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Cao J, An GS, Li RQ, Hou ZJ, Li J, Jin QQ, Du QX, Sun JH. Novel Strategy for Human Deep Vein Thrombosis Diagnosis Based on Metabolomics and Stacking Machine Learning. Anal Chem 2024; 96:14560-14570. [PMID: 39197159 DOI: 10.1021/acs.analchem.4c02973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2024]
Abstract
Deep vein thrombosis (DVT) is a serious health issue that often leads to considerable morbidity and mortality. Diagnosis of DVT in a clinical setting, however, presents considerable challenges. The fusion of metabolomics techniques and machine learning methods has led to high diagnostic and prognostic accuracy for various pathological conditions. This study explored the synergistic potential of dual-platform metabolomics (specifically, gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS)) to expand the detection of metabolites and improve the precision of DVT diagnosis. Sixty-one differential metabolites were identified in serum from DVT patients: 22 from GC-MS and 39 from LC-MS. Among these, five key metabolites were highlighted by SHapley Additive exPlanations (SHAP)-guided feature engineering and then used to develop a stacking diagnostic model. Additionally, a user-friendly interface application system was developed to streamline and automate the application of the diagnostic model, enhancing its practicality and accessibility for clinical use. This work showed that the integration of dual-platform metabolomics with a stacking machine learning model enables faster and more accurate diagnosis of DVT in clinical environments.
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Affiliation(s)
- Jie Cao
- School of Forensic Medicine, Shanxi Medical University, Yuci District, Jinzhong, Shanxi 030600, People's Republic of China
| | - Guo-Shuai An
- School of Forensic Medicine, Shanxi Medical University, Yuci District, Jinzhong, Shanxi 030600, People's Republic of China
| | - Rong-Qi Li
- School of Forensic Medicine, Shanxi Medical University, Yuci District, Jinzhong, Shanxi 030600, People's Republic of China
| | - Ze-Jin Hou
- School of Forensic Medicine, Shanxi Medical University, Yuci District, Jinzhong, Shanxi 030600, People's Republic of China
| | - Jian Li
- School of Forensic Medicine, Shanxi Medical University, Yuci District, Jinzhong, Shanxi 030600, People's Republic of China
| | - Qian-Qian Jin
- School of Forensic Medicine, Shanxi Medical University, Yuci District, Jinzhong, Shanxi 030600, People's Republic of China
| | - Qiu-Xiang Du
- School of Forensic Medicine, Shanxi Medical University, Yuci District, Jinzhong, Shanxi 030600, People's Republic of China
| | - Jun-Hong Sun
- School of Forensic Medicine, Shanxi Medical University, Yuci District, Jinzhong, Shanxi 030600, People's Republic of China
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Sun N, Yang AP, Wang SM, Zhu GL, Liu J, Wang TY, Wang ZJ, Qi BW, Liu XY, Lv SX, Li MH, Fu Q. Mechanism of synergistic remediation of soil phenanthrene contamination in paddy fields by rice-crab coculture and bioaugmentation with Pseudomonas sp. ENVIRONMENT INTERNATIONAL 2023; 182:108315. [PMID: 37963424 DOI: 10.1016/j.envint.2023.108315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/30/2023] [Accepted: 11/07/2023] [Indexed: 11/16/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are persistent and harmful pollutants with high priority concern in agricultural fields. This work constructed a rice-crab coculture and bioaugmentation (RCM) system to remediate phenanthrene (a model PAH) contamination in rice fields. The results showed that RCM had a higher remediation performance of phenanthrene in rice paddy compared with rice cultivation alone, microbial addition alone, and crab-rice coculture, reaching a remediation efficiency of 88.92 % in 42 d. The concentration of phenanthrene in the rice plants decreased to 6.58 mg/kg, and its bioconcentration effect was efficiently inhibited in the RCM system. In addition, some low molecular weight organic acids of rice root increased by 12.87 %∼73.87 %, and some amino acids increased by 140 %∼1150 % in RCM. Bioturbation of crabs improves soil aeration structure and microbial migration, and adding Pseudomonas promoted the proliferation of some plant growth-promoting rhizobacteria (PGPRs), which facilitated the degradation of phenanthrene. This coupling rice-crab coculture with bioaugmentation had favorable effects on soil enzyme activity, microbial community structure, and PAH degradation genes in paddy fields, enhancing the removal of and resistance to PAH contamination in paddy fields and providing new strategies for achieving a balance between production and remediation in contaminated paddy fields.
