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Li H, Tian S, Shang F, Shi X, Zhang Y, Cao Y. Impacts of oxbow lake evolution on sediment microbial community structure in the Yellow River source region. ENVIRONMENTAL RESEARCH 2024; 252:119042. [PMID: 38692420 DOI: 10.1016/j.envres.2024.119042] [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: 03/01/2024] [Revised: 04/26/2024] [Accepted: 04/27/2024] [Indexed: 05/03/2024]
Abstract
Oxbow lake formation and evolution have significant impacts on the fragile Yellow River Basin ecosystem. However, the effects of different oxbow lake evolutionary stages on sediment microbial community structure are not yet understood comprehensively. Therefore, microbial community structure in three stages of oxbow lake succession, namely, lotic lake (early stage), semi-lotic lake (middle stage), and lentic lake (late stage), was investigated in the present study in the Yellow River Basin on the Qinghai-Tibet Plateau. Amplicon sequencing was employed to reveal differences in microbial community diversity and composition. The bacterial and fungal communities in sediment were significantly different among the three succession stages and were driven by different environmental factors. In particular, bacterial community structure was influenced primarily by nitrate-nitrogen (N), microbial biomass phosphorus, and total carbon (C) and organic C in the early, middle, and late stages, respectively. Conversely, fungal community structure was influenced primarily by ammonium-N in the early stage and by moisture content in the middle and late stages. However, the predicted functions of the microbial communities did not exhibit significant differences across the three succession stages. Both bacteria and fungi were influenced significantly by stochastic factors. Homogeneous selection had a high relative contribution to bacteria community assembly in the middle stage, whereas the relative contributions of heterogeneous selection processes to fungal community assembly increased through the three stages. As succession time increased, the total number of keystone species increased gradually, and the late succession stage had high network complexity and the highest network stability. The findings could facilitate further elucidation of the evolution mechanisms of oxbow lake source area, high-altitude river evolution dynamics, in addition to aiding a deeper understanding of the long-term ecological evolution patterns of source river ecosystems.
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Affiliation(s)
- Huinan Li
- School of Life Sciences, Henan University, Kaifeng, Henan, 475004, China
| | - Shimin Tian
- Yellow River Institute of Hydraulic Research, Henan Key Laboratory of Ecological Environment Protection and Restoration of Yellow River Basin, YRCC, Zhengzhou, 450003, China.
| | - Fude Shang
- School of Life Sciences, Henan University, Kaifeng, Henan, 475004, China.
| | - Xiaoyu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, Henan, 475004, China
| | - Yang Zhang
- Yellow River Institute of Hydraulic Research, Henan Key Laboratory of Ecological Environment Protection and Restoration of Yellow River Basin, YRCC, Zhengzhou, 450003, China
| | - Yongtao Cao
- Yellow River Institute of Hydraulic Research, Henan Key Laboratory of Ecological Environment Protection and Restoration of Yellow River Basin, YRCC, Zhengzhou, 450003, China
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2
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Chen P, Huang P, Yu H, Yu H, Xie W, Wang Y, Zhou Y, Chen L, Zhang M, Yao R. Strigolactones shape the assembly of root-associated microbiota in response to phosphorus availability. mSystems 2024; 9:e0112423. [PMID: 38780241 DOI: 10.1128/msystems.01124-23] [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: 10/20/2023] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Plants rely on strigolactones (SLs) to regulate their development and form symbiotic relationships with microbes as part of the adaptive phosphorus (P) efficiency strategies. However, the impact of SLs on root-associated microbial communities in response to P availability remains unknown. Here, root microbiota of SL biosynthesis (max3-11) and perception (d14-1) were compared to wild-type Col-0 plants under different P concentrations. Using high-throughput sequencing, the relationship between SLs, P concentrations, and the root-associated microbiota was investigated to reveal the variation in microbial diversity, composition, and interaction. Plant genotypes and P availability played important but different roles in shaping the root-associated microbial community. Importantly, SLs were found to attract Acinetobacter in low P conditions, which included an isolated CP-2 (Acinetobacter soli) that could promote plant growth in cocultivation experiments. Moreover, SLs could change the topologic structure within co-occurrence networks and increase the number of keystone taxa (e.g., Rhizobiaceae and Acidobacteriaceae) to enhance microbial community stability. This study reveals the key role of SLs in mediating root-associated microbiota interactions.IMPORTANCEStrigolactones (SLs) play a crucial role in plant development and their symbiotic relationships with microbes, particularly in adapting to phosphorus levels. Using high-throughput sequencing, we compared the root microbiota of plants with SL biosynthesis and perception mutants to wild-type plants under different phosphorus concentrations. These results found that SLs can attract beneficial microbes in low phosphorus conditions to enhance plant growth. Additionally, SLs affect microbial network structures, increasing the stability of microbial communities. This study highlights the key role of SLs in shaping root-associated microbial interactions, especially in response to phosphorus availability.
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Affiliation(s)
- Pubo Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Pingliang Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Haiyang Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Huang Yu
- School of Resource and Environment and Safety Engineering, University of South China, Hengyang, China
| | - Weicheng Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Yuehua Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Yu Zhou
- Hunan Institute of Microbiology, Changsha, China
| | - Li Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou, China
| | - Meng Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou, China
| | - Ruifeng Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou, China
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3
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Wu WF, Li XY, Chen SC, Jin BJ, Wu CY, Li G, Sun CL, Zhu YG, Lin XY. Nitrogen fertilization modulates rice phyllosphere functional genes and pathogens through fungal communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172622. [PMID: 38642761 DOI: 10.1016/j.scitotenv.2024.172622] [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: 01/25/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
The phyllosphere is a vital yet often neglected habitat hosting diverse microorganisms with various functions. However, studies regarding how the composition and functions of the phyllosphere microbiome respond to agricultural practices, like nitrogen fertilization, are limited. This study investigated the effects of long-term nitrogen fertilization with different levels (CK, N90, N210, N330) on the functional genes and pathogens of the rice phyllosphere microbiome. Results showed that the relative abundance of many microbial functional genes in the rice phyllosphere was significantly affected by nitrogen fertilization, especially those involved in C fixation and denitrification genes. Different nitrogen fertilization levels have greater effects on fungal communities than bacteria communities in the rice phyllosphere, and network analysis and structural equation models further elucidate that fungal communities not only changed bacterial-fungal inter-kingdom interactions in the phyllosphere but also contributed to the variation of biogeochemical cycle potential. Besides, the moderate nitrogen fertilization level (N210) was associated with an enrichment of beneficial microbes in the phyllosphere, while also resulting in the lowest abundance of pathogenic fungi (1.14 %). In contrast, the highest abundance of pathogenic fungi (1.64 %) was observed in the highest nitrogen fertilization level (N330). This enrichment of pathogen due to high nitrogen level was also regulated by the fungal communities, as revealed through SEM analysis. Together, we demonstrated that the phyllosphere fungal communities were more sensitive to the nitrogen fertilization levels and played a crucial role in influencing phyllosphere functional profiles including element cycling potential and pathogen abundance. This study expands our knowledge regarding the role of phyllosphere fungal communities in modulating the element cycling and plant health in sustainable agriculture.
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Affiliation(s)
- Wei-Feng Wu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Xin-Yuan Li
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Song-Can Chen
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Bing-Jie Jin
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Chun-Yan Wu
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Cheng-Liang Sun
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yong-Guan Zhu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Xian-Yong Lin
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China.
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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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Wang Z, Yuan J, Wang R, Xu S, Zhou J. Distinct fungal communities affecting opposite galanthamine accumulation patterns in two Lycoris species. Microbiol Res 2024; 286:127791. [PMID: 38851007 DOI: 10.1016/j.micres.2024.127791] [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: 03/18/2024] [Revised: 05/10/2024] [Accepted: 05/27/2024] [Indexed: 06/10/2024]
Abstract
Lycoris radiata is the main source of galanthamine, a clinical drug used in Alzheimer's disease; however, the galanthamine content in L. radiata is low. Lycoris aurea is another Lycoris species with high galanthamine content. Fungal endophytes can enhance plant secondary metabolite accumulation; thus, we compared the fungal communities in these two Lycoris species to identify certain fungal taxa in L. aurea capable of enhancing galanthamine accumulation. Several fungal endophytes, which were enriched in, exclusively isolated from L. aurea, or showed significant correlations with galanthamine, were demonstrated to enhance the accumulation of only galanthamine but no other Amaryllidaceae alkaloids (AAs) in L. radiata. These fungal endophytes mainly upregulated the downstream genes in the biosynthesis pathways of AAs in L. radiata, suggesting that they may allocate more precursors for galanthamine biosynthesis. This study demonstrated that fungal endophytes from L. aurea with higher galanthamine content can specifically enhance the accumulation of this medicinal alkaloid in other Lycoris species, thereby increasing the galanthamine source and reducing galanthamine separation and purification costs. This study broadens our understanding of the complex interactions between plant secondary metabolites and fungal endophytes.
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Affiliation(s)
- Ziying Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Jie Yuan
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Ren Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Sheng Xu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China.
| | - Jiayu Zhou
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China.
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6
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Ding Y, Wang L, Wang H, Li H. Dynamic Succession of Natural Microbes during the Ecolly Grape Growth under Extremely Simplified Eco-Cultivation. Foods 2024; 13:1580. [PMID: 38790880 PMCID: PMC11120413 DOI: 10.3390/foods13101580] [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: 03/17/2024] [Revised: 04/26/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
The composition and continuous succession of natural microbial communities during grape growth play important roles in grape health and flavor quality as well as in characterizing the regional wine terroir. This study explored the diversity and dynamics of fruit epidermal microbes at each growth and developmental stage of Ecolly grapes under an extremely simplified eco-cultivation model, analyzed microbial interactions and associations of weather parameters to specific communities, and emphasized metabolic functional characteristics of microecology. The results indicated that the natural microbial community changed significantly during the grape growth phase. The dominant fungal genera mainly included Gibberella, Alternaria, Filobasidium, Naganishia, Ascochyta, Apiotrichum, Comoclathris, and Aureobasidium, and the dominant bacterial genera mainly contained Sediminibacterium, Ralstonia, Pantoea, Bradyrhizobium, Brevundimonas, Mesorhizobium, Planococcus, and Planomicrobium. In summary, filamentous fungi gradually shifted to basidiomycetous yeasts along with fruit ripening, with a decline in the number of Gram-negative bacteria and a relative increase in Gram-positive bacteria. The community assembly process reflects the fact that microbial ecology may be influenced by a variety of factors, but the fungal community was more stable, and the bacterial community fluctuated more from year to year, which may reflect their response to weather conditions over the years. Overall, our study helps to comprehensively profile the ecological characteristics of the grape microbial system, highlights the natural ecological viticulture concept, and promotes the sustainable development of the grape and wine industry.
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Affiliation(s)
- Yinting Ding
- College of Enology, Northwest A&F University, Xianyang 712100, China; (Y.D.); (L.W.); (H.W.)
| | - Lin Wang
- College of Enology, Northwest A&F University, Xianyang 712100, China; (Y.D.); (L.W.); (H.W.)
| | - Hua Wang
- College of Enology, Northwest A&F University, Xianyang 712100, China; (Y.D.); (L.W.); (H.W.)
- China Wine Industry Technology Institute, Yinchuan 750021, China
- Shaanxi Engineering Research Center for Viti-Viniculture, Xianyang 712100, China
- Engineering Research Center for Viti-Viniculture, National Forestry and Grassland Administration, Xianyang 712100, China
| | - Hua Li
- College of Enology, Northwest A&F University, Xianyang 712100, China; (Y.D.); (L.W.); (H.W.)
- China Wine Industry Technology Institute, Yinchuan 750021, China
- Shaanxi Engineering Research Center for Viti-Viniculture, Xianyang 712100, China
- Engineering Research Center for Viti-Viniculture, National Forestry and Grassland Administration, Xianyang 712100, China
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Lan X, Ning Z, Jia Y, Lin W, Xiao E, Cheng Q, Cai Q, Xiao T. The rhizosphere microbiome reduces the uptake of arsenic and tungsten by Blechnum orientale by increasing nutrient cycling in historical tungsten mining area soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171429. [PMID: 38442750 DOI: 10.1016/j.scitotenv.2024.171429] [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: 01/03/2024] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/07/2024]
Abstract
The growth of pioneer plants in metal mining area soil is closely related to their minimal uptake of toxic elements. Pioneer plants can inhibit the uptake of toxic elements by increasing nutrient uptake. However, few studies have focused on the mechanisms by which the rhizosphere microbiome affect nutrient cycling and their impact on the uptake of toxic elements by pioneer plants. In this study, we selected Blechnum orientale to investigate the potential roles of the rhizosphere microbiome in nutrient cycling and plant growth in a historical tungsten (W) mining area. Our results showed that while the arsenic (As) and W contents in the soil were relatively high, the enrichment levels of As and W in the B. orientale were relatively low. Furthermore, we found that the As and W contents in plants were significantly negatively correlated with soil nutrients (S, P and Mo), suggesting that elevated levels of these soil nutrients could inhibit As and W uptake by B. orientale. Importantly, we found that these nutrients were also identified as the most important factors shaping rhizosphere microbial attributes, including microbial diversity, ecological clusters, and keystone OTUs. Moreover, the genera, keystone taxa and microbial functional genes enriched in the rhizosphere soils from mining areas played a key role in nutrient (S, P and Mo) bioavailability, which could further increase the nutrient uptake by B. orientale. Taken together, our results suggest that rhizosphere microorganisms can improve pioneer plant growth by inhibiting toxic element accumulation via the increase in nutrient cycling in former W mining areas.
