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Agarwal P, Vibhandik R, Agrahari R, Daverey A, Rani R. Role of Root Exudates on the Soil Microbial Diversity and Biogeochemistry of Heavy Metals. Appl Biochem Biotechnol 2024; 196:2673-2693. [PMID: 37191824 DOI: 10.1007/s12010-023-04465-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2023] [Indexed: 05/17/2023]
Abstract
Due to extensive industrialization and escalation in pollution, the world is facing problems related to soil heavy metal pollution. The traditional ways of soil remediation are neither feasible nor cost-effective in most of the real-world scenarios, where metal concentration is relatively low in soil. Therefore, phytoremediation using plants and plant secretions to remediate heavy metal-contaminated soil is recently getting more attention. The plant root exudates act as an ecological driver in the rhizospheric region where they influence and guide the microbial community to function in such a way that can be advantageous for plant growth. They also promote phytoremediation process by altering the bioavailability of pollutants in soil. Root exudates affect the biogeochemical properties of heavy metals as well. In this review, existing literature on the role of root exudates (natural as well as artificial) on the phytoremediation of heavy metal-contaminated (particularly lead) soil is reviewed. The effect of root exudates on the biogeochemistry of lead in soil is also discussed.
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Affiliation(s)
- Priyanka Agarwal
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, Teliyarganj, Uttar Pradesh, 211004, India
| | - Rutuja Vibhandik
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, Teliyarganj, Uttar Pradesh, 211004, India
| | - Roma Agrahari
- Department of Biochemical Engineering, Harcourt Butler Technical University, Kanpur, Uttar Pradesh, 208002, India
| | - Achlesh Daverey
- School of Environment and Natural Resources, Doon University, Dehradun, Uttarakhand, 248001, India
| | - Radha Rani
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, Teliyarganj, Uttar Pradesh, 211004, India.
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Eroğlu ÇG, Bennett AA, Steininger-Mairinger T, Hann S, Puschenreiter M, Wirth J, Gfeller A. Neighbour-induced changes in root exudation patterns of buckwheat results in altered root architecture of redroot pigweed. Sci Rep 2024; 14:8679. [PMID: 38622223 PMCID: PMC11018816 DOI: 10.1038/s41598-024-58687-3] [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: 11/29/2023] [Accepted: 04/02/2024] [Indexed: 04/17/2024] Open
Abstract
Roots are crucial in plant adaptation through the exudation of various compounds which are influenced and modified by environmental factors. Buckwheat root exudate and root system response to neighbouring plants (buckwheat or redroot pigweed) and how these exudates affect redroot pigweed was investigated. Characterising root exudates in plant-plant interactions presents challenges, therefore a split-root system which enabled the application of differential treatments to parts of a single root system and non-destructive sampling was developed. Non-targeted metabolome profiling revealed that neighbour presence and identity induces systemic changes. Buckwheat and redroot pigweed neighbour presence upregulated 64 and 46 metabolites, respectively, with an overlap of only 7 metabolites. Root morphology analysis showed that, while the presence of redroot pigweed decreased the number of root tips in buckwheat, buckwheat decreased total root length and volume, surface area, number of root tips, and forks of redroot pigweed. Treatment with exudates (from the roots of buckwheat and redroot pigweed closely interacting) on redroot pigweed decreased the total root length and number of forks of redroot pigweed seedlings when compared to controls. These findings provide understanding of how plants modify their root exudate composition in the presence of neighbours and how this impacts each other's root systems.
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Affiliation(s)
- Çağla Görkem Eroğlu
- Herbology in Field Crops, Plant Production Systems, Agroscope, Nyon, Switzerland
| | - Alexandra A Bennett
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190, Vienna, Austria
| | - Teresa Steininger-Mairinger
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190, Vienna, Austria
| | - Stephan Hann
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190, Vienna, Austria
| | - Markus Puschenreiter
- Department of Forest and Soil Sciences, Institute of Soil Research, Rhizosphere Ecology & Biogeochemistry Group, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 24, 3430, Tulln, Austria
| | - Judith Wirth
- Herbology in Field Crops, Plant Production Systems, Agroscope, Nyon, Switzerland
| | - Aurélie Gfeller
- Herbology in Field Crops, Plant Production Systems, Agroscope, Nyon, Switzerland.
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Mészárošová L, Kuťáková E, Kohout P, Münzbergová Z, Baldrian P. Plant effects on microbiome composition are constrained by environmental conditions in a successional grassland. ENVIRONMENTAL MICROBIOME 2024; 19:8. [PMID: 38268048 PMCID: PMC10809484 DOI: 10.1186/s40793-024-00550-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
BACKGROUND Below-ground microbes mediate key ecosystem processes and play a vital role in plant nutrition and health. Understanding the composition of the belowground microbiome is therefore important for maintaining ecosystem stability. The structure of the belowground microbiome is largely determined by individual plants, but it is not clear how far their influence extends and, conversely, what the influence of other plants growing nearby is. RESULTS To determine the extent to which a focal host plant influences its soil and root microbiome when growing in a diverse community, we sampled the belowground bacterial and fungal communities of three plant species across a primary successional grassland sequence. The magnitude of the host effect on its belowground microbiome varied among microbial groups, soil and root habitats, and successional stages characterized by different levels of diversity of plant neighbours. Soil microbial communities were most strongly structured by sampling site and showed significant spatial patterns that were partially driven by soil chemistry. The influence of focal plant on soil microbiome was low but tended to increase with succession and increasing plant diversity. In contrast, root communities, particularly bacterial, were strongly structured by the focal plant species. Importantly, we also detected a significant effect of neighbouring plant community composition on bacteria and fungi associating with roots of the focal plants. The host influence on root microbiome varied across the successional grassland sequence and was highest in the most diverse site. CONCLUSIONS Our results show that in a species rich natural grassland, focal plant influence on the belowground microbiome depends on environmental context and is modulated by surrounding plant community. The influence of plant neighbours is particularly pronounced in root communities which may have multiple consequences for plant community productivity and stability, stressing the importance of plant diversity for ecosystem functioning.
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Affiliation(s)
- Lenka Mészárošová
- Institute of Microbiology of the CAS, v. v. i., Vídeňská 1083, Prague 4, 142 20, Czech Republic.
