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Dos-Santos CM, Nascimento WBA, Cesar MJSC, Baldani JI, Schwab S. Diversity of bacteria of the genus Sphingomonas associated with sugarcane (Saccharum spp.) culm apoplast fluid and their agrotechnological potential. World J Microbiol Biotechnol 2024; 40:304. [PMID: 39155347 DOI: 10.1007/s11274-024-04111-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 08/13/2024] [Indexed: 08/20/2024]
Abstract
In sugarcane, sequences related to the genus Sphingomonas have been widely detected by microbiome studies. In this work, the presence of bacteria of this genus was confirmed using culture-dependent and independent techniques. A collection of thirty isolates was obtained using semispecific cultivation conditions, and a specific PCR assay was applied to help confirm the isolates as belonging to the genus. A series of laboratory evaluations were carried out to identify potential properties among the isolates in the collection, which consequently allowed the identification of some most promising isolates for the development of new agricultural bioinputs. In a separate analysis, the culture-independent fluorescence in situ hybridization (FISH) methodology was applied to demonstrate the natural occurrence of Sphingomonas in different organs and tissues of sugarcane. The results showed the presence of bacteria of the genus in the spaces between cells (apoplast) of the culm parenchyma, in vessels in the region of the leaf vein, on the adaxial surface of the leaf blade, and on the root surface, sometimes close to the base of root hairs, which suggests extensive colonization on the host plant. In summary, the present study corroborates previous metagenomic amplicon sequencing results that indicated a high occurrence of Sphingomonas associated with sugarcane. This is the first study that uses approaches other than amplicon sequencing to confirm the occurrence of the genus in sugarcane and, at the same time, demonstrates potentially beneficial activities to be explored by sugarcane cultivation.
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Affiliation(s)
- Carlos M Dos-Santos
- Embrapa Agrobiologia, Rodovia BR 465, Km 7, Seropédica, Rio de Janeiro State, 23891-000, Brazil
- Pró-Reitoria de Pesquisa e Pós-Graduação, Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465, Km 7, Seropédica, Rio de Janeiro State, 23897-000, Brazil
- Instituto SENAI de Inovação em Química Verde, Rio de Janeiro, Rio de Janeiro State, 20271-030, Brazil
| | - W Bruno A Nascimento
- Embrapa Agrobiologia, Rodovia BR 465, Km 7, Seropédica, Rio de Janeiro State, 23891-000, Brazil
- Instituto de Agronomia, Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465, Km 7, Seropédica, Rio de Janeiro State, 23897-000, Brazil
| | - M Joana S C Cesar
- Embrapa Agrobiologia, Rodovia BR 465, Km 7, Seropédica, Rio de Janeiro State, 23891-000, Brazil
- Instituto de Ciências Biológicas e da Saúde, Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465, Km 7, Seropédica, Rio de Janeiro State, 23897-000, Brazil
| | - José Ivo Baldani
- Embrapa Agrobiologia, Rodovia BR 465, Km 7, Seropédica, Rio de Janeiro State, 23891-000, Brazil
| | - Stefan Schwab
- Embrapa Agrobiologia, Rodovia BR 465, Km 7, Seropédica, Rio de Janeiro State, 23891-000, Brazil.
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Engelhardt IC, Holden N, Daniell TJ, Dupuy LX. Mobility and growth in confined spaces are important mechanisms for the establishment of Bacillus subtilis in the rhizosphere. MICROBIOLOGY (READING, ENGLAND) 2024; 170. [PMID: 39106481 DOI: 10.1099/mic.0.001477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2024]
Abstract
The rhizosphere hosts complex and abundant microbiomes whose structure and composition are now well described by metagenomic studies. However, the dynamic mechanisms that enable micro-organisms to establish along a growing plant root are poorly characterized. Here, we studied how a motile bacterium utilizes the microhabitats created by soil pore space to establish in the proximity of plant roots. We have established a model system consisting of Bacillus subtilis and lettuce seedlings co-inoculated in transparent soil microcosms. We carried out live imaging experiments and developed image analysis pipelines to quantify the abundance of the bacterium as a function of time and position in the pore space. Results showed that the establishment of the bacterium in the rhizosphere follows a precise sequence of events where small islands of mobile bacteria were first seen forming near the root tip within the first 12-24 h of inoculation. Biofilm was then seen forming on the root epidermis at distances of about 700-1000 µm from the tip. Bacteria accumulated predominantly in confined pore spaces within 200 µm from the root or the surface of a particle. Using probabilistic models, we could map the complete sequence of events and propose a conceptual model of bacterial establishment in the pore space. This study therefore advances our understanding of the respective role of growth and mobility in the efficient colonization of bacteria in the rhizosphere.
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Affiliation(s)
- Ilonka C Engelhardt
- Department of Geosciences, University of Tuebingen, Tuebingen 72074, Germany
| | - Nicola Holden
- Department of Rural Land Use, Scotland's Rural College, Aberdeen AB21 9YA, UK
| | - Tim J Daniell
- Molecular Microbiology: Biochemistry to Disease, School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK
| | - Lionel X Dupuy
- Department of Conservation of Natural Resources, Neiker, Derio 48160, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao 48009, Spain
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Li J, Hong M, Lv J, Tang R, Wang R, Yang Y, Liu N. Enhancement on migration and biodegradation of Diaphorobacter sp. LW2 mediated by Pythium ultimum in soil with different particle sizes. Front Microbiol 2024; 15:1391553. [PMID: 38841075 PMCID: PMC11150788 DOI: 10.3389/fmicb.2024.1391553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/02/2024] [Indexed: 06/07/2024] Open
Abstract
Introduction The composition and structure of natural soil are very complex, leading to the difficult contact between hydrophobic organic compounds and degrading-bacteria in contaminated soil, making pollutants hard to be removed from the soil. Several researches have reported the bacterial migration in unsaturated soil mediated by fungal hyphae, but bacterial movement in soil of different particle sizes or in heterogeneous soil was unclear. The remediation of contaminated soil enhanced by hyphae still needs further research. Methods In this case, the migration and biodegradation of Diaphorobacter sp. LW2 in soil was investigated in presence of Pythium ultimum. Results Hyphae could promote the growth and migration of LW2 in culture medium. It was also confirmed that LW2 was able to migrate in the growth direction and against the growth direction along hyphae. Mediated by hyphae, motile strain LW2 translocated over 3 cm in soil with different particle size (CS1, 1.0-2.0 mm; CS2, 0.5-1.0mm; MS, 0.25-0.5 mm and FS, <0.25 mm), and it need shorter time in bigger particle soils. In inhomogeneous soil, hyphae participated in the distribution of introduced bacteria, and the total number of bacteria increased. Pythium ultimum enhanced the migration and survival of LW2 in soil, improving the bioremediation of polluted soil. Discussion The results of this study indicate that the mobilization of degrading bacteria mediated by Pythium ultimum in soil has great potential for application in bioremediation of contaminated soil.
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Affiliation(s)
- Jialu Li
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, China
- National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, Jilin University, Changchun, China
| | - Mei Hong
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, China
- National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, Jilin University, Changchun, China
| | - Jing Lv
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, China
- National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, Jilin University, Changchun, China
| | - Rui Tang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, China
- National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, Jilin University, Changchun, China
| | - Ruofan Wang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, China
- National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, Jilin University, Changchun, China
| | - Yadong Yang
- School of Environmental Science and Engineering, Jiangsu Engineering Research Center of Biomass Waste Pyrolytic Carbonization & Application, Yancheng Institute of Technology, Yancheng, China
| | - Na Liu
- Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, China
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Schmidt H, Gorka S, Seki D, Schintlmeister A, Woebken D. Gold-FISH enables targeted NanoSIMS analysis of plant-associated bacteria. THE NEW PHYTOLOGIST 2023; 240:439-451. [PMID: 37381111 PMCID: PMC10962543 DOI: 10.1111/nph.19112] [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: 03/08/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023]
Abstract
Bacteria colonize plant roots and engage in reciprocal interactions with their hosts. However, the contribution of individual taxa or groups of bacteria to plant nutrition and fitness is not well characterized due to a lack of in situ evidence of bacterial activity. To address this knowledge gap, we developed an analytical approach that combines the identification and localization of individual bacteria on root surfaces via gold-based in situ hybridization with correlative NanoSIMS imaging of incorporated stable isotopes, indicative of metabolic activity. We incubated Kosakonia strain DS-1-associated, gnotobiotically grown rice plants with 15 N-N2 gas to detect in situ N2 fixation activity. Bacterial cells along the rhizoplane showed heterogeneous patterns of 15 N enrichment, ranging from the natural isotope abundance levels up to 12.07 at% 15 N (average and median of 3.36 and 2.85 at% 15 N, respectively, n = 697 cells). The presented correlative optical and chemical imaging analysis is applicable to a broad range of studies investigating plant-microbe interactions. For example, it enables verification of the in situ metabolic activity of host-associated commercialized strains or plant growth-promoting bacteria, thereby disentangling their role in plant nutrition. Such data facilitate the design of plant-microbe combinations for improvement of crop management.
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Affiliation(s)
- Hannes Schmidt
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
| | - Stefan Gorka
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
- Doctoral School in Microbiology and Environmental ScienceUniversity of ViennaVienna1030Austria
| | - David Seki
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
- Large‐Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
| | - Dagmar Woebken
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
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Wu Y, Fu C, Peacock CL, Sørensen SJ, Redmile-Gordon MA, Xiao KQ, Gao C, Liu J, Huang Q, Li Z, Song P, Zhu Y, Zhou J, Cai P. Cooperative microbial interactions drive spatial segregation in porous environments. Nat Commun 2023; 14:4226. [PMID: 37454222 PMCID: PMC10349867 DOI: 10.1038/s41467-023-39991-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/05/2023] [Indexed: 07/18/2023] Open
Abstract
The role of microbial interactions and the underlying mechanisms that shape complex biofilm communities are poorly understood. Here we employ a microfluidic chip to represent porous subsurface environments and show that cooperative microbial interactions between free-living and biofilm-forming bacteria trigger active spatial segregation to promote their respective dominance in segregated microhabitats. During initial colonization, free-living and biofilm-forming microbes are segregated from the mixed planktonic inoculum to occupy the ambient fluid and grain surface. Contrary to spatial exclusion through competition, the active spatial segregation is induced by cooperative interactions which improves the fitness of both biofilm and planktonic populations. We further show that free-living Arthrobacter induces the surface colonization by scavenging the biofilm inhibitor, D-amino acids and receives benefits from the public goods secreted by the biofilm-forming strains. Collectively, our results reveal how cooperative microbial interactions may contribute to microbial coexistence in segregated microhabitats and drive subsurface biofilm community succession.
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Affiliation(s)
- Yichao Wu
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Chengxia Fu
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Caroline L Peacock
- School of Earth and Environment, University of Leeds, Leeds, LS2 9JT, UK
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Marc A Redmile-Gordon
- Department of Environmental Horticulture, Royal Horticultural Society, Wisley, Surrey, GU23 6QB, UK
| | - Ke-Qing Xiao
- School of Earth and Environment, University of Leeds, Leeds, LS2 9JT, UK
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Chunhui Gao
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Jun Liu
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Zixue Li
- School of Physics, Huazhong University of Science and Technology, Wuhan, China
| | - Peiyi Song
- School of Physics, Huazhong University of Science and Technology, Wuhan, China
| | - Yongguan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, USA
| | - Peng Cai
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China.