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Affiliation(s)
- Xiaolong Lan
- School of Chemistry and Environmental Engineering, Hanshan Normal University, Chaozhou 521041, China
| | - Zengping Ning
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Yanlong Jia
- School of Chemistry and Environmental Engineering, Hanshan Normal University, Chaozhou 521041, China.
| | - Wenjie Lin
- School of Chemistry and Environmental Engineering, Hanshan Normal University, Chaozhou 521041, China.
| | - Enzong Xiao
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Qianyun Cheng
- School of Geography, Hanshan Normal University, Chaozhou 521041, China
| | - Qiaoxue Cai
- School of Chemistry and Environmental Engineering, Hanshan Normal University, Chaozhou 521041, China
| | - Tangfu Xiao
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
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Cao T, Shi M, Zhang J, Ji H, Wang X, Sun J, Chen Z, Li Q, Song X. Nitrogen fertilization practices alter microbial communities driven by clonal integration in Moso bamboo. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171581. [PMID: 38461973 DOI: 10.1016/j.scitotenv.2024.171581] [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: 01/11/2024] [Revised: 03/03/2024] [Accepted: 03/06/2024] [Indexed: 03/12/2024]
Abstract
Nitrogen (N) fertilization is crucial for maintaining plant productivity. Clonal plants can share resources between connected ramets through clonal integration influencing microbial communities and regulating soil biogeochemical cycling, especially in the rhizosphere. However, the effect of various N fertilization practices on microbial communities in the rhizosphere of clonal ramets remain unknown. In this study, clonal fragments of Moso bamboo (Phyllostachys edulis), consisting of a parent ramet, an offspring ramet, and an interconnecting rhizome, were established in the field. NH4NO3 solution was applied to the parent, offspring ramets or rhizomes to investigate the effect of fertilization practices on the structure and function of rhizosphere microbial communities. The differences in N availability, microbial biomass and community composition, and abundance of nitrifying genes among rhizosphere soils of ramets gradually decreased during the rapid growth of Moso bamboo, irrespective of fertilization practice. The soil N availability variation, particularly in NO3-, caused by fertilization practices altered the rhizosphere microbial community. Soil N availability and stable microbial biomass N in parent fertilization were the highest, being 9.0 % and 18.7 %, as well as 60.8 % and 90.4 % higher than rhizome and offspring fertilizations, respectively. The microbial network nodes and links in rhizome fertilization were 1.8 and 7.5 times higher than in parent and offspring fertilization, respectively. However, the diversity of bacterial community and abundance of nitrifying and denitrifying genes were the highest in offspring fertilization among three practices, which may be associated with increased N loss. Collectively, the rhizosphere microbial community characteristics depended on fertilization practices by altering the clonal integration of N in Moso bamboo. Parent and rhizome fertilization were favorable for N retention in plant-soil system and resulted in more stable microbial functions than offspring fertilization. Our findings provide new insights into precision fertilization for the sustainable Moso bamboo forest management.
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Affiliation(s)
- Tingting Cao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Man Shi
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Junbo Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Hangxiang Ji
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Xiao Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Jilei Sun
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Zhenxiong Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Quan Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Xinzhang Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China.
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9
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Wang Y, Zhang Y, Yang Z, Fei J, Zhou X, Rong X, Peng J, Luo G. Intercropping improves maize yield and nitrogen uptake by regulating nitrogen transformation and functional microbial abundance in rhizosphere soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 358:120886. [PMID: 38648726 DOI: 10.1016/j.jenvman.2024.120886] [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: 09/17/2023] [Revised: 04/03/2024] [Accepted: 04/10/2024] [Indexed: 04/25/2024]
Abstract
Intercropping-driven changes in nitrogen (N)-acquiring microbial genomes and functional expression regulate soil N availability and plant N uptake. However, present data seem to be limited to a specific community, obscuring the viewpoint of entire N-acquiring microbiomes and functions. Taking maize intercropped with legumes (peanut and soybean) and non-legumes (gingelly and sweet potato) as models, we studied the effects of intercropping on N transformations and N-acquiring microbiomes in rhizosphere soil across four maize growth stages. Meanwhile, we compiled promising strategies such as random forest analysis and structural equation model for the exploitation of the associations between microbe-driven N dynamics and soil-plant N trade-offs and maize productivity. Compared with monoculture, maize intercropping significantly increased the denitrification rate of rhizosphere soils across four maize growth stages, net N mineralization in the elongation and flowering stages, and the nitrification rate in the seedling and mature stages. The abundance of most N-acquiring microbial populations was influenced significantly by intercropping patterns and maize growth stages. Soil available N components (NH4+-N, NO3--N, and dissolved organic N content) showed a highly direct effect on plant N uptake, which mainly mediated by N transformations (denitrification rate) and N-acquiring populations (amoB, nirK3, and hzsB genes). Overall, the adaptation of N-acquiring microbiomes to changing rhizosphere micro-environments caused by intercropping patterns and maize development could promote soil N transformations and dynamics to meet demand of maize for N nutrient. This would offer another unique perspective to manage the benefits of the highly N-effective and production-effective intercropping ecosystems.
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Affiliation(s)
- Yizhe Wang
- College of Resources, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China
| | - Yuping Zhang
- College of Resources, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China.
| | - Ziyu Yang
- College of Resources, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China
| | - Jiangchi Fei
- College of Resources, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China.
| | - Xuan Zhou
- Institute of Soil and Fertilizer, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Xiangmin Rong
- College of Resources, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
| | - Jianwei Peng
- College of Resources, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
| | - Gongwen Luo
- College of Resources, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China.
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10
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Yang L, Fan W, Xu Y. Qu-omics elucidates the formation and spatio-temporal differentiation mechanism underlying the microecology of high temperature Daqu. Food Chem 2024; 438:137988. [PMID: 37979262 DOI: 10.1016/j.foodchem.2023.137988] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/06/2023] [Accepted: 11/11/2023] [Indexed: 11/20/2023]
Abstract
Even if fermented in the same qu-room, Daqu will form various microecologies. A gradual differentiation of microbial population niches was observed within different qu-layers, manifesting as variations in the abundance of dominant microorganisms including Bacillus, Saccharopolyspora, Weissella, Kroppenstedtia, Thermoascus, Thermomyces, Saccharomycopsis, and Rasamsonia. Moreover, distinctions were observed in the functional expression of microorganisms, including Aspergillus, Virgibacillus, Oceanobacillus, and Neurospora. The community in middle layer Daqu exhibited characteristics of high compactness and niche diversity, which facilitated efficient substrate utilization. During the initial phase, the upper Daqu community demonstrated heightened activity. However, in the middle and lower layers, fungi and bacteria respectively exhibited greater functional expression. The key environmental factors regulating the assembly of communities in the upper and middle layers were pH and temperature, respectively, and the lower was moisture and acidity. Notably, deterministic assembly exerted a stronger influence on fungi.
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Affiliation(s)
- Liang Yang
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Ave, Wuxi 214122, Jiangsu, China; Department of Brewing Engineering, Moutai Institute, Luban Ave, Renhuai 564507, Guizhou, China
| | - Wenlai Fan
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Ave, Wuxi 214122, Jiangsu, China.
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Ave, Wuxi 214122, Jiangsu, China.
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11
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Xiong C, K. Singh B, Zhu YG, Hu HW, Li PP, Han YL, Han LL, Zhang QB, Wang JT, Liu SY, Wu CF, Ge AH, Zhang LM, He JZ. Microbial species pool-mediated diazotrophic community assembly in crop microbiomes during plant development. mSystems 2024; 9:e0105523. [PMID: 38501864 PMCID: PMC11019923 DOI: 10.1128/msystems.01055-23] [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: 10/02/2023] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Plant-associated diazotrophs strongly relate to plant nitrogen (N) supply and growth. However, our knowledge of diazotrophic community assembly and microbial N metabolism in plant microbiomes is largely limited. Here we examined the assembly and temporal dynamics of diazotrophic communities across multiple compartments (soils, epiphytic and endophytic niches of root and leaf, and grain) of three cereal crops (maize, wheat, and barley) and identified the potential N-cycling pathways in phylloplane microbiomes. Our results demonstrated that the microbial species pool, influenced by site-specific environmental factors (e.g., edaphic factors), had a stronger effect than host selection (i.e., plant species and developmental stage) in shaping diazotrophic communities across the soil-plant continuum. Crop diazotrophic communities were dominated by a few taxa (~0.7% of diazotrophic phylotypes) which were mainly affiliated with Methylobacterium, Azospirillum, Bradyrhizobium, and Rhizobium. Furthermore, eight dominant taxa belonging to Azospirillum and Methylobacterium were identified as keystone diazotrophic taxa for three crops and were potentially associated with microbial network stability and crop yields. Metagenomic binning recovered 58 metagenome-assembled genomes (MAGs) from the phylloplane, and the majority of them were identified as novel species (37 MAGs) and harbored genes potentially related to multiple N metabolism processes (e.g., nitrate reduction). Notably, for the first time, a high-quality MAG harboring genes involved in the complete denitrification process was recovered in the phylloplane and showed high identity to Pseudomonas mendocina. Overall, these findings significantly expand our understanding of ecological drivers of crop diazotrophs and provide new insights into the potential microbial N metabolism in the phyllosphere.IMPORTANCEPlants harbor diverse nitrogen-fixing microorganisms (i.e., diazotrophic communities) in both belowground and aboveground tissues, which play a vital role in plant nitrogen supply and growth promotion. Understanding the assembly and temporal dynamics of crop diazotrophic communities is a prerequisite for harnessing them to promote plant growth. In this study, we show that the site-specific microbial species pool largely shapes the structure of diazotrophic communities in the leaves and roots of three cereal crops. We further identify keystone diazotrophic taxa in crop microbiomes and characterize potential microbial N metabolism pathways in the phyllosphere, which provides essential information for developing microbiome-based tools in future sustainable agricultural production.
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Affiliation(s)
- Chao Xiong
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Pei-Pei Li
- College of Resource and Environmental Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yan-Lai Han
- College of Resource and Environmental Sciences, Henan Agricultural University, Zhengzhou, China
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qin-Bing Zhang
- Soil and Fertilizer Station of Qilin District, Qujing, Yunnan Province, China
| | - Jun-Tao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia
| | - Si-Yi Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chuan-Fa Wu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resource and Environmental Sciences, Henan Agricultural University, Zhengzhou, China
| | - An-Hui Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
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12
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Ali Q, Sami A, Haider MZ, Ashfaq M, Javed MA. Antioxidant production promotes defense mechanism and different gene expression level in Zea mays under abiotic stress. Sci Rep 2024; 14:7114. [PMID: 38531994 DOI: 10.1038/s41598-024-57939-6] [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: 11/10/2023] [Accepted: 03/22/2024] [Indexed: 03/28/2024] Open
Abstract
The growth and productivity of maize are severely affected by soil salinity. The crucial determinants for the future performance of plants are productive for seed germination and seedling establishment; however, both stages are liable to soil salinity. For grain, maize is an economically significant crop sensitive to abiotic stresses. However, little is known about defense responses by the salinity-induced antioxidant and oxidative stress in maize. In our work, the commercially available maize variety Raka-Poshi was grown in pots for 30 days under greenhouse conditions. To evaluate the salt-induced oxidative/antioxidant responses in maize for salt stress 0, 25, 50, 75, 100 and 150 mM concentrations, treatments were provided using sodium chloride (NaCl). All the biochemical indices were calculated under all NaCl concentrations, while drought was induced by up to 50% irrigation water. After 30 days of seed germination, the maize leaves were collected for the measurement of lipid peroxidase or malondialdehyde (MDA), glutathione reductase (GR), guaiacol peroxidase (GPOD), hydrogen peroxide (H2O2), superoxide dismutase (SOD), lipoxygenase (LOX), catalase (CAT), ascorbate peroxidase (APOD) and glutathione-S-transferase (GST). The results revealed a 47% reduction under 150 mM NaCl and 50% drought stress conditions. The results have shown that the successive increase of NaCl concentrations and drought caused an increase in catalase production. With successive increase in NaCl concentration and drought stress, lower levels of H2O2, SOD, and MDA were detected in maize leaves. The results regarding the morphology of maize seedlings indicated a successive reduction in the root length and shoot length under applications of salt and drought stress, while root-to-shoot weights were found to be increased under drought stress and decreased under salt stress conditions During gene expression analysis collectively indicate that, under drought stress conditions, the expression levels of all nine mentioned enzyme-related genes were consistently downregulated.
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Affiliation(s)
- Qurban Ali
- Department of Plant Breeding and Genetics, Faculty of Agriculture, University of the Punjab, Lahore, 54590, Pakistan.
| | - Adnan Sami
- Department of Plant Breeding and Genetics, Faculty of Agriculture, University of the Punjab, Lahore, 54590, Pakistan
| | - Muhammad Zeshan Haider
- Department of Plant Breeding and Genetics, Faculty of Agriculture, University of the Punjab, Lahore, 54590, Pakistan
| | - Muhammad Ashfaq
- Department of Plant Breeding and Genetics, Faculty of Agriculture, University of the Punjab, Lahore, 54590, Pakistan
| | - Muhammad Arshad Javed
- Department of Plant Breeding and Genetics, Faculty of Agriculture, University of the Punjab, Lahore, 54590, Pakistan.
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13
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Zhang Y, Du Y, Zhang Z, Islam W, Zeng F. Unveiling the diversity, composition, and dynamics of phyllosphere microbial communities in Alhagi sparsifolia across desert basins and seasons in Xinjiang, China. Front Microbiol 2024; 15:1361756. [PMID: 38591034 PMCID: PMC10999668 DOI: 10.3389/fmicb.2024.1361756] [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: 12/26/2023] [Accepted: 03/07/2024] [Indexed: 04/10/2024] Open
Abstract
Phyllosphere microbes residing on plant leaf surfaces for maintaining plant health have gained increasing recognition. However, in desert ecosystems, knowledge about the variety, composition, and coexistence patterns of microbial communities in the phyllosphere remains limited. This study, conducted across three basins (Turpan-TLF, Tarim-CL, and Dzungaria-MSW) and three seasons (spring, summer, and autumn) in Xinjiang, China, aimed to explore the diversity and composition of microbial communities in the phyllosphere, encompassing both bacteria and fungi in Alhagi sparsifolia. We also investigated the co-occurrence patterns, influencing factors, and underlying mechanisms driving these dynamics. Results indicate that phyllosphere bacteria exhibited lower diversity indices (ACE, Shannon, Simpson, Fisher phylogenetic diversity, and Richness) in spring compared to summer and autumn, while the Goods Coverage Index (GCI) was higher in spring. Conversely, diversity indices and GCI of phyllosphere fungi showed an opposite trend. Interestingly, the lowest level of multi-functionality and niche width in phyllosphere bacteria occurred in spring, while the highest level was observed in phyllosphere fungi. Furthermore, the study revealed that no significant differences in multi-functionality were found among the regions (CL, MSW, and TLF). Network analysis highlighted that during spring, phyllosphere bacteria exhibited the lowest number of nodes, edges, and average degree, while phyllosphere fungi had the highest. Surprisingly, the multi-functionality of both phyllosphere bacteria and fungi showed no significant correlation with climatic and environmental factors but displayed a significant association with the morphological characteristics and physicochemical properties of leaves. Structural Equation Model indicated that the morphological characteristics of leaves significantly influenced the multi-functionality of phyllosphere bacteria and fungi. However, the indirect and total effects of climate on multi-functionality were greater than the effects of physicochemical properties and morphological characteristics of leaves. These findings offer new insights into leaf phyllosphere microbial community structure, laying a theoretical foundation for vegetation restoration and rational plant resource utilization in desert ecosystems.
