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Wang D, He X, Baer M, Lami K, Yu B, Tassinari A, Salvi S, Schaaf G, Hochholdinger F, Yu P. Lateral root enriched Massilia associated with plant flowering in maize. MICROBIOME 2024; 12:124. [PMID: 38982519 PMCID: PMC11234754 DOI: 10.1186/s40168-024-01839-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 05/16/2024] [Indexed: 07/11/2024]
Abstract
BACKGROUND Beneficial associations between plants and soil microorganisms are critical for crop fitness and resilience. However, it remains obscure how microorganisms are assembled across different root compartments and to what extent such recruited microbiomes determine crop performance. Here, we surveyed the root transcriptome and the root and rhizosphere microbiome via RNA sequencing and full-length (V1-V9) 16S rRNA gene sequencing from genetically distinct monogenic root mutants of maize (Zea mays L.) under different nutrient-limiting conditions. RESULTS Overall transcriptome and microbiome display a clear assembly pattern across the compartments, i.e., from the soil through the rhizosphere to the root tissues. Co-variation analysis identified that genotype dominated the effect on the microbial community and gene expression over the nutrient stress conditions. Integrated transcriptomic and microbial analyses demonstrated that mutations affecting lateral root development had the largest effect on host gene expression and microbiome assembly, as compared to mutations affecting other root types. Cooccurrence and trans-kingdom network association analysis demonstrated that the keystone bacterial taxon Massilia (Oxalobacteraceae) is associated with root functional genes involved in flowering time and overall plant biomass. We further observed that the developmental stage drives the differentiation of the rhizosphere microbial assembly, especially the associations of the keystone bacteria Massilia with functional genes in reproduction. Taking advantage of microbial inoculation experiments using a maize early flowering mutant, we confirmed that Massilia-driven maize growth promotion indeed depends on flowering time. CONCLUSION We conclude that specific microbiota supporting lateral root formation could enhance crop performance by mediating functional gene expression underlying plant flowering time in maize. Video Abstract.
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Affiliation(s)
- Danning Wang
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
| | - Xiaoming He
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
| | - Marcel Baer
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
| | - Klea Lami
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
- Plant Nutrition, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
| | - Baogang Yu
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
| | - Alberto Tassinari
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, 40127, Italy
| | - Silvio Salvi
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, 40127, Italy
| | - Gabriel Schaaf
- Plant Nutrition, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
| | - Frank Hochholdinger
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
| | - Peng Yu
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany.
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany.
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Ortúzar M, Riesco R, Criado M, Alonso MDP, Trujillo ME. Unraveling the dynamic interplay of microbial communities associated to Lupinus angustifolius in response to environmental and cultivation conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174277. [PMID: 38944300 DOI: 10.1016/j.scitotenv.2024.174277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/05/2024] [Accepted: 06/23/2024] [Indexed: 07/01/2024]
Abstract
Microorganisms form dynamic communities with plants, providing benefits such as nutrient acquisition and stress resilience. Understanding how these microorganisms are affected by environmental factors such as growth conditions and soil characteristics are essential for harnessing these communities for sustainable agriculture practices and their response to climate change. The microbiome associated to Lupinus angustifolius, a legume native in Europe, with a high protein value and stress resilience was characterized for the first time. Using 16S rRNA gene and ITS amplicon sequencing, we characterized the compositional and temporal changes of the bacterial and fungal communities associated to the soil, rhizosphere, and plant compartments where Lupinus angustifolius grows naturally. Our results suggest that the main difference in the soil microbial communities is related to the edaphic properties, although environmental factors such as temperature, humidity or rainfall also influenced the composition of the soil microbial communities. We also characterized the bacterial communities associated with the rhizosphere, roots, nodules, and leaves of wild plants collected in the field and compared them against plants obtained under greenhouse conditions. In the plant compartments, the bacterial composition appeared to be more affected by the growing conditions (field vs greenhouse), than by soil characteristics or location. These results can be used to identify key taxa that may play crucial roles in the development and adaptation of the host plant and its associated microbiota to environmental changes and highlight the importance of characterizing the plant microbiomes in their natural habitats. Soil, influenced by climatic seasons, shapes the plant microbiome assembly. Lupinus recruits a core microbiome across rhizosphere, roots, nodules, and leaves, that is stable across locations. However, cultivation conditions may alter microbiome dynamics, impacting the adaptability of its components. Wild plants show a resilient and adaptable microbiome while germination and cultivation in greenhouse conditions alter its composition and vulnerability.
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Affiliation(s)
- Maite Ortúzar
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain.
| | - Raúl Riesco
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain.
| | - Marco Criado
- Area of Edaphology and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, University of Salamanca, 37007 Salamanca, Spain.
| | - María Del Pilar Alonso
- Area of Edaphology and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, University of Salamanca, 37007 Salamanca, Spain.
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain.
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3
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Rowson M, Jolly M, Dickson S, Gifford ML, Carré I. Timely symbiosis: circadian control of legume-rhizobia symbiosis. Biochem Soc Trans 2024; 52:1419-1430. [PMID: 38779952 DOI: 10.1042/bst20231307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/10/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024]
Abstract
Legumes house nitrogen-fixing endosymbiotic rhizobia in specialised polyploid cells within root nodules. This results in a mutualistic relationship whereby the plant host receives fixed nitrogen from the bacteria in exchange for dicarboxylic acids. This plant-microbe interaction requires the regulation of multiple metabolic and physiological processes in both the host and symbiont in order to achieve highly efficient symbiosis. Recent studies have showed that the success of symbiosis is influenced by the circadian clock of the plant host. Medicago and soybean plants with altered clock mechanisms showed compromised nodulation and reduced plant growth. Furthermore, transcriptomic analyses revealed that multiple genes with key roles in recruitment of rhizobia to plant roots, infection and nodule development were under circadian control, suggesting that appropriate timing of expression of these genes may be important for nodulation. There is also evidence for rhythmic gene expression of key nitrogen fixation genes in the rhizobium symbiont, and temporal coordination between nitrogen fixation in the bacterial symbiont and nitrogen assimilation in the plant host may be important for successful symbiosis. Understanding of how circadian regulation impacts on nodule establishment and function will identify key plant-rhizobial connections and regulators that could be targeted to increase the efficiency of this relationship.
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Affiliation(s)
- Monique Rowson
- School of Life Sciences, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Matthew Jolly
- School of Life Sciences, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Suzanna Dickson
- School of Life Sciences, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Miriam L Gifford
- School of Life Sciences, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, The University of Warwick, Coventry CV4 7AL, U.K
| | - Isabelle Carré
- School of Life Sciences, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
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4
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Ji C, Guo J, Ma Y, Xu X, Zang T, Liu S, An Z, Yang M, He X, Zheng W. Application Progress of Culturomics in the Isolated Culture of Rhizobacteria: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7586-7595. [PMID: 38530921 DOI: 10.1021/acs.jafc.3c08885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Comprehending the structure and function of rhizobacteria components and their regulation are crucial for sustainable agricultural management. However, obtaining comprehensive species information for most bacteria in the natural environment, particularly rhizobacteria, presents a challenge using traditional culture methods. To obtain diverse and pure cultures of rhizobacteria, this study primarily reviews the evolution of rhizobacteria culturomics and associated culture methods. Furthermore, it explores new strategies for enhancing the application of culturomics, providing valuable insights into efficiently enriching and isolate target bacterial strains/groups from the environment. The findings will help improve rhizobacteria's culturability and enrich the functional bacterial library.
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Affiliation(s)
- Chao Ji
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Junli Guo
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Ying Ma
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Xiangfu Xu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Tongyu Zang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Sentao Liu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Zhenzhen An
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Min Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Xiahong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan 650201, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, Yunnan 650224, China
| | - Wenjie Zheng
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan 650201, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, Yunnan 650224, China
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Fu Q, Qiu Y, Zhao J, Li J, Xie S, Liao Q, Fu X, Huang Y, Yao Z, Dai Z, Qiu Y, Yang Y, Li F, Chen H. Monotonic trends of soil microbiomes, metagenomic and metabolomic functioning across ecosystems along water gradients in the Altai region, northwestern China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169351. [PMID: 38123079 DOI: 10.1016/j.scitotenv.2023.169351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/21/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
To investigate microbial communities and their contributions to carbon and nutrient cycling along water gradients can enhance our comprehension of climate change impacts on ecosystem services. Thus, we conducted an assessment of microbial communities, metagenomic functions, and metabolomic profiles within four ecosystems, i.e., desert grassland (DG), shrub-steppe (SS), forest (FO), and marsh (MA) in the Altai region of Xinjiang, China. Our results showed that soil total carbon (TC), total nitrogen, NH4+, and NO3- increased, but pH decreased with soil water gradients. Microbial abundances and richness also increased with soil moisture except the abundances of fungi and protists being lowest in MA. A shift in microbial community composition is evident along the soil moisture gradient, with Proteobacteria, Basidiomycota, and Evosea proliferating but a decline in Actinobacteria and Cercozoa. The β-diversity of microbiomes, metagenomic, and metabolomic functioning were correlated with soil moisture gradients and have significant associations with specific soil factors of TC, NH4+, and pH. Metagenomic functions associated with carbohydrate and DNA metabolisms, as well as phages, prophages, TE, plasmids functions diminished with moisture, whereas the genes involved in nitrogen and potassium metabolism, along with certain biological interactions and environmental information processing functions, demonstrated an augmentation. Additionally, MA harbored the most abundant metabolomics dominated by lipids and lipid-like molecules and organic oxygen compounds, except certain metabolites showing decline trends along water gradients, such as N'-Hydroxymethylnorcotinine and 5-Hydroxyenterolactone. Thus, our study suggests that future ecosystem succession facilitated by changes in rainfall patterns will significantly alter soil microbial taxa, functional potential, and metabolite fractions.
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Affiliation(s)
- Qi Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yingbo Qiu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jiayi Zhao
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jiaxin Li
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Siqi Xie
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Qiuchang Liao
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xianheng Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yu Huang
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Zhiyuan Yao
- School of Civil and Environmental Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Zhongmin Dai
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yunpeng Qiu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Furong Li
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
| | - Huaihai Chen
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
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6
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Marschmann GL, Tang J, Zhalnina K, Karaoz U, Cho H, Le B, Pett-Ridge J, Brodie EL. Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model. Nat Microbiol 2024; 9:421-433. [PMID: 38316928 PMCID: PMC10847045 DOI: 10.1038/s41564-023-01582-w] [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: 04/20/2023] [Accepted: 12/08/2023] [Indexed: 02/07/2024]
Abstract
Soil microbiomes are highly diverse, and to improve their representation in biogeochemical models, microbial genome data can be leveraged to infer key functional traits. By integrating genome-inferred traits into a theory-based hierarchical framework, emergent behaviour arising from interactions of individual traits can be predicted. Here we combine theory-driven predictions of substrate uptake kinetics with a genome-informed trait-based dynamic energy budget model to predict emergent life-history traits and trade-offs in soil bacteria. When applied to a plant microbiome system, the model accurately predicted distinct substrate-acquisition strategies that aligned with observations, uncovering resource-dependent trade-offs between microbial growth rate and efficiency. For instance, inherently slower-growing microorganisms, favoured by organic acid exudation at later plant growth stages, exhibited enhanced carbon use efficiency (yield) without sacrificing growth rate (power). This insight has implications for retaining plant root-derived carbon in soils and highlights the power of data-driven, trait-based approaches for improving microbial representation in biogeochemical models.