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Davoudpour Y, Kümmel S, Musat N, Richnow HH, Schmidt M. Tracking deuterium uptake in hydroponically grown maize roots using correlative helium ion microscopy and Raman micro-spectroscopy. PLANT METHODS 2023; 19:71. [PMID: 37452400 PMCID: PMC10347822 DOI: 10.1186/s13007-023-01040-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Investigations into the growth and self-organization of plant roots is subject to fundamental and applied research in various areas such as botany, agriculture, and soil science. The growth activity of the plant tissue can be investigated by isotope labeling experiments with heavy water and subsequent detection of the deuterium in non-exchangeable positions incorporated into the plant biomass. Commonly used analytical methods to detect deuterium in plants are based on mass-spectrometry or neutron-scattering and they either suffer from elaborated sample preparation, destruction of the sample during analysis, or low spatial resolution. Confocal Raman micro-spectroscopy (CRM) can be considered a promising method to overcome the aforementioned challenges. The substitution of hydrogen with deuterium results in the measurable shift of the CH-related Raman bands. By employing correlative approaches with a high-resolution technique, such as helium ion microscopy (HIM), additional structural information can be added to CRM isotope maps and spatial resolution can be further increased. For that, it is necessary to develop a comprehensive workflow from sample preparation to data processing. RESULTS A workflow to prepare and analyze roots of hydroponically grown and deuterium labeled Zea mays by correlative HIM-CRM micro-analysis was developed. The accuracy and linearity of deuterium detection by CRM were tested and confirmed with samples of deuterated glucose. A set of root samples taken from deuterated Zea mays in a time-series experiment was used to test the entire workflow. The deuterium content in the roots measured by CRM was close to the values obtained by isotope-ratio mass spectrometry. As expected, root tips being the most actively growing root zone had incorporated the highest amount of deuterium which increased with increasing time of labeling. Furthermore, correlative HIM-CRM analysis allowed for obtaining the spatial distribution pattern of deuterium and lignin in root cross-sections. Here, more active root zones with higher deuterium incorporation showed less lignification. CONCLUSIONS We demonstrated that CRM in combination with deuterium labeling can be an alternative and reliable tool for the analysis of plant growth. This approach together with the developed workflow has the potential to be extended to complex systems such as plant roots grown in soil.
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Affiliation(s)
- Yalda Davoudpour
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.
| | - Steffen Kümmel
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Hans Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Matthias Schmidt
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
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Wang J, Chen S, Sun R, Liu B, Waghmode T, Hu C. Spatial and temporal dynamics of the bacterial community under experimental warming in field-grown wheat. PeerJ 2023; 11:e15428. [PMID: 37334112 PMCID: PMC10276554 DOI: 10.7717/peerj.15428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/25/2023] [Indexed: 06/20/2023] Open
Abstract
Climate change may lead to adverse effects on agricultural crops, plant microbiomes have the potential to help hosts counteract these effects. While plant-microbe interactions are known to be sensitive to temperature, how warming affects the community composition and functioning of plant microbiomes in most agricultural crops is still unclear. Here, we utilized a 10-year field experiment to investigate the effects of warming on root zone carbon availability, microbial activity and community composition at spatial (root, rhizosphere and bulk soil) and temporal (tillering, jointing and ripening stages of plants) scales in field-grown wheat (Triticum aestivum L.). The dissolved organic carbon and microbial activity in the rhizosphere were increased by soil warming and varied considerably across wheat growth stages. Warming exerted stronger effects on the microbial community composition in the root and rhizosphere samples than in the bulk soil. Microbial community composition, particularly the phyla Actinobacteria and Firmicutes, shifted considerably in response to warming. Interestingly, the abundance of a number of known copiotrophic taxa, such as Pseudomonas and Bacillus, and genera in Actinomycetales increased in the roots and rhizosphere under warming and the increase in these taxa implies that they may play a role in increasing the resilience of plants to warming. Taken together, we demonstrated that soil warming along with root proximity and plant growth status drives changes in the microbial community composition and function in the wheat root zone.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, The Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuaimin Chen
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, The Chinese Academy of Sciences, Shijiazhuang, Hebei, China
| | - Ruibo Sun
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, The Chinese Academy of Sciences, Shijiazhuang, Hebei, China
| | - Binbin Liu
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, The Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- Xiong’an Institute of Innovation, Chinese Academy of Sciences, Xiong’an New Area, China
| | - Tatoba Waghmode
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, The Chinese Academy of Sciences, Shijiazhuang, Hebei, China
| | - Chunsheng Hu
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, The Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- Xiong’an Institute of Innovation, Chinese Academy of Sciences, Xiong’an New Area, China
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Cao Z, Zuo W, Wang L, Chen J, Qu Z, Jin F, Dai L. Spatial profiling of microbial communities by sequential FISH with error-robust encoding. Nat Commun 2023; 14:1477. [PMID: 36932092 PMCID: PMC10023729 DOI: 10.1038/s41467-023-37188-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
Spatial analysis of microbiomes at single cell resolution with high multiplexity and accuracy has remained challenging. Here we present spatial profiling of a microbiome using sequential error-robust fluorescence in situ hybridization (SEER-FISH), a highly multiplexed and accurate imaging method that allows mapping of microbial communities at micron-scale. We show that multiplexity of RNA profiling in microbiomes can be increased significantly by sequential rounds of probe hybridization and dissociation. Combined with error-correction strategies, we demonstrate that SEER-FISH enables accurate taxonomic identification in complex microbial communities. Using microbial communities composed of diverse bacterial taxa isolated from plant rhizospheres, we apply SEER-FISH to quantify the abundance of each taxon and map microbial biogeography on roots. At micron-scale, we identify clustering of microbial cells from multiple species on the rhizoplane. Under treatment of plant metabolites, we find spatial re-organization of microbial colonization along the root and alterations in spatial association among microbial taxa. Taken together, SEER-FISH provides a useful method for profiling the spatial ecology of complex microbial communities in situ.
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Affiliation(s)
- Zhaohui Cao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenlong Zuo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Lanxiang Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Junyu Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zepeng Qu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Fan Jin
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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9
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Fluorescence in situ hybridisation in Carnoy's fixed tonsil tissue. Sci Rep 2022; 12:12395. [PMID: 35858968 PMCID: PMC9300673 DOI: 10.1038/s41598-022-16309-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 07/07/2022] [Indexed: 11/18/2022] Open
Abstract
Fluorescence in situ hybridisation (FISH) is a powerful molecular technique that enables direct visualisation of specific bacterial species. Few studies have established FISH protocols for tonsil tissue in Carnoy’s fixative, accordingly limiting its application to investigate the pathogenesis of tonsillar hyperplasia. Tonsil tissue from 24 children undergoing tonsillectomy for either recurrent tonsillitis or sleep-disordered breathing were obtained during a previous study. The specificity of each of the five FISH probes (Fusobacterium spp., Bacteroides spp., Streptococcus spp., Haemophilus influenzae and Pseudomonas spp.) were successfully optimised using pure and mixed bacterial isolates, and in Carnoy’s fixed tonsil tissue. Bacteroides spp. were present in 100% of patients with microcolonies. In comparison, the prevalence of Fusobacterium spp. was 93.8%, Streptococcus spp. 85.7%, H. influenzae 82.35% and Pseudomonas spp. 76.5%. Notable differences in the organisation of bacterial taxa within a single microcolony were also observed. This is the first study to establish a robust FISH protocol identifying multiple aerobic and anaerobic bacteria in Carnoy’s fixed tonsil tissue. This protocol provides a strong foundation for combining histological and microbiological analyses of Carnoy’s fixed tonsil samples. It may also have important implications on the analysis of microorganisms in other human tissues prepared using the same techniques.
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Fulk EM, Gao X, Lu LC, Redeker KR, Masiello CA, Silberg JJ. Nondestructive Chemical Sensing within Bulk Soil Using 1000 Biosensors Per Gram of Matrix. ACS Synth Biol 2022; 11:2372-2383. [PMID: 35715210 DOI: 10.1021/acssynbio.2c00083] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gene expression can be monitored in hard-to-image environmental materials using gas-reporting biosensors, but these outputs have only been applied in autoclaved matrices that are hydrated with rich medium. To better understand the compatibility of indicator gas reporting with environmental samples, we evaluated how matrix hydration affects the gas signal of an engineered microbe added to a sieved soil. A gas-reporting microbe presented a gas signal in a forest soil (Alfisol) when hydrated to an environmentally relevant osmotic pressure. When the gas signal was concentrated prior to analysis, a biosensor titer of 103 cells/gram of soil produced a significant signal when soil was supplemented with halides. A signal was also observed without halide amendment, but a higher cell titer (106 cells/gram of soil) was required. A sugar-regulated gas biosensor was able to report with a similar level of sensitivity when added to an unsterilized soil matrix, illustrating how gas concentration enables biosensing within a soil containing environmental microbes. These results establish conditions where engineered microbes can report on gene expression in living environmental matrices with decreased perturbation of the soil environment compared to previously reported approaches, using biosensor titers that are orders of magnitude lower than the number of cells typically observed in a gram of soil.
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Affiliation(s)
- Emily M Fulk
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, 6100 Main Street, MS-180, Houston, Texas 77005, United States
| | - Xiaodong Gao
- Department of Earth, Environmental and Planetary Sciences, Rice University, 6100 Main St, MS-126, Houston, Texas 77005, United States
| | - Li Chieh Lu
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Kelly R Redeker
- Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Caroline A Masiello
- Department of Earth, Environmental and Planetary Sciences, Rice University, 6100 Main St, MS-126, Houston, Texas 77005, United States.,Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, 6100 Main Street, MS-60, Houston, Texas 77005, United States
| | - Jonathan J Silberg
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States.,Department of Bioengineering, Rice University, 6100 Main Street, MS-142, Houston, Texas 77005, United States.,Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, MS-362, Houston, Texas 77005, United States
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Ultra-Wideband Microwave Imaging System for Root Phenotyping. SENSORS 2022; 22:s22052031. [PMID: 35271178 PMCID: PMC8914630 DOI: 10.3390/s22052031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 11/18/2022]
Abstract
The roots are a vital organ for plant growth and health. The opaque surrounding environment of the roots and the complicated growth process means that in situ and non-destructive root phenotyping face great challenges, which thus spur great research interests. The existing methods for root phenotyping are either unable to provide high-precision and high accuracy in situ detection, or they change the surrounding root environment and are destructive to root growth and health. Thus,we propose and develop an ultra-wideband microwave scanning method that uses time reversal to achieve in situ root phenotyping nondestructively. To verify the method’s feasibility, we studied an electromagnetic numerical model that simulates the transmission signal of two ultra-wideband microwave antennas. The simulated signal of roots with different shapes shows the proposed system’s capability to measure the root size in the soil. Experimental validations were conducted considering three sets of measurements with different sizes, numbers and locations, and the experimental results indicate that the developed imaging system was able to differentiate root sizes and numbers with high contrast. The reconstruction from both simulations and experimental measurements provided accurate size estimation of the carrots in the soil, which indicates the system’s potential for root imaging.
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12
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Aufrecht J, Khalid M, Walton CL, Tate K, Cahill JF, Retterer ST. Hotspots of root-exuded amino acids are created within a rhizosphere-on-a-chip. LAB ON A CHIP 2022; 22:954-963. [PMID: 35089295 DOI: 10.1039/d1lc00705j] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The rhizosphere is a challenging ecosystem to study from a systems biology perspective due to its diverse chemical, physical, and biological characteristics. In the past decade, microfluidic platforms (e.g. plant-on-a-chip) have created an alternative way to study whole rhizosphere organisms, like plants and microorganisms, under reduced-complexity conditions. However, in reducing the complexity of the environment, it is possible to inadvertently alter organism phenotype, which biases laboratory data compared to in situ experiments. To build back some of the complexity of the rhizosphere in a fully-defined, parameterized approach we have developed a rhizosphere-on-a-chip platform that mimics the physical structure of soil. We demonstrate, through computational simulation, how this synthetic soil structure can influence the emergence of molecular "hotspots" and "hotmoments" that arise naturally from the plant's exudation of labile carbon compounds. We establish the amenability of the rhizosphere-on-a-chip for long-term culture of Brachypodium distachyon, and experimentally validate the presence of exudate hotspots within the rhizosphere-on-a-chip pore spaces using liquid microjunction surface sampling probe mass spectrometry.