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Affiliation(s)
- Yulin Zhang
- College of Ecology and Environmental, Xinjiang University, Urumqi, China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
| | - Yi Du
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhihao Zhang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
| | - Waqar Islam
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
| | - Fanjiang Zeng
- College of Ecology and Environmental, Xinjiang University, Urumqi, China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
- University of Chinese Academy of Sciences, Beijing, China
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14
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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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15
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Argiroff WA, Carrell AA, Klingeman DM, Dove NC, Muchero W, Veach AM, Wahl T, Lebreux SJ, Webb AB, Peyton K, Schadt CW, Cregger MA. Seasonality and longer-term development generate temporal dynamics in the Populus microbiome. mSystems 2024; 9:e0088623. [PMID: 38421171 PMCID: PMC10949431 DOI: 10.1128/msystems.00886-23] [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: 08/22/2023] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
Abstract
Temporal variation in community composition is central to our understanding of the assembly and functioning of microbial communities, yet the controls over temporal dynamics for microbiomes of long-lived plants, such as trees, remain unclear. Temporal variation in tree microbiomes could arise primarily from seasonal (i.e., intra-annual) fluctuations in community composition or from longer-term changes across years as host plants age. To test these alternatives, we experimentally isolated temporal variation in plant microbiome composition using a common garden and clonally propagated plants, and we used amplicon sequencing to characterize bacterial/archaeal and fungal communities in the leaf endosphere, root endosphere, and rhizosphere of two Populus spp. over four seasons across two consecutive years. Microbial community composition differed among seasons and years (which accounted for up to 21% of the variation in microbial community composition) and was correlated with seasonal dissimilarity in climatic conditions. However, microbial community dissimilarity was also positively correlated with time, reflecting longer-term compositional shifts as host trees aged. Together, our findings demonstrate that temporal patterns in tree microbiomes arise from both seasonal fluctuations and longer-term changes, which interact to generate unique seasonal patterns each year. In addition to shedding light on two important controls over the assembly of plant microbiomes, our results also suggest future studies of tree microbiomes should account for background temporal dynamics when testing the drivers of spatial patterns in microbial community composition and temporal responses of plant microbiomes to environmental change.IMPORTANCEMicrobiomes are integral to the health of host plants, but we have a limited understanding of the factors that control how the composition of plant microbiomes changes over time. Especially little is known about the microbiome of long-lived trees, relative to annual and non-woody plants. We tested how tree microbiomes changed between seasons and years in poplar (genus Populus), which are widespread and ecologically important tree species that also serve as important biofuel feedstocks. We found the composition of bacterial, archaeal, and fungal communities differed among seasons, but these seasonal differences depended on year. This dependence was driven by longer-term changes in microbial composition as host trees developed across consecutive years. Our findings suggest that temporal variation in tree microbiomes is driven by both seasonal fluctuations and longer-term (i.e., multiyear) development.
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Affiliation(s)
- William A. Argiroff
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Alyssa A. Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Dawn M. Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Nicholas C. Dove
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Allison M. Veach
- Department of Integrative Biology, The University of Texas, San Antonio, Texas, USA
| | - Toni Wahl
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Steven J. Lebreux
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Amber B. Webb
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Kellie Peyton
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Christopher W. Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Melissa A. Cregger
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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Guo J, Ning H, Li Y, Xu Q, Shen Q, Ling N, Guo S. Assemblages of rhizospheric and root endospheric mycobiota and their ecological associations with functional traits of rice. mBio 2024; 15:e0273323. [PMID: 38319112 PMCID: PMC10936437 DOI: 10.1128/mbio.02733-23] [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: 10/18/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
The soil-root interface harbors complex fungal communities that play vital roles in the fitness of host plants. However, little is known about the assembly rules and potential functions of rhizospheric and endospheric mycobiota. A greenhouse experiment was conducted to explore the fungal communities inhabiting the rhizosphere and roots of 87 rice cultivars at the tillering stage via amplicon sequencing of the fungal internal transcribed spacer 1 region. The potential relationships between these communities and host plant functional traits were also investigated using Procrustes analysis, generalized additive model fitting, and correlation analysis. The fungal microbiota exhibited greater richness, higher diversity, and lower structural variability in the rhizosphere than in the root endosphere. Compared with the root endosphere, the rhizosphere supported a larger coabundance network, with greater connectivity and stronger cohesion. Null model-based analyses revealed that dispersal limitation was primarily responsible for rhizosphere fungal community assembly, while ecological drift was the dominant process in the root endosphere. The community composition of fungi in the rhizosphere was shown to be more related to plant functional traits, such as the root/whole plant biomass, root:shoot biomass ratio, root/shoot nitrogen (N) content, and root/shoot/whole plant N accumulation, than to that in the root endosphere. Overall, at the early stage of rice growth, diverse and complex rhizospheric fungal communities are shaped by stochastic-based processes and exhibit stronger associations with plant functional traits. IMPORTANCE The assembly processes and functions of root-associated mycobiota are among the most fascinating yet elusive topics in microbial ecology. Our results revealed that stochastic forces (dispersal limitation or ecological drift) act on fungal community assembly in both the rice rhizosphere and root endosphere at the early stage of plant growth. In addition, high covariations between the rhizosphere fungal community compositions and plant functional trait profiles were clearly demonstrated in the present study. This work provides empirical evidence of the root-associated fungal assembly principles and ecological relationships of plant functional traits with rhizospheric and root endospheric mycobiota, thereby potentially providing novel perspectives for enhancing plant performance.
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Affiliation(s)
- Junjie Guo
- State Key Lab of Biocontrol, School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong, China
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Huiling Ning
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Yong Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qicheng Xu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Ning Ling
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Shiwei Guo
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
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Quijia Pillajo J, Chapin LJ, Quiroz-Moreno CD, Altland JE, Jones ML. Nutrient availability and plant phenological stage influence the substrate microbiome in container-grown Impatiens walleriana 'Xtreme Red'. BMC PLANT BIOLOGY 2024; 24:176. [PMID: 38448825 PMCID: PMC10916185 DOI: 10.1186/s12870-024-04854-7] [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: 11/28/2023] [Accepted: 02/22/2024] [Indexed: 03/08/2024]
Abstract
BACKGROUND The microbiome plays a fundamental role in plant health and performance. Soil serves as a reservoir of microbial diversity where plants attract microorganisms via root exudates. The soil has an important impact on the composition of the rhizosphere microbiome, but greenhouse ornamental plants are commonly grown in soilless substrates. While soil microbiomes have been extensively studied in traditional agriculture to improve plant performance, health, and sustainability, information about the microbiomes of soilless substrates is still limited. Thus, we conducted an experiment to explore the microbiome of a peat-based substrate used in container production of Impatiens walleriana, a popular greenhouse ornamental plant. We investigated the effects of plant phenological stage and fertilization level on the substrate microbiome. RESULTS Impatiens plants grown under low fertilization rates were smaller and produced more flowers than plants grown under optimum and high fertilization. The top five bacterial phyla present in the substrate were Proteobacteria, Actinobacteria, Bacteriodota, Verrucomicrobiota, and Planctomycetota. We found a total of 2,535 amplicon sequence variants (ASV) grouped into 299 genera. The substrate core microbiome was represented by only 1.8% (48) of the identified ASV. The microbiome community composition was influenced by plant phenological stage and fertilizer levels. Phenological stage exhibited a stronger influence on microbiome composition than fertilizer levels. Differential abundance analysis using DESeq2 identified more ASVs significantly affected (enriched or depleted) in the high fertilizer levels at flowering. As observed for community composition, the effect of plant phenological stage on microbial community function was stronger than fertilizer level. Phenological stage and fertilizer treatments did not affect alpha-diversity in the substrate. CONCLUSIONS In container-grown ornamental plants, the substrate serves as the main microbial reservoir for the plant, and the plant and agricultural inputs (fertilization) modulate the microbial community structure and function of the substrate. The differences observed in substrate microbiome composition across plant phenological stage were explained by pH, total organic carbon (TOC) and fluoride, and across fertilizer levels by pH and phosphate (PO4). Our project provides an initial diversity profile of the bacteria occurring in soilless substrates, an underexplored source of microbial diversity.
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Affiliation(s)
- Juan Quijia Pillajo
- Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH, 44691, USA
| | - Laura J Chapin
- Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH, 44691, USA
| | - Cristian D Quiroz-Moreno
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA
| | - James E Altland
- Application Technology Research Unit, United States Department of Agriculture (USDA)-Agricultural Research Service, Wooster, OH, 44691, USA
| | - Michelle L Jones
- Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH, 44691, USA.
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18
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Yang J, Du Z, Huang C, Li W, Xi B, Zhu L, Wu X. Dynamics of microbial functional guilds involved in the humification process during aerobic composting of chicken manure on an industrial scale. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:21044-21056. [PMID: 38381293 DOI: 10.1007/s11356-024-32390-2] [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: 11/22/2023] [Accepted: 02/05/2024] [Indexed: 02/22/2024]
Abstract
Proper composting treatment of poultry manure waste is recommended before its use as a fertilizer. This involves many bioprocesses driven by microorganisms. Therefore, it is important to understand microbial mechanisms behind these bioprocesses in manure composting systems. Many efforts have been made to study the microbial community structure and diversity in these systems using high-throughput sequencing techniques. However, the dynamics of microbial interaction and functionality, especially for key microbial functional guilds, are not yet fully understood. To address these knowledge gaps, we collected samples from a 150-day industrial chicken manure composting system and performed the microbial network analysis based on the sequencing data. We found that the family Bacillaceae and genus Bacillus might play important roles in organic matter biodegradation at the mesophilic/thermophilic phases. Genera Virgibacillus, Gracilibacillus, Nocardiopsis, Novibacillus, and Bacillaceae_BM62 were identified as the key ones for humic acid synthesis at the mature phases. These findings improve our understanding about the fundamental mechanisms behind manure composting and can aid the development of microbial agents to promote manure composting performance.
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Affiliation(s)
- Jie Yang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, No. 8 Dayangfang, Beiyuan Road, Chaoyang District, Beijing, 100012, China
- State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Zhe Du
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, No. 8 Dayangfang, Beiyuan Road, Chaoyang District, Beijing, 100012, China
- State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Caihong Huang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, No. 8 Dayangfang, Beiyuan Road, Chaoyang District, Beijing, 100012, China.
- State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Wei Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, No. 8 Dayangfang, Beiyuan Road, Chaoyang District, Beijing, 100012, China
- State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, No. 8 Dayangfang, Beiyuan Road, Chaoyang District, Beijing, 100012, China
- State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Lin Zhu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, No. 8 Dayangfang, Beiyuan Road, Chaoyang District, Beijing, 100012, China
- State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Xinxin Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, No. 8 Dayangfang, Beiyuan Road, Chaoyang District, Beijing, 100012, China
- State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
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19
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Li H, Zou Y, Song W, Xin J, Gao J. Effects of frequency and amount of stover mulching on the microbial community composition and structure in the endosphere and rhizosphere. Front Microbiol 2024; 15:1372471. [PMID: 38468854 PMCID: PMC10925793 DOI: 10.3389/fmicb.2024.1372471] [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: 01/18/2024] [Accepted: 02/13/2024] [Indexed: 03/13/2024] Open
Abstract
Stover mulching, as a sustainable agricultural conservation practice, has been shown to effectively increase soil organic matter and enhance crop yields. The impact of stover mulching on soil microorganisms has been extensively studied. However, less attention has been given to endophytic and rhizospheric microorganisms that have closer relationships with crops. How do the quality and frequency of stover mulching affect the composition and structure of these endosphere and rhizosphere microbial communities? And what is their influence on critical indicators of soil health such as bacterial plant pathogen and Rhizobiales? These questions remain unresolved. Therefore, we investigated the responses of the microbial functional guilds in the endosphere and rhizosphere to maize stover mulching qualities (0%, 33%, 67%, and total stover mulching every year) and frequencies (once every 3 years and twice every 3 years) under 10-year no-till management. Results showed significant correlations between Bacillales and Rhizobiales orders and soil SOC, NO3-N, and NH4+N; Hypocreales and Eurotiales orders were significantly correlated with soil NO3-N, with the Aspergillus genus also showing a significant correlation with soil SOC. The frequency and quality of stover mulching had a significant effect on root and rhizospheric microbial communities, with the lowest relative abundance of bacterial plant pathogens and highest relative abundance of nitrogen-fixing bacteria such as Rhizobiales and Hypocreales observed under F1/3 and F2/3 conditions. The most complex structures in endosphere and rhizospheric microbial communities were found under Q33 and Q67 conditions, respectively. This research indicates that from a soil health perspective, low-frequency high-coverage stover mulching is beneficial for the composition of endosphere and rhizosphere microbial communities, while moderate coverage levels are conducive to more complex structures within these communities. This study holds significant ecological implications for agricultural production and crop protection.
