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Kończak B, Wiesner-Sękala M, Ziembińska-Buczyńska A. The European trees phyllosphere characteristics and its potential in air bioremediation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 349:123977. [PMID: 38621454 DOI: 10.1016/j.envpol.2024.123977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/08/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
The air pollution remediation is naturally carried out by plants. Their overground parts called phyllosphere are a type of a natural filter on which pollutants can be adsorb. Moreover, microbial communities living in phyllosphere perform a variety of biochemical processes removing also chemical pollutants. As their pollution is nowadays a burning issue especially for highly developed countries, the development of effective and ecological technologies for air treatment are of the utmost importance. The use of phyllosphere bacteria in the process of air bioremediation is a promising technology. This article reviews the role of phyllospheric bacteria in air bioremediation processes especially linked with the moderate climate plants. Research results published so far indicate that phyllosphere bacteria are able to metabolize the air pollutants but their potential is strictly determined by plant-phyllospheric bacteria interaction. The European tree species most commonly used for this purpose are also presented. The collected information filled the gap in the practical use of tree species in air bioremediation in the moderate climate zone.
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Affiliation(s)
- B Kończak
- Department of Water Protection, Central Mining Institute - National Research Institute, Plac Gwarków 1, 40-166, Katowice, Poland.
| | - M Wiesner-Sękala
- Department of Water Protection, Central Mining Institute - National Research Institute, Plac Gwarków 1, 40-166, Katowice, Poland.
| | - A Ziembińska-Buczyńska
- Department of Environmental Biotechnology, Faculty of Power and Environmental Engineering, Silesian University of Technology, str. Akademicka 2, 44-100, Gliwice, Poland.
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Saha BK, Roy V, Saha J, Chatterjee A, Pal A. Study of mercury resistance and Fourier transform infrared spectroscopy-based metabolic profiling of a potent Bacillus tropicus strain from forest soil. J Basic Microbiol 2024; 64:e2300351. [PMID: 37847888 DOI: 10.1002/jobm.202300351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/01/2023] [Accepted: 10/07/2023] [Indexed: 10/19/2023]
Abstract
Mercury (Hg) is a highly toxic heavy metal and Hg-resistant indigenous bacterial isolates may offer a green and cost-effective bioremediation strategy to counter Hg contamination. In this study, a potent Hg-resistant bacterium was isolated from the forest soil of a bird sanctuary. Identification using matrix-assisted laser desorption ionization-time of flight mass spectrometry depicted the isolate as a strain of Bacillus tropicus, validated by morphological, biochemical, and molecular studies. The isolate demonstrated biological Hg removal efficiency and capacity of 50.67% and 19.76 mg g-1 , respectively. The plasmid borne resistance determinant, merA, encoding mercuric reductase, was detected in the bacterium endowing it with effective Hg volatilization and resistance capability. A Fourier-transform infrared spectroscopic comparative metabolic profiling revealed the involvement of various functional groups like -COOH, -CH2 , -OH, PO4 - and so on, resulting in differential spectral patterns of the bacterium both in control and Hg-exposed situations. A temporal variance in metabolic signature was also observed during the early and mid-log phase of growth in the presence of Hg. The bacterium described in this study is the first indigenous Hg-resistant strain isolated from the Uttar Dinajpur region, which could be further explored and exploited as a potent bioresource for Hg remediation.
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Affiliation(s)
- Barnan K Saha
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal, India
| | - Vivek Roy
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal, India
| | - Jayanti Saha
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal, India
- Department of Botany, Acharya Prafulla Chandra Roy Government College, Himachal Bihar, Matigara, Siliguri, West Bengal, India
| | - Abhik Chatterjee
- Design, Synthesis & Simulation Laboratory, Department of Chemistry, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal, India
| | - Ayon Pal
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal, India
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Pfendler S, Ciadamidaro L, Ozaki S, Bonin A, Taberlet P, Zappelini C, Maillard F, Blaudez D, Chalot M. Differential effects of tree species identity on rhizospheric bacterial and fungal community richness and composition across multiple trace element-contaminated sites. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168600. [PMID: 37981137 DOI: 10.1016/j.scitotenv.2023.168600] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 11/21/2023]
Abstract
Soil microbial communities play a key role in plant nutrition and stress tolerance. This is particularly true in sites contaminated by trace metals, which often have low fertility and stressful conditions for woody plants in particular. However, we have limited knowledge of the abiotic and biotic factors affecting the richness and composition of microbial communities inhabiting the rhizosphere of plants in contaminated sites. Using high-throughput amplicon sequencing, we studied the rhizospheric bacterial and fungal community structures of 14 woody plant families planted in three contrasting sites contaminated by metals (Pb, Cd, Zn, Mn, Fe, S). The rhizospheric bacterial communities in the given sites showed no significant difference between the various woody species but did differ significantly between sites. The Proteobacteria phylum was dominant, accounting for over 25 % of the overall relative abundance, followed by Actinobacteria, Bacteroidetes and Gemmatimonadetes. Site was also the main driver of fungal community composition, yet unlike bacteria, tree species identity significantly affected fungal communities. The Betulaceae, Salicaceae and Fagaceae families had a high proportion of Basidiomycota, particularly ectomycorrhizal fungi, and the lowest diversity and richness. The other tree families and the unplanted soil harboured a greater abundance of Ascomycota and Mucoromycota. Consequently, for both bacteria and fungi, the site effect significantly impacted their community richness and composition, while the influence of plants on the richness and composition of rhizospheric microbial communities stayed consistent across sites and was dependent on the microbial kingdom. Finally, we highlighted the importance of considering this contrasting response of plant rhizospheric microbial communities in relation to their host identity, particularly to improve assisted revegetation efforts at contaminated sites.
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Affiliation(s)
- Stéphane Pfendler
- Université de Franche-Comté, CNRS, Chrono-environnement, F-25200 Montbéliard, France.
| | - Lisa Ciadamidaro
- Université de Franche-Comté, CNRS, Chrono-environnement, F-25200 Montbéliard, France
| | - Shinji Ozaki
- Université de Franche-Comté, CNRS, Chrono-environnement, F-25200 Montbéliard, France
| | - Aurélie Bonin
- Université Grenoble Alpes, CNRS, LECA, Laboratoire d'Ecologie Alpine, F-38000 Grenoble, France
| | - Pierre Taberlet
- Université Grenoble Alpes, CNRS, LECA, Laboratoire d'Ecologie Alpine, F-38000 Grenoble, France; UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, Norway
| | - Cyril Zappelini
- Université de Franche-Comté, CNRS, Chrono-environnement, F-25200 Montbéliard, France
| | - François Maillard
- Université de Franche-Comté, CNRS, Chrono-environnement, F-25200 Montbéliard, France
| | - Damien Blaudez
- Université de Lorraine, CNRS, LIEC, F-54000 Nancy, France
| | - Michel Chalot
- Université de Franche-Comté, CNRS, Chrono-environnement, F-25200 Montbéliard, France; Université de Lorraine, Faculté des Sciences et Technologies, F-54000 Nancy, France
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Xiong Q, Yang J, Ni S. Microbiome-Mediated Protection against Pathogens in Woody Plants. Int J Mol Sci 2023; 24:16118. [PMID: 38003306 PMCID: PMC10671361 DOI: 10.3390/ijms242216118] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/23/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
Pathogens, especially invasive species, have caused significant global ecological, economic, and social losses in forests. Plant disease research has traditionally focused on direct interactions between plants and pathogens in an appropriate environment. However, recent research indicates that the microbiome can interact with the plant host and pathogens to modulate plant resistance or pathogen pathogenicity, thereby altering the outcome of plant-pathogen interactions. Thus, this presents new opportunities for studying the microbial management of forest diseases. Compared to parallel studies on human and crop microbiomes, research into the forest tree microbiome and its critical role in forest disease progression has lagged. The rapid development of microbiome sequencing and analysis technologies has resulted in the rapid accumulation of a large body of evidence regarding the association between forest microbiomes and diseases. These data will aid the development of innovative, effective, and environmentally sustainable methods for the microbial management of forest diseases. Herein, we summarize the most recent findings on the dynamic structure and composition of forest tree microbiomes in belowground and aboveground plant tissues (i.e., rhizosphere, endosphere, and phyllosphere), as well as their pleiotropic impact on plant immunity and pathogen pathogenicity, highlighting representative examples of biological control agents used to modulate relevant tree microbiomes. Lastly, we discuss the potential application of forest tree microbiomes in disease control as well as their future prospects and challenges.
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Affiliation(s)
- Qin Xiong
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (J.Y.); (S.N.)
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Hakobyan A, Velte S, Sickel W, Quandt D, Stoll A, Knief C. Tillandsia landbeckii phyllosphere and laimosphere as refugia for bacterial life in a hyperarid desert environment. MICROBIOME 2023; 11:246. [PMID: 37936139 PMCID: PMC10631034 DOI: 10.1186/s40168-023-01684-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/28/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND The lack of water is a major constraint for microbial life in hyperarid deserts. Consequently, the abundance and diversity of microorganisms in common habitats such as soil are strongly reduced, and colonization occurs primarily by specifically adapted microorganisms that thrive in particular refugia to escape the harsh conditions that prevail in these deserts. We suggest that plants provide another refugium for microbial life in hyperarid deserts. We studied the bacterial colonization of Tillandsia landbeckii (Bromeliaceae) plants, which occur in the hyperarid regions of the Atacama Desert in Chile, one of the driest and oldest deserts on Earth. RESULTS We detected clear differences between the bacterial communities being plant associated to those of the bare soil surface (PERMANOVA, R2 = 0.187, p = 0.001), indicating that Tillandsia plants host a specific bacterial community, not only dust-deposited cells. Moreover, the bacterial communities in the phyllosphere were distinct from those in the laimosphere, i.e., on buried shoots (R2 = 0.108, p = 0.001), indicating further habitat differentiation within plant individuals. The bacterial taxa detected in the phyllosphere are partly well-known phyllosphere colonizers, but in addition, some rather unusual taxa (subgroup2 Acidobacteriae, Acidiphilum) and insect endosymbionts (Wolbachia, "Candidatus Uzinura") were found. The laimosphere hosted phyllosphere-associated as well as soil-derived taxa. The phyllosphere bacterial communities showed biogeographic patterns across the desert (R2 = 0.331, p = 0.001). These patterns were different and even more pronounced in the laimosphere (R2 = 0.467, p = 0.001), indicating that different factors determine community assembly in the two plant compartments. Furthermore, the phyllosphere microbiota underwent temporal changes (R2 = 0.064, p = 0.001). CONCLUSIONS Our data demonstrate that T. landbeckii plants host specific bacterial communities in the phyllosphere as well as in the laimosphere. Therewith, these plants provide compartment-specific refugia for microbial life in hyperarid desert environments. The bacterial communities show biogeographic patterns and temporal variation, as known from other plant microbiomes, demonstrating environmental responsiveness and suggesting that bacteria inhabit these plants as viable microorganisms. Video Abstract.
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Affiliation(s)
- Anna Hakobyan
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
| | - Stefanie Velte
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
| | - Wiebke Sickel
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
- Institute of Biodiversity, Johann Heinrich Von Thünen Institute, Brunswick, Germany
| | - Dietmar Quandt
- Nees Institute for Biodiversity of Plants, University of Bonn, Bonn, Germany
| | - Alexandra Stoll
- Centro de Estudios Avanzados en Zonas Áridas Ceaza, La Serena, Chile
- Instituto de Investigación Multidisciplinar en Ciencia y Tecnología, Universidad de La Serena, La Serena, Chile
| | - Claudia Knief
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany.