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Affiliation(s)
- Jayde Aufrecht
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Muneeba Khalid
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Courtney L Walton
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Kylee Tate
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - John F Cahill
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Scott T Retterer
- Center for Nanophase Materials Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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13
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Huang Y, Dong Y, Ren Y, Wang S, Li Y, Du K, Lin X, Yang M. Niches and Seasonal Changes, Rather Than Transgenic Events, Affect the Microbial Community of Populus × euramericana ‘Neva’. Front Microbiol 2022; 12:805261. [PMID: 35154035 PMCID: PMC8831546 DOI: 10.3389/fmicb.2021.805261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/27/2021] [Indexed: 01/05/2023] Open
Abstract
Exploring the complex spatiotemporal changes and colonization mechanism of microbial communities will enable microbial communities to be better used to serve agricultural and ecological operations. In addition, evaluating the impact of transgenic plants on endogenous microbial communities is necessary for their commercial application. In this study, microbial communities of Populus × euramericana ‘Neva’ carrying Cry1Ac-Cry3A-BADH genes (ECAA1 line), Populus × euramericana ‘Neva’ carrying Cry1Ac-Cry3A-NTHK1 genes (ECAB1 line), and non-transgenic Populus × euramericana ‘Neva’ from rhizosphere soil, roots, and phloem collected in different seasons were compared and analyzed. Our analyses indicate that the richness and diversity of bacterial communities were higher in the three Populus × euramericana ‘Neva’ habitats than in those of fungi. Bacterial and fungal genetic-distance-clustering results were similar; rhizosphere soil clustered in one category, with roots and phloem in another. The diversity and evenness values of the microbial community were: rhizosphere soil > phloem > root system. The bacterial communities in the three habitats were dominated by the Proteobacteria, and fungal communities were dominated by the Ascomycota. The community composition and abundance of each part were quite different; those of Populus × euramericana ‘Neva’ were similar among seasons, but community abundance fluctuated. Seasonal fluctuation in the bacterial community was greatest in rhizosphere soil, while that of the fungal community was greatest in phloem. The transgenic lines ECAA1 and ECAB1 had a bacterial and fungal community composition similar to that of the control samples, with no significant differences in community structure or diversity among the lines. The abundances of operational taxonomic units (OTUs) were low, and differed significantly among the lines. These differences did not affect the functioning of the whole specific community. Sampling time and location were the main driving factors of changes in the Populus × euramericana ‘Neva’ microbial community. Transgenic events did not affect the Populus × euramericana ‘Neva’ rhizosphere or endophytic microbial communities. This study provides a reference for the safety evaluation of transgenic plants and the internal colonization mechanism of microorganisms in plants.
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Affiliation(s)
- Yali Huang
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Yan Dong
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Yachao Ren
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Shijie Wang
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Yongtan Li
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Kejiu Du
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Xin Lin
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding, China
- Agricultural Office of Kenfeng Subdistrict Office, Tangshan, China
| | - Minsheng Yang
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
- *Correspondence: Minsheng Yang,
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14
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Liu Y, Patko D, Engelhardt I, George TS, Stanley-Wall NR, Ladmiral V, Ameduri B, Daniell TJ, Holden N, MacDonald MP, Dupuy LX. Plant-environment microscopy tracks interactions of Bacillus subtilis with plant roots across the entire rhizosphere. Proc Natl Acad Sci U S A 2021; 118:e2109176118. [PMID: 34819371 PMCID: PMC8640753 DOI: 10.1073/pnas.2109176118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2021] [Indexed: 11/18/2022] Open
Abstract
Our understanding of plant-microbe interactions in soil is limited by the difficulty of observing processes at the microscopic scale throughout plants' large volume of influence. Here, we present the development of three-dimensional live microscopy for resolving plant-microbe interactions across the environment of an entire seedling growing in a transparent soil in tailor-made mesocosms, maintaining physical conditions for the culture of both plants and microorganisms. A tailor-made, dual-illumination light sheet system acquired photons scattered from the plant while fluorescence emissions were simultaneously captured from transparent soil particles and labeled microorganisms, allowing the generation of quantitative data on samples ∼3,600 mm3 in size, with as good as 5 µm resolution at a rate of up to one scan every 30 min. The system tracked the movement of Bacillus subtilis populations in the rhizosphere of lettuce plants in real time, revealing previously unseen patterns of activity. Motile bacteria favored small pore spaces over the surface of soil particles, colonizing the root in a pulsatile manner. Migrations appeared to be directed toward the root cap, the point of "first contact," before the subsequent colonization of mature epidermis cells. Our findings show that microscopes dedicated to live environmental studies present an invaluable tool to understand plant-microbe interactions.
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Affiliation(s)
- Yangminghao Liu
- School of Science and Engineering, University of Dundee, Dundee DD1 4HN, United Kingdom
| | - Daniel Patko
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
- Department of Conservation of Natural Resources, Neiker, Derio 48160, Spain
| | - Ilonka Engelhardt
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
- Department of Conservation of Natural Resources, Neiker, Derio 48160, Spain
| | - Timothy S George
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | | | - Vincent Ladmiral
- Institut Charles Gerhardt de Montpellier, Université de Montpellier, CNRS, ENSCM, Montpellier 34090, France
| | - Bruno Ameduri
- Institut Charles Gerhardt de Montpellier, Université de Montpellier, CNRS, ENSCM, Montpellier 34090, France
| | - Tim J Daniell
- Plants, Photosynthesis and Soil, School of Biosciences, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Nicola Holden
- Northern Faculty, Scotland's Rural College, Aberdeen AB21 9YA, United Kingdom
| | - Michael P MacDonald
- School of Science and Engineering, University of Dundee, Dundee DD1 4HN, United Kingdom;
| | - Lionel X Dupuy
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom;
- Department of Conservation of Natural Resources, Neiker, Derio 48160, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao 48009, Spain
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15
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Usyskin-Tonne A, Hadar Y, Minz D. Spike Formation Is a Turning Point Determining Wheat Root Microbiome Abundance, Structures and Functions. Int J Mol Sci 2021; 22:11948. [PMID: 34769377 PMCID: PMC8585012 DOI: 10.3390/ijms222111948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/24/2021] [Accepted: 10/29/2021] [Indexed: 11/17/2022] Open
Abstract
Root selection of their associated microbiome composition and activities is determined by the plant's developmental stage and distance from the root. Total gene abundance, structure and functions of root-associated and rhizospheric microbiomes were studied throughout wheat growth season under field conditions. On the root surface, abundance of the well-known wheat colonizers Proteobacteria and Actinobacteria decreased and increased, respectively, during spike formation, whereas abundance of Bacteroidetes was independent of spike formation. Metagenomic analysis combined with functional co-occurrence networks revealed a significant impact of plant developmental stage on its microbiome during the transition from vegetative growth to spike formation. For example, gene functions related to biofilm and sensorial movement, antibiotic production and resistance and carbons and amino acids and their transporters. Genes associated with these functions were also in higher abundance in root vs. the rhizosphere microbiome. We propose that abundance of transporter-encoding genes related to carbon and amino acid, may mirror the availability and utilization of root exudates. Genes related to antibiotic resistance mechanisms were abundant during vegetative growth, while after spike formation, genes related to the biosynthesis of various antibiotics were enriched. This observation suggests that during root colonization and biofilm formation, bacteria cope with competitor's antibiotics, whereas in the mature biofilm stage, they invest in inhibiting new colonizers. Additionally, there is higher abundance of genes related to denitrification in rhizosphere compared to root-associated microbiome during wheat growth, possibly due to competition with the plant over nitrogen in the root vicinity. We demonstrated functional and phylogenetic division in wheat root zone microbiome in both time and space: pre- and post-spike formation, and root-associated vs. rhizospheric niches. These findings shed light on the dynamics of plant-microbe and microbe-microbe interactions in the developing root zone.
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Affiliation(s)
- Alla Usyskin-Tonne
- Soil, Water and Environmental Sciences, Volcani Research Center, Rishon LeZion 7505101, Israel;
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel;
| | - Yitzhak Hadar
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel;
| | - Dror Minz
- Soil, Water and Environmental Sciences, Volcani Research Center, Rishon LeZion 7505101, Israel;
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16
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Armbruster CR, Marshall CW, Garber AI, Melvin JA, Zemke AC, Moore J, Zamora PF, Li K, Fritz IL, Manko CD, Weaver ML, Gaston JR, Morris A, Methé B, DePas WH, Lee SE, Cooper VS, Bomberger JM. Adaptation and genomic erosion in fragmented Pseudomonas aeruginosa populations in the sinuses of people with cystic fibrosis. Cell Rep 2021; 37:109829. [PMID: 34686349 PMCID: PMC8667756 DOI: 10.1016/j.celrep.2021.109829] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/09/2021] [Accepted: 09/22/2021] [Indexed: 10/20/2022] Open
Abstract
Pseudomonas aeruginosa notoriously adapts to the airways of people with cystic fibrosis (CF), yet how infection-site biogeography and associated evolutionary processes vary as lifelong infections progress remains unclear. Here we test the hypothesis that early adaptations promoting aggregation influence evolutionary-genetic trajectories by examining longitudinal P. aeruginosa from the sinuses of six adults with CF. Highly host-adapted lineages harbored mutator genotypes displaying signatures of early genome degradation associated with recent host restriction. Using an advanced imaging technique (MiPACT-HCR [microbial identification after passive clarity technique]), we find population structure tracks with genome degradation, with the most host-adapted, genome-degraded P. aeruginosa (the mutators) residing in small, sparse aggregates. We propose that following initial adaptive evolution in larger populations under strong selection for aggregation, P. aeruginosa persists in small, fragmented populations that experience stronger effects of genetic drift. These conditions enrich for mutators and promote degenerative genome evolution. Our findings underscore the importance of infection-site biogeography to pathogen evolution.
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Affiliation(s)
- Catherine R Armbruster
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | | | - Arkadiy I Garber
- Biodesign Center for Mechanisms of Evolution and School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Jeffrey A Melvin
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Anna C Zemke
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - John Moore
- Department of Otolaryngology, University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Paula F Zamora
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Kelvin Li
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Ian L Fritz
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Christopher D Manko
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Madison L Weaver
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Jordan R Gaston
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Alison Morris
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Barbara Methé
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - William H DePas
- Department of Pediatrics, Children's Hospital of Pittsburgh and University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Stella E Lee
- Department of Otolaryngology, University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA.
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA; Pittsburgh Center for Evolutionary Biology & Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
| | - Jennifer M Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
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17
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Kawasaki A, Dennis PG, Forstner C, Raghavendra AKH, Richardson AE, Watt M, Mathesius U, Gilliham M, Ryan PR. The microbiomes on the roots of wheat (Triticum aestivum L.) and rice (Oryza sativa L.) exhibit significant differences in structure between root types and along root axes. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:871-888. [PMID: 33934748 DOI: 10.1071/fp20351] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/22/2021] [Indexed: 05/06/2023]
Abstract
There is increasing interest in understanding how the microbial communities on roots can be manipulated to improve plant productivity. Root systems are not homogeneous organs but are comprised of different root types of various ages and anatomies that perform different functions. Relatively little is known about how this variation influences the distribution and abundance of microorganisms on roots and in the rhizosphere. Such information is important for understanding how root-microbe interactions might affect root function and prevent diseases. This study tested specific hypotheses related to the spatial variation of bacterial and fungal communities on wheat (Triticum aestivum L.) and rice (Oryza sativa L.) roots grown in contrasting soils. We demonstrate that microbial communities differed significantly between soil type, between host species, between root types, and with position along the root axes. The magnitude of variation between different root types and along individual roots was comparable with the variation detected between different plant species. We discuss the general patterns that emerged in this variation and identify bacterial and fungal taxa that were consistently more abundant on specific regions of the root system. We argue that these patterns should be measured more routinely so that localised root-microbe interactions can be better linked with root system design, plant health and performance.