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Affiliation(s)
- Haowen Li
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Yawen Zou
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Wenchen Song
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Jiaxun Xin
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Jian Gao
- School of Ecology and Environment, Baotou Teachers’ College, Inner Mongolia University of Science and Technology, Baotou, China
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20
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Wang M, Ge AH, Ma X, Wang X, Xie Q, Wang L, Song X, Jiang M, Yang W, Murray JD, Wang Y, Liu H, Cao X, Wang E. Dynamic root microbiome sustains soybean productivity under unbalanced fertilization. Nat Commun 2024; 15:1668. [PMID: 38395981 PMCID: PMC10891064 DOI: 10.1038/s41467-024-45925-5] [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: 05/25/2023] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Root-associated microbiomes contribute to plant growth and health, and are dynamically affected by plant development and changes in the soil environment. However, how different fertilizer regimes affect quantitative changes in microbial assembly to effect plant growth remains obscure. Here, we explore the temporal dynamics of the root-associated bacteria of soybean using quantitative microbiome profiling (QMP) to examine its response to unbalanced fertilizer treatments (i.e., lacking either N, P or K) and its role in sustaining plant growth after four decades of unbalanced fertilization. We show that the root-associated bacteria exhibit strong succession during plant development, and bacterial loads largely increase at later stages, particularly for Bacteroidetes. Unbalanced fertilization has a significant effect on the assembly of the soybean rhizosphere bacteria, and in the absence of N fertilizer the bacterial community diverges from that of fertilized plants, while lacking P fertilizer impedes the total load and turnover of rhizosphere bacteria. Importantly, a SynCom derived from the low-nitrogen-enriched cluster is capable of stimulating plant growth, corresponding with the stabilized soybean productivity in the absence of N fertilizer. These findings provide new insights in the quantitative dynamics of the root-associated microbiome and highlight a key ecological cluster with prospects for sustainable agricultural management.
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Affiliation(s)
- 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, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - An-Hui Ge
- 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, 200032, China
| | - Xingzhu Ma
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, 150086, China
| | - Xiaolin Wang
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Qiujin Xie
- 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, 200032, China
| | - Like 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, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianwei Song
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mengchen Jiang
- 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, 200032, China
| | - Weibing Yang
- 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, 200032, China
| | - Jeremy D Murray
- 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, 200032, China
| | - Yayu Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China
| | - Xiaofeng Cao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, 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, 200032, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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21
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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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Dong C, Shao Q, Ran Q, Li X, Han Y. Interactions of rhizosphere microbiota-environmental factors-pharmacological active ingredients of Eucommia ulmoides. PLANTA 2024; 259:59. [PMID: 38311641 DOI: 10.1007/s00425-024-04338-w] [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: 08/26/2023] [Accepted: 01/09/2024] [Indexed: 02/06/2024]
Abstract
MAIN CONCLUSION The composition, diversity and co-occurrence patterns of the rhizosphere microbiota of E. ulmoides were significantly influenced by environmental factors, and which were potentially associated with the contents of pharmacological active ingredients. Eucommia ulmoides is an important perennial medicinal plant. However, little is known about the interactions among microbiota, environmental factors (EFs), and pharmacological active ingredients (PAIs) of E. ulmoides. Herein, we analyzed the interactions among rhizosphere microbiota-EFs-PAIs of E. ulmoides by amplicon sequencing and multi-analytical approach. Our results revealed variations in the dominant genera, diversity, and co-occurrence networks of the rhizosphere microbiota of E. ulmoides across different geographical locations. Notably, available nitrogen exerted the strongest influence on fungal dominant genera, while pH significantly impacted bacterial dominant genera. Rainfall and relative humidity exhibited pronounced effects on the α-diversity of fungal groups, whereas available phosphorus influenced the number of nodes in fungal co-occurrence networks. Altitude and total phosphorus had substantial effects on the average degree and nodes in bacterial co-occurrence networks. Furthermore, the dominant genera, diversity and co-occurrence network of rhizosphere microbiota of E. ulmoides were significantly correlated with the content of PAIs. Specifically, the abundance of rhizosphere dominant genera Filobasidium, Hannaella and Nitrospira were significantly correlated with the content of pinoresinol diglucoside (PD). Similarly, the abundance of Vishniacozyma and Bradyrhizobium correlated significantly with the content of geniposidic acid (GC), while the abundance of Gemmatimonas was significantly correlated with the content of aucubin. Moreover, the bacterial co-occurrence network parameters including average degree, density, and edge, were significantly correlated with the content of GC and aucubin. The α-diversity index Chao1 also displayed a significant correlation with the content of PD. These findings contribute to a more comprehensive understanding of the interactions between medicinal plants and microbes.
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Affiliation(s)
- Chunbo Dong
- Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Fungus Resources, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Qiuyu Shao
- Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Fungus Resources, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Qingsong Ran
- Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Fungus Resources, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Xu Li
- Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Fungus Resources, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Yanfeng Han
- Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Fungus Resources, Guizhou University, Guiyang, 550025, Guizhou, China.
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23
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Li Y, Tao S, Liang Y. Time-Course Responses of Apple Leaf Endophytes to the Infection of Gymnosporangium yamadae. J Fungi (Basel) 2024; 10:128. [PMID: 38392801 PMCID: PMC10890309 DOI: 10.3390/jof10020128] [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: 12/26/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
Apple rust, caused by Gymnosporangium yamadae, poses a significant challenge to apple production. Prior studies have underscored the pivotal role played by endophytic microbial communities, intimately linked with the host, in influencing plant diseases and their pathogenic outcomes. The objective of this study is to scrutinize alternations in endophytic microbial communities within apple leaves at different stages of apple rust using high-throughput sequencing technology. The findings revealed a discernible pattern characterized by an initial increase and subsequent decrease in the alpha diversity of microbial communities in diseased leaves. A microbial co-occurrence network analysis revealed that the complexity of the bacterial community in diseased leaves diminished initially and then rebounded during the progression of the disease. Additionally, employing the PICRUSt2 platform, this study provided preliminary insights into the functions of microbial communities at specific disease timepoints. During the spermogonial stage, endophytic bacteria particularly exhibited heightened activity in genetic information processing, metabolism, and environmental information processing pathways. Endophytic fungi also significantly enriched a large number of metabolic pathways during the spermogonial stage and aecial stage, exhibiting abnormally active life activities. These findings establish a foundation for comprehending the role of host endophytes in the interaction between pathogens and hosts. Furthermore, they offer valuable insights for the development and exploitation of plant endophytic resources, thereby contributing to enhanced strategies for managing apple rust.
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Affiliation(s)
- Yunfan Li
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing 100083, China
| | - Siqi Tao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing 100083, China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan 518000, China
| | - Yingmei Liang
- Museum of Beijing Forestry University, Beijing Forestry University, Beijing 100083, China
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Gao M, Xiong C, Tsui CKM, Cai L. Pathogen invasion increases the abundance of predatory protists and their prey associations in the plant microbiome. Mol Ecol 2024; 33:e17228. [PMID: 38037712 DOI: 10.1111/mec.17228] [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: 07/07/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023]
Abstract
Soil and plant-associated protistan communities play a key role in shaping bacterial and fungal communities, primarily through their function as top-down predators. However, our understanding of how pathogen invasion influences these protistan communities and their relationships with bacterial and fungal communities remains limited. Here, we studied the protistan communities along the soil-plant continuum of healthy chilli peppers and those affected by Fusarium wilt disease (FWD), and integrated bacterial and fungal community data from our previous research. Our research showed that FWD was associated with a significant enrichment of phagotrophic protists in roots, and also increased the proportion and connectivity of these protists (especially Cercozoa and Ciliophora) in both intra- and inter-kingdom networks. Furthermore, the microbiome of diseased plants not only showed a higher relative abundance of functional genes related to bacterial anti-predator responses than healthy plants, but also contained a greater abundance of metagenome-assembled genomes with functional traits involved in this response. The increased microbial inter-kingdom associations between bacteria and protists, coupled with the notable bacterial anti-predator feedback in the microbiome of diseased plants, suggest that FWD may catalyse the associations between protists and their microbial prey. These findings highlight the potential role of predatory protists in influencing microbial assembly and functionality through top-down forces under pathogenic stress.
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Affiliation(s)
- Min Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Chao Xiong
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Clement K M Tsui
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- National Center for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Solanki MK, Joshi NC, Singh PK, Singh SK, Santoyo G, Basilio de Azevedo LC, Kumar A. From concept to reality: Transforming agriculture through innovative rhizosphere engineering for plant health and productivity. Microbiol Res 2024; 279:127553. [PMID: 38007891 DOI: 10.1016/j.micres.2023.127553] [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: 10/01/2023] [Revised: 11/14/2023] [Accepted: 11/19/2023] [Indexed: 11/28/2023]
Abstract
The plant rhizosphere is regarded as a microbial hotspot due to a wide array of root exudates. These root exudates comprise diverse organic compounds such as phenolic, polysaccharides, flavonoids, fatty acids, and amino acids that showed chemotactic responses towards microbial communities and mediate significant roles in root colonization. The rhizospheric microbiome is a crucial driver of plant growth and productivity, contributing directly or indirectly by facilitating nutrient acquisition, phytohormone modulation, and phosphate solubilization under normal and stressful conditions. Moreover, these microbial candidates protect plants from pathogen invasion by secreting antimicrobial and volatile organic compounds. To enhance plant fitness and yield, rhizospheric microbes are frequently employed as microbial inoculants. However, recent developments have shifted towards targeted rhizosphere engineering or microbial recruitments as a practical approach to constructing desired plant rhizospheres for specific outcomes. The rhizosphere, composed of plants, microbes, and soil, can be modified in several ways to improve inoculant efficiency. Rhizosphere engineering is achieved through three essential mechanisms: a) plant-mediated modifications involving genetic engineering, transgenics, and gene editing of plants; b) microbe-mediated modifications involving genetic alterations of microbes through upstream or downstream methodologies; and c) soil amendments. These mechanisms shape the rhizospheric microbiome, making plants more productive and resilient under different stress conditions. This review paper comprehensively summarizes the various aspects of rhizosphere engineering and their potential applications in maintaining plant health and achieving optimum agricultural productivity.
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Affiliation(s)
- Manoj Kumar Solanki
- Department of Life Sciences and Biological Sciences, IES University, Bhopal, Madhya Pradesh, India; Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032 Katowice, Poland
| | - Naveen Chandra Joshi
- Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh, 201313, India
| | - Prashant Kumar Singh
- Department of Biotechnology, Pachhunga University College Campus, Mizoram University (A Central University), Aizawl 796001, India
| | - Sandeep Kumar Singh
- Department of Microbiology, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mexico
| | - Lucas Carvalho Basilio de Azevedo
- Instituto de Ciências Agrárias, Campus Glória-Bloco CCG, Universidade Federal de Uberlândia, RodoviaBR-050, KM 78, S/N, Uberlândia CEP 38410-337, Brazil
| | - Ajay Kumar
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, 201313, India.
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Chen M, Zhou S, Xiang P, Wang Y, Luo X, Zhang X, Wen D. Elevated CO 2 and nitrogen addition enhance the symbiosis and functions of rhizosphere microorganisms under cadmium exposure. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 351:120012. [PMID: 38171127 DOI: 10.1016/j.jenvman.2023.120012] [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: 10/06/2023] [Revised: 12/30/2023] [Accepted: 12/30/2023] [Indexed: 01/05/2024]
Abstract
Soil microbes are fundamental to ecosystem health and productivity. How soil microbial communities are influenced by elevated atmospheric carbon dioxide (eCO2) concentration and nitrogen (N) deposition under heavy metal pollution remains uncertain, despite global exposure of terrestrial ecosystems to eCO2, high N deposition and heavy metal stress. Here, we conducted a four year's open-top chamber experiment to assess the effects of soil cadmium (Cd) treatment (10 kg hm-2 year-1) alone and combined treatments of Cd with eCO2 concentration (700 ppm) and/or N addition (100 kg hm-2 year-1) on tree growth and rhizosphere microbial community. Relative to Cd treatment alone, eCO2 concentration in Cd contaminated soil increased the complexity of microbial networks, including the number links, average degree and positive/negative ratios. The combined effect of eCO2 and N addition in Cd contaminated soil not only increased the complexity of microbial networks, but also enhanced the abundance of microbial urealysis related UreC and nitrifying related amoA1 and amoA2, and the richness of arbuscular mycorrhiza fungi (AMF), thereby improving the symbiotic functions between microorganisms and plants. Results from correlation analysis and structural equation model (SEM) further demonstrated that eCO2 concentration and N addition acted on functions and networks differently. Elevated CO2 positively regulated microbial networks and functions through phosphorus (P) and Cd concentration in roots, while N addition affected microbial functions through soil available N and soil organic carbon (SOC) concentration and microbial network through soil Cd concentration. Overall, our findings highlight that eCO2 concentration and N addition make microbial communities towards ecosystem health that may mitigate Cd stress, and provide new insights into the microbiology supporting phytoremediation for Cd contaminated sites in current and future global change scenarios.