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Jiao R, Wu B, Liang Z, Gao P, Gao X. GLV reveal species differences and responses to environment in alpine shrub Rosa sericea complex. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:166146. [PMID: 37595914 DOI: 10.1016/j.scitotenv.2023.166146] [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: 05/23/2023] [Revised: 07/20/2023] [Accepted: 08/06/2023] [Indexed: 08/20/2023]
Abstract
Plant Volatile components are an ecological adaptation mechanism of plants that can reflect species differences and environment information where it is located. The alpine shrub Rosa sericea complex consists of several allied species, which are morphologically similar and difficult to distinguish, they are typical distribution along the elevation in the Himalayas and the Transverse Ranges. We selected two typical areas to find that the different species could be distinguished by their "green leaf volatile components" (GLV) composition as well as their geographical location, and it was evident that species with glands had higher sesquiterpene content. Correlation analysis revealed the relation between volatile components and ecology factors (climate factors, soil factors, phyllospheric microorganisms). Our study adds a new perspective and basis for the environmental adaptations of different species in the alpine shrub Rosa sericea complex from a chemical ecology perspective.
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Affiliation(s)
- Ruifang Jiao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Xingke Road 723, Guangzhou 510650, China
| | - Bohan Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Zhenlong Liang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Gao
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
| | - Xinfen Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
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Lacson MLB, Arbotante CA, Magdayao MJTE, Bundalian RD, Anas ARJ. Ultra-high-performance liquid chromatography-tandem high-resolution elevated mass spectrometry profiling of anti-methicillin-resistant Staphylococcus aureus metabolites from the endophytic bacteria collected from the weeds of a previous dumpsite. J Chromatogr A 2023; 1706:464228. [PMID: 37556933 DOI: 10.1016/j.chroma.2023.464228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/08/2023] [Accepted: 07/19/2023] [Indexed: 08/11/2023]
Abstract
The culturable endophytic bacteria from the weeds Cleome rutidosperma of the family Cleomaceae and Digitaria sanguinalis of the family Poaceae obtained from a previous dumpsite in Pampanga, Philippines have been assessed for their anti-methicillin-resistant Staphylococcus aureus (MRSA) activity, and the analytes with such activity should be identified. However, due to the limited amounts collected from the isolation process, 1.8 mg yield of compound 1 from the endophyte of C. rutidosperma and 1.2 mg of a mixture from the endophyte of D. sanguinalis were selected for LC-MSE analysis. The production of compounds from the culturable endophytic bacteria Pseudomonas aeruginosa- determined by gene-sequencing, an untargeted and data-independent analysis (DIA) by ultra-high performance liquid chromatography-high resolution-elevated energy mass spectrometry (UHPLC-HR-MSE) technique was employed to profile the metabolites present in the two high-performance liquid chromatography (HPLC) fractions. The analytes present from P. aeruginosa detected by UHPLC-HR-MSE isolated from C. rutidosperma was phenazine-1-carboxylic acid (1), and for D. sanguinalis were chamigrenal (2), dialkyl resorcinol (3), and a pyoverdine elicitor (4). This study proves that UHPLC-HR-MSE could identify the anti-MRSA constituents in P. aeruginosa from commensal weeds C. rutidosperma and D. sanguinalis. The UHPLC-HR-MSE could help strengthen metabolomics antibacterial research and its related applications from a future perspective. Application of metabolomics research using UHPLC-HR-MSE could enhance the rehabilitation of dumpsites by the microbial community present.
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Affiliation(s)
- Mona Lisa B Lacson
- Center for Advanced Research and Innovation, Office of the Vice President for Research and Innovation, Angeles University Foundation, Pampanga 2009 Philippines; College of Allied Medical Professions, Angeles University Foundation, Pampanga 2009 Philippines.
| | - Carolyn A Arbotante
- College of Arts and Sciences, Angeles University Foundation, Pampanga 2009 Philippines
| | - Ma Jamaica Trexy E Magdayao
- Applied Chemistry Laboratory Regional Research Center, University of the Philippines Visayas, Miag-ao, Iloilo 5023 Philippines
| | - Reynaldo Dl Bundalian
- Center for Advanced Research and Innovation, Office of the Vice President for Research and Innovation, Angeles University Foundation, Pampanga 2009 Philippines.
| | - Andrea Roxanne J Anas
- Department of Brain Function, Division of Stress Adaptation and Protection, Research Institute of Environmental Medicine, Nagoya University, Chikusa-Ku, Nagoya 464-8601, Japan; Department of Molecular Pharmacokinetics, Division of Clinical Pharmacology, Graduate School of Medicine Nagoya University, Chikusa-Ku, Nagoya 464-8601, Japan.
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Zhou R, Duan GL, García-Palacios P, Yang G, Cui HL, Yan M, Yin Y, Yi XY, Li L, Delgado-Baquerizo M, Zhu YG. Environmental factors and host genotype control foliar epiphytic microbial community of wild soybeans across China. Front Microbiol 2023; 14:1065302. [PMID: 36992926 PMCID: PMC10041966 DOI: 10.3389/fmicb.2023.1065302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 02/16/2023] [Indexed: 03/14/2023] Open
Abstract
IntroductionThe microbiome inhabiting plant leaves is critical for plant health and productivity. Wild soybean (Glycine soja), which originated in China, is the progenitor of cultivated soybean (Glycine max). So far, the community structure and assembly mechanism of phyllosphere microbial community on G. soja were poorly understood.MethodsHere, we combined a national-scale survey with high-throughput sequencing and microsatellite data to evaluate the contribution of host genotype vs. climate in explaining the foliar microbiome of G. soja, and the core foliar microbiota of G. soja were identified.ResultsOur findings revealed that both the host genotype and environmental factors (i.e., geographic location and climatic conditions) were important factors regulating foliar community assembly of G. soja. Host genotypes explained 0.4% and 3.6% variations of the foliar bacterial and fungal community composition, respectively, while environmental factors explained 25.8% and 19.9% variations, respectively. We further identified a core microbiome thriving on the foliage of all G. soja populations, including bacterial (dominated by Methylobacterium-Methylorubrum, Pantoea, Quadrisphaera, Pseudomonas, and Sphingomonas) and fungal (dominated by Cladosporium, Alternaria, and Penicillium) taxa.ConclusionOur study revealed the significant role of host genetic distance as a driver of the foliar microbiome of the wild progenitor of soya, as well as the effects of climatic changes on foliar microbiomes. These findings would increase our knowledge of assembly mechanisms in the phyllosphere of wild soybeans and suggest the potential to manage the phyllosphere of soya plantations by plant breeding and selecting specific genotypes under climate change.
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Affiliation(s)
- Rui Zhou
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Gui-Lan Duan
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pablo García-Palacios
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Guang Yang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Hui-Ling Cui
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ming Yan
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yue Yin
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xing-Yun Yi
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lv Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Sevilla, Spain
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- *Correspondence: Yong-Guan Zhu,
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Anguita-Maeso M, Navas-Cortés JA, Landa BB. Insights into the Methodological, Biotic and Abiotic Factors Influencing the Characterization of Xylem-Inhabiting Microbial Communities of Olive Trees. PLANTS (BASEL, SWITZERLAND) 2023; 12:912. [PMID: 36840260 PMCID: PMC9967459 DOI: 10.3390/plants12040912] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Vascular pathogens are the causal agents of some of the most devastating plant diseases in the world, which can cause, under specific conditions, the destruction of entire crops. These plant pathogens activate a range of physiological and immune reactions in the host plant following infection, which may trigger the proliferation of a specific microbiome to combat them by, among others, inhibiting their growth and/or competing for space. Nowadays, it has been demonstrated that the plant microbiome can be modified by transplanting specific members of the microbiome, with exciting results for the control of plant diseases. However, its practical application in agriculture for the control of vascular plant pathogens is hampered by the limited knowledge of the plant endosphere, and, in particular, of the xylem niche. In this review, we present a comprehensive overview of how research on the plant microbiome has evolved during the last decades to unravel the factors and complex interactions that affect the associated microbial communities and their surrounding environment, focusing on the microbial communities inhabiting the xylem vessels of olive trees (Olea europaea subsp. europaea), the most ancient and important woody crop in the Mediterranean Basin. For that purpose, we have highlighted the role of xylem composition and its associated microorganisms in plants by describing the methodological approaches explored to study xylem microbiota, starting from the methods used to extract xylem microbial communities to their assessment by culture-dependent and next-generation sequencing approaches. Additionally, we have categorized some of the key biotic and abiotic factors, such as the host plant niche and genotype, the environment and the infection with vascular pathogens, that can be potential determinants to critically affect olive physiology and health status in a holobiont context (host and its associated organisms). Finally, we have outlined future directions and challenges for xylem microbiome studies based on the recent advances in molecular biology, focusing on metagenomics and culturomics, and bioinformatics network analysis. A better understanding of the xylem olive microbiome will contribute to facilitate the exploration and selection of specific keystone microorganisms that can live in close association with olives under a range of environmental/agronomic conditions. These microorganisms could be ideal targets for the design of microbial consortia that can be applied by endotherapy treatments to prevent or control diseases caused by vascular pathogens or modify the physiology and growth of olive trees.
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Zhuang X, Wang Y, Wang H, Dong Y, Li X, Wang S, Fan H, Wu S. Comparison of the efficiency and microbial mechanisms of chemical- and bio-surfactants in remediation of petroleum hydrocarbon. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 314:120198. [PMID: 36165831 DOI: 10.1016/j.envpol.2022.120198] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/04/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Surfactant-enhanced remediation (SER) is one of the most effective methods for petroleum hydrocarbon-contaminated sites compared to single physical and chemical methods. However, biosurfactants are not as commonly used as chemical surfactants, and the actual remediation effects and related mechanisms remain undefined. Therefore, to comprehensively compare the remediation effects and biological mechanisms of biosurfactants and chemical surfactants, soil column leaching experiments including two biosurfactants (rhamnolipids and lipopeptide) and three commercially used chemical surfactants (Tween 80, Triton X-100, and Berol 226SA) were conducted. After seven days of leaching, rhamnolipids exhibited the highest petroleum hydrocarbon removal rate of 61.01%, which was superior to that of chemical surfactants (11.73-18.75%) in n-alkanes C10-C30. Meanwhile, rhamnolipids exhibited a great degradation advantage of n-alkanes C13-C28, which was 1.22-30.55 times that of chemical surfactants. Compared to chemical surfactants, biosurfactants significantly upregulated the soil's biological functions, including soil conductivity (80.90-155.56%), and soil enzyme activities of lipase (90.31-497.10%), dehydrogenase (325.00-655.56%), core enzyme activities of petroleum hydrocarbon degradation, and quorum sensing between species. Biosurfactants significantly changed the composition of Pseudomonas, Citrobacter, Acidobacteriota, and Enterobacter at the genus level. Meanwhile, chemical surfactants had less influence on the bacterial community and interactions between species. Moreover, the biosurfactants enhanced the microbial interactions and centrality of petroleum hydrocarbon degraders in the community based on the network. Overall, this work provides a systematic comparison and understanding of the chemical- and bio-surfactants used in bioremediation. In the future, we intend to apply biosurfactants to practical petroleum hydrocarbon-contaminated fields to observe realistic remediation effects and compare their functional mechanisms.