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Affiliation(s)
- Akitomo Kawasaki
- CSIRO Agriculture and Food, PO Box 1700, Canberra, ACT 2601, Australia; and Present address: NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW 2568, Australia
| | - Paul G Dennis
- School of Earth and Environmental Sciences, Faculty of Sciences, The University of Queensland, St Lucia, Qld 4072, Australia
| | - Christian Forstner
- School of Earth and Environmental Sciences, Faculty of Sciences, The University of Queensland, St Lucia, Qld 4072, Australia
| | - Anil K H Raghavendra
- School of Earth and Environmental Sciences, Faculty of Sciences, The University of Queensland, St Lucia, Qld 4072, Australia; and Present address: NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW 2568, Australia
| | - Alan E Richardson
- CSIRO Agriculture and Food, PO Box 1700, Canberra, ACT 2601, Australia
| | - Michelle Watt
- School of BioSciences, University of Melbourne, Parkville, Vic. 3010, Australia
| | - Ulrike Mathesius
- Division of Plant Sciences, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Matthew Gilliham
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA 5064, Australia
| | - Peter R Ryan
- CSIRO Agriculture and Food, PO Box 1700, Canberra, ACT 2601, Australia; and Corresponding author.
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18
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Bhattacharyya A, Pablo CHD, Mavrodi OV, Weller DM, Thomashow LS, Mavrodi DV. Rhizosphere plant-microbe interactions under water stress. ADVANCES IN APPLIED MICROBIOLOGY 2021; 115:65-113. [PMID: 34140134 DOI: 10.1016/bs.aambs.2021.03.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Climate change, with its extreme temperature, weather and precipitation patterns, is a major global concern of dryland farmers, who currently meet the challenges of climate change agronomically and with growth of drought-tolerant crops. Plants themselves compensate for water stress by modifying aerial surfaces to control transpiration and altering root hydraulic conductance to increase water uptake. These responses are complemented by metabolic changes involving phytohormone network-mediated activation of stress response pathways, resulting in decreased photosynthetic activity and the accumulation of metabolites to maintain osmotic and redox homeostasis. Phylogenetically diverse microbial communities sustained by plants contribute to host drought tolerance by modulating phytohormone levels in the rhizosphere and producing water-sequestering biofilms. Drylands of the Inland Pacific Northwest, USA, illustrate the interdependence of dryland crops and their associated microbiota. Indigenous Pseudomonas spp. selected there by long-term wheat monoculture suppress root diseases via the production of antibiotics, with soil moisture a critical determinant of the bacterial distribution, dynamics and activity. Those pseudomonads producing phenazine antibiotics on wheat had more abundant rhizosphere biofilms and provided improved tolerance to drought, suggesting a role of the antibiotic in alleviation of drought stress. The transcriptome and metabolome studies suggest the importance of wheat root exudate-derived osmoprotectants for the adaptation of these pseudomonads to the rhizosphere lifestyle and support the idea that the exchange of metabolites between plant roots and microorganisms profoundly affects and shapes the belowground plant microbiome under water stress.
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Affiliation(s)
- Ankita Bhattacharyya
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Clint H D Pablo
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Olga V Mavrodi
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - David M Weller
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Linda S Thomashow
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Dmitri V Mavrodi
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States.
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19
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Priya P, Aneesh B, Harikrishnan K. Genomics as a potential tool to unravel the rhizosphere microbiome interactions on plant health. J Microbiol Methods 2021; 185:106215. [PMID: 33839214 DOI: 10.1016/j.mimet.2021.106215] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 12/12/2022]
Abstract
Intense agricultural practices to meet rising food demands have caused ecosystem perturbations. For sustainable crop production, biological agents are gaining attention, but exploring their functional potential on a multi-layered complex ecosystem like the rhizosphere is challenging. This review explains the significance of genomics as a culture-independent molecular tool to understand the diversity and functional significance of the rhizosphere microbiome for sustainable agriculture. It discusses the recent significant studies in the rhizosphere environment carried out using evolving techniques like metagenomics, metatranscriptomics, and metaproteomics, their challenges, constraints infield application, and prospective solutions. The recent advances in techniques such as nanotechnology for the development of bioformulations and visualization techniques contemplating environmental safety were also discussed. The need for development of metagenomic data sets of regionally important crops, their plant microbial interactions and agricultural practices for narrowing down significant data from huge databases have been suggested. The role of taxonomical and functional diversity of soil microbiota in understanding soil suppression and part played by the microbial metabolites in the process have been analyzed and discussed in the context of 'omics' approach. 'Omics' studies have revealed important information about microbial diversity, their responses to various biotic and abiotic stimuli, and the physiology of disease suppression. This can be translated to crop sustainability and combinational approaches with advancing visualization and analysis methodologies fix the existing knowledge gap to a huge extend. With improved data processing and standardization of the methods, details of plant-microbe interactions can be successfully decoded to develop sustainable agricultural practices.
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Affiliation(s)
- P Priya
- Environmental Biology Lab, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.
| | - B Aneesh
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences Cochin University of Science and Technology, Cochin, Kerala, India.
| | - K Harikrishnan
- Environmental Biology Lab, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.
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20
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Birt HWG, Pattison AB, Dennis PG. Sampling Microbiomes Associated with Different Plant Compartments. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2232:23-29. [PMID: 33161535 DOI: 10.1007/978-1-0716-1040-4_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The microbiome is known to influence plant fitness and differs significantly between plant compartments. To characterize the communities associated with different plant compartments, it is necessary to separate plant tissues in a manner that is suitable for microbiome analysis. Here, we describe a standardized protocol for sampling the microbiomes associated with bulk soil, the apical and basal ectorhizosphere, the apical and ectorhizosphere, the rhizome, pseudostem, and leaves of Musa spp. The approach can easily be modified for work with other plants.
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Affiliation(s)
- Henry W G Birt
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Anthony B Pattison
- Department of Agriculture and Fisheries, Centre for Wet Tropic Agriculture, South Johnstone, QLD, Australia
| | - Paul G Dennis
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD, Australia.
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21
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Biessy A, Filion M. Phloroglucinol Derivatives in Plant-Beneficial Pseudomonas spp.: Biosynthesis, Regulation, and Functions. Metabolites 2021; 11:metabo11030182. [PMID: 33804595 PMCID: PMC8003664 DOI: 10.3390/metabo11030182] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/12/2021] [Accepted: 03/17/2021] [Indexed: 11/16/2022] Open
Abstract
Plant-beneficial Pseudomonas spp. aggressively colonize the rhizosphere and produce numerous secondary metabolites, such as 2,4-diacetylphloroglucinol (DAPG). DAPG is a phloroglucinol derivative that contributes to disease suppression, thanks to its broad-spectrum antimicrobial activity. A famous example of this biocontrol activity has been previously described in the context of wheat monoculture where a decline in take-all disease (caused by the ascomycete Gaeumannomyces tritici) has been shown to be associated with rhizosphere colonization by DAPG-producing Pseudomonas spp. In this review, we discuss the biosynthesis and regulation of phloroglucinol derivatives in the genus Pseudomonas, as well as investigate the role played by DAPG-producing Pseudomonas spp. in natural soil suppressiveness. We also tackle the mode of action of phloroglucinol derivatives, which can act as antibiotics, signalling molecules and, in some cases, even as pathogenicity factors. Finally, we discuss the genetic and genomic diversity of DAPG-producing Pseudomonas spp. as well as its importance for improving the biocontrol of plant pathogens.
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22
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Bonkowski M, Tarkka M, Razavi BS, Schmidt H, Blagodatskaya E, Koller R, Yu P, Knief C, Hochholdinger F, Vetterlein D. Spatiotemporal Dynamics of Maize ( Zea mays L.) Root Growth and Its Potential Consequences for the Assembly of the Rhizosphere Microbiota. Front Microbiol 2021; 12:619499. [PMID: 33815308 PMCID: PMC8010349 DOI: 10.3389/fmicb.2021.619499] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 02/16/2021] [Indexed: 12/20/2022] Open
Abstract
Numerous studies have shown that plants selectively recruit microbes from the soil to establish a complex, yet stable and quite predictable microbial community on their roots – their “microbiome.” Microbiome assembly is considered as a key process in the self-organization of root systems. A fundamental question for understanding plant-microbe relationships is where a predictable microbiome is formed along the root axis and through which microbial dynamics the stable formation of a microbiome is challenged. Using maize as a model species for which numerous data on dynamic root traits are available, this mini-review aims to give an integrative overview on the dynamic nature of root growth and its consequences for microbiome assembly based on theoretical considerations from microbial community ecology.
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Affiliation(s)
- Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Mika Tarkka
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Bahar S Razavi
- Department of Soil and Plant Microbiome, Christian-Albrecht University of Kiel, Kiel, Germany
| | - Hannes Schmidt
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Evgenia Blagodatskaya
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany
| | - Robert Koller
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Peng Yu
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Claudia Knief
- Institute of Crop Science and Resource Conservation - Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
| | - Frank Hochholdinger
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Doris Vetterlein
- Department of Soil System Science, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany.,Soil Science, Martin-Luther-University Halle-Wittenberg, Halle, Germany
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23
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Munoz‐Ucros J, Zwetsloot MJ, Cuellar‐Gempeler C, Bauerle TL. Spatiotemporal patterns of rhizosphere microbiome assembly: From ecological theory to agricultural application. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.13850] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Juana Munoz‐Ucros
- School of Integrative Plant Science Cornell University Ithaca NY USA
| | | | | | - Taryn L. Bauerle
- School of Integrative Plant Science Cornell University Ithaca NY USA
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24
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Leaf-FISH: In Situ Hybridization Method for Visualizing Bacterial Taxa on Plant Surfaces. Methods Mol Biol 2021. [PMID: 33576986 DOI: 10.1007/978-1-0716-1115-9_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
High-resolution, spatial characterization of microbial communities is critical for the accurate understanding of microbe-microbe and microbe-plant interactions in leaf surfaces (phyllosphere). However, leaves are specially challenging surfaces for imaging methods due to their high autofluorescence. In this chapter we describe the Leaf-FISH method. Leaf-FISH is a fluorescence in situ hybridization (FISH) method specially adapted to the requirements of plant tissues. Leaf-FISH uses a combination of leaf pretreatments coupled with spectral imaging confocal microscopy and image post-processing to visualize bacterial taxa on a structural-informed context recreated from the residual background autofluorescence of the tissues. Leaf-FISH is suitable for simultaneous identification of multiple bacterial taxa using multiple taxon-specific fluorescently labeled oligonucleotide probes (combinatorial labeling).
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25
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Bhatia R, Gulati D, Sethi G. Biofilms and nanoparticles: applications in agriculture. Folia Microbiol (Praha) 2021; 66:159-170. [PMID: 33528768 DOI: 10.1007/s12223-021-00851-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 01/04/2021] [Indexed: 02/04/2023]
Abstract
A profound need to explore eco-friendly methods to practice sustainable agriculture leads to the research and exploration of plant growth-promoting rhizobacteria (PGPRs). Biofilms are assemblages of microbial communities within a self-secreted exopolymeric matrix, adhering to different biotic and abiotic surfaces and performing a variety of desired and undesired functions. Biofilm formation by PGPRs is governed by effective root colonization of the host plant in providing plant growth promotion and stress management. Biofilms can also provide a suitable environment for the synthesis and entrapment of nanoparticles. Together, nanoparticles and PGPRs may contribute towards biocontrol and crop management. This review discusses the significance of biofilms in agriculture and their confluence with different types of nanoparticles for plant protection and improved crop production.