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Affiliation(s)
- Minghao Chen
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Science, Guangzhou, 510650, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuyidan Zhou
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Science, Guangzhou, 510650, China
| | - Ping Xiang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Science, Guangzhou, 510650, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yutao Wang
- Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Xianzhen Luo
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Science, Guangzhou, 510650, China
| | - Xiaofeng Zhang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Science, Guangzhou, 510650, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dazhi Wen
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Science, Guangzhou, 510650, China; College of Life Sciences, Gannan Normal University, Ganzhou, Jiangxi, 341000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Liang J, Wei C, Song X, Wang R, Shi H, Tan J, Cheng D, Wang W, Wang X. Bacterial wilt affects the structure and assembly of microbial communities along the soil-root continuum. ENVIRONMENTAL MICROBIOME 2024; 19:6. [PMID: 38229154 DOI: 10.1186/s40793-024-00548-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 01/02/2024] [Indexed: 01/18/2024]
Abstract
BACKGROUND Beneficial root-associated microbiomes play crucial roles in enhancing plant growth and suppressing pathogenic threats, and their application for defending against pathogens has garnered increasing attention. Nonetheless, the dynamics of microbiome assembly and defense mechanisms during pathogen invasion remain largely unknown. In this study, we aimed to investigate the diversity and assembly of microbial communities within four niches (bulk soils, rhizosphere, rhizoplane, and endosphere) under the influence of the bacterial plant pathogen Ralstonia solanacearum. RESULTS Our results revealed that healthy tobacco plants exhibited more diverse community compositions and more robust co-occurrence networks in root-associated niches compared to diseased tobacco plants. Stochastic processes (dispersal limitation and drift), rather than determinism, dominated the assembly processes, with a higher impact of drift observed in diseased plants than in healthy ones. Furthermore, during the invasion of R. solanacearum, the abundance of Fusarium genera, a known potential pathogen of Fusarium wilt, significantly increased in diseased plants. Moreover, the response strategies of the microbiomes to pathogens in diseased and healthy plants diverged. Diseased microbiomes recruited beneficial microbial taxa, such as Streptomyces and Bacilli, to mount defenses against pathogens, with an increased presence of microbial taxa negatively correlated with the pathogen. Conversely, the potential defense strategies varied across niches in healthy plants, with significant enrichments of functional genes related to biofilm formation in the rhizoplane and antibiotic biosynthesis in the endosphere. CONCLUSION Our study revealed the varied community composition and assembly mechanism of microbial communities between healthy and diseased tobacco plants along the soil-root continuum, providing new insights into niche-specific defense mechanisms against pathogen invasions. These findings may underscore the potential utilization of different functional prebiotics to enhance plants' ability to fend off pathogens.
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Affiliation(s)
- Jinchang Liang
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 266101, Qingdao, China
| | - Chengjian Wei
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 266101, Qingdao, China
- College of Agriculture, Guangxi University, 530004, Nanning, China
| | - Xueru Song
- Engineering Center for Biological Control of Diseases and Pests in Tobacco Industry, 653100, Yuxi, China
| | - Rui Wang
- Enshi Tobacco Science and Technology Center, 445000, Enshi, China
| | - Heli Shi
- Enshi Tobacco Science and Technology Center, 445000, Enshi, China
| | - Jun Tan
- Enshi Tobacco Science and Technology Center, 445000, Enshi, China
| | - Dejie Cheng
- College of Agriculture, Guangxi University, 530004, Nanning, China
| | - Wenjing Wang
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 266101, Qingdao, China
| | - Xiaoqiang Wang
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 266101, Qingdao, China.
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Shi Z, Yang M, Li K, Yang L, Yang L. Influence of cultivation duration on microbial taxa aggregation in Panax ginseng soils across ecological niches. Front Microbiol 2024; 14:1284191. [PMID: 38282744 PMCID: PMC10813202 DOI: 10.3389/fmicb.2023.1284191] [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: 08/29/2023] [Accepted: 12/22/2023] [Indexed: 01/30/2024] Open
Abstract
Introduction Microbial communities are crucial for plant health and productivity. However, the influence of cultivation age on the ecological processes in assembling plant microbiomes at various ecological niches remains unclear. Methods We selected 12 samples from ginseng farmlands with different cultivation years (N4: 4 years old, N6: 6 years old). We used soil physicochemical properties, enzyme activities, and high-throughput sequencing (16S rDNA and ITS) to examine the rhizoplane (RP), rhizosphere (RS), and bulk soil (BS). Results Our results indicated that cultivation years significantly affect the soil microbiome's diversity and community composition across different ecological niches. The BS microbiome experienced the largest effect, while the RS experienced the smallest. N6 showed a greater impact than N4. This effect was more pronounced on the fungal communities than the bacterial communities of various ecological niches and can be closely related to the soil's physicochemical properties. In N4 soils, we observed an upward trend in both the number of ASVs (amplicon sequence variations) and the diversity of soil microbial taxa across various ecological niches. In N4RP, the bacteria Sphingomonas, known for degrading toxic soil compounds, was present. All ecological niches in N4 showed significant enrichment of Tetracladium fungi, positively associated with crop yield (N4RP at 6.41%, N4RS at 11.31%, and N4BS at 3.45%). In N6 soils, we noted a stark decline in fungal diversity within the BS, with a 57.5% reduction in ASVs. Moreover, Sphingomonas was abundantly present in N6RS and N6BS soils. The relative abundance of the pathogen-inhibiting fungus Exophiala in N6RP and N6RS reached 34.18% and 13.71%, respectively, marking increases of 4.9-fold and 7.7-fold. Additionally, another pathogeninhibiting fungus, Humicola, showed significant enrichment in N6BS, with a 7.5-fold increase. The phenolic acid-producing fungus Pseudogymnoascus in N6RP, N6RS, and N6BS showed increases of 2.41-fold, 2.55-fold, and 4.32-fold, respectively. We hypothesize that functional genes related to the metabolism of terpenoids and polyketides, as well as signaling molecules and interactions, regulate soil microbial taxa in ginseng from different cultivation years. Discussion In conclusion, our study enhances understanding of plant-microbe interactions and aids the sustainable development of medicinal plants, particularly by addressing ginseng succession disorder.
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Affiliation(s)
| | | | | | - Li Yang
- Cultivation Base of State Key Laboratory for Ecological Restoration and Ecosystem Management, College of Traditional Chinese Medicine, Jilin Agricultural University, Changchun, China
| | - Limin Yang
- Cultivation Base of State Key Laboratory for Ecological Restoration and Ecosystem Management, College of Traditional Chinese Medicine, Jilin Agricultural University, Changchun, China
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Wang W, Li D, Qiu X, Yang J, Liu L, Wang E, Yuan H. Selective regulation of endophytic bacteria and gene expression in soybean by water-soluble humic materials. ENVIRONMENTAL MICROBIOME 2024; 19:2. [PMID: 38178261 PMCID: PMC10768371 DOI: 10.1186/s40793-023-00546-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/24/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND As part of the plant microbiome, endophytic bacteria play an essential role in plant growth and resistance to stress. Water-soluble humic materials (WSHM) is widely used in sustainable agriculture as a natural and non-polluting plant growth regulator to promote the growth of plants and beneficial bacteria. However, the mechanisms of WSHM to promote plant growth and the evidence for commensal endophytic bacteria interaction with their host remain largely unknown. Here, 16S rRNA gene sequencing, transcriptomic analysis, and culture-based methods were used to reveal the underlying mechanisms. RESULTS WSHM reduced the alpha diversity of soybean endophytic bacteria, but increased the bacterial interactions and further selectively enriched the potentially beneficial bacteria. Meanwhile, WSHM regulated the expression of various genes related to the MAPK signaling pathway, plant-pathogen interaction, hormone signal transduction, and synthetic pathways in soybean root. Omics integration analysis showed that Sphingobium was the genus closest to the significantly changed genes in WSHM treatment. The inoculation of endophytic Sphingobium sp. TBBS4 isolated from soybean significantly improved soybean nodulation and growth by increasing della gene expression and reducing ethylene release. CONCLUSION All the results revealed that WSHM promotes soybean nodulation and growth by selectively regulating soybean gene expression and regulating the endophytic bacterial community, Sphingobium was the key bacterium involved in plant-microbe interaction. These findings refined our understanding of the mechanism of WSHM promoting soybean nodulation and growth and provided novel evidence for plant-endophyte interaction.
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Affiliation(s)
- Wenqian Wang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
| | - Dongmei Li
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
| | - Xiaoqian Qiu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
| | - Jinshui Yang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
| | - Liang Liu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, C.P. 11340, Ciudad de México, México
| | - Hongli Yuan
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian District, 100193, Beijing, China.
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Huang WF, Li J, Huang JA, Liu ZH, Xiong LG. Review: Research progress on seasonal succession of phyllosphere microorganisms. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 338:111898. [PMID: 37879538 DOI: 10.1016/j.plantsci.2023.111898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/15/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023]
Abstract
Phyllosphere microorganisms have recently attracted the attention of scientists studying plant microbiomes. The origin, diversity, functions, and interactions of phyllosphere microorganisms have been extensively explored. Many experiments have demonstrated seasonal cycles of phyllosphere microbes. However, a comprehensive comparison of these separate investigations to characterize seasonal trends in phyllosphere microbes of woody and herbaceous plants has not been conducted. In this review, we explored the dynamic changes of phyllosphere microorganisms in woody and non-woody plants with the passage of the season, sought to find the driving factors, summarized these texts, and thought about future research trends regarding the application of phyllosphere microorganisms in agricultural production. Seasonal trends in phyllosphere microorganisms of herbaceous and woody plants have similarities and differences, but extensive experimental validation is needed. Climate, insects, hosts, microbial interactions, and anthropogenic activities are the diverse factors that influence seasonal variation in phyllosphere microorganisms.
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Affiliation(s)
- Wen-Feng Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Juan Li
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Jian-An Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Zhong-Hua Liu
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Li-Gui Xiong
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China.
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Uwaremwe C, Bao W, Daoura BG, Mishra S, Zhang X, Shen L, Xia S, Yang X. Shift in the rhizosphere soil fungal community associated with root rot infection of Plukenetia volubilis Linneo caused by Fusarium and Rhizopus species. Int Microbiol 2023:10.1007/s10123-023-00470-x. [PMID: 38158469 DOI: 10.1007/s10123-023-00470-x] [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: 10/12/2023] [Revised: 11/14/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Plukenetia volubilis Linneo is an oleaginous plant belonging to the family Euphorbiaceae. Due to its seeds containing a high content of edible oil and rich in vitamins, P. volubilis is cultivated as an economical plant worldwide. However, the cultivation and growth of P. volubilis is challenged by phytopathogen invasion leading to production loss. METHODS In the current study, we tested the pathogenicity of fungal pathogens isolated from root rot infected P. volubilis plant tissues by inoculating them into healthy P. volubilis seedlings. Metagenomic sequencing was used to assess the shift in the fungal community of P. volubilis rhizosphere soil after root rot infection. RESULTS Four Fusarium isolates and two Rhizopus isolates were found to be root rot causative agents of P. volubilis as they induced typical root rot symptoms in healthy seedlings. The metagenomic sequencing data showed that root rot infection altered the rhizosphere fungal community. In root rot infected soil, the richness and diversity indices increased or decreased depending on pathogens. The four most abundant phyla across all samples were Ascomycota, Glomeromycota, Basidiomycota, and Mortierellomycota. In infected soil, the relative abundance of each phylum increased or decreased depending on the pathogen and functional taxonomic classification. CONCLUSIONS Based on our results, we concluded that Fusarium and Rhizopus species cause root rot infection of P. volubilis. In root rot infected P. volubilis, the shift in the rhizosphere fungal community was pathogen-dependent. These findings may serve as a key point for a future study on the biocontrol of root rot of P. volubilis.
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Affiliation(s)
- Constantine Uwaremwe
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China.
| | - Wenjie Bao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bachir Goudia Daoura
- Department of Biology, Faculty of Sciences and Technology, Dan Dicko Dankoulodo University, POBox, 465, Maradi, Niger
| | - Sandhya Mishra
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
- National Field Scientific Observation and Research Station of Forest Ecosystem in Ailao Mountain, Yunnan, 665000, China
| | - Xianxian Zhang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lingjie Shen
- College of Biology and Chemistry, Pu'er University, Pu'er, 665000, China
| | - Shangwen Xia
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
- National Field Scientific Observation and Research Station of Forest Ecosystem in Ailao Mountain, Yunnan, 665000, China
| | - Xiaodong Yang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China.
- National Field Scientific Observation and Research Station of Forest Ecosystem in Ailao Mountain, Yunnan, 665000, China.
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Zhang Y, Ding CT, Jiang T, Liu YH, Wu Y, Zhou HW, Zhang LS, Chen Y. Community structure and niche differentiation of endosphere bacterial microbiome in Camellia oleifera. Microbiol Spectr 2023; 11:e0133523. [PMID: 37847029 PMCID: PMC10715075 DOI: 10.1128/spectrum.01335-23] [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: 03/27/2023] [Accepted: 09/10/2023] [Indexed: 10/18/2023] Open
Abstract
IMPORTANCE Microorganisms inhabited various tissues of plants and play a key role in promoting plant growth, nutritional absorption, and resistance. Our research indicates that the diversity of Camellia oleifera endophytic bacterial communities is highly dependent on the plant compartment. Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Chloroflexi, and Verrucomicrobia are dominant bacteria phyla. The tissues of Camellia oleifera contain various bacteria with nitrogen fixation potential, host life promotion, and plant defense. This study provides a scientific theoretical basis for an in-depth discussion of plant-endosphere microbial interaction and better exploration of benign interaction of beneficial microorganisms and plants.
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Affiliation(s)
- Yan Zhang
- Institute of Jiangxi Oil-tea Camellia, Jiujiang University, Jiujiang, Jiangxi, China
| | - Chu Ting Ding
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang City, Jiangxi Province, China
| | - Taoya Jiang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang City, Jiangxi Province, China
| | - Yu Hua Liu
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang City, Jiangxi Province, China
| | - Yang Wu
- Institute of Jiangxi Oil-tea Camellia, Jiujiang University, Jiujiang, Jiangxi, China
| | - Hui Wen Zhou
- Institute of Jiangxi Oil-tea Camellia, Jiujiang University, Jiujiang, Jiangxi, China
| | - Li Sha Zhang
- Institute of Jiangxi Oil-tea Camellia, Jiujiang University, Jiujiang, Jiangxi, China
| | - Ye Chen
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang City, Jiangxi Province, China
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Jiang H, Luo J, Liu Q, Ogunyemi SO, Ahmed T, Li B, Yu S, Wang X, Yan C, Chen J, Li B. Rice bacterial leaf blight drives rhizosphere microbial assembly and function adaptation. Microbiol Spectr 2023; 11:e0105923. [PMID: 37846986 PMCID: PMC10715139 DOI: 10.1128/spectrum.01059-23] [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: 03/09/2023] [Accepted: 08/27/2023] [Indexed: 10/18/2023] Open
Abstract
IMPORTANCE Our results suggest that rhizosphere bacteria are more sensitive to bacterial leaf blight (BLB) than fungi. BLB infection decreased the diversity of the rhizosphere bacterial community but increased the complexity and size of the rhizosphere microbial community co-occurrence networks. In addition, the relative abundance of the genera Streptomyces, Chitinophaga, Sphingomonas, and Bacillus increased significantly. Finally, these findings contribute to the understanding of plant-microbiome interactions by providing critical insight into the ecological mechanisms by which rhizosphere microbes respond to phyllosphere diseases. In addition, it also lays the foundation and provides data to support the use of plant microbes to promote plant health in sustainable agriculture, providing critical insight into ecological mechanisms.