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Affiliation(s)
- Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China; Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yaxin Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haoyu Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yuzhu Dong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianglong Li
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shijie Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haonan Fan
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shanghua Wu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Ciadamidaro L, Pfendler S, Girardclos O, Zappelini C, Binet P, Bert V, Khasa D, Blaudez D, Chalot M. Mycorrhizal inoculation effects on growth and the mycobiome of poplar on two phytomanaged sites after 7-year-short rotation coppicing. FRONTIERS IN PLANT SCIENCE 2022; 13:993301. [PMID: 36388565 PMCID: PMC9650387 DOI: 10.3389/fpls.2022.993301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
AIMS Afforestation of trace-element contaminated soils, notably with fast growing trees, has been demonstrated to be an attractive option for bioremediation due to the lower costs and dispersion of contaminants than conventional cleanup methods. Mycorrhizal fungi form symbiotic associations with plants, contributing to their tolerance towards toxic elements and actively participating to the biorestoration processes. The aim of this study was to deepen our understanding on the effects of mycorrhizal inoculation on plant development and fungal community at two trace-element contaminated sites (Pierrelaye and Fresnes-sur-Escaut, France) planted with poplar (Populus trichocarpa x Populus maximowiczii). METHODS The 2 sites were divided into 4 replicated field blocks with a final plant density of 2200 tree h-1. Half of the trees were inoculated with a commercial inoculum made of a mix of mycorrhizal species. The sites presented different physico-chemical characteristics (e.g., texture: sandy soil versus silty-loam soil and organic matter: 5.7% versus 3.4% for Pierrelaye and Fresnes-sur-Escaut, respectively) and various trace element contamination levels. RESULTS After 7 years of plantation, inoculation showed a significant positive effect on poplar biomass production at the two sites. Fungal composition study demonstrated a predominance of the phylum Ascomycota at both sites, with a dominance of Geopora Arenicola and Mortierella elongata, and a higher proportion of ectomycorrhizal and endophytic fungi (with the highest values observed in Fresnes-sur-Escaut: 45% and 28% for ECM and endophytic fungi, respectively), well known for their capacity to have positive effects on plant development in stressful conditions. Furthermore, Pierrelaye site showed higher frequency (%) of mycorrhizal tips for ectomycorrhizal fungi (ECM) and higher intensity (%) of mycorrhizal root cortex colonization for arbuscular mycorrhizal fungi (AMF) than Fresnes-sur-Escaut site, which translates in a higher level of diversity. CONCLUSIONS Finally, this study demonstrated that this biofertilization approach could be recommended as an appropriate phytomanagement strategy, due to its capacity to significantly improve poplar productivity without any perturbations in soil mycobiomes.
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Affiliation(s)
- Lisa Ciadamidaro
- Chrono-environnement UMR6249, CNRS, Université Bourgogne Franche-Comté, Besançon, France
| | - Stéphane Pfendler
- Laboratoire Chrono-environnement UMR6249, CNRS, Université Bourgogne Franche-Comté, Besançon, France
| | - Olivier Girardclos
- Laboratoire Chrono-environnement UMR6249, CNRS, Université Bourgogne Franche-Comté, Besançon, France
| | - Cyril Zappelini
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Philippe Binet
- Laboratoire Chrono-environnement UMR6249, CNRS, Université Bourgogne Franche-Comté, Besançon, France
| | - Valerie Bert
- INERIS, Clean Technologies and Circular Economy Unit, SIT, Parc Technologique Alata, BP2, Verneuil-en- Halatte, France
| | - Damase Khasa
- Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | | | - Michel Chalot
- Laboratoire Chrono-environnement UMR6249, CNRS, Université Bourgogne Franche-Comté, Besançon, France
- Université de Lorraine, Faculté des Sciences et Technologies, Nancy, France
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Agbavor C, Mirza BS, Wait A. The Effects of Phyllosphere Bacteria on Plant Physiology and Growth of Soybean Infected with Pseudomonas syringae. PLANTS (BASEL, SWITZERLAND) 2022; 11:2634. [PMID: 36235499 PMCID: PMC9571934 DOI: 10.3390/plants11192634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/28/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
Phyllosphere bacteria are an important determinant of plant growth and resistance to pathogens. However, the efficacy of phyllosphere bacteria in regulating infection of Pseudomonas syringae pv. glycinea (Psg) and its influence on soybean growth and physiology is unknown. In a greenhouse study, we assessed the influence of a phyllosphere bacterial consortium (BC) of 13 species isolated from field-grown soybean leaves on uninfected and deliberately Psg infected soybean plants. We measured Psg density on infected leaves with and without the application of the BC. The BC application resulted in a significant reduction in Psg cells. We also measured plant biomass, nodule mass and number, gas exchange, and leaf chlorophyll and nitrogen in four treatment groups: control plants, plants with a BC and no infection (BC), plants with BC and infected with Psg (BC + Psg), and plants infected with Psg alone. For all variables, plants infected with Psg alone showed significant reduction in measured variables compared to both BC treatments. Therefore, the bacterial consortium was effective in controlling the negative effects of Psg on growth and physiology. The BC treatment sometimes resulted in increases in measured variables such as plant biomass, nodule numbers, and leaf chlorophyll as compared to control and BC + Psg treatments. Overall, the positive influence of BC treatment on plant growth and physiology highlights its potential applications to increase crop yield and control bacterial pathogens.
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Affiliation(s)
| | - Babur S. Mirza
- Correspondence: ; Tel.: +1-417-836-5062; Fax: +1-417-836-4204
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13
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Yeo FKS, Cheok YH, Wan Ismail WN, Kueh-Tai FF, Lam TTY, Chong YL. Genotype and organ effect on the occupancy of phyllosphere prokaryotes in different rice landraces. Arch Microbiol 2022; 204:600. [PMID: 36056990 DOI: 10.1007/s00203-022-03209-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/26/2022] [Accepted: 08/19/2022] [Indexed: 11/02/2022]
Abstract
Bacteria community provides essential ecological services to rice plants. The bacterial diversity of rice varies across host plant genotype and organs. This study employed 16S rDNA amplicon sequencing to characterise the bacterial community associated with three rice landraces using leaf blade and stem samples. The prokaryotic community found in these rice landraces comprised of two kingdoms, 12 phyla, 25 classes, 40 orders, 80 families, and 118 genera. Proteobacteria (53.9%) was the most abundant phylum. The most abundant genus was an undefined genus under Cyanobacteria (33.0%). Homogeneity of prokaryotic community was observed across the three rice landraces, which may suggest a high similarity in biological and genetical properties of the rice landraces. The difference in prokaryotic composition between leaf blade and stem was depicted based on principal coordinate analysis. This study observed that the prokaryotic inhabitants in rice plants is predominantly determined by rice plant organs.
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Affiliation(s)
- Freddy Kuok San Yeo
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Yin Hui Cheok
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Wan Nurainie Wan Ismail
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Felicia Fui Kueh-Tai
- Agriculture Research Centre, Semongok, 12th Mile, Kuching-Serian Road, P.O. Box 977, 93720, Kuching, Sarawak, Malaysia
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, Li Ka Shing, Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Yee Ling Chong
- Department of Science and Environmental Studies, Faculty of Liberal Arts and Social Sciences, The Education University of Hong Kong, 10 Lo Ping Road, Ting Kok, Hong Kong SAR, China
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Effects of three regeneration methods on the growth and bacterial community diversity of Populus × euramericana. PLoS One 2022; 17:e0273306. [PMID: 36018851 PMCID: PMC9416986 DOI: 10.1371/journal.pone.0273306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/06/2022] [Indexed: 11/19/2022] Open
Abstract
To study the effects of different regeneration methods on the growth and bacterial community diversity of Populus × euramericana cv. ‘74/76’ (poplar 107), we investigated the growth of poplar 107 trees under three regeneration methods in 2017 and 2020, and sequenced the 16S rDNA V5–V7 regions in stem endophytic, root endophytic, and rhizosphere soil bacteria present in samples from the three regeneration methods using the Illumina high-throughput sequencing platform. The growth analysis showed that stump grafting regeneration (ST) and stump sprouting regeneration (SP) presented similar tree height and diameter at breast height (DBH), which were significantly lower by planted seedling regeneration (CK). The high-throughput sequencing results showed that the rhizosphere soil bacteria appeared to be significantly more diverse and rich than the root and stem endophytic bacteria. Cluster analysis showed that the similarity of bacterial community structure among the rhizosphere soil, root, and stem was small. Thus, the three sample types showed significant differences in bacteria. While comparing the two years, 2020 was significantly more diverse and rich than 2017. With the increase in stand age, the abundance of Proteobacteria increased and the abundance of Acidobacteria decreased. Among the three regeneration methods, ST significantly increased the diversity of stem endophytic bacteria. Chthoniobacter was enriched in SP, which promoted the decomposition of organic matter, and more plant growth promoting rhizobacteria (PGPR) were accumulated in the rhizosphere of SP and ST. The composition of the bacterial community was similar in the three regeneration methods, but the community composition was different. Regeneration and transformation of poplar plantations can be better carried out by stump grafting and stump sprouting.
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Yu Y, Li Z, Liu Y, Wang F, Liu Y, Zhao J, Li Y, Gao Y, Zhu N. Roles of plant-associated microorganisms in regulating the fate of Hg in croplands: A perspective on potential pathways in maintaining sustainable agriculture. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 834:155204. [PMID: 35421489 DOI: 10.1016/j.scitotenv.2022.155204] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
In heavy metal-contaminated croplands, plant-associated microorganisms play important roles in the adaptation of crops to heavy metals. Plant-associated microbes can interact with Hg and stimulate plant resistance to Hg toxicity, which is crucial for impeding Hg accumulation along the food chain. The roles of rhizosphere microorganisms for the improvement of plant growth and Hg resistance have drawn great research attention. However, the interactions among plant-endophyte-Hg have been neglected although they might be important for in vivo Hg detoxification. In this study, we systematically summarized 1) the roles of plant-associated microorganisms in Hg detoxification and plant growth, 2) Hg methylation and demethylation driven by plant-associated microbes, 3) the relationships between plant-associated microbes and Hg biogeochemical cycling. The possible mechanisms underlying crop-endophyte-Hg interactions were discussed, although limited studies on this aspect are available to date. The challenges and perspectives of plant-endophytes in dampening Hg phytotoxicity and controlling Hg accumulation in croplands were proposed on the basis of the present knowledge. Taken together, this work provides evidence for further understanding the interactions between soil-plant-endophyte-Hg systems and as well as new interpretations and perspectives into regulating the fate of Hg in croplands.