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Affiliation(s)
- Nan Sun
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Efficient Use of Agricultural Water Resources, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Northeast Agricultural University, Harbin 150030, China; Northeast Agricultural University/Heilongjiang Academy of Environmental Science Joint Postdoctoral Mobile Station, Harbin 150030, China
| | - An-Pei Yang
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin 150030, China; Research Center for Ecological Agriculture and Soil-Water Environment Restoration, Northeast Agricultural University, Harbin 150030, China
| | - Si-Ming Wang
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin 150030, China; Research Center for Ecological Agriculture and Soil-Water Environment Restoration, Northeast Agricultural University, Harbin 150030, China
| | - Guang-Lei Zhu
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin 150030, China; Research Center for Ecological Agriculture and Soil-Water Environment Restoration, Northeast Agricultural University, Harbin 150030, China
| | - Jin Liu
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin 150030, China; Research Center for Ecological Agriculture and Soil-Water Environment Restoration, Northeast Agricultural University, Harbin 150030, China
| | - Tian-Yi Wang
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin 150030, China; Research Center for Ecological Agriculture and Soil-Water Environment Restoration, Northeast Agricultural University, Harbin 150030, China
| | - Zi-Jian Wang
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin 150030, China; Research Center for Ecological Agriculture and Soil-Water Environment Restoration, Northeast Agricultural University, Harbin 150030, China
| | - Bo-Wei Qi
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin 150030, China; Research Center for Ecological Agriculture and Soil-Water Environment Restoration, Northeast Agricultural University, Harbin 150030, China
| | - Xin-Ying Liu
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin 150030, China; Research Center for Ecological Agriculture and Soil-Water Environment Restoration, Northeast Agricultural University, Harbin 150030, China
| | - Shao-Xuan Lv
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin 150030, China; Research Center for Ecological Agriculture and Soil-Water Environment Restoration, Northeast Agricultural University, Harbin 150030, China
| | - Ming-Hang Li
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin 150030, China; Research Center for Ecological Agriculture and Soil-Water Environment Restoration, Northeast Agricultural University, Harbin 150030, China
| | - Qiang Fu
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin 150030, China.
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Steinauer K, Thakur MP, Emilia Hannula S, Weinhold A, Uthe H, van Dam NM, Martijn Bezemer T. Root exudates and rhizosphere microbiomes jointly determine temporal shifts in plant-soil feedbacks. PLANT, CELL & ENVIRONMENT 2023; 46:1885-1899. [PMID: 36794528 DOI: 10.1111/pce.14570] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 01/10/2023] [Accepted: 02/13/2023] [Indexed: 05/04/2023]
Abstract
Plants influence numerous soil biotic factors that can alter the performance of later growing plants-defined as plant-soil feedback (PSF). Here, we investigate whether PSF effects are linked with the temporal changes in root exudate diversity and the rhizosphere microbiome of two common grassland species (Holcus lanatus and Jacobaea vulgaris). Both plant species were grown separately establishing conspecific and heterospecific soils. In the feedback phase, we determined plant biomass, measured root exudate composition, and characterised rhizosphere microbial communities weekly (eight time points). Over time, we found a strong negative conspecific PSF on J. vulgaris in its early growth phase which changed into a neutral PSF, whereas H. lanatus exhibited a more persistent negative PSF. Root exudate diversity increased considerably over time for both plant species. Rhizosphere microbial communities were distinct in conspecific and heterospecific soils and showed strong temporal patterns. Bacterial communities converged over time. Using path models, PSF effects could be linked to the temporal dynamics of root exudate diversity, whereby shifts in rhizosphere microbial diversity contributed to temporal variation in PSF to a lesser extent. Our results highlight the importance of root exudates and rhizosphere microbial communities in driving temporal changes in the strength of PSF effects.