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Affiliation(s)
- Gianna L Marschmann
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jinyun Tang
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kateryna Zhalnina
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Heejung Cho
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Beatrice Le
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life and Environmental Sciences Department, University of California Merced, Merced, CA, USA
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA.
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7
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Kitz F, Wachter H, Spielmann F, Hammerle A, Wohlfahrt G. Root and rhizosphere contribution to the net soil COS exchange. PLANT AND SOIL 2023; 498:325-339. [PMID: 38665878 PMCID: PMC11039419 DOI: 10.1007/s11104-023-06438-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 12/02/2023] [Indexed: 04/28/2024]
Abstract
Background and aims Partitioning the measured net ecosystem carbon dioxide (CO2) exchange into gross primary productivity (GPP) and ecosystem respiration remains a challenge, which scientists try to tackle by using the properties of the trace gas carbonyl sulfide (COS). Its similar pathway into and within the leaf makes it a potential photosynthesis proxy. The application of COS as an effective proxy depends, among other things, on a robust inventory of potential COS sinks and sources within ecosystems. While the soil received some attention during the last couple of years, the role of plant roots is mostly unknown. In our study, we investigated the effects of live roots on the soil COS exchange. Methods An experimental setup was devised to measure the soil and the belowground plant parts of young beech trees observed over the course of 9 months. Results During the growing season, COS emissions were significantly lower when roots were present compared to chambers only containing soil, while prior to the growing season, with photosynthetically inactive trees, the presence of roots increased COS emissions. The difference in the COS flux between root-influenced and uninfluenced soil was fairly constant within each month, with diurnal variations in the COS flux driven primarily by soil temperature changes rather than the presence or absence of roots. Conclusion While the mechanisms by which roots influence the COS exchange are largely unknown, their contribution to the overall ground surface COS exchange should not be neglected when quantifying the soil COS exchange. Supplementary Information The online version contains supplementary material available at 10.1007/s11104-023-06438-0.
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Affiliation(s)
- Florian Kitz
- Universität Innsbruck, Institut für Ökologie, Sternwartestraße 15, Innsbruck, 6020 Austria
| | - Herbert Wachter
- Universität Innsbruck, Institut für Ökologie, Sternwartestraße 15, Innsbruck, 6020 Austria
| | - Felix Spielmann
- Universität Innsbruck, Institut für Ökologie, Sternwartestraße 15, Innsbruck, 6020 Austria
| | - Albin Hammerle
- Universität Innsbruck, Institut für Ökologie, Sternwartestraße 15, Innsbruck, 6020 Austria
| | - Georg Wohlfahrt
- Universität Innsbruck, Institut für Ökologie, Sternwartestraße 15, Innsbruck, 6020 Austria
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8
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Ikeda H, Uchikawa T, Kondo Y, Takahashi N, Shishikui T, Watahiki MK, Kubota A, Endo M. Circadian Clock Controls Root Hair Elongation through Long-Distance Communication. PLANT & CELL PHYSIOLOGY 2023; 64:1289-1300. [PMID: 37552691 DOI: 10.1093/pcp/pcad076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/06/2023] [Accepted: 07/13/2023] [Indexed: 08/10/2023]
Abstract
Plants adapt to periodic environmental changes, such as day and night, by using circadian clocks. Cell division and elongation are primary steps to adjust plant development according to their environments. In Arabidopsis, hypocotyl elongation has been studied as a representative model to understand how the circadian clock regulates cell elongation. However, it remains unknown whether similar phenomena exist in other organs, such as roots, where circadian clocks regulate physiological responses. Here, we show that root hair elongation is controlled by both light and the circadian clock. By developing machine-learning models to automatically analyze the images of root hairs, we found that genes encoding major components of the central oscillator, such as TIMING OF CAB EXPRESSION1 (TOC1) or CIRCADIAN CLOCK ASSOCIATED1 (CCA1), regulate the rhythmicity of root hair length. The partial illumination of light to either shoots or roots suggested that light received in shoots is mainly responsible for the generation of root hair rhythmicity. Furthermore, grafting experiments between wild-type (WT) and toc1 plants demonstrated that TOC1 in shoots is responsible for the generation of root hair rhythmicity. Our results illustrate the combinational effects of long-distance signaling and the circadian clock on the regulation of root hair length.
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Affiliation(s)
- Hikari Ikeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan
| | - Taiga Uchikawa
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan
| | - Yohei Kondo
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, 444-8787 Japan
| | - Nozomu Takahashi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, 332-0012 Japan
| | - Takuma Shishikui
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan
| | - Masaaki K Watahiki
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
- Faculty of Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Akane Kubota
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan
| | - Motomu Endo
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan
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9
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de Barros Dantas LL, Eldridge BM, Dorling J, Dekeya R, Lynch DA, Dodd AN. Circadian regulation of metabolism across photosynthetic organisms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:650-668. [PMID: 37531328 PMCID: PMC10953457 DOI: 10.1111/tpj.16405] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 08/04/2023]
Abstract
Circadian regulation produces a biological measure of time within cells. The daily cycle in the availability of light for photosynthesis causes dramatic changes in biochemical processes in photosynthetic organisms, with the circadian clock having crucial roles in adaptation to these fluctuating conditions. Correct alignment between the circadian clock and environmental day-night cycles maximizes plant productivity through its regulation of metabolism. Therefore, the processes that integrate circadian regulation with metabolism are key to understanding how the circadian clock contributes to plant productivity. This forms an important part of exploiting knowledge of circadian regulation to enhance sustainable crop production. Here, we examine the roles of circadian regulation in metabolic processes in source and sink organ structures of Arabidopsis. We also evaluate possible roles for circadian regulation in root exudation processes that deposit carbon into the soil, and the nature of the rhythmic interactions between plants and their associated microbial communities. Finally, we examine shared and differing aspects of the circadian regulation of metabolism between Arabidopsis and other model photosynthetic organisms, and between circadian control of metabolism in photosynthetic and non-photosynthetic organisms. This synthesis identifies a variety of future research topics, including a focus on metabolic processes that underlie biotic interactions within ecosystems.
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Affiliation(s)
| | - Bethany M. Eldridge
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Jack Dorling
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Richard Dekeya
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Deirdre A. Lynch
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Antony N. Dodd
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
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10
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Géron A, Werner J, Wattiez R, Matallana-Surget S. Towards the discovery of novel molecular clocks in Prokaryotes. Crit Rev Microbiol 2023:1-13. [PMID: 37330701 DOI: 10.1080/1040841x.2023.2220789] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 01/17/2023] [Accepted: 02/15/2023] [Indexed: 06/19/2023]
Abstract
Diel cycle is of enormous biological importance as it imposes daily oscillation in environmental conditions, which temporally structures most ecosystems. Organisms developed biological time-keeping mechanisms - circadian clocks - that provide a significant fitness advantage over competitors by optimising the synchronisation of their biological activities. While circadian clocks are ubiquitous in Eukaryotes, they are so far only characterised in Cyanobacteria within Prokaryotes. However, growing evidence suggests that circadian clocks are widespread in the bacterial and archaeal domains. As Prokaryotes are at the heart of crucial environmental processes and are essential to human health, unravelling their time-keeping systems provides numerous applications in medical research, environmental sciences, and biotechnology. In this review, we elaborate on how novel circadian clocks in Prokaryotes offer research and development perspectives. We compare and contrast the different circadian systems in Cyanobacteria and discuss about their evolution and taxonomic distribution. We necessarily provide an updated phylogenetic analysis of bacterial and archaeal species that harbour homologs of the main cyanobacterial clock components. Finally, we elaborate on new potential clock-controlled microorganisms that represent opportunities of ecological and industrial relevance in prokaryotic groups such as anoxygenic photosynthetic bacteria, methanogenic archaea, methanotrophs or sulphate-reducing bacteria.
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Affiliation(s)
- Augustin Géron
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK
- Proteomic and Microbiology Department, University of Mons, Mons, Belgium
| | - Johannes Werner
- High Performance and Cloud Computing Group, Zentrum für Datenverarbeitung (ZDV), University of Tübingen, Tübingen, Germany
| | - Ruddy Wattiez
- Proteomic and Microbiology Department, University of Mons, Mons, Belgium
| | - Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK
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11
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Wollmuth EM, Angert ER. Microbial circadian clocks: host-microbe interplay in diel cycles. BMC Microbiol 2023; 23:124. [PMID: 37161348 PMCID: PMC10173096 DOI: 10.1186/s12866-023-02839-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 03/28/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Circadian rhythms, observed across all domains of life, enable organisms to anticipate and prepare for diel changes in environmental conditions. In bacteria, a circadian clock mechanism has only been characterized in cyanobacteria to date. These clocks regulate cyclical patterns of gene expression and metabolism which contribute to the success of cyanobacteria in their natural environments. The potential impact of self-generated circadian rhythms in other bacterial and microbial populations has motivated extensive research to identify novel circadian clocks. MAIN TEXT Daily oscillations in microbial community composition and function have been observed in ocean ecosystems and in symbioses. These oscillations are influenced by abiotic factors such as light and the availability of nutrients. In the ocean ecosystems and in some marine symbioses, oscillations are largely controlled by light-dark cycles. In gut systems, the influx of nutrients after host feeding drastically alters the composition and function of the gut microbiota. Conversely, the gut microbiota can influence the host circadian rhythm by a variety of mechanisms including through interacting with the host immune system. The intricate and complex relationship between the microbiota and their host makes it challenging to disentangle host behaviors from bacterial circadian rhythms and clock mechanisms that might govern the daily oscillations observed in these microbial populations. CONCLUSIONS While the ability to anticipate the cyclical behaviors of their host would likely be enhanced by a self-sustained circadian rhythm, more evidence and further studies are needed to confirm whether host-associated heterotrophic bacteria possess such systems. In addition, the mechanisms by which heterotrophic bacteria might respond to diel cycles in environmental conditions has yet to be uncovered.
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Affiliation(s)
- Emily M Wollmuth
- Department of Microbiology, Cornell University, 123 Wing Drive, Ithaca, NY, 14853, USA
| | - Esther R Angert
- Department of Microbiology, Cornell University, 123 Wing Drive, Ithaca, NY, 14853, USA.
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12
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Xu H, Wang X, Wei J, Zuo Y, Wang L. The Regulatory Networks of the Circadian Clock Involved in Plant Adaptation and Crop Yield. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091897. [PMID: 37176955 PMCID: PMC10181312 DOI: 10.3390/plants12091897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
Global climatic change increasingly threatens plant adaptation and crop yields. By synchronizing internal biological processes, including photosynthesis, metabolism, and responses to biotic and abiotic stress, with external environmental cures, such as light and temperature, the circadian clock benefits plant adaptation and crop yield. In this review, we focus on the multiple levels of interaction between the plant circadian clock and environmental factors, and we summarize recent progresses on how the circadian clock affects yield. In addition, we propose potential strategies for better utilizing the current knowledge of circadian biology in crop production in the future.