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Affiliation(s)
- Yue Yu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, Jiangsu, China; State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing 100048, China
| | - Zhanming Li
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, Jiangsu, China; State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing 100048, China; School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Yonghua Liu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, & CAS-HKU Joint Laboratory of Metallomics on Health and Environment, & Beijing Metallomics Facility, & National Consortium for Excellence in Metallomics, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China; School of Chemical and Biological Engineering, Taiyuan University of Science and Technology, Taiyuan 030000, Shanxi, China
| | - Fang Wang
- State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing 100048, China
| | - Yurong Liu
- State Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiating Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, & CAS-HKU Joint Laboratory of Metallomics on Health and Environment, & Beijing Metallomics Facility, & National Consortium for Excellence in Metallomics, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Yufeng Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, & CAS-HKU Joint Laboratory of Metallomics on Health and Environment, & Beijing Metallomics Facility, & National Consortium for Excellence in Metallomics, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Yuxi Gao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, & CAS-HKU Joint Laboratory of Metallomics on Health and Environment, & Beijing Metallomics Facility, & National Consortium for Excellence in Metallomics, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Nali Zhu
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
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Sahu KP, Kumar A, Sakthivel K, Reddy B, Kumar M, Patel A, Sheoran N, Gopalakrishnan S, Prakash G, Rathour R, Gautam RK. Deciphering core phyllomicrobiome assemblage on rice genotypes grown in contrasting agroclimatic zones: implications for phyllomicrobiome engineering against blast disease. ENVIRONMENTAL MICROBIOME 2022; 17:28. [PMID: 35619157 PMCID: PMC9134649 DOI: 10.1186/s40793-022-00421-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 05/09/2022] [Indexed: 05/16/2023]
Abstract
BACKGROUND With its adapted microbial diversity, the phyllosphere contributes microbial metagenome to the plant holobiont and modulates a host of ecological functions. Phyllosphere microbiome (hereafter termed phyllomicrobiome) structure and the consequent ecological functions are vulnerable to a host of biotic (Genotypes) and abiotic factors (Environment) which is further compounded by agronomic transactions. However, the ecological forces driving the phyllomicrobiome assemblage and functions are among the most understudied aspects of plant biology. Despite the reports on the occurrence of diverse prokaryotic phyla such as Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria in phyllosphere habitat, the functional characterization leading to their utilization for agricultural sustainability is not yet explored. Currently, the metabarcoding by Next-Generation-Sequencing (mNGS) technique is a widely practised strategy for microbiome investigations. However, the validation of mNGS annotations by culturomics methods is not integrated with the microbiome exploration program. In the present study, we combined the mNGS with culturomics to decipher the core functional phyllomicrobiome of rice genotypes varying for blast disease resistance planted in two agroclimatic zones in India. There is a growing consensus among the various stakeholder of rice farming for an ecofriendly method of disease management. Here, we proposed phyllomicrobiome assisted rice blast management as a novel strategy for rice farming in the future. RESULTS The tropical "Island Zone" displayed marginally more bacterial diversity than that of the temperate 'Mountain Zone' on the phyllosphere. Principal coordinate analysis indicated converging phyllomicrobiome profiles on rice genotypes sharing the same agroclimatic zone. Interestingly, the rice genotype grown in the contrasting zones displayed divergent phyllomicrobiomes suggestive of the role of environment on phyllomicrobiome assembly. The predominance of phyla such as Proteobacteria, Actinobacteria, and Firmicutes was observed in the phyllosphere irrespective of the genotypes and climatic zones. The core-microbiome analysis revealed an association of Acidovorax, Arthrobacter, Bacillus, Clavibacter, Clostridium, Cronobacter, Curtobacterium, Deinococcus, Erwinia, Exiguobacterium, Hymenobacter, Kineococcus, Klebsiella, Methylobacterium, Methylocella, Microbacterium, Nocardioides, Pantoea, Pedobacter, Pseudomonas, Salmonella, Serratia, Sphingomonas and Streptomyces on phyllosphere. The linear discriminant analysis (LDA) effect size (LEfSe) method revealed distinct bacterial genera in blast-resistant and susceptible genotypes, as well as mountain and island climate zones. SparCC based network analysis of phyllomicrobiome showed complex intra-microbial cooperative or competitive interactions on the rice genotypes. The culturomic validation of mNGS data confirmed the occurrence of Acinetobacter, Aureimonas, Curtobacterium, Enterobacter, Exiguobacterium, Microbacterium, Pantoea, Pseudomonas, and Sphingomonas in the phyllosphere. Strikingly, the contrasting agroclimatic zones showed genetically identical bacterial isolates suggestive of vertical microbiome transmission. The core-phyllobacterial communities showed secreted and volatile compound mediated antifungal activity on M. oryzae. Upon phyllobacterization (a term coined for spraying bacterial cells on the phyllosphere), Acinetobacter, Aureimonas, Pantoea, and Pseudomonas conferred immunocompetence against blast disease. Transcriptional analysis revealed activation of defense genes such as OsPR1.1, OsNPR1, OsPDF2.2, OsFMO, OsPAD4, OsCEBiP, and OsCERK1 in phyllobacterized rice seedlings. CONCLUSIONS PCoA indicated the key role of agro-climatic zones to drive phyllomicrobiome assembly on the rice genotypes. The mNGS and culturomic methods showed Acinetobacter, Aureimonas, Curtobacterium, Enterobacter, Exiguobacterium, Microbacterium, Pantoea, Pseudomonas, and Sphingomonas as core phyllomicrobiome of rice. Genetically identical Pantoea intercepted on the phyllosphere from the well-separated agroclimatic zones is suggestive of vertical transmission of phyllomicrobiome. The phyllobacterization showed potential for blast disease suppression by direct antibiosis and defense elicitation. Identification of functional core-bacterial communities on the phyllosphere and their co-occurrence dynamics presents an opportunity to devise novel strategies for rice blast management through phyllomicrobiome reengineering in the future.
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Affiliation(s)
- Kuleshwar Prasad Sahu
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - A Kumar
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - K Sakthivel
- Division of Field Crop Improvement and Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, 744101, India
| | - Bhaskar Reddy
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Mukesh Kumar
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Asharani Patel
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Neelam Sheoran
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | - Ganesan Prakash
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Rajeev Rathour
- Department of Agricultural Biotechnology, CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, 176062, India
| | - R K Gautam
- Division of Field Crop Improvement and Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, 744101, India
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Gréau L, Blaudez D, Heintz D, Zumsteg J, Billet D, Cébron A. Response of Poplar and Associated Fungal Endophytic Communities to a PAH Contamination Gradient. Int J Mol Sci 2022; 23:ijms23115909. [PMID: 35682588 PMCID: PMC9180295 DOI: 10.3390/ijms23115909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 01/27/2023] Open
Abstract
Microbial populations associated to poplar are well described in non-contaminated and metal-contaminated environments but more poorly in the context of polycyclic aromatic hydrocarbon (PAH) contamination. This study aimed to understand how a gradient of phenanthrene (PHE) contamination affects poplar growth and the fungal microbiome in both soil and plant endosphere (roots, stems and leaves). Plant growth and fitness parameters indicated that the growth of Populus canadensis was impaired when PHE concentration increased above 400 mg kg-1. Values of alpha-diversity indicators of fungal diversity and richness were not affected by the PHE gradient. The PHE contamination had a stronger impact on the fungal community composition in the soil and root compartments compared to that of the aboveground organs. Most of the indicator species whose relative abundance was correlated with PHE contamination decreased along the gradient indicating a toxic effect of PHE on these fungal OTUs (Operational Taxonomic Units). However, the relative abundance of some OTUs such as Cadophora, Alternaria and Aspergillus, potentially linked to PHE degradation or being plant-beneficial taxa, increased along the gradient. Finally, this study allowed a deeper understanding of the dual response of plant and fungal communities in the case of a soil PAH contamination gradient leading to new perspectives on fungal assisted phytoremediation.
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Affiliation(s)
- Lilian Gréau
- Université de Lorraine, CNRS, LIEC, 54000 Nancy, France; (L.G.); (D.B.); (D.B.)
| | - Damien Blaudez
- Université de Lorraine, CNRS, LIEC, 54000 Nancy, France; (L.G.); (D.B.); (D.B.)
| | - Dimitri Heintz
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France; (D.H.); (J.Z.)
| | - Julie Zumsteg
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France; (D.H.); (J.Z.)
| | - David Billet
- Université de Lorraine, CNRS, LIEC, 54000 Nancy, France; (L.G.); (D.B.); (D.B.)
- Pôle de Compétences en Biologie Environnementale, Université de Lorraine, CNRS, LIEC, 54000 Nancy, France
| | - Aurélie Cébron
- Université de Lorraine, CNRS, LIEC, 54000 Nancy, France; (L.G.); (D.B.); (D.B.)
- Correspondence:
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The Application of Mixed Organic and Inorganic Fertilizers Drives Soil Nutrient and Bacterial Community Changes in Teak Plantations. Microorganisms 2022; 10:microorganisms10050958. [PMID: 35630402 PMCID: PMC9145699 DOI: 10.3390/microorganisms10050958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/21/2022] [Accepted: 04/28/2022] [Indexed: 11/17/2022] Open
Abstract
Appropriate fertilization can enhance forest productivity by maintaining soil fertility and improving the structure of the bacterial community. However, there is still uncertainty surrounding the effects of combined application of organic and inorganic fertilizers on soil nutrient status and bacterial community structure. A fertilization experiment was set up in an eight-year-old teak plantation with five treatments involved: mixed organic and NPK compound fertilizers (OCF), mixed organic and phosphorus fertilizers (OPF), mixed organic, NPK and phosphorus fertilizers (OCPF), mixed NPK and phosphorus fertilizers (CPF) and no fertilization (CK). Soil chemical properties and bacterial communities were investigated, and the co-occurrence pattern of the bacterial community under different fertilization treatments was compared. The results showed that the contents of soil organic matter and nitrate nitrogen, and the soil pH values were the highest after OCPF treatment, which were 20.39%, 90.91% and 8.16% higher than CK, respectively. The richness and diversity of bacteria underwent no obvious changes, but the structure of the soil’s bacterial community was significantly altered by fertilization. Of the dominant bacteria taxa, the relative abundance increased for Gemmatimonadetes, Myxococcota, ADurb.Bin063-13 and Candidatus_Koribacter, and decreased for Chloroflexi, Proteobacteria, JG30-KF-AS9 and Acidothermus under OCPF treatment in comparison to CK. The number of nodes and edges, the average degree and the network density of bacterial community co-occurrence networks were the greatest in OCPF treatment, indicating that application of OCPF could make the network structure of soil bacteria more stable and complex. Moreover, soil pH and organic matter were significantly correlated with bacterial community structure and were considered the main influencing factors. These findings highlight that the combined application of organic, NPK and phosphorus fertilizers is highly beneficial for improving soil quality and optimizing bacterial community structure in teak plantations.
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Xu N, Zhao Q, Zhang Z, Zhang Q, Wang Y, Qin G, Ke M, Qiu D, Peijnenburg WJGM, Lu T, Qian H. Phyllosphere Microorganisms: Sources, Drivers, and Their Interactions with Plant Hosts. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:4860-4870. [PMID: 35435673 DOI: 10.1021/acs.jafc.2c01113] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The leaves of plants are colonized by various microorganisms. In comparison to the rhizosphere, less is known about the characteristics and ecological functions of phyllosphere microorganisms. Phyllosphere microorganisms mainly originate from soil, air, and seeds. The composition of phyllosphere microorganisms is mainly affected by ecological and abiotic factors. Phyllosphere microorganisms execute multiple ecological functions by influencing leaf functions and longevity, seed mass, fruit development, and homeostasis of host growth. A plant can respond to phyllosphere microorganisms by secondary metabolite secretion and its immune system. Meanwhile, phyllosphere microorganisms play an important role in ecological stability and environmental safety assessment. However, as a result of the instability of the phyllosphere environment and the poor cultivability of phyllosphere microorganisms in the current research, there are still many limitations, such as the lack of insight into the mechanisms of plant-microorganism interactions, the roles of phyllosphere microorganisms in plant growth processes, the responses of phyllosphere microorganisms to plant metabolites, etc. This review summarizes the latest progress made in the research of the phyllosphere in recent years. This is beneficial for deepening our understanding of phyllosphere microorganisms and promoting the research of plant-atmosphere interactions, plant pathogens, and plant biological control.
