251
|
Liu WL, Zhang CB, Han WJ, Guan M, Liu SY, Ge Y, Chang J. Fungal Denitrification Activity in Vertical Flow Constructed Wetlands as Impacted by Plant Species Richness, Carbon, Nitrogen and pH Amendments. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2017; 99:748-752. [PMID: 29116334 DOI: 10.1007/s00128-017-2207-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 11/02/2017] [Indexed: 06/07/2023]
Abstract
To control potential fungal denitrification rate (PFDR) in vertical flow simulated wetlands (VFSW) microcosms, thirty VFSW microcosms were established and planted with three plant species richness levels (i.e. unplanted, monoculture, and four-species polyculture treatment), and effects of carbon, nitrogen and pH amendments on the PFDR were investigated using a room-incubating method. Among seven carbon compounds, sodium citrate, glycerol, glucose and sodium succinate were more effective in enhancing PFDRs. These enhanced effects were dependant on a given species richness level. Sodium nitrite mostly stimulated PFDRs to a greater extent than the other three nitrogen compound amendments at any richness level. Treatments with pH 5.6 or 8.4 had significantly greater PFDRs than the treatment with pH 2.8 in the three species richness levels. However, no effect of plant species richness on the PFDR was observed among any carbon, nitrogen and pH amendments. Current results suggest carbon, nitrogen and pH factors should be considered when mediating fungal denitrification in VFSW microcosms.
Collapse
Affiliation(s)
- W L Liu
- School of Civil Engineering and Architecture, Taizhou University, Jiaojiang, 318000, China
| | - C B Zhang
- School of Life Sciences, Taizhou University, Jiaojiang, 318000, China.
| | - W J Han
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - M Guan
- School of Life Sciences, Taizhou University, Jiaojiang, 318000, China
| | - S Y Liu
- School of Civil Engineering and Architecture, Taizhou University, Jiaojiang, 318000, China
| | - Y Ge
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - J Chang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| |
Collapse
|
252
|
Uksa M, Buegger F, Gschwendtner S, Lueders T, Kublik S, Kautz T, Athmann M, Köpke U, Munch JC, Schloter M, Fischer D. Bacteria utilizing plant-derived carbon in the rhizosphere of Triticum aestivum change in different depths of an arable soil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:729-741. [PMID: 28892269 DOI: 10.1111/1758-2229.12588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Root exudates shape microbial communities at the plant-soil interface. Here we compared bacterial communities that utilize plant-derived carbon in the rhizosphere of wheat in different soil depths, including topsoil, as well as two subsoil layers up to 1 m depth. The experiment was performed in a greenhouse using soil monoliths with intact soil structure taken from an agricultural field. To identify bacteria utilizing plant-derived carbon, 13 C-CO2 labelling of plants was performed for two weeks at the EC50 stage, followed by isopycnic density gradient centrifugation of extracted DNA from the rhizosphere combined with 16S rRNA gene-based amplicon sequencing. Our findings suggest substantially different bacterial key players and interaction mechanisms between plants and bacteria utilizing plant-derived carbon in the rhizosphere of subsoils and topsoil. Among the three soil depths, clear differences were found in 13 C enrichment pattern across abundant operational taxonomic units (OTUs). Whereas, OTUs linked to Proteobacteria were enriched in 13 C mainly in the topsoil, in both subsoil layers OTUs related to Cohnella, Paenibacillus, Flavobacterium showed a clear 13 C signal, indicating an important, so far overseen role of Firmicutes and Bacteriodetes in the subsoil rhizosphere.
Collapse
Affiliation(s)
- Marie Uksa
- Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
- Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, D-70599 Stuttgart, Germany
| | - Franz Buegger
- Institute of Biochemical Plant Pathology, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
| | - Silvia Gschwendtner
- Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
| | - Tillmann Lueders
- Institute for Groundwater Ecology, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
| | - Timo Kautz
- Institute of Organic Agriculture, University of Bonn, D-53115 Bonn, Germany
| | - Miriam Athmann
- Institute of Organic Agriculture, University of Bonn, D-53115 Bonn, Germany
| | - Ulrich Köpke
- Institute of Organic Agriculture, University of Bonn, D-53115 Bonn, Germany
| | - Jean Charles Munch
- Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, D-70599 Stuttgart, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
- Chair for Soil Science, Research Department Ecology and Ecosystem Management, Technische Universität München, D-85350 Freising-Weihenstephan, Germany
| | - Doreen Fischer
- Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
| |
Collapse
|
253
|
Wu H, Wang X, He X, Zhang S, Liang R, Shen J. Effects of root exudates on denitrifier gene abundance, community structure and activity in a micro-polluted constructed wetland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 598:697-703. [PMID: 28456121 DOI: 10.1016/j.scitotenv.2017.04.150] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/19/2017] [Accepted: 04/19/2017] [Indexed: 06/07/2023]
Abstract
In micro-polluted constructed wetland (CW), the low pollutant concentrations and the low COD/N ratios (chemical oxygen demand: total nitrogen in influent), make the biological treatment more difficult. It is expected that root exudates drive microbial-based transformations within plant rhizosphere. In this research, the roles of root exudates of three aquatic plants (Phragmites australis, Typha angustifolia and Cyperus alternifolius) in improving the growth of heterotrophic denitrifying bacteria were determined in a micro-polluted CW. In studied root rhizospheres, the total organic carbon (TOC) released from the plant roots varied significantly among plant species and seasons; the average TOC ranged from 0.1715 to 0.9221mgg-1rootDMd-1, which could fuel a denitrification rate of approximately 156-841kgNO3--Nha-1year-1 if all were used by the denitrifying bacteria; the abundances of nirK- and nirS-encoding bacteria were significantly influenced by the concentration of sucrose and glucose (0.869≤r≤0.933, p<0.05), and microbial community richness and diversity had response to root exudates. The results revealed that root exudates can act as endogenous carbon sources for heterotrophic denitrifying bacteria and ultimately determine the microbe distribution patterns in micro-polluted CW.
Collapse
Affiliation(s)
- Hailu Wu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai 200240, China
| | - Xinze Wang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai 200240, China.
| | - Xiaojuan He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai 200240, China
| | - Shengbo Zhang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai 200240, China
| | - Rubing Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai 200240, China
| | - Jian Shen
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai 200240, China
| |
Collapse
|
254
|
Verzeaux J, Hirel B, Dubois F, Lea PJ, Tétu T. Agricultural practices to improve nitrogen use efficiency through the use of arbuscular mycorrhizae: Basic and agronomic aspects. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 264:48-56. [PMID: 28969802 DOI: 10.1016/j.plantsci.2017.08.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 08/08/2017] [Accepted: 08/11/2017] [Indexed: 05/21/2023]
Abstract
Nitrogen cycling in agroecosystems is heavily dependent upon arbuscular mycorrhizal fungi (AMF) present in the soil microbiome. These fungi develop obligate symbioses with various host plant species, thus increasing their ability to acquire nutrients. However, AMF are particularly sensitive to physical, chemical and biological disturbances caused by human actions that limit their establishment. For a more sustainable agriculture, it will be necessary to further investigate which agricultural practices could be favorable to maximize the benefits of AMF to improve crop nitrogen use efficiency (NUE), thus reducing nitrogen (N) fertilizer usage. Direct seeding, mulch-based cropping systems prevent soil mycelium disruption and increase AMF propagule abundance. Such cropping systems lead to more efficient root colonization by AMF and thus a better establishment of the plant/fungal symbiosis. In addition, the use of continuous cover cropping systems can also enhance the formation of more efficient interconnected hyphal networks between mycorrhizae colonized plants. Taking into account both fundamental and agronomic aspects of mineral nutrition by plant/AMF symbioses, we have critically described, how improving fungal colonization through the reduction of soil perturbation and maintenance of an ecological balance could be helpful for increasing crop NUE.
Collapse
Affiliation(s)
- Julien Verzeaux
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, FRE 3498 CNRS UPJV), Laboratoire d'Agroécologie, Ecophysiologie et Biologie intégrative, Université de Picardie Jules Verne, 33 rue St Leu, 80039 Amiens Cedex, France
| | - Bertrand Hirel
- Intitut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 INRA-Agro-ParisTech, Equipe de Recherche Labellisée, Centre National de la Recherche Scientifique (CNRS) 3559, RD10, F-78026 Versailles Cedex, France.
| | - Frédéric Dubois
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, FRE 3498 CNRS UPJV), Laboratoire d'Agroécologie, Ecophysiologie et Biologie intégrative, Université de Picardie Jules Verne, 33 rue St Leu, 80039 Amiens Cedex, France
| | - Peter J Lea
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom
| | - Thierry Tétu
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, FRE 3498 CNRS UPJV), Laboratoire d'Agroécologie, Ecophysiologie et Biologie intégrative, Université de Picardie Jules Verne, 33 rue St Leu, 80039 Amiens Cedex, France
| |
Collapse
|
255
|
Sun L, Ataka M, Kominami Y, Yoshimura K. Relationship between fine-root exudation and respiration of two Quercus species in a Japanese temperate forest. TREE PHYSIOLOGY 2017; 37:1011-1020. [PMID: 28338964 DOI: 10.1093/treephys/tpx026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 03/01/2017] [Indexed: 05/07/2023]
Abstract
Plants allocate a considerable amount of carbon (C) to fine roots as respiration and exudation. Fine-root exudation could stimulate microbial activity, which further contributes to soil heterotrophic respiration. Although both root respiration and exudation are important components of belowground C cycling, how they relate to each other is less well known. In this study, we aimed to explore this relationship on mature trees growing in the field. The measurements were performed on two canopy species, Quercus serrata Thunb. and Quercus glauca, in a warm temperate forest. The respiration and exudation rates of the same fine-root segment were measured in parallel with a syringe-basis incubation and a closed static chamber, respectively. We also measured root traits and ectomycorrhizal colonization ratio because these indexes commonly relate to root respiration and reflect root physiology. The microbial activity enhanced by root exudation was investigated by comparing the dissolved organic carbon (DOC) and microbial biomass carbon (MBC) between rhizosphere soils and bulk soils. Mean DOC concentration and MBC were ca two times higher in the rhizosphere soils and positively related to exudation rates, indicating that exudation further relates to the C dynamics in the soils. Flux rates of exudation and respiration were positively correlated with each other. Both root exudation and respiration rates positively related to ectomycorrhizal colonization and root tissue nitrogen, and therefore the relationship between the two fluxes may be attributed to fine-root activity. The flux rates of root respiration were 8.7 and 10.5 times as much as those of exudation on a root-length basis and a root-weight basis, respectively. In spite of the fact that flux rates of respiration and exudation varied enormously among the fine-root segments of the two Quercus species, exudation was in proportion to respiration. This result gives new insight into the fine-root C-allocation strategy and the belowground C dynamics.