- University of Chemistry and Technology, Technická 5, Praha 6, 166 28, Czech Republic.
| | - Eliška Kuťáková
- Institute of Botany of the CAS, v. v. i., Zámek 1, Průhonice, 252 43, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague 2, 128 01, Czech Republic
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Skogsmarksgränd 17, Umeå, 901 83, Sweden
| | - Petr Kohout
- Institute of Microbiology of the CAS, v. v. i., Vídeňská 1083, Prague 4, 142 20, Czech Republic
| | - Zuzana Münzbergová
- Institute of Botany of the CAS, v. v. i., Zámek 1, Průhonice, 252 43, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague 2, 128 01, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the CAS, v. v. i., Vídeňská 1083, Prague 4, 142 20, Czech Republic
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Ndour PMS, Bargaz A, Rchiad Z, Pawlett M, Clark IM, Mauchline TH, Harris J, Lyamlouli K. Microbial Catabolic Activity: Methods, Pertinence, and Potential Interest for Improving Microbial Inoculant Efficiency. MICROBIAL ECOLOGY 2023; 86:2211-2230. [PMID: 37280438 DOI: 10.1007/s00248-023-02250-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/24/2023] [Indexed: 06/08/2023]
Abstract
Microbial catabolic activity (MCA) defined as the degrading activity of microorganisms toward various organic compounds for their growth and energy is commonly used to assess soil microbial function potential. For its measure, several methods are available including multi-substrate-induced respiration (MSIR) measurement which allow to estimate functional diversity using selected carbon substrates targeting specific biochemical pathways. In this review, the techniques used to measure soil MCA are described and compared with respect to their accuracy and practical use. Particularly the efficiency of MSIR-based approaches as soil microbial function indicators was discussed by (i) showing their sensitivity to different agricultural practices including tillage, amendments, and cropping systems and (ii) by investigating their relationship with soil enzyme activities and some soil chemical properties (pH, soil organic carbon, cation exchange capacity). We highlighted the potential of these MSIR-based MCA measurements to improve microbial inoculant composition and to determine their potential effects on soil microbial functions. Finally, we have proposed ideas for improving MCA measurement notably through the use of molecular tools and stable isotope probing which can be combined with classic MSIR methods. Graphical abstract describing the interrelation between the different parts and the concepts developed in the review.
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Affiliation(s)
- Papa Mamadou Sitor Ndour
- College for Sustainable Agriculture and Environmental Sciences, AgroBioSciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco.
- Cranfield Soil and AgriFood Institute, School of Applied Sciences, Cranfield University, Cranfield, MK43 0AL, UK.
| | - Adnane Bargaz
- College for Sustainable Agriculture and Environmental Sciences, AgroBioSciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Zineb Rchiad
- Institute of Biological Sciences (ISSB), Faculty of Medical Sciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Mark Pawlett
- Cranfield Soil and AgriFood Institute, School of Applied Sciences, Cranfield University, Cranfield, MK43 0AL, UK
| | - Ian M Clark
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Tim H Mauchline
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Jim Harris
- Cranfield Soil and AgriFood Institute, School of Applied Sciences, Cranfield University, Cranfield, MK43 0AL, UK
| | - Karim Lyamlouli
- College for Sustainable Agriculture and Environmental Sciences, AgroBioSciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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Subrahmaniam HJ, Lind Salomonsen C, Radutoiu S, Ehlers BK, Glasius M. Unraveling the secrets of plant roots: Simplified method for large scale root exudate sampling and analysis in Arabidopsis thaliana. OPEN RESEARCH EUROPE 2023; 3:12. [PMID: 37645513 PMCID: PMC10445920 DOI: 10.12688/openreseurope.15377.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/18/2023] [Indexed: 08/31/2023]
Abstract
Background Plants exude a plethora of compounds to communicate with their environment. Although much is known about above-ground plant communication, we are only beginning to fathom the complexities of below-ground chemical communication channels. Studying root-exuded compounds and their role in plant communication has been difficult due to the lack of standardized methodologies. Here, we develop an interdisciplinary workflow to explore the natural variation in root exudate chemical composition of the model plant Arabidopsis thaliana. We highlight key challenges associated with sampling strategies and develop a framework for analyzing both narrow- and broad-scale patterns of root exudate composition in a large set of natural A. thaliana accessions. Methods Our method involves cultivating individual seedlings in vitro inside a plastic mesh, followed by a short hydroponic sampling period in small quantities of ultrapure water. The mesh makes it easy to handle plants of different sizes and allows for large-scale characterization of individual plant root exudates under axenic conditions. This setup can also be easily extended for prolonged temporal exudate collection experiments. Furthermore, the short sampling time minimizes the duration of the experiment while still providing sufficient signal even with small volume of the sampling solution. We used ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS) for untargeted metabolic profiling, followed by tentative compound identification using MZmine3 and SIRIUS 5 software, to capture a broad overview of root exudate composition in A. thaliana accessions. Results Based on 28 replicates of the Columbia genotype (Col-0) compared with 10 random controls, MZmine3 annotated 354 metabolites to be present only in Col-0 by negative ionization. Of these, 254 compounds could be annotated by SIRIUS 5 software. Conclusions The methodology developed in this study can be used to broadly investigate the role of root exudates as chemical signals in plant belowground interactions.