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Affiliation(s)
- Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Qianqiu Zhao
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Science, Urumqi, Xinjiang 830011, People's Republic of China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Yan Wang
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Guoyan Qin
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Mingjing Ke
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Danyan Qiu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - W J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, 2300 RA Leiden, Netherlands
- National Institute of Public Health and the Environment (RIVM), Center for Safety of Substances and Products, Post Office Box 1, 3720 BA Bilthoven, Netherlands
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
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20
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Singh S, Ramakrishna W. Application of CRISPR-Cas9 in plant-plant growth-promoting rhizobacteria interactions for next Green Revolution. 3 Biotech 2021; 11:492. [PMID: 34840925 PMCID: PMC8590643 DOI: 10.1007/s13205-021-03041-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/20/2021] [Indexed: 12/21/2022] Open
Abstract
Agriculture's beginnings resulted in the domestication of numerous plant species as well as the use of natural resources. Food grain production took about 10,000 years to reach a billion tonnes in 1960, however, it took only 40 years to achieve 2 billion tonnes in year 2000. The creation of genetically modified crops, together with the use of enhanced agronomic practices, resulted in this remarkable increase, dubbed the "Green Revolution". Plants and bacteria that interact with each other in nature are co-evolving, according to Red Queen dynamics. Plant microorganisms, also known as plant microbiota, are an essential component of plant life. Plant-microbe (PM) interactions can be beneficial or harmful to hosts, depending on the health impact. The significance of microbiota in plant growth promotion (PGP) and stress resistance is well known. Our understanding of the community composition of the plant microbiome and important driving forces has advanced significantly. As a result, utilising the plant microbiota is a viable strategy for the next Green Revolution for meeting food demand. The utilisation of newer methods to understand essential genetic and molecular components of the multiple PM interactions is required for their application. The use of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-mediated genome editing (GE) techniques to investigate PM interactions is of tremendous interest. The implementation of GE techniques to boost the ability of microorganisms or plants for agronomic trait development will be enabled by a comprehensive understanding of PM interactions. This review focuses on using GE approaches to investigate the principles of PM interactions, disease resistance, PGP activity, and future implications in agriculture in plants or associated microbiota.
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Affiliation(s)
- Sudiksha Singh
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Ghudda, Bathinda, Punjab 151401 India
| | - Wusirika Ramakrishna
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Ghudda, Bathinda, Punjab 151401 India
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21
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Li S, Dong L, Lian WH, Lin ZL, Lu CY, Xu L, Li L, Hozzein WN, Li WJ. Exploring untapped potential of Streptomyces spp. in Gurbantunggut Desert by use of highly selective culture strategy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 790:148235. [PMID: 34380255 DOI: 10.1016/j.scitotenv.2021.148235] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 06/13/2023]
Abstract
Streptomycetes have been, for over 70 years, one of the most abundant sources for the discovery of new antibiotics and clinic drugs. However, in recent decades, it has been more and more difficult to obtain new phylotypes of the genus Streptomyces by using conventional samples and culture strategies. In this study, we combined culture-dependent and culture-independent approaches to better explore the Streptomyces communities in desert sandy soils. Moreover, two different culture strategies termed Conventional Culture Procedure (CCP) and Streptomycetes Culture Procedure (SCP) were employed to evaluate the isolation efficiency of Streptomyces spp. with different intensities of selectivity. The 16S rRNA gene amplicon analysis revealed a very low abundance (0.04-0.37%, average 0.22%) of Streptomyces in all the desert samples, conversely the percentage of Streptomyces spp. obtained by the culture-dependent method was very high (5.20-39.57%, average 27.76%), especially in the rhizospheric sand soils (38.40-39.57%, average 38.99%). Meanwhile, a total of 1589 pure cultures were isolated successfully, dominated by Streptomyces (29.52%), Microvirga (8.06%) and Bacillus (7.68%). In addition, 400 potential new species were obtained, 48 of which belonged to the genus Streptomyces. More importantly, our study demonstrated the SCP strategy which had highly selectivity could greatly expand the number and phylotypes of Streptomyces spp. by almost 4-fold than CCP strategy. These results provide insights on the diversity investigation of desert Streptomyces, and it could be reference for researchers to bring more novel actinobacteria strains from the environment into culture.
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Affiliation(s)
- Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
| | - Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Zhi-Liang Lin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Chun-Yan Lu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Lu Xu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Wael N Hozzein
- Zoology Department, College of Science, King Saud University, Riyadh 999088, Saudi Arabia; Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef 62511, Egypt
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China.
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22
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Bashir I, War AF, Rafiq I, Reshi ZA, Rashid I, Shouche YS. Phyllosphere microbiome: Diversity and functions. Microbiol Res 2021; 254:126888. [PMID: 34700185 DOI: 10.1016/j.micres.2021.126888] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/15/2021] [Accepted: 09/30/2021] [Indexed: 12/28/2022]
Abstract
Phyllosphere or aerial surface of plants represents the globally largest and peculiar microbial habitat that inhabits diverse and rich communities of bacteria, fungi, viruses, cyanobacteria, actinobacteria, nematodes, and protozoans. These hyperdiverse microbial communities are related to the host's specific functional traits and influence the host's physiology and the ecosystem's functioning. In the last few years, significant advances have been made in unravelling several aspects of phyllosphere microbiology, including diversity and microbial community composition, dynamics, and functional interactions. This review highlights the current knowledge about the assembly, structure, and composition of phyllosphere microbial communities across spatio-temporal scales, besides functional significance of different microbial communities to the plant host and the surrounding environment. The knowledge will help develop strategies for modelling and manipulating these highly beneficial microbial consortia for furthering scientific inquiry into their interactions with the host plants and also for their useful and economic utilization.
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Affiliation(s)
- Iqra Bashir
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India.
| | - Aadil Farooq War
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Iflah Rafiq
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Zafar A Reshi
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Irfan Rashid
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
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23
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Tao J, Cao P, Xiao Y, Wang Z, Huang Z, Jin J, Liu Y, Yin H, Liu T, Zhou Z. Distribution of the potential pathogenic Alternaria on plant leaves determines foliar fungal communities around the disease spot. ENVIRONMENTAL RESEARCH 2021; 200:111715. [PMID: 34297933 DOI: 10.1016/j.envres.2021.111715] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/14/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
Plant leaves are colonized by a remarkably diverse fungal microbiome, which contributes to host plant growth and health. However, responses of foliar fungal community to phytopathogen invasion and measures of the fungal community taken to resist or assist pathogens remain elusive. By utilizing high-throughput sequencing of internal transcribed spacer (ITS) amplicons, we studied the relationships between the foliar fungal community around the disease spot and the pathogen of brown spot disease. The pathogenic Alternaria was found to follow a dramatically decreased trend from the disease spot to its surrounding fungal communities, whose community structure also diverged substantially away from the disease spot community. With the increase of pathogenic Alternaria, diversity indexes, including Shannon, Pielou and Simpson, showed a trend of increasing first and then decreasing. Total network links and the average path distance exhibited strong negative and positive correlations with Alternaria, respectively. Five keystone members showed direct interactions with pathogenic Alternaria. Members of Botryosphaeria, Paraphoma and Plectosphaerella might act as key 'pathogen facilitators' to increase the severity and development of brown spot disease, while Pleospora and Ochrocladosporium might be important 'pathogen antagonists' to suppress the expansion of pathogenic Alternaria. Our study provides new insights in developing new strategies for leaf disease prediction or prevention.
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Affiliation(s)
- Jiemeng Tao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China; School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Yansong Xiao
- Chenzhou Tobacco Company of Hunan Province, Chenzhou, 423000, China
| | - Zhenhua Wang
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, 427000, China
| | - Zhihua Huang
- Yuxi Tobacco Company of Yunnan Province, Yuxi, 653100, China
| | - Jingjing Jin
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Yongjun Liu
- Central South Agricultural Experiment Station of China Tobacco, Changsha, 410004, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Tianbo Liu
- Central South Agricultural Experiment Station of China Tobacco, Changsha, 410004, China; College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China.
| | - Zhicheng Zhou
- Central South Agricultural Experiment Station of China Tobacco, Changsha, 410004, China.
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24
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Suo Y, Tang N, Li H, Corti G, Jiang L, Huang Z, Zhang Z, Huang J, Wu Z, Feng C, Zhang X. Long-term effects of phytoextraction by a poplar clone on the concentration, fractionation, and transportation of heavy metals in mine tailings. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:47528-47539. [PMID: 33895954 DOI: 10.1007/s11356-021-13864-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
Mine tailings are one of main causes of diffused heavy metal pollution since the heavy metals in there may acquire mobility. The current knowledge of the processes at work in long-term phytoremediation by woody species remains insufficient. Through a 4-year field study, we evaluated the phytoextraction efficiency of Populus deltoides CL. 'Xianglin 90' grown on a mine tailing co-polluted by Cd, Cu, Cr, Ni, Pb, and Zn. The concentrations of Cd, Cu, Ni, Pb, and Zn in the rhizospheric soil were reduced by amounts ranging from 12.86 to 42.19% during the study period. Bioconcentration factors and translocation factors showed that the accumulation of Cd and Zn occurring in the shoots was the most effective. Combined with the considerable biomass produced by poplar, the extracted amounts of Cd and Zn could reach 0.61 g and 10.66 g plant-1, respectively, in which the shoots account for 77.3% (Cd) and 89.0% (Zn) of the overall extraction amounts. Acid-soluble Cd and Zn increased by 5.49% and 4.29%, respectively, in the rhizosphere compared to the bulk soil, indicating that poplar enhanced the mobility of Cd and Zn in the rhizosphere, which explained its ability for bioaccumulation and root-shoot translocation. Moreover, calculated time required to address the issue of Cd and Zn pollution was theoretically shortened by more than half from 2015 to 2019. This study brings new insights into the long-term effects of phytoextraction on the concentration, fractionation, and transportation of heavy metals and confirms the potential of poplar as a Cd and Zn remediation species.
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Affiliation(s)
- Yange Suo
- School of Mechanical and Energy Engineering, Zhejiang University of Science and Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Ning Tang
- School of Mechanical and Energy Engineering, Zhejiang University of Science and Technology, Hangzhou, Zhejiang, People's Republic of China
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, Hunan, People's Republic of China
| | - Hui Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, Hunan, People's Republic of China
| | - Giuseppe Corti
- Department of Agrarian, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Lijuan Jiang
- Central South University of Forestry and Technology, Changsha, Hunan, People's Republic of China
| | - Zhongliang Huang
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, Hunan, People's Republic of China
| | - Zhiguo Zhang
- School of Mechanical and Energy Engineering, Zhejiang University of Science and Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Jing Huang
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, Hunan, People's Republic of China
| | - Zijian Wu
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, Hunan, People's Republic of China
| | - Chongling Feng
- Central South University of Forestry and Technology, Changsha, Hunan, People's Republic of China
| | - Xuan Zhang
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, Hunan, People's Republic of China.
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25
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Chaudhry V, Runge P, Sengupta P, Doehlemann G, Parker JE, Kemen E. Shaping the leaf microbiota: plant-microbe-microbe interactions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:36-56. [PMID: 32910810 PMCID: PMC8210630 DOI: 10.1093/jxb/eraa417] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/07/2020] [Indexed: 05/28/2023]
Abstract
The aerial portion of a plant, namely the leaf, is inhabited by pathogenic and non-pathogenic microbes. The leaf's physical and chemical properties, combined with fluctuating and often challenging environmental factors, create surfaces that require a high degree of adaptation for microbial colonization. As a consequence, specific interactive processes have evolved to establish a plant leaf niche. Little is known about the impact of the host immune system on phyllosphere colonization by non-pathogenic microbes. These organisms can trigger plant basal defenses and benefit the host by priming for enhanced resistance to pathogens. In most disease resistance responses, microbial signals are recognized by extra- or intracellular receptors. The interactions tend to be species specific and it is unclear how they shape leaf microbial communities. In natural habitats, microbe-microbe interactions are also important for shaping leaf communities. To protect resources, plant colonizers have developed direct antagonistic or host manipulation strategies to fight competitors. Phyllosphere-colonizing microbes respond to abiotic and biotic fluctuations and are therefore an important resource for adaptive and protective traits. Understanding the complex regulatory host-microbe-microbe networks is needed to transfer current knowledge to biotechnological applications such as plant-protective probiotics.