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Affiliation(s)
- Hubiao Jiang
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou , China
| | - Jinyan Luo
- Department of Plant Quarantine, Shanghai Extension and Service Center of Agriculture Technology, Shanghai, China
| | - Quanhong Liu
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou , China
| | - Solabomi Olaitan Ogunyemi
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou , China
| | - Temoor Ahmed
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou , China
| | - Bing Li
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou , China
| | - Shanhong Yu
- Taizhou Academy of Agricultural Sciences, Taizhou, China
| | - Xiao Wang
- Ningbo Jiangbei District Agricultural Technology Extension Service Station, Ningbo , China
| | - Chenqi Yan
- Institute of Biotechnology, Ningbo Academy of Agricultural Sciences, Ningbo, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Bin Li
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou , China
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Cirillo V, Romano I, Woo SL, Di Stasio E, Lombardi N, Comite E, Pepe O, Ventorino V, Maggio A. Inoculation with a microbial consortium increases soil microbial diversity and improves agronomic traits of tomato under water and nitrogen deficiency. FRONTIERS IN PLANT SCIENCE 2023; 14:1304627. [PMID: 38126011 PMCID: PMC10731302 DOI: 10.3389/fpls.2023.1304627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
Microbial-based biostimulants, functioning as biotic and abiotic stress protectants and growth enhancers, are becoming increasingly important in agriculture also in the context of climate change. The search for new products that can help reduce chemical inputs under a variety of field conditions is the new challenge. In this study, we tested whether the combination of two microbial growth enhancers with complementary modes of action, Azotobacter chroococcum 76A and Trichoderma afroharzianum T22, could facilitate tomato adaptation to a 30% reduction of optimal water and nitrogen requirements. The microbial inoculum increased tomato yield (+48.5%) under optimal water and nutrient conditions. In addition, the microbial application improved leaf water potential under stress conditions (+9.5%), decreased the overall leaf temperature (-4.6%), and increased shoot fresh weight (+15%), indicating that this consortium could act as a positive regulator of plant water relations under limited water and nitrogen availability. A significant increase in microbial populations in the rhizosphere with applications of A. chroococcum 76A and T. afroharzianum T22 under stress conditions, suggested that these inoculants could enhance soil microbial abundance, including the abundance of native beneficial microorganisms. Sampling time, limited water and nitrogen regimes and microbial inoculations all affected bacterial and fungal populations in the rhizospheric soil. Overall, these results indicated that the selected microbial consortium could function as plant growth enhancer and stress protectant, possibly by triggering adaptation mechanisms via functional changes in the soil microbial diversity and relative abundance.
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Affiliation(s)
- Valerio Cirillo
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Ida Romano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Sheridan L. Woo
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
- National Research Council, Institute for Sustainable Plant Protection, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Portici, Italy
| | - Emilio Di Stasio
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Nadia Lombardi
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Ernesto Comite
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Olimpia Pepe
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Portici, Italy
| | - Valeria Ventorino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Portici, Italy
| | - Albino Maggio
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
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Singh P, Vaishnav A, Liu H, Xiong C, Singh HB, Singh BK. Seed biopriming for sustainable agriculture and ecosystem restoration. Microb Biotechnol 2023; 16:2212-2222. [PMID: 37490280 PMCID: PMC10686123 DOI: 10.1111/1751-7915.14322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023] Open
Abstract
The utilization of microbial inoculants in the realm of sustainable agricultural and ecosystem restoration has witnessed a surge in recent decades. This rise is largely attributed to advancements in our understanding of plant-microbe interactions, the urgency to reduce the dependence on agrochemicals and the growing societal demand for sustainable strategies in ecosystem management. However, despite the rapid growth of bio-inoculants sector, certain limitations persist concerning their efficacy and performance under the field condition. Here, we propose that seed biopriming, an effective microbial inoculant technique integrating both biological agents (the priming of beneficial microbes on seeds) and physiological aspects (hydration of seeds for improved metabolically activity), has a significant potential to mitigate these limitations. This method increases the protection of seeds against soil-borne pathogens and soil pollutants, such as salts and heavy metals, while promoting germination rate and uniformity, leading to overall improved primary productivity and soil health. Furthermore, we argue that a microbial coating on seeds can facilitate transgenerational associations of beneficial microbes, refine plant and soil microbiomes, and maintain soil legacies of beneficial microflora. This review article aims to improve our understanding of the seed biopriming approach as a potent and valuable tool in achieving sustainable agriculture and successful ecosystem restoration.
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Affiliation(s)
- Prachi Singh
- Rabindranath Tagore Agriculture College, DeogharBirsa Agriculture UniversityRanchiJharkhandIndia
| | - Anukool Vaishnav
- Department of BiotechnologyGLA UniversityMathuraUttar PradeshIndia
| | - Hongwei Liu
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
| | - Chao Xiong
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
| | | | - Brajesh K. Singh
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
- Global Centre for Land‐Based InnovationWestern Sydney UniversityPenrithNew South WalesAustralia
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Acuña JJ, Hu J, Inostroza NG, Valenzuela T, Perez P, Epstein S, Sessitsch A, Zhang Q, Jorquera MA. Endophytic bacterial communities in ungerminated and germinated seeds of commercial vegetables. Sci Rep 2023; 13:19829. [PMID: 37963999 PMCID: PMC10645892 DOI: 10.1038/s41598-023-47099-4] [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: 07/26/2023] [Accepted: 11/09/2023] [Indexed: 11/16/2023] Open
Abstract
Chile is a prominent seed exporter globally, but the seed microbiome of vegetables (46% of seeds) and its role in the early stages of plant growth have remained largely unexplored. Here, we employed DNA metabarcoding analysis to investigate the composition and putative functions of endophytic bacterial communities in ungerminated and germinated seeds of the commercial vegetables Apiaceae (parsley and carrot), Asteraceae (lettuce), Brassicaceae (cabbage and broccoli), and Solanaceae (tomato). Bacterial quantification showed 104 to 108 copies of the 16S rRNA gene per gram of ungerminated and germinated seeds. Alpha diversity analysis (e.g., Chao1, Shannon, and Simpson indices) did not indicate significant differences (Kruskal-Wallis test) between ungerminated and germinated seeds, except for Solanaceae. However, beta diversity (PCoA) analysis showed distinctions (Adonis test) between ungerminated and germinated seeds, except Apiaceae. Pseudomonadota and Bacillota were identified as the dominant and specialist taxa in both ungerminated and germinated seed samples. Chemoheterotrophy and fermentation were predicted as the main microbial functional groups in the endophytic bacterial community. Notably, a considerable number of the 143 isolated endophytic strains displayed plant growth-promoting traits (10 to 64%) and biocontrol activity (74% to 82%) against plant pathogens (Xanthomonas and Pseudomonas). This study revealed the high variability in the abundance, diversity, composition, and functionality of endophytic bacteria between ungerminated and germinated seeds in globally commercialized vegetables. Furthermore, potential beneficial endophytic bacteria contained in their seed microbiomes that may contribute to the microbiome of the early stages, development, growth and progeny of vegetables were found.
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Affiliation(s)
- Jacquelinne J Acuña
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Millennium Institute Center for Genome Regulation (MI-CGR), Valenzuela Puelma 10207, 7800003, Santiago, La Reina, Chile
| | - Jingming Hu
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, 361102, China
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Nitza G Inostroza
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Tamara Valenzuela
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Pablo Perez
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Slava Epstein
- College of Science, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, USA
| | - Angela Sessitsch
- Health & Bioresources, AIT Austrian Institute of Technology, Konrad-Lorenz-Straße 24, 3430, Tulln, Austria
| | - Qian Zhang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, 361102, China.
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China.
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile.
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile.
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Li T, Gao J. Attribution of dispersal limitation can better explain the assembly patterns of plant microbiota. FRONTIERS IN PLANT SCIENCE 2023; 14:1168760. [PMID: 37941678 PMCID: PMC10628812 DOI: 10.3389/fpls.2023.1168760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023]
Abstract
Disentangling community assembly processes is crucial for fully understanding the function of microbiota in agricultural ecosystems. However, numerous plant microbiome surveys have gradually revealed that stochastic processes dominate the assembly of the endophytic root microbiota in conflict with strong host filtering effects, which is an important issue. Resolving such conflicts or inconsistencies will not only help accurately predict the composition and structure of the root endophytic microbiota and its driving mechanisms, but also provide important guidance on the correlation between the relative importance of deterministic and stochastic processes in the assembly of the root endophytic microbiota, and crop productivity and nutritional quality. Here, we propose that the inappropriate division of dispersal limitation may be the main reason for such inconsistency, which can be resolved after the proportion of dispersal limitation is incorporated into the deterministic processes. The rationality of this adjustment under the framework of the formation of a holobiont between the microbiome and the plant host is herein explained, and a potential theoretical framework for dynamic assembly patterns of endophytic microbiota along the soil-plant continuum is proposed. Considering that the assembly of root endophytic microbiota is complicated, we suggest caution and level-by-level verification from deterministic processes to neutral components to stochastic processes when deciding on the attribution of dispersal limitation in the future to promote the expansion and application of microbiome engineering in sustainable agricultural development based on community assembly patterns.
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Affiliation(s)
| | - Jiangyun Gao
- Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
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Li X, Wang C, Zhu X, Ntoukakis V, Cernava T, Jin D. Exploration of phyllosphere microbiomes in wheat varieties with differing aphid resistance. ENVIRONMENTAL MICROBIOME 2023; 18:78. [PMID: 37876011 PMCID: PMC10594911 DOI: 10.1186/s40793-023-00534-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/10/2023] [Indexed: 10/26/2023]
Abstract
BACKGROUND Leaf-associated microbes play an important role in plant development and response to exogenous stress. Insect herbivores are known to alter the phyllosphere microbiome. However, whether the host plant's defense against insects is related to the phyllosphere microbiome remains mostly elusive. Here, we investigated bacterial communities in the phyllosphere and endosphere of eight wheat cultivars with differing aphid resistance, grown in the same farmland. RESULTS The bacterial community in both the phyllosphere and endosphere showed significant differences among most wheat cultivars. The phyllosphere was connected to more complex and stable microbial networks than the endosphere in most wheat cultivars. Moreover, the genera Pantoea, Massilia, and Pseudomonas were found to play a major role in shaping the microbial community in the wheat phyllosphere. Additionally, wheat plants showed phenotype-specific associations with the genera Massilia and Pseudomonas. The abundance of the genus Exiguobacterium in the phyllosphere exhibited a significant negative correlation with the aphid hazard grade in the wheat plants. CONCLUSION Communities of leaf-associated microbes in wheat plants were mainly driven by the host genotype. Members of the genus Exiguobacterium may have adverse effects on wheat aphids. Our findings provide new clues supporting the development of aphid control strategies based on phyllosphere microbiome engineering.
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Affiliation(s)
- Xinan Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China
- Henan Engineering Research Center of Biological Pesticide & Fertilizer Development and Synergistic Application, School of Resource and Environmental Sciences, Henan Institute of Science and Technology, 453003, Xinxiang, China
| | - Chao Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China
| | - Xun Zhu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China.
| | - Vardis Ntoukakis
- School of Life Sciences, University of Warwick, CV4 7AL, Coventry, UK
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK
| | - Decai Jin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China.
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Zhang Y, Zhao Q, Uroz S, Gao T, Li J, He F, Rosazlina R, Martin F, Xu L. The cultivation regimes of Morchella sextelata trigger shifts in the community assemblage and ecological traits of soil bacteria. Front Microbiol 2023; 14:1257905. [PMID: 37808313 PMCID: PMC10552182 DOI: 10.3389/fmicb.2023.1257905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/05/2023] [Indexed: 10/10/2023] Open
Abstract
The successful large-scale cultivation of morel mushrooms (Morchella sextelata) requires a comprehensive understanding of the soil bacterial communities associated with morel-farming beds, as the interactions between fungi and bacteria play a crucial role in shaping the soil microbiome. In this study, we investigated the temporal distribution and ecological characteristics of soil bacteria associated with morel fruiting bodies at different stages, specifically the conidial and primordial stages, under two cropping regimes, non-continuous cropping (NCC) and continuous cropping (CC). Our findings revealed a significant reduction in the yield of morel primordia during the third year following 2 years of CC (0.29 ± 0.25 primordia/grid), in comparison to the NCC regime (12.39 ± 6.09 primordia/grid). Furthermore, inoculation with morel mycelia had a notable impact on soil bacterial diversity, decreasing it in the NCC regime and increasing the number of generalist bacterial members in the CC regime. The latter regime also led to the accumulation of nutrients in the soil beds, resulting in a shift from a stochastic to a deterministic process in the composition of the bacterial community, which differed from the NCC regime. Additionally, mycelial inoculation had a positive effect on the abundance of potential copiotrophic/denitrifying and N-fixing bacteria while decreasing the abundance of oligotrophic/nitrifying bacteria. Interestingly, this effect was more pronounced in the NCC regime than in the CC regime. These results suggest that the increase in potential copiotrophic/denitrifying and N-fixing bacteria facilitated the decomposition of nutrients in exogenous nutrient bags by morel mushrooms, thereby maintaining nitrogen balance in the soil. Overall, our study provides valuable insights into the interactions between morel mycelia and the associated soil bacteriome as well as the influence of different cultivation regimes on these interactions. These findings contribute to our understanding of the complex dynamics of the soil microbiome and can inform strategies for optimizing morel mushroom cultivation.