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Affiliation(s)
- Harihar Jaishree Subrahmaniam
- Department of Ecoscience, Aarhus University, 8000 Aarhus C, Denmark
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
- Department of Molecular Biology and Genetics - Plant Molecular Biology, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Simona Radutoiu
- Department of Molecular Biology and Genetics - Plant Molecular Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Bodil K. Ehlers
- Department of Ecoscience, Aarhus University, 8000 Aarhus C, Denmark
| | - Marianne Glasius
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
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Rathore N, Hanzelková V, Dostálek T, Semerád J, Schnablová R, Cajthaml T, Münzbergová Z. Species phylogeny, ecology, and root traits as predictors of root exudate composition. THE NEW PHYTOLOGIST 2023. [PMID: 37421208 DOI: 10.1111/nph.19060] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/04/2023] [Indexed: 07/10/2023]
Abstract
Root traits including root exudates are key factors affecting plant interactions with soil and thus play an important role in determining ecosystem processes. The drivers of their variation, however, remain poorly understood. We determined the relative importance of phylogeny and species ecology in determining root traits and analyzed the extent to which root exudate composition can be predicted by other root traits. We measured different root morphological and biochemical traits (including exudate profiles) of 65 plant species grown in a controlled system. We tested phylogenetic conservatism in traits and disentangled the individual and overlapping effects of phylogeny and species ecology on traits. We also predicted root exudate composition using other root traits. Phylogenetic signal differed greatly among root traits, with the strongest signal in phenol content in plant tissues. Interspecific variation in root traits was partly explained by species ecology, but phylogeny was more important in most cases. Species exudate composition could be partly predicted by specific root length, root dry matter content, root biomass, and root diameter, but a large part of variation remained unexplained. In conclusion, root exudation cannot be easily predicted based on other root traits and more comparative data on root exudation are needed to understand their diversity.
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Affiliation(s)
- Nikita Rathore
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czech Republic
| | - Věra Hanzelková
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Albertov 6, 128 00, Prague, Czech Republic
| | - Tomáš Dostálek
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Albertov 6, 128 00, Prague, Czech Republic
| | - Jaroslav Semerád
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czech Republic
| | - Renáta Schnablová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czech Republic
| | - Tomáš Cajthaml
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czech Republic
| | - Zuzana Münzbergová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Albertov 6, 128 00, Prague, Czech Republic
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Volynchikova E, Kim KD. Anti-Oomycete Activity and Pepper Root Colonization of Pseudomonas plecoglossicida YJR13 and Pseudomonas putida YJR92 against Phytophthora capsici. THE PLANT PATHOLOGY JOURNAL 2023; 39:123-135. [PMID: 36760054 PMCID: PMC9929162 DOI: 10.5423/ppj.oa.01.2023.0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/17/2023] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Previously, Pseudomonas plecoglossicida YJR13 and Pseudomonas putida YJR92 from a sequential screening procedure were proven to effectively control Phytophthora blight caused by Phytophthora capsici. In this study, we further investigated the anti-oomycete activities of these strains against mycelial growth, zoospore germination, and germ tube elongation of P. capsici. We also investigated root colonization ability of the bacterial strains in square dishes, including cell motility (swimming and swarming motilities) and biofilm formation. Both strains significantly inhibited mycelial growth in liquid and solid V8 juice media and M9 minimal media, zoospore germination, and germ tube elongation compared with Bacillus vallismortis EXTN-1 (positive biocontrol strain), Sphingomonas aquatilis KU408 (negative biocontrol strain), and MgSO4 solution (untreated control). In diluted (nutrient-deficient) V8 juice broth, the tested strain populations were maintained at >108 cells/ml, simultaneously providing mycelial inhibitory activity. Additionally, these strains colonized pepper roots at a 106 cells/ml concentration for 7 days. The root colonization of the strains was supported by strong swimming and swarming activities, biofilm formation, and chemotactic activity towards exudate components (amino acids, organic acids, and sugars) of pepper roots. Collectively, these results suggest that strains YJR13 and YJR92 can effectively suppress Phytophthora blight of pepper through direct anti-oomycete activities against mycelial growth, zoospore germination and germ tube elongation. Bacterial colonization of pepper roots may be mediated by cell motility and biofilm formation together with chemotaxis to root exudates.
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Affiliation(s)
| | - Ki Deok Kim
- Corresponding author: Phone) +82-2-3290-3065, FAX) +82-2-925-1970, E-mail)
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Lohse M, Santangeli M, Steininger-Mairinger T, Oburger E, Reemtsma T, Lechtenfeld OJ, Hann S. The effect of root hairs on exudate composition: a comparative non-targeted metabolomics approach. Anal Bioanal Chem 2023; 415:823-840. [PMID: 36547703 PMCID: PMC9883335 DOI: 10.1007/s00216-022-04475-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/10/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022]
Abstract
Root exudation is a major pathway of organic carbon input into soils. It affects soil physical properties, element solubility as well as speciation, and impacts the microbial community in the rhizosphere. Root exudates contain a large number of primary and secondary plant metabolites, and the amount and composition are highly variable depending on plant species and developmental stage. Detailed information about exudate composition will allow for a better understanding of exudate-driven rhizosphere processes and their feedback loops. Although non-targeted metabolomics by high-resolution mass spectrometry is an established tool to characterize root exudate composition, the extent and depth of the information obtained depends strongly on the analytical approach applied. Here, two genotypes of Zea mays L., differing in root hair development, were used to compare six mass spectrometric approaches for the analysis of root exudates. Reversed-phase liquid chromatography and hydrophilic interaction liquid chromatography combined with time-of-flight mass spectrometry (LC-TOF-MS), as well as direct infusion Fourier-transform ion cyclotron resonance mass spectrometry (DI-FT-ICR-MS), were applied with positive and negative ionization mode. By using the same statistical workflow, the six approaches resulted in different numbers of detected molecular features, ranging from 176 to 889, with a fraction of 48 to 69% of significant features (fold change between the two genotypes of > 2 and p-value < 0.05). All approaches revealed the same trend between genotypes, namely up-regulation of most metabolites in the root hair defective mutant (rth3). These results were in agreement with the higher total carbon and nitrogen exudation rate of the rth3-mutant as compared to the corresponding wild-type maize (WT). However, only a small fraction of features were commonly found across the different analytical approaches (20-79 features, 13-31% of the rth3-mutant up-regulated molecular formulas), highlighting the need for different mass spectrometric approaches to obtain a more comprehensive view into the composition of root exudates. In summary, 111 rth3-mutant up-regulated compounds (92 different molecular formulas) were detected with at least two different analytical approaches, while no WT up-regulated compound was found by both, LC-TOF-MS and DI-FT-ICR-MS. Zea mays L. exudate features obtained with multiple analytical approaches in our study were matched against the metabolome database of Zea mays L. (KEGG) and revealed 49 putative metabolites based on their molecular formula.