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Affiliation(s)
- Hang Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiling Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Wei
- College of Life Sciences, Changchun Normal University, Changchun 130032, China
| | - Yi Zuo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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13
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Pacheco AR, Vorholt JA. Resolving metabolic interaction mechanisms in plant microbiomes. Curr Opin Microbiol 2023; 74:102317. [PMID: 37062173 DOI: 10.1016/j.mib.2023.102317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 04/18/2023]
Abstract
Metabolic interactions are fundamental to the assembly and functioning of microbiomes, including those of plants. However, disentangling the molecular basis of these interactions and their specific roles remains a major challenge. Here, we review recent applications of experimental and computational methods toward the elucidation of metabolic interactions in plant-associated microbiomes. We highlight studies that span various scales of taxonomic and environmental complexity, including those that test interaction outcomes in vitro and in planta by deconstructing microbial communities. We also discuss how the continued integration of multiple methods can further reveal the general ecological characteristics of plant microbiomes, as well as provide strategies for applications in areas such as improved plant protection, bioremediation, and sustainable agriculture.
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Affiliation(s)
- Alan R Pacheco
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
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14
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McLaughlin S, Zhalnina K, Kosina S, Northen TR, Sasse J. The core metabolome and root exudation dynamics of three phylogenetically distinct plant species. Nat Commun 2023; 14:1649. [PMID: 36964135 PMCID: PMC10039077 DOI: 10.1038/s41467-023-37164-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 03/01/2023] [Indexed: 03/26/2023] Open
Abstract
Root exudates are plant-derived, exported metabolites likely shaping root-associated microbiomes by acting as nutrients and signals. However, root exudation dynamics are unclear and thus also, if changes in exudation are reflected in changes in microbiome structure. Here, we assess commonalities and differences between exudates of different plant species, diurnal exudation dynamics, as well as the accompanying methodological aspects of exudate sampling. We find that exudates should be collected for hours rather than days as many metabolite abundances saturate over time. Plant growth in sterile, nonsterile, or sugar-supplemented environments significantly alters exudate profiles. A comparison of Arabidopsis thaliana, Brachypodium distachyon, and Medicago truncatula shoot, root, and root exudate metabolite profiles reveals clear differences between these species, but also a core metabolome for tissues and exudates. Exudate profiles also exhibit a diurnal signature. These findings add to the methodological and conceptual groundwork for future exudate studies to improve understanding of plant-microbe interactions.
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Affiliation(s)
- Sarah McLaughlin
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology, Berkeley, CA, USA
- Institute for Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Kateryna Zhalnina
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology, Berkeley, CA, USA
| | - Suzanne Kosina
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology, Berkeley, CA, USA
| | - Trent R Northen
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology, Berkeley, CA, USA.
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Joelle Sasse
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology, Berkeley, CA, USA.
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Institute for Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.
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15
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Tixier A, Forest M, Prudent M, Durey V, Zwieniecki M, Barnard RL. Root exudation of carbon and nitrogen compounds varies over the day-night cycle in pea: The role of diurnal changes in internal pools. PLANT, CELL & ENVIRONMENT 2023; 46:962-974. [PMID: 36562125 DOI: 10.1111/pce.14523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Rhizodeposition is the export of organic compounds from plant roots to the soil. Carbon allocation towards rhizodeposition has to be balanced with allocation for other physiological functions, which depend on both newly assimilated and stored nonstructural carbohydrate (NSC). To test whether the exudation of primary metabolites scales with plant NSC status, we studied diurnal dynamics of NSC and amino acid (AA) pools and fluxes within the plant and the rhizosphere. These diurnal dynamics were measured in the field and under hydroponic-controlled conditions. Further, C-limiting treatments offered further insight into the regulation of rhizodeposition. The exudation of primary metabolites fluctuated diurnally. The diurnal dynamics of soluble sugars (SS) and AA concentrations in tissues coincided with exudate pool fluctuations in the rhizosphere. SS and AA pools in the rhizosphere increased with NSC and AA pools in the roots. C starvation treatments offset the balance of exudates: AA exudate content in the rhizosphere significantly decreased while SS exudate content remained stable. Our results suggest that rhizodeposition is to some extent controlled by plant C:N status. We propose that SS exudation is less controlled than AA exudation because N assimilation depends on controlled C supply while SS exudation relies to a greater extent on passive diffusion mechanisms.
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Affiliation(s)
- Aude Tixier
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Marion Forest
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Marion Prudent
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Vincent Durey
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Maciej Zwieniecki
- Department of Plant Sciences, University of California, Davis, California, USA
| | - Romain L Barnard
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
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16
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Poupin MJ, Ledger T, Roselló-Móra R, González B. The Arabidopsis holobiont: a (re)source of insights to understand the amazing world of plant-microbe interactions. ENVIRONMENTAL MICROBIOME 2023; 18:9. [PMID: 36803555 PMCID: PMC9938593 DOI: 10.1186/s40793-023-00466-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
As holobiont, a plant is intrinsically connected to its microbiomes. However, some characteristics of these microbiomes, such as their taxonomic composition, biological and evolutionary role, and especially the drivers that shape them, are not entirely elucidated. Reports on the microbiota of Arabidopsis thaliana first appeared more than ten years ago. However, there is still a lack of a comprehensive understanding of the vast amount of information that has been generated using this holobiont. The main goal of this review was to perform an in-depth, exhaustive, and systematic analysis of the literature regarding the Arabidopsis-microbiome interaction. A core microbiota was identified as composed of a few bacterial and non-bacterial taxa. The soil (and, to a lesser degree, air) were detected as primary microorganism sources. From the plant perspective, the species, ecotype, circadian cycle, developmental stage, environmental responses, and the exudation of metabolites were crucial factors shaping the plant-microbe interaction. From the microbial perspective, the microbe-microbe interactions, the type of microorganisms belonging to the microbiota (i.e., beneficial or detrimental), and the microbial metabolic responses were also key drivers. The underlying mechanisms are just beginning to be unveiled, but relevant future research needs were identified. Thus, this review provides valuable information and novel analyses that will shed light to deepen our understanding of this plant holobiont and its interaction with the environment.
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Affiliation(s)
- M J Poupin
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, 7941169, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - T Ledger
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, 7941169, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - R Roselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), Illes Balears, Majorca, Spain
| | - B González
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, 7941169, Santiago, Chile.
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile.
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile.
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17
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DeWolf E, Brock MT, Calder WJ, Kliebenstein DJ, Katz E, Li B, Morrison HG, Maïgnien L, Weinig C. The rhizosphere microbiome and host plant glucosinolates exhibit feedback cycles in Brassica rapa. Mol Ecol 2023; 32:741-751. [PMID: 36373270 DOI: 10.1111/mec.16782] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022]
Abstract
The rhizosphere microbiome influences many aspects of plant fitness, including production of secondary compounds and defence against insect herbivores. Plants also modulate the composition of the microbial community in the rhizosphere via secretion of root exudates. We tested both the effect of the rhizosphere microbiome on plant traits, and host plant effects on rhizosphere microbes using recombinant inbred lines (RILs) of Brassica rapa that differ in production of glucosinolates (GLS), secondary metabolites that contribute to defence against insect herbivores. First, we investigated the effect of genetic variation in GLS production on the composition of the rhizosphere microbiome. Using a Bayesian Dirichlet-multinomial regression model (DMBVS), we identified both negative and positive associations between bacteria from six genera and the concentration of five GLS compounds produced in plant roots. Additionally, we tested the effects of microbial inoculation (an intact vs. disrupted soil microbiome) on GLS production and insect damage in these RILs. We found a significant microbial treatment × genotype interaction, in which total GLS was higher in the intact relative to the disrupted microbiome treatment in some RILs. However, despite differences in GLS production between microbial treatments, we observed no difference in insect damage between treatments. Together, these results provide evidence for a full feedback cycle of plant-microbe interactions mediated by GLS; that is, GLS compounds produced by the host plant "feed-down" to influence rhizosphere microbial community and rhizosphere microbes "feed-up" to influence GLS production.
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Affiliation(s)
- Ella DeWolf
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA.,Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, USA
| | - Marcus T Brock
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA
| | | | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California Davis, Davis, California, USA
| | - Ella Katz
- Department of Plant Sciences, University of California Davis, Davis, California, USA
| | - Baohua Li
- Department of Plant Sciences, University of California Davis, Davis, California, USA.,College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Hilary G Morrison
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Lois Maïgnien
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA.,Laboratory of Microbiology of Extreme Environments, UMR 6197, Institut Européen de la Mer, Université de Bretagne Occidentale, Plouzane, France
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA.,Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, USA
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18
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Wei Y, Quan F, Lan G, Wu Z, Yang C. Space Rather than Seasonal Changes Explained More of the Spatiotemporal Variation of Tropical Soil Microbial Communities. Microbiol Spectr 2022; 10:e0184622. [PMID: 36416607 PMCID: PMC9769686 DOI: 10.1128/spectrum.01846-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 11/03/2022] [Indexed: 11/24/2022] Open
Abstract
Soil microbiomes play an essential role in maintaining soil geochemical cycle and function. Although there have been some reports on the diversity patterns and drivers of the tropical forest soil microbial community, how space and seasonal changes affect spatiotemporal distribution at the regional scales are poorly understood. Based on 260 soil samples, we investigated the spatiotemporal patterns of rubber plantations and rainforest soil microbial communities across the whole of Hainan Island, China during the dry and rainy seasons. We examined soil bacterial and fungal composition and diversity and the main drivers of these microbes using Illumina sequencing and assembly. Our results revealed that the diversity (both alpha and beta) spatiotemporal variation in microbial communities is highly dependent on regional location rather than seasonal changes. For example, the site explained 28.5% and 37.2% of the variation in alpha diversity for soil bacteria and fungi, respectively, and explained 34.6% of the bacterial variance and 14.3% of the fungal variance in beta diversity. Soil pH, mean annual temperature, and mean annual precipitation were the most important factors associated with the distribution of soil microbial communities. Furthermore, we identified that variations in edaphic (e.g., soil pH) and climatic factors (e.g., mean annual temperature [MAT] and mean annual precipitation [MAP]) were mainly caused by regional sites (P < 0.001). Collectively, our work provides empirical evidence that space, rather than seasonal changes, explained more of the spatiotemporal variation of soil microbial communities in tropical forests, mediated by regional location-induced changes in climatic factors and edaphic properties. IMPORTANCE The soil microbiomes communities of the two forests were not only affected by environmental factors (e.g., edaphic and climatic factors), but also by different dominant geographic factors. In particular, our work showed that spatial variation in bacterial and fungal community composition was mainly dominated by edaphic properties (e.g., pH) and climatic factors (e.g., MAT and MAP). Moreover, the environmental factors were mainly explained by geographic location effect rather than by seasonal effect, and environmental dissimilarity significantly increased with geographic distance. In conclusion, our study provides solid empirical evidence that space rather than season explained more of the spatiotemporal variation of soil microbial communities in the tropical forest.
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Affiliation(s)
- Yaqing Wei
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou City, Hainan Province, People’s Republic of China
- Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou City, Hainan Province, People’s Republic of China
- College of Ecology and Environment, Hainan University, Haikou, China
| | - Fei Quan
- School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
- Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou City, Hainan Province, People’s Republic of China
| | - Guoyu Lan
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou City, Hainan Province, People’s Republic of China
- Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou City, Hainan Province, People’s Republic of China
| | - Zhixiang Wu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou City, Hainan Province, People’s Republic of China
- Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou City, Hainan Province, People’s Republic of China
| | - Chuan Yang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou City, Hainan Province, People’s Republic of China
- Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou City, Hainan Province, People’s Republic of China
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19
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Xu X, Dodd AN. Is there crosstalk between circadian clocks in plants and the rhizomicrobiome? BMC Biol 2022; 20:241. [PMID: 36303146 PMCID: PMC9615303 DOI: 10.1186/s12915-022-01443-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/10/2022] Open
Abstract
Circadian clocks occur across the kingdoms of life, including some fungi and bacteria present in the root-associated soil known as the rhizosphere. Recent work from Amy Newman and colleagues, published in BMC Biology, has discovered that the circadian clock in Arabidopsis plants affects the rhythmicity of rhizosphere microbial communities This brings into play the exciting question of whether there is a bidirectional rhythmic interaction between plants and their rhizomicrobiome. Here, we discuss how the findings of Newman et al. suggest that soil microbiomes can have both self-sustained and plant-imposed rhythmicity, and the challenges of plant-microbiome circadian clock research.