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Affiliation(s)
- Vasvi Chaudhry
- Department of Microbial Interactions, IMIT/ZMBP, University of
Tübingen, Tübingen, Germany
| | - Paul Runge
- Department of Microbial Interactions, IMIT/ZMBP, University of
Tübingen, Tübingen, Germany
- Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Priyamedha Sengupta
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences
(CEPLAS), University of Cologne, Center for Molecular Biosciences, Cologne,
Germany
| | - Gunther Doehlemann
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences
(CEPLAS), University of Cologne, Center for Molecular Biosciences, Cologne,
Germany
| | - Jane E Parker
- Max Planck Institute for Plant Breeding Research, Köln, Germany
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences
(CEPLAS), University of Cologne, Center for Molecular Biosciences, Cologne,
Germany
| | - Eric Kemen
- Department of Microbial Interactions, IMIT/ZMBP, University of
Tübingen, Tübingen, Germany
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26
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Kumar M, Kumar A, Sahu KP, Patel A, Reddy B, Sheoran N, Krishnappa C, Rajashekara H, Bhagat S, Rathour R. Deciphering core-microbiome of rice leaf endosphere: Revelation by metagenomic and microbiological analysis of aromatic and non-aromatic genotypes grown in three geographical zones. Microbiol Res 2021; 246:126704. [PMID: 33486428 DOI: 10.1016/j.micres.2021.126704] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/20/2020] [Accepted: 01/06/2021] [Indexed: 11/16/2022]
Abstract
We have deciphered the leaf endophytic-microbiome of aromatic (cv. Pusa Basmati-1) and non-aromatic (cv. BPT-5204) rice-genotypes grown in the mountain and plateau-zones of India by both metagenomic NGS (mNGS) and conventional microbiological methods. Microbiome analysis by sequencing V3-V4 region of ribosomal gene revealed marginally more bacterial operational taxonomic units (OTU) in the mountain zone at Palampur and Almora than plateau zone at Hazaribagh. Interestingly, the rice leaf endophytic microbiomes in mountain zone were found clustered separately from that of plateau-zone. The Bray-Curtis dissimilarity indices indicated influence of geographical location as compared to genotype per se for shaping rice endophytic microbiome composition. Bacterial phyla, Proteobacteria followed by Bacteroidetes, Firmicutes, and Actinobacteria were found abundant in all three locations. The core-microbiome analysis devulged association of Acidovorax; Acinetobacter; Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium; Aureimonas; Bradyrhizobium; Burkholderia-Caballeronia-Paraburkholderia; Enterobacter; Pantoea; Pseudomonas; Sphingomonas; and Stenotrophomonas with the leaf endosphere. The phyllosphere and spermosphere microbiota appears to have contributed to endophytic microbiota of rice leaf. SparCC network analysis of the endophytic-microbiome showed complex cooperative and competitive intra-microbial interactions among the microbial communities. Microbiological validation of mNGS data further confirmed the presence of core and transient genera such as Acidovorax, Alcaligenes, Bacillus, Chryseobacterium, Comamonas, Curtobacterium, Delftia, Microbacterium, Ochrobactrum, Pantoea, Pseudomonas, Rhizobium, Rhodococcus, Sphingobacterium, Staphylococcus, Stenotrophomonas, and Xanthomonas in the rice genotypes. We isolated, characterized and identified core-endophytic microbial communities of rice leaf for developing microbiome assisted crop management by microbiome reengineering in future.
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Affiliation(s)
- Mukesh Kumar
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Aundy Kumar
- ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | | | - Asharani Patel
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Bhaskar Reddy
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Neelam Sheoran
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | | | - Someshwar Bhagat
- ICAR-Central Rainfed Upland Rice Research Station (NRRI), Hazaribagh, Jharkhand, India
| | - Rajeev Rathour
- CSK-Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, India
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27
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Raveau R, Fontaine J, Hijri M, Lounès-Hadj Sahraoui A. The Aromatic Plant Clary Sage Shaped Bacterial Communities in the Roots and in the Trace Element-Contaminated Soil More Than Mycorrhizal Inoculation - A Two-Year Monitoring Field Trial. Front Microbiol 2020; 11:586050. [PMID: 33424786 PMCID: PMC7794003 DOI: 10.3389/fmicb.2020.586050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/14/2020] [Indexed: 01/04/2023] Open
Abstract
To cope with soil contamination by trace elements (TE), phytomanagement has attracted much attention as being an eco-friendly and cost-effective green approach. In this context, aromatic plants could represent a good option not only to immobilize TE, but also to use their biomass to extract essential oils, resulting in high added-value products suitable for non-food valorization. However, the influence of aromatic plants cultivation on the bacterial community structure and functioning in the rhizosphere microbiota remains unknown. Thus, the present study aims at determining in TE-aged contaminated soil (Pb - 394 ppm, Zn - 443 ppm, and Cd - 7ppm, respectively, 11, 6, and 17 times higher than the ordinary amounts in regional agricultural soils) the effects of perennial clary sage (Salvia sclarea L.) cultivation, during two successive years of growth and inoculated with arbuscular mycorrhizal fungi, on rhizosphere bacterial diversity and community structure. Illumina MiSeq amplicon sequencing targeting bacterial 16S rRNA gene was used to assess bacterial diversity and community structure changes. Bioinformatic analysis of sequencing datasets resulted in 4691 and 2728 bacterial Amplicon Sequence Variants (ASVs) in soil and root biotopes, respectively. Our findings have shown that the cultivation of clary sage displayed a significant year-to-year effect, on both bacterial richness and community structures. We found that the abundance of plant-growth promoting rhizobacteria significantly increased in roots during the second growing season. However, we didn't observe any significant effect of mycorrhizal inoculation neither on bacterial diversity nor on community structure. Our study brings new evidence in TE-contaminated areas of the effect of a vegetation cover with clary sage cultivation on the microbial soil functioning.
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Affiliation(s)
- Robin Raveau
- Université du Littoral Côte d’Opale, Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV), Calais, France
| | - Joël Fontaine
- Université du Littoral Côte d’Opale, Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV), Calais, France
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale (IRBV) de l’Université de Montréal, Montreal, QC, Canada
- AgroBioSciences, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Anissa Lounès-Hadj Sahraoui
- Université du Littoral Côte d’Opale, Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV), Calais, France
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28
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Lefèvre E, Gardner CM, Gunsch CK. A novel PCR-clamping assay reducing plant host DNA amplification significantly improves prokaryotic endo-microbiome community characterization. FEMS Microbiol Ecol 2020; 96:5850752. [PMID: 32490528 DOI: 10.1093/femsec/fiaa110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/01/2020] [Indexed: 11/12/2022] Open
Abstract
Due to the sequence homology between the bacterial 16S rRNA gene and plant chloroplast and mitochondrial DNA, the taxonomic characterization of plant microbiome using amplicon-based high throughput sequencing often results in the overwhelming presence of plant-affiliated reads, preventing the thorough description of plant-associated microbial communities. In this work we developed a PCR blocking primer assay targeting the taxonomically informative V5-V6 region of the 16S rRNA gene in order to reduce plant DNA co-amplification, and increase diversity coverage of associated prokaryotic communities. Evaluation of our assay on the characterization of the prokaryotic endophytic communities of Zea mays, Pinus taeda and Spartina alternifora leaves led to significantly reducing the proportion of plant reads, yielded 20 times more prokaryotic reads and tripled the number of detected OTUs compared to a commonly used V5-V6 PCR protocol. To expand the application of our PCR-clamping assay across a wider taxonomic spectrum of plant hosts, we additionally provide an alignment of chloroplast and mitochondrial DNA sequences encompassing more than 200 terrestrial plant families as a supporting tool for customizing our blocking primers.
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Affiliation(s)
- Emilie Lefèvre
- Department of Civil and Environmental Engineering, Duke University, 127 Hudson Hall, Box 90287, Durham, NC 27708, USA
| | - Courtney M Gardner
- Department of Civil and Environmental Engineering, Washington State University, 405 Spokane street, Sloan 101, Box 642910, Pullman, WA 99164, USA
| | - Claudia K Gunsch
- Department of Civil and Environmental Engineering, Duke University, 127 Hudson Hall, Box 90287, Durham, NC 27708, USA
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29
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Wang X, Dong G, Liu X, Zhang S, Li C, Lu X, Xia T. Poly-γ-glutamic acid-producing bacteria reduced Cd uptake and effected the rhizosphere microbial communities of lettuce. JOURNAL OF HAZARDOUS MATERIALS 2020; 398:123146. [PMID: 32768845 DOI: 10.1016/j.jhazmat.2020.123146] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/04/2020] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
Poly-γ-glutamic acid (γ-PGA) could efficiently stabilize heavy metals in the environment. This study characterized the effects of two plant growth-promoting and γ-PGA-producing bacteria Bacillus subtilis W7 and Bacillus amyloliquefaciens W25 on Cd immobilization and γ-PGA production in soil filtrate and on the biomass and Cd uptake by lettuce in Cd-contaminated soil, the impact of these strains on the rhizosphere soil bacterial community was also evaluated. The strains reduced Cd concentration (16-75 %) in soil filtrate and strain W25 had a higher ability of producing γ-PGA and immobilizing Cd than strain W7. Compared with the control, the strains significantly increased the biomass (41-85 %) and reduced Cd uptake (19-41 %) by lettuce, reduced available Cd content (25-37 %) and increased the relative abundance of γ-PGA-producing bacteria (24-30 %) in Cd-contaminated soil, among which the effects of strain W25 were better than that of strain W7. Besides, these isolates also increased soil pH value, urease activity and the relative abundance of plant growth-promoting and metal-immobilizing bacteria such as Sphingomonas and Bacillus. In summary, the two strains reduced soil available Cd and lettuce Cd uptake by increasing the pH value, urease activity and the abundance of γ-PGA-producing bacteria, and regulating bacterial community structure in rhizosphere soil.
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Affiliation(s)
- Xiaohan Wang
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, PR China
| | - Geyu Dong
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, PR China
| | - Xingwang Liu
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, PR China
| | - Shengkui Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, PR China
| | - Can Li
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, PR China
| | - Xianqin Lu
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, PR China
| | - Tao Xia
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, PR China.
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Durand A, Maillard F, Foulon J, Chalot M. Interactions between Hg and soil microbes: microbial diversity and mechanisms, with an emphasis on fungal processes. Appl Microbiol Biotechnol 2020; 104:9855-9876. [PMID: 33043392 DOI: 10.1007/s00253-020-10795-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/06/2020] [Accepted: 07/21/2020] [Indexed: 11/25/2022]
Abstract
Mercury (Hg) is a highly toxic metal with no known biological function, and it can be highly bioavailable in terrestrial ecosystems. Although fungi are important contributors to a number of soil processes including plant nutrient uptake and decomposition, little is known about the effect of Hg on fungi. Fungi accumulate the largest amount of Hg and are the organisms capable of the highest bioaccumulation of Hg. While referring to detailed mechanisms in bacteria, this mini-review emphasizes the progress made recently on this topic and represents the first step towards a better understanding of the mechanisms underlying Hg tolerance and accumulation in fungal species and hence on the role of fungi within the Hg cycle at Hg-contaminated sites. KEY POINTS: • The fungal communities are more resilient than bacterial communities to Hg exposure. • The exposure to Hg is a threat to microbial soil functions involved in both C and nutrient cycles. • Fungal (hyper)accumulation of Hg may be important for the Hg cycle in terrestrial environments. • Understanding Hg tolerance and accumulation by fungi may lead to new remediation biotechnologies.
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Affiliation(s)
- Alexis Durand
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211, Montbéliard, France
- Laboratoire Sols et Environnement, UMR 1120, Université de Lorraine - INRAE, 2 avenue de la Forêt de Haye BP 20 163, 54505, Vandœuvre-lès-Nancy, France
| | - François Maillard
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211, Montbéliard, France
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Julie Foulon
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211, Montbéliard, France
- Institut des Sciences de la Mer de Rimouski, Université du Québec à Rimouski, 310 Allée des Ursulines, C.P. 3300, Rimouski, QC, G5L 3A1, Canada
| | - Michel Chalot
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211, Montbéliard, France.