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Affiliation(s)
- Martin Lohse
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research - UFZ, 04318, Leipzig, Germany
| | - Michael Santangeli
- Department of Forest and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna (BOKU), 3430, Tulln an Der Donau, Austria
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190, Vienna, Austria
| | - Teresa Steininger-Mairinger
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190, Vienna, Austria
| | - Eva Oburger
- Department of Forest and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna (BOKU), 3430, Tulln an Der Donau, Austria.
| | - Thorsten Reemtsma
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research - UFZ, 04318, Leipzig, Germany
- Institute of Analytical Chemistry, University of Leipzig, 04103, Leipzig, Germany
| | - Oliver J Lechtenfeld
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research - UFZ, 04318, Leipzig, Germany.
- ProVIS, Centre for Chemical Microscopy, Helmholtz Centre for Environmental Research, UFZ, 04318, Leipzig, Germany.
| | - Stephan Hann
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190, Vienna, Austria
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Ghatak A, Chaturvedi P, Waldherr S, Subbarao GV, Weckwerth W. PANOMICS at the interface of root-soil microbiome and BNI. TRENDS IN PLANT SCIENCE 2023; 28:106-122. [PMID: 36229336 DOI: 10.1016/j.tplants.2022.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 08/10/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Nitrification and denitrification are soil biological processes responsible for large nitrogen losses from agricultural soils and generation of the greenhouse gas (GHG) N2O. Increased use of nitrogen fertilizer and the resulting decline in nitrogen use efficiency (NUE) are a major concern in agroecosystems. This nitrogen cycle in the rhizosphere is influenced by an intimate soil microbiome-root exudate interaction and biological nitrification inhibition (BNI). A PANOMICS approach can dissect these processes. We review breakthroughs in this area, including identification and characterization of root exudates by metabolomics and proteomics, which facilitate better understanding of belowground chemical communications and help identify new biological nitrification inhibitors (BNIs). We also address challenges for advancing the understanding of the role root exudates play in biotic and abiotic stresses.
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Affiliation(s)
- Arindam Ghatak
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria.
| | - Steffen Waldherr
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Guntur Venkata Subbarao
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Ibaraki 305-8686, Japan
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria.
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Heuermann D, Döll S, Schweneker D, Feuerstein U, Gentsch N, von Wirén N. Distinct metabolite classes in root exudates are indicative for field- or hydroponically-grown cover crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1122285. [PMID: 37089658 PMCID: PMC10118039 DOI: 10.3389/fpls.2023.1122285] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
Introduction Plants release a large variety of metabolites via their roots to shape physico-chemical soil properties and biological processes in the rhizosphere. While hydroponic growth conditions facilitate accessibility of the root system and recovery of root exudates, the natural soil environment can alter root metabolism and exudate secretion, raising the question to what extent the quantity and composition of root exudates released in hydroponic growth systems reflect those recovered from soil-grown roots. Methods Using a root washing method, we sampled root exudates from four field-grown cover crop species with wide taxonomic distance, namely white mustard, lacy phacelia, bristle oat, and Egyptian clover. A set of primary metabolites and secondary metabolites were analysed in a targeted and untargeted LC-MS-based approach, respectively, for comparison with exudates obtained from hydroponically cultured plants. Results and discussion We found that hydroponically cultivated plants released a larger amount of total carbon, but that the recovery of total carbon was not indicative for the diversity of metabolites in root exudates. In the field, root exudates from phacelia and clover contained 2.4 to 3.8 times more secondary metabolites, whereas carbon exudation in hydroponics was 5- to 4-fold higher. The composition of the set of metabolites identified using the untargeted approach was much more distinct among all species and growth conditions than that of quantified primary metabolites. Among secondary metabolite classes, the presence of lipids and lipid-like molecules was highly indicative for field samples, while the release of a large amount of phenylpropanoids, organoheterocyclic compounds or benzenoids was characteristic for clover, mustard or oat, respectively, irrespective of the cultivation condition. However, at the compound level the bulk of released metabolites was specific for cultivation conditions in every species, which implies that hydroponically sampled root exudates poorly reflect the metabolic complexity of root exudates recovered from field-grown plants.
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Affiliation(s)
- Diana Heuermann
- Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, Seeland, Germany
| | - Stefanie Döll
- Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Dörte Schweneker
- Deutsche Saatveredelung Aktiengesellschaft (AG), Asendorf, Germany
| | - Ulf Feuerstein
- Deutsche Saatveredelung Aktiengesellschaft (AG), Asendorf, Germany
| | - Norman Gentsch
- Institute of Soil Science, Leibniz Universität Hannover, Hannover, Germany
| | - Nicolaus von Wirén
- Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, Seeland, Germany
- *Correspondence: Nicolaus von Wirén,
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Whalen ED, Grandy AS, Sokol NW, Keiluweit M, Ernakovich J, Smith RG, Frey SD. Clarifying the evidence for microbial- and plant-derived soil organic matter, and the path toward a more quantitative understanding. GLOBAL CHANGE BIOLOGY 2022; 28:7167-7185. [PMID: 36043234 DOI: 10.1111/gcb.16413] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
Predicting and mitigating changes in soil carbon (C) stocks under global change requires a coherent understanding of the factors regulating soil organic matter (SOM) formation and persistence, including knowledge of the direct sources of SOM (plants vs. microbes). In recent years, conceptual models of SOM formation have emphasized the primacy of microbial-derived organic matter inputs, proposing that microbial physiological traits (e.g., growth efficiency) are dominant controls on SOM quantity. However, recent quantitative studies have challenged this view, suggesting that plants make larger direct contributions to SOM than is currently recognized by this paradigm. In this review, we attempt to reconcile these perspectives by highlighting that variation across estimates of plant- versus microbial-derived SOM may arise in part from methodological limitations. We show that all major methods used to estimate plant versus microbial contributions to SOM have substantial shortcomings, highlighting the uncertainty in our current quantitative estimates. We demonstrate that there is significant overlap in the chemical signatures of compounds produced by microbes, plant roots, and through the extracellular decomposition of plant litter, which introduces uncertainty into the use of common biomarkers for parsing plant- and microbial-derived SOM, especially in the mineral-associated organic matter (MAOM) fraction. Although the studies that we review have contributed to a deeper understanding of microbial contributions to SOM, limitations with current methods constrain quantitative estimates. In light of recent advances, we suggest that now is a critical time to re-evaluate long-standing methods, clearly define their limitations, and develop a strategic plan for improving the quantification of plant- and microbial-derived SOM. From our synthesis, we outline key questions and challenges for future research on the mechanisms of SOM formation and stabilization from plant and microbial pathways.