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Affiliation(s)
- Xinming Xu
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Antony N Dodd
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7RU, UK.
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20
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Newman A, Picot E, Davies S, Hilton S, Carré IA, Bending GD. Circadian rhythms in the plant host influence rhythmicity of rhizosphere microbiota. BMC Biol 2022; 20:235. [PMID: 36266698 PMCID: PMC9585842 DOI: 10.1186/s12915-022-01430-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 09/30/2022] [Indexed: 11/18/2022] Open
Abstract
Background Recent studies demonstrated that microbiota inhabiting the plant rhizosphere exhibit diel changes in abundance. To investigate the impact of plant circadian rhythms on bacterial and fungal rhythms in the rhizosphere, we analysed temporal changes in fungal and bacterial communities in the rhizosphere of Arabidopsis plants overexpressing or lacking function of the circadian clock gene LATE ELONGATED HYPOCOTYL (LHY). Results Under diel light–dark cycles, the knock-out mutant lhy-11 and the gain-of-function mutant lhy-ox both exhibited gene expression rhythms with altered timing and amplitude compared to wild-type plants. Distinct sets of bacteria and fungi were found to display rhythmic changes in abundance in the rhizosphere of both of these mutants, suggesting that abnormal patterns of rhythmicity in the plant host caused temporal reprogramming of the rhizosphere microbiome. This was associated with changes in microbial community structure, including changes in the abundance of fungal guilds known to impact on plant health. Under constant environmental conditions, microbial rhythmicity persisted in the rhizosphere of wild-type plants, indicating control by a circadian oscillator. In contrast, loss of rhythmicity in lhy-ox plants was associated with disrupted rhythms for the majority of rhizosphere microbiota. Conclusions These results show that aberrant function of the plant circadian clock is associated with altered rhythmicity of rhizosphere bacteria and fungi. In the long term, this leads to changes in composition of the rhizosphere microbiome, with potential consequences for plant health. Further research will be required to understand the functional implications of these changes and how they impact on plant health and productivity. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01430-z.
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Affiliation(s)
- Amy Newman
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, West Midlands, UK.,Present address: National STEM Learning Centre, University of York, York, YO10 5DD, UK
| | - Emma Picot
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, West Midlands, UK
| | - Sian Davies
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, West Midlands, UK.,Present address: Micropathology Ltd, Venture Centre, Sir William Lyons Road, Coventry, CV4 7EZ, UK
| | - Sally Hilton
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, West Midlands, UK.,Present address: Micropathology Ltd, Venture Centre, Sir William Lyons Road, Coventry, CV4 7EZ, UK
| | - Isabelle A Carré
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, West Midlands, UK.
| | - Gary D Bending
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, West Midlands, UK
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21
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Durán P, Ellis TJ, Thiergart T, Ågren J, Hacquard S. Climate drives rhizosphere microbiome variation and divergent selection between geographically distant Arabidopsis populations. THE NEW PHYTOLOGIST 2022; 236:608-621. [PMID: 35794837 DOI: 10.1111/nph.18357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Disentangling the contribution of climatic and edaphic factors to microbiome variation and local adaptation in plants requires an experimental approach to uncouple their effects and test for causality. We used microbial inocula, soil matrices and plant genotypes derived from two natural Arabidopsis thaliana populations in northern and southern Europe in an experiment conducted in climatic chambers mimicking seasonal changes in temperature, day length and light intensity of the home sites of the two genotypes. The southern A. thaliana genotype outperformed the northern genotype in the southern climate chamber, whereas the opposite was true in the northern climate chamber. Recipient soil matrix, but not microbial composition, affected plant fitness, and effects did not differ between genotypes. Differences between chambers significantly affected rhizosphere microbiome assembly, although these effects were small in comparison with the shifts induced by physicochemical differences between soil matrices. The results suggest that differences in seasonal changes in temperature, day length and light intensity between northern and southern Europe have strongly influenced adaptive differentiation between the two A. thaliana populations, whereas effects of differences in soil factors have been weak. By contrast, below-ground differences in soil characteristics were more important than differences in climate for rhizosphere microbiome differentiation.
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Affiliation(s)
- Paloma Durán
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- LIPME, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Castanet-Tolosan, 31326, France
| | - Thomas James Ellis
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden
- Gregor Mendel Institute of Molecular Plant Sciences, Austrian Academy of Sciences, Doktor-Bohr-Gasse 3, 1030, Vienna, Austria
| | - Thorsten Thiergart
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Jon Ågren
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden
| | - Stéphane Hacquard
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
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22
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Davis W, Endo M, Locke JCW. Spatially specific mechanisms and functions of the plant circadian clock. PLANT PHYSIOLOGY 2022; 190:938-951. [PMID: 35640123 PMCID: PMC9516738 DOI: 10.1093/plphys/kiac236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
Like many organisms, plants have evolved a genetic network, the circadian clock, to coordinate processes with day/night cycles. In plants, the clock is a pervasive regulator of development and modulates many aspects of physiology. Clock-regulated processes range from the correct timing of growth and cell division to interactions with the root microbiome. Recently developed techniques, such as single-cell time-lapse microscopy and single-cell RNA-seq, are beginning to revolutionize our understanding of this clock regulation, revealing a surprising degree of organ, tissue, and cell-type specificity. In this review, we highlight recent advances in our spatial view of the clock across the plant, both in terms of how it is regulated and how it regulates a diversity of output processes. We outline how understanding these spatially specific functions will help reveal the range of ways that the clock provides a fitness benefit for the plant.
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Affiliation(s)
- William Davis
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Motomu Endo
- Authors for correspondence: (M.E.); (J.C.W.L.)
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23
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Henríquez-Urrutia M, Spanner R, Olivares-Yánez C, Seguel-Avello A, Pérez-Lara R, Guillén-Alonso H, Winkler R, Herrera-Estrella AH, Canessa P, Larrondo LF. Circadian oscillations in Trichoderma atroviride and the role of core clock components in secondary metabolism, development, and mycoparasitism against the phytopathogen Botrytis cinerea. eLife 2022; 11:71358. [PMID: 35950750 PMCID: PMC9427114 DOI: 10.7554/elife.71358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
Circadian clocks are important for an individual’s fitness, and recent studies have underlined their role in the outcome of biological interactions. However, the relevance of circadian clocks in fungal–fungal interactions remains largely unexplored. We sought to characterize a functional clock in the biocontrol agent Trichoderma atroviride to assess its importance in the mycoparasitic interaction against the phytopathogen Botrytis cinerea. Thus, we confirmed the existence of circadian rhythms in T. atroviride, which are temperature-compensated and modulated by environmental cues such as light and temperature. Nevertheless, the presence of such molecular rhythms appears to be highly dependent on the nutritional composition of the media. Complementation of a clock null (Δfrq) Neurospora crassa strain with the T. atroviride-negative clock component (tafrq) restored core clock function, with the same period observed in the latter fungus, confirming the role of tafrq as a bona fide core clock component. Confrontation assays between wild-type and clock mutant strains of T. atroviride and B. cinerea, in constant light or darkness, revealed an inhibitory effect of light on T. atroviride’s mycoparasitic capabilities. Interestingly, when confrontation assays were performed under light/dark cycles, T. atroviride’s overgrowth capacity was enhanced when inoculations were at dawn compared to dusk. Deleting the core clock-negative element FRQ in B. cinerea, but not in T. atroviride, was vital for the daily differential phenotype, suggesting that the B. cinerea clock has a more significant influence on the result of this interaction. Additionally, we observed that T. atroviride clock components largely modulate development and secondary metabolism in this fungus, including the rhythmic production of distinct volatile organic compounds (VOCs). Thus, this study provides evidence on how clock components impact diverse aspects of T. atroviride lifestyle and how daily changes modulate fungal interactions and dynamics.
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Affiliation(s)
- Marlene Henríquez-Urrutia
- Molecular Genetics and Microbiology department, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rebecca Spanner
- Molecular Genetics and Microbiology department, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Consuelo Olivares-Yánez
- Millennium Science Initiative Program, Millennium Institute for Integrative Biology, Santiago, Chile
| | - Aldo Seguel-Avello
- Molecular Genetics and Microbiology department, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rodrigo Pérez-Lara
- Molecular Genetics and Microbiology department, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Hector Guillén-Alonso
- Department of Biotechnology and Biochemistry, Cinvestav Unidad Irapuato, Irapuato, Mexico
| | - Robert Winkler
- Department of Biotechnology and Biochemistry, Cinvestav Unidad Irapuato, Irapuato, Mexico
| | | | - Paulo Canessa
- Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago, Chile
| | - Luis F Larrondo
- Molecular Genetics and Microbiology department, Pontificia Universidad Católica de Chile, Santiago, Chile
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24
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Luo X, Yang Y, Xie S, Wang W, Li N, Wen C, Zhu S, Chen L. Drying and rewetting induce changes in biofilm characteristics and the subsequent release of metal ions. JOURNAL OF HAZARDOUS MATERIALS 2022; 433:128832. [PMID: 35390615 DOI: 10.1016/j.jhazmat.2022.128832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/15/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Drying and rewetting can markedly influence the microbial structure and function of river biofilm communities and potentially result in the release of metal ions from biofilms containing metals. However, little information is available on the response of metal-enriched biofilms to drying and rewetting over time. In this study, natural biofilms were allowed to develop in four rotating annular bioreactors for 2-11 weeks, followed by drying for 5 days and rewetting for another 5 days. Subsequently, we assessed Zn, Cd, and As desorption from the biofilms and other related parameters (microbial community structure, biofilm morphology, enzyme activity, and surface components as well as characteristics). High-throughput sequencing of the 16 S rRNA gene and confocal laser scanning microscopy revealed that the biofilm architecture and bacterial communities were distinct in different growth phases and under drying and rewetting conditions (permutational multivariate analysis of variance; p = 0.001). Proteobacteria was the dominant bacterial phylum, accounting for 69.7-90.1% of the total content. Kinetic experiments revealed that the drying and rewetting process increased metal desorption from the biofilm matrix. The desorption of heavy metals was affected by the age of the biofilm, with the maximum amount of metal ions released from 2-week-old biofilms (one-way ANOVA, Zn: p < 0.001; Cd: p = 0.008; As: p < 0.001). The modifications in biofilm properties and decreased diversity of the bacterial community (paired t-test, p < 0.05) after drying and rewetting decreased the number of specific binding sites for metal ions. In addition, negatively charged arsenate and other anions in the liquid phase could compete with As ions for adsorption sites to promote the release of As(V) and/or reductive desorption of As(III). The results of this study and their interpretation are expected to help refine the behaviors of heavy metals in the aquatic environment.
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Affiliation(s)
- Xia Luo
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China.
| | - Yuanhao Yang
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China
| | - Shanshan Xie
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China
| | - Wenwen Wang
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China
| | - Nihong Li
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China
| | - Chen Wen
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China
| | - Shijun Zhu
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China
| | - Liqiang Chen
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China.