Collapse
Affiliation(s)
- Lijuan Sun
- Lab of Forest Ecology, Graduate School of Agriculture, Kyoto University, Kitashirakawa OiwakeCho, Kyoto 606-8502, Japan
- Graduate School of Agriculture, Kyoto University, Main Building of Agriculture School, Kitashirakawa OiwakeCho, Kyoto 606-8502, Japan
| | - Mioko Ataka
- Kansai Research Center, Forestry and Forest Product Research Institute, Japan
| | - Yuji Kominami
- Kansai Research Center, Forestry and Forest Product Research Institute, Japan
| | - Kenichi Yoshimura
- Lab of Forest Hydrology, Graduate School of Agriculture, Kyoto University, Kitashirakawa OiwakeCho, Kyoto 606-8502, Japan
| |
Collapse
|
256
|
Coskun D, Britto DT, Shi W, Kronzucker HJ. How Plant Root Exudates Shape the Nitrogen Cycle. TRENDS IN PLANT SCIENCE 2017; 22:661-673. [PMID: 28601419 DOI: 10.1016/j.tplants.2017.05.004] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 05/23/2023]
Abstract
Although the global nitrogen (N) cycle is largely driven by soil microbes, plant root exudates can profoundly modify soil microbial communities and influence their N transformations. A detailed understanding is now beginning to emerge regarding the control that root exudates exert over two major soil N processes - nitrification and N2 fixation. We discuss recent breakthroughs in this area, including the identification of root exudates as nitrification inhibitors and as signaling compounds facilitating N-acquisition symbioses. We indicate gaps in current knowledge, including questions of how root exudates affect newly discovered microbial players and N-cycle components. A better understanding of these processes is urgent given the widespread inefficiencies in agricultural N use and their links to N pollution and climate change.
Collapse
Affiliation(s)
- Devrim Coskun
- Department of Biological Sciences and Canadian Centre for World Hunger Research (CCWHR), University of Toronto, Toronto M1C 1A4, ON, Canada; Département de Phytologie, Faculté des Sciences de l'Agriculture et de l'Alimentation (FSAA), Université Laval, Québec G1V 0A6, QC, Canada
| | - Dev T Britto
- Department of Biological Sciences and Canadian Centre for World Hunger Research (CCWHR), University of Toronto, Toronto M1C 1A4, ON, Canada
| | - Weiming Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Herbert J Kronzucker
- Department of Biological Sciences and Canadian Centre for World Hunger Research (CCWHR), University of Toronto, Toronto M1C 1A4, ON, Canada; School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| |
Collapse
|
257
|
Li M, Yang Y, Feng F, Zhang B, Chen S, Yang C, Gu L, Wang F, Zhang J, Chen A, Lin W, Chen X, Zhang Z. Differential proteomic analysis of replanted Rehmannia glutinosa roots by iTRAQ reveals molecular mechanisms for formation of replant disease. BMC PLANT BIOLOGY 2017; 17:116. [PMID: 28693420 PMCID: PMC5504617 DOI: 10.1186/s12870-017-1060-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 06/22/2017] [Indexed: 05/07/2023]
Abstract
BACKGROUND The normal growth of Rehmannia glutinosa, a widely used medicinal plant in China, is severely disturbed by replant disease. The formation of replant disease commonly involves interactions among plants, allelochemicals and microbes; however, these relationships remain largely unclear. As a result, no effective measures are currently available to treat replant disease. RESULTS In this study, an integrated R. glutinosa transcriptome was constructed, from which an R. glutinosa protein library was obtained. iTRAQ technology was then used to investigate changes in the proteins in replanted R. glutinosa roots, and the proteins that were expressed in response to replant disease were identified. An integrated R. glutinosa transcriptome from different developmental stages of replanted and normal-growth R. glutinosa produced 65,659 transcripts, which were accurately translated into 47,818 proteins. Using this resource, a set of 189 proteins was found to be significantly differentially expressed between normal-growth and replanted R. glutinosa. Of the proteins that were significantly upregulated in replanted R. glutinosa, most were related to metabolism, immune responses, ROS generation, programmed cell death, ER stress, and lignin synthesis. CONCLUSIONS By integrating these key events and the results of previous studies on replant disease formation, a new picture of the damaging mechanisms that cause replant disease stress emerged. Replant disease altered the metabolic balance of R. glutinosa, activated immune defence systems, increased levels of ROS and antioxidant enzymes, and initiated the processes of cell death and senescence in replanted R. glutinosa. Additionally, lignin deposition in R. glutinosa roots that was caused by replanting significantly inhibited tuberous root formation. These key processes provide important insights into the underlying mechanisms leading to the formation of replant disease and also for the subsequent development of new control measures to improve production and quality of replanted plants.
Collapse
Affiliation(s)
- Mingjie Li
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanhui Yang
- College of Bioengineering, Henan University of Technology, Zhengzhou, China
| | - Fajie Feng
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bao Zhang
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuqiang Chen
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chuyun Yang
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Li Gu
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Junyi Zhang
- College of Chemical Engineering, Huaqiao University, Xiamen, China
| | - Aiguo Chen
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenxiong Lin
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Zhongyi Zhang
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
258
|
Ibort P, Molina S, Núñez R, Zamarreño ÁM, García-Mina JM, Ruiz-Lozano JM, Orozco-Mosqueda MDC, Glick BR, Aroca R. Tomato ethylene sensitivity determines interaction with plant growth-promoting bacteria. ANNALS OF BOTANY 2017; 120:101-122. [PMID: 28586422 PMCID: PMC5737082 DOI: 10.1093/aob/mcx052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/20/2017] [Indexed: 05/29/2023]
Abstract
BACKGROUND AND AIMS Plant growth-promoting bacteria (PGPB) are soil micro-organisms able to interact with plants and stimulate their growth, positively affecting plant physiology and development. Although ethylene plays a key role in plant growth, little is known about the involvement of ethylene sensitivity in bacterial inoculation effects on plant physiology. Thus, the present study was pursued to establish whether ethylene perception is critical for plant-bacteria interaction and growth induction by two different PGPB strains, and to assess the physiological effects of these strains in juvenile and mature tomato ( Solanum lycopersicum ) plants. METHODS An experiment was performed with the ethylene-insensitive tomato never ripe and its isogenic wild-type line in which these two strains were inoculated with either Bacillus megaterium or Enterobacter sp. C7. Plants were grown until juvenile and mature stages, when biomass, stomatal conductance, photosynthesis as well as nutritional, hormonal and metabolic statuses were analysed. KEY RESULTS Bacillus megaterium promoted growth only in mature wild type plants. However, Enterobacter C7 PGPB activity affected both wild-type and never ripe plants. Furthermore, PGPB inoculation affected physiological parameters and root metabolite levels in juvenile plants; meanwhile plant nutrition was highly dependent on ethylene sensitivity and was altered at the mature stage. Bacillus megaterium inoculation improved carbon assimilation in wild-type plants. However, insensitivity to ethylene compromised B. megaterium PGPB activity, affecting photosynthetic efficiency, plant nutrition and the root sugar content. Nevertheless, Enterobacter C7 inoculation modified the root amino acid content in addition to stomatal conductance and plant nutrition. CONCLUSIONS Insensitivity to ethylene severely impaired B. megaterium interaction with tomato plants, resulting in physiological modifications and loss of PGPB activity. In contrast, Enterobacter C7 inoculation stimulated growth independently of ethylene perception and improved nitrogen assimilation in ethylene-insensitive plants. Thus, ethylene sensitivity is a determinant for B. megaterium , but is not involved in Enterobacter C7 PGPB activity.
Collapse
Affiliation(s)
- Pablo Ibort
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín (EEZ-CSIC), Profesor Albareda 1, 18008 Granada, Spain
| | - Sonia Molina
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín (EEZ-CSIC), Profesor Albareda 1, 18008 Granada, Spain
| | - Rafael Núñez
- Scientific Instrumental Service, Estación Experimental del Zaidín (EEZ-CSIC), Profesor Albareda 1, 18008 Granada, Spain
| | - Ángel María Zamarreño
- Department of Environmental Biology, Agricultural Chemistry and Biology Group-CMI Roullier, Faculty of Sciences, University of Navarra, Irunlarrea 1, 31008 Pamplona, Spain
| | - José María García-Mina
- Department of Environmental Biology, Agricultural Chemistry and Biology Group-CMI Roullier, Faculty of Sciences, University of Navarra, Irunlarrea 1, 31008 Pamplona, Spain
| | - Juan Manuel Ruiz-Lozano
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín (EEZ-CSIC), Profesor Albareda 1, 18008 Granada, Spain
| | | | - Bernard R. Glick
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Ricardo Aroca
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín (EEZ-CSIC), Profesor Albareda 1, 18008 Granada, Spain
| |
Collapse
|
259
|
Abstract
Plant roots and soil microorganisms interact with each other mainly in the rhizosphere. Changes in the community structure of the rhizosphere microbiome are influenced by many factors. In this study, we determined the community structure of rhizosphere bacteria in cotton, and studied the variation of rhizosphere bacterial community structure in different soil types and developmental stages using TM-1, an upland cotton cultivar (Gossypium hirsutum L.) and Hai 7124, a sea island cotton cultivar (G. barbadense L.) by high-throughput sequencing technology. Six bacterial phyla were found dominantly in cotton rhizosphere bacterial community including Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Proteobacteria, and Verrucomicrobia. The abundance of Acidobacteria, Cyanobacteria, Firmicutes, Planctomycetes and Proteobacteria were largely influenced by cotton root. Bacterial α-diversity in rhizosphere was lower than that of bulk soil in nutrient-rich soil, but higher in cotton continuous cropping field soil. The β-diversity in nutrient-rich soil was greater than that in continuous cropping field soil. The community structure of the rhizosphere bacteria varied significantly during different developmental stages. Our results provided insights into the dynamics of cotton rhizosphere bacterial community and would facilitate to improve cotton growth and development through adjusting soil bacterial community structure artificially.
Collapse
|
260
|
Guyonnet JP, Vautrin F, Meiffren G, Labois C, Cantarel AAM, Michalet S, Comte G, Haichar FEZ. The effects of plant nutritional strategy on soil microbial denitrification activity through rhizosphere primary metabolites. FEMS Microbiol Ecol 2017; 93:3003321. [PMID: 28334144 DOI: 10.1093/femsec/fix022] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/17/2017] [Indexed: 11/12/2022] Open
Abstract
The aim of this study was to determine (i) whether plant nutritional strategy affects the composition of primary metabolites exuded into the rhizosphere and (ii) the impact of exuded metabolites on denitrification activity in soil. We answered this question by analysing primary metabolite content extracted from the root-adhering soil (RAS) and the roots of three grasses representing different nutrient management strategies: conservative (Festuca paniculata), intermediate (Bromus erectus) and exploitative (Dactylis glomerata). We also investigated the impact of primary metabolites on soil microbial denitrification enzyme activity without carbon addition, comparing for each plant RAS and bulk soils. Our data show that plant nutritional strategy impacts on primary metabolite composition of root extracts or RAS. Further we show, for the first time, that RAS-extracted primary metabolites are probably better indicators to explain plant nutrient strategy than root-extracted ones. In addition, our results show that some primary metabolites present in the RAS were well correlated with soil microbial denitrification activity with positive relationships found between denitrification and the presence of some organic acids and negative ones with the presence of xylose. We demonstrated that the analysis of primary metabolites extracted from the RAS is probably more pertinent to evaluate the impact of plant on soil microbial community functioning.