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Affiliation(s)
- Ranjana Bhatia
- Department of Biotechnology, University Institute of Engineering and Technology, Panjab University, Chandigarh, 160014, India.
| | - Divij Gulati
- Department of Biotechnology, University Institute of Engineering and Technology, Panjab University, Chandigarh, 160014, India
| | - Gavin Sethi
- Department of Biotechnology, University Institute of Engineering and Technology, Panjab University, Chandigarh, 160014, India
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26
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de la Fuente Cantó C, Simonin M, King E, Moulin L, Bennett MJ, Castrillo G, Laplaze L. An extended root phenotype: the rhizosphere, its formation and impacts on plant fitness. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:951-964. [PMID: 32324287 DOI: 10.1111/tpj.14781] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/03/2020] [Accepted: 04/09/2020] [Indexed: 05/13/2023]
Abstract
Plants forage soil for water and nutrients, whose distribution is patchy and often dynamic. To improve their foraging activities, plants have evolved mechanisms to modify the physicochemical properties and microbial communities of the rhizosphere, i.e. the soil compartment under the influence of the roots. This dynamic interplay in root-soil-microbiome interactions creates emerging properties that impact plant nutrition and health. As a consequence, the rhizosphere can be considered an extended root phenotype, a manifestation of the effects of plant genes on their environment inside and/or outside of the organism. Here, we review current understanding of how plants shape the rhizosphere and the benefits it confers to plant fitness. We discuss future research challenges and how applying their solutions in crops will enable us to harvest the benefits of the extended root phenotype.
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Affiliation(s)
- Carla de la Fuente Cantó
- UMR DIADE, Université de Montpellier, Institut de Recherche pour le Développement (IRD), Montpellier, France
| | - Marie Simonin
- UMR DIADE, Université de Montpellier, Institut de Recherche pour le Développement (IRD), Montpellier, France
- UMR IPME, IRD, Cirad, Université de Montpellier, Montpellier, France
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Eoghan King
- UMR IPME, IRD, Cirad, Université de Montpellier, Montpellier, France
| | - Lionel Moulin
- UMR IPME, IRD, Cirad, Université de Montpellier, Montpellier, France
| | - Malcolm J Bennett
- Future Food Beacon of Excellence, School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Gabriel Castrillo
- Future Food Beacon of Excellence, School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Laurent Laplaze
- UMR DIADE, Université de Montpellier, Institut de Recherche pour le Développement (IRD), Montpellier, France
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Dakar, Senegal
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27
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Zi H, Jiang Y, Cheng X, Li W, Huang X. Change of rhizospheric bacterial community of the ancient wild tea along elevational gradients in Ailao mountain, China. Sci Rep 2020; 10:9203. [PMID: 32514187 PMCID: PMC7280300 DOI: 10.1038/s41598-020-66173-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 05/11/2020] [Indexed: 11/10/2022] Open
Abstract
The rhizospheric microbial community is one of the major environmental factors affecting the distribution and fitness of plants. Ancient wild tea plants are rare genetic resource distributed in Southwest China. In this study, we investigated that rhizospheric bacterial communities of ancient wild tea plants along the elevational gradients (2050, 2200, 2350 and 2500 m) in QianJiaZhai Reserve of Ailao Mountains. According to the Illumina MiSeq sequencing of 16 S rRNA gene amplicons, Proteobacteria, Acidobacteria and Actinobacteria were the dominant phyla with the relative abundance 43.12%, 21.61% and 14.84%, respectively. The Variibacter was the most dominant genus in rhizosphere of ancient wild tea plant. Phylogenetic null modeling analysis suggested that rhizospheric bacterial communities of ancient wild tea plants were more phylogenetically clustered than expected by chance. The bacterial community at 2050 m was unique with the highest alpha diversity, tend to cluster the nearest taxon and simple co-occurrence network structure. The unique bacterial community was correlated to multiple soil factors, and the content soil ammonium nitrogen (NH4+-N) was the key factor affecting the diversity and distribution of bacterial community along the elevational gradients. This study provided the necessary basic information for the protection of ancient tea trees and cultivation of tea plants.
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Affiliation(s)
- Haiyun Zi
- Southwest Landscape Architecture Engineering Research Center of State Forestry and Grassland Administration, College of Landscape Architecture and Horticulture, Southwest Forestry University, Yunnan, Kunming, 650224, China
| | - Yonglei Jiang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Xiaomao Cheng
- Southwest Landscape Architecture Engineering Research Center of State Forestry and Grassland Administration, College of Landscape Architecture and Horticulture, Southwest Forestry University, Yunnan, Kunming, 650224, China
| | - Wanting Li
- Southwest Landscape Architecture Engineering Research Center of State Forestry and Grassland Administration, College of Landscape Architecture and Horticulture, Southwest Forestry University, Yunnan, Kunming, 650224, China
| | - Xiaoxia Huang
- Southwest Landscape Architecture Engineering Research Center of State Forestry and Grassland Administration, College of Landscape Architecture and Horticulture, Southwest Forestry University, Yunnan, Kunming, 650224, China.
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Microbial inoculum development for ameliorating crop drought stress: A case study of Variovorax paradoxus 5C-2. N Biotechnol 2020; 56:103-113. [DOI: 10.1016/j.nbt.2019.12.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 12/24/2019] [Accepted: 12/29/2019] [Indexed: 01/01/2023]
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Tracy SR, Nagel KA, Postma JA, Fassbender H, Wasson A, Watt M. Crop Improvement from Phenotyping Roots: Highlights Reveal Expanding Opportunities. TRENDS IN PLANT SCIENCE 2020; 25:105-118. [PMID: 31806535 DOI: 10.1016/j.tplants.2019.10.015] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 05/21/2023]
Abstract
Root systems determine the water and nutrients for photosynthesis and harvested products, underpinning agricultural productivity. We highlight 11 programs that integrated root traits into germplasm for breeding, relying on phenotyping. Progress was successful but slow. Today's phenotyping technologies will speed up root trait improvement. They combine multiple new alleles in germplasm for target environments, in parallel. Roots and shoots are detected simultaneously and nondestructively, seed to seed measures are automated, and field and laboratory technologies are increasingly linked. Available simulation models can aid all phenotyping decisions. This century will see a shift from single root traits to rhizosphere selections that can be managed dynamically on farms and a shift to phenotype-based improvement to accommodate the dynamic complexity of whole crop systems.
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Affiliation(s)
- Saoirse R Tracy
- School of Agriculture & Food Science, University College Dublin, Dublin, Ireland
| | - Kerstin A Nagel
- Institute for Bio and Geosciences-2, Plant Sciences, Forschungszentrum Juelich GmbH, 52428 Juelich, Germany
| | - Johannes A Postma
- Institute for Bio and Geosciences-2, Plant Sciences, Forschungszentrum Juelich GmbH, 52428 Juelich, Germany
| | - Heike Fassbender
- Institute for Bio and Geosciences-2, Plant Sciences, Forschungszentrum Juelich GmbH, 52428 Juelich, Germany
| | - Anton Wasson
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Michelle Watt
- Institute for Bio and Geosciences-2, Plant Sciences, Forschungszentrum Juelich GmbH, 52428 Juelich, Germany.
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30
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Canarini A, Kaiser C, Merchant A, Richter A, Wanek W. Root Exudation of Primary Metabolites: Mechanisms and Their Roles in Plant Responses to Environmental Stimuli. FRONTIERS IN PLANT SCIENCE 2019; 10:157. [PMID: 30881364 PMCID: PMC6407669 DOI: 10.3389/fpls.2019.00157] [Citation(s) in RCA: 297] [Impact Index Per Article: 59.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 01/29/2019] [Indexed: 05/19/2023]
Abstract
Root exudation is an important process determining plant interactions with the soil environment. Many studies have linked this process to soil nutrient mobilization. Yet, it remains unresolved how exudation is controlled and how exactly and under what circumstances plants benefit from exudation. The majority of root exudates including primary metabolites (sugars, amino acids, and organic acids) are believed to be passively lost from the root and used by rhizosphere-dwelling microbes. In this review, we synthetize recent advances in ecology and plant biology to explain and propose mechanisms by which root exudation of primary metabolites is controlled, and what role their exudation plays in plant nutrient acquisition strategies. Specifically, we propose a novel conceptual framework for root exudates. This framework is built upon two main concepts: (1) root exudation of primary metabolites is driven by diffusion, with plants and microbes both modulating concentration gradients and therefore diffusion rates to soil depending on their nutritional status; (2) exuded metabolite concentrations can be sensed at the root tip and signals are translated to modify root architecture. The flux of primary metabolites through root exudation is mostly located at the root tip, where the lack of cell differentiation favors diffusion of metabolites to the soil. We show examples of how the root tip senses concentration changes of exuded metabolites and translates that into signals to modify root growth. Plants can modify the concentration of metabolites either by controlling source/sink processes or by expressing and regulating efflux carriers, therefore challenging the idea of root exudation as a purely unregulated passive process. Through root exudate flux, plants can locally enhance concentrations of many common metabolites, which can serve as sensors and integrators of the plant nutritional status and of the nutrient availability in the surrounding environment. Plant-associated micro-organisms also constitute a strong sink for plant carbon, thereby increasing concentration gradients of metabolites and affecting root exudation. Understanding the mechanisms of and the effects that environmental stimuli have on the magnitude and type of root exudation will ultimately improve our knowledge of processes determining soil CO2 emissions, ecosystem functioning, and how to improve the sustainability of agricultural production.
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Affiliation(s)
- Alberto Canarini
- Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry Meets Microbiology’, University of Vienna, Vienna, Austria
- *Correspondence: Alberto Canarini,
| | - Christina Kaiser
- Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry Meets Microbiology’, University of Vienna, Vienna, Austria
| | - Andrew Merchant
- Faculty of Science, Sydney Institute of Agriculture, The University of Sydney, Sydney, NSW, Australia
| | - Andreas Richter
- Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry Meets Microbiology’, University of Vienna, Vienna, Austria
| | - Wolfgang Wanek
- Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry Meets Microbiology’, University of Vienna, Vienna, Austria
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Zhang J, Guo T, Wang P, Tian H, Wang Y, Cheng J. Characterization of diazotrophic growth-promoting rhizobacteria isolated from ginger root soil as antagonists against Ralstonia solanacearum. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1533431] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Jian Zhang
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, PR China
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Hefei, PR China
| | - Tingting Guo
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, PR China
- School of Life Sciences, Anhui Agricultural University, Hefei, PR China
| | - Pengcheng Wang
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, PR China
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Hefei, PR China
| | - Hongmei Tian
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, PR China
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Hefei, PR China
| | - Yan Wang
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, PR China
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Hefei, PR China
| | - Jingyi Cheng
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, PR China
- School of Horticulture, Anhui Agricultural University, Hefei, PR China
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32
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Li P, Xue Y, Shi J, Pan A, Tang X, Ming F. The response of dominant and rare taxa for fungal diversity within different root environments to the cultivation of Bt and conventional cotton varieties. MICROBIOME 2018; 6:184. [PMID: 30336777 PMCID: PMC6194802 DOI: 10.1186/s40168-018-0570-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 10/02/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Bacillus thuringiensis (Bt) crops have been cultivated at a large scale over the past several decades, which have raised concern about unintended effects on natural environments. Microbial communities typically contain numerous rare taxa that make up the majority of community populations. However, the response of dominant and rare taxa for fungal diversity to the different root environments of Bt plants remains unclear. RESULTS We quantified fungal population sizes and community composition via quantitative PCR of ITS genes and 18S rRNA gene sequencing of, respectively, that were associated with Bt and conventional cotton variety rhizosphere soils from different plant growth stages. qPCR analyses indicated that fungal abundances reached their peak at the seedling stage and that the taproots and lateral root rhizospheres of the Bt cotton SGK321 were significantly different. However, no significant differences in population sizes were detected between the same root zones from Bt and the conventional cotton varieties. The overall patterns of fungal genera abundances followed that of the dominant genera, whereas overall patterns of fungal genera richness followed those of the rare genera. These results suggest that the dominant and rare taxa play different roles in the maintenance of rhizosphere microhabitat ecosystems. Cluster analyses indicated a separation of fungal communities based on the lateral roots or taproots from the three cotton varieties at the seedling stage, suggesting that root microhabitats had marked effects on fungal community composition. Redundancy analyses indicated that pH was more correlated to soil fungal community composition than Bt protein content. CONCLUSIONS In conclusion, these results indicate that dominant and rare fungal taxa differentially contribute to community dynamics in different root microhabitats of both Bt and conventional cotton varieties. Moreover, these results showed that the rhizosphere fungal community of Bt cotton did not respond significantly to the presence of Bt protein when compared to the two conventional cotton varieties.