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Affiliation(s)
- Emily D Whalen
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - A Stuart Grandy
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Noah W Sokol
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Marco Keiluweit
- School of Earth & Sustainability and Stockbridge School of Agriculture, University of Massachusetts, Amherst, Massachusetts, USA
| | - Jessica Ernakovich
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Richard G Smith
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Serita D Frey
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
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12
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Mishra AK, Sudalaimuthuasari N, Hazzouri KM, Saeed EE, Shah I, Amiri KMA. Tapping into Plant-Microbiome Interactions through the Lens of Multi-Omics Techniques. Cells 2022; 11:3254. [PMID: 36291121 PMCID: PMC9600287 DOI: 10.3390/cells11203254] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 10/21/2023] Open
Abstract
This review highlights the pivotal role of root exudates in the rhizosphere, especially the interactions between plants and microbes and between plants and plants. Root exudates determine soil nutrient mobilization, plant nutritional status, and the communication of plant roots with microbes. Root exudates contain diverse specialized signaling metabolites (primary and secondary). The spatial behavior of these metabolites around the root zone strongly influences rhizosphere microorganisms through an intimate compatible interaction, thereby regulating complex biological and ecological mechanisms. In this context, we reviewed the current understanding of the biological phenomenon of allelopathy, which is mediated by phytotoxic compounds (called allelochemicals) released by plants into the soil that affect the growth, survival, development, ecological infestation, and intensification of other plant species and microbes in natural communities or agricultural systems. Advances in next-generation sequencing (NGS), such as metagenomics and metatranscriptomics, have opened the possibility of better understanding the effects of secreted metabolites on the composition and activity of root-associated microbial communities. Nevertheless, understanding the role of secretory metabolites in microbiome manipulation can assist in designing next-generation microbial inoculants for targeted disease mitigation and improved plant growth using the synthetic microbial communities (SynComs) tool. Besides a discussion on different approaches, we highlighted the advantages of conjugation of metabolomic approaches with genetic design (metabolite-based genome-wide association studies) in dissecting metabolome diversity and understanding the genetic components of metabolite accumulation. Recent advances in the field of metabolomics have expedited comprehensive and rapid profiling and discovery of novel bioactive compounds in root exudates. In this context, we discussed the expanding array of metabolomics platforms for metabolome profiling and their integration with multivariate data analysis, which is crucial to explore the biosynthesis pathway, as well as the regulation of associated pathways at the gene, transcript, and protein levels, and finally their role in determining and shaping the rhizomicrobiome.
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Affiliation(s)
- Ajay Kumar Mishra
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Naganeeswaran Sudalaimuthuasari
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Khaled M. Hazzouri
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Esam Eldin Saeed
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Iltaf Shah
- Department of Chemistry (Biochemistry), College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Khaled M. A. Amiri
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
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13
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Murillo-Roos M, Abdullah HSM, Debbar M, Ueberschaar N, Agler MT. Cross-feeding niches among commensal leaf bacteria are shaped by the interaction of strain-level diversity and resource availability. THE ISME JOURNAL 2022; 16:2280-2289. [PMID: 35768644 PMCID: PMC9381498 DOI: 10.1038/s41396-022-01271-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 05/20/2022] [Accepted: 06/10/2022] [Indexed: 12/27/2022]
Abstract
Leaf microbiomes play crucial roles in plant health, making it important to understand the origins and functional relevance of their diversity. High strain-level leaf bacterial genetic diversity is known to be relevant for interactions with hosts, but little is known about its relevance for interactions with the multitude of diverse co-colonizing microorganisms. In leaves, nutrients like amino acids are major regulators of microbial growth and activity. Using metabolomics of leaf apoplast fluid, we found that different species of the plant genus Flaveria considerably differ in the concentrations of high-cost amino acids. We investigated how these differences affect bacterial community diversity and assembly by enriching leaf bacteria in vitro with only sucrose or sucrose + amino acids as possible carbon sources. Enrichments from F. robusta were dominated by Pantoea sp. and Pseudomonas sp., regardless of carbon source. The latter was unable to grow on sucrose alone but persisted in the sucrose-only enrichment thanks to exchange of diverse metabolites from Pantoea sp. Individual Pseudomonas strains in the enrichments had high genetic similarity but still displayed clear niche partitioning, enabling distinct strains to cross-feed in parallel. Pantoea strains were also closely related, but individuals enriched from F. trinervia fed Pseudomonas more poorly than those from F. robusta. This can be explained in part by the plant environment, since some cross-feeding interactions were selected for, when experimentally evolved in a poor (sucrose-only) environment but selected against in a rich (sucrose + amino acids) one. Together, our work shows that leaf bacterial diversity is functionally relevant in cross-feeding interactions and strongly suggests that the leaf resource environment can shape these interactions and thereby indirectly drive bacterial diversity.
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Affiliation(s)
- Mariana Murillo-Roos
- Plant Microbiosis Lab, Department of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Hafiz Syed M Abdullah
- Plant Microbiosis Lab, Department of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Mossaab Debbar
- Plant Microbiosis Lab, Department of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Nico Ueberschaar
- Mass Spectrometry Platform, Friedrich Schiller University Jena, Jena, Germany
| | - Matthew T Agler
- Plant Microbiosis Lab, Department of Microbiology, Friedrich Schiller University Jena, Jena, Germany.
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14
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Panchal P, Preece C, Peñuelas J, Giri J. Soil carbon sequestration by root exudates. TRENDS IN PLANT SCIENCE 2022; 27:749-757. [PMID: 35606255 DOI: 10.1016/j.tplants.2022.04.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 04/22/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Root exudates are well-known 'labile' sources of soil carbon that can prime microbial activity. Recent investigations suggest that the stability of labile carbon inputs in soil mostly depends upon the physical, chemical, and biological properties of the surroundings. Here, we propose that, in some ecosystems, such as forests and grasslands, root exudates can function as a source of soil organic carbon (SOC) that can be stabilized through various mechanisms leading to long-term sequestration. Increasing soil carbon sequestration is important for capturing atmospheric CO2 and combating climate change issues. Thus, there is an urgent need to preserve existing ecosystems and to adopt strategies such as afforestation, reforestation, and establishment of artificial grasslands to foster carbon sequestration through higher root exudate inputs in the soil.