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Affiliation(s)
- Katja Steinauer
- Department of Terrestrial Ecology, The Netherlands Institute of Ecology, Wageningen, The Netherlands
- Institute of Plant Science, University of Bern, Bern, Switzerland
| | - Madhav P Thakur
- Department of Terrestrial Ecology, The Netherlands Institute of Ecology, Wageningen, The Netherlands
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - S Emilia Hannula
- Department of Terrestrial Ecology, The Netherlands Institute of Ecology, Wageningen, The Netherlands
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | - Alexander Weinhold
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Henriette Uthe
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Nicole M van Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
- Molecular Interaction Ecology, Institute of Water and Wetland Research (IWWR), Radboud University, Nijmegen, The Netherlands
| | - T Martijn Bezemer
- Department of Terrestrial Ecology, The Netherlands Institute of Ecology, Wageningen, The Netherlands
- Section Plant Ecology and Phytochemistry, Institute of Biology, Leiden University, Leiden, The Netherlands
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McLaughlin S, Zhalnina K, Kosina S, Northen TR, Sasse J. The core metabolome and root exudation dynamics of three phylogenetically distinct plant species. Nat Commun 2023; 14:1649. [PMID: 36964135 PMCID: PMC10039077 DOI: 10.1038/s41467-023-37164-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 03/01/2023] [Indexed: 03/26/2023] Open
Abstract
Root exudates are plant-derived, exported metabolites likely shaping root-associated microbiomes by acting as nutrients and signals. However, root exudation dynamics are unclear and thus also, if changes in exudation are reflected in changes in microbiome structure. Here, we assess commonalities and differences between exudates of different plant species, diurnal exudation dynamics, as well as the accompanying methodological aspects of exudate sampling. We find that exudates should be collected for hours rather than days as many metabolite abundances saturate over time. Plant growth in sterile, nonsterile, or sugar-supplemented environments significantly alters exudate profiles. A comparison of Arabidopsis thaliana, Brachypodium distachyon, and Medicago truncatula shoot, root, and root exudate metabolite profiles reveals clear differences between these species, but also a core metabolome for tissues and exudates. Exudate profiles also exhibit a diurnal signature. These findings add to the methodological and conceptual groundwork for future exudate studies to improve understanding of plant-microbe interactions.
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Affiliation(s)
- Sarah McLaughlin
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology, Berkeley, CA, USA
- Institute for Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Kateryna Zhalnina
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology, Berkeley, CA, USA
| | - Suzanne Kosina
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology, Berkeley, CA, USA
| | - Trent R Northen
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology, Berkeley, CA, USA.
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Joelle Sasse
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology, Berkeley, CA, USA.
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Institute for Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.
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5
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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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6
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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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An Y, Sun H, Zhang W, Sun Y, Li S, Yu Z, Yang R, Hu T, Yang P. Distinct rhizosphere soil responses to nitrogen in relation to microbial biomass and community composition at initial flowering stages of alfalfa cultivars. FRONTIERS IN PLANT SCIENCE 2022; 13:938865. [PMID: 36092415 PMCID: PMC9449485 DOI: 10.3389/fpls.2022.938865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
In the long-term growth process, alfalfa rhizosphere forms specific microbiome to provide nutrition for its growth and development. However, the effects of different perennial alfalfa cultivars on changes in the rhizosphere soil characteristics and microbiome are not well understood. In this study, 12 perennial alfalfa cultivars were grown continuously for eight years. Rhizosphere samples were tested using Illumina sequencing of the 16S rRNA gene coupled with co-occurrence network analysis to explore the relationship between alfalfa (biomass and crude protein content), soil properties, and the microbial composition and diversity. Redundancy analysis showed SOC and pH had the greatest impact on the composition of the rhizosphere microbial community. Moreover, microbial diversity also contributes to microbial composition. Soil properties (AP, EC, SOC and pH) exhibited a significant positive correlation with soil bacterial communities, which was attributed to the differences between plant cultivars. Partial least squares path modeling (PLS-PM) revealed that microbial biomass and community composition rather than diversity, are the dominant determinants in the rhizosphere soil nitrogen content of perennial alfalfa. Our findings demonstrate that the soil microbial biomass and composition of rhizosphere bacterial communities are strongly affected by cultivar, driving the changes in soil nitrogen content, and variances in the selective capacities of plants.