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Affiliation(s)
- Peng Li
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
- State Key Laboratory of Genetic Engineering, Institute of Genetics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China.
| | - Yong Xue
- Institute of Eco-Environment and Plant Protection, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Jialiang Shi
- Dezhou Academy of Agricultural Sciences, Dezhou, 253000, China
| | - Aihu Pan
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Xueming Tang
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
| | - Feng Ming
- State Key Laboratory of Genetic Engineering, Institute of Genetics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China.
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33
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Biessy A, Filion M. Phenazines in plant-beneficialPseudomonasspp.: biosynthesis, regulation, function and genomics. Environ Microbiol 2018; 20:3905-3917. [DOI: 10.1111/1462-2920.14395] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/20/2018] [Accepted: 08/24/2018] [Indexed: 12/01/2022]
Affiliation(s)
- Adrien Biessy
- Department of Biology; Université de Moncton; Moncton New Brunswick Canada
| | - Martin Filion
- Department of Biology; Université de Moncton; Moncton New Brunswick Canada
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Li P, Li Y, Shi J, Yu Z, Pan A, Tang X, Ming F. Impact of transgenic Cry1Ac + CpTI cotton on diversity and dynamics of rhizosphere bacterial community of different root environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:233-243. [PMID: 29751306 DOI: 10.1016/j.scitotenv.2018.05.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/02/2018] [Accepted: 05/02/2018] [Indexed: 06/08/2023]
Abstract
The objective of this study was to characterize the diversity and dynamics of rhizosphere bacterial community, especially the response of dominant and rare bacterial taxa to the cultivation of Bt cotton for different root environments at different growth stages. qPCR analyses indicated that bacterial abundances of the taproots and lateral root rhizospheres of the Bt cotton SGK321 were significantly different at seedling and bolling stages. But no significant differences were detected between the same root zones from Bt and the conventional cotton varieties. Total bacterial genera had similar pattern with dominant genera in abundance, and with rare genera in richness to the changes of bacterial community, respectively. Although the rhizosphere bacterial diversity of the three cotton varieties changed in taproot and lateral root, no significant differences were detected in the same root environments between Bt and conventional cotton. Moreover, Soil pH was more correlated with variations in the bacterial community composition than Bt proteins. In conclusion, these results revealed no indication that rhizosphere bacterial community of Bt cotton had different response to increased Bt protein regarding the same root environment. In particular, dominant and rare bacterial taxa showed the variation in diversity and community composition in different root microhabitats.
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Affiliation(s)
- Peng Li
- State Key Laboratory of Genetic Engineering, Institute of Genetics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China; The Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Yongchun Li
- School of Environmental and Resources, Zhejiang Agriculture and Forestry University, Lin'an, Zhejiang 311300, China
| | - Jialiang Shi
- Dezhou Academy of Agricultural Sciences, Dezhou 253000, China
| | - Zhibo Yu
- Faculty of Sciences, Paris-Sud University, 300-91405 Orsay, France
| | - Aihu Pan
- The Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Xueming Tang
- The Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.
| | - Feng Ming
- State Key Laboratory of Genetic Engineering, Institute of Genetics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China.
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35
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LeTourneau MK, Marshall MJ, Cliff JB, Bonsall RF, Dohnalkova AC, Mavrodi DV, Devi SI, Mavrodi OV, Harsh JB, Weller DM, Thomashow LS. Phenazine‐1‐carboxylic acid and soil moisture influence biofilm development and turnover of rhizobacterial biomass on wheat root surfaces. Environ Microbiol 2018; 20:2178-2194. [DOI: 10.1111/1462-2920.14244] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 04/15/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Melissa K. LeTourneau
- Department of Crop & Soil SciencesWashington State UniversityPullmanWA 99164‐6420 USA
| | - Matthew J. Marshall
- Earth & Biological Sciences DirectoratePacific Northwest National LaboratoryRichlandWA 99352 USA
| | - John B. Cliff
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWA 99352 USA
| | - Robert F. Bonsall
- Department of Plant PathologyWashington State UniversityPullmanWA 99164‐6420 USA
| | - Alice C. Dohnalkova
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWA 99352 USA
| | - Dmitri V. Mavrodi
- Department of Biological SciencesUniversity of Southern MississippiHattiesburgMS 39406‐0001 USA
| | - S. Indira Devi
- Institute of Bioresources and Sustainable DevelopmentTakyelpat ManipurImphal 795001 India
| | - Olga V. Mavrodi
- Department of Biological SciencesUniversity of Southern MississippiHattiesburgMS 39406‐0001 USA
| | - James B. Harsh
- Department of Crop & Soil SciencesWashington State UniversityPullmanWA 99164‐6420 USA
| | - David M. Weller
- United States Department of Agriculture – Agricultural Research ServiceWheat Health, Genetics, and Quality Research UnitPullmanWA 99164‐6430 USA
| | - Linda S. Thomashow
- United States Department of Agriculture – Agricultural Research ServiceWheat Health, Genetics, and Quality Research UnitPullmanWA 99164‐6430 USA
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36
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Zhang H, Chen F, Zhao HZ, Lu JS, Zhao MJ, Hong Q, Huang X. Colonization on Cucumber Root and Enhancement of Chlorimuron-ethyl Degradation in the Rhizosphere by Hansschlegelia zhihuaiae S113 and Root Exudates. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:4584-4591. [PMID: 29672047 DOI: 10.1021/acs.jafc.8b00041] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The colonization of Hansschlegelia zhihuaiae S113 and its degradation of the herbicide chlorimuron-ethyl in the cucumber rhizosphere was investigated. The results reveal that S113 colonized the cucumber roots (2.14 × 105cells per gram of roots) and were able to survive in the rhizosphere (maintained for 20 d). The root exudates promoted colonization on roots and increased the degradation of chlorimuron-ethyl by S113. Five organic acids in cucumber-root exudates were detected and identified by HPLC. Citric acid and fumaric acid significantly stimulated S113 colonization on cucumber roots, with 18.4 and 15.5% increases, respectively, compared with the control. After irrigation with an S113 solution for 10 days, chlorimuron-ethyl could not be detected in the roots, seedlings, or rhizosphere soil, which allowed for improved cucumber growth. Therefore, the degradation mechanism of chlorimuron-ethyl residues by S113 in the rhizosphere could be applied in situ for the bioremediation of chlorimuron-ethyl contaminated soil to ensure crop safety.
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Affiliation(s)
- Hao Zhang
- College of Life Sciences , Nanjing Agricultural University , Nanjing 210095 , PR China
- School of Life Science and Technology , Nanyang Normal University , Nanyang 473061 , PR China
| | - Feng Chen
- College of Life Sciences , Nanjing Agricultural University , Nanjing 210095 , PR China
| | - Hua-Zhu Zhao
- College of Life Sciences , Nanjing Agricultural University , Nanjing 210095 , PR China
| | - Jia-Sen Lu
- College of Life Sciences , Nanjing Agricultural University , Nanjing 210095 , PR China
| | - Meng-Jun Zhao
- College of Life Sciences , Nanjing Agricultural University , Nanjing 210095 , PR China
| | - Qing Hong
- College of Life Sciences , Nanjing Agricultural University , Nanjing 210095 , PR China
| | - Xing Huang
- College of Life Sciences , Nanjing Agricultural University , Nanjing 210095 , PR China
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Tissue Localization and Variation of Major Symbionts in Haemaphysalis longicornis, Rhipicephalus haemaphysaloides, and Dermacentor silvarum in China. Appl Environ Microbiol 2018. [PMID: 29523550 DOI: 10.1128/aem.00029-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Ticks are important disease vectors, as they transmit a variety of human and animal pathogens worldwide. Symbionts that coevolved with ticks confer crucial benefits to their host in nutrition metabolism, fecundity, and vector competence. Although over 100 tick species have been identified in China, general information on tick symbiosis is limited. Here, we visualized the tissue distribution of Coxiella sp. and Rickettsia sp. in lab-reared Haemaphysalis longicornis and Rhipicephalus haemaphysaloides by fluorescent in situ hybridization. We found that Coxiella sp. colonized exclusively the Malpighian tubules and ovaries of H. longicornis, while Rickettsia sp. additionally colonized the midgut of R. haemaphysaloides We also investigated the population structure of microbiota in Dermacentor silvarum ticks collected from Inner Mongolia, China, and found that Coxiella, Rickettsia, and Pseudomonas are the three dominant genera. No significant difference in microbiota composition was found between male and female D. silvarum ticks. We again analyzed the tissue localization of Coxiella sp. and Rickettsia sp. and found that they displayed tissue tropisms similar to those in R. haemaphysaloides, except that Rickettsia sp. colonized the nuclei of spermatids instead of ovaries in D. silvarum Altogether, our results suggest that Coxiella sp. and Rickettsia sp. are the main symbionts in the three ticks and reside primarily in midgut, Malpighian tubules, and reproductive tissues, but their tissue distribution varies in association with species and sexes.IMPORTANCE Tick-borne diseases constitute a major public health burden, as they are increasing in frequency and severity worldwide. The presence of symbionts helps ticks to metabolize nutrients, promotes fecundity, and influences pathogen infections. Increasing numbers of tick-borne pathogens have been identified in China; however, knowledge of native ticks, especially tick symbiosis, is limited. In this study, we analyze the distribution of Coxiella sp. and Rickettsia sp. in tissues of laboratory-reared Haemaphysalis longicornis and Rhipicephalus haemaphysaloides and field-collected Dermacentor silvarum We found that the localization patterns of Coxiella sp. in three Chinese tick species were similar to those of other tick species. We also found a previously undefined intracellular localization of Rickettsia sp. in tick midgut and spermatids. In addition, we demonstrate that tissue tropisms of symbionts vary between species and sexes. Our findings provide new insights into the tissue localization of symbionts in native Chinese ticks and pave the way for further understanding of their functional capabilities and symbiotic interactions with ticks.
