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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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2
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Musa OI, Akande SA, Ijah UJJ, Abioye OP, Maude AM, Samuel JO, Mustapha A, Abdulrahim AM, Gusdanis ACG. Biofilms communities in the soil: characteristic and interactions using mathematical model. Res Microbiol 2024; 175:104149. [PMID: 37923049 DOI: 10.1016/j.resmic.2023.104149] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/17/2023] [Accepted: 10/22/2023] [Indexed: 11/07/2023]
Abstract
There are many different kinds of microorganisms in the soil, and many of them are biofilms because they can make supracellular compounds. Surface-associated microorganisms in a biofilm are encased in a hydrated extracellular polymeric substance that aids in adherence and survival. Numerous different kinds of microorganisms call the soil home. Strong interactions with and among species are made possible by biofilms; this, in turn, might increase the effectiveness with which organic compounds and poisons in soil are degraded. This encouraged us to take a close look at soil biofilm ecosystems, which we do in this paper. In this research, we will look at how soil biofilms arise and how that affects the composition of microbial communities and their function in the soil. Recent years have seen an uptick in interest in questions about biofilm structure and the social interactions of various bacteria. Many concepts elucidating the underlying mathematics of biofilm growth are also presented. Since biofilms are so widespread, this breakthrough in soil biofilm inquiry might help scientists understand soil microbiomes better. Mathematical models further extrapolate the relationships between microbial communities and gives a more precise information as to what is happening in a biofilm. Biofilms can help plants cope with a variety of environmental challenges. Soil quality, plant nourishment, plant protection, bioremediation, and climate change are all influenced by the interplay of biofilm communities. Thus, biofilms play an important role in the development of environmentally friendly and sustainable agriculture.
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Affiliation(s)
- Ojeba Innocent Musa
- Department of Microbiology, Skyline University Nigeria, Kano State, Nigeria.
| | | | | | - Olabisi Peter Abioye
- Department of Microbiology, Federal University of Technology, Minna Niger State, Nigeria
| | - Asmau Mohammed Maude
- Department of Microbiology, Federal University of Technology, Minna Niger State, Nigeria
| | - Job Oloruntoba Samuel
- Department of Microbiology, Federal University of Technology, Minna Niger State, Nigeria
| | - Adamu Mustapha
- Department of Microbiology, Federal University of Technology, Minna Niger State, Nigeria
| | - Al-Musbahu Abdulrahim
- Department of Mathematics, Federal University of Technology, Minna Niger State, Nigeria
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3
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Fu X, Huang Y, Fu Q, Qiu Y, Zhao J, Li J, Wu X, Yang Y, Liu H, Yang X, Chen H. Critical transition of soil microbial diversity and composition triggered by plant rhizosphere effects. FRONTIERS IN PLANT SCIENCE 2023; 14:1252821. [PMID: 38023904 PMCID: PMC10676204 DOI: 10.3389/fpls.2023.1252821] [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: 07/04/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023]
Abstract
Over the years, microbial community composition in the rhizosphere has been extensively studied as the most fascinating topic in microbial ecology. In general, plants affect soil microbiota through rhizodeposits and changes in abiotic conditions. However, a consensus on the response of microbiota traits to the rhizosphere and bulk soils in various ecosystems worldwide regarding community diversity and structure has not been reached yet. Here, we conducted a meta-analysis of 101 studies to investigate the microbial community changes between the rhizosphere and bulk soils across various plant species (maize, rice, vegetables, other crops, herbaceous, and woody plants). Our results showed that across all plant species, plant rhizosphere effects tended to reduce the rhizosphere soil pH, especially in neutral or slightly alkaline soils. Beta-diversity of bacterial community was significantly separated between into rhizosphere and bulk soils. Moreover, r-strategists and copiotrophs (e.g. Proteobacteria and Bacteroidetes) enriched by 24-27% in the rhizosphere across all plant species, while K-strategists and oligotrophic (e.g. Acidobacteria, Gemmatimonadete, Nitrospirae, and Planctomycetes) decreased by 15-42% in the rhizosphere. Actinobacteria, Firmicutes, and Chloroflexi are also depleted by in the plant rhizosphere compared with the bulk soil by 7-14%. The Actinobacteria exhibited consistently negative effect sizes across all plant species, except for maize and vegetables. In Firmicutes, both herbaceous and woody plants showed negative responses to rhizosphere effects, but those in maize and rice were contrarily enriched in the rhizosphere. With regards to Chloroflexi, apart from herbaceous plants showing a positive effect size, the plant rhizosphere effects were consistently negative across all other plant types. Verrucomicrobia exhibited a significantly positive effect size in maize, whereas herbaceous plants displayed a negative effect size in the rhizosphere. Overall, our meta-analysis exhibited significant changes in microbial community structure and diversity responding to the plant rhizosphere effects depending on plant species, further suggesting the importance of plant rhizosphere to environmental changes influencing plants and subsequently their controls over the rhizosphere microbiota related to nutrient cycling and soil health.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Xian Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Huaihai Chen
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, Guangdong, China
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Fu X, Fu Q, Zhu X, Yang X, Chen H, Li S. Microdiversity sustains the distribution of rhizosphere-associated bacterial species from the root surface to the bulk soil region in maize crop fields. FRONTIERS IN PLANT SCIENCE 2023; 14:1266218. [PMID: 37905168 PMCID: PMC10613529 DOI: 10.3389/fpls.2023.1266218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/22/2023] [Indexed: 11/02/2023]
Abstract
Over the years, the microbial community of maize (Zea mays) rhizosphere has been extensively studied; however, the role of microdiversity sustain rhizosphere-associated microbial species distribution from root surface to bulk soil in mature maize is still unclear. Although operational taxonomic units (OTUs) have been used to classify species, amplicon sequence variants (ASVs) have been shown to be effective in representing microdiversity within OTUs at a finer genetic scale. Therefore, the aim of this study was to examine the role of microdiversity in influencing the distribution of rhizosphere-associated microbial species across environmental gradients from root surface to bulk soil at the OTU and ASV levels. Here, the microbial community structures of bulk, loosely bound, and tightly bound soil samples from maize rhizosphere were examined at OTU and ASV levels. The results showed that OTU and ASV methods exhibited similar microbial community structures in rhizosphere. Additionally, different ecotypes with varying distributions and habitat preferences were observed within the same bacterial OTU at the ASV level, indicating a rich bacterial microdiversity. In contrast, the fungal community exhibited low microdiversity, with no significant relationship between fungal microdiversity and persistence and variability. Moreover, the ecotypes observed within the bacterial OTUs were found to be positively or negatively associated with environmental factors, such as soil organic carbon (SOC), NO3 --N, NH4 +-N contents, and pH. Overall, the results showed that the rich microdiversity could sustain the distribution of rhizosphere-associated bacterial species across environmental gradients from root surface to bulk soil. Further genetic analyses of rhizosphere-associated bacterial species could have considerable implications for potential mediation of microdiversity for sustainable crop production.