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25
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Spatiotemporal Heterogeneity and Intragenus Variability in Rhizobacterial Associations with
Brassica rapa
Growth. mSystems 2022; 7:e0006022. [PMID: 35575562 PMCID: PMC9239066 DOI: 10.1128/msystems.00060-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial communities in the rhizosphere are distinct from those in soils and are influenced by stochastic and deterministic processes during plant development. These communities contain bacteria capable of promoting growth in host plants through various strategies. While some interactions are characterized in mechanistic detail using model systems, others can be inferred from culture-independent methods, such as 16S amplicon sequencing, using machine learning methods that account for this compositional data type. To characterize assembly processes and identify community members associated with plant growth amid the spatiotemporal variability of the rhizosphere, we grew Brassica rapa in a greenhouse time series with amended and reduced microbial treatments. Inoculation with a native soil community increased plant leaf area throughout the time series by up to 28%. Despite identifying spatially and temporally variable amplicon sequence variants (ASVs) in both treatments, inoculated communities were more highly connected and assembled more deterministically overall. Using a generalized linear modeling approach controlling for spatial variability, we identified 43 unique ASVs that were positively or negatively associated with leaf area, biomass, or growth rates across treatments and time stages. ASVs of the genus Flavobacterium dominated rhizosphere communities and showed some of the strongest positive and negative correlations with plant growth. Members of this genus, and growth-associated ASVs more broadly, exhibited variable connectivity in networks independent of growth association (positive or negative). These findings suggest host-rhizobacterial interactions vary temporally at narrow taxonomic scales and present a framework for identifying rhizobacteria that may work independently or in concert to improve agricultural yields. IMPORTANCE The rhizosphere, the zone of soil surrounding plant roots, is a hot spot for microbial activity, hosting bacteria capable of promoting plant growth in ways like increasing nutrient availability or fighting plant pathogens. This microbial system is highly diverse and most bacteria are unculturable, so to identify specific bacteria associated with plant growth, we used culture-independent community DNA sequencing combined with machine learning techniques. We identified 43 specific bacterial sequences associated with the growth of the plant Brassica rapa in different soil microbial treatments and at different stages of plant development. Most associations between bacterial abundances and plant growth were positive, although similar bacterial groups sometimes had different effects on growth. Why this happens will require more research, but overall, this study provides a way to identify native bacteria from plant roots that might be isolated and applied to boost agricultural yields.
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26
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Achom M, Roy P, Lagunas B, Picot E, Richards L, Bonyadi-Pour R, Pardal AJ, Baxter L, Richmond BL, Aschauer N, Fletcher EM, Rowson M, Blackwell J, Rich-Griffin C, Mysore KS, Wen J, Ott S, Carré IA, Gifford ML. Plant circadian clock control of Medicago truncatula nodulation via regulation of nodule cysteine-rich peptides. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2142-2156. [PMID: 34850882 PMCID: PMC8982390 DOI: 10.1093/jxb/erab526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 11/30/2021] [Indexed: 06/13/2023]
Abstract
Legumes house nitrogen-fixing endosymbiotic rhizobia in specialized polyploid cells within root nodules, which undergo tightly regulated metabolic activity. By carrying out expression analysis of transcripts over time in Medicago truncatula nodules, we found that the circadian clock enables coordinated control of metabolic and regulatory processes linked to nitrogen fixation. This involves the circadian clock-associated transcription factor LATE ELONGATED HYPOCOTYL (LHY), with lhy mutants being affected in nodulation. Rhythmic transcripts in root nodules include a subset of nodule-specific cysteine-rich peptides (NCRs) that have the LHY-bound conserved evening element in their promoters. Until now, studies have suggested that NCRs act to regulate bacteroid differentiation and keep the rhizobial population in check. However, these conclusions came from the study of a few members of this very large gene family that has complex diversified spatio-temporal expression. We suggest that rhythmic expression of NCRs may be important for temporal coordination of bacterial activity with the rhythms of the plant host, in order to ensure optimal symbiosis.
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Affiliation(s)
- Mingkee Achom
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Proyash Roy
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Beatriz Lagunas
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Emma Picot
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Luke Richards
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Roxanna Bonyadi-Pour
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Alonso J Pardal
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Laura Baxter
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Bethany L Richmond
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Nadine Aschauer
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Eleanor M Fletcher
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Monique Rowson
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Joseph Blackwell
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Charlotte Rich-Griffin
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Kirankumar S Mysore
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401, USA
| | - Jiangqi Wen
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401, USA
| | - Sascha Ott
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Isabelle A Carré
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Miriam L Gifford
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
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27
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Van Syoc E, Albeke SE, Scasta JD, van Diepen LT. Quantifying the immediate response of the soil microbial community to different grazing intensities on irrigated pastures. AGRICULTURE, ECOSYSTEMS & ENVIRONMENT 2022; 326:107805. [PMID: 35068628 PMCID: PMC8782393 DOI: 10.1016/j.agee.2021.107805] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Grazing is known to affect soil microbial communities, nutrient cycling, and forage quantity and quality over time. However, a paucity of information exists for the immediate changes in the soil physicochemical and microbial environment in response to different grazing strategies. Soil microbes drive nutrient cycling and are involved in plant-soil-microbe relationships, making them potentially vulnerable to plant-driven changes in the soil environment caused by grazing. To test the hypothesis that variable grazing intensities modulate immediate effects on the soil microbial community, we conducted a grazing trial of three management approaches; high-intensity, short-duration grazing (HDG), low-intensity, medium-duration grazing (LDG), and no grazing (NG). Soil and vegetation samples were collected before grazing and 24 hours, 1 week, and 4 weeks after HDG grazing ended. Soil labile carbon (C) and nitrogen (N) pools, vegetation biomass, and soil microbial diversity and functional traits were determined, including extracellular enzymatic assays and high-throughput sequencing of the bacterial 16S rRNA and fungal ITS2 regions. We found that labile soil C and inorganic N increased following the LDG grazing while C-cycling extracellular enzymatic activities increased in response to HDG grazing but both total extracellular enzymatic activity profiles and soil abiotic profiles were mostly affected by temporal fluxes. The soil fungal community composition was strongly affected by the interaction of sampling time and grazing treatment, while the soil bacterial community composition was largely affected by sampling time with a lesser impact from grazing treatment. We identified several key fungal taxa that may influence immediate responses to grazing and modulate plant-soil-microbe interactions. There was strong evidence of temporal influences on soil biogeochemical variables and the soil microbiome, even within our narrow sampling scheme. Our results indicate that the soil ecosystem is dynamic and responsive to different grazing strategies within very short time scales, showing the need for further research to understand plant-soil-microbe interactions and how these feedback mechanisms can inform sustainable land management.
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Affiliation(s)
- Emily Van Syoc
- Department of Ecosystem Science and Management, University of Wyoming, Wyoming, USA
- Integrative & Biomedical Physiology and Clinical & Translational Sciences Dual-Title Ph.D. Program, The Pennsylvania State University, Pennsylvania, USA
| | - Shannon E. Albeke
- Wyoming Geographic Information Science Center, University of Wyoming, Wyoming, USA
| | - John Derek Scasta
- Department of Ecosystem Science and Management, University of Wyoming, Wyoming, USA
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28
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Ponsford JCB, Hubbard CJ, Harrison JG, Maignien L, Buerkle CA, Weinig C. Whole-Genome Duplication and Host Genotype Affect Rhizosphere Microbial Communities. mSystems 2022; 7:e0097321. [PMID: 35014873 PMCID: PMC8751390 DOI: 10.1128/msystems.00973-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/15/2021] [Indexed: 01/04/2023] Open
Abstract
The composition of microbial communities found in association with plants is influenced by host phenotype and genotype. However, the ways in which specific genetic architectures of host plants shape microbiomes are unknown. Genome duplication events are common in the evolutionary history of plants and influence many important plant traits, and thus, they may affect associated microbial communities. Using experimentally induced whole-genome duplication (WGD), we tested the effect of WGD on rhizosphere bacterial communities in Arabidopsis thaliana. We performed 16S rRNA amplicon sequencing to characterize differences between microbiomes associated with specific host genetic backgrounds (Columbia versus Landsberg) and ploidy levels (diploid versus tetraploid). We modeled relative abundances of bacterial taxa using a hierarchical Bayesian approach. We found that host genetic background and ploidy level affected rhizosphere community composition. We then tested to what extent microbiomes derived from a specific genetic background or ploidy level affected plant performance by inoculating sterile seedlings with microbial communities harvested from a prior generation. We found a negative effect of the tetraploid Columbia microbiome on growth of all four plant genetic backgrounds. These findings suggest an interplay between host genetic background and ploidy level and bacterial community assembly with potential ramifications for host fitness. Given the prevalence of ploidy-level variation in both wild and managed plant populations, the effects on microbiomes of this aspect of host genetic architecture could be a widespread driver of differences in plant microbiomes. IMPORTANCE Plants influence the composition of their associated microbial communities, yet the underlying host-associated genetic determinants are typically unknown. Genome duplication events are common in the evolutionary history of plants and affect many plant traits. Using Arabidopsis thaliana, we characterized how whole-genome duplication affected the composition of rhizosphere bacterial communities and how bacterial communities associated with two host plant genetic backgrounds and ploidy levels affected subsequent plant growth. We observed an interaction between ploidy level and genetic background that affected both bacterial community composition and function. This research reveals how genome duplication, a widespread genetic feature of both wild and crop plant species, influences bacterial assemblages and affects plant growth.
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Affiliation(s)
| | - Charley J. Hubbard
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA
- Program in Ecology, University of Wyoming, Laramie, Wyoming, USA
| | | | - Lois Maignien
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, Massachusetts, USA
- Laboratory of Microbiology of Extreme Environments, UMR 6197, Institut Européen de la Mer, Université de Bretagne Occidentale, Plouzane, France
| | - C. Alex Buerkle
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA
- Program in Ecology, University of Wyoming, Laramie, Wyoming, USA
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA
- Program in Ecology, University of Wyoming, Laramie, Wyoming, USA
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, USA
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29
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Ruocco M, Barrote I, Hofman JD, Pes K, Costa MM, Procaccini G, Silva J, Dattolo E. Daily Regulation of Key Metabolic Pathways in Two Seagrasses Under Natural Light Conditions. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.757187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The circadian clock is an endogenous time-keeping mechanism that enables organisms to adapt to external environmental cycles. It produces rhythms of plant metabolism and physiology, and interacts with signaling pathways controlling daily and seasonal environmental responses through gene expression regulation. Downstream metabolic outputs, such as photosynthesis and sugar metabolism, besides being affected by the clock, can also contribute to the circadian timing itself. In marine plants, studies of circadian rhythms are still way behind in respect to terrestrial species, which strongly limits the understanding of how they coordinate their physiology and energetic metabolism with environmental signals at sea. Here, we provided a first description of daily timing of key core clock components and clock output pathways in two seagrass species, Cymodocea nodosa and Zostera marina (order Alismatales), co-occurring at the same geographic location, thus exposed to identical natural variations in photoperiod. Large differences were observed between species in the daily timing of accumulation of transcripts related to key metabolic pathways, such as photosynthesis and sucrose synthesis/transport, highlighting the importance of intrinsic biological, and likely ecological attributes of the species in determining the periodicity of functions. The two species exhibited a differential sensitivity to light-to-dark and dark-to-light transition times and could adopt different growth timing based on a differential strategy of resource allocation and mobilization throughout the day, possibly coordinated by the circadian clock. This behavior could potentially derive from divergent evolutionary adaptations of the species to their bio-geographical range of distributions.