- Faculté des Sciences et Technologies, Université de Lorraine, BP 70239, 54506, Vandoeuvre-les-Nancy, France.
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Wang Z, Zhu Y, Jing R, Wu X, Li N, Liu H, Zhang X, Wang W, Liu Y. High-throughput sequencing-based analysis of the composition and diversity of endophytic bacterial community in seeds of upland rice. Arch Microbiol 2020; 203:609-620. [PMID: 32995980 DOI: 10.1007/s00203-020-02058-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/17/2020] [Accepted: 09/19/2020] [Indexed: 01/07/2023]
Abstract
Upland rice is an ecotype crop resulting from the long-term domestication and evolution of rice in dry land without a water layer. Generally, the stems and leaves are thick and luxuriant, while the leaves also typically broad and light. The root system is developed with abundant root hair, and the osmotic pressure of the root and cell juice concentration in the leaves is high, while this plant is drought-resistant, heat-resistant, and water absorbent. This study aims to reveal the "core flora" of the endophytes in upland rice seeds by examining their diversity and community structures. It further intends to reveal the impact of the soil environment on the formation of endophyte community structures in upland rice seeds by comparing the environmental soil microorganisms in upland rice habitats. In this study, high-throughput sequencing technology based on the Illumina Hiseq 2500 platform was used to investigate the structure and diversity of endophytic bacterial communities using upland rice varieties collected from different locations and soil samples from unified planting sites as materials. Here, 42 endophytic OTUs were found to coexist in the 14 samples. At the phylum level, the first dominant phyla in all the samples were Proteobacteria (93.81-99.99%). At the genus level, Pantoea (8.77-87.77%), Pseudomonas (1.15-61.58%), Methylobacterium (0.40-4.64%), Sphingomonas (0.26-3.85%), Microbacterium (0.01-4.67%) and Aurantimonas (0.04-4.34%), which represent the core microflora in upland rice seeds, served as the dominant genera that coexisted in all the upland rice seeds tested. This study significant for the isolation, screening, functional evaluation, and re-action of various functional microorganisms in upland rice to improve its agronomic traits. It also provides a specific reference for the interaction between microorganisms and plants.
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Affiliation(s)
- Zhishan Wang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Yongqiang Zhu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center At Shanghai, Shanghai, 201203, China
| | - Ruixue Jing
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Xianyu Wu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Ni Li
- State Key Laboratory of Hybrid Rice (Hunan Hybrid Rice Research Center), Changsha, 410125, China
| | - Hai Liu
- State Key Laboratory of Hybrid Rice (Hunan Hybrid Rice Research Center), Changsha, 410125, China
| | - Xiaoxia Zhang
- 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, China.
| | - Weiping Wang
- State Key Laboratory of Hybrid Rice (Hunan Hybrid Rice Research Center), Changsha, 410125, China.
| | - Yang Liu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
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Álvarez-López V, Zappelini C, Durand A, Chalot M. Pioneer trees of Betula pendula at a red gypsum landfill harbour specific structure and composition of root-associated microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 726:138530. [PMID: 32315851 DOI: 10.1016/j.scitotenv.2020.138530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/02/2020] [Accepted: 04/05/2020] [Indexed: 06/11/2023]
Abstract
The study of root-associated microbial communities is important to understand the natural processes involved in plant recolonisation at degraded areas. Root associated bacterial and fungal communities of woody species colonising a red gypsum landfill (a metal-enriched environment) were characterised through metabarcoding. Among trees naturally growing on the landfill, Betula pendula is the only tree species in the centre of the area, whereas companion tree species such as Populus nigra, P. tremula and Salix purpurea were present on the edges. The bacterial community was dominated by Proteobacteria (38%), Actinobacteria (35%) and Bacteroidetes (20%) and the most abundant bacterial OTU belonged to the family Streptomycetaceae. The fungal community was dominated by Ascomycota (60%) and Basidiomycota (30%) and the most abundant family was Pyronemataceae. Analysis of similarities, heatmap and hierarchical cluster analysis showed that B. pendula grown in the centre of the landfill harboured a specific microbial community, which was unique and different, not only from other tree species (Populus or Salix spp.), but also from other B. pendula growing at the edges. Our findings on relevant indicator OTUs associated to the birches located in the centre of the landfill (such as Otu00716 Catellatospora sp. (family Micromonosporaceae, phylum Actinobacteria) or Otu4_35502 Russula sp. (family Russulaceae, phylum Basidiomycota)) may have important implications for the successful revegetation of these harsh environments using microbial-based phytostabilisation approaches.
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Affiliation(s)
- Vanessa Álvarez-López
- Université de Bourgogne Franche-Comté, UMR CNRS Laboratoire Chrono-environnement, Montbéliard, France.
| | - Cyril Zappelini
- Université de Bourgogne Franche-Comté, UMR CNRS Laboratoire Chrono-environnement, Montbéliard, France
| | - Alexis Durand
- Université de Bourgogne Franche-Comté, UMR CNRS Laboratoire Chrono-environnement, Montbéliard, France
| | - Michel Chalot
- Université de Bourgogne Franche-Comté, UMR CNRS Laboratoire Chrono-environnement, Montbéliard, France; Université de Lorraine, F-54000 Nancy, France
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BenIsrael M, Wanner P, Fernandes J, Burken JG, Aravena R, Parker BL, Haack EA, Tsao DT, Dunfield KE. Quantification of toluene phytoextraction rates and microbial biodegradation functional profiles at a fractured bedrock phytoremediation site. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 707:135890. [PMID: 31865073 DOI: 10.1016/j.scitotenv.2019.135890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/27/2019] [Accepted: 11/30/2019] [Indexed: 05/28/2023]
Abstract
This field study evaluated the efficacy of a mature hybrid poplar phytoremediation system for the remediation of toluene in a fractured bedrock aquifer site. Phytoextraction activity of the trees and the ecology and biodegradation potential of root-colonizing bacteria that ultimately influence how much toluene is transported from the roots and phytoextracted to the aboveground point of measurement were explored. Peak-season toluene mass removal rates ranging from 313 to 743 μg/day were quantified using passive in planta contaminant sampling techniques and continuous heat dissipation transpiration measurements in tree stems. Root bacterial microbiome structure and biodegradation potential were evaluated via high-throughput sequencing and predictive metagenomic functional modelling of bacterial 16S rRNA genes in roots. Poplar roots were colonized mostly by Proteobacteria, Actinobacteria, and Bacteroidetes. Distinct, more uniform communities were observed in roots associated with trees planted in the toluene source area compared to other areas, with differences apparent at lower taxonomic levels. Significant enrichment of Streptomyces in roots was observed in the source area, implicating that genus as a potentially important poplar endophyte at toluene-impacted sites. Moreover, significantly greater aerobic toluene biodegradation capacity was predicted in these roots compared to other areas using taxonomic functional modelling. Together with passive sampling, the molecular results provided supporting evidence of biodegradation activity in the source area and contextualized the detected phytoextraction patterns. These results support the application of phytoremediation systems for aromatic hydrocarbons in environments with complex geology and demonstrate field-validated monitoring techniques to assess phytoextraction and biodegradation in these systems.
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Affiliation(s)
- Michael BenIsrael
- School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Philipp Wanner
- G(360) Institute for Groundwater Research, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Jeremy Fernandes
- G(360) Institute for Groundwater Research, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Joel G Burken
- Civil, Architectural and Environmental Engineering, Missouri University of Science and Technology, 1401 N. Pine St., Rolla, MO 65409-0030, USA
| | - Ramon Aravena
- Department of Earth and Environmental Sciences, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Beth L Parker
- G(360) Institute for Groundwater Research, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Elizabeth A Haack
- EcoMetrix Inc., 6800 Campobello Road, Mississauga, ON L5N 2L8, Canada
| | - David T Tsao
- BP Corporation North America Inc., 150 W Warrenville Road #605-2E, Naperville, IL 60563, USA
| | - Kari E Dunfield
- School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada.
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Yadav AN, Singh J, Rastegari AA, Yadav N. Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications. ACTA ACUST UNITED AC 2020. [PMCID: PMC7123684 DOI: 10.1007/978-3-030-38453-1_5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The phyllosphere referred to the total aerial plant surfaces (above-ground portions), as habitat for microorganisms. Microorganisms establish compositionally complex communities on the leaf surface. The microbiome of phyllosphere is rich in diversity of bacteria, fungi, actinomycetes, cyanobacteria, and viruses. The diversity, dispersal, and community development on the leaf surface are based on the physiochemistry, environment, and also the immunity of the host plant. A colonization process is an important event where both the microbe and the host plant have been benefited. Microbes commonly established either epiphytic or endophytic mode of life cycle on phyllosphere environment, which helps the host plant and functional communication with the surrounding environment. To the scientific advancement, several molecular techniques like metagenomics and metaproteomics have been used to study and understand the physiology and functional relationship of microbes to the host and its environment. Based on the available information, this chapter describes the basic understanding of microbiome in leaf structure and physiology, microbial interactions, especially bacteria, fungi, and actinomycetes, and their adaptation in the phyllosphere environment. Further, the detailed information related to the importance of the microbiome in phyllosphere to the host plant and their environment has been analyzed. Besides, biopotentials of the phyllosphere microbiome have been reviewed.
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Affiliation(s)
- Ajar Nath Yadav
- Department of Biotechnology, Eternal University, Baru Sahib, Himachal Pradesh India
| | - Joginder Singh
- Department of Microbiology, Lovely Professional University, Phagwara, Punjab India
| | | | - Neelam Yadav
- Gopi Nath PG College, Veer Bahadur Singh Purvanchal University, Ghazipur, Uttar Pradesh India
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Mao X, Kusstatscher P, Li H, Chen X, Berg G, Yang M, Cernava T. Microbiome-Guided Exploration of the Microbial Assemblage of the Exotic Beverage "Insect Tea" Native to Southwestern China. Front Microbiol 2020; 10:3087. [PMID: 32063890 PMCID: PMC7000658 DOI: 10.3389/fmicb.2019.03087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/20/2019] [Indexed: 01/06/2023] Open
Abstract
Insect tea is a unique beverage that is native to Southwestern China and traditionally produced by local farmers in an elaborate process. It consists of insect larvae excrements that are commonly obtained from meal moths (Pyralis farinalis Linnaeus 1758) reared on a specific plant-based diet. We have reconstructed the whole production process under laboratory conditions in order to obtain microbiome-level insights into this uncommon beverage and to trace back the origin of the prevalent bacteria in the final product. The bacterial community composition was specific for each production stage, with a high proportion of Streptomycetacea, Pseudonocaridaceae, Enterococcaceae, and Enterobacteriaceae in the insect tea. A large proportion of the constituents was traced back to the producing insect (13.2%) and its excrements (43.8%), while the initial plant-based substrate for tea production was found to contribute only 0.6% of the traceable bacteria in the final product. Moreover, an enrichment of Enterobactericeae was observed during the analyzed process steps and verified with complementary analyses. The cultivation experiments indicated a high occurrence of viable bacteria in the tea at 2.7 × 105 ± 1.2 × 105 cfu g-1. The isolated bacteria included Bordetella petrii and Enterococcus spp. that were recovered from a commercial product. By implementing an integrative approach, the insect tea was shown to harbor a species-rich bacterial community that can be traced back to certain plant and insect microbiome constituents from distinct production steps. Moreover, the microbial profile of the insect tea was found to be unique for a food product so far and contained several bacterial groups that are considered from the current perspective as food contaminants or yet unreported in other beverages. Due to the high number of viable bacteria, the tea harbors a so far undescribed dynamic component that might have implications for human health.