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Aufrecht JA, Timm CM, Bible A, Morrell‐Falvey JL, Pelletier DA, Doktycz MJ, Retterer ST. Quantifying the Spatiotemporal Dynamics of Plant Root Colonization by Beneficial Bacteria in a Microfluidic Habitat. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/adbi.201800048] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jayde A. Aufrecht
- Bioscience Division Oak Ridge National Laboratory Oak Ridge TN 37831 USA
- Bredesen Center University of Tennessee Knoxville TN 37996 USA
| | - Collin M. Timm
- Bioscience Division Oak Ridge National Laboratory Oak Ridge TN 37831 USA
| | - Amber Bible
- Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville TN 37996 USA
| | - Jennifer L. Morrell‐Falvey
- Bioscience Division Oak Ridge National Laboratory Oak Ridge TN 37831 USA
- Bredesen Center University of Tennessee Knoxville TN 37996 USA
- Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville TN 37996 USA
| | - Dale A. Pelletier
- Bioscience Division Oak Ridge National Laboratory Oak Ridge TN 37831 USA
| | - Mitchel J. Doktycz
- Bioscience Division Oak Ridge National Laboratory Oak Ridge TN 37831 USA
- Bredesen Center University of Tennessee Knoxville TN 37996 USA
- Center for Nanophase Materials Sciences Oak Ridge National Laboratory Oak Ridge TN 37831 USA
| | - Scott T. Retterer
- Bioscience Division Oak Ridge National Laboratory Oak Ridge TN 37831 USA
- Bredesen Center University of Tennessee Knoxville TN 37996 USA
- Center for Nanophase Materials Sciences Oak Ridge National Laboratory Oak Ridge TN 37831 USA
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Peredo EL, Simmons SL. Leaf-FISH: Microscale Imaging of Bacterial Taxa on Phyllosphere. Front Microbiol 2018; 8:2669. [PMID: 29375531 PMCID: PMC5767230 DOI: 10.3389/fmicb.2017.02669] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/21/2017] [Indexed: 11/13/2022] Open
Abstract
Molecular methods for microbial community characterization have uncovered environmental and plant-associated factors shaping phyllosphere communities. Variables undetectable using bulk methods can play an important role in shaping plant-microbe interactions. Microscale analysis of bacterial dynamics in the phyllosphere requires imaging techniques specially adapted to the high autoflouresence and 3-D structure of the leaf surface. We present an easily-transferable method (Leaf-FISH) to generate high-resolution tridimensional images of leaf surfaces that allows simultaneous visualization of multiple bacterial taxa in a structurally informed context, using taxon-specific fluorescently labeled oligonucleotide probes. Using a combination of leaf pretreatments coupled with spectral imaging confocal microscopy, we demonstrate the successful imaging bacterial taxa at the genus level on cuticular and subcuticular leaf areas. Our results confirm that different bacterial species, including closely related isolates, colonize distinct microhabitats in the leaf. We demonstrate that highly related Methylobacterium species have distinct colonization patterns that could not be predicted by shared physiological traits, such as carbon source requirements or phytohormone production. High-resolution characterization of microbial colonization patterns is critical for an accurate understanding of microbe-microbe and microbe-plant interactions, and for the development of foliar bacteria as plant-protective agents.
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Affiliation(s)
- Elena L Peredo
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, MA, United States
| | - Sheri L Simmons
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, MA, United States
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Honeker LK, Neilson JW, Root RA, Gil-Loaiza J, Chorover J, Maier RM. Bacterial Rhizoplane Colonization Patterns of Buchloe dactyloides Growing in Metalliferous Mine Tailings Reflect Plant Status and Biogeochemical Conditions. MICROBIAL ECOLOGY 2017; 74:853-867. [PMID: 28577167 PMCID: PMC5654687 DOI: 10.1007/s00248-017-0998-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 05/16/2017] [Indexed: 05/28/2023]
Abstract
Plant establishment during phytostabilization of legacy mine tailings in semiarid regions is challenging due to low pH, low organic carbon, low nutrients, and high toxic metal(loid) concentrations. Plant-associated bacterial communities are particularly important under these harsh conditions because of their beneficial services to plants. We hypothesize that bacterial colonization profiles on rhizoplane surfaces reflect deterministic processes that are governed by plant health and the root environment. The aim of this study was to identify associations between bacterial colonization patterns on buffalo grass (Buchloe dactyloides) rhizoplanes and both plant status (leaf chlorophyll and plant cover) and substrate biogeochemistry (pH, electrical conductivity, total organic carbon, total nitrogen, and rhizosphere microbial community). Buffalo grass plants from mesocosm- and field-scale phytostabilization trials conducted with tailings from the Iron King Mine and Humboldt Smelter Superfund Site in Dewey-Humboldt, Arizona, were analyzed. These tailings are extremely acidic and have arsenic and lead concentrations of 2-4 g kg-1 substrate. Bacterial communities on rhizoplanes and in rhizosphere-associated substrate were characterized using fluorescence in situ hybridization and 16S rRNA gene amplicon sequencing, respectively. The results indicated that the metabolic status of rhizoplane bacterial colonizers is significantly related to plant health. Principal component analysis revealed that root-surface Alphaproteobacteria relative abundance was associated most strongly with substrate pH and Gammaproteobacteria relative abundance associated strongly with substrate pH and plant cover. These factors also affected the phylogenetic profiles of the associated rhizosphere communities. In summary, rhizoplane bacterial colonization patterns are plant specific and influenced by plant status and rhizosphere biogeochemical conditions.
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Affiliation(s)
- Linnea K Honeker
- Department of Soil, Water, and Environmental Science, University of Arizona, P.O. Box 210038, Tucson, AZ, 85721, USA
| | - Julia W Neilson
- Department of Soil, Water, and Environmental Science, University of Arizona, P.O. Box 210038, Tucson, AZ, 85721, USA.
| | - Robert A Root
- Department of Soil, Water, and Environmental Science, University of Arizona, P.O. Box 210038, Tucson, AZ, 85721, USA
| | - Juliana Gil-Loaiza
- Department of Soil, Water, and Environmental Science, University of Arizona, P.O. Box 210038, Tucson, AZ, 85721, USA
| | - Jon Chorover
- Department of Soil, Water, and Environmental Science, University of Arizona, P.O. Box 210038, Tucson, AZ, 85721, USA
| | - Raina M Maier
- Department of Soil, Water, and Environmental Science, University of Arizona, P.O. Box 210038, Tucson, AZ, 85721, USA
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Oleghe E, Naveed M, Baggs EM, Hallett PD. Plant exudates improve the mechanical conditions for root penetration through compacted soils. PLANT AND SOIL 2017; 421:19-30. [PMID: 31997836 PMCID: PMC6956916 DOI: 10.1007/s11104-017-3424-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/11/2017] [Indexed: 05/10/2023]
Abstract
BACKGROUND AND AIM Plant exudates greatly affect the physical behaviour of soil, but measurements of the impact of exudates on compression characteristics are missing. Our aim is to provide these data and explore how plant exudates may enhance the restructuring of compacted soils following cycles of wetting and drying. METHODS Two soils were amended with Chia (Salvia hispanica) seed exudate at 5 concentrations, compacted in cores to 200 kPa stress (equivalent to tractor stress), equilibrated to -50 kPa matric potential, and then compacted to 600 kPa (equivalent to axial root stress) followed by 3 cycles of wetting and drying and recompression to 600 kPa at -50 kPa matric potential. Penetration resistance (PR), compression index (CC) and pore characteristics were measured at various steps. RESULTS PR decreased and CC increased with increasing exudate concentration. At 600 kPa compression, 1.85 mg exudate g-1 soil increased CC from 0.37 to 0.43 for sandy loam soil and from 0.50 to 0.54 for clay loam soil. After 3 wetting-drying cycles the clay loam was more resillient than the sandy loam soil, with resilience increasing with greater exudate concentration. Root growth modelled on PR data suggested plant exudates significantly eased root elongation in soil. CONCLUSION Plant exudates improve compression characteristics of soils, easing penetration and enhancing recovery of root induced soil compaction.
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Affiliation(s)
- E. Oleghe
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU UK
- Department of Soil Science, Ambrose Alli University, P.M.B 14, Ekpoma, Edo State Nigeria
| | - M. Naveed
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU UK
| | - E. M. Baggs
- The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG UK
| | - P. D. Hallett
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU UK
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Hao DC, Xiao PG. Rhizosphere Microbiota and Microbiome of Medicinal Plants: From Molecular Biology to Omics Approaches. CHINESE HERBAL MEDICINES 2017. [DOI: 10.1016/s1674-6384(17)60097-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Matsumoto A, Takahashi Y. Endophytic actinomycetes: promising source of novel bioactive compounds. J Antibiot (Tokyo) 2017; 70:514-519. [PMID: 28270688 DOI: 10.1038/ja.2017.20] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/26/2016] [Accepted: 01/26/2017] [Indexed: 12/20/2022]
Abstract
Endophytic actinomycetes associated with plant roots are a relatively untapped source of potential new bioactive compounds. This is becoming increasingly important, as the returns from discovery research on soil-dwelling microbes, have been continuously diminishing. We have isolated more than 1000 strains of actinomycetes from plant roots in our search for novel bioactive compounds, identified and assayed their bioactive metabolites, as well as investigated their biosynthetic genes for generating secondary metabolites. This has resulted in the discovery of several interesting compounds. Creation of plant root clone libraries enabled us to confirm that we had, indeed, isolated endophytes. In this paper, we introduce our approach to this promising line of research, incorporating data from other publications, and illustrate the potential that endophytic actinomycetes offer as a new source of novel lead compounds.
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Affiliation(s)
- Atsuko Matsumoto
- Kitasato Institute for Life Sciences, Laboratory of Microbial Functions, Kitasato University, Tokyo, Japan
| | - Yōko Takahashi
- Kitasato Institute for Life Sciences, Laboratory of Microbial Functions, Kitasato University, Tokyo, Japan
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Honeker LK, Root RA, Chorover J, Maier RM. Resolving colocalization of bacteria and metal(loid)s on plant root surfaces by combining fluorescence in situ hybridization (FISH) with multiple-energy micro-focused X-ray fluorescence (ME μXRF). J Microbiol Methods 2016; 131:23-33. [PMID: 27693754 PMCID: PMC5127750 DOI: 10.1016/j.mimet.2016.09.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 09/26/2016] [Accepted: 09/26/2016] [Indexed: 02/08/2023]
Abstract
Metal(loid)-contamination of the environment due to anthropogenic activities is a global problem. Understanding the fate of contaminants requires elucidation of biotic and abiotic factors that influence metal(loid) speciation from molecular to field scales. Improved methods are needed to assess micro-scale processes, such as those occurring at biogeochemical interfaces between plant tissues, microbial cells, and metal(loid)s. Here we present an advanced method that combines fluorescence in situ hybridization (FISH) with synchrotron-based multiple-energy micro-focused X-ray fluorescence microprobe imaging (ME μXRF) to examine colocalization of bacteria and metal(loid)s on root surfaces of plants used to phytostabilize metalliferous mine tailings. Bacteria were visualized on a small root section using SytoBC nucleic acid stain and FISH probes targeting the domain Bacteria and a specific group (Alphaproteobacteria, Gammaproteobacteria, or Actinobacteria). The same root region was then analyzed for elemental distribution and metal(loid) speciation of As and Fe using ME μXRF. The FISH and ME μXRF images were aligned using ImageJ software to correlate microbiological and geochemical results. Results from quantitative analysis of colocalization show a significantly higher fraction of As colocalized with Fe-oxide plaques on the root surfaces (fraction of overlap 0.49±0.19) than to bacteria (0.072±0.052) (p<0.05). Of the bacteria that colocalized with metal(loid)s, Actinobacteria, known for their metal tolerance, had a higher correlation with both As and Fe than Alphaproteobacteria or Gammaproteobacteria. This method demonstrates how coupling these micro-techniques can expand our understanding of micro-scale interactions between roots, metal(loid)s and microbes, information that should lead to improved mechanistic models of metal(loid) speciation and fate.
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Affiliation(s)
- Linnea K Honeker
- Department of Soil, Water, and Environmental Science, P.O. Box 210038, University of Arizona, Tucson, AZ 85721, United States.
| | - Robert A Root
- Department of Soil, Water, and Environmental Science, P.O. Box 210038, University of Arizona, Tucson, AZ 85721, United States.
| | - Jon Chorover
- Department of Soil, Water, and Environmental Science, P.O. Box 210038, University of Arizona, Tucson, AZ 85721, United States.
| | - Raina M Maier
- Department of Soil, Water, and Environmental Science, P.O. Box 210038, University of Arizona, Tucson, AZ 85721, United States.