Collapse
|
261
|
Effects of Selected Root Exudate Components on Nitrogen Removal and Development of Denitrifying Bacteria in Constructed Wetlands. WATER 2017. [DOI: 10.3390/w9060430] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
262
|
Alufasi R, Gere J, Chakauya E, Lebea P, Parawira W, Chingwaru W. Mechanisms of pathogen removal by macrophytes in constructed wetlands. ACTA ACUST UNITED AC 2017. [DOI: 10.1080/21622515.2017.1325940] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Richwell Alufasi
- Department of Biological Sciences, Faculty of Science, Bindura University of Science Education, Bindura, Zimbabwe
| | - Jephris Gere
- Department of Biological Sciences, Faculty of Science, Bindura University of Science Education, Bindura, Zimbabwe
| | - Ereck Chakauya
- Council for Scientific and Industrial Research (CSIR), Biosciences, Pretoria, South Africa
| | - Phiyani Lebea
- Council for Scientific and Industrial Research (CSIR), Biosciences, Pretoria, South Africa
| | - Wilson Parawira
- Department of Biological Sciences, Faculty of Science, Bindura University of Science Education, Bindura, Zimbabwe
| | - Walter Chingwaru
- Department of Biological Sciences, Faculty of Science, Bindura University of Science Education, Bindura, Zimbabwe
| |
Collapse
|
263
|
Ktari A, Gueddou A, Nouioui I, Miotello G, Sarkar I, Ghodhbane-Gtari F, Sen A, Armengaud J, Gtari M. Host Plant Compatibility Shapes the Proteogenome of Frankia coriariae. Front Microbiol 2017; 8:720. [PMID: 28512450 PMCID: PMC5411423 DOI: 10.3389/fmicb.2017.00720] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/06/2017] [Indexed: 01/24/2023] Open
Abstract
Molecular signaling networks in the actinorhizal rhizosphere select host-compatible Frankia strains, trigger the infection process and eventually the genesis of nitrogen-fixing nodules. The molecular triggers involved remain difficult to ascertain. Root exudates (RE) are highly dynamic substrates that play key roles in establishing the rhizosphere microbiome. RE are known to induce the secretion by rhizobia of Nod factors, polysaccharides, and other proteins in the case of legume symbiosis. Next-generation proteomic approach was here used to decipher the key bacterial signals matching the first-step recognition of host plant stimuli upon treatment of Frankia coriariae strain BMG5.1 with RE derived from compatible (Coriaria myrtifolia), incompatible (Alnus glutinosa), and non-actinorhizal (Cucumis melo) host plants. The Frankia proteome dynamics were mainly driven by host compatibility. Both metabolism and signal transduction were the dominant activities for BMG5.1 under the different RE conditions tested. A second set of proteins that were solely induced by C. myrtifolia RE and were mainly linked to cell wall remodeling, signal transduction and host signal processing activities. These proteins may footprint early steps in receptive recognition of host stimuli before subsequent events of symbiotic recruitment.
Collapse
Affiliation(s)
- Amir Ktari
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) and Université de Carthage (INSAT)Tunis, Tunisia
| | - Abdellatif Gueddou
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) and Université de Carthage (INSAT)Tunis, Tunisia
| | - Imen Nouioui
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) and Université de Carthage (INSAT)Tunis, Tunisia
| | - Guylaine Miotello
- CEA, DRF, Joliot, Lab Innovative Technologies for Detection and DiagnosticBagnols-sur-Cèze, France
| | - Indrani Sarkar
- Department of Botany, NBU Bioinformatics Facility, University of North BengalSiliguri, India
| | - Faten Ghodhbane-Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) and Université de Carthage (INSAT)Tunis, Tunisia
| | - Arnab Sen
- Department of Botany, NBU Bioinformatics Facility, University of North BengalSiliguri, India
| | - Jean Armengaud
- CEA, DRF, Joliot, Lab Innovative Technologies for Detection and DiagnosticBagnols-sur-Cèze, France
| | - Maher Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) and Université de Carthage (INSAT)Tunis, Tunisia
| |
Collapse
|
264
|
Massalha H, Korenblum E, Tholl D, Aharoni A. Small molecules below-ground: the role of specialized metabolites in the rhizosphere. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:788-807. [PMID: 28333395 DOI: 10.1111/tpj.13543] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 03/17/2017] [Accepted: 03/21/2017] [Indexed: 05/18/2023]
Abstract
Soil communities are diverse taxonomically and functionally. This ecosystem experiences highly complex networks of interactions, but may also present functionally independent entities. Plant roots, a metabolically active hotspot in the soil, take an essential part in below-ground interactions. While plants are known to release an extremely high portion of the fixated carbon to the soil, less information is known about the composition and role of C-containing compounds in the rhizosphere, in particular those involved in chemical communication. Specialized metabolites (or secondary metabolites) produced by plants and their associated microbes have a critical role in various biological activities that modulate the behavior of neighboring organisms. Thus, elucidating the chemical composition and function of specialized metabolites in the rhizosphere is a key element in understanding interactions in this below-ground environment. Here, we review key classes of specialized metabolites that occur as mostly non-volatile compounds in root exudates or are emitted as volatile organic compounds (VOCs). The role of these metabolites in below-ground interactions and response to nutrient deficiency, as well as their tissue and cell type-specific biosynthesis and release are discussed in detail.
Collapse
Affiliation(s)
- Hassan Massalha
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Elisa Korenblum
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Dorothea Tholl
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| |
Collapse
|
265
|
Cordovil CMDS, de Varennes A, Pinto RMDS, Alves TF, Mendes P, Sampaio SC. Decomposition rate and enzymatic activity of composted municipal waste and poultry manure in the soil in a biofuel crops field. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:2245-2255. [PMID: 27620351 DOI: 10.1002/jsfa.8035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 09/01/2016] [Accepted: 09/08/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Biofuel crops are gaining importance because of the need to replace non-renewable sources. Also, due to the increasing amounts of wastes generated, there is the need to recycle them to the soil, both to fertilize crops and to improve soil physical properties through organic matter increase and microbiological changes in the rhizosphere. We therefore studied the influence of six biofuel crops (elephant grass, giant cane, sugarcane, blue gum, black cottonwood, willow) on the decomposition rate and enzymatic activity of composted municipal solid waste and poultry manure. Organic amendments were incubated in the field (litterbag method), buried near each plant or bare soil. Biomass decrease and dehydrogenase, urease and acid phosphatase level in amendments was monitored over a 180-day period. Soil under the litterbags was analysed for the same enzymatic activity and organic matter fractions (last sampling). After 365 days, a fractionation of organic matter was carried out in both amendments and soil under the litterbags. RESULTS For compost, willow and sugarcane generally led to the greatest enzymatic activity, at the end of the experiment. For manure, dehydrogenase activity decreased sharply with time, the smallest value near sugarcane, while phosphatase and urease generally presented the highest values, at the beginning or after 90 days' incubation. Clustering showed that plant species could be grouped based on biomass and enzymes measured over time. CONCLUSIONS Plant species influenced the decomposition rate and enzymatic activities of the organic amendments. Overall, mineralization of both amendments was associated with a greater urease activity in soils. Dehydrogenase activity in manure was closely associated with urease activity. © 2016 Society of Chemical Industry.
Collapse
Affiliation(s)
| | - Amarilis de Varennes
- Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | | | - Tiago Filipe Alves
- Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - Pedro Mendes
- Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - Sílvio César Sampaio
- Research Group on Water Resources and Environmental Sanitation, Western Paraná State University, UNIOESTE/Cascavel/ CCET/PGEAGRI, 85819-110, Cascavel, PR, Brazil
| |
Collapse
|
266
|
Zhang R, Vivanco JM, Shen Q. The unseen rhizosphere root-soil-microbe interactions for crop production. Curr Opin Microbiol 2017; 37:8-14. [PMID: 28433932 DOI: 10.1016/j.mib.2017.03.008] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/22/2017] [Indexed: 02/03/2023]
Abstract
The underground root-soil-microbe interactions are extremely complex, but vitally important for aboveground plant growth, health and fitness. The pressure to reduce our reliance on agrochemicals, and sustainable efforts to develop agriculture makes rhizosphere interactions' research a hotspot. Recent advances provide new insights about the signals, pathways, functions and mechanisms of these interactions. In this review, we provide an overview about recent progress in rhizosphere interaction networks in crops. We also discuss a holistic view of the root-soil-rhizomicrobiome interactions achieved through the advances of omics and bioinformatics technologies, and the potential strategies to manage the complex rhizosphere interactions for enhancing crop production.
Collapse
Affiliation(s)
- Ruifu Zhang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China; Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Jorge M Vivanco
- Department of Horticulture and Landscape Architecture and Center for Rhizosphere Biology, Colorado State University, Fort Collins, CO 80523, United States
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China.
| |
Collapse
|
267
|
Dong T, Li J, Liao Y, Chen BJW, Xu X. Root-mediated sex recognition in a dioecious tree. Sci Rep 2017; 7:801. [PMID: 28400562 PMCID: PMC5429744 DOI: 10.1038/s41598-017-00894-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 03/16/2017] [Indexed: 01/14/2023] Open
Abstract
Recent studies have demonstrated that plants can determine the identity of neighbouring roots (e.g., self and non-self, kin and non-kin), but whether they can discriminate by sex remains an open question. Here, we predict that dioecious plants can modulate their root performance in response to local root conditions related to sex. Female and male Populus cathayana cuttings were planted in a greenhouse in root-owner (one individual without a root neighbour) or root-sharer pairs (two individuals with roots neighbouring each other) with equal amounts of nutrients and space per plant in three combinations (females-females, males-males or females-males); root morphology, biomass and allocation were investigated. P. cathayana root-sharers altered their root growth in same-sex but not in different-sex combinations. Females enhanced root growth and allocation but decreased root proliferation (greater diameter with reduced branching and specific root length) in the presence of a female root neighbour, while males reduced root growth but increased root morphological proliferation in contact with another male. Therefore, the effect of a neighbour of the same sex differed from that of a neighbour of the opposite sex, which suggests that these plants can recognize the sexual identity of their neighbours.
Collapse
Affiliation(s)
- Tingfa Dong
- Key Laboratory of Southwest China Wildlife Resources Conservation, Ministry of Education, and College of Life Sciences, China West Normal University, Nanchong, Sichuan, 637009, China
| | - Junyu Li
- Key Laboratory of Southwest China Wildlife Resources Conservation, Ministry of Education, and College of Life Sciences, China West Normal University, Nanchong, Sichuan, 637009, China
- School of Urban-rural Planning and Landscape Architecture, Xuchang University, Xuchang, 461000, China
| | - Yongmei Liao
- Key Laboratory of Southwest China Wildlife Resources Conservation, Ministry of Education, and College of Life Sciences, China West Normal University, Nanchong, Sichuan, 637009, China
| | - Bin J W Chen
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiao Xu
- Key Laboratory of Southwest China Wildlife Resources Conservation, Ministry of Education, and College of Life Sciences, China West Normal University, Nanchong, Sichuan, 637009, China.
| |
Collapse
|
268
|
Eisenhauer N, Lanoue A, Strecker T, Scheu S, Steinauer K, Thakur MP, Mommer L. Root biomass and exudates link plant diversity with soil bacterial and fungal biomass. Sci Rep 2017; 7:44641. [PMID: 28374800 PMCID: PMC5379681 DOI: 10.1038/srep44641] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/13/2017] [Indexed: 11/30/2022] Open
Abstract
Plant diversity has been shown to determine the composition and functioning of soil biota. Although root-derived organic inputs are discussed as the main drivers of soil communities, experimental evidence is scarce. While there is some evidence that higher root biomass at high plant diversity increases substrate availability for soil biota, several studies have speculated that the quantity and diversity of root inputs into the soil, i.e. though root exudates, drive plant diversity effects on soil biota. Here we used a microcosm experiment to study the role of plant species richness on the biomass of soil bacteria and fungi as well as fungal-to-bacterial ratio via root biomass and root exudates. Plant diversity significantly increased shoot biomass, root biomass, the amount of root exudates, bacterial biomass, and fungal biomass. Fungal biomass increased most with increasing plant diversity resulting in a significant shift in the fungal-to-bacterial biomass ratio at high plant diversity. Fungal biomass increased significantly with plant diversity-induced increases in root biomass and the amount of root exudates. These results suggest that plant diversity enhances soil microbial biomass, particularly soil fungi, by increasing root-derived organic inputs.