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Affiliation(s)
- Xianheng Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resource, Shaanxi, China
| | - Qi Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Xiaozheng Zhu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resource, Shaanxi, China
| | - Xian Yang
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Huaihai Chen
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Shiqing Li
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resource, Shaanxi, China
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Nitrogen-Fixing Symbiotic Paraburkholderia Species: Current Knowledge and Future Perspectives. NITROGEN 2023. [DOI: 10.3390/nitrogen4010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
A century after the discovery of rhizobia, the first Beta-proteobacteria species (beta-rhizobia) were isolated from legume nodules in South Africa and South America. Since then, numerous species belonging to the Burkholderiaceae family have been isolated. The presence of a highly branching lineage of nodulation genes in beta-rhizobia suggests a long symbiotic history. In this review, we focus on the beta-rhizobial genus Paraburkholderia, which includes two main groups: the South American mimosoid-nodulating Paraburkholderia and the South African predominantly papilionoid-nodulating Paraburkholderia. Here, we discuss the latest knowledge on Paraburkholderia nitrogen-fixing symbionts in each step of the symbiosis, from their survival in the soil, through the first contact with the legumes until the formation of an efficient nitrogen-fixing symbiosis in root nodules. Special attention is given to the strain P. phymatum STM815T that exhibits extraordinary features, such as the ability to: (i) enter into symbiosis with more than 50 legume species, including the agriculturally important common bean, (ii) outcompete other rhizobial species for nodulation of several legumes, and (iii) endure stressful soil conditions (e.g., high salt concentration and low pH) and high temperatures.
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Metagenomic insights into taxonomic, functional diversity and inhibitors of microbial biofilms. Microbiol Res 2022; 265:127207. [DOI: 10.1016/j.micres.2022.127207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/17/2022] [Accepted: 09/18/2022] [Indexed: 11/21/2022]
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Sarenqimuge S, Rahman S, Wang Y, von Tiedemann A. Dormancy and germination of microsclerotia of Verticillium longisporum are regulated by soil bacteria and soil moisture levels but not by nutrients. Front Microbiol 2022; 13:979218. [PMID: 36212810 PMCID: PMC9539216 DOI: 10.3389/fmicb.2022.979218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022] Open
Abstract
The soil-borne pathogen Verticillium longisporum infects roots of its host plant, oilseed rape, and systemically colonizes stems where it finally forms microsclerotia at crop maturity. Once returned to the soil after harvest, microsclerotia undergo a stage of dormancy, in which they may survive for several years. Since there is neither efficient chemical control nor effective resistance in oilseed rape cultivars to control the disease, alternative control strategies may consist in regulating the germination and dormancy of microsclerotia in the soil. Therefore, a series of experiments were conducted to explore the effects of nutrients, soil moisture, and the soil microbiome on germination of dormant microsclerotia. Experiments with microsclerotia exposed in vitro to different nutrients indicated that under sterile conditions the stimulating effect of nutrients on microsclerotia germination was not enhanced as compared to water. Moreover, further assays revealed a strong inhibitory effect of unsterile soil on microsclerotia germination. Accordingly, oilseed rape plants inoculated with microsclerotia of V. longisporum showed severe infection with V. longisporum when grown in autoclaved soil, in contrast to plants grown in unsterile soil. These experiments indicate a crucial role of soil fungistasis and thus the soil microbiome on microsclerotia germination. Further bioassays demonstrated that viable soil bacteria obtained from the rhizosphere of oilseed rape plants and bulk field soil effectively inhibited microsclerotia germination, whereas dead bacteria and bacterial culture filtrates hardly suppressed germination. A putative inhibitory role of volatile organic compounds (VOCs) produced by soil bacteria was confirmed in two-compartment Petri dishes, where microsclerotia germination and colony growth were significantly inhibited. Bacterial VOCs were collected and analyzed by GC–MS. In total, 45 VOCs were identified, among which two acid and two alcohol compounds were emitted by all tested bacteria. A bioassay, conducted with corresponding pure chemicals in two-compartment Petri dishes, indicated that all acidic volatile compounds, including 3-methylbutanoic acid, 2-methylbutanoic acid, hexanoic acid, and 2-methylpropionic acid, induced strong inhibitory effects on microsclerotia. We conclude that bacterial acidic volatiles play a key role in the fungistatic effect on microsclerotia of V. longisporum in the soil and could thus be targeted for development of novel strategies to control this pathogen by artificially regulating dormancy of microsclerotia in soil.
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Affiliation(s)
- Sarenqimuge Sarenqimuge
- Plant Pathology and Plant Protection Division, Department of Crop Sciences, Faculty of Agriculture, Georg-August University Göttingen, Göttingen, Germany
| | - Shahinoor Rahman
- Agricultural Entomology Division, Department of Crop Sciences, Faculty of Agriculture, Georg-August University Göttingen, Göttingen, Germany
| | - Yao Wang
- Plant Pathology and Plant Protection Division, Department of Crop Sciences, Faculty of Agriculture, Georg-August University Göttingen, Göttingen, Germany
| | - Andreas von Tiedemann
- Plant Pathology and Plant Protection Division, Department of Crop Sciences, Faculty of Agriculture, Georg-August University Göttingen, Göttingen, Germany
- *Correspondence: Andreas von Tiedemann,
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Appidi MR, Bible AN, Carper DL, Jawdy SS, Giannone RJ, Hettich RL, Morrell-Falvey J, Abraham PE. Development of an Experimental Approach to Achieve Spatially Resolved Plant Root-Associated Metaproteomics Using an Agar-Plate System. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:639-649. [PMID: 35349304 DOI: 10.1094/mpmi-01-22-0011-ta] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Plant-microbe interactions in the rhizosphere play a vital role in plant health and productivity. The composition and function of root-associated microbiomes is strongly influenced by their surrounding environment, which is often customized by their host. How microbiomes change with respect to space and time across plant roots remains poorly understood, and methodologies that facilitate spatiotemporal metaproteomic studies of root-associated microbiomes are yet to be realized. Here, we developed a method that provides spatially resolved metaproteome measurements along plant roots embedded in agar-plate culture systems, which have long been used to study plants. Spatially defined agar "plugs" of interest were excised and subsequently processed using a novel peptide extraction method prior to metaproteomics, which was used to infer both microbial community composition and function. As a proof-of-principle, a previously studied 10-member community constructed from a Populus root system was grown in an agar plate with a 3-week-old Populus trichocarpa plant. Metaproteomics was performed across two time points (24 and 48 h) for three distinct locations (root base, root tip, and a region distant from the root). The spatial resolution of these measurements provides evidence that microbiome composition and expression changes across the plant root interface. Interrogation of the individual microbial proteomes revealed functional profiles related to their behavioral associations with the plant root, in which chemotaxis and augmented metabolism likely supported predominance of the most abundant member. This study demonstrated a novel peptide extraction method for studying plant agar-plate culture systems, which was previously unsuitable for (meta)proteomic measurements.