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30
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Hotta CT. From crops to shops: how agriculture can use circadian clocks. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7668-7679. [PMID: 34363668 DOI: 10.1093/jxb/erab371] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/06/2021] [Indexed: 06/13/2023]
Abstract
Knowledge about environmental and biological rhythms can lead to more sustainable agriculture in a climate crisis and resource scarcity scenario. When rhythms are considered, more efficient and cost-effective management practices can be designed for food production. The circadian clock is used to anticipate daily and seasonal changes, organize the metabolism during the day, integrate internal and external signals, and optimize interaction with other organisms. Plants with a circadian clock in synchrony with the environment are more productive and use fewer resources. In medicine, chronotherapy is used to increase drug efficacy, reduce toxicity, and understand the health effects of circadian clock disruption. Here, I show evidence of why circadian biology can be helpful in agriculture. However, as evidence is scattered among many areas, they frequently lack field testing, integrate poorly with other rhythms, or suffer inconsistent results. These problems can be mitigated if researchers of different areas start collaborating under a new study area-circadian agriculture.
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Affiliation(s)
- Carlos Takeshi Hotta
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
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31
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Miller SL, Gans MR. Largely invariant communities of bacterial endophytes in the nonphotosynthetic mycoheterotrophic plant Pterospora andromedea. AMERICAN JOURNAL OF BOTANY 2021; 108:2208-2219. [PMID: 34606096 DOI: 10.1002/ajb2.1754] [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: 08/10/2020] [Revised: 07/21/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Mycoheterotrophic plants rely on fungi to obtain their carbon requirements. Recent experiments demonstrated the presence of endophytic bacteria associated with mycoheterotrophs. Although mycoheterotrophs show high specificity for their fungal partners, it is not known whether they also show high specificity for associated bacteria or whether the bacteria have a definite function in the symbiosis. METHODS Two 16S rRNA sequencing experiments were designed to explore endophytic microbial community composition and function in root ball fractions of the mycoheterotroph Pterospora andromedea (Ericaceae), and rhizosphere soil and control soil 5 m away from each plant. One experiment compared microbial assemblages in fractions of six plants to those in rhizosphere and control soil samples. Another experiment documented bacterial endophyte diversity in root balls of 97 plants from across North America. RESULTS Soil samples were similar in bacterial community structure but were significantly more diverse and less consistently structured than were bacterial communities within root balls. The proportion of endophytic bacterial species varied slightly but not their community composition despite differences in P. andromedea lineage, geography, conifer species, and fungi. Predictive metagenomic profiling of the endophytes in P. andromedea-only root ball fractions showed many of the bacterial endophytes likely function in N-metabolism and N-fixation. CONCLUSIONS Our results document a consistent and largely invariant community of endophytic bacteria in P. andromedea across biotic and abiotic environmental conditions at a continental scale. It is unknown what role these bacteria may play in the quad-partite symbiotic network centered on P. andromedea; however, the predictive metagenomic profiling suggests a possible function in N-metabolism or N-fixation. Discovery of a ubiquitous community of endophytic bacteria with a putative function centered on N-metabolism or N-fixation could have a previously unrecognized impact on understanding of mycoheterotroph ecophysiology.
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Affiliation(s)
- Steven L Miller
- Department of Botany, University of Wyoming, 1000 University Avenue, Laramie, WY, 82071, USA
| | - Maya R Gans
- Department of Botany, University of Wyoming, 1000 University Avenue, Laramie, WY, 82071, USA
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32
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Lu T, Zhang Z, Li Y, Zhang Q, Cui H, Sun L, Peijnenburg WJGM, Peñuelas J, Zhu L, Zhu YG, Chen J, Qian H. Does biological rhythm transmit from plants to rhizosphere microbes? Environ Microbiol 2021; 23:6895-6906. [PMID: 34658124 DOI: 10.1111/1462-2920.15820] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 10/07/2021] [Indexed: 11/28/2022]
Abstract
Plant physiological and metabolic processes are modulated by rhythmic gene expression in a large part. Meanwhile, plants are also regulated by rhizosphere microorganisms, which are fed by root exudates and provide beneficial functions to their plant host. Whether the biorhythms in plants would transfer to the rhizosphere microbial community is still uncertain and their intricate connection remains poorly understood. Here, we investigated the role of the Arabidopsis circadian clock in shaping the rhizosphere microbial community using wild-type plants and clock mutants (cca1-1 and toc1-101) with transcriptomic, metabolomic and 16S rRNA gene sequencing analysis throughout a 24-h period. Deficiencies of the central circadian clock led to abnormal diurnal rhythms for thousands of expressed genes and dozens of root exudates. The bacterial community failed to follow obvious patterns in the 24-h period, and there was lack of coordination with plant growth in the clock mutants. Our results suggest that the robust rhythmicity of genes and root exudation due to circadian clock in plants is an important driving force for the positive succession of rhizosphere communities, which will feedback on plant development.
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Affiliation(s)
- Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - Yan Li
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - Hengzheng Cui
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - Liwei Sun
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - W J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, Leiden, 2300 RA, The Netherlands
| | - Josep Peñuelas
- CSIC, Global Ecology Unit, CREAF- CSIC-UAB, Barcelona, Catalonia, Spain.,CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
| | - Lizhong Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China
| | - Jianmeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
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Nimmo HG, Laird J. Arabidopsis thaliana PRR7 Provides Circadian Input to the CCA1 Promoter in Shoots but not Roots. FRONTIERS IN PLANT SCIENCE 2021; 12:750367. [PMID: 34733306 PMCID: PMC8559795 DOI: 10.3389/fpls.2021.750367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/23/2021] [Indexed: 05/24/2023]
Abstract
The core of the plant circadian clock involves multiple interlocking gene expression loops and post-translational controls along with inputs from light and metabolism. The complexity of the interactions is such that few specific functions can be ascribed to single components. In previous work, we reported differences in the operation of the clocks in Arabidopsis shoots and roots, including the effects of mutations of key clock components. Here, we have used luciferase imaging to study prr7 mutants expressing CCA1::LUC and GI::LUC markers. In mature shoots expressing CCA1::LUC, loss of PRR7 radically altered behaviour in light:dark cycles and caused loss of rhythmicity in constant light but had little effect on roots. In contrast, in mature plants expressing GI::LUC, loss of PRR7 had little effect in light:dark cycles but in constant light increased the circadian period in shoots and reduced it in roots. We conclude that most or all of the circadian input to the CCA1 promoter in shoots is mediated by PRR7 and that loss of PRR7 has organ-specific effects. The results emphasise the differences in operation of the shoot and root clocks, and the importance of studying clock mutants in both light:dark cycles and constant light.
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O'Brien AM, Ginnan NA, Rebolleda-Gómez M, Wagner MR. Microbial effects on plant phenology and fitness. AMERICAN JOURNAL OF BOTANY 2021; 108:1824-1837. [PMID: 34655479 DOI: 10.1002/ajb2.1743] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
Plant development and the timing of developmental events (phenology) are tightly coupled with plant fitness. A variety of internal and external factors determine the timing and fitness consequences of these life-history transitions. Microbes interact with plants throughout their life history and impact host phenology. This review summarizes current mechanistic and theoretical knowledge surrounding microbe-driven changes in plant phenology. Overall, there are examples of microbes impacting every phenological transition. While most studies have focused on flowering time, microbial effects remain important for host survival and fitness across all phenological phases. Microbe-mediated changes in nutrient acquisition and phytohormone signaling can release plants from stressful conditions and alter plant stress responses inducing shifts in developmental events. The frequency and direction of phenological effects appear to be partly determined by the lifestyle and the underlying nature of a plant-microbe interaction (i.e., mutualistic or pathogenic), in addition to the taxonomic group of the microbe (fungi vs. bacteria). Finally, we highlight biases, gaps in knowledge, and future directions. This biotic source of plasticity for plant adaptation will serve an important role in sustaining plant biodiversity and managing agriculture under the pressures of climate change.
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Affiliation(s)
- Anna M O'Brien
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Nichole A Ginnan
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | - María Rebolleda-Gómez
- Department of Ecology and Evolutionary Biology, University of California-Irvine, Irvine, CA, USA
| | - Maggie R Wagner
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, USA
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Abstract
Circadian clocks are important to much of life on Earth and are of inherent interest to humanity, implicated in fields ranging from agriculture and ecology to developmental biology and medicine. New techniques show that it is not simply the presence of clocks, but coordination between them that is critical for complex physiological processes across the kingdoms of life. Recent years have also seen impressive advances in synthetic biology to the point where parallels can be drawn between synthetic biological and circadian oscillators. This review will emphasize theoretical and experimental studies that have revealed a fascinating dichotomy of coupling and heterogeneity among circadian clocks. We will also consolidate the fields of chronobiology and synthetic biology, discussing key design principles of their respective oscillators.
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Affiliation(s)
- Chris N Micklem
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK.,The Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CH3 0HE, UK
| | - James C W Locke
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
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Light exposure mediates circadian rhythms of rhizosphere microbial communities. THE ISME JOURNAL 2021; 15:2655-2664. [PMID: 33746202 PMCID: PMC8397761 DOI: 10.1038/s41396-021-00957-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 02/01/2023]
Abstract
Microbial community circadian rhythms have a broad influence on host health and even though light-induced environmental fluctuations could regulate microbial communities, the contribution of light to the circadian rhythms of rhizosphere microbial communities has received little attention. To address this gap, we monitored diel changes in the microbial communities in rice (Oryza sativa L.) rhizosphere soil under light-dark and constant dark regimes, identifying microbes with circadian rhythms caused by light exposure and microbial circadian clocks, respectively. While rhizosphere microbial communities displayed circadian rhythms under light-dark and constant dark regimes, taxa possessing circadian rhythms under the two conditions were dissimilar. Light exposure concealed microbial circadian clocks as a regulatory driver, leading to fewer ecological niches in light versus dark communities. These findings disentangle regulation mechanisms for circadian rhythms in the rice rhizosphere microbial communities and highlight the role of light-induced regulation of rhizosphere microbial communities.
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Novel Microdialysis Technique Reveals a Dramatic Shift in Metabolite Secretion during the Early Stages of the Interaction between the Ectomycorrhizal Fungus Pisolithus microcarpus and Its Host Eucalyptus grandis. Microorganisms 2021; 9:microorganisms9091817. [PMID: 34576712 PMCID: PMC8465077 DOI: 10.3390/microorganisms9091817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/23/2021] [Accepted: 08/23/2021] [Indexed: 12/28/2022] Open
Abstract
The colonisation of tree roots by ectomycorrhizal (ECM) fungi is the result of numerous signalling exchanges between organisms, many of which occur before physical contact. However, information is lacking about these exchanges and the compounds that are secreted by each organism before contact. This is in part due to a lack of low disturbance sampling methods with sufficient temporal and spatial resolution to capture these exchanges. Using a novel in situ microdialysis approach, we sampled metabolites released from Eucalyptus grandis and Pisolithus microcarpus independently and during indirect contact over a 48-h time-course using UPLC-MS. A total of 560 and 1530 molecular features (MFs; ESI- and ESI+ respectively) were identified with significant differential abundance from control treatments. We observed that indirect contact between organisms altered the secretion of MFs to produce a distinct metabolomic profile compared to either organism independently. Many of these MFs were produced within the first hour of contact and included several phenylpropanoids, fatty acids and organic acids. These findings show that the secreted metabolome, particularly of the ECM fungus, can rapidly shift during the early stages of pre-symbiotic contact and highlight the importance of observing these early interactions in greater detail. We present microdialysis as a useful tool for examining plant–fungal signalling with high temporal resolution and with minimal experimental disturbance.