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Affiliation(s)
- Poonam Panchal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Catherine Preece
- Plants and Ecosystems (PLECO), Biology Department, University of Antwerp, BE-2610 Wilrijk, Belgium; CREAF, Cerdanyola del Vallès 08193, Catalonia, Spain
| | - Josep Peñuelas
- CREAF, Cerdanyola del Vallès 08193, Catalonia, Spain; CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra 08193, Catalonia, Spain
| | - Jitender Giri
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
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15
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Maity S, Guchhait R, Sarkar MB, Pramanick K. Occurrence and distribution of micro/nanoplastics in soils and their phytotoxic effects: A review. PLANT, CELL & ENVIRONMENT 2022; 45:1011-1028. [PMID: 35060135 DOI: 10.1111/pce.14248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/06/2021] [Accepted: 11/25/2021] [Indexed: 06/14/2023]
Abstract
Some recent studies have reviewed the occurrence and phytotoxicity of micro/nanoplastics, but their distribution in the soil environment, mechanisms of uptake by roots and the mode of action are unclear. Thus, this review comprehensively represents the relative abundance of micro/nanoplastics in different soil types and their toxicities in plants with insights into their partitioning to different soil matrices, uptake mechanisms, and the mode of action. Partitioning of micro/nanoplastics to different soil matrices (like-soil particles, naturally occurring soil organic matters, pore waters and soil fauna) could modify their bioavailability to plants. The small micro/nanoplastic particles can be taken up by roots through the apoplastic and symplastic pathways. In this regard, cellular endocytosis and aquaporin might play a significant role. The shape of the polymers can also regulate their uptake, and the polymers with spherical shapes are more easily absorbed by roots than the polymers with other shapes. Bioaccumulation of micro/nanoplastic induces oxidative stress, which, in turn, causes alterations of gene expressions and different metabolic pathways responsible for plant growth, biomass production and synthesis of secondary metabolites.
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Affiliation(s)
- Sukhendu Maity
- Integrative Biology Research Unit (IBRU) Lab, Department of Life Sciences, Presidency University, Kolkata, India
| | - Rajkumar Guchhait
- Integrative Biology Research Unit (IBRU) Lab, Department of Life Sciences, Presidency University, Kolkata, India
- Department of Zoology, Mahishadal Raj College, Purba Medinipur, India
| | | | - Kousik Pramanick
- Integrative Biology Research Unit (IBRU) Lab, Department of Life Sciences, Presidency University, Kolkata, India
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16
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Field Studies on the Effect of Bioaugmentation with Bacillus amyloliquefaciens FZB42 on Plant Accumulation of Rare Earth Elements and Selected Trace Elements. MINERALS 2022. [DOI: 10.3390/min12040409] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This study is an investigation of the effect of soil bioaugmentation (inoculation) on a field scale with the commercially available product RhizoVital®42, containing Bacillus amyloliquefaciens FZB4, on element bioavailability, plant biomass production, as well as accumulation of rare earth elements (REEs), germanium, and selected trace elements. Zea mays and Helianthus annuus were selected as test plants. Post-harvest, results showed inoculation increased biomass production of Z. mays and H. annuus by 24% and 26%, albeit insignificant at p ≤ 0.05. Bioaugmentation enhanced Z. mays shoot content of P, Cd, and Ge by percentages between 73% and 80% (significant only for Ge) and decreased shoot content of REET, Pb, and Cu by 28%, 35%, and 59%, respectively. For H. annuus grown on bioaugmented soil, shoot content of Ca, Cu, Ge, REET, and Pb increased by over 40%, with a negligible decrease observed for Cd. Summarily, results suggest that bioaugmentation with Bacillus amyloliquefaciens FZB42 could enhance biomass production, increase soil element bioavailability enhance, and increase or reduce plant accumulation of target elements. Additionally, differences in P use efficiency could influence bioaugmentation effects on P accumulation.
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17
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Naeem I, Asif T, Zhang T, Guan Y, Wu X, Tariq H, Wang D. Mixing effects of three Eurasian plants on root decomposition in the existence of living plant community in a meadow steppe. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 811:151400. [PMID: 34742802 DOI: 10.1016/j.scitotenv.2021.151400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 06/13/2023]
Abstract
In grasslands, roots of different plant species decay in combination in the presence of living plants, besides, most root decomposition studies are conducted on how roots of plants decomposed alone or in artificial compositions in the absence of living plants. Therefore, we evaluated how roots of different perennial plants induced effects on decomposition process under living plants and their associated mechanisms. By using litter bag technique, we determined the root decomposition process of three perennial plants, Leymus chinensis, Phragmites australis, and Kalimeris integrifolia grown in monocultures, bi- and tri-species mixtures, after 12 months of incubation under living plants and bare soil communities. We found both additive and non-additive effects on decomposition dynamics indicating that root mass losses of compositions cannot be calculated from decaying rates of individual species. The rich-nutrient roots of K. integrifolia in monocultures and in mixtures with other plant species decayed faster. Compared with bare soil, microbial activities were enhanced under living plant communities and hence stimulated decomposition rates. Our results indicated that microbial activities are important but secondary factors to root physico-chemical properties impacting root decomposition rates. In conclusion, the empirical relationships developed here are helpful to better understand the effects of root properties and microbial activities on decay rates.
