's stress tolerance. The review also recognizes the growing prominence of microbial inoculants in modern rice cultivation for their eco-friendliness and sustainability. We discuss ongoing efforts to optimize these inoculants, providing insights into the rigorous processes involved in their formulation and strategic deployment. In conclusion, this review emphasizes the importance of microbial interventions in bolstering rice agriculture and ensuring its resilience in the face of rising environmental challenges.
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Affiliation(s)
- Jintong Zhao
- Gembloux Agro-Bio Tech, University of Liege, TERRA - Teaching & Research Center, Plant Sciences, 5030 Gembloux, Belgium; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoxia Yu
- School of Water Resources & Environmental Engineering, East China University of Technology, Nanchang, Jiangxi 330000, China
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Sanya Institute, Hainan, Academy of Agricultural Sciences, Sanya 572000, China
| | - Ligang Hou
- Rice Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, Jilin 136100, China
| | - Ningfeng Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuan Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Pierre Delaplace
- Gembloux Agro-Bio Tech, University of Liege, TERRA - Teaching & Research Center, Plant Sciences, 5030 Gembloux, Belgium
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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