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Affiliation(s)
- Manasa R Appidi
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
- Department of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, U.S.A
| | - Amber N Bible
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | - Dana L Carper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | - Sara S Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | - Richard J Giannone
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | | | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
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Ganugi P, Fiorini A, Ardenti F, Caffi T, Bonini P, Taskin E, Puglisi E, Tabaglio V, Trevisan M, Lucini L. Nitrogen use efficiency, rhizosphere bacterial community, and root metabolome reprogramming due to maize seed treatment with microbial biostimulants. PHYSIOLOGIA PLANTARUM 2022; 174:e13679. [PMID: 35362106 PMCID: PMC9324912 DOI: 10.1111/ppl.13679] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/26/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Seed inoculation with beneficial microorganisms has gained importance as it has been proven to show biostimulant activity in plants, especially in terms of abiotic/biotic stress tolerance and plant growth promotion, representing a sustainable way to ensure yield stability under low input sustainable agriculture. Nevertheless, limited knowledge is available concerning the molecular and physiological processes underlying the root-inoculant symbiosis or plant response at the root system level. Our work aimed to integrate the interrelationship between agronomic traits, rhizosphere microbial population and metabolic processes in roots, following seed treatment with either arbuscular mycorrhizal fungi (AMF) or Plant Growth-Promoting Rhizobacteria (PGPR). To this aim, maize was grown under open field conditions with either optimal or reduced nitrogen availability. Both seed treatments increased nitrogen uptake efficiency under reduced nitrogen supply revealed some microbial community changes among treatments at root microbiome level and limited yield increases, while significant changes could be observed at metabolome level. Amino acid, lipid, flavone, lignan, and phenylpropanoid concentrations were mostly modulated. Integrative analysis of multi-omics datasets (Multiple Co-Inertia Analysis) highlighted a strong correlation between the metagenomics and the untargeted metabolomics datasets, suggesting a coordinate modulation of root physiological traits.
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Affiliation(s)
- Paola Ganugi
- Department for Sustainable Food ProcessUniversità Cattolica del Sacro CuorePiacenzaItaly
| | - Andrea Fiorini
- Department of Sustainable Crop ProductionUniversità Cattolica del Sacro CuorePiacenzaItaly
| | - Federico Ardenti
- Department of Sustainable Crop ProductionUniversità Cattolica del Sacro CuorePiacenzaItaly
| | - Tito Caffi
- Department of Sustainable Crop ProductionUniversità Cattolica del Sacro CuorePiacenzaItaly
| | | | - Eren Taskin
- Department for Sustainable Food ProcessUniversità Cattolica del Sacro CuorePiacenzaItaly
| | - Edoardo Puglisi
- Department for Sustainable Food ProcessUniversità Cattolica del Sacro CuorePiacenzaItaly
| | - Vincenzo Tabaglio
- Department of Sustainable Crop ProductionUniversità Cattolica del Sacro CuorePiacenzaItaly
| | - Marco Trevisan
- Department for Sustainable Food ProcessUniversità Cattolica del Sacro CuorePiacenzaItaly
| | - Luigi Lucini
- Department for Sustainable Food ProcessUniversità Cattolica del Sacro CuorePiacenzaItaly
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Belinato JR, Costa CP, Almeida A, Rocha SM, Augusto F. Mapping Aspergillus niger Metabolite Biomarkers for In Situ and Early Evaluation of Table Grapes Contamination. Foods 2021; 10:2870. [PMID: 34829150 PMCID: PMC8624196 DOI: 10.3390/foods10112870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 12/02/2022] Open
Abstract
The Aspergillus niger exometabolome was recently investigated using advanced gas chromatography in tandem with multivariate analysis, which allowed a metabolite biomarker pattern to be proposed. Microbial metabolomics patterns have gained enormous relevance, mainly due to the amount of information made available, which may be useful in countless processes. One of the great challenges in microbial metabolomics is related to applications in more complex systems of metabolomics information obtained from studies carried out in culture media, as complications may occur due to the dynamic nature of biological systems. Thus, the main objective of this research was to evaluate the applicability of the A. niger metabololite biomarkers pattern for in situ and early evaluation of table grapes contamination, used as study model. A. niger is a ubiquitous fungus responsible for food contamination, being reported as one of the main agents of the black mold disease, a serious post-harvest pathology of table grapes. This work included analysis from 1 day of growth time of pure A. niger cultures, A. niger cultures obtained from previously contaminated grapes, and finally, an in situ solid-phase microextraction (SPME) approach directly on previously contaminated table grapes. Supervised multivariate analysis was performed which revealed that after 1 day of inoculation it was possible to detect A. niger biomarkers, which can be extremely useful in making this type of method possible for the rapid detection of food contamination. The results obtained confirm the potential applicability of the pattern of A. niger biomarkers for early detection of the fungi (after 1 day of contamination), and may be further explored for access food susceptibility to fungi contamination, based on direct analysis of the food item.
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Affiliation(s)
- Joao Raul Belinato
- Institute of Chemistry, University of Campinas and National Institute of Science and Technology in Bioanalysis (INCTBio), Campinas 13083-970, Brazil;
| | - Carina Pedrosa Costa
- Department of Chemistry & LAQV-REQUIMTE, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Adelaide Almeida
- Department of Biology & CESAM, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Silvia M. Rocha
- Department of Chemistry & LAQV-REQUIMTE, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Fabio Augusto
- Institute of Chemistry, University of Campinas and National Institute of Science and Technology in Bioanalysis (INCTBio), Campinas 13083-970, Brazil;
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Yanagisawa N, Kozgunova E, Grossmann G, Geitmann A, Higashiyama T. Microfluidics-Based Bioassays and Imaging of Plant Cells. PLANT & CELL PHYSIOLOGY 2021; 62:1239-1250. [PMID: 34027549 PMCID: PMC8579190 DOI: 10.1093/pcp/pcab067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/13/2021] [Accepted: 05/23/2021] [Indexed: 05/03/2023]
Abstract
Many plant processes occur in the context of and in interaction with a surrounding matrix such as soil (e.g. root growth and root-microbe interactions) or surrounding tissues (e.g. pollen tube growth through the pistil), making it difficult to study them with high-resolution optical microscopy. Over the past decade, microfabrication techniques have been developed to produce experimental systems that allow researchers to examine cell behavior in microstructured environments that mimic geometrical, physical and/or chemical aspects of the natural growth matrices and that cannot be generated using traditional agar plate assays. These microfabricated environments offer considerable design flexibility as well as the transparency required for high-resolution, light-based microscopy. In addition, microfluidic platforms have been used for various types of bioassays, including cellular force assays, chemoattraction assays and electrotropism assays. Here, we review the recent use of microfluidic devices to study plant cells and organs, including plant roots, root hairs, moss protonemata and pollen tubes. The increasing adoption of microfabrication techniques by the plant science community may transform our approaches to investigating how individual plant cells sense and respond to changes in the physical and chemical environment.