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Kawasaki A, Donn S, Ryan PR, Mathesius U, Devilla R, Jones A, Watt M. Microbiome and Exudates of the Root and Rhizosphere of Brachypodium distachyon, a Model for Wheat. PLoS One 2016; 11:e0164533. [PMID: 27727301 PMCID: PMC5058512 DOI: 10.1371/journal.pone.0164533] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 09/27/2016] [Indexed: 01/31/2023] Open
Abstract
The rhizosphere microbiome is regulated by plant genotype, root exudates and environment. There is substantial interest in breeding and managing crops that host root microbial communities that increase productivity. The eudicot model species Arabidopsis has been used to investigate these processes, however a model for monocotyledons is also required. We characterized the rhizosphere microbiome and root exudates of Brachypodium distachyon, to develop it as a rhizosphere model for cereal species like wheat. The Brachypodium rhizosphere microbial community was dominated by Burkholderiales. However, these communities were also dependent on how tightly they were bound to roots, the root type they were associated with (nodal or seminal roots), and their location along the roots. Moreover, the functional gene categories detected in microorganisms isolated from around root tips differed from those isolated from bases of roots. The Brachypodium rhizosphere microbiota and root exudate profiles were similar to those reported for wheat rhizospheres, and different to Arabidopsis. The differences in root system development and cell wall chemistry between monocotyledons and eudicots may also influence the microorganism composition of these major plant types. Brachypodium is a promising model for investigating the microbiome of wheat.
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Affiliation(s)
| | - Suzanne Donn
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Peter R. Ryan
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Ulrike Mathesius
- Division of Plant Science, Research School of Biology, Australian National University, ACT, Australia
| | | | - Amanda Jones
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Michelle Watt
- CSIRO Agriculture and Food, Canberra, ACT, Australia
- Institute of Bio and Geosciences (IBG 2), Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
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Exposing the Three-Dimensional Biogeography and Metabolic States of Pathogens in Cystic Fibrosis Sputum via Hydrogel Embedding, Clearing, and rRNA Labeling. mBio 2016; 7:mBio.00796-16. [PMID: 27677788 PMCID: PMC5040109 DOI: 10.1128/mbio.00796-16] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Physiological resistance to antibiotics confounds the treatment of many chronic bacterial infections, motivating researchers to identify novel therapeutic approaches. To do this effectively, an understanding of how microbes survive in vivo is needed. Though much can be inferred from bulk approaches to characterizing complex environments, essential information can be lost if spatial organization is not preserved. Here, we introduce a tissue-clearing technique, termed MiPACT, designed to retain and visualize bacteria with associated proteins and nucleic acids in situ on various spatial scales. By coupling MiPACT with hybridization chain reaction (HCR) to detect rRNA in sputum samples from cystic fibrosis (CF) patients, we demonstrate its ability to survey thousands of bacteria (or bacterial aggregates) over millimeter scales and quantify aggregation of individual species in polymicrobial communities. By analyzing aggregation patterns of four prominent CF pathogens, Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus sp., and Achromobacter xylosoxidans, we demonstrate a spectrum of aggregation states: from mostly single cells (A. xylosoxidans), to medium-sized clusters (S. aureus), to a mixture of single cells and large aggregates (P. aeruginosa and Streptococcus sp.). Furthermore, MiPACT-HCR revealed an intimate interaction between Streptococcus sp. and specific host cells. Lastly, by comparing standard rRNA fluorescence in situ hybridization signals to those from HCR, we found that different populations of S. aureus and A. xylosoxidans grow slowly overall yet exhibit growth rate heterogeneity over hundreds of microns. These results demonstrate the utility of MiPACT-HCR to directly capture the spatial organization and metabolic activity of bacteria in complex systems, such as human sputum. The advent of metagenomic and metatranscriptomic analyses has improved our understanding of microbial communities by empowering us to identify bacteria, calculate their abundance, and profile gene expression patterns in complex environments. We are still technologically limited, however, in regards to the many questions that bulk measurements cannot answer, specifically in assessing the spatial organization of microbe-microbe and microbe-host interactions. Here, we demonstrate the power of an enhanced optical clearing method, MiPACT, to survey important aspects of bacterial physiology (aggregation, host interactions, and growth rate), in situ, with preserved spatial information when coupled to rRNA detection by HCR. Our application of MiPACT-HCR to cystic fibrosis patient sputum revealed species-specific aggregation patterns, yet slow growth characterized the vast majority of bacterial cells regardless of their cell type. More broadly, MiPACT, coupled with fluorescent labeling, promises to advance the direct study of microbial communities in diverse environments, including microbial habitats within mammalian systems.
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Pascual J, Blanco S, García-López M, García-Salamanca A, Bursakov SA, Genilloud O, Bills GF, Ramos JL, van Dillewijn P. Assessing Bacterial Diversity in the Rhizosphere of Thymus zygis Growing in the Sierra Nevada National Park (Spain) through Culture-Dependent and Independent Approaches. PLoS One 2016; 11:e0146558. [PMID: 26741495 PMCID: PMC4711807 DOI: 10.1371/journal.pone.0146558] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/19/2015] [Indexed: 11/19/2022] Open
Abstract
Little is known of the bacterial communities associated with the rhizosphere of wild plant species found in natural settings. The rhizosphere bacterial community associated with wild thyme, Thymus zygis L., plants was analyzed using cultivation, the creation of a near-full length 16S rRNA gene clone library and 454 amplicon pyrosequencing. The bacterial community was dominated by Proteobacteria (mostly Alphaproteobacteria and Betaproteobacteria), Actinobacteria, Acidobacteria, and Gemmatimonadetes. Although each approach gave a different perspective of the bacterial community, all classes/subclasses detected in the clone library and the cultured bacteria could be found in the pyrosequencing datasets. However, an exception caused by inconclusive taxonomic identification as a consequence of the short read length of pyrotags together with the detection of singleton sequences which corresponded to bacterial strains cultivated from the same sample highlight limitations and considerations which should be taken into account when analysing and interpreting amplicon datasets. Amplicon pyrosequencing of replicate rhizosphere soil samples taken a year later permit the definition of the core microbiome associated with Thymus zygis plants. Abundant bacterial families and predicted functional profiles of the core microbiome suggest that the main drivers of the bacterial community in the Thymus zygis rhizosphere are related to the nutrients originating from the plant root and to their participation in biogeochemical cycles thereby creating an intricate relationship with this aromatic plant to allow for a feedback ecological benefit.
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Affiliation(s)
- Javier Pascual
- Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Granada, Spain
- MEDINA Foundation, Centre of Excellence for Innovative Medicines Research, Granada, Spain
| | - Silvia Blanco
- Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Granada, Spain
| | - Marina García-López
- MEDINA Foundation, Centre of Excellence for Innovative Medicines Research, Granada, Spain
| | - Adela García-Salamanca
- Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Granada, Spain
| | - Sergey A. Bursakov
- Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Granada, Spain
| | - Olga Genilloud
- MEDINA Foundation, Centre of Excellence for Innovative Medicines Research, Granada, Spain
| | - Gerald F. Bills
- MEDINA Foundation, Centre of Excellence for Innovative Medicines Research, Granada, Spain
| | - Juan L. Ramos
- Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Granada, Spain
| | - Pieter van Dillewijn
- Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Granada, Spain
- * E-mail:
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Schiltz S, Gaillard I, Pawlicki-Jullian N, Thiombiano B, Mesnard F, Gontier E. A review: what is the spermosphere and how can it be studied? J Appl Microbiol 2015; 119:1467-81. [PMID: 26332271 DOI: 10.1111/jam.12946] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/27/2015] [Accepted: 08/15/2015] [Indexed: 11/27/2022]
Abstract
The spermosphere is the zone surrounding seeds where interactions between the soil, microbial communities and germinating seeds take place. The concept of the spermosphere is usually only applied during germination sensu stricto. Despite the transient nature of this very small zone of soil around the germinating seed, the microbial activities which occur there may have long-lasting impacts on plants. The spermosphere is indirectly characterized by either (i) seed exudates, which could be inhibitors or stimulators of micro-organism growth or (ii) the composition of the microbiome on and around the germinating seeds. The microbial communities present in the spermosphere directly reflect that of the germination medium or are host-dependent and influenced quantitatively and qualitatively by host exudates. Despite its strong impact on the future development of plants, the spermosphere remains little studied. This can be explained by the technical difficulties related to characterizing this concept due to its short duration, small size and biomass, and the number and complexity of the interactions that take place. However, recent technical methods, such as metabolite profiling, combining phenotypic methods with DNA- and RNA-based methods, could be used to investigate seed exudates, microbial communities and their interactions with the soil environment.
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Affiliation(s)
- S Schiltz
- Biologie des Plantes et Innovation (BIOPI), Université de Picardie Jules Verne, Amiens, France
| | - I Gaillard
- Biologie des Plantes et Innovation (BIOPI), Université de Picardie Jules Verne, Amiens, France
| | - N Pawlicki-Jullian
- Biologie des Plantes et Innovation (BIOPI), Université de Picardie Jules Verne, Amiens, France
| | - B Thiombiano
- Biologie des Plantes et Innovation (BIOPI), Université de Picardie Jules Verne, Amiens, France
| | - F Mesnard
- Biologie des Plantes et Innovation (BIOPI), Université de Picardie Jules Verne, Amiens, France
| | - E Gontier
- Biologie des Plantes et Innovation (BIOPI), Université de Picardie Jules Verne, Amiens, France
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Downie HF, Adu MO, Schmidt S, Otten W, Dupuy LX, White PJ, Valentine TA. Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis. PLANT, CELL & ENVIRONMENT 2015; 38:1213-32. [PMID: 25211059 DOI: 10.1111/pce.12448] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 08/02/2014] [Accepted: 08/25/2014] [Indexed: 05/19/2023]
Abstract
The morphology of roots and root systems influences the efficiency by which plants acquire nutrients and water, anchor themselves and provide stability to the surrounding soil. Plant genotype and the biotic and abiotic environment significantly influence root morphology, growth and ultimately crop yield. The challenge for researchers interested in phenotyping root systems is, therefore, not just to measure roots and link their phenotype to the plant genotype, but also to understand how the growth of roots is influenced by their environment. This review discusses progress in quantifying root system parameters (e.g. in terms of size, shape and dynamics) using imaging and image analysis technologies and also discusses their potential for providing a better understanding of root:soil interactions. Significant progress has been made in image acquisition techniques, however trade-offs exist between sample throughput, sample size, image resolution and information gained. All of these factors impact on downstream image analysis processes. While there have been significant advances in computation power, limitations still exist in statistical processes involved in image analysis. Utilizing and combining different imaging systems, integrating measurements and image analysis where possible, and amalgamating data will allow researchers to gain a better understanding of root:soil interactions.
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Affiliation(s)
- H F Downie
- The SIMBIOS Centre, Abertay University, Dundee, DD1 1HG, UK
- Ecological Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK
| | - M O Adu
- Ecological Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Leicestershire, LE12 5RD, UK
| | - S Schmidt
- The SIMBIOS Centre, Abertay University, Dundee, DD1 1HG, UK
| | - W Otten
- The SIMBIOS Centre, Abertay University, Dundee, DD1 1HG, UK
| | - L X Dupuy
- Ecological Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK
| | - P J White
- Ecological Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK
- King Saud University, Riyadh, Saudi Arabia
| | - T A Valentine
- Ecological Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK
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Effects of Colonization of the Roots of Domestic Rice (Oryza sativa L. cv. Amaroo) by Burkholderia pseudomallei. Appl Environ Microbiol 2015; 81:4368-75. [PMID: 25911477 DOI: 10.1128/aem.00317-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 03/30/2015] [Indexed: 11/20/2022] Open
Abstract
Burkholderia pseudomallei is a saprophytic bacterium that causes melioidosis and is often isolated from rice fields in Southeast Asia, where the infection incidence is high among rice field workers. The aim of this study was to investigate the relationship between this bacterium and rice through growth experiments where the effect of colonization of domestic rice (Oryza sativa L. cv Amaroo) roots by B. pseudomallei could be observed. When B. pseudomallei was exposed to surface-sterilized seeds, the growth of both the root and the aerosphere was retarded compared to that in controls. The organism was found to localize in the root hairs and endodermis of the plant. A biofilm formed around the root and root structures that were colonized. Growth experiments with a wild rice species (Oryza meridionalis) produced similar retardation of growth, while another domestic cultivar (O. sativa L. cv Koshihikari) did not show retarded growth. Here we report B. pseudomallei infection and inhibition of O. sativa L. cv Amaroo, which might provide insights into plant interactions with this important human pathogen.
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