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Affiliation(s)
- Yan Zhang
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
- Xi'an Key Laboratory of Plant Stress Physiology and Ecological Restoration Technology, Key Laboratory of Natural Product Development and Anticancer Innovative Drug Research in Qinling, School of Biological and Environmental Engineering, Xi'an University, Xi'an, Shaanxi, China
| | - Qi Zhao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Stéphane Uroz
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, France
| | - Tianpeng Gao
- Xi'an Key Laboratory of Plant Stress Physiology and Ecological Restoration Technology, Key Laboratory of Natural Product Development and Anticancer Innovative Drug Research in Qinling, School of Biological and Environmental Engineering, Xi'an University, Xi'an, Shaanxi, China
- The Engineering Research Center of Mining Pollution Treatment and Ecological Restoration of Gansu Province, Lanzhou City University, Lanzhou, China
| | - Jing Li
- Xi'an Key Laboratory of Plant Stress Physiology and Ecological Restoration Technology, Key Laboratory of Natural Product Development and Anticancer Innovative Drug Research in Qinling, School of Biological and Environmental Engineering, Xi'an University, Xi'an, Shaanxi, China
| | - Fengqin He
- Xi'an Key Laboratory of Plant Stress Physiology and Ecological Restoration Technology, Key Laboratory of Natural Product Development and Anticancer Innovative Drug Research in Qinling, School of Biological and Environmental Engineering, Xi'an University, Xi'an, Shaanxi, China
| | - Rusly Rosazlina
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Francis Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, France
| | - Lingling Xu
- Xi'an Key Laboratory of Plant Stress Physiology and Ecological Restoration Technology, Key Laboratory of Natural Product Development and Anticancer Innovative Drug Research in Qinling, School of Biological and Environmental Engineering, Xi'an University, Xi'an, Shaanxi, China
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, France
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Kenmotsu H, Masuma T, Murakami J, Hirose Y, Eki T. Distinct prokaryotic and eukaryotic communities and networks in two agricultural fields of central Japan with different histories of maize-cabbage rotation. Sci Rep 2023; 13:15435. [PMID: 37723228 PMCID: PMC10507100 DOI: 10.1038/s41598-023-42291-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 09/07/2023] [Indexed: 09/20/2023] Open
Abstract
Crop rotation is an important agricultural practice for homeostatic crop cultivation. Here, we applied high-throughput sequencing of ribosomal RNA gene amplicons to investigate soil biota in two fields of central Japan with different histories of maize-cabbage rotation. We identified 3086 eukaryotic and 17,069 prokaryotic sequence variants (SVs) from soil samples from two fields rotating two crops at three different growth stages. The eukaryotic and prokaryotic communities in the four sample groups of two crops and two fields were clearly distinguished using β-diversity analysis. Redundancy analysis showed the relationships of the communities in the fields to pH and nutrient, humus, and/or water content. The complexity of eukaryotic and prokaryotic networks was apparently higher in the cabbage-cultivated soils than those in the maize-cultivated soils. The node SVs (nSVs) of the networks were mainly derived from two eukaryotic phyla: Ascomycota and Cercozoa, and four prokaryotic phyla: Pseudomonadota, Acidobacteriota, Actinomycetota, and Gemmatimonadota. The networks were complexed by cropping from maize to cabbage, suggesting the formation of a flexible network under crop rotation. Ten out of the 16 eukaryotic nSVs were specifically found in the cabbage-cultivated soils were derived from protists, indicating the potential contribution of protists to the formation of complex eukaryotic networks.
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Affiliation(s)
- Harutaro Kenmotsu
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan
| | - Tomoro Masuma
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan
| | - Junya Murakami
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan
- Research Center for Agrotechnology and Biotechnology, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan
| | - Toshihiko Eki
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan.
- Research Center for Agrotechnology and Biotechnology, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan.
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Wei X, Fu T, He G, Zhong Z, Yang M, Lou F, He T. Characteristics of rhizosphere and bulk soil microbial community of Chinese cabbage ( Brassica campestris) grown in Karst area. Front Microbiol 2023; 14:1241436. [PMID: 37789857 PMCID: PMC10542900 DOI: 10.3389/fmicb.2023.1241436] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/24/2023] [Indexed: 10/05/2023] Open
Abstract
Understanding the rhizosphere soil microbial community and its relationship with the bulk soil microbial community is critical for maintaining soil health and fertility and improving crop yields in Karst regions. The microbial communities in the rhizosphere and bulk soils of a Chinese cabbage (Brassica campestris) plantation in a Karst region, as well as their relationships with soil nutrients, were examined in this study using high-throughput sequencing technologies of 16S and ITS amplicons. The aim was to provide theoretical insights into the healthy cultivation of Chinese cabbage in a Karst area. The findings revealed that the rhizosphere soil showed higher contents of organic matter (OM), alkaline hydrolyzable nitrogen (AN), available phosphorus (AP), total phosphorus (TP), available potassium (AK), total potassium (TK), total nitrogen (TN), catalase (CA), urease (UR), sucrase (SU), and phosphatase (PHO), in comparison with bulk soil, while the pH value showed the opposite trend. The diversity of bacterial and fungal communities in the bulk soil was higher than that in the rhizosphere soil, and their compositions differed between the two types of soil. In the rhizosphere soil, Proteobacteria, Acidobacteriota, Actinobacteriota, and Bacteroidota were the dominant bacterial phyla, while Olpidiomycota, Ascomycota, Mortierellomycota, and Basidiomycota were the predominant fungal phyla. In contrast, the bulk soil was characterized by bacterial dominance of Proteobacteria, Acidobacteriota, Chloroflexi, and Actinobacteriota and fungal dominance of Ascomycota, Olpidiomycota, Mortierellomycota, and Basidiomycota. The fungal network was simpler than the bacterial network, and both networks exhibited less complexity in the rhizosphere soil compared with the bulk soil. Moreover, the rhizosphere soil harbored a higher proportion of beneficial Rhizobiales. The rhizosphere soil network was less complicated than the network in bulk soil by building a bacterial-fungal co-occurrence network. Furthermore, a network of relationships between soil properties and network keystone taxa revealed that the rhizosphere soil keystone taxa were more strongly correlated with soil properties than those in the bulk soil; despite its lower complexity, the rhizosphere soil contains a higher abundance of bacteria which are beneficial for cabbage growth compared with the bulk soil.
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Affiliation(s)
- Xiaoliao Wei
- College of Agriculture, Guizhou University, Guiyang, China
| | - Tianling Fu
- Engineering Key Laboratory for Pollution Control and Resource Reuse Technology of Mountain Livestock Breeding, Institute of New Rural Development, Guizhou University, Guiyang, China
| | - Guandi He
- College of Agriculture, Guizhou University, Guiyang, China
| | - Zhuoyan Zhong
- College of Agriculture, Guizhou University, Guiyang, China
| | - Mingfang Yang
- College of Agriculture, Guizhou University, Guiyang, China
| | - Fei Lou
- College of Agriculture, Guizhou University, Guiyang, China
| | - Tengbing He
- College of Agriculture, Guizhou University, Guiyang, China
- Engineering Key Laboratory for Pollution Control and Resource Reuse Technology of Mountain Livestock Breeding, Institute of New Rural Development, Guizhou University, Guiyang, China
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Lin C, Li LJ, Ren K, Zhou SYD, Isabwe A, Yang LY, Neilson R, Yang XR, Cytryn E, Zhu YG. Phagotrophic protists preserve antibiotic-resistant opportunistic human pathogens in the vegetable phyllosphere. ISME COMMUNICATIONS 2023; 3:94. [PMID: 37660098 PMCID: PMC10475086 DOI: 10.1038/s43705-023-00302-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/04/2023]
Abstract
Food safety of leafy greens is an emerging public health issue as they can harbor opportunistic human pathogens (OHPs) and expose OHPs to consumers. Protists are an integral part of phyllosphere microbial ecosystems. However, our understanding of protist-pathogen associations in the phyllosphere and their consequences on public health remains poor. Here, we examined phyllosphere protists, human pathogen marker genes (HPMGs), and protist endosymbionts from four species of leafy greens from major supermarkets in Xiamen, China. Our results showed that Staphylococcus aureus and Klebsiella pneumoniae were the dominant human pathogens in the vegetable phyllosphere. The distribution of HPMGs and protistan communities differed between vegetable species, of which Chinese chive possessed the most diverse protists and highest abundance of HPMGs. HPMGs abundance positively correlated with the diversity and relative abundance of phagotrophic protists. Whole genome sequencing further uncovered that most isolated phyllosphere protists harbored multiple OHPs which carried antibiotic resistance genes, virulence factors, and metal resistance genes and had the potential to HGT. Colpoda were identified as key phagotrophic protists which positively linked to OHPs and carried diverse resistance and virulence potential endosymbiont OHPs including Pseudomonas nitroreducens, Achromobacter xylosoxidans, and Stenotrophomonas maltophilia. We highlight that phyllosphere protists contribute to the transmission of resistant OHPs through internalization and thus pose risks to the food safety of leafy greens and human health. Our study provides insights into the protist-OHP interactions in the phyllosphere, which will help in food safety surveillance and human health.
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Affiliation(s)
- Chenshuo Lin
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, 100049, Beijing, China
| | - Li-Juan Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, 100049, Beijing, China
| | - Kexin Ren
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Shu-Yi-Dan Zhou
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Xingke Road 723, Tianhe District, Guangzhou, 510650, China
| | - Alain Isabwe
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Le-Yang Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, 100049, Beijing, China
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Eddie Cytryn
- Department of Soil Chemistry, Plant Nutrition and Microbiology, Institute of Soil, Water and Environmental Sciences, The Volcani Institute, Agriculture Research Organization, 7528809, Rishon Lezion, Israel
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China.
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China.
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Wang L, Jiao Y, Bi Y, Hu Y, Jiang Y, Wang S, Wang S. Nodulation number tempers the relative importance of stochastic processes in the assembly of soybean root-associated communities. ISME COMMUNICATIONS 2023; 3:89. [PMID: 37640896 PMCID: PMC10462722 DOI: 10.1038/s43705-023-00296-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023]
Abstract
Identifying the ecological forces that structure root-associated microbial communities is an essential step toward more sustainable agriculture. Legumes are widely utilized as model plants to study selective forces and their functioning in plant-microbial interactions owing to their ability to establish mutualism with rhizobia. Root nodules act as symbiotic organs to optimize the cost-benefit balance in this mutualistic relationship by modulating the number of nodules. However, it is not known whether the number of nodules is related to the structure of root-associated bacterial communities. Here, the root-associated bacterial communities of soybean grown in native soil by means of soybean cultivars with super- or normal nodulation were investigated across four developmental stages. We compared ecological processes between communities and found decreased relative importance of neutral processes for super-nodulating soybean, although the overall structures resembled those of normal-nodulating soybean. We identified the generalist core bacterial populations in each root-associated compartment, that are shared across root-associated niches, and persist through developmental stages. Within core bacterial species, the relative abundances of bacterial species in the rhizosphere microbiome were linked to host-plant functional traits and can be used to predict these traits from microbes using machine learning algorithms. These findings broaden the comprehensive understanding of the ecological forces and associations of microbiotas in various root-associated compartments and provide novel insights to integrate beneficial plant microbiomes into agricultural production to enhance plant performance.
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Affiliation(s)
- Lei Wang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, 150030, Harbin, PR China
- School of Resources and Environment, Northeast Agricultural University, 150030, Harbin, PR China
| | - Yan Jiao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, 150030, Harbin, PR China
| | - Yingdong Bi
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, 150028, Harbin, PR China
| | - Yanli Hu
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, 150030, Harbin, PR China
| | - Yan Jiang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, 150030, Harbin, PR China
| | - Shaodong Wang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, 150030, Harbin, PR China.
| | - Sui Wang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, 150030, Harbin, PR China.
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Wang Z, Liu J, Xu H, Liu J, Zhao Z, Gong X. Core Microbiome and Microbial Community Structure in Coralloid Roots of Cycas in Ex Situ Collection of Kunming Botanical Garden in China. Microorganisms 2023; 11:2144. [PMID: 37763988 PMCID: PMC10537389 DOI: 10.3390/microorganisms11092144] [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: 07/14/2023] [Revised: 08/12/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Endophytes are essential in plant succession and evolution, and essential for stress resistance. Coralloid root is a unique root structure found in cycads that has played a role in resisting adverse environments, yet the core taxa and microbial community of different Cycas species have not been thoroughly investigated. Using amplicon sequencing, we successfully elucidated the microbiomes present in coralloid roots of 10 Cycas species, representing all four sections of Cycas in China. We found that the endophytic bacteria in coralloid roots, i.e., Cyanobacteria, were mainly composed of Desmonostoc_PCC-7422, Nostoc_PCC-73102 and unclassified_f__Nostocaceae. Additionally, the Ascomycota fungi of Exophiala, Paraboeremia, Leptobacillium, Fusarium, Alternaria, and Diaporthe were identified as the core fungi taxa. The Ascomycota fungi of Nectriaceae, Herpotrichiellaceae, Cordycipitaceae, Helotiaceae, Diaporthaceae, Didymellaceae, Clavicipitaceae and Pleosporaceae were identified as the core family taxa in coralloid roots of four sections. High abundance but low diversity of bacterial community was detected in the coralloid roots, but no significant difference among species. The fungal community exhibited much higher complexity compared to bacteria, and diversity was noted among different species or sections. These core taxa, which were a subset of the microbiome that frequently occurred in all, or most, individuals of Cycas species, represent targets for the development of Cycas conservation.
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Affiliation(s)
- Zhaochun Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China;
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (J.L.)
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Jian Liu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (J.L.)
| | - Haiyan Xu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China;
| | - Jiating Liu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (J.L.)
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Zhiwei Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China;
| | - Xun Gong
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (J.L.)
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Demarquest G, Lajoie G. Bacterial endophytes of sugar maple leaves vary more idiosyncratically than epiphytes across a large geographic area. FEMS Microbiol Ecol 2023; 99:fiad079. [PMID: 37442613 DOI: 10.1093/femsec/fiad079] [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: 04/17/2023] [Revised: 07/04/2023] [Accepted: 07/12/2023] [Indexed: 07/15/2023] Open
Abstract
Bacteria from the leaf surface and the leaf tissue have been attributed with several beneficial properties for their plant host. Though physically connected, the microbial ecology of these compartments has mostly been studied separately such that we lack an integrated understanding of the processes shaping their assembly. We sampled leaf epiphytes and endophytes from the same individuals of sugar maple across the northern portion of its range to evaluate if their community composition was driven by similar processes within and across populations differing in plant traits and overall abiotic environment. Leaf compartment explained most of the variation in community diversity and composition across samples. Leaf epiphytic communities were driven more by host and site characteristics than endophytic communities, whose community composition was more idiosyncratic across samples. Our results suggest a greater importance of priority effects and opportunistic colonization in driving community assembly of leaf endophytes. Understanding the comparative assembly of bacterial communities at the surface and inside plant leaves may be particularly useful for leveraging their respective potential for improving the health of plants in natural and anthropized ecosystems.
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Affiliation(s)
- Garance Demarquest
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 rue Sherbrooke E, H1X 2B2 Montréal, Canada
- Université de Rennes, Agro-Campus Ouest, 65 Rue de Saint-Brieuc, 35042 Rennes, France
| | - Geneviève Lajoie
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 rue Sherbrooke E, H1X 2B2 Montréal, Canada
- Jardin Botanique de Montréal, 4101 rue Sherbrooke E, H1X 2B2 Montréal, Canada
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Kong W, Qiu L, Ishii S, Jia X, Su F, Song Y, Hao M, Shao M, Wei X. Contrasting response of soil microbiomes to long-term fertilization in various highland cropping systems. ISME COMMUNICATIONS 2023; 3:81. [PMID: 37596350 PMCID: PMC10439144 DOI: 10.1038/s43705-023-00286-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/20/2023]
Abstract
Soil microbiomes play important roles in supporting agricultural ecosystems. However, it is still not well-known how soil microbiomes and their functionality respond to fertilization in various cropping systems. Here we examined the effects of 36 years of phosphorus, nitrogen, and manure application on soil bacterial communities, functionality and crop productivity in three contrasting cropping systems (i.e., continuous leguminous alfalfa (AC), continuous winter wheat (WC), and grain-legume rotation of winter wheat + millet - pea - winter wheat (GLR)) in a highland region of China's Loess Plateau. We showed that long-term fertilization significantly affected soil bacterial communities and that the effects varied with cropping system. Compared with the unfertilized control, fertilization increased soil bacterial richness and diversity in the leguminous AC system, whereas it decreased those in the GLR system. Fertilization, particularly manure application, enlarged the differences in soil bacterial communities among cropping systems. Soil bacterial communities were mostly affected by the soil organic carbon and nitrogen contents in the WC and GLR systems, but by the soil available phosphorous content in the AC system. Crop productivity was closely associated with the abundance of fertilization-responsive taxa in the three cropping systems. Our study highlights that legume and non-legume cropping systems should be disentangled when assessing the responses of soil microbial communities to long-term fertilizer application.
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Affiliation(s)
- Weibo Kong
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, 712100, China
| | - Liping Qiu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, 712100, China
| | - Satoshi Ishii
- BioTechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA
- Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, 55108, USA
| | - Xiaoxu Jia
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, 100101, Beijing, China
| | - Fuyuan Su
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, 712100, China
| | - Yu Song
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - Mingde Hao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, 712100, China
| | - Mingan Shao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, 712100, China
- CAS Center for Excellence in Quaternary Science and Global Change, Xi'an, 710061, Shaanxi, China
| | - Xiaorong Wei
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, 712100, China.
- CAS Center for Excellence in Quaternary Science and Global Change, Xi'an, 710061, Shaanxi, China.
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Wei X, Fu T, He G, Zhong Z, Yang M, Lou F, He T. Types of vegetables shape composition, diversity, and co-occurrence networks of soil bacteria and fungi in karst areas of southwest China. BMC Microbiol 2023; 23:194. [PMID: 37468849 PMCID: PMC10354930 DOI: 10.1186/s12866-023-02929-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/03/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Microorganisms are of significant importance in soil. Yet their association with specific vegetable types remains poorly comprehended. This study investigates the composition of bacterial and fungal communities in soil by employing high-throughput sequencing of 16 S rRNA genes and ITS rRNA genes while considering the cultivation of diverse vegetable varieties. RESULTS The findings indicate that the presence of cultivated vegetables influenced the bacterial and fungal communities leading to discernible alterations when compared to uncultivated soil. In particular, the soil of leafy vegetables (such as cabbage and kale) exhibited higher bacterial α-diversity than melon and fruit vegetable (such as cucumber and tomato), while fungal α-diversity showed an inverse pattern. The prevailing bacterial phyla in both leafy vegetable and melon and fruit vegetable soils were Proteobacteria, Acidobacteriota, Actinobacteriota, and Chloroflexi. In leafy vegetable soil, dominant fungal phyla included Ascomycota, Olpidiomycota, Mortierellomycota, and Basidiomycota whereas in melon and fruit vegetable soil. Ascomycota, Mortierellomycota, Basidiomycota, and Rozellomycota held prominence. Notably, the relative abundance of Ascomycota was lower in leafy vegetable soil compared to melon and fruit vegetable soil. Moreover, leafy vegetable soil exhibited a more complex and stable co-occurrence network in comparison to melon and fruit vegetable soil. CONCLUSION The findings enhance our understanding of how cultivated soil bacteria and fungi respond to human disturbance, thereby providing a valuable theoretical basis for soil health in degraded karst areas of southwest China.
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Affiliation(s)
- Xiaoliao Wei
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Tianling Fu
- Institute of New Rural Development, Engineering Key Laboratory for Pollution Control and Resource Reuse Technology of Mountain Livestock Breeding, Guizhou University, Huaxi District, Guiyang City, 550025, Guizhou Province, PR China
| | - Guandi He
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Zhuoyan Zhong
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Mingfang Yang
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Fei Lou
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Tengbing He
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China.
- Institute of New Rural Development, Engineering Key Laboratory for Pollution Control and Resource Reuse Technology of Mountain Livestock Breeding, Guizhou University, Huaxi District, Guiyang City, 550025, Guizhou Province, PR China.
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48
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Sun X, Sharon O, Sharon A. Distinct Features Based on Partitioning of the Endophytic Fungi of Cereals and Other Grasses. Microbiol Spectr 2023; 11:e0061123. [PMID: 37166321 PMCID: PMC10269846 DOI: 10.1128/spectrum.00611-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/18/2023] [Indexed: 05/12/2023] Open
Abstract
Endophytic fungi form a significant part of the plant mycobiome. Defining core members is crucial to understanding the assembly mechanism of fungal endophytic communities (FECs) and identifying functionally important community members. We conducted a meta-analysis of FECs in stems of wheat and five wild cereal species and generated a landscape of the fungal endophytic assemblages in this group of plants. The analysis revealed that several Ascomycota members and basidiomycetous yeasts formed an important compartment of the FECs in these plants. We observed a weak spatial autocorrelation at the regional scale and high intrahost variations in the FECs, suggesting a space-related heterogeneity. Accordingly, we propose that the heterogeneity among subcommunities should be a criterion to define the core endophytic members. Analysis of the subcommunities and meta-communities showed that the core and noncore members had distinct roles in various assembly processes, such as stochasticity, universal dynamics, and network characteristics, within each host. The distinct features identified between the community partitions of endophytes aid in understanding the principles that govern the assembly and function of natural communities. These findings can assist in designing synthetic microbiomes. IMPORTANCE This study proposes a novel method for diagnosing core microbiotas based on prevalence of community members in a meta-community, which could be determined and supported statistically. Using this approach, the study found stratification in community assembly processes within fungal endophyte communities (FECs) in the stems of wheat and cereal-related wild species. The core and noncore partitions of the FECs exhibited certain degrees of determinism from different aspects. Further analysis revealed abundant and consistent interactions between rare taxa, which might contribute to the determinism process in noncore partitions. Despite minor differences in FEC compositions, wheat FECs showed distinct patterns in community assembly processes compared to wild species, suggesting the effects of domestication on FECs. Overall, our study provided a new approach for identifying core microbiota and provides insights into the community assembly processes within FECs in wheat and related wild species.
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Affiliation(s)
- Xiang Sun
- School of Life Sciences, Hebei University, Baoding, Hebei, China
| | - Or Sharon
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Amir Sharon
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
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Che J, Wu Y, Yang H, Wang S, Wu W, Lyu L, Wang X, Li W. Root Niches of Blueberry Imprint Increasing Bacterial-Fungal Interkingdom Interactions along the Soil-Rhizosphere-Root Continuum. Microbiol Spectr 2023; 11:e0533322. [PMID: 37222589 PMCID: PMC10269492 DOI: 10.1128/spectrum.05333-22] [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: 12/28/2022] [Accepted: 05/10/2023] [Indexed: 05/25/2023] Open
Abstract
Plant root-associated microbiomes play critical roles in promoting plant health, productivity, and tolerance to biotic/abiotic stresses. Blueberry (Vaccinium spp.) is adapted to acidic soils, while the interactions of the root-associated microbiomes in this specific habitat under various root microenvironments remain elusive. Here, we investigated the diversity and community composition of bacterial and fungal communities in various blueberry root niches (bulk soil, rhizosphere soil, and root endosphere). The results showed that blueberry root niches significantly affected root-associated microbiome diversity and community composition compared to those of the three host cultivars. Deterministic processes gradually increased along the soil-rhizosphere-root continuum in both bacterial and fungal communities. The co-occurrence network topological features showed that both bacterial and fungal community complexity and intensive interactions decreased along the soil-rhizosphere-root continuum. Different compartment niches clearly influenced bacterial-fungal interkingdom interactions, which were significantly higher in the rhizosphere, and positive interactions gradually dominated the co-occurrence networks from the bulk soil to the endosphere. The functional predictions showed that rhizosphere bacterial and fungal communities may have higher cellulolysis and saprotrophy capacities, respectively. Collectively, the root niches not only affected microbial diversity and community composition but also enhanced the positive interkingdom interactions between bacterial and fungal communities along the soil-rhizosphere-root continuum. This provides an essential basis for manipulating synthetic microbial communities for sustainable agriculture. IMPORTANCE The blueberry root-associated microbiome plays an essential role in its adaptation to acidic soils and in limiting the uptake of soil nutrients by its poor root system. Studies on the interactions of the root-associated microbiome in the various root niches may deepen our understanding of the beneficial effects in this particular habitat. Our study extended the research on the diversity and composition of microbial communities in different blueberry root compartment niches. Root niches dominated the root-associated microbiome compared to that of the host cultivar, and deterministic processes increased from the bulk soil to the endosphere. In addition, bacterial-fungal interkingdom interactions were significantly higher in the rhizosphere, and those positive interactions progressively dominated the co-occurrence network along the soil-rhizosphere-root continuum. Collectively, root niches dominantly affected the root-associated microbiome and the positive interkingdom interactions increased, potentially providing benefits for the blueberry.
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Affiliation(s)
- Jilu Che
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yaqiong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Hao Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Shaoyi Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Wenlong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Lianfei Lyu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Xiaomin Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Weilin Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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Bourak K, Sare AR, Allaoui A, Jijakli MH, Massart S. Impact of Two Phosphorus Fertilizer Formulations on Wheat Physiology, Rhizosphere, and Rhizoplane Microbiota. Int J Mol Sci 2023; 24:9879. [PMID: 37373026 DOI: 10.3390/ijms24129879] [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: 04/21/2023] [Revised: 05/29/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Phosphorus (P) is the second most important macronutrient for crop growth and a limiting factor in food production. Choosing the right P fertilizer formulation is important for crop production systems because P is not mobile in soils, and placing phosphate fertilizers is a major management decision. In addition, root microorganisms play an important role in helping phosphorus fertilization management by regulating soil properties and fertility through different pathways. Our study evaluated the impact of two phosphorous formulations (polyphosphates and orthophosphates) on physiological traits of wheat related to yield (photosynthetic parameters, biomass, and root morphology) and its associated microbiota. A greenhouse experiment was conducted using agricultural soil deficient in P (1.49%). Phenotyping technologies were used at the tillering, stem elongation, heading, flowering, and grain-filling stages. The evaluation of wheat physiological traits revealed highly significant differences between treated and untreated plants but not between phosphorous fertilizers. High-throughput sequencing technologies were applied to analyse the wheat rhizosphere and rhizoplane microbiota at the tillering and the grain-filling growth stages. The alpha- and beta-diversity analyses of bacterial and fungal microbiota revealed differences between fertilized and non-fertilized wheat, rhizosphere, and rhizoplane, and the tillering and grain-filling growth stages. Our study provides new information on the composition of the wheat microbiota in the rhizosphere and rhizoplane during growth stages (Z39 and Z69) under polyphosphate and orthophosphate fertilization. Hence, a deeper understanding of this interaction could provide better insights into managing microbial communities to promote beneficial plant-microbiome interactions for P uptake.
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Affiliation(s)
- Kaoutar Bourak
- Terra Research Center, Integrated and Urban Plant Pathology Laboratory, Liege University, Gembloux Agro-Bio-Tech, B-5030 Gembloux, Belgium
- Microbiology Laboratory, African Genome Center (AGC), Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco
| | - Abdoul Razack Sare
- Terra Research Center, Integrated and Urban Plant Pathology Laboratory, Liege University, Gembloux Agro-Bio-Tech, B-5030 Gembloux, Belgium
| | - Abdelmounaaim Allaoui
- Microbiology Laboratory, African Genome Center (AGC), Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco
| | - M Haissam Jijakli
- Terra Research Center, Integrated and Urban Plant Pathology Laboratory, Liege University, Gembloux Agro-Bio-Tech, B-5030 Gembloux, Belgium
| | - Sébastien Massart
- Terra Research Center, Integrated and Urban Plant Pathology Laboratory, Liege University, Gembloux Agro-Bio-Tech, B-5030 Gembloux, Belgium
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