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Affiliation(s)
- Naoki Yanagisawa
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Nagoya Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Elena Kozgunova
- Department of Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Schänzlestr. 1, Freiburg, Baden-Württemberg 79104, Germany
| | - Guido Grossmann
- Institute of Cell and Interaction Biology, Heinrich Heine University Düsseldorf, Universitätsstr. 1, Düsseldorf 40225, Germany
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Baden-Württemberg 69120, Germany
| | - Anja Geitmann
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Québec H9X 3V9, Canada
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Nagoya Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo City, Tokyo 113-0033, Japan
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Kashiwagi FM, Wendler Miranda B, de Oliveira Pedrosa F, de Souza EM, Müller-Santos M. Control of Gene Expression With Quercetin-Responsive Modular Circuits. Front Bioeng Biotechnol 2021; 9:730967. [PMID: 34604189 PMCID: PMC8481877 DOI: 10.3389/fbioe.2021.730967] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/23/2021] [Indexed: 12/02/2022] Open
Abstract
Control of gene expression is crucial for several biotechnological applications, especially for implementing predictable and controllable genetic circuits. Such circuits are often implemented with a transcriptional regulator activated by a specific signal. These regulators should work independently of the host machinery, with low gratuitous induction or crosstalk with host components. Moreover, the signal should also be orthogonal, recognized only by the regulator with minimal interference with the host operation. In this context, transcriptional regulators activated by plant metabolites as flavonoids emerge as candidates to control gene expression in bacteria. However, engineering novel circuits requires the characterization of the genetic parts (e.g., genes, promoters, ribosome binding sites, and terminators) in the host of interest. Therefore, we decomposed the QdoR regulatory system of B. subtilis, responsive to the flavonoid quercetin, and reassembled its parts into genetic circuits programmed to have different levels of gene expression and noise dependent on the concentration of quercetin. We showed that only one of the promoters regulated by QdoR worked well in E. coli, enabling the construction of other circuits induced by quercetin. The QdoR expression was modulated with constitutive promoters of different transcriptional strengths, leading to low expression levels when QdoR was highly expressed and vice versa. E. coli strains expressing high and low levels of QdoR were mixed and induced with the same quercetin concentration, resulting in two stable populations expressing different levels of their gene reporters. Besides, we demonstrated that the level of QdoR repression generated different noise levels in gene expression dependent on the concentration of quercetin. The circuits presented here can be exploited in applications requiring adjustment of gene expression and noise using a highly available and natural inducer as quercetin.
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Affiliation(s)
- Fernanda Miyuki Kashiwagi
- Postgraduate Program in Science (Biochemistry), Department of Biochemistry and Molecular Biology, Nitrogen Fixation Laboratory, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Brenno Wendler Miranda
- Biological Sciences Undergraduate Course, Department of Biochemistry and Molecular Biology, Nitrogen Fixation Laboratory, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Fabio de Oliveira Pedrosa
- Nitrogen Fixation Laboratory, Department of Biochemistry and Molecular Biology, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Emanuel Maltempi de Souza
- Nitrogen Fixation Laboratory, Department of Biochemistry and Molecular Biology, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Marcelo Müller-Santos
- Nitrogen Fixation Laboratory, Department of Biochemistry and Molecular Biology, Federal University of Paraná (UFPR), Curitiba, Brazil
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Sun H, Jiang S, Jiang C, Wu C, Gao M, Wang Q. A review of root exudates and rhizosphere microbiome for crop production. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:54497-54510. [PMID: 34431053 DOI: 10.1007/s11356-021-15838-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/02/2021] [Indexed: 05/04/2023]
Abstract
Increasing crop yields and ensuring food security is a major global challenge. In order to increase crop production, chemical fertilizers and pesticides are excessively used. However, the significance of root exudates is understudied. Beneficial interactions between plant and rhizosphere microbiome are critical for plant fitness and health. In this review, we discuss the application and progress of current research methods and technologies in terms of root exudates and rhizosphere microbiome. We summarize how root exudates promote plant access to nitrogen, phosphorus, and iron, and how root exudates strengthen plant immunity to cope with biotic stress by regulating the rhizosphere microbiome, and thereby reducing dependence on fertilizers and pesticides. Optimizing these interactions to increase plant nutrient uptake and resistance to biotic stresses offers one of the few untapped opportunities to confront sustainability issues in food security. To overcome the limitations of current research, combination of multi-omics, imaging technology together with synthetic communities has the potential to uncover the interaction mechanisms and to fill the knowledge gap for their applications in agriculture to achieve sustainable development.
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Affiliation(s)
- Haishu Sun
- Department of Environmental Engineering, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Shanxue Jiang
- School of Ecology and Environment, Beijing Technology and Business University, Beijing, 100048, China
- State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing, 100048, China
| | - Cancan Jiang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Chuanfu Wu
- Department of Environmental Engineering, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Key Laboratory on Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, 10083, China
| | - Ming Gao
- Department of Environmental Engineering, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Key Laboratory on Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, 10083, China
| | - Qunhui Wang
- Department of Environmental Engineering, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
- Beijing Key Laboratory on Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, 10083, China.
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Mendoza-Suárez M, Andersen SU, Poole PS, Sánchez-Cañizares C. Competition, Nodule Occupancy, and Persistence of Inoculant Strains: Key Factors in the Rhizobium-Legume Symbioses. FRONTIERS IN PLANT SCIENCE 2021; 12:690567. [PMID: 34489993 PMCID: PMC8416774 DOI: 10.3389/fpls.2021.690567] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/19/2021] [Indexed: 05/06/2023]
Abstract
Biological nitrogen fixation by Rhizobium-legume symbioses represents an environmentally friendly and inexpensive alternative to the use of chemical nitrogen fertilizers in legume crops. Rhizobial inoculants, applied frequently as biofertilizers, play an important role in sustainable agriculture. However, inoculants often fail to compete for nodule occupancy against native rhizobia with inferior nitrogen-fixing abilities, resulting in low yields. Strains with excellent performance under controlled conditions are typically selected as inoculants, but the rates of nodule occupancy compared to native strains are rarely investigated. Lack of persistence in the field after agricultural cycles, usually due to the transfer of symbiotic genes from the inoculant strain to naturalized populations, also limits the suitability of commercial inoculants. When rhizobial inoculants are based on native strains with a high nitrogen fixation ability, they often have superior performance in the field due to their genetic adaptations to the local environment. Therefore, knowledge from laboratory studies assessing competition and understanding how diverse strains of rhizobia behave, together with assays done under field conditions, may allow us to exploit the effectiveness of native populations selected as elite strains and to breed specific host cultivar-rhizobial strain combinations. Here, we review current knowledge at the molecular level on competition for nodulation and the advances in molecular tools for assessing competitiveness. We then describe ongoing approaches for inoculant development based on native strains and emphasize future perspectives and applications using a multidisciplinary approach to ensure optimal performance of both symbiotic partners.