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Affiliation(s)
- Yunru An
- College of Grassland Agriculture, Northwest A&F University, Xianyang, China
| | - Haoyang Sun
- College of Grassland Agriculture, Northwest A&F University, Xianyang, China
| | - Wei Zhang
- College of Grassland Agriculture, Northwest A&F University, Xianyang, China
| | - Yunfu Sun
- College of Grassland Agriculture, Northwest A&F University, Xianyang, China
| | - Shuxia Li
- College of Agricultural, Ningxia University, Yinchuan, China
| | - Zhouchang Yu
- College of Grassland Agriculture, Northwest A&F University, Xianyang, China
| | - Rongchen Yang
- College of Grassland Agriculture, Northwest A&F University, Xianyang, China
| | - Tianming Hu
- College of Grassland Agriculture, Northwest A&F University, Xianyang, China
| | - Peizhi Yang
- College of Grassland Agriculture, Northwest A&F University, Xianyang, China
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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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Clover Root Exudates Favor Novosphingobium sp. HR1a Establishment in the Rhizosphere and Promote Phenanthrene Rhizoremediation. mSphere 2021; 6:e0041221. [PMID: 34378981 PMCID: PMC8386446 DOI: 10.1128/msphere.00412-21] [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] [Indexed: 11/20/2022] Open
Abstract
Rhizoremediation is based on the ability of microorganisms to metabolize nutrients from plant root exudates and, thereby, to cometabolize or even mineralize toxic environmental contaminants. Novosphingobium sp. HR1a is a bacterial strain able to degrade a wide variety of polycyclic aromatic hydrocarbons (PAHs). Here, we have demonstrated that the number of CFU in microcosms vegetated with clover was almost 2 orders of magnitude higher than that in nonvegetated microcosms or microcosms vegetated with rye-grass or grass. Strain HR1a was able to eliminate 92% of the phenanthrene in the microcosms with clover after 9 days. We have studied the molecular basis of the interaction between strain HR1a and clover by phenomic, metabolomic, and transcriptomic analyses. By measuring the relative concentrations of several metabolites exudated by clover both in the presence and in the absence of the bacteria, we identified some compounds that were probably consumed in the rhizosphere; the transcriptomic analyses confirmed the expression of genes involved in the catabolism of these compounds. By using a transcriptional fusion of the green fluorescent protein (GFP) to the promoter of the gene encoding the dioxygenase involved in the degradation of PAHs, we have demonstrated that this gene is induced at higher levels in clover microcosms than in nonvegetated microcosms. Therefore, the positive interaction between clover and Novosphingobium sp. HR1a during rhizoremediation is a result of the bacterial utilization of different carbon and nitrogen sources released during seedling development and the capacity of clover exudates to induce the PAH degradation pathway. IMPORTANCE The success of an eco-friendly and cost-effective strategy for soil decontamination is conditioned by the understanding of the ecology of plant-microorganism interactions. Although many studies have been published about the bacterial metabolic capacities in the rhizosphere and about rhizoremediation of contaminants, there are fewer studies dealing with the integration of bacterial metabolic capacities in the rhizosphere during PAH bioremediation, and some aspects still remain controversial. Some authors have postulated that the presence of easily metabolizable carbon sources in root exudates might repress the expression of genes required for contaminant degradation, while others found that specific rhizosphere compounds can induce such genes. Novosphingobium sp. HR1a, which is our model organism, has two characteristics desirable in bacteria for use in remediation: its ubiquity and the capacity to degrade a wide variety of contaminants. We have demonstrated that this bacterium consumes several rhizospheric compounds without repression of the genes required for the mineralization of PAHs. In fact, some compounds even induced their expression.
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10
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Compton KK, Scharf BE. Rhizobial Chemoattractants, the Taste and Preferences of Legume Symbionts. FRONTIERS IN PLANT SCIENCE 2021; 12:686465. [PMID: 34017351 PMCID: PMC8129513 DOI: 10.3389/fpls.2021.686465] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 04/12/2021] [Indexed: 05/21/2023]
Abstract
The development of host-microbe interactions between legumes and their cognate rhizobia requires localization of the bacteria to productive sites of initiation on the plant roots. This end is achieved by the motility apparatus that propels the bacterium and the chemotaxis system that guides it. Motility and chemotaxis aid rhizobia in their competitiveness for space, resources, and nodulation opportunities. Here, we examine studies on chemotaxis of three major model rhizobia, namely Sinorhizobium meliloti, Rhizobium leguminosarum, and Bradyrhizobium japonicum, cataloging their range of attractant molecules and correlating this in the context of root and seed exudate compositions. Current research areas will be summarized, gaps in knowledge discussed, and future directions described.