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Wang L, Zhou A, Li J, Yang M, Bu F, Ge L, Chen L, Huang W. Circadian rhythms driving a fast-paced root clock implicate species-specific regulation in Medicago truncatula. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1537-1554. [PMID: 34009694 DOI: 10.1111/jipb.13138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/13/2021] [Indexed: 06/12/2023]
Abstract
Plants have a hierarchical circadian structure comprising multiple tissue-specific oscillators that operate at different speeds and regulate the expression of distinct sets of genes in different organs. However, the identity of the genes differentially regulated by the circadian clock in different organs, such as roots, and how their oscillations create functional specialization remain unclear. Here, we profiled the diurnal and circadian landscapes of the shoots and roots of Medicago truncatula and identified the conserved regulatory sequences contributing to transcriptome oscillations in each organ. We found that the light-dark cycles strongly affect the global transcriptome oscillation in roots, and many clock genes oscillate only in shoots. Moreover, many key genes involved in nitrogen fixation are regulated by circadian rhythms. Surprisingly, the root clock runs faster than the shoot clock, which is contrary to the hierarchical circadian structure showing a slow-paced root clock in both detached and intact Arabidopsis thaliana (L.) Heynh. roots. Our result provides important clues about the species-specific circadian regulatory mechanism, which is often overlooked, and possibly coordinates the timing between shoots and roots independent of the current prevailing model.
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Affiliation(s)
- Liping Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Anqi Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Mingkang Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Fan Bu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Liangfa Ge
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, 510642, China
| | - Liang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Wei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
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39
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Dibner RR, Weaver AM, Brock MT, Custer GF, Morrison HG, Maignien L, Weinig C. Time outweighs the effect of host developmental stage on microbial community composition. FEMS Microbiol Ecol 2021; 97:6321163. [PMID: 34259857 DOI: 10.1093/femsec/fiab102] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/12/2021] [Indexed: 01/04/2023] Open
Abstract
Thousands of microbial taxa in the soil form symbioses with host plants, and due to their contribution to plant performance, these microbes are often considered an extension of the host genome. Given microbial effects on host performance, it is important to understand factors that govern microbial community assembly. Host developmental stage could affect rhizosphere microbial diversity while, alternatively, microbial assemblages could change simply as a consequence of time and the opportunity for microbial succession. Previous studies suggest that rhizosphere microbial assemblages shift across plant developmental stages, but time since germination is confounded with developmental stage. We asked how elapsed time and potential microbial succession relative to host development affected microbial diversity in the rhizosphere using monogenic flowering-time mutants of Arabidopsis thaliana. Under our experimental design, different developmental stages were present among host genotypes after the same amount of time following germination, e.g. at 76 days following germination some host genotypes were flowering while others were fruiting or senescing. We found that elapsed time was a strong predictor of microbial diversity whereas there were few differences among developmental stages. Our results support the idea that time and, likely, microbial succession more strongly affect microbial community assembly than host developmental stage.
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Affiliation(s)
- Reilly R Dibner
- University of Wyoming, Botany, USA; University of Wyoming, EPSCoR, USA
| | - A Monique Weaver
- The University of Iowa Roy J and Lucille A Carver College of Medicine, Molecular Otolaryngology and Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, USA; The University of Iowa, Interdisciplinary PhD Program in Genetics, USA
| | | | - Gordon F Custer
- University of Wyoming, Department of Ecosystem Science and Management, USA; University of Wyoming, Program in Ecology, USA
| | - Hilary G Morrison
- Marine Biological Laboratory, Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, USA
| | - Lois Maignien
- UBO, CNRS, IFREMER, France; Marine Biological Laboratory, Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, USA
| | - Cynthia Weinig
- University of Wyoming, Department of Botany, USA; University of Wyoming, Program in Ecology, USA; University of Wyoming, Department of Molecular Biology, USA
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40
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Assessing the potential to harness the microbiome through plant genetics. Curr Opin Biotechnol 2021; 70:167-173. [PMID: 34126329 DOI: 10.1016/j.copbio.2021.05.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/07/2021] [Accepted: 05/23/2021] [Indexed: 12/17/2022]
Abstract
Microbial communities are influenced by a complex system of host effects, including traits involved in physical barriers, immunity, hormones, metabolisms and nutrient homeostasis. Variation of host control within species is governed by many genes of small effect and is sensitive to biotic and abiotic environments. On the flip side, these host impacts seem targeted on particular microbial species, with that impact percolating through the microbial community. There is not yet evidence that the nature and strength of these interactions differs between fungal and bacterial communities, or among different compartments of the plant. The challenge of deciphering how systems of host traits impact systems of microbial associates is vast but holds promise for developing novel strategies to improve plant health.
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41
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Steed G, Ramirez DC, Hannah MA, Webb AAR. Chronoculture, harnessing the circadian clock to improve crop yield and sustainability. Science 2021; 372:372/6541/eabc9141. [PMID: 33926926 DOI: 10.1126/science.abc9141] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human health is dependent on a plentiful and nutritious supply of food, primarily derived from crop plants. Rhythmic supply of light as a result of the day and night cycle led to the evolution of circadian clocks that modulate most plant physiology, photosynthesis, metabolism, and development. To regulate crop traits and adaptation, breeders have indirectly selected for variation at circadian genes. The pervasive impact of the circadian system on crops suggests that future food production might be improved by modifying circadian rhythms, engineering the timing of transgene expression, and applying agricultural treatments at the most effective time of day. We describe the applied research required to take advantage of circadian biology in agriculture to increase production and reduce inputs.
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Affiliation(s)
- Gareth Steed
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Dora Cano Ramirez
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Matthew A Hannah
- BASF, BBCC-Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Gent, Belgium
| | - Alex A R Webb
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK.
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42
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Durr J, Reyt G, Spaepen S, Hilton S, Meehan C, Qi W, Kamiya T, Flis P, Dickinson HG, Feher A, Shivshankar U, Pavagadhi S, Swarup S, Salt D, Bending GD, Gutierrez-Marcos J. A Novel Signaling Pathway Required for Arabidopsis Endodermal Root Organization Shapes the Rhizosphere Microbiome. PLANT & CELL PHYSIOLOGY 2021; 62:248-261. [PMID: 33475132 PMCID: PMC8112839 DOI: 10.1093/pcp/pcaa170] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The Casparian strip (CS) constitutes a physical diffusion barrier to water and nutrients in plant roots, which is formed by the polar deposition of lignin polymer in the endodermis tissue. The precise pattern of lignin deposition is determined by the scaffolding activity of membrane-bound Casparian Strip domain proteins (CASPs), but little is known of the mechanism(s) directing this process. Here, we demonstrate that Endodermis-specific Receptor-like Kinase 1 (ERK1) and, to a lesser extent, ROP Binding Kinase1 (RBK1) are also involved in regulating CS formation, with the former playing an essential role in lignin deposition as well as in the localization of CASP1. We show that ERK1 is localized to the cytoplasm and nucleus of the endodermis and that together with the circadian clock regulator, Time for Coffee (TIC), forms part of a novel signaling pathway necessary for correct CS organization and suberization of the endodermis, with their single or combined loss of function resulting in altered root microbiome composition. In addition, we found that other mutants displaying defects in suberin deposition at the CS also display altered root exudates and microbiome composition. Thus, our work reveals a complex network of signaling factors operating within the root endodermis that establish both the CS diffusion barrier and influence the microbial composition of the rhizosphere.
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Affiliation(s)
- Julius Durr
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Guilhem Reyt
- Division of Plant and Crop Sciences, Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Stijn Spaepen
- Department of Plant Microbe Interactions & Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Carl-von-Linn�-Weg 10, K�ln 50829, Germany
- Centre for Microbial and Plant Genetics, Leuven Institute for Beer Research, University of Leuven, Gaston Geenslaan 1 B-3001, Belgium
| | - Sally Hilton
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Cathal Meehan
- Division of Plant and Crop Sciences, Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Wu Qi
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Takehiro Kamiya
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Paulina Flis
- Division of Plant and Crop Sciences, Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Hugh G Dickinson
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Attila Feher
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, Temesv�ri krt. 62, Szeged H-6726, Hungary
| | - Umashankar Shivshankar
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| | - Shruti Pavagadhi
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| | - Sanjay Swarup
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| | - David Salt
- Division of Plant and Crop Sciences, Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Gary D Bending
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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Ma X, Li H, Zhang J, Shen J. Spatiotemporal Pattern of Acid Phosphatase Activity in Soils Cultivated With Maize Sensing to Phosphorus-Rich Patches. FRONTIERS IN PLANT SCIENCE 2021; 12:650436. [PMID: 33927739 PMCID: PMC8076754 DOI: 10.3389/fpls.2021.650436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
AIMS Acid phosphatase (APase) secretion by roots allows plants to mobilize organic phosphorus (P) in low P soils. However, the spatiotemporal dynamics of soil APase activity in response to P-rich patches remain unclear. METHODS Here, we grew maize in rhizoboxes with two contrasting soil types and different localized P supplies. In situ soil zymography was applied to examine the spatial-temporal variation of APase activity. RESULTS We found P-rich patches can induce the secretion of APase from roots, indicating that even mineral P fertilizers were localized apply, mobilization of soil organic P by roots can also be enhanced; APase hotspot areas and APase activities in the rhizosphere and bulk soil of the same rhizobox showed opposite diurnal rhythms across the whole soil profile. The APase hotspot area was 10-140% larger at noon than at midnight in the rhizosphere, which is consistent with the diurnal rhythm of photosynthesis. In contrast, in bulk soil, the area was 18-200% larger at midnight than at noon, which led to spatiotemporal niche differentiation with regard to the utilization of soil organic P; this alleviated competition between plants and soil microorganisms. CONCLUSION Our findings showed that APase secretion of roots was plastic in P-rich patches and showed an opposite diurnal rhythm with soil microorganisms in bulk soil.
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Affiliation(s)
- Xiaofan Ma
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Haigang Li
- Inner Mongolia Key Laboratory of Soil Quality and Nutrient Resources, Key Laboratory of Grassland Resource (IMAU), Ministry of Education, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Junling Zhang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Jianbo Shen
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
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44
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Xu L, Pierroz G, Wipf HML, Gao C, Taylor JW, Lemaux PG, Coleman-Derr D. Holo-omics for deciphering plant-microbiome interactions. MICROBIOME 2021; 9:69. [PMID: 33762001 PMCID: PMC7988928 DOI: 10.1186/s40168-021-01014-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/02/2021] [Indexed: 05/02/2023]
Abstract
Host-microbiome interactions are recognized for their importance to host health. An improved understanding of the molecular underpinnings of host-microbiome relationships will advance our capacity to accurately predict host fitness and manipulate interaction outcomes. Within the plant microbiome research field, unlocking the functional relationships between plants and their microbial partners is the next step to effectively using the microbiome to improve plant fitness. We propose that strategies that pair host and microbial datasets-referred to here as holo-omics-provide a powerful approach for hypothesis development and advancement in this area. We discuss several experimental design considerations and present a case study to highlight the potential for holo-omics to generate a more holistic perspective of molecular networks within the plant microbiome system. In addition, we discuss the biggest challenges for conducting holo-omics studies; specifically, the lack of vetted analytical frameworks, publicly available tools, and required technical expertise to process and integrate heterogeneous data. Finally, we conclude with a perspective on appropriate use-cases for holo-omics studies, the need for downstream validation, and new experimental techniques that hold promise for the plant microbiome research field. We argue that utilizing a holo-omics approach to characterize host-microbiome interactions can provide important opportunities for broadening system-level understandings and significantly inform microbial approaches to improving host health and fitness. Video abstract.
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Affiliation(s)
- Ling Xu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Grady Pierroz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Heidi M.-L. Wipf
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Cheng Gao
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Peggy G. Lemaux
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Devin Coleman-Derr
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
- Plant Gene Expression Center, USDA-ARS, Albany, CA USA
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45
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Marín O, González B, Poupin MJ. From Microbial Dynamics to Functionality in the Rhizosphere: A Systematic Review of the Opportunities With Synthetic Microbial Communities. FRONTIERS IN PLANT SCIENCE 2021; 12:650609. [PMID: 34149752 PMCID: PMC8210828 DOI: 10.3389/fpls.2021.650609] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/15/2021] [Indexed: 05/07/2023]
Abstract
Synthetic microbial communities (SynComs) are a useful tool for a more realistic understanding of the outcomes of multiple biotic interactions where microbes, plants, and the environment are players in time and space of a multidimensional and complex system. Toward a more in-depth overview of the knowledge that has been achieved using SynComs in the rhizosphere, a systematic review of the literature on SynComs was performed to identify the overall rationale, design criteria, experimental procedures, and outcomes of in vitro or in planta tests using this strategy. After an extensive bibliography search and a specific selection process, a total of 30 articles were chosen for further analysis, grouping them by their reported SynCom size. The reported SynComs were constituted with a highly variable number of members, ranging from 3 to 190 strains, with a total of 1,393 bacterial isolates, where the three most represented phyla were Proteobacteria, Actinobacteria, and Firmicutes. Only four articles did not reference experiments with SynCom on plants, as they considered only microbial in vitro studies, whereas the others chose different plant models and plant-growth systems; some of them are described and reviewed in this article. Besides, a discussion on different approaches (bottom-up and top-down) to study the microbiome role in the rhizosphere is provided, highlighting how SynComs are an effective system to connect and fill some knowledge gaps and to have a better understanding of the mechanisms governing these multiple interactions. Although the SynCom approach is already helpful and has a promising future, more systematic and standardized studies are needed to harness its full potential.
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Affiliation(s)
- Olga Marín
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Bernardo González
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - María Josefina Poupin
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
- *Correspondence: María Josefina Poupin
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Rheault K, Lachance D, Morency MJ, Thiffault É, Guittonny M, Isabel N, Martineau C, Séguin A. Plant Genotype Influences Physicochemical Properties of Substrate as Well as Bacterial and Fungal Assemblages in the Rhizosphere of Balsam Poplar. Front Microbiol 2020; 11:575625. [PMID: 33329437 PMCID: PMC7719689 DOI: 10.3389/fmicb.2020.575625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/26/2020] [Indexed: 01/09/2023] Open
Abstract
Abandoned unrestored mines are an important environmental concern as they typically remain unvegetated for decades, exposing vast amounts of mine waste to erosion. Several factors limit the revegetation of these sites, including extreme abiotic and unfavorable biotic conditions. However, some pioneer tree species having high levels of genetic diversity, such as balsam poplar (Populus balsamifera), can naturally colonize these sites and initiate plant succession. This suggests that some tree genotypes are likely more suited for acclimation to the conditions of mine wastes. In this study, we selected two contrasting mine waste storage facilities (waste rock from a gold mine and tailings from a molybdenum mine) from the Abitibi region of Quebec (Canada), on which poplars were found to have grown naturally. First, we assessed in situ the impact of vegetation presence on each mine waste type. The presence of balsam poplars improved soil health locally by modifying the physicochemical properties (e.g., higher nutrient content and pH) of the mine wastes and causing an important shift in their bacterial and fungal community compositions, going from lithotrophic communities that dominate mine waste environments to heterotrophic communities involved in nutrient cycling. Next, in a greenhouse experiment we assessed the impact of plant genotype when grown in these mine wastes. Ten genotypes of P. balsamifera were collected locally, found growing either at the mine sites or in the surrounding natural forest. Tree growth was monitored over two growing seasons, after which the effects of genotype-by-environment interactions were assessed by measuring the physicochemical properties of the substrates and the changes in microbial community assembly. Although substrate type was identified as the main driver of rhizosphere microbiome diversity and community structure, a significant effect due to tree genotype was also detected, particularly for bacterial communities. Plant genotype also influenced aboveground tree growth and the physicochemical properties of the substrates. These results highlight the influence of balsam poplar genotype on the soil environment and the potential importance of tree genotype selection in the context of mine waste revegetation.
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Affiliation(s)
- Karelle Rheault
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Denis Lachance
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Marie-Josée Morency
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Évelyne Thiffault
- Renewable Materials Research Centre, Department of Wood and Forest Sciences, Université Laval, Quebec City, QC, Canada
| | - Marie Guittonny
- Research Institute of Mines and Environment (RIME), Université du Québec en Abitibi-Témiscamingue, Rouyn-Noranda, QC, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Christine Martineau
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Armand Séguin
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
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Exploring Rice Root Microbiome; The Variation, Specialization and Interaction of Bacteria and Fungi In Six Tropic Savanna Regions in Ghana. SUSTAINABILITY 2020. [DOI: 10.3390/su12145835] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We investigated the root microbiomes of rice sampled from six major rice-producing regions in Ghana using Illumina MiSeq high-throughput amplicon sequencing analysis. The result showed that both bacterial and fungal community compositions were significantly varied across the regions. Bacterial communities were shaped predominantly by biotic factors, including root fungal diversity and abundance. In contrast, fungal communities were influenced by abiotic factors such as soil nitrate, total carbon and soil pH. A negative correlation between the diversity and abundance of root fungi with soil nitrate (NO3-) level was observed. It suggested that there were direct and indirect effects of NO3- on the root-associated bacterial and fungal community composition. The gradient of soil nitrate from North to South parts of Ghana may influence the composition of rice root microbiome. Bacterial community composition was shaped by fungal diversity and abundance; whereas fungal community composition was shaped by bacterial abundance. It suggested the mutualistic interaction of bacteria and fungi at the community level in the rice root microbiome. Specific bacterial and fungal taxa were detected abundantly in the ‘Northern’ regions of Ghana, which were very low or absent from the samples of other regions. The analysis of indicator species suggested that an ‘ecological specialization’ may have occurred which enabled specific microbial taxa to adapt to the local environment, such as the low-nitrate condition in the Northern regions.
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Nimmo HG, Laird J, Bindbeutel R, Nusinow DA. The evening complex is central to the difference between the circadian clocks of Arabidopsis thaliana shoots and roots. PHYSIOLOGIA PLANTARUM 2020; 169:442-451. [PMID: 32303120 DOI: 10.1111/ppl.13108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/26/2020] [Accepted: 04/10/2020] [Indexed: 05/25/2023]
Abstract
The circadian clock regulates the timing of many aspects of plant physiology, and this requires entrainment of the clock to the prevailing day:night cycle. Different plant cells and tissues can oscillate with different free-running periods, so coordination of timing across the plant is crucial. Previous work showed that a major difference between the clock in mature shoots and roots involves light inputs. The objective of this work was to define, in Arabidopsis thaliana, the operation of the root clock in more detail, and in particular how it responds to light quality. Luciferase imaging was used to study the shoot and root clocks in several null mutants of clock components and in lines with aberrant expression of phytochromes. Mutations in each of the components of the evening complex (EARLY FLOWERING 3 and 4, and LUX ARRHYTHMO) were found to have specific effects on roots, by affecting either rhythmicity or period and its response to light quality. The data suggest that the evening complex is a key part of the light input mechanism that differs between shoots and roots and show that roots sense red light via phytochrome B.
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Affiliation(s)
- Hugh G Nimmo
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Janet Laird
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
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Alvarez Y, Glotfelty LG, Blank N, Dohnalová L, Thaiss CA. The Microbiome as a Circadian Coordinator of Metabolism. Endocrinology 2020; 161:bqaa059. [PMID: 32291454 PMCID: PMC7899566 DOI: 10.1210/endocr/bqaa059] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 04/13/2020] [Indexed: 12/15/2022]
Abstract
The microbiome is critically involved in the regulation of systemic metabolism. An important but poorly understood facet of this regulation is the diurnal activity of the microbiome. Herein, we summarize recent developments in our understanding of the diurnal properties of the microbiome and their integration into the circadian regulation of organismal metabolism. The microbiome may be involved in the detrimental consequences of circadian disruption for host metabolism and the development of metabolic disease. At the same time, the mechanisms by which microbiome diurnal activity is integrated into host physiology reveal several translational opportunities by which the time of day can be harnessed to optimize microbiome-based therapies. The study of circadian microbiome properties may thus provide a new avenue for treating disorders associated with circadian disruption from the gut.
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Affiliation(s)
- Yelina Alvarez
- Microbiology Department, Institute for Immunology, and Institute for Diabetes, Obesity & Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lila G Glotfelty
- Microbiology Department, Institute for Immunology, and Institute for Diabetes, Obesity & Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Niklas Blank
- Microbiology Department, Institute for Immunology, and Institute for Diabetes, Obesity & Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - Lenka Dohnalová
- Microbiology Department, Institute for Immunology, and Institute for Diabetes, Obesity & Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Christoph A Thaiss
- Microbiology Department, Institute for Immunology, and Institute for Diabetes, Obesity & Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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Qu Q, Zhang Z, Peijnenburg WJGM, Liu W, Lu T, Hu B, Chen J, Chen J, Lin Z, Qian H. Rhizosphere Microbiome Assembly and Its Impact on Plant Growth. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:5024-5038. [PMID: 32255613 DOI: 10.1021/acs.jafc.0c00073] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Microorganisms colonizing the plant rhizosphere provide a number of beneficial functions for their host. Although an increasing number of investigations clarified the great functional capabilities of rhizosphere microbial communities, the understanding of the precise mechanisms underlying the impact of rhizosphere microbiome assemblies is still limited. Also, not much is known about the various beneficial functions of the rhizosphere microbiome. In this review, we summarize the current knowledge of biotic and abiotic factors that shape the rhizosphere microbiome as well as the rhizosphere microbiome traits that are beneficial to plants growth and disease-resistance. We give particular emphasis on the impact of plant root metabolites on rhizosphere microbiome assemblies and on how the microbiome contributes to plant growth, yield, and disease-resistance. Finally, we introduce a new perspective and a novel method showing how a synthetic microbial community construction provides an effective approach to unravel the plant-microbes and microbes-microbes interplays.
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Affiliation(s)
- Qian Qu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P.R. China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P.R. China
| | - W J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, 2300 RA Leiden, The Netherlands
- National Institute of Public Health and the Environment (RIVM), Center for Safety of Substances and Products, P.O. Box 1, 3720BA Bilthoven, The Netherlands
| | - Wanyue Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, P.R. China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P.R. China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, P.R. China
| | - Jianmeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P.R. China
| | - Jun Chen
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P.R. China
| | - Zhifen Lin
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, P.R. China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P.R. China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, P.R. China
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