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Affiliation(s)
| | - Stig U. Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Philip S. Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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Jiang Z, Nero T, Mukherjee S, Olson R, Yan J. Searching for the Secret of Stickiness: How Biofilms Adhere to Surfaces. Front Microbiol 2021; 12:686793. [PMID: 34305846 PMCID: PMC8295476 DOI: 10.3389/fmicb.2021.686793] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/28/2021] [Indexed: 01/01/2023] Open
Abstract
Bacterial biofilms are communities of cells enclosed in an extracellular polymeric matrix in which cells adhere to each other and to foreign surfaces. The development of a biofilm is a dynamic process that involves multiple steps, including cell-surface attachment, matrix production, and population expansion. Increasing evidence indicates that biofilm adhesion is one of the main factors contributing to biofilm-associated infections in clinics and biofouling in industrial settings. This review focuses on describing biofilm adhesion strategies among different bacteria, including Vibrio cholerae, Pseudomonas aeruginosa, and Staphylococcus aureus. Techniques used to characterize biofilm adhesion are also reviewed. An understanding of biofilm adhesion strategies can guide the development of novel approaches to inhibit or manipulate biofilm adhesion and growth.
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Affiliation(s)
- Zhaowei Jiang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, United States
| | - Thomas Nero
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, United States
| | - Sampriti Mukherjee
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, United States
| | - Rich Olson
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, CT, United States
| | - Jing Yan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, United States.,Quantitative Biology Institute, Yale University, New Haven, CT, United States
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16
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Elhady A, Topalović O, Heuer H. Plants Specifically Modulate the Microbiome of Root-Lesion Nematodes in the Rhizosphere, Affecting Their Fitness. Microorganisms 2021; 9:microorganisms9040679. [PMID: 33806116 PMCID: PMC8064444 DOI: 10.3390/microorganisms9040679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/20/2021] [Accepted: 03/22/2021] [Indexed: 12/31/2022] Open
Abstract
Plant-parasitic nematodes are a major constraint on agricultural production. They significantly impede crop yield. To complete their parasitism, they need to locate, disguise, and interact with plant signals exuded in the rhizosphere of the host plant. A specific subset of the soil microbiome can attach to the surface of nematodes in a specific manner. We hypothesized that host plants recruit species of microbes as helpers against attacking nematode species, and that these helpers differ among plant species. We investigated to what extend the attached microbial species are determined by plant species, their root exudates, and how these microbes affect nematodes. We conditioned the soil microbiome in the rhizosphere of different plant species, then employed culture-independent and culture-dependent methods to study microbial attachment to the cuticle of the phytonematode Pratylenchus penetrans. Community fingerprints of nematode-attached fungi and bacteria showed that the plant species govern the microbiome associated with the nematode cuticle. Bacteria isolated from the cuticle belonged to Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Sphingobacteria, and Firmicutes. The isolates Microbacterium sp. i.14, Lysobacter capsici i.17, and Alcaligenes sp. i.37 showed the highest attachment rates to the cuticle. The isolates Bacillus cereus i.24 and L. capsici i.17 significantly antagonized P. penetrans after attachment. Significantly more bacteria attached to P. penetrans in microbiome suspensions from bulk soil or oat rhizosphere compared to Ethiopian mustard rhizosphere. However, the latter caused a better suppression of the nematode. Conditioning the cuticle of P. penetrans with root exudates significantly decreased the number of Microbacterium sp. i.14 attaching to the cuticle, suggesting induced changes of the cuticle structure. These findings will lead to a more knowledge-driven exploitation of microbial antagonists of plant-parasitic nematodes for plant protection.
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Affiliation(s)
- Ahmed Elhady
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI)–Federal Research Centre for Cultivated Plants, 38104 Braunschweig, Germany; (O.T.); (H.H.)
- Department of Plant Protection, Faculty of Agriculture, Benha University, Moshtohor 13736, Egypt
- Correspondence: or
| | - Olivera Topalović
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI)–Federal Research Centre for Cultivated Plants, 38104 Braunschweig, Germany; (O.T.); (H.H.)
| | - Holger Heuer
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI)–Federal Research Centre for Cultivated Plants, 38104 Braunschweig, Germany; (O.T.); (H.H.)
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17
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Sharma R, Shrivas VL, Sharma S. Effect of substitution of chemical fertilizer by bioinoculants on plant performance and rhizospheric bacterial community: case study with Cajanus cajan. Braz J Microbiol 2021; 52:373-386. [PMID: 33415718 DOI: 10.1007/s42770-020-00418-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/22/2020] [Indexed: 11/29/2022] Open
Abstract
Improper nutrient management is one of the major limitations linked with cultivation of Cajanus cajan. This calls for an urgent need for a promising alternative, employing both bioinoculants and chemical fertilizer. Present study attempted to understand the impact of bioinoculants {Azotobacter chroococcum, Bacillus megaterium, and Pseudomonas fluorescens (ABP)} as their mono-inoculations, triple-inoculation, and their combination with different doses of fertilizer on (a) plant parameters, (b) soil nitrogen (N) economy, (c) resident bacterial community, (d) genes and transcripts involved in N cycle, and to evaluate the extent to which fertilizer could be replaced by ABP without compromising on grain yield. Bradyrhizobium sp. was used in all the treatments (as it was recommended for C. cajan). Combined application of bioinoculants and 75% of recommended dose of fertilizer (RDF) led to 1.28-fold enhancement in grain yield as compared to RDF alone. Apart from exerting a positive impact on grain yield, the combined application of ABP and fertilizer led to an improvement in soil fertility, and modified the culturable rhizospheric bacterial community involved in N cycle. Integrated use of bioinoculants and fertilizer led to better N substrate utilization and hence, metabolic diversity when compared with application of fertilizer alone. An increase in the transcripts of nifH gene at the harvest stage in the soil treated with ABP alone and its combination with fertilizer, over individual treatment with fertilizer was observed. The combined use of ABP and fertilizer shaped the resident bacterial community towards a more beneficial community, which helped in increasing soil nitrogen turnover and hence, soil fertility as a whole.
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Affiliation(s)
- Richa Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Vijay Laxmi Shrivas
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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18
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Islam W, Noman A, Naveed H, Huang Z, Chen HYH. Role of environmental factors in shaping the soil microbiome. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:41225-41247. [PMID: 32829437 DOI: 10.1007/s11356-020-10471-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/10/2020] [Indexed: 05/09/2023]
Abstract
The soil microbiome comprises one of the most important and complex components of all terrestrial ecosystems as it harbors millions of microbes including bacteria, fungi, archaea, viruses, and protozoa. Together, these microbes and environmental factors contribute to shaping the soil microbiome, both spatially and temporally. Recent advances in genomic and metagenomic analyses have enabled a more comprehensive elucidation of the soil microbiome. However, most studies have described major modulators such as fungi and bacteria while overlooking other soil microbes. This review encompasses all known microbes that may exist in a particular soil microbiome by describing their occurrence, abundance, diversity, distribution, communication, and functions. Finally, we examined the role of several abiotic factors involved in the shaping of the soil microbiome.
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Affiliation(s)
- Waqar Islam
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China
- Faculty of Natural Resources Management, Lakehead University, 955 Oliver Rd, Thunder Bay, ON, P7B 5E1, Canada
| | - Ali Noman
- Department of Botany, Government College University, Faisalabad, 38000, Pakistan
| | - Hassan Naveed
- College of Life Science, Leshan Normal University, Leshan, 614004, Sichuan, China
| | - Zhiqun Huang
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China.
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China.
| | - Han Y H Chen
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China.
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China.