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Affiliation(s)
| | - Birgit E. Scharf
- Department of Biological Sciences, Life Sciences I, Virginia Tech, Blacksburg, VA, United States
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11
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Delory BM, Schempp H, Spachmann SM, Störzer L, van Dam NM, Temperton VM, Weinhold A. Soil chemical legacies trigger species-specific and context-dependent root responses in later arriving plants. PLANT, CELL & ENVIRONMENT 2021; 44:1215-1230. [PMID: 33455010 DOI: 10.1111/pce.13999] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 01/06/2021] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Soil legacies play an important role for the creation of priority effects. However, we still poorly understand to what extent the metabolome found in the soil solution of a plant community is conditioned by its species composition and whether soil chemical legacies affect subsequent species during assembly. To test these hypotheses, we collected soil solutions from forb or grass communities and evaluated how the metabolome of these soil solutions affected the growth, biomass allocation and functional traits of a forb (Dianthus deltoides) and a grass species (Festuca rubra). Results showed that the metabolomes found in the soil solutions of forb and grass communities differed in composition and chemical diversity. While soil chemical legacies did not have any effect on F. rubra, root foraging by D. deltoides decreased when plants received the soil solution from a grass or a forb community. Structural equation modelling showed that reduced soil exploration by D. deltoides arose via either a root growth-dependent pathway (forb metabolome) or a root trait-dependent pathway (grass metabolome). Reduced root foraging was not connected to a decrease in total N uptake. Our findings reveal that soil chemical legacies can create belowground priority effects by affecting root foraging in later arriving plants.
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Affiliation(s)
- Benjamin M Delory
- Ecosystem Functioning and Services, Institute of Ecology, Leuphana University of Lüneburg, Lüneburg, Germany
| | - Hannes Schempp
- Ecosystem Functioning and Services, Institute of Ecology, Leuphana University of Lüneburg, Lüneburg, Germany
| | - Sina Maria Spachmann
- Ecosystem Functioning and Services, Institute of Ecology, Leuphana University of Lüneburg, Lüneburg, Germany
| | - Laura Störzer
- Ecosystem Functioning and Services, Institute of Ecology, Leuphana University of Lüneburg, Lüneburg, Germany
| | - Nicole M van Dam
- Molecular Interaction Ecology, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Vicky M Temperton
- Ecosystem Functioning and Services, Institute of Ecology, Leuphana University of Lüneburg, Lüneburg, Germany
| | - Alexander Weinhold
- Molecular Interaction Ecology, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
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12
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Highly Species-Specific Foliar Metabolomes of Diverse Woody Species and Relationships with the Leaf Economics Spectrum. Cells 2021; 10:cells10030644. [PMID: 33805842 PMCID: PMC7999030 DOI: 10.3390/cells10030644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/08/2021] [Accepted: 03/10/2021] [Indexed: 11/17/2022] Open
Abstract
Plants show an extraordinary diversity in chemical composition and are characterized by different functional traits. However, relationships between the foliar primary and specialized metabolism in terms of metabolite numbers and composition as well as links with the leaf economics spectrum have rarely been explored. We investigated these relationships in leaves of 20 woody species from the Mediterranean region grown as saplings in a common garden, using a comparative ecometabolomics approach that included (semi-)polar primary and specialized metabolites. Our analyses revealed significant positive correlations between both the numbers and relative composition of primary and specialized metabolites. The leaf metabolomes were highly species-specific but in addition showed some phylogenetic imprints. Moreover, metabolomes of deciduous species were distinct from those of evergreens. Significant relationships were found between the primary metabolome and nitrogen content and carbon/nitrogen ratio, important traits of the leaf economics spectrum, ranging from acquisitive (mostly deciduous) to conservative (evergreen) leaves. A comprehensive understanding of various leaf traits and their coordination in different plant species may facilitate our understanding of plant functioning in ecosystems. Chemodiversity is thereby an important component of biodiversity.
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13
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Hoang SA, Lamb D, Seshadri B, Sarkar B, Choppala G, Kirkham MB, Bolan NS. Rhizoremediation as a green technology for the remediation of petroleum hydrocarbon-contaminated soils. JOURNAL OF HAZARDOUS MATERIALS 2021; 401:123282. [PMID: 32634659 DOI: 10.1016/j.jhazmat.2020.123282] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 05/22/2023]
Abstract
Rhizoremediation is increasingly becoming a green and sustainable alternative to physico-chemical methods for remediation of contaminated environments through the utilization of symbiotic relationship between plants and their associated soil microorganisms in the root zone. The overall efficiency can be enhanced by identifying suitable plant-microbe combinations for specific contaminants and supporting the process with the application of appropriate soil amendments. This approach not only involves promoting the existing activity of plants and soil microbes, but also introduces an adequate number of microorganisms with specific catabolic activity. Here, we reviewed recent literature on the main mechanisms and key factors in the rhizoremediation process with a particular focus on soils contaminated with total petroleum hydrocarbon (TPH). We then discuss the potential of different soil amendments to accelerate the remediation efficiency based on biostimulation and bioaugmentation processes. Notwithstanding some successes in well-controlled environments, rhizoremediation of TPH under field conditions is still not widespread and considered less attractive than physico-chemical methods. We catalogued the major pitfalls of this remediation approach at the field scale in TPH-contaminated sites and, provide some applicable situations for the future successful use of in situ rhizoremediation of TPH-contaminated soils.
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Affiliation(s)
- Son A Hoang
- Global Centre for Environmental Remediation (GCER), Advanced Technology Centre (ATC) Building, Faculty of Science, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia; Division of Urban Infrastructural Engineering, Mien Trung University of Civil Engineering, Phu Yen 56000, Viet Nam
| | - Dane Lamb
- Global Centre for Environmental Remediation (GCER), Advanced Technology Centre (ATC) Building, Faculty of Science, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Balaji Seshadri
- Global Centre for Environmental Remediation (GCER), Advanced Technology Centre (ATC) Building, Faculty of Science, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Binoy Sarkar
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom
| | - Girish Choppala
- Global Centre for Environmental Remediation (GCER), Advanced Technology Centre (ATC) Building, Faculty of Science, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - M B Kirkham
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Nanthi S Bolan
- Global Centre for Environmental Remediation (GCER), Advanced Technology Centre (ATC) Building, Faculty of Science, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia.
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14
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Dietz S, Herz K, Gorzolka K, Jandt U, Bruelheide H, Scheel D. Root exudate composition of grass and forb species in natural grasslands. Sci Rep 2020; 10:10691. [PMID: 32612150 PMCID: PMC7329890 DOI: 10.1038/s41598-019-54309-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 09/25/2019] [Indexed: 11/08/2022] Open
Abstract
Plants exude a diverse cocktail of metabolites into the soil as response to exogenous and endogenous factors. So far, root exudates have mainly been studied under artificial conditions due to methodological difficulties. In this study, each five perennial grass and forb species were investigated for polar and semi-polar metabolites in exudates under field conditions. Metabolite collection and untargeted profiling approaches combined with a novel classification method allowed the designation of 182 metabolites. The composition of exuded polar metabolites depended mainly on the local environment, especially soil conditions, whereas the pattern of semi-polar metabolites was primarily affected by the species identity. The profiles of both polar and semi-polar metabolites differed between growth forms, with grass species being generally more similar to each other and more responsive to the abiotic environment than forb species. This study demonstrated the feasibility of investigating exudates under field conditions and to identify the driving factors of exudate composition.