Collapse
Affiliation(s)
- Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.,Institute of Biology, Leipzig University, Johannisallee 21, 04103 Leipzig, Germany
| | - Arnaud Lanoue
- Université François Rabelais de Tours. EA 2106 Plant Biotechnology and Biomolecules, 31 Avenue Monge, F-37200 Tours, France
| | - Tanja Strecker
- Georg August University Göttingen, J.F. Blumenbach Institute of Zoology and Anthropology, Berliner Str. 28, 37073 Göttingen, Germany
| | - Stefan Scheu
- Georg August University Göttingen, J.F. Blumenbach Institute of Zoology and Anthropology, Berliner Str. 28, 37073 Göttingen, Germany
| | - Katja Steinauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.,Institute of Biology, Leipzig University, Johannisallee 21, 04103 Leipzig, Germany
| | - Madhav P Thakur
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.,Institute of Biology, Leipzig University, Johannisallee 21, 04103 Leipzig, Germany
| | - Liesje Mommer
- Plant Ecology and Nature Conservation group, Wageningen University, PO Box 47, 6700 AA Wageningen, The Netherlands
| |
Collapse
|
269
|
Weiller F, Moore JP, Young P, Driouich A, Vivier MA. The Brassicaceae species Heliophila coronopifolia produces root border-like cells that protect the root tip and secrete defensin peptides. ANNALS OF BOTANY 2017; 119:803-813. [PMID: 27481828 PMCID: PMC5379576 DOI: 10.1093/aob/mcw141] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 05/03/2016] [Accepted: 06/02/2016] [Indexed: 05/16/2023]
Abstract
Background and Aims Root border cells and border-like cells (BLCs), the latter originally described in Arabidopsis thaliana , have been described as cells released at the root tips of the species in which they occur. BLCs are thought to provide protection to root meristems similar to classical root border cells. In addition, four defensin peptides (Hc-AFP1-4) have previously been characterized from Heliophila coronopifolia , a South African semi-desert flower, and found to be strongly antifungal. This provided an opportunity to evaluate if the BLCs of H. coronopifolia indeed produce these defensins, which would provide evidence towards a defence role for BLCs. Methods Fluorescence microscopy, using live-cell-imaging technology, was used to characterize the BLCs of H. coronopifolia . Quantitative real-time PCR (qRT-PCR) analysis and immunofluorescence microscopy was used to characterize these defensin peptides. Key Results BLCs originated at the root apical meristem and formed a protective sheath at the tip and along the sides as the root elongated in solid medium. BLCs have a cellulose-enriched cell wall, intact nuclei and are embedded in a layer of pectin-rich mucilage. Pectinase treatments led to the dissolution of the sheath and dissociation of the root BLCs. Hc-AFP1-4 genes were all expressed in root tissues, but Hc-AFP3 transcripts were the most abundant in these tissues as measured by qRT-PCR. A polyclonal antibody that was cross-reactive with all four defensins, and probably recognizing a general plant defensin epitope, was used in fluorescence microscopy analysis to examine the presence of the peptides in the root tip and BLCs. Data confirmed the peptides present in the root tip tissues, the mucilage sheath and the BLCs. Conclusions This study provides a link between defensin peptides and BLCs, both embedded in a protective pectin mucilage sheath, during normal plant growth and development. The presence of the Hc-AFP3 defensin peptides in the BLCs suggests a role for these cells in root protection.
Collapse
Affiliation(s)
- Florent Weiller
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Faculty of AgriSciences, Stellenbosch University, Matieland 7602, South Africa
- Laboratoire Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV), Grand Réseau de Recherche VASI de Haute Normandie, Normandie Université, Université de Rouen, 76821 Mont Saint Aignan cedex, France
| | - John P. Moore
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Faculty of AgriSciences, Stellenbosch University, Matieland 7602, South Africa
| | - Philip Young
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Faculty of AgriSciences, Stellenbosch University, Matieland 7602, South Africa
| | - Azeddine Driouich
- Laboratoire Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV), Grand Réseau de Recherche VASI de Haute Normandie, Normandie Université, Université de Rouen, 76821 Mont Saint Aignan cedex, France
| | - Melané A. Vivier
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Faculty of AgriSciences, Stellenbosch University, Matieland 7602, South Africa
| |
Collapse
|
270
|
Rugova A, Puschenreiter M, Koellensperger G, Hann S. Elucidating rhizosphere processes by mass spectrometry – A review. Anal Chim Acta 2017; 956:1-13. [DOI: 10.1016/j.aca.2016.12.044] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/27/2016] [Accepted: 12/28/2016] [Indexed: 12/20/2022]
|
271
|
Chen S, Ma H, Guo Z, Feng Y, Lin J, Zhang M, Zhong M. Quantitative proteomics analysis reveals the tolerance of Mirabilis jalapa L. to petroleum contamination. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:7375-7382. [PMID: 28108917 DOI: 10.1007/s11356-017-8403-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/04/2017] [Indexed: 04/15/2023]
Abstract
Petroleum is not only an important energy resource but is also a major soil pollutant. To gain better insight into the adaptability mechanism of Mirabilis jalapa to petroleum-contaminated soil, the protein profiles of M. jalapa root were investigated using label-free quantitative proteomics technique. After exposing to petroleum-contaminated soil for 24 h, 34 proteins significantly changed their protein abundance and most of the proteins increased in protein abundance (91.18%). Combined with gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses as well as data from previous studies, our results revealed that M. jalapa enhanced tolerance to petroleum by changing antioxidation and detoxification, cell wall organization, amino acid and carbohydrate metabolism, transportation and protein process, and so on. These metabolism alterations could result in the production and secretion of low molecular carbohydrate, amino acid, and functional protein, which enhanced the bioavailability of petroleum and reducing the toxicity of the petroleum. Taken together, these results provided novel information for better understanding of the tolerance of M. jalapa to petroleum stress.
Collapse
Affiliation(s)
- Shuisen Chen
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Hui Ma
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Zhifu Guo
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Yaping Feng
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Jingwei Lin
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Menghua Zhang
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Ming Zhong
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang, 110866, China.
| |
Collapse
|
272
|
Steinauer K, Chatzinotas A, Eisenhauer N. Root exudate cocktails: the link between plant diversity and soil microorganisms? Ecol Evol 2016; 6:7387-7396. [PMID: 28725406 PMCID: PMC5513276 DOI: 10.1002/ece3.2454] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 08/13/2016] [Accepted: 08/15/2016] [Indexed: 12/22/2022] Open
Abstract
Higher plant diversity is often associated with higher soil microbial biomass and diversity, which is assumed to be partly due to elevated root exudate diversity. However, there is little experimental evidence that diversity of root exudates shapes soil microbial communities. We tested whether higher root exudate diversity enhances soil microbial biomass and diversity in a plant diversity gradient, thereby negating significant plant diversity effects on soil microbial properties. We set up plant monocultures and two- and three-species mixtures in microcosms using functionally dissimilar plants and soil of a grassland biodiversity experiment in Germany. Artificial exudate cocktails were added by combining the most common sugars, organic acids, and amino acids found in root exudates. We applied four different exudate cocktails: two exudate diversity levels (low- and high-diversity) and two nutrient-enriched levels (carbon- and nitrogen-enriched), and a control with water only. Soil microorganisms were more carbon- than nitrogen-limited. Cultivation-independent fingerprinting analysis revealed significantly different soil microbial communities among exudate diversity treatments. Most notably and according to our hypothesis, adding diverse exudate cocktails negated the significant plant diversity effect on soil microbial properties. Our findings provide the first experimental evidence that root exudate diversity is a crucial link between plant diversity and soil microorganisms.
Collapse
Affiliation(s)
- Katja Steinauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of BiologyLeipzig UniversityLeipzigGermany
| | - Antonis Chatzinotas
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Department of Environmental MicrobiologyHelmholtz Centre for Environmental Research‐UFZLeipzigGermany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of BiologyLeipzig UniversityLeipzigGermany
| |
Collapse
|
273
|
Chen X, Fukushi K. Development of an innovative decentralized treatment system for the reclamation and reuse of strong wastewater from rural community: Effects of elevated CO2 concentrations. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2016; 180:401-408. [PMID: 27262339 DOI: 10.1016/j.jenvman.2016.05.071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/20/2016] [Accepted: 05/27/2016] [Indexed: 06/05/2023]
Abstract
In a previous study, a soil-plant-based natural treatment system was successfully developed for post-treatment of anaerobically digested strong wastewater full of potential nutrients (nitrogen, phosphorus, and potassium). For upgraded performance, an innovative decentralized treatment system was further developed, in which an anaerobic digestion stage and a natural treatment system stage are placed within a greenhouse. This allows the CO2 generated by the processing of wastewater and biogas consumption to be sequestrated within the greenhouse for elevating its concentration level and potentially enhance nutrient removal and recovery from the applied wastewater. To investigate the feasibility of the system, a bench-scale experiment was conducted using CO2 chambers. Valuable Kentucky bluegrass was planted in two soil types (red ball earth and black soil) at three CO2 concentrations (340 ppm, 900 ppm, and 1400 ppm). The results confirmed the positive effects of elevated CO2 concentration on the biomass production and turf quality of Kentucky bluegrass as well as the resulting higher nutrient recovery efficiencies. More importantly, it was demonstrated that the elevated CO2 concentration significantly stimulated the soil nitrifying microorganisms and thus improved the nitrogen removal efficiency (a critical issue in ecological wastewater treatment). A CO2 concentration of 1400 ppm is therefore recommended for use in the system. The mechanism underlying this phenomenon was shown to be an indirect effect, in which the higher CO2 concentration first positively influenced growing plants, which then stimulated the soil nitrifier communities. The effects of soil type (a design parameter) and hydraulic and nutrient loading rates (an operational parameter) on system performance were also examined. The results favored black soil for system establishment. Based on the findings of this study, our proposed system is thought to have the potential to be scaled up and adopted by rural communities worldwide for the reclamation and reuse of strong wastewater, addressing the agricultural non-point source pollution, and achieving the sustainable development.
Collapse
Affiliation(s)
- Xiaochen Chen
- Department of Urban Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Kensuke Fukushi
- Integrated Research System for Sustainability Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.
| |
Collapse
|
274
|
Jia H, Wang H, Lu H, Jiang S, Dai M, Liu J, Yan C. Rhizodegradation potential and tolerance of Avicennia marina (Forsk.) Vierh in phenanthrene and pyrene contaminated sediments. MARINE POLLUTION BULLETIN 2016; 110:112-118. [PMID: 27373941 DOI: 10.1016/j.marpolbul.2016.06.075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 06/13/2016] [Accepted: 06/22/2016] [Indexed: 06/06/2023]
Abstract
A pot experiment was conducted to investigate the dissipation of phenanthrene and pyrene in spiked sediments with presence of Avicennia marina (Forsk.) Vierh. The rhizosphere environment was set up using a self-design nylon rhizo-bag which divided the sediment into the rhizosphere and non-rhizosphere. Results showed that the dissipation of phenanthrene and pyrene were significantly enhanced in the rhizosphere compared with non-rhizosphere sediments. Plant roots promoted dissipation significantly greater than the contribution of direct plant uptake and accumulation of phenanthrene and pyrene. The activities of antioxidant and detoxification enzymes in roots and leaves significantly increased against oxidative stress with increasing PAH concentrations. Furthermore, a significant relationship (R(2)>0.91) between dissolved organic carbon (DOC) concentrations and the residual of PAHs in rhizosphere and non-rhizosphere sediments was observed after 120days planting. Results indicated that rhizome mediation with A. marina is a useful approach to promote the depletion of PAHs in contaminated mangrove sediments.