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Affiliation(s)
- Xin Mao
- College of Forestry, Guizhou University, Guiyang, China
- Institute of Entomology, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang, China
| | - Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Haoxi Li
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang, China
- College of Tobacco Science, Guizhou University, Guiyang, China
| | - Xiaoyulong Chen
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang, China
- College of Tobacco Science, Guizhou University, Guiyang, China
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Maofa Yang
- Institute of Entomology, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang, China
- College of Tobacco Science, Guizhou University, Guiyang, China
| | - Tomislav Cernava
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang, China
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- College of Tobacco Science, Guizhou University, Guiyang, China
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Anguita-Maeso M, Olivares-García C, Haro C, Imperial J, Navas-Cortés JA, Landa BB. Culture-Dependent and Culture-Independent Characterization of the Olive Xylem Microbiota: Effect of Sap Extraction Methods. FRONTIERS IN PLANT SCIENCE 2020; 10:1708. [PMID: 32038682 PMCID: PMC6988092 DOI: 10.3389/fpls.2019.01708] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/04/2019] [Indexed: 05/03/2023]
Abstract
Microbial endophytes are well known to protect host plants against pathogens, thus representing a promising strategy for the control of xylem-colonizing pathogens. To date, the vast majority of microbial communities inhabiting the olive xylem are unknown; therefore, this work pursues the characterization of the xylem-limited microbiome and determines whether the culture isolation medium, olive genotype, and the plant material used to analyze it can have an effect on the bacterial populations retrieved. Macerated xylem tissue and xylem sap extracted with the Scholander chamber from olive branches obtained from two cultivated and a wild olive genotypes were analyzed using culture-dependent and -independent approaches. In the culture-dependent approach using four solid culture media, a total of 261 bacterial isolates were identified after performing Sanger sequencing of 16S rRNA. Culturable bacteria clustered into 34 genera, with some effect of culture media for bacterial isolation. The cultivated bacteria belonged to four phyla and the most abundant genera included Frigoribacterium (18.8%), Methylobacterium (16.4%), and Sphingomonas (14.6%). On the other hand, in the culture-independent approach conducted using Illumina MiSeq 16S rRNA amplicon sequencing [next-generation sequencing (NGS)] of the xylem extracts, we identified a total of 48 operational taxonomic units (OTUs) belonging to five phyla, being Sphingomonas (30.1%), Hymenobacter (24.1%) and Methylobacterium (22.4%) the most representative genera (>76% of reads). In addition, the results indicated significant differences in the bacterial communities detected in the xylem sap depending on the genotype of the olive tree studied and, to a minor extent, on the type of sap extraction method used. Among the total genera identified using NGS, 14 (41.2%) were recovered in the culture collection, whereas 20 (58.8%) in the culture collection were not captured by the NGS approach. Some of the xylem-inhabiting bacteria isolated are known biocontrol agents of plant pathogens, whereas for others little information is known and are first reported for olive. Consequently, the potential role of these bacteria in conferring olive tree protection against xylem pathogens should be explored in future research.
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Affiliation(s)
- Manuel Anguita-Maeso
- Institute for Sustainable Agriculture, Spanish National Research Council (CSIC), Córdoba, Spain
| | | | - Carmen Haro
- Institute for Sustainable Agriculture, Spanish National Research Council (CSIC), Córdoba, Spain
| | - Juan Imperial
- Institute of Agricultural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Juan A. Navas-Cortés
- Institute for Sustainable Agriculture, Spanish National Research Council (CSIC), Córdoba, Spain
| | - Blanca B. Landa
- Institute for Sustainable Agriculture, Spanish National Research Council (CSIC), Córdoba, Spain
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Burges A, Fievet V, Oustriere N, Epelde L, Garbisu C, Becerril JM, Mench M. Long-term phytomanagement with compost and a sunflower - Tobacco rotation influences the structural microbial diversity of a Cu-contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 700:134529. [PMID: 31693956 DOI: 10.1016/j.scitotenv.2019.134529] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/15/2019] [Accepted: 09/16/2019] [Indexed: 06/10/2023]
Abstract
At a former wood preservation site contaminated with Cu, various phytomanagement options have been assessed in the last decade through physicochemical, ecotoxicological and biological assays. In a field trial at this site, phytomanagement with a crop rotation based on tobacco and sunflower, combined with the incorporation of compost and dolomitic limestone, has proved to be efficient in Cu-associated risk mitigation, ecological soil functions recovery and net gain of economic and social benefits. To demonstrate the long-term effectiveness and sustainability of phytomanagement, we assessed here the influence of this remediation option on the diversity, composition and structure of microbial communities over time, through a metabarcoding approach. After 9 years of phytomanagement, no overall effect was identified on microbial diversity; the soil amendments, notably the repeated compost application, led to shifts in soil microbial populations. This phytomanagement option induced changes in the composition of soil microbial communities, promoting the growth of microbial groups belonging to Alphaproteobacteria, many being involved in N cycling. Populations of Nitrososphaeria, which are crucial in nitrification, as well as taxa from phyla Planctomycetacia, Chloroflexi and Gemmatimonadetes, which are tolerant to metal contamination and adapted to oligotrophic soil conditions, decreased in amended phytomanaged plots. Our study provides an insight into population dynamics within soil microbial communities under long-term phytomanagement, in line with the assessment of soil ecological functions and their recovery.
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Affiliation(s)
- Aritz Burges
- UMR BIOGECO INRA 1202, University of Bordeaux, Bât. B2, allée Geoffroy St-Hilaire, F-33615 Pessac Cedex, France; University of the Basque Country (UPV/EHU), Department of Plant Biology and Ecology, P.O. Box 644, E-48080 Bilbao, Spain.
| | - Virgil Fievet
- UMR BIOGECO INRA 1202, University of Bordeaux, Bât. B2, allée Geoffroy St-Hilaire, F-33615 Pessac Cedex, France
| | - Nadège Oustriere
- Laboratoire Génie Civil et Géoenvironnement (LGCGE), Yncréa Hauts-de-France, Institut Supérieur d'Agriculture, 48 Bld Vauban, 59046 Lille Cedex, France
| | - Lur Epelde
- NEIKER-Tecnalia, Department of Ecology and Natural Resources, Soil Microbial Ecology Group, c/ Berreaga 1, E-48160 Derio, Spain
| | - Carlos Garbisu
- NEIKER-Tecnalia, Department of Ecology and Natural Resources, Soil Microbial Ecology Group, c/ Berreaga 1, E-48160 Derio, Spain
| | - Jose María Becerril
- University of the Basque Country (UPV/EHU), Department of Plant Biology and Ecology, P.O. Box 644, E-48080 Bilbao, Spain
| | - Michel Mench
- UMR BIOGECO INRA 1202, University of Bordeaux, Bât. B2, allée Geoffroy St-Hilaire, F-33615 Pessac Cedex, France
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Schlechter RO, Miebach M, Remus-Emsermann MNP. Driving factors of epiphytic bacterial communities: A review. J Adv Res 2019; 19:57-65. [PMID: 31341670 PMCID: PMC6630024 DOI: 10.1016/j.jare.2019.03.003] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 12/29/2022] Open
Abstract
The physicochemistry of leaves is unique and is a major driver of leaf colonisation. Competition and cooperation may be major drivers of bacterial colonisation. Leaves respond to bacterial colonisation locally and systemically. How leaf responses shape bacterial colonisation patterns is unclear. Plant-microbe interaction should be studied at the micrometer resolution.
Bacteria establish complex, compositionally consistent communities on healthy leaves. Ecological processes such as dispersal, diversification, ecological drift, and selection as well as leaf surface physicochemistry and topology impact community assembly. Since the leaf surface is an oligotrophic environment, species interactions such as competition and cooperation may be major contributors to shape community structure. Furthermore, the plant immune system impacts on microbial community composition, as plant cells respond to bacterial molecules and shape their responses according to the mixture of molecules present. Such tunability of the plant immune network likely enables the plant host to differentiate between pathogenic and non-pathogenic colonisers, avoiding costly immune responses to non-pathogenic colonisers. Plant immune responses are either systemically distributed or locally confined, which in turn affects the colonisation pattern of the associated microbiota. However, how each of these factors impacts the bacterial community is unclear. To better understand this impact, bacterial communities need to be studied at a micrometre resolution, which is the scale that is relevant to the members of the community. Here, current insights into the driving factors influencing the assembly of leaf surface-colonising bacterial communities are discussed, with a special focus on plant host immunity as an emerging factor contributing to bacterial leaf colonisation.
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Affiliation(s)
- Rudolf O Schlechter
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Moritz Miebach
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Mitja N P Remus-Emsermann
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
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Zappelini C, Alvarez-Lopez V, Capelli N, Guyeux C, Chalot M. Streptomyces Dominate the Soil Under Betula Trees That Have Naturally Colonized a Red Gypsum Landfill. Front Microbiol 2018; 9:1772. [PMID: 30123206 PMCID: PMC6085467 DOI: 10.3389/fmicb.2018.01772] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/16/2018] [Indexed: 11/13/2022] Open
Abstract
The successful restoration of well-engineered tailings storage facilities is needed to avoid mine tailings problems. This study characterized the bacterial communities from vegetated and non-vegetated soils from a red gypsum landfill resulting from the industrial extraction of titanium. A set of 275 bacteria was isolated from vegetated soil and non-vegetated soil areas and taxonomically characterized using BOX-PCR. The study also evaluated the ability of a subset of 88 isolated bacteria on their ability to produce plant growth promoting (PGP) traits [indoleacetic acid (IAA) production, phosphate solubilization, and siderophore production] and their tolerance to potentially toxic elements (PTEs). Twenty strains were chosen for further analysis to produce inoculum for birch-challenging experiments. Principal component analysis (PCA) showed that the set of pedological parameters (pH, granulometry, carbon, organic matter, and Mg content) alone explained approximately 40% of the differences between the two soils. The highest density of total culturable bacteria was found in the vegetated soil, and it was much higher than that in the non-vegetated soil. The Actinobacteria phyla dominated the culturable soil community (70% in vegetated soil and 95% in non-vegetated soil), while the phyla Firmicutes (including the genus Bacillus) and Bacteroides (including the genera Pedobacter and Olivibacter) were found only in the vegetated soil fraction. Additional genera (Rhizobium, Variovorax, and Ensifer) were found solely in the vegetated soil. The vegetated soil bacteria harbored the most beneficial PGP bacteria with 12% of the isolates showing three or more PGP traits. The strains with higher metal tolerances in our study were Phyllobacterium sp. WR140 (RO1.15), Phyllobacterium sp. WR140 (R01.34), and Streptomyces sp. (R04.15), all isolated from the vegetated soil. Among the isolates tested in challenging experiments, Phyllobacterium (R01.34) and Streptomyces sp. (R05.33) have the greatest potential to act as PGP rhizobacteria and therefore to be used in the biological restoration of tailings dumps.
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Affiliation(s)
- Cyril Zappelini
- Laboratoire Chrono-Environnement, UMR CNRS 6249, Université Bourgogne Franche-Comté, Montbéliard, France
| | - Vanessa Alvarez-Lopez
- Laboratoire Chrono-Environnement, UMR CNRS 6249, Université Bourgogne Franche-Comté, Montbéliard, France
| | - Nicolas Capelli
- Laboratoire Chrono-Environnement, UMR CNRS 6249, Université Bourgogne Franche-Comté, Montbéliard, France
| | - Christophe Guyeux
- Département d'Informatique des Systèmes Complexes, Institut FEMTO-ST (UMR 6174 CNRS), Université Bourgogne Franche-Comté, Besançon, France
| | - Michel Chalot
- Laboratoire Chrono-Environnement, UMR CNRS 6249, Université Bourgogne Franche-Comté, Montbéliard, France.,Faculté des Sciences et Technologies, Université de Lorraine, Nancy, France
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