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Affiliation(s)
- Sophie Dietz
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany.
| | - Katharina Herz
- Martin Luther University Halle-Wittenberg, Institute of Biology/Geobotany and Botanical Garden, Am Kirchtor 1, 06108, Halle [Saale], Germany
| | - Karin Gorzolka
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Ute Jandt
- Martin Luther University Halle-Wittenberg, Institute of Biology/Geobotany and Botanical Garden, Am Kirchtor 1, 06108, Halle [Saale], Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Helge Bruelheide
- Martin Luther University Halle-Wittenberg, Institute of Biology/Geobotany and Botanical Garden, Am Kirchtor 1, 06108, Halle [Saale], Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Dierk Scheel
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
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15
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Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands. ISME JOURNAL 2019; 14:463-475. [PMID: 31659233 PMCID: PMC6976627 DOI: 10.1038/s41396-019-0543-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/14/2019] [Accepted: 10/16/2019] [Indexed: 12/25/2022]
Abstract
The active bacterial rhizobiomes and root exudate profiles of phytometers of six plant species growing in central European temperate grassland communities were investigated in three regions located up to 700 km apart, across diverse edaphic conditions and along a strong land use gradient. The recruitment process from bulk soil communities was identified as the major direct driver of the composition of active rhizosphere bacterial communities. Unexpectedly, the effect of soil properties, particularly soil texture, water content, and soil type, strongly dominated over plant properties and the composition of polar root exudates of the primary metabolism. While plant species-specific selection of bacteria was minor, the RNA-based composition of active rhizosphere bacteria substantially differed between rhizosphere and bulk soil. Although other variables could additionally be responsible for the consistent enrichment of particular bacteria in the rhizosphere, distinct bacterial OTUs were linked to the presence of specific polar root exudates independent of individual plant species. Our study also identified numerous previously unknown taxa that are correlated with rhizosphere dynamics and hence represent suitable targets for future manipulations of the plant rhizobiome.
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16
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Welk A, Welk E, Baudis M, Böckelmann J, Bruelheide H. Plant species' range type determines local responses to biotic interactions and land use. Ecology 2019; 100:e02890. [PMID: 31509229 DOI: 10.1002/ecy.2890] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/24/2019] [Accepted: 07/22/2019] [Indexed: 12/24/2022]
Abstract
Geographic plant distribution is often assumed to be predominantly limited directly by the climatic tolerances of species. However, the role of climate is now known to be mainly an indirect one mostly mediating dispersal and establishment, species interactions, or habitat characteristics, which all are often modified by human land use. In these complex systems, negative biotic interactions are predicted to increase in relative importance toward benign climatic conditions. We tested this hypothesis experimentally by exposing plant species with different geographic distribution ranges to different climates, biotic interactions, and land use. Thereby, species predominantly distributed in regions with benign climatic conditions were expected to be better able to cope with negative biotic interactions than species from regions with environmentally stressful climatic conditions. We present results of a fully crossed two-year transplantation field experiment replicated in 45 plots in three study regions along a precipitation gradient across Germany. We manipulated biotic interactions (presence/absence of competition and mollusk herbivory) in grasslands of different management regimes (meadows, mown pastures, pastures). The transplanted phytometers consisted of six congeneric species pairs, each representing one oceanic and one distinctly more continental range type. The oceanic range type is predominantly distributed in benign climatic conditions in Western Europe, while the more continental type is distributed in regions with more stressful climatic conditions in Eastern Europe. This experimental setting allowed us to study the impact of negative biotic interactions along an abiotic stress gradient under realistic land-use conditions. Under competition and mollusk herbivory, growth performance was more strongly reduced in continental compared to oceanic species. Range types also differed in their responses to grassland management. Differences in survival between the congeneric species were found to be region-specific and largely unaffected by biotic interactions and land use. In consequence, our results suggest that local responses to biotic interactions and land-use practices of otherwise very similar plant species can differ strongly depending on species' large-scale geographical distribution. Regionally differing responses to biotic interactions also show that local conditions can drastically change responses expected from macroecological theory.
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Affiliation(s)
- Astrid Welk
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, D-06108, Halle (Saale), Germany
| | - Erik Welk
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, D-06108, Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103, Leipzig, Germany
| | - Mathias Baudis
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, D-06108, Halle (Saale), Germany
| | - Jörg Böckelmann
- Department of Botany and Biodiversity Research, Division of Tropical Ecology and Animal Biodiversity, University of Vienna, Rennweg 14, A-1030, Wien, Austria
| | - Helge Bruelheide
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, D-06108, Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103, Leipzig, Germany
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