Collapse
Affiliation(s)
- Hui Jia
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, PR China
| | - He Wang
- Xuzhou Medical University, Affiliated Hospital, Xuzhou 221009, PR China
| | - Haoliang Lu
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, PR China
| | - Shan Jiang
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, PR China; Biogeochemistry Research Group, Geography Department, Trinity College, University of Dublin, Ireland
| | - Minyue Dai
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, PR China
| | - Jingchun Liu
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, PR China
| | - Chongling Yan
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, PR China.
| |
Collapse
|
275
|
Jia H, Lu H, Dai M, Hong H, Liu J, Yan C. Effect of root exudates on sorption, desorption, and transport of phenanthrene in mangrove sediments. MARINE POLLUTION BULLETIN 2016; 109:171-177. [PMID: 27293074 DOI: 10.1016/j.marpolbul.2016.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 05/05/2016] [Accepted: 06/02/2016] [Indexed: 05/28/2023]
Abstract
The effect of root exudates on the environmental behaviors of phenanthrene in mangrove sediments is poorly understood. In order to evaluate their influence, comprehensive laboratory experiments were performed using batch equilibrium and thin-layer chromatography (TLC) analyses. In the presence of root exudates, sorption of phenanthrene was inhibited, whereas desorption and mobility were promoted, and were elevated as root exudate concentrations increased. Among the three representative low molecular weight organic acids (LMWOAs) (citric, oxalic, and acetic acids), citric acid promoted desorption and mobility of phenanthrene more effectively than the other two. In addition, application of artificial root exudates (AREs) enhanced phenanthrene desorption, and mobility was always lower than that with the same concentration of LMWOAs, suggesting that LMWOAs predominantly affected the fate of phenanthrene in sediments. The results of this study could enhance our understanding of the mobility of persistent organic pollutants in sediment-water system.
Collapse
Affiliation(s)
- Hui Jia
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, PR China
| | - Haoliang Lu
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, PR China
| | - Minyue Dai
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, PR China
| | - Hualong Hong
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, PR China
| | - Jingchun Liu
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, PR China
| | - Chongling Yan
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, PR China.
| |
Collapse
|
276
|
Frasier I, Quiroga A, Noellemeyer E. Effect of different cover crops on C and N cycling in sorghum NT systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 562:628-639. [PMID: 27107651 DOI: 10.1016/j.scitotenv.2016.04.058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/18/2016] [Accepted: 04/09/2016] [Indexed: 06/05/2023]
Abstract
In many no-till (NT) systems, residue input is low and fallow periods excessive, for which reasons soil degradation occurs. Cover crops could improve organic matter, biological activity, and soil structure. In order to study changes in soil carbon, nitrogen and microbial biomass a field experiment (2010-2012) was set up with sorghum (Sorghum bicolor Moench.) monoculture and with cover crops. Treatments were control (NT with bare fallow), rye (Secale cereale L.) (R), rye with nitrogen fertilization (R+N), vetch (Vicia villosa Roth.) (V), and rye-vetch mixture (VR) cover crops. A completely randomized block design with 4 replicates was used. Soil was sampled once a year at 0.06 and 0.12m depth for total C, microbial biomass carbon (MBC) and-nitrogen (MBN) determinations. Shoot and root biomass of sorghum and cover crops, litter biomass, and their respective carbon and nitrogen contents were determined. Soil temperatures at 0.06 and 0.12m depth, volumetric water contents and nitrate concentrations were determined at sowing, and harvest of each crop, and during sorghum's vegetative phase. NT led to a small increase in MBC and MBN, despite low litter and root biomass residue. Cover crops increased litter, root biomass, total C, MBC, and MBN. Relationships between MBC, MBN, and root-C and -N adjusted to logistic models (R(2)=0.61 and 0.43 for C and N respectively). Litter cover improved soil moisture to 45-50% water filled pore space and soil temperatures not exceeding 25°C during the warmest month. Microbial biomass stabilized at 20.1gCm(-2) and 1.9gNm(-2) in the upper 0.06m. Soil litter disappearance was a good indicator of mineral N availability. These findings support the view that cover crops, specifically legumes in NT systems can increase soil ecosystem services related to water and carbon storage, habitat for biodiversity, and nutrient availability.
Collapse
Affiliation(s)
- Ileana Frasier
- Facultad de Agronomía Universidad Nacional de La Pampa, Santa Rosa, La Pampa, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina; Instituto Nacional de Tecnología Agropecuaria, EEA Anguil, La Pampa, Argentina
| | - Alberto Quiroga
- Facultad de Agronomía Universidad Nacional de La Pampa, Santa Rosa, La Pampa, Argentina; Instituto Nacional de Tecnología Agropecuaria, EEA Anguil, La Pampa, Argentina
| | - Elke Noellemeyer
- Facultad de Agronomía Universidad Nacional de La Pampa, Santa Rosa, La Pampa, Argentina.
| |
Collapse
|
277
|
Hawes M, Allen C, Turgeon BG, Curlango-Rivera G, Minh Tran T, Huskey DA, Xiong Z. Root Border Cells and Their Role in Plant Defense. ANNUAL REVIEW OF PHYTOPATHOLOGY 2016; 54:143-161. [PMID: 27215971 DOI: 10.1146/annurev-phyto-080615-100140] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Root border cells separate from plant root tips and disperse into the soil environment. In most species, each root tip can produce thousands of metabolically active cells daily, with specialized patterns of gene expression. Their function has been an enduring mystery. Recent studies suggest that border cells operate in a manner similar to mammalian neutrophils: Both cell types export a complex of extracellular DNA (exDNA) and antimicrobial proteins that neutralize threats by trapping pathogens and thereby preventing invasion of host tissues. Extracellular DNases (exDNases) of pathogens promote virulence and systemic spread of the microbes. In plants, adding DNase I to root tips eliminates border cell extracellular traps and abolishes root tip resistance to infection. Mutation of genes encoding exDNase activity in plant-pathogenic bacteria (Ralstonia solanacearum) and fungi (Cochliobolus heterostrophus) results in reduced virulence. The study of exDNase activities in plant pathogens may yield new targets for disease control.
Collapse
Affiliation(s)
- Martha Hawes
- Department of Soil, Water and Environmental Sciences, Bio5 Institute, University of Arizona, Tucson, Arizona 85721; , ,
| | - Caitilyn Allen
- Department of Plant Pathology, University of Wisconsin, Madison, Wisconsin 53706; ,
| | - B Gillian Turgeon
- School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology Section, Cornell University, Ithaca, New York 14853;
| | - Gilberto Curlango-Rivera
- Department of Soil, Water and Environmental Sciences, Bio5 Institute, University of Arizona, Tucson, Arizona 85721; , ,
| | - Tuan Minh Tran
- Department of Plant Pathology, University of Wisconsin, Madison, Wisconsin 53706; ,
| | - David A Huskey
- Department of Soil, Water and Environmental Sciences, Bio5 Institute, University of Arizona, Tucson, Arizona 85721; , ,
| | - Zhongguo Xiong
- School of Plant Science, Bio5 Institute, University of Arizona, Tucson, Arizona 85721;
| |
Collapse
|
278
|
Shah AN, Iqbal J, Ullah A, Yang G, Yousaf M, Fahad S, Tanveer M, Hassan W, Tung SA, Wang L, Khan A, Wu Y. Allelopathic potential of oil seed crops in production of crops: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:14854-14867. [PMID: 27263104 DOI: 10.1007/s11356-016-6969-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 05/24/2016] [Indexed: 06/05/2023]
Abstract
Agricultural production enhancement has been realized by more consumption of fossil energy such as fertilizer and agrochemicals. However, the production provides the present human with sufficient and diversified commodities, but at the same time, deprives in some extent the resources from the future human as well. In the other hand, it is known that synthetic herbicides face worldwide threats to human's health and environment as well. Therefore, it is a great challenge for agricultural sustainable development. The current review has been focussed on various oilseed crop species which launch efficient allelopathic intervention, either with weeds or other crops. Crop allelopathic properties can make one species more persistent to a native species. Therefore, these crops are potentially harmful to both naturalized as well as agricultural settings. On the other side, allelopathic crops provide strong potential for the development of cultivars that are more highly weed suppressive in managed settings. It is possible to utilize companion plants that have no deleterious effect on neighbor crops and can be included in intercropping system, thus, a mean of contributing to agricultural sustainable development. In mixed culture, replacement method, wherein differing densities of a neighbor species are planted, has been used to study phytotoxic/competitive effects. So, to use alternative ways for weed suppression has become very crucial. Allelochemicals have the ability to create eco-friendly products for weed management, which is beneficial for agricultural sustainable development. Our present study assessed the potential of four oilseed crops for allelopathy on other crops and associated weeds.
Collapse
Affiliation(s)
- Adnan Noor Shah
- MOA Key Laboratory of Crop Eco physiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Javaid Iqbal
- Ghazi University, Dera Ghazi Khan, 32200, Punjab, Pakistan
| | - Abid Ullah
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Guozheng Yang
- MOA Key Laboratory of Crop Eco physiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
| | - Muhammad Yousaf
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Shah Fahad
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Mohsin Tanveer
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Waseem Hassan
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Shahbaz Atta Tung
- MOA Key Laboratory of Crop Eco physiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Leishan Wang
- MOA Key Laboratory of Crop Eco physiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Aziz Khan
- MOA Key Laboratory of Crop Eco physiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yingying Wu
- MOA Key Laboratory of Crop Eco physiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| |
Collapse
|
279
|
Kimani VN, Chen L, Liu Y, Raza W, Zhang N, Mungai LK, Shen Q, Zhang R. Characterization of extracellular polymeric substances ofBacillus amyloliquefaciensSQR9 induced by root exudates of cucumber. J Basic Microbiol 2016; 56:1183-1193. [DOI: 10.1002/jobm.201600104] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/16/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Veronicah Njeri Kimani
- Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization; National Engineering Research Center for Organic-based Fertilizers; Nanjing Agricultural University; Nanjing P.R. China
| | - Lin Chen
- Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization; National Engineering Research Center for Organic-based Fertilizers; Nanjing Agricultural University; Nanjing P.R. China
| | - Yunpeng Liu
- Key Laboratory of Microbial Resources Collection and Preservation; Ministry of Agriculture; Institute of Agricultural Resources and Regional Planning; Chinese Academy of Agricultural Sciences; Beijing P.R. China
| | - Waseem Raza
- Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization; National Engineering Research Center for Organic-based Fertilizers; Nanjing Agricultural University; Nanjing P.R. China
| | - Nan Zhang
- Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization; National Engineering Research Center for Organic-based Fertilizers; Nanjing Agricultural University; Nanjing P.R. China
| | | | - Qirong Shen
- Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization; National Engineering Research Center for Organic-based Fertilizers; Nanjing Agricultural University; Nanjing P.R. China
| | - Ruifu Zhang
- Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization; National Engineering Research Center for Organic-based Fertilizers; Nanjing Agricultural University; Nanjing P.R. China
- Key Laboratory of Microbial Resources Collection and Preservation; Ministry of Agriculture; Institute of Agricultural Resources and Regional Planning; Chinese Academy of Agricultural Sciences; Beijing P.R. China
| |
Collapse
|
280
|
Ren L, Huo H, Zhang F, Hao W, Xiao L, Dong C, Xu G. The components of rice and watermelon root exudates and their effects on pathogenic fungus and watermelon defense. PLANT SIGNALING & BEHAVIOR 2016; 11:e1187357. [PMID: 27217091 PMCID: PMC4977455 DOI: 10.1080/15592324.2016.1187357] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 04/30/2016] [Accepted: 05/02/2016] [Indexed: 05/26/2023]
Abstract
Watermelon (Citrullus lanatus) is susceptible to wilt disease caused by the fungus Fusarium oxysporum f. sp niveum (FON). Intercropping management of watermelon/aerobic rice (Oryza sativa) alleviates watermelon wilt disease, because some unidentified component(s) in rice root exudates suppress FON sporulation and spore germination. Here, we show that the phenolic acid p-coumaric acid is present in rice root exudates only, and it inhibits FON spore germination and sporulation. We found that exogenously applied p-coumaric acid up-regulated the expression of ClPR3 in roots, as well as increased chitinase activity in leaves. Furthermore, exogenously applied p-coumaric acid increased β-1,3-glucanase activity in watermelon roots. By contrast, we found that ferulic acid was secreted by watermelon roots, but not by rice roots, and that it stimulated spore germination and sporulation of FON. Exogenous application of ferulic acid down-regulated ClPR3 expression and inhibited chitinase activity in watermelon leaves. Salicylic acid was detected in both watermelon and rice root exudates, which stimulated FON spore germination at low concentrations and suppressed spore germination at high concentrations. Exogenously applied salicylic acid did not alter ClPR3 expression, but did increase chitinase and β-1,3-glucanase activities in watermelon leaves. Together, our results show that the root exudates of phenolic acids were different between rice and watermelon, which lead to their special ecological roles on pathogenic fungus and watermelon defense.
Collapse
Affiliation(s)
- Lixuan Ren
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Hongwei Huo
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Fang Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Wenya Hao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Avic Fertilizer Corporation Limited, Beijing, China
| | - Liang Xiao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, China
| | - Caixia Dong
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, China
| | - Guohua Xu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, China
| |
Collapse
|
281
|
Miao CP, Mi QL, Qiao XG, Zheng YK, Chen YW, Xu LH, Guan HL, Zhao LX. Rhizospheric fungi of Panax notoginseng: diversity and antagonism to host phytopathogens. J Ginseng Res 2016; 40:127-34. [PMID: 27158233 PMCID: PMC4845048 DOI: 10.1016/j.jgr.2015.06.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 05/04/2015] [Accepted: 06/14/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Rhizospheric fungi play an essential role in the plant-soil ecosystem, affecting plant growth and health. In this study, we evaluated the fungal diversity in the rhizosphere soil of 2-yr-old healthy Panax notoginseng cultivated in Wenshan, China. METHODS Culture-independent Illumina MiSeq and culture-dependent techniques, combining molecular and morphological characteristics, were used to analyze the rhizospheric fungal diversity. A diffusion test was used to challenge the phytopathogens of P. notoginseng. RESULTS A total of 16,130 paired-end reads of the nuclear ribosomal internal transcribed spacer 2 were generated and clustered into 860 operational taxonomic units at 97% sequence similarity. All the operational taxonomic units were assigned to five phyla and 79 genera. Zygomycota (46.2%) and Ascomycota (37.8%) were the dominant taxa; Mortierella and unclassified Mortierellales accounted for a large proportion (44.9%) at genus level. The relative abundance of Fusarium and Phoma sequences was high, accounting for 12.9% and 5.5%, respectively. In total, 113 fungal isolates were isolated from rhizosphere soil. They were assigned to five classes, eight orders (except for an Incertae sedis), 26 genera, and 43 species based on morphological characteristics and phylogenetic analysis of the internal transcribed spacer. Fusarium was the most isolated genus with six species (24 isolates, 21.2%). The abundance of Phoma was also relatively high (8.0%). Thirteen isolates displayed antimicrobial activity against at least one test fungus. CONCLUSION Our results suggest that diverse fungi including potential pathogenic ones exist in the rhizosphere soil of 2-yr-old P. notoginseng and that antagonistic isolates may be useful for biological control of pathogens.
Collapse
Affiliation(s)
- Cui-Ping Miao
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Qi-Li Mi
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
- Technology Center, China Tobacco Yunnan Industrial Co., Ltd, Kunming, China
| | - Xin-Guo Qiao
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - You-Kun Zheng
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - You-Wei Chen
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Li-Hua Xu
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Hui-Lin Guan
- School of Energy and Environment Science, Yunnan Normal University, Kunming, China
| | - Li-Xing Zhao
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| |
Collapse
|
282
|
Pérez-Jaramillo JE, Mendes R, Raaijmakers JM. Impact of plant domestication on rhizosphere microbiome assembly and functions. PLANT MOLECULAR BIOLOGY 2016; 90:635-44. [PMID: 26085172 PMCID: PMC4819786 DOI: 10.1007/s11103-015-0337-7] [Citation(s) in RCA: 283] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/04/2015] [Indexed: 05/18/2023]
Abstract
The rhizosphere microbiome is pivotal for plant health and growth, providing defence against pests and diseases, facilitating nutrient acquisition and helping plants to withstand abiotic stresses. Plants can actively recruit members of the soil microbial community for positive feedbacks, but the underlying mechanisms and plant traits that drive microbiome assembly and functions are largely unknown. Domestication of plant species has substantially contributed to human civilization, but also caused a strong decrease in the genetic diversity of modern crop cultivars that may have affected the ability of plants to establish beneficial associations with rhizosphere microbes. Here, we review how plants shape the rhizosphere microbiome and how domestication may have impacted rhizosphere microbiome assembly and functions via habitat expansion and via changes in crop management practices, root exudation, root architecture, and plant litter quality. We also propose a "back to the roots" framework that comprises the exploration of the microbiome of indigenous plants and their native habitats for the identification of plant and microbial traits with the ultimate goal to reinstate beneficial associations that may have been undermined during plant domestication.
Collapse
Affiliation(s)
- Juan E Pérez-Jaramillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands
- Sylvius Laboratories, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, Embrapa Environment, Rodovia SP 340 - km 127.5, Jaguariúna, 13820-000, Brazil
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands.
- Sylvius Laboratories, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
| |
Collapse
|
283
|
Haichar FEZ, Heulin T, Guyonnet JP, Achouak W. Stable isotope probing of carbon flow in the plant holobiont. Curr Opin Biotechnol 2016; 41:9-13. [PMID: 27019410 DOI: 10.1016/j.copbio.2016.02.023] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 01/27/2023]
Abstract
Microbial communities associated with a plant host, constituting a holobiont, affect the physiology and growth of the plant via metabolites that are mainly derived from their photosynthates. The structure and function of active microbial communities that assimilate root exudates can be tracked by using stable isotope probing (SIP) approaches. This article reviews results from ongoing SIP research in plant-microbe interactions, with a specific focus on investigating the fate of fresh and recalcitrant carbon in the rhizosphere with 13C enriched-root exudates, in addition to identifying key players in carbon cycling. Finally, we discuss new SIP applications that have the potential to identify novel enzymes implicated in rhizoremediation or plant genes dedicated to root exudation by combining SIP approaches and genome wide associations studies.
Collapse
Affiliation(s)
- Feth El Zahar Haichar
- Université Lyon1, CNRS, UMR5557, INRA, USC1364, Ecologie Microbienne, 69622 Villeurbanne, France.
| | - Thierry Heulin
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA/Cadarache, St-Paul-lez-Durance, France
| | - Julien P Guyonnet
- Université Lyon1, CNRS, UMR5557, INRA, USC1364, Ecologie Microbienne, 69622 Villeurbanne, France
| | - Wafa Achouak
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA/Cadarache, St-Paul-lez-Durance, France
| |
Collapse
|
284
|
Jia H, Lu H, Liu J, Li J, Dai M, Yan C. Effects of root exudates on the leachability, distribution, and bioavailability of phenanthrene and pyrene from mangrove sediments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:5566-5576. [PMID: 26573317 DOI: 10.1007/s11356-015-5772-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 11/05/2015] [Indexed: 06/05/2023]
Abstract
In this study, column leaching experiments were used to evaluate the leachability, distribution and bioavailability of phenanthrene and pyrene by root exudates from contaminated mangrove sediments. We observed that root exudates significantly promoted the release and enhanced the bioavailability of phenanthrene and pyrene from sediment columns. The concentration of phenanthrene and pyrene and cumulative content released from the analyzed sediment samples following root exudate rinsing decreased in the following order: citric acid > oxalic acid > malic acid. After elution, the total concentrations of phenanthrene and pyrene in sediment layers followed a descending order of bottom (9-12 cm) > middle (5-7 cm) > top (0-3 cm). Furthermore, a positive correlation between leachate pH values and PAH concentrations of the leachate was found. Consequently, the addition of root exudates can increase the leachability and bioavailability of phenanthrene and pyrene.
Collapse
Affiliation(s)
- Hui Jia
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, 361102, China
| | - Haoliang Lu
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, 361102, China
| | - Jingchun Liu
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, 361102, China
| | - Jian Li
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, 361102, China
| | - Minyue Dai
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, 361102, China
| | - Chongling Yan
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, 361102, China.
| |
Collapse
|
285
|
Bardon C, Poly F, Piola F, Pancton M, Comte G, Meiffren G, Haichar FEZ. Mechanism of biological denitrification inhibition: procyanidins induce an allosteric transition of the membrane-bound nitrate reductase through membrane alteration. FEMS Microbiol Ecol 2016; 92:fiw034. [PMID: 26906096 DOI: 10.1093/femsec/fiw034] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2016] [Indexed: 12/14/2022] Open
Abstract
Recently, it has been shown that procyanidins from Fallopia spp. inhibit bacterial denitrification, a phenomenon called biological denitrification inhibition (BDI). However, the mechanisms involved in such a process remain unknown. Here, we investigate the mechanisms of BDI involving procyanidins, using the model strain Pseudomonas brassicacearum NFM 421. The aerobic and anaerobic (denitrification) respiration, cell permeability and cell viability of P. brassicacearum were determined as a function of procyanidin concentration. The effect of procyanidins on the bacterial membrane was observed using transmission electronic microscopy. Bacterial growth, denitrification, NO3- and NO2-reductase activity, and the expression of subunits of NO3- (encoded by the gene narG) and NO2-reductase (encoded by the gene nirS) under NO3 or NO2 were measured with and without procyanidins. Procyanidins inhibited the denitrification process without affecting aerobic respiration at low concentrations. Procyanidins also disturbed cell membranes without affecting cell viability. They specifically inhibited NO3- but not NO2-reductase.Pseudomonas brassicacearum responded to procyanidins by over-expression of the membrane-bound NO3-reductase subunit (encoded by the gene narG). Our results suggest that procyanidins can specifically inhibit membrane-bound NO3-reductase inducing enzymatic conformational changes through membrane disturbance and that P. brassicacearum responds by over-expressing membrane-bound NO3-reductase. Our results lead the way to a better understanding of BDI.
Collapse
Affiliation(s)
- Clément Bardon
- Université de Lyon, UMR 5557 LEM, Université Lyon 1, CNRS, INRA USC 1364, F-69622 Villeurbanne Cedex, France Université de Lyon, UMR5023 LEHNA, Université Lyon 1, CNRS, ENTPE, F-69622 Villeurbanne Cedex, France
| | - Franck Poly
- Université de Lyon, UMR 5557 LEM, Université Lyon 1, CNRS, INRA USC 1364, F-69622 Villeurbanne Cedex, France
| | - Florence Piola
- Université de Lyon, UMR5023 LEHNA, Université Lyon 1, CNRS, ENTPE, F-69622 Villeurbanne Cedex, France
| | - Muriel Pancton
- Université de Lyon, UMR5276 LGLTPE, Université Lyon 1, CNRS, ENTPE, F-69622 Villeurbanne Cedex, France
| | - Gilles Comte
- Université de Lyon, UMR 5557 LEM, Université Lyon 1, CNRS, INRA USC 1364, F-69622 Villeurbanne Cedex, France
| | - Guillaume Meiffren
- Université de Lyon, UMR 5557 LEM, Université Lyon 1, CNRS, INRA USC 1364, F-69622 Villeurbanne Cedex, France
| | - Feth el Zahar Haichar
- Université de Lyon, UMR 5557 LEM, Université Lyon 1, CNRS, INRA USC 1364, F-69622 Villeurbanne Cedex, France
| |
Collapse
|
286
|
Mining the genome of Rhodococcus fascians, a plant growth-promoting bacterium gone astray. N Biotechnol 2016; 33:706-717. [PMID: 26877150 DOI: 10.1016/j.nbt.2016.01.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/16/2015] [Accepted: 01/05/2016] [Indexed: 11/21/2022]
Abstract
Rhodococcus fascians is a phytopathogenic Gram-positive Actinomycete with a very broad host range encompassing especially dicotyledonous herbaceous perennials, but also some monocots, such as the Liliaceae and, recently, the woody crop pistachio. The pathogenicity of R. fascians strain D188 is known to be encoded by the linear plasmid pFiD188 and to be dictated by its capacity to produce a mixture of cytokinins. Here, we show that D188-5, the nonpathogenic plasmid-free derivative of the wild-type strain D188 actually has a plant growth-promoting effect. With the availability of the genome sequence of R. fascians, the chromosome of strain D188 was mined for putative plant growth-promoting functions and the functionality of some of these activities was tested. This analysis together with previous results suggests that the plant growth-promoting activity of R. fascians is due to production of plant growth modulators, such as auxin and cytokinin, combined with degradation of ethylene through 1-amino-cyclopropane-1-carboxylic acid deaminase. Moreover, R. fascians has several functions that could contribute to efficient colonization and competitiveness, but there is little evidence for a strong impact on plant nutrition. Possibly, the plant growth promotion encoded by the D188 chromosome is imperative for the epiphytic phase of the life cycle of R. fascians and prepares the plant to host the bacteria, thus ensuring proper continuation into the pathogenic phase.
Collapse
|
287
|
Postma A, Slabbert E, Postma F, Jacobs K. Soil bacterial communities associated with natural and commercialCyclopiaspp. FEMS Microbiol Ecol 2016; 92:fiw016. [DOI: 10.1093/femsec/fiw016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2016] [Indexed: 12/16/2022] Open
|
288
|
Extracellular Trapping of Soil Contaminants by Root Border Cells: New Insights into Plant Defense. AGRONOMY-BASEL 2016. [DOI: 10.3390/agronomy6010005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
289
|
Mueller P, Jensen K, Megonigal JP. Plants mediate soil organic matter decomposition in response to sea level rise. GLOBAL CHANGE BIOLOGY 2016; 22:404-414. [PMID: 26342160 DOI: 10.1111/gcb.13082] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 08/20/2015] [Indexed: 06/05/2023]
Abstract
Tidal marshes have a large capacity for producing and storing organic matter, making their role in the global carbon budget disproportionate to land area. Most of the organic matter stored in these systems is in soils where it contributes 2-5 times more to surface accretion than an equal mass of minerals. Soil organic matter (SOM) sequestration is the primary process by which tidal marshes become perched high in the tidal frame, decreasing their vulnerability to accelerated relative sea level rise (RSLR). Plant growth responses to RSLR are well understood and represented in century-scale forecast models of soil surface elevation change. We understand far less about the response of SOM decomposition to accelerated RSLR. Here we quantified the effects of flooding depth and duration on SOM decomposition by exposing planted and unplanted field-based mesocosms to experimentally manipulated relative sea level over two consecutive growing seasons. SOM decomposition was quantified as CO2 efflux, with plant- and SOM-derived CO2 separated via δ(13) CO2 . Despite the dominant paradigm that decomposition rates are inversely related to flooding, SOM decomposition in the absence of plants was not sensitive to flooding depth and duration. The presence of plants had a dramatic effect on SOM decomposition, increasing SOM-derived CO2 flux by up to 267% and 125% (in 2012 and 2013, respectively) compared to unplanted controls in the two growing seasons. Furthermore, plant stimulation of SOM decomposition was strongly and positively related to plant biomass and in particular aboveground biomass. We conclude that SOM decomposition rates are not directly driven by relative sea level and its effect on oxygen diffusion through soil, but indirectly by plant responses to relative sea level. If this result applies more generally to tidal wetlands, it has important implications for models of SOM accumulation and surface elevation change in response to accelerated RSLR.
Collapse
Affiliation(s)
- Peter Mueller
- Applied Plant Ecology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Kai Jensen
- Applied Plant Ecology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | | |
Collapse
|
290
|
Xu L, Cui H, Zheng X, Zhu Z, Liang J, Zhou J. Immobilization of copper and cadmium by hydroxyapatite combined with phytoextraction and changes in microbial community structure in a smelter-impacted soil. RSC Adv 2016. [DOI: 10.1039/c6ra23487a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Soil heavy metal fraction and microbial community structure can be changed by combined remediation of hydroxyapatite and plants.
Collapse
Affiliation(s)
- Lei Xu
- Institute of Soil Science
- Chinese Academy of Sciences
- Nanjing 210008
- China
- National Engineering and Technology Research Center for Red Soil Improvement
| | - Hongbiao Cui
- School of Earth and Environment
- Anhui University of Science and Technology
- Huainan 232001
- China
| | - Xuebo Zheng
- Institute of Soil Science
- Chinese Academy of Sciences
- Nanjing 210008
- China
- National Engineering and Technology Research Center for Red Soil Improvement
| | - Zhenqiu Zhu
- Institute of Soil Science
- Chinese Academy of Sciences
- Nanjing 210008
- China
- National Engineering and Technology Research Center for Red Soil Improvement
| | - Jiani Liang
- Institute of Soil Science
- Chinese Academy of Sciences
- Nanjing 210008
- China
- National Engineering and Technology Research Center for Red Soil Improvement
| | - Jing Zhou
- Institute of Soil Science
- Chinese Academy of Sciences
- Nanjing 210008
- China
- National Engineering and Technology Research Center for Red Soil Improvement
| |
Collapse
|
291
|
Dovana F, Mucciarelli M, Mascarello M, Fusconi A. In Vitro Morphogenesis of Arabidopsis to Search for Novel Endophytic Fungi Modulating Plant Growth. PLoS One 2015; 10:e0143353. [PMID: 26641657 PMCID: PMC4671684 DOI: 10.1371/journal.pone.0143353] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/03/2015] [Indexed: 11/20/2022] Open
Abstract
Fungal endophytes have shown to affect plant growth and to confer stress tolerance to the host; however, effects of endophytes isolated from water plants have been poorly investigated. In this study, fungi isolated from stems (stem-E) and roots (root-E) of Mentha aquatica L. (water mint) were identified, and their morphogenetic properties analysed on in vitro cultured Arabidopsis (L.) Heynh., 14 and 21 days after inoculation (DAI). Nineteen fungi were analysed and, based on ITS analysis, 17 isolates showed to be genetically distinct. The overall effect of water mint endophytes on Arabidopsis fresh (FW) and dry weight (DW) was neutral and positive, respectively, and the increased DW, mainly occurring 14 DAI, was possibly related to plant defence mechanism. Only three fungi increased both FW and DW of Arabidopsis at 14 and 21 DAI, thus behaving as plant growth promoting (PGP) fungi. E-treatment caused a reduction of root depth and primary root length in most cases and inhibition-to-promotion of root area and lateral root length, from 14 DAI. Only Phoma macrostoma, among the water mint PGP fungi, increased both root area and depth, 21 DAI. Root depth and area 14 DAI were shown to influence DWs, indicating that the extension of the root system, and thus nutrient uptake, was an important determinant of plant dry biomass. Reduction of Arabidopsis root depth occurred to a great extent when plants where treated with stem-E while root area decreased or increased under the effects of stem-E and root-E, respectively, pointing to an influence of the endophyte origin on root extension. M. aquatica and many other perennial hydrophytes have growing worldwide application in water pollution remediation. The present study provided a model for directed screening of endophytes able to modulate plant growth in the perspective of future field applications of these fungi.
Collapse
Affiliation(s)
- Francesco Dovana
- Department of Sciences and Innovative Technology, University of Piemonte Orientale, Alessandria, Italy
| | - Marco Mucciarelli
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Maurizio Mascarello
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Anna Fusconi
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| |
Collapse
|
292
|
Chitarra W, Siciliano I, Ferrocino I, Gullino ML, Garibaldi A. Effect of Elevated Atmospheric CO2 and Temperature on the Disease Severity of Rocket Plants Caused by Fusarium Wilt under Phytotron Conditions. PLoS One 2015; 10:e0140769. [PMID: 26469870 PMCID: PMC4607163 DOI: 10.1371/journal.pone.0140769] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/30/2015] [Indexed: 11/20/2022] Open
Abstract
The severity of F. oxysporum f.sp. conglutinans on rocket plants grown under simulated climate change conditions has been studied. The rocket plants were cultivated on an infested substrate (4 log CFU g-1) and a non-infested substrate over three cycles. Pots were placed in six phytotrons in order to simulate different environmental conditions: 1) 400-450 ppm CO2, 18-22°C; 2) 800-850 ppm CO2, 18-22°C; 3) 400-450 ppm CO2, 22-26°C, 4) 800-850 ppm CO2, 22-26°C, 5) 400-450 ppm CO2, 26-30°C; 6) 800-850 ppm CO2, 26-30°C. Substrates from the infested and control samples were collected from each phytotron at 0, 60 and 120 days after transplanting. The disease index, microbial abundance, leaf physiological performances, root exudates and variability in the fungal profiles were monitored. The disease index was found to be significantly influenced by higher levels of temperature and CO2. Plate counts showed that fungal and bacterial development was not affected by the different CO2 and temperature levels, but a significant decreasing trend was observed from 0 up to 120 days. Conversely, the F. oxysporum f.sp. conglutinans plate counts did not show any significantly decrease from 0 up to 120 days. The fungal profiles, evaluated by means of polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE), showed a relationship to temperature and CO2 on fungal diversity profiles. Different exudation patterns were observed when the controls and infested plants were compared, and it was found that both CO2 and temperature can influence the release of compounds from the roots of rocket plants. In short, the results show that global climate changes could influence disease incidence, probably through plant-mediated effects, caused by soilborne pathogens.
Collapse
Affiliation(s)
- Walter Chitarra
- Centre for Innovation in the Agro-Environmental Sector, AGROINNOVA, University of Torino, Largo P. Braccini 2, Grugliasco (TO), Italy
| | - Ilenia Siciliano
- Centre for Innovation in the Agro-Environmental Sector, AGROINNOVA, University of Torino, Largo P. Braccini 2, Grugliasco (TO), Italy
| | - Ilario Ferrocino
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Largo P. Braccini 2, Grugliasco (TO), Italy
| | - Maria Lodovica Gullino
- Centre for Innovation in the Agro-Environmental Sector, AGROINNOVA, University of Torino, Largo P. Braccini 2, Grugliasco (TO), Italy
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Largo P. Braccini 2, Grugliasco (TO), Italy
| | - Angelo Garibaldi
- Centre for Innovation in the Agro-Environmental Sector, AGROINNOVA, University of Torino, Largo P. Braccini 2, Grugliasco (TO), Italy
| |
Collapse
|
293
|
Schiltz S, Gaillard I, Pawlicki-Jullian N, Thiombiano B, Mesnard F, Gontier E. A review: what is the spermosphere and how can it be studied? J Appl Microbiol 2015; 119:1467-81. [PMID: 26332271 DOI: 10.1111/jam.12946] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/27/2015] [Accepted: 08/15/2015] [Indexed: 11/27/2022]
Abstract
The spermosphere is the zone surrounding seeds where interactions between the soil, microbial communities and germinating seeds take place. The concept of the spermosphere is usually only applied during germination sensu stricto. Despite the transient nature of this very small zone of soil around the germinating seed, the microbial activities which occur there may have long-lasting impacts on plants. The spermosphere is indirectly characterized by either (i) seed exudates, which could be inhibitors or stimulators of micro-organism growth or (ii) the composition of the microbiome on and around the germinating seeds. The microbial communities present in the spermosphere directly reflect that of the germination medium or are host-dependent and influenced quantitatively and qualitatively by host exudates. Despite its strong impact on the future development of plants, the spermosphere remains little studied. This can be explained by the technical difficulties related to characterizing this concept due to its short duration, small size and biomass, and the number and complexity of the interactions that take place. However, recent technical methods, such as metabolite profiling, combining phenotypic methods with DNA- and RNA-based methods, could be used to investigate seed exudates, microbial communities and their interactions with the soil environment.
Collapse
Affiliation(s)
- S Schiltz
- Biologie des Plantes et Innovation (BIOPI), Université de Picardie Jules Verne, Amiens, France
| | - I Gaillard
- Biologie des Plantes et Innovation (BIOPI), Université de Picardie Jules Verne, Amiens, France
| | - N Pawlicki-Jullian
- Biologie des Plantes et Innovation (BIOPI), Université de Picardie Jules Verne, Amiens, France
| | - B Thiombiano
- Biologie des Plantes et Innovation (BIOPI), Université de Picardie Jules Verne, Amiens, France
| | - F Mesnard
- Biologie des Plantes et Innovation (BIOPI), Université de Picardie Jules Verne, Amiens, France
| | - E Gontier
- Biologie des Plantes et Innovation (BIOPI), Université de Picardie Jules Verne, Amiens, France
| |
Collapse
|
294
|
Ranjan K, Paula FS, Mueller RC, Jesus EDC, Cenciani K, Bohannan BJM, Nüsslein K, Rodrigues JLM. Forest-to-pasture conversion increases the diversity of the phylum Verrucomicrobia in Amazon rainforest soils. Front Microbiol 2015; 6:779. [PMID: 26284056 PMCID: PMC4519759 DOI: 10.3389/fmicb.2015.00779] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 07/15/2015] [Indexed: 11/13/2022] Open
Abstract
The Amazon rainforest is well known for its rich plant and animal diversity, but its bacterial diversity is virtually unexplored. Due to ongoing and widespread deforestation followed by conversion to agriculture, there is an urgent need to quantify the soil biological diversity within this tropical ecosystem. Given the abundance of the phylum Verrucomicrobia in soils, we targeted this group to examine its response to forest-to-pasture conversion. Both taxonomic and phylogenetic diversities were higher for pasture in comparison to primary and secondary forests. The community composition of Verrucomicrobia in pasture soils was significantly different from those of forests, with a 11.6% increase in the number of sequences belonging to subphylum 3 and a proportional decrease in sequences belonging to the class Spartobacteria. Based on 99% operational taxonomic unit identity, 40% of the sequences have not been detected in previous studies, underscoring the limited knowledge regarding the diversity of microorganisms in tropical ecosystems. The abundance of Verrucomicrobia, measured with quantitative PCR, was strongly correlated with soil C content (r = 0.80, P = 0.0016), indicating their importance in metabolizing plant-derived carbon compounds in soils.
Collapse
Affiliation(s)
- Kshitij Ranjan
- Department of Biology, The University of Texas at Arlington Arlington, TX, USA
| | - Fabiana S Paula
- Department of Biology, The University of Texas at Arlington Arlington, TX, USA
| | - Rebecca C Mueller
- Institute of Ecology and Evolution, University of Oregon Eugene, OR, USA
| | | | - Karina Cenciani
- Centro de Energia Nuclear na Agricultura, University of Sao Paulo Piracicaba, Brazil
| | | | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | - Jorge L M Rodrigues
- Department of Land, Air and Water Resources, University of California, Davis Davis, CA, USA
| |
Collapse
|
295
|
Sugiyama A, Yamazaki Y, Yamashita K, Takahashi S, Nakayama T, Yazaki K. Developmental and nutritional regulation of isoflavone secretion from soybean roots. Biosci Biotechnol Biochem 2015; 80:89-94. [PMID: 26168358 DOI: 10.1080/09168451.2015.1062714] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 06/09/2015] [Indexed: 12/26/2022]
Abstract
Isoflavones play important roles in plant-microbe interactions in rhizospheres. Soybean roots secrete daidzein and genistein to attract rhizobia. Despite the importance of isoflavones in plant-microbe interactions, little is known about the developmental and nutritional regulation of isoflavone secretion from soybean roots. In this study, soybeans were grown in hydroponic culture, and isoflavone contents in tissues, isoflavone secretion from the roots, and the expression of isoflavone conjugates hydrolyzing beta-glucosidase (ICHG) were investigated. Isoflavone contents did not show strong growth-dependent changes, while secretion of daidzein from the roots dramatically changed, with higher secretion during vegetative stages. Coordinately, the expression of ICHG also peaked at vegetative stages. Nitrogen deficiency resulted in 8- and 15-fold increases in secretion of daidzein and genistein, respectively, with no induction of ICHG. Taken together, these results suggest that large amounts of isoflavones were secreted during vegetative stages via the hydrolysis of (malonyl)glucosides with ICHG.
Collapse
Affiliation(s)
- Akifumi Sugiyama
- a Research Institute for Sustainable Humanosphere , Kyoto University , Uji , Japan
| | - Yumi Yamazaki
- a Research Institute for Sustainable Humanosphere , Kyoto University , Uji , Japan
| | - Kazuaki Yamashita
- a Research Institute for Sustainable Humanosphere , Kyoto University , Uji , Japan
| | - Seiji Takahashi
- b Department of Biomolecular Engineering , Graduate School of Engineering, Tohoku University , Aoba, Sendai , Japan
| | - Toru Nakayama
- b Department of Biomolecular Engineering , Graduate School of Engineering, Tohoku University , Aoba, Sendai , Japan
| | - Kazufumi Yazaki
- a Research Institute for Sustainable Humanosphere , Kyoto University , Uji , Japan
| |
Collapse
|
296
|
Akhter A, Hage-Ahmed K, Soja G, Steinkellner S. Compost and biochar alter mycorrhization, tomato root exudation, and development of Fusarium oxysporum f. sp. lycopersici. FRONTIERS IN PLANT SCIENCE 2015; 6:529. [PMID: 26217373 PMCID: PMC4498038 DOI: 10.3389/fpls.2015.00529] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 06/29/2015] [Indexed: 05/21/2023]
Abstract
Soil amendments like compost and biochar are known to affect soil properties, plant growth as well as soil borne plant pathogens. Complex interactions based on microbial activity and abiotic characteristics are supposed to be responsible for suppressive properties of certain substrates, however, the specific mechanisms of action are still widely unknown. In the present study, the main focus was on the development of the soil borne pathogen, Fusarium oxysporum f.sp. lycopersici (Fol) in tomato (Solanum lycopersicum L.) and changes in root exudates of tomato plants grown in different soil substrate compositions, such as compost (Comp) alone at application rate of 20% (v/v), and in combination with wood biochar (WB; made from beech wood chips) or green waste biochar (GWB; made from garden waste residues) at application rate of 3% (v/v), and/or with additional arbuscular mycorrhizal fungi (AMF). The association of GWB and AMF had a positive effect on tomato plants growth unlike to the plants grown in WB containing a soil substrate. The AMF root colonization was not enhanced by the addition of WB or GWB in the soil substrate, though a bio-protective effect of mycorrhization was evident in both biochar amended treatments against Fol. Compost and biochars altered root exudates differently, which is evident from variable response of in vitro growth and development of Fol. The microconidia germination was highest in root exudates from plants grown in the soil containing compost and GWB, whereas root exudates of plants from a substrate containing WB suppressed the mycelial growth and development of Fol. In conclusion, the plant growth response and disease suppression in biochar containing substrates with additional AMF was affected by the feedstock type. Moreover, application of compost and biochars in the soil influence the quality and composition of root exudates with respect to their effects on soil-dwelling fungi.
Collapse
Affiliation(s)
- Adnan Akhter
- Division of Plant Protection, Department of Crop Sciences, University of Natural Resources and Life Sciences ViennaTulln, Austria
| | - Karin Hage-Ahmed
- Division of Plant Protection, Department of Crop Sciences, University of Natural Resources and Life Sciences ViennaTulln, Austria
| | - Gerhard Soja
- Department of Health and Environment, Austrian Institute of TechnologyTulln, Austria
| | - Siegrid Steinkellner
- Division of Plant Protection, Department of Crop Sciences, University of Natural Resources and Life Sciences ViennaTulln, Austria
| |
Collapse
|
297
|
Fryday S, Tiede K, Stein J. Scientific services to support EFSA systematic reviews: Lot 5 Systematic literature review on the neonicotinoids (namely active substances clothianidin, thiamethoxam and imidacloprid) and the risks to bees (Tender specifications RC/EFSA/PRAS/2013/03). ACTA ACUST UNITED AC 2015. [DOI: 10.2903/sp.efsa.2015.en-756] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
298
|
|
299
|
Carbon Turnover during Effluent Application to the Land: A Potential Role for Vegetation? WATER 2015. [DOI: 10.3390/w7010288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
300
|
Woo DK, Quijano JC, Kumar P, Chaoka S, Bernacchi CJ. Threshold dynamics in soil carbon storage for bioenergy crops. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:12090-8. [PMID: 25207669 DOI: 10.1021/es5023762] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Because of increasing demands for bioenergy, a considerable amount of land in the midwestern United States could be devoted to the cultivation of second-generation bioenergy crops, such as switchgrass and miscanthus. The foliar carbon/nitrogen ratio (C/N) in these bioenergy crops at harvest is significantly higher than the ratios in replaced crops, such as corn or soybean. We show that there is a critical soil organic matter C/N ratio, where microbial biomass can be impaired as microorganisms become dependent upon net immobilization. The simulation results show that there is a threshold effect in the amount of aboveground litter input in the soil after harvest that will reach a critical organic matter C/N ratio in the soil, triggering a reduction of the soil microbial population, with significant consequences in other microbe-related processes, such as decomposition and mineralization. These thresholds are approximately 25 and 15% of aboveground biomass for switchgrass and miscanthus, respectively. These results suggest that values above these thresholds could result in a significant reduction of decomposition and mineralization, which, in turn, would enhance the sequestration of atmospheric carbon dioxide in the topsoil and reduce inorganic nitrogen losses when compared to a corn-corn-soybean rotation.
Collapse
Affiliation(s)
- Dong K Woo
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign , 205 North Mathews Avenue, Urbana, Illinois 61801-2352, United States
| | | | | | | | | |
Collapse
|