- Faculty of Natural Resources Management, Lakehead University, 955 Oliver Rd, Thunder Bay, ON, P7B 5E1, Canada.
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19
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Pandit A, Adholeya A, Cahill D, Brau L, Kochar M. Microbial biofilms in nature: unlocking their potential for agricultural applications. J Appl Microbiol 2020; 129:199-211. [PMID: 32034822 DOI: 10.1111/jam.14609] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/23/2020] [Accepted: 02/05/2020] [Indexed: 12/17/2022]
Abstract
Soil environments are dynamic and the plant rhizosphere harbours a phenomenal diversity of micro-organisms which exchange signals and beneficial nutrients. Bipartite beneficial or symbiotic interactions with host roots, such as mycorrhizae and various bacteria, are relatively well characterized. In addition, a tripartite interaction also exists between plant roots, arbuscular mycorrhizal fungi (AMF) and associated bacteria. Bacterial biofilms exist as a sheet of bacterial cells in association with AMF structures, embedded within a self-produced exopolysaccharide matrix. Such biofilms may play important functional roles within these tripartite interactions. However, the details about such interactions in the rhizosphere and their relevant functional relationships have not been elucidated. This review explores the current understanding of naturally occurring microbial biofilms, and their interaction with biotic surfaces, especially AMF. The possible roles played by bacterial biofilms and the potential for their application for a more productive and sustainable agriculture is discussed in this review.
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Affiliation(s)
- A Pandit
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, TERI Gram, Gwal Pahari, Gurugram, Haryana, India
- School of Life and Environmental Sciences, Deakin University, Geelong, Vic, Australia
| | - A Adholeya
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, TERI Gram, Gwal Pahari, Gurugram, Haryana, India
| | - D Cahill
- School of Life and Environmental Sciences, Deakin University, Geelong, Vic, Australia
| | - L Brau
- School of Life and Environmental Sciences, Deakin University, Geelong, Vic, Australia
| | - M Kochar
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, TERI Gram, Gwal Pahari, Gurugram, Haryana, India
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20
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Sahu J, Vaishnav A, Singh HB. Insights in Plant-Microbe Interaction through Genomics Approach (Part 1). Curr Genomics 2020; 21:155. [PMID: 33071608 PMCID: PMC7521037 DOI: 10.2174/138920292103200625161718] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Jagajjit Sahu
- 1National Center for Cell Sciences (NCCS), University of Pune Campus, University Road, Ganeshkhind, Pune-411007, Maharashtra, India; 2Somvanshi Research Foundation, 13/21 Vikas Nagar, Lucknow-226022, Uttar Pradesh, India; 3Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University, Mathura-281121, Uttar Pradesh, India
| | - Anukool Vaishnav
- 1National Center for Cell Sciences (NCCS), University of Pune Campus, University Road, Ganeshkhind, Pune-411007, Maharashtra, India; 2Somvanshi Research Foundation, 13/21 Vikas Nagar, Lucknow-226022, Uttar Pradesh, India; 3Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University, Mathura-281121, Uttar Pradesh, India
| | - Harikesh B Singh
- 1National Center for Cell Sciences (NCCS), University of Pune Campus, University Road, Ganeshkhind, Pune-411007, Maharashtra, India; 2Somvanshi Research Foundation, 13/21 Vikas Nagar, Lucknow-226022, Uttar Pradesh, India; 3Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University, Mathura-281121, Uttar Pradesh, India
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Wang C, Masoudi A, Wang M, Yang J, Shen R, Man M, Yu Z, Liu J. Community structure and diversity of the microbiomes of two microhabitats at the root-soil interface: implications of meta-analysis of the root-zone soil and root endosphere microbial communities in Xiong'an New Area. Can J Microbiol 2020; 66:605-622. [PMID: 32526152 DOI: 10.1139/cjm-2020-0061] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The diversity of the microbial compositions of the root-zone soil (the rhizosphere-surrounding soil) and root endosphere (all inner root tissues) of Pinus tabulaeformis Carr. and Ginkgo biloba L. were evaluated in Xiong'an New Area using high-throughput sequencing; the influence of the soil edaphic parameters on microbial community compositions was also evaluated. Our results showed that both the taxonomic and phylogenetic diversities of the root endosphere were lower than those of the root-zone soil, but the variation in the endosphere microbial community structure was remarkably higher than that of the root-zone soil. Spearman correlation analysis showed that the soil organic matter, total nitrogen, total phosphate, total potassium, ratio of carbon to nitrogen, and pH significantly explained the α-diversity of the bacterial community and that total nitrogen differentially contributed to the α-diversity of the fungal community. Variation partitioning analysis showed that plant species had a greater influence on microbial composition variations than did any other soil property, although soil chemical parameters explained more variation when integrated. Together, our results suggest that both plant species and soil chemical parameters played a critical role in shaping the microbial community composition.
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Affiliation(s)
- Can Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P.R. China
| | - Abolfazl Masoudi
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P.R. China
| | - Min Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P.R. China
| | - Jia Yang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P.R. China
| | - Ruowen Shen
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P.R. China
| | - Meng Man
- Library of Hebei Normal University, Hebei Normal University, Shijiazhuang 050024, P.R. China
| | - Zhijun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P.R. China
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P.R. China
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22
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Kavamura VN, Robinson RJ, Hughes D, Clark I, Rossmann M, Melo ISD, Hirsch PR, Mendes R, Mauchline TH. Wheat dwarfing influences selection of the rhizosphere microbiome. Sci Rep 2020; 10:1452. [PMID: 31996781 PMCID: PMC6989667 DOI: 10.1038/s41598-020-58402-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/14/2020] [Indexed: 12/23/2022] Open
Abstract
The development of dwarf wheat cultivars combined with high levels of agrochemical inputs during the green revolution resulted in high yielding cropping systems. However, changes in wheat cultivars were made without considering impacts on plant and soil microbe interactions. We studied the effect of these changes on root traits and on the assembly of rhizosphere bacterial communities by comparing eight wheat cultivars ranging from tall to semi-dwarf plants grown under field conditions. Wheat breeding influenced root diameter and specific root length (SRL). Rhizosphere bacterial communities from tall cultivars were distinct from those associated with semi-dwarf cultivars, with higher differential abundance of Actinobacteria, Bacteroidetes and Proteobacteria in tall cultivars, compared with a higher differential abundance of Verrucomicrobia, Planctomycetes and Acidobacteria in semi-dwarf cultivars. Predicted microbial functions were also impacted and network analysis revealed a greater level of connectedness between microbial communities in the tall cultivars relative to semi-dwarf cultivars. Taken together, results suggest that the development of semi-dwarf plants might have affected the ability of plants to recruit and sustain a complex bacterial community network in the rhizosphere.
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Affiliation(s)
- Vanessa N Kavamura
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Rebekah J Robinson
- Plant Pathology Laboratory, Royal Horticultural Society, RHS Garden Wisley, Woking, Surrey, GU23 6QB, United Kingdom
| | - David Hughes
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Ian Clark
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Maike Rossmann
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna-SP, Brazil
| | - Itamar Soares de Melo
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna-SP, Brazil
| | - Penny R Hirsch
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna-SP, Brazil
| | - Tim H Mauchline
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom.
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Wu L, Yang B, Li M, Chen J, Xiao Z, Wu H, Tong Q, Luo X, Lin W. Modification of Rhizosphere Bacterial Community Structure and Functional Potentials to Control Pseudostellaria heterophylla Replant Disease. PLANT DISEASE 2020; 104:25-34. [PMID: 31726014 DOI: 10.1094/pdis-04-19-0833-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Replant disease caused by negative plant-soil feedback commonly occurs in a Pseudostellaria heterophylla monoculture regime. Here, barcoded pyrosequencing of 16S ribosomal DNA amplicons combined with phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis was applied to study the shifts in soil bacterial community structure and functional potentials in the rhizosphere of P. heterophylla under consecutive monoculture and different soil amendments (i.e., bio-organic fertilizer application [MF] and paddy-upland rotation [PR]). The results showed that the yield of tuberous roots decreased under P. heterophylla consecutive monoculture and then increased after MF and PR treatments, which was consistent with the changes in soil bacterial diversity. Both principal coordinate analysis and the unweighted pair-group method with arithmetic means cluster analysis showed the distinct difference in bacterial community structure between the consecutively monocultured soil (relatively unhealthy soil) and other relatively healthy soils (i.e., newly planted soil, MF, and PR). Furthermore, taxonomic analysis showed that consecutive monoculture of P. heterophylla significantly decreased the relative abundances of the families Burkholderiaceae and Acidobacteriaceae (subgroup 1), whereas it increased the population density of families Xanthomonadaceae, Phyllobacteriaceae, Sphingobacteriaceae, and Alcaligenaceae, and Fusarium oxysporum. In contrast, the MF and PR treatments recovered the soil microbiome and decreased F. oxysporum abundance through the different ways; for example, the introduction of beneficial microorganisms (in MF) or the switching between anaerobic and aerobic conditions (in PR). In addition, PICRUSt analysis revealed the higher abundances of membrane transport, cell motility, and DNA repair in the consecutively monocultured soil, which might contribute to the root colonization and survival for certain bacterial pathogens under monoculture. These findings highlight the close association between replant disease of P. heterophylla and the variations in structure and potential functions of rhizosphere bacterial community.
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Affiliation(s)
- Linkun Wu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University
| | - Bo Yang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University
| | - Manlin Li
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University
| | - Jun Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University
| | - Zhigang Xiao
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University
| | - Hongmiao Wu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University
| | - Qingyu Tong
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University
| | - Xiaomian Luo
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University
| | - Wenxiong Lin
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University
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Tovi N, Frenk S, Hadar Y, Minz D. Host Specificity and Spatial Distribution Preference of Three Pseudomonas Isolates. Front Microbiol 2019; 9:3263. [PMID: 30687261 PMCID: PMC6335278 DOI: 10.3389/fmicb.2018.03263] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 12/14/2018] [Indexed: 12/17/2022] Open
Abstract
Plant hosts recruit and maintain a distinct root-associated microbiota based on host and bacterium traits. However, past studies disregarded microbial strain-host specificity and spatial micro-heterogeneity of the root compartment. Using genetic manipulation, confocal laser scanning microscopy, real-time quantitative PCR, and genome sequencing we characterized the colonization patterns of three Pseudomonas spp. isolates native to wheat roots, on the micro-scale. Namely, isolates P. fluorescens NT0133, P. stutzeri NT124, and P. stutzeri NT128. All three isolates preferentially colonized wheat over cucumber roots that served as control for host specificity. Furthermore, not only had the isolates strong host specificity but each isolate had a distinct spatial distribution on the root, all within a few millimeters. Isolate P. stutzeri-NT0124 preferentially colonized root tips, whereas P. fluorescens-NT0133 showed a preference for zones distant from the tip. In contrast, isolate P. stutzeri-NT0128 had no preference for a specific niche on the root. While all isolates maintained genetic potential for motility and biofilm formation their phenotype varied significantly and corresponded to their niche preference. These results demonstrate the importance of spatial colonization patterns, governed by both niche and bacterial characteristics which will have great importance in future attempts to manipulate the plant microbiome by constructing synthetic microbial consortia.
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Affiliation(s)
- Nesli Tovi
- Department of Soil, Water, and Environmental Sciences, Agricultural Research Organization–Volcani Center, Rishon LeZion, Israel
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Sammy Frenk
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Dror Minz
- Department of Soil, Water, and Environmental Sciences, Agricultural Research Organization–Volcani Center, Rishon LeZion, Israel
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Bravo A, Ruiz-Cruz S, Alkorta I, Espinosa M. When Humans Met Superbugs: Strategies to Tackle Bacterial Resistances to Antibiotics. Biomol Concepts 2018; 9:216-226. [PMID: 30811343 DOI: 10.1515/bmc-2018-0021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 12/17/2018] [Indexed: 12/25/2022] Open
Abstract
Bacterial resistance to antibiotics poses enormous health and economic burdens to our society, and it is of the essence to explore old and new ways to deal with these problems. Here we review the current status of multi-resistance genes and how they spread among bacteria. We discuss strategies to deal with resistant bacteria, namely the search for new targets and the use of inhibitors of protein-protein interactions, fragment-based methods, or modified antisense RNAs. Finally, we discuss integrated approaches that consider bacterial populations and their niches, as well as the role of global regulators that activate and/or repress the expression of multiple genes in fluctuating environments and, therefore, enable resistant bacteria to colonize new niches. Understanding how the global regulatory circuits work is, probably, the best way to tackle bacterial resistance.
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Affiliation(s)
- Alicia Bravo
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Sofia Ruiz-Cruz
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Itziar Alkorta
- Instituto BIOFISIKA (CSIC, UPV/EHU), Departamento de Bioquímica y Biología Molecular, Universidad del Pais Vasco, P.O. Box 644, 48080 Bilbao, Spain
| | - Manuel Espinosa
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, 9, 28040 Madrid, Spain
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Wheatley RM, Poole PS. Mechanisms of bacterial attachment to roots. FEMS Microbiol Rev 2018; 42:448-461. [PMID: 29672765 DOI: 10.1093/femsre/fuy014] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 04/14/2018] [Indexed: 11/13/2022] Open
Abstract
The attachment of bacteria to roots constitutes the first physical step in many plant-microbe interactions. These interactions exert both positive and negative influences on agricultural systems depending on whether a growth-promoting, symbiotic or pathogenic relationship transpires. A common biphasic mechanism of root attachment exists across agriculturally important microbial species, including Rhizobium, Agrobacterium, Pseudomonas, Azospirillum and Salmonella. Attachment studies have revealed how plant-microbe interactions develop, and how to manipulate these relationships for agricultural benefit. Here, we review our current understanding of the molecular mechanisms governing plant-microbe root attachment and draw together a common biphasic model.
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Affiliation(s)
- Rachel M Wheatley
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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Field KJ, Pressel S. Unity in diversity: structural and functional insights into the ancient partnerships between plants and fungi. THE NEW PHYTOLOGIST 2018; 220:996-1011. [PMID: 29696662 DOI: 10.1111/nph.15158] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 03/06/2018] [Indexed: 05/16/2023]
Abstract
Contents Summary 996 I. Introduction 996 II. An ancient, and diverse, symbiosis 998 III. Structural diversity in ancient plant-fungal partnerships 1000 IV. Mycorrhizal unity in host plant nutrition 1002 V. Plant-to-fungus carbon transfer 1003 VI. From individuals to networks 1003 VII. Diverse responses of mycorrhizal functioning to dynamic environments 1006 VIII. Summary of future research direction 1007 Acknowledgements 1006 References 1006 SUMMARY: Mycorrhizal symbiosis is an ancient and widespread mutualism between plants and fungi that facilitated plant terrestrialisation > 500 million years ago, with key roles in ecosystem functioning at multiple scales. Central to the symbiosis is the bidirectional exchange of plant-fixed carbon for fungal-acquired nutrients. Within this unifying role of mycorrhizas, considerable diversity in structure and function reflects the diversity of the partners involved. Early diverging plants form mutualisms not only with arbuscular mycorrhizal Glomeromycotina fungi, but also with poorly characterised Mucoromycotina, which may also colonise the roots of 'higher' plants as fine root endophytes. Functional diversity in these symbioses depends on both fungal and plant life histories and is influenced by the environment. Recent studies have highlighted the roles of lipids/fatty acids in plant-to-fungus carbon transport and potential contributions of Glomeromycotina fungi to plant nitrogen nutrition. Together with emerging appreciation of mycorrhizal networks as multi-species resource-sharing systems, these insights are broadening our views on mycorrhizas and their roles in nutrient cycling. It is crucial that the diverse array of biotic and abiotic factors that together shape the dynamics of carbon-for-nutrient exchange between plants and fungi are integrated, in addition to embracing the unfolding and potentially key role of Mucoromycotina fungi in these processes.
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Affiliation(s)
- Katie J Field
- Centre for Plant Sciences, School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Silvia Pressel
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
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Wu L, Chen J, Khan MU, Wang J, Wu H, Xiao Z, Zhang Z, Lin W. Rhizosphere Fungal Community Dynamics Associated with Rehmannia glutinosa Replant Disease in a Consecutive Monoculture Regime. PHYTOPATHOLOGY 2018; 108:1493-1500. [PMID: 29975158 DOI: 10.1094/phyto-02-18-0038-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Consecutive monoculture of Rehmannia glutinosa in the same field leads to a severe decline in both quality and yield of tuberous roots, the most useful part in traditional Chinese medicine. Fungi are an important and diverse group of microorganisms in the soil ecosystem and play crucial roles in soil health. In this study, high-throughput pyrosequencing of internal transcribed spacer 2 ribosomal DNA amplicons was applied to gain insight into how consecutive monoculture practice influence and stimulate R. glutinosa rhizosphere and bulk soil fungal communities. The results from nonmetric multidimensional scaling ordination and clustering analysis revealed distinctive differences between rhizosphere and bulk soil fungal communities. However, longer-term monocultured bulk soils were more similar to the rhizosphere soils in comparison with the shorter-term monocultured bulk soils. Moreover, consecutive monoculture caused a gradual shift in the composition and structure of the soil fungal community. The cultivation of this plant led to the appearance of some exclusive operational taxonomic units in rhizosphere or bulk soils that were assigned to the genera Fusarium, Rhizoctonia, and so on. Furthermore, the sum of the relative abundance of species of Fusarium, Cylindrocarpon, and Gibberella (belonging to the family Nectriaceae); Rhizoctonia, Thanatephorus, and Ceratobasidium (belonging to the family Ceratobasidiaceae); and Lectera and Plectosporium (belonging to the family Plectosphaerellaceae) was significantly higher in consecutively monocultured (CM) than in newly planted (NP) soil in both rhizosphere and bulk soils. In particular, Fusarium abundance was significantly higher in CM than in NP in the rhizosphere, and higher in rhizosphere soils than in bulk soils for each treatment. A pathogenicity test showed that both Fusarium strains isolated were pathogenic to R. glutinosa seedlings. In addition, the culture filtrate and mycotoxins produced by Fusarium oxysporum significantly repressed the growth of the antagonistic bacterium, Pseudomonas aeruginosa. In conclusion, consecutive monoculture of R. glutinosa restructured the fungal communities in both rhizosphere and bulk soils but bulk effects developed more slowly over time in comparison with rhizosphere effects. Furthermore, microbial interactions might lead to a reduction in the abundance of beneficial microbes.
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Affiliation(s)
- Linkun Wu
- First, second, third, fourth, fifth, sixth, and eighth authors: College of Life Sciences and Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring; seventh and eighth authors: Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Province University; and seventh author: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P.R. China
| | - Jun Chen
- First, second, third, fourth, fifth, sixth, and eighth authors: College of Life Sciences and Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring; seventh and eighth authors: Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Province University; and seventh author: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P.R. China
| | - Muhammad Umar Khan
- First, second, third, fourth, fifth, sixth, and eighth authors: College of Life Sciences and Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring; seventh and eighth authors: Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Province University; and seventh author: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P.R. China
| | - Juanying Wang
- First, second, third, fourth, fifth, sixth, and eighth authors: College of Life Sciences and Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring; seventh and eighth authors: Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Province University; and seventh author: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P.R. China
| | - Hongmiao Wu
- First, second, third, fourth, fifth, sixth, and eighth authors: College of Life Sciences and Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring; seventh and eighth authors: Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Province University; and seventh author: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P.R. China
| | - Zhigang Xiao
- First, second, third, fourth, fifth, sixth, and eighth authors: College of Life Sciences and Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring; seventh and eighth authors: Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Province University; and seventh author: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P.R. China
| | - Zhongyi Zhang
- First, second, third, fourth, fifth, sixth, and eighth authors: College of Life Sciences and Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring; seventh and eighth authors: Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Province University; and seventh author: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P.R. China
| | - Wenxiong Lin
- First, second, third, fourth, fifth, sixth, and eighth authors: College of Life Sciences and Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring; seventh and eighth authors: Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Province University; and seventh author: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P.R. China
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A Sustainable Agricultural Future Relies on the Transition to Organic Agroecological Pest Management. SUSTAINABILITY 2018. [DOI: 10.3390/su10062023] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Abstract
Rhizobia are some of the best-studied plant microbiota. These oligotrophic Alphaproteobacteria or Betaproteobacteria form symbioses with their legume hosts. Rhizobia must exist in soil and compete with other members of the microbiota before infecting legumes and forming N2-fixing bacteroids. These dramatic lifestyle and developmental changes are underpinned by large genomes and even more complex pan-genomes, which encompass the whole population and are subject to rapid genetic exchange. The ability to respond to plant signals and chemoattractants and to colonize nutrient-rich roots are crucial for the competitive success of these bacteria. The availability of a large body of genomic, physiological, biochemical and ecological studies makes rhizobia unique models for investigating community interactions and plant colonization.
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