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Affiliation(s)
- Iqra Naeem
- Institute of Grassland Science/School of Environment, Key Laboratory of Vegetation Ecology, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Northeast Normal University, Changchun, Jilin 130024, PR China
| | - Talal Asif
- Peatland Ecology Research Group (PERG), Centre for Northern Studies, Department of Plant Sciences, Université Laval, Quebec, Québec, Canada
| | - Tianyu Zhang
- Institute of Grassland Science/School of Environment, Key Laboratory of Vegetation Ecology, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Northeast Normal University, Changchun, Jilin 130024, PR China
| | - Yue Guan
- Institute of Grassland Science/School of Environment, Key Laboratory of Vegetation Ecology, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Northeast Normal University, Changchun, Jilin 130024, PR China
| | - Xuefeng Wu
- Institute of Grassland Science/School of Environment, Key Laboratory of Vegetation Ecology, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Northeast Normal University, Changchun, Jilin 130024, PR China
| | - Hina Tariq
- Department of Forestry and Range Management, PMAS Arid Agriculture University, Rawalpindi 46300, Pakistan
| | - Deli Wang
- Institute of Grassland Science/School of Environment, Key Laboratory of Vegetation Ecology, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Northeast Normal University, Changchun, Jilin 130024, PR China.
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18
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Geisen S, Heinen R, Andreou E, van Lent T, ten Hooven FC, Thakur MP. Contrasting effects of soil microbial interactions on growth-defence relationships between early- and mid-successional plant communities. THE NEW PHYTOLOGIST 2022; 233:1345-1357. [PMID: 34242435 PMCID: PMC9292498 DOI: 10.1111/nph.17609] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
Plants allocate resources to processes related to growth and enemy defence. Simultaneously, they interact with complex soil microbiomes that also affect plant performance. While the influence of individual microbial groups on single plants is increasingly studied, effects of microbial interactions on growth, defence and growth-defence relationships remain unknown, especially at the plant community level. We investigated how three microbial groups (bacteria, fungi, protists), alone and in full-factorial combinations, affect plant performance and potential growth-defence relationships by measuring phenolics composition in early- and mid-successional grass and forb communities in a glasshouse experiment. Microbial groups did not affect plant growth and only fungi increased defence compounds in early- and mid-successional forbs, while grasses were not affected. Shoot biomass-defence relationships were negatively correlated in most microbial treatments in early-successional forbs, but positively in several microbial treatments in mid-successional forbs. The growth-defence relationship was generally negative in early-successional but not in mid-successional grasses. The presence of different microbiomes commonly removed the observed growth-defence relationships. We conclude that soil microorganisms and their interactions can shift growth-defence relationships differentially for plant functional groups and the relationships vary between successional stages. Microbial interaction-induced growth-defence shifts might therefore underlie distinct plant strategies and fitness.
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Affiliation(s)
- Stefan Geisen
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)Wageningen6708PBthe Netherlands
- Laboratory of NematologyWageningen UniversityWageningen6708PBthe Netherlands
| | - Robin Heinen
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)Wageningen6708PBthe Netherlands
- Lehrstuhl für Terrestrische Ökologie, Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und UmweltTechnische Universität MünchenFreising85354Germany
| | - Elena Andreou
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)Wageningen6708PBthe Netherlands
| | - Teun van Lent
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)Wageningen6708PBthe Netherlands
- Laboratory of NematologyWageningen UniversityWageningen6708PBthe Netherlands
| | - Freddy C. ten Hooven
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)Wageningen6708PBthe Netherlands
| | - Madhav P. Thakur
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)Wageningen6708PBthe Netherlands
- Institute of Ecology and EvolutionUniversity of BernBern3012Switzerland
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19
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Semchenko M, Xue P, Leigh T. Functional diversity and identity of plant genotypes regulate rhizodeposition and soil microbial activity. THE NEW PHYTOLOGIST 2021; 232:776-787. [PMID: 34235741 DOI: 10.1111/nph.17604] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Our understanding of the linkages between plant diversity and soil carbon and nutrient cycling is primarily derived from studies at the species level, while the importance and mechanisms of diversity effects at the genotype level are poorly understood. Here we examine how genotypic diversity and identity, and associated variation in functional traits, within a common grass species, Anthoxanthum odoratum, modified rhizodeposition, soil microbial activity and litter decomposition. Root litter quality was not significantly affected by plant genotypic diversity, but decomposition was enhanced in soils with the legacy of higher genotypic diversity. Plant genotypic diversity and identity modified rhizodeposition and associated microbial activity via two independent pathways. Plant genotypic diversity enhanced soil functioning via positive effects on variation in specific leaf area and total rhizodeposition. Genotype identity affected both rhizodeposit quantity and quality, and these effects were mediated by differences in mean specific leaf area, shoot mass and plant height. Rhizodeposition was more strongly predicted by aboveground than belowground traits, suggesting strong linkages between photosynthesis and root exudation. Our study demonstrates that functional diversity and identity of plant genotypes modulates belowground carbon supply and quality, representing an important but overlooked pathway by which biodiversity affects ecosystem functioning.
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Affiliation(s)
- Marina Semchenko
- Department of Earth and Environmental Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Piao Xue
- Department of Earth and Environmental Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
- Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Tokyo, 153-8902, Japan
| | - Tomas Leigh
- Department of Earth and Environmental Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
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20
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Rolli E, Vergani L, Ghitti E, Patania G, Mapelli F, Borin S. 'Cry-for-help' in contaminated soil: a dialogue among plants and soil microbiome to survive in hostile conditions. Environ Microbiol 2021; 23:5690-5703. [PMID: 34139059 PMCID: PMC8596516 DOI: 10.1111/1462-2920.15647] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/25/2021] [Accepted: 06/16/2021] [Indexed: 12/20/2022]
Abstract
An open question in environmental ecology regards the mechanisms triggered by root chemistry to drive the assembly and functionality of a beneficial microbiome to rapidly adapt to stress conditions. This phenomenon, originally described in plant defence against pathogens and predators, is encompassed in the ‘cry‐for‐help’ hypothesis. Evidence suggests that this mechanism may be part of the adaptation strategy to ensure the holobiont fitness in polluted environments. Polychlorinated biphenyls (PCBs) were considered as model pollutants due to their toxicity, recalcitrance and poor phyto‐extraction potential, which lead to a plethora of phytotoxic effects and rise environmental safety concerns. Plants have inefficient detoxification processes to catabolize PCBs, even leading to by‐products with a higher toxicity. We propose that the ‘cry‐for‐help’ mechanism could drive the exudation‐mediated recruitment and sustainment of the microbial services for PCBs removal, exerted by an array of anaerobic and aerobic microbial degrading populations working in a complex metabolic network. Through this synergistic interaction, the holobiont copes with the soil contamination, releasing the plant from the pollutant stress by the ecological services provided by the boosted metabolism of PCBs microbial degraders. Improving knowledge of root chemistry under PCBs stress is, therefore, advocated to design rhizoremediation strategies based on plant microbiome engineering.
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Affiliation(s)
- Eleonora Rolli
- Department of Food, Environmental and Nutritional Sciences, DeFENS, University of Milan, Via Celoria 2, Milan, 20133, Italy
| | - Lorenzo Vergani
- Department of Food, Environmental and Nutritional Sciences, DeFENS, University of Milan, Via Celoria 2, Milan, 20133, Italy
| | - Elisa Ghitti
- Department of Food, Environmental and Nutritional Sciences, DeFENS, University of Milan, Via Celoria 2, Milan, 20133, Italy
| | - Giovanni Patania
- Department of Food, Environmental and Nutritional Sciences, DeFENS, University of Milan, Via Celoria 2, Milan, 20133, Italy
| | - Francesca Mapelli
- Department of Food, Environmental and Nutritional Sciences, DeFENS, University of Milan, Via Celoria 2, Milan, 20133, Italy
| | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences, DeFENS, University of Milan, Via Celoria 2, Milan, 20133, Italy
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21
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Li H, Bölscher T, Winnick M, Tfaily MM, Cardon ZG, Keiluweit M. Simple Plant and Microbial Exudates Destabilize Mineral-Associated Organic Matter via Multiple Pathways. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:3389-3398. [PMID: 33587629 DOI: 10.1021/acs.est.0c04592] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Most mineral-associated organic matter (MAOM) is protected against microbial attack, thereby contributing to long-term carbon storage in soils. However, the extent to which reactive compounds released by plants and microbes may destabilize MAOM and so enhance microbial access, as well as the underlying mechanisms, remain unclear. Here, we tested the ability of functionally distinct model exudates-ligands, reductants, and simple sugars-to promote microbial utilization of monomeric MAOM, bound via outer-sphere complexes to common iron and aluminum (hydr)oxide minerals. The strong ligand oxalic acid induced rapid MAOM mineralization, coinciding with greater sorption to and dissolution of minerals, suggestive of direct MAOM mobilization mechanisms. In contrast, the simple sugar glucose caused slower MAOM mineralization, but stimulated microbial activity and metabolite production, indicating an indirect microbially-mediated mechanism. Catechol, acting as reductant, promoted both mechanisms. While MAOM on ferrihydrite showed the greatest vulnerability to both direct and indirect mechanisms, MAOM on other (hydr)oxides was more susceptible to direct mechanisms. These findings suggest that MAOM persistence, and thus long-term carbon storage within a given soil, is not just a function of mineral reactivity but also depends on the capacity of plant roots and associated microbes to produce reactive compounds capable of triggering specific destabilization mechanisms.
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Affiliation(s)
- Hui Li
- Stockbridge School of Agriculture and School of Earth & Sustainability, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Tobias Bölscher
- Stockbridge School of Agriculture and School of Earth & Sustainability, University of Massachusetts, Amherst, Massachusetts 01003, United States
- Department of Biology, Lund University, 223 62 Lund, Sweden
| | - Matthew Winnick
- Department of Geosciences, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Malak M Tfaily
- Department of Environmental Science, University of Arizona, Tucson, Arizona 85719, United States
| | - Zoe G Cardon
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, United States
| | - Marco Keiluweit
- Stockbridge School of Agriculture and School of Earth & Sustainability, University of Massachusetts, Amherst, Massachusetts 01003, United States
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22
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Volkov V, Schwenke H. A Quest for Mechanisms of Plant Root Exudation Brings New Results and Models, 300 Years after Hales. PLANTS 2020; 10:plants10010038. [PMID: 33375713 PMCID: PMC7823307 DOI: 10.3390/plants10010038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 12/27/2022]
Abstract
The review summarizes some of our current knowledge on the phenomenon of exudation from the cut surface of detached roots with emphasis on results that were mostly established over the last fifty years. The phenomenon is quantitatively documented in the 18th century (by Hales in 1727). By the 19th century, theories mainly ascribed exudation to the secretion of living root cells. The 20th century favored the osmometer model of root exudation. Nevertheless, growing insights into the mechanisms of water transport and new or rediscovered observations stimulated the quest for a more adequate exudation model. The historical overview shows how understanding of exudation changed with time following experimental opportunities and novel ideas from different areas of knowledge. Later theories included cytoskeleton-dependent micro-pulsations of turgor in root cells to explain the observed water exudation. Recent progress in experimental biomedicine led to detailed study of channels and transporters for ion transport via cellular membranes and to the discovery of aquaporins. These universal molecular entities have been incorporated to the more complex models of water transport via plant roots. A new set of ideas and explanations was based on cellular osmoregulation by mechanosensitive ion channels. Thermodynamic calculations predicted the possibility of water transport against osmotic forces based on co-transport of water with ions via cation-chloride cotransporters. Recent observations of rhizodermis exudation, exudation of roots without an external aqueous medium, segments cut from roots, pulses of exudation, a phase shifting of water uptake and exudation, and of effects of physiologically active compounds (like ion channel blockers, metabolic agents, and cytoskeletal agents) will likely refine our understanding of the phenomenon. So far, it seems that more than one mechanism is responsible for root pressure and root exudation, processes which are important for refilling of embolized xylem vessels. However, recent advances in ion and water transport research at the molecular level suggest potential future directions to understanding of root exudation and new models awaiting experimental testing.
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Affiliation(s)
- Vadim Volkov
- Department of Plant Sciences, College of Agricultural and Environmental Sciences, University of California, Davis, CA 95616, USA
- K.A. Timiriazev Institute of Plant Physiology RAS, 35 Botanicheskaya St., Moscow 127276, Russia
- Correspondence: (V.V.); (H.S.)
| | - Heiner Schwenke
- Max Planck Institute for the History of Science, Boltzmannstraße 22, 14195 Berlin, Germany
- Correspondence: (V.V.); (H.S.)
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