1
|
Geyer JK, Grunberg RL, Wang J, Mitchell CE. Leaf age structures phyllosphere microbial communities in the field and greenhouse. Front Microbiol 2024; 15:1429166. [PMID: 39206365 PMCID: PMC11349622 DOI: 10.3389/fmicb.2024.1429166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024] Open
Abstract
The structure of the leaf microbiome can alter host fitness and change in response to abiotic and biotic factors, like seasonality, climate, and leaf age. However, relatively few studies consider the influence of host age on microbial communities at a time scale of a few days, a short time scale relevant to microbes. To understand how host age modulates changes in the fungal and bacterial leaf microbiome on a short time scale, we ran independent field and greenhouse-based studies and characterized phyllosphere communities using next-generation sequencing approaches. Our field study characterized changes in the fungal and bacterial phyllosphere by examining leaves of different relative ages across individuals, whereas the greenhouse study examined changes in the fungal microbiome by absolute leaf age across individuals. Together, these results indicate that fungal communities are susceptible to change as a leaf ages as evidenced by shifts in the diversity of fungal taxa both in the field and the greenhouse. Similarly, there were increases in the diversity of fungal taxa by leaf age in the greenhouse. In bacterial communities in the field, we observed changes in the diversity, composition, and relative abundance of common taxa. These findings build upon previous literature characterizing host-associated communities at longer time scales and provide a foundation for targeted work examining how specific microbial taxa might interact with each other, such as fine-scale interactions between pathogenic and non-pathogenic species.
Collapse
Affiliation(s)
- Julie K. Geyer
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Rita L. Grunberg
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Wilson Center for Science and Justice at Duke Law, Durham, NC, United States
| | - Jeremy Wang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Charles E. Mitchell
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Environment, Ecology, and Energy Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| |
Collapse
|
2
|
Poupin MJ, González B. Embracing complexity in plant-microbiome systems. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e70000. [PMID: 39189551 PMCID: PMC11348195 DOI: 10.1111/1758-2229.70000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 07/27/2024] [Indexed: 08/28/2024]
Abstract
Despite recent advances in understanding the role of microorganisms in plant holobiont metabolism, physiology, and fitness, several relevant questions are yet to be answered, with implications for ecology, evolution, and sustainable agriculture. This article explores some of these questions and discusses emerging research areas in plant microbiomes. Firstly, it emphasizes the need to move beyond taxonomic characterization towards understanding microbial functions within plant ecosystems. Secondly, controlling methodological biases and enhancing OMICS technologies' standardization is imperative for a deeper comprehension of plant-microbiota interactions. Furthermore, while plant microbiota research has primarily centred on bacteria and fungi, other microbial players such as archaea, viruses, and microeukaryotes have been largely overlooked. Emerging evidence highlights their presence and potential roles, underscoring the need for thorough assessments. Future research should aim to elucidate the ecological microbial interactions, their impact on plant performance, and how the plant context shapes microbial community dynamics. Finally, a discussion is provided on how the multiple layers of abiotic and biotic factors influencing the spatiotemporal dynamics of plant-microbiome systems require in-depth attention. Examples illustrate how synthetic communities and computational methods such as machine learning and artificial intelligence provide alternatives to tackle these challenges and analyse the plant holobiont as a complex system.
Collapse
Affiliation(s)
- María Josefina Poupin
- Laboratorio de Bioingeniería, Facultad de Ingeniería y CienciasUniversidad Adolfo IbáñezSantiagoChile
- Center of Applied Ecology and Sustainability (CAPES)SantiagoChile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN‐SAP)SantiagoChile
| | - Bernardo González
- Laboratorio de Bioingeniería, Facultad de Ingeniería y CienciasUniversidad Adolfo IbáñezSantiagoChile
- Center of Applied Ecology and Sustainability (CAPES)SantiagoChile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN‐SAP)SantiagoChile
| |
Collapse
|
3
|
Zhang Y, Gan G, Li Y, Li W, Jiang Y, Wang P, Hu J, Wang N, Quan X, Liu J, Raza W, Xu Y, Hohmann P, Jousset A, Wang Y, Shen Q, Jiang G, Wei Z. Exploring the temporal dynamics of a disease suppressive rhizo-microbiome in eggplants. iScience 2024; 27:110319. [PMID: 39055957 PMCID: PMC11269921 DOI: 10.1016/j.isci.2024.110319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/03/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024] Open
Abstract
The rhizosphere microbiome is important for plant health, yet their contributions to disease resistance and assembly dynamics remain unclear. This study employed rhizosphere microbiome transplantation (RMT) to delineate the impact of the rhizosphere microbiome and the immune response of eggplant (Solanum melongena) on resistance to bacterial wilt caused by Ralstonia solanacearum. We first identified disease-suppressive and disease-conducive rhizosphere microbiome in a susceptible tomato recipient. Using a non-destructive rhizobox and 16S rRNA amplicon sequencing, we monitored the dynamics of both microbiome types during the eggplant development. Most differences were observed at the early stage and then diminished over time. The suppressive microbiome maintained a higher proportion of initial community members throughout eggplant development and exhibited stronger deterministic processes in the early stage, underscoring the importance of plant selection in recruiting protective microbes for rhizosphere immunity. Our study sheds light on the development of microbiome-based strategies for plant disease management and resistance breeding.
Collapse
Affiliation(s)
- Yuling Zhang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Guiyun Gan
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530000, China
| | - Yarong Li
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Weiliu Li
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530000, China
| | - Yaqin Jiang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530000, China
| | - Peng Wang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530000, China
| | - Jie Hu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, the Netherlands
| | - Ningqi Wang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaowen Quan
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Jialin Liu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Waseem Raza
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Yangchun Xu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Pierre Hohmann
- Department of Biology, Healthcare and the Environment, Universitat de Barcelona, 08028 Barcelona, Spain
- BonaPlanta, 08241 Manresa, Spain
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Yikui Wang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530000, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Gaofei Jiang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530000, China
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
4
|
Tyborski N, Koehler T, Steiner FA, Tung SY, Wild AJ, Carminati A, Mueller CW, Vidal A, Wolfrum S, Pausch J, Lueders T. Consistent prokaryotic community patterns along the radial root axis of two Zea mays L. landraces across two distinct field locations. Front Microbiol 2024; 15:1386476. [PMID: 39091306 PMCID: PMC11292614 DOI: 10.3389/fmicb.2024.1386476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 06/25/2024] [Indexed: 08/04/2024] Open
Abstract
The close interconnection of plants with rhizosphere- and root-associated microorganisms is well recognized, and high expectations are raised for considering their symbioses in the breeding of future crop varieties. However, it is unclear how consistently plant-mediated selection, a potential target in crop breeding, influences microbiome members compared to selection imposed by the agricultural environment. Landraces may have traits shaping their microbiome, which were lost during the breeding of modern varieties, but knowledge about this is scarce. We investigated prokaryotic community composition along the radial root axis of two European maize (Zea mays L.) landraces. A sampling gradient included bulk soil, a distal and proximal rhizosphere fraction, and the root compartment. Our study was replicated at two field locations with differing edaphic and climatic conditions. Further, we tested for differences between two plant developmental stages and two precipitation treatments. Community data were generated by metabarcoding of the V4 SSU rRNA region. While communities were generally distinct between field sites, the effects of landrace variety, developmental stage, and precipitation treatment were comparatively weak and not statistically significant. Under all conditions, patterns in community composition corresponded strongly to the distance to the root. Changes in α- and β-diversity, as well as abundance shifts of many taxa along this gradient, were similar for both landraces and field locations. Most affected taxa belonged to a core microbiome present in all investigated samples. Remarkably, we observed consistent enrichment of Actinobacteriota (particularly Streptomyces, Lechevalieria) and Pseudomonadota (particularly Sphingobium) toward the root. Further, we report a depletion of ammonia-oxidizers along this axis at both field sites. We identified clear enrichment and depletion patterns in microbiome composition along the radial root axis of Z. mays. Many of these were consistent across two distinct field locations, plant developmental stages, precipitation treatments, and for both landraces. This suggests a considerable influence of plant-mediated effects on the microbiome. We propose that the affected taxa have key roles in the rhizosphere and root microbiome of Z. mays. Understanding the functions of these taxa appears highly relevant for the development of methods aiming to promote microbiome services for crops.
Collapse
Affiliation(s)
- Nicolas Tyborski
- Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Tina Koehler
- Root-Soil Interaction, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Franziska A. Steiner
- Soil Science, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Shu-Yin Tung
- Institute for Agroecology and Organic Farming, Bavarian State Research Center for Agriculture (LfL), Freising, Germany
- TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Andreas J. Wild
- Agroecology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Andrea Carminati
- Physics of Soils and Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Carsten W. Mueller
- Soil Science, Institute of Ecology, Technical University of Berlin, Berlin, Germany
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
| | - Alix Vidal
- Soil Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Sebastian Wolfrum
- Institute for Agroecology and Organic Farming, Bavarian State Research Center for Agriculture (LfL), Freising, Germany
| | - Johanna Pausch
- Agroecology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Tillmann Lueders
- Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| |
Collapse
|
5
|
Jorrin B, Haskett TL, Knights HE, Martyn A, Underwood TJ, Dolliver J, Ledermann R, Poole PS. Stable, fluorescent markers for tracking synthetic communities and assembly dynamics. MICROBIOME 2024; 12:81. [PMID: 38715147 PMCID: PMC11075435 DOI: 10.1186/s40168-024-01792-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/09/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND After two decades of extensive microbiome research, the current forefront of scientific exploration involves moving beyond description and classification to uncovering the intricate mechanisms underlying the coalescence of microbial communities. Deciphering microbiome assembly has been technically challenging due to their vast microbial diversity but establishing a synthetic community (SynCom) serves as a key strategy in unravelling this process. Achieving absolute quantification is crucial for establishing causality in assembly dynamics. However, existing approaches are primarily designed to differentiate a specific group of microorganisms within a particular SynCom. RESULTS To address this issue, we have developed the differential fluorescent marking (DFM) strategy, employing three distinguishable fluorescent proteins in single and double combinations. Building on the mini-Tn7 transposon, DFM capitalises on enhanced stability and broad applicability across diverse Proteobacteria species. The various DFM constructions are built using the pTn7-SCOUT plasmid family, enabling modular assembly, and facilitating the interchangeability of expression and antibiotic cassettes in a single reaction. DFM has no detrimental effects on fitness or community assembly dynamics, and through the application of flow cytometry, we successfully differentiated, quantified, and tracked a diverse six-member SynCom under various complex conditions like root rhizosphere showing a different colonisation assembly dynamic between pea and barley roots. CONCLUSIONS DFM represents a powerful resource that eliminates dependence on sequencing and/or culturing, thereby opening new avenues for studying microbiome assembly. Video Abstract.
Collapse
Affiliation(s)
- Beatriz Jorrin
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK.
| | - Timothy L Haskett
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Hayley E Knights
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Anna Martyn
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Thomas J Underwood
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Jessica Dolliver
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Raphael Ledermann
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Philip S Poole
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| |
Collapse
|
6
|
Nisha FA, Tagoe JNA, Pease AB, Horne SM, Ugrinov A, Geddes BA, Prüß BM. Plant seedlings of peas, tomatoes, and cucumbers exude compounds that are needed for growth and chemoattraction of Rhizobium leguminosarum bv. viciae 3841 and Azospirillum brasilense Sp7. Can J Microbiol 2024; 70:150-162. [PMID: 38427979 DOI: 10.1139/cjm-2023-0217] [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] [Indexed: 03/03/2024]
Abstract
This study characterizes seedling exudates of peas, tomatoes, and cucumbers at the level of chemical composition and functionality. A plant experiment confirmed that Rhizobium leguminosarum bv. viciae 3841 enhanced growth of pea shoots, while Azospirillum brasilense Sp7 supported growth of pea, tomato, and cucumber roots. Chemical analysis of exudates after 1 day of seedling incubation in water yielded differences between the exudates of the three plants. Most remarkably, cucumber seedling exudate did not contain detectable sugars. All exudates contained amino acids, nucleobases/nucleosides, and organic acids, among other compounds. Cucumber seedling exudate contained reduced glutathione. Migration on semi solid agar plates containing individual exudate compounds as putative chemoattractants revealed that R. leguminosarum bv. viciae was more selective than A. brasilense, which migrated towards any of the compounds tested. Migration on semi solid agar plates containing 1:1 dilutions of seedling exudate was observed for each of the combinations of bacteria and exudates tested. Likewise, R. leguminosarum bv. viciae and A. brasilense grew on each of the three seedling exudates, though at varying growth rates. We conclude that the seedling exudates of peas, tomatoes, and cucumbers contain everything that is needed for their symbiotic bacteria to migrate and grow on.
Collapse
Affiliation(s)
- Fatema A Nisha
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - Janice N A Tagoe
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - Amanda B Pease
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - Shelley M Horne
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - Angel Ugrinov
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, USA
| | - Barney A Geddes
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - Birgit M Prüß
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| |
Collapse
|
7
|
Pacheco-Moreno A, Bollmann-Giolai A, Chandra G, Brett P, Davies J, Thornton O, Poole P, Ramachandran V, Brown JKM, Nicholson P, Ridout C, DeVos S, Malone JG. The genotype of barley cultivars influences multiple aspects of their associated microbiota via differential root exudate secretion. PLoS Biol 2024; 22:e3002232. [PMID: 38662644 PMCID: PMC11045101 DOI: 10.1371/journal.pbio.3002232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
Plant-associated microbes play vital roles in promoting plant growth and health, with plants secreting root exudates into the rhizosphere to attract beneficial microbes. Exudate composition defines the nature of microbial recruitment, with different plant species attracting distinct microbiota to enable optimal adaptation to the soil environment. To more closely examine the relationship between plant genotype and microbial recruitment, we analysed the rhizosphere microbiomes of landrace (Chevallier) and modern (NFC Tipple) barley (Hordeum vulgare) cultivars. Distinct differences were observed between the plant-associated microbiomes of the 2 cultivars, with the plant-growth promoting rhizobacterial genus Pseudomonas substantially more abundant in the Tipple rhizosphere. Striking differences were also observed between the phenotypes of recruited Pseudomonas populations, alongside distinct genotypic clustering by cultivar. Cultivar-driven Pseudomonas selection was driven by root exudate composition, with the greater abundance of hexose sugars secreted from Tipple roots attracting microbes better adapted to growth on these metabolites and vice versa. Cultivar-driven selection also operates at the molecular level, with both gene expression and the abundance of ecologically relevant loci differing between Tipple and Chevallier Pseudomonas isolates. Finally, cultivar-driven selection is important for plant health, with both cultivars showing a distinct preference for microbes selected by their genetic siblings in rhizosphere transplantation assays.
Collapse
Affiliation(s)
- Alba Pacheco-Moreno
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | | | - Govind Chandra
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Paul Brett
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Jack Davies
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Owen Thornton
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Philip Poole
- Department of Biology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Vinoy Ramachandran
- Department of Biology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - James K. M. Brown
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Paul Nicholson
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Chris Ridout
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- New Heritage Barley, Norwich Research Park, Norwich, United Kingdom
| | - Sarah DeVos
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- New Heritage Barley, Norwich Research Park, Norwich, United Kingdom
| | - Jacob G. Malone
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| |
Collapse
|
8
|
Seitz VA, McGivem BB, Borton MA, Chaparro JM, Schipanski ME, Prenni JE, Wrighton KC. Cover Crop Root Exudates Impact Soil Microbiome Functional Trajectories in Agricultural Soils. RESEARCH SQUARE 2024:rs.3.rs-3956430. [PMID: 38410449 PMCID: PMC10896397 DOI: 10.21203/rs.3.rs-3956430/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Background Cover cropping is an agricultural practice that uses secondary crops to support the growth of primary crops through various mechanisms including erosion control, weed suppression, nutrient management, and enhanced biodiversity. Cover crops may elicit some of these ecosystem services through chemical interactions with the soil microbiome via root exudation, or the release of plant metabolites from roots. Phytohormones are one metabolite type exuded by plants that activate the rhizosphere microbiome, yet managing this chemical interaction remains an untapped mechanism for optimizing plant-soil microbiome interactions. Currently, there is limited understanding on the diversity of cover crop phytohormone root exudation patterns and how these chemical messages selectively enrich specific microbial taxa and functionalities in agricultural soils. Results Here, we link variability in cover crop root exudate composition to changes in soil microbiome functionality. Exudate chemical profiles from 4 cover crop species (Sorghum bicolor, Vicia villosa, Brassica napus, and Secale cereal) were used as the chemical inputs to decipher microbial responses. These distinct exudate profiles, along with a no exudate control, were amended to agricultural soil microcosms with microbial responses tracked over time using metabolomes and genome-resolved metatranscriptomes. Our findings illustrated microbial metabolic patterns were unique in response to cover crop exudate inputs over time, particularly by sorghum and cereal rye amended microcosms where we identify novel microbial members (at the genera and family level) who produced IAA and GA4 over time. We also identify broad changes in microbial nitrogen cycling in response chemical inputs. Conclusions We highlight that root exudate amendments alter microbial community function and phytohormone metabolisms, particularly in response to root exudates isolated from cereal rye and sorghum plants. Additionally, we constructed a soil microbial genomic catalog of microorganisms responding to commonly used cover crops, a public resource for agriculturally-relevant microbes. Many of our exudate-stimulated microorganisms are representatives from poorly characterized or novel taxa, highlighting the yet to be discovered metabolic reservoir harbored in agricultural soils. Our findings emphasize the tractability of high-resolution multiomics approaches to investigate processes relevant for agricultural soils, opening the possibility of targeting specific soil biogeochemical outcomes through biological precision agricultural practices that use cover crops and the microbiome as levers for enhanced crop production.
Collapse
|
9
|
Ghitti E, Rolli E, Vergani L, Borin S. Flavonoids influence key rhizocompetence traits for early root colonization and PCB degradation potential of Paraburkholderia xenovorans LB400. FRONTIERS IN PLANT SCIENCE 2024; 15:1325048. [PMID: 38371405 PMCID: PMC10869545 DOI: 10.3389/fpls.2024.1325048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/15/2024] [Indexed: 02/20/2024]
Abstract
Introduction Flavonoids are among the main plant root exudation components, and, in addition to their role in symbiosis, they can broadly affect the functionality of plant-associated microbes: in polluted environments, for instance, flavonoids can induce the expression of the enzymatic degradative machinery to clean-up soils from xenobiotics like polychlorinated biphenyls (PCBs). However, their involvement in root community recruitment and assembly involving non-symbiotic beneficial interactions remains understudied and may be crucial to sustain the holobiont fitness under PCB stress. Methods By using a set of model pure flavonoid molecules and a natural blend of root exudates (REs) with altered flavonoid composition produced by Arabidopsis mutant lines affected in flavonoid biosynthesis and abundance (null mutant tt4, flavonoid aglycones hyperproducer tt8, and flavonoid conjugates hyperaccumulator ttg), we investigated flavonoid contribution in stimulating rhizocompetence traits and the catabolic potential of the model bacterial strain for PCB degradation Paraburkholderia xenovorans LB400. Results Flavonoids influenced the traits involved in bacterial recruitment in the rhizoplane by improving chemotaxis and motility responses, by increasing biofilm formation and by promoting the growth and activation of the PCB-degradative pathway of strain LB400, being thus potentially exploited as carbon sources, stimulating factors and chemoattractant molecules. Indeed, early rhizoplane colonization was favored in plantlets of the tt8 Arabidopsis mutant and reduced in the ttg line. Bacterial growth was promoted by the REs of mutant lines tt4 and tt8 under control conditions and reduced upon PCB-18 stress, showing no significant differences compared with the WT and ttg, indicating that unidentified plant metabolites could be involved. PCB stress presumably altered the Arabidopsis root exudation profile, although a sudden "cry-for-help" response to recruit strain LB400 was excluded and flavonoids appeared not to be the main determinants. In the in vitro plant-microbe interaction assays, plant growth promotion and PCB resistance promoted by strain LB400 seemed to act through flavonoid-independent mechanisms without altering bacterial colonization efficiency and root adhesion pattern. Discussions This study further contributes to elucidate the vast array of functions provided by flavonoids in orchestrating the early events of PCB-degrading strain LB400 recruitment in the rhizosphere and to support the holobiont fitness by stimulating the catabolic machinery involved in xenobiotics decomposition and removal.
Collapse
Affiliation(s)
| | - Eleonora Rolli
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | | | | |
Collapse
|
10
|
Zhang X, Wu Y, Liu S, Li J, Jiang Z, Luo H, Huang X. Plant growth and development of tropical seagrass determined rhizodeposition and its related microbial community. MARINE POLLUTION BULLETIN 2024; 199:115940. [PMID: 38150979 DOI: 10.1016/j.marpolbul.2023.115940] [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: 10/07/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/29/2023]
Abstract
In the recent study, we investigated the seasonal variations in root exudation and microbial community structure in the rhizosphere of seagrass Enhalus acoroides in the South China Sea. We found that the quantity and quality of root exudates varied seasonally, with higher exudation rates and more bioavailable dissolved organic matter (DOM) during the seedling and vegetative stages in spring and summer. Using Illumina NovaSeq sequencing, we analyzed bacterial and fungal communities and discovered that microbial diversity and composition were influenced by root exudate characteristics s and seagrass biomass, which were strongly dependent on seagrass growth stages. Certain bacterial groups, such as Ruegeria, Sulfurovum, Photobacterium, and Ralstonia were closely associated with root exudation and may contribute to sulfur cycling, nitrogen fixation, and carbon remineralization, which were important for plant early development. Similarly, specific fungal taxa, including Astraeus, Alternaria, Rocella, and Tomentella, were enriched in spring and summer and showed growth-promoting abilities. Overall, our study suggests that seagrass secretes different compounds in its exudates at various developmental stages, shaping the rhizosphere microbial assemblages.
Collapse
Affiliation(s)
- Xia Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou 510301, China
| | - Yunchao Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou 510301, China
| | - Songlin Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinlong Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhijian Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongxue Luo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoping Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
11
|
Ojeda-Rivera JO, Ulloa M, Pérez-Zavala FG, Nájera-González HR, Roberts PA, Yong-Villalobos L, Yadav H, Chávez Montes RA, Herrera-Estrella L, Lopez-Arredondo D. Enhanced phenylpropanoid metabolism underlies resistance to Fusarium oxysporum f. sp. vasinfectum race 4 infection in the cotton cultivar Pima-S6 ( Gossypium barbadense L.). Front Genet 2024; 14:1271200. [PMID: 38259617 PMCID: PMC10800685 DOI: 10.3389/fgene.2023.1271200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/24/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction: Fusarium oxysporum f. sp. vasinfectum (FOV) race 4 (FOV4) is a highly pathogenic soil-borne fungus responsible for Fusarium wilt in cotton (Gossypium spp.) and represents a continuing threat to cotton production in the southwest states of the United States, including California, New Mexico, and Texas. Pima (G. barbadense L.) cotton, which is highly valued for its fiber quality, has been shown to be more susceptible to this pathogen than Upland (G. hirsutum L.) cotton. Still, some Pima cultivars present resistance to FOV4 infection. Methods: To gain insights into the FOV4-resistance mechanism, we performed comparative transcriptional and metabolomic analyses between FOV4-susceptible and FOV4-resistant Pima cotton entries. FOV4-resistant Pima-S6 and FOV4-susceptible Pima S-7 and Pima 3-79 cotton plants were infected with FOV4 in the greenhouse, and the roots harvested 11 days post-infection for further analysis. Results: We found that an enhanced root phenylpropanoid metabolism in the resistant Pima-S6 cultivar determines FOV4-resistance. Gene-ontology enrichment of phenylpropanoid biosynthesis and metabolism categories correlated with the accumulation of secondary metabolites in Pima-S6 roots. Specifically, we found esculetin, a coumarin, an inhibitor of Fusarium's growth, accumulated in the roots of Pima-S6 even under non-infected conditions. Genes related to the phenylpropanoid biosynthesis and metabolism, including phenylalanine ammonia-lyase 2 (PAL2) and pleiotropic drug resistance 12 (PDR12) transporter, were found to be upregulated in Pima-S6 roots. Discussion: Our results highlight an essential role for the phenylpropanoid synthesis pathway in FOV4 resistance in Pima-S6 cotton. These genes represent attractive research prospects for FOV4-disease resistance and breeding approaches of other cotton cultivars of economic relevance.
Collapse
Affiliation(s)
- Jonathan Odilón Ojeda-Rivera
- Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Science Department, Texas Tech University, Lubbock, TX, United States
| | - Mauricio Ulloa
- Plant Stress and Germplasm Development Research, U.S. Department of Agriculture-Agricultural Research Service, Plains Area, Cropping Systems Research Laboratory, Lubbock, TX, United States
| | - Francisco G. Pérez-Zavala
- Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Science Department, Texas Tech University, Lubbock, TX, United States
| | - Héctor-Rogelio Nájera-González
- Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Science Department, Texas Tech University, Lubbock, TX, United States
| | - Philip A. Roberts
- Department of Nematology, University of California, Riverside, CA, United States
| | - Lenin Yong-Villalobos
- Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Science Department, Texas Tech University, Lubbock, TX, United States
| | - Himanshu Yadav
- Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Science Department, Texas Tech University, Lubbock, TX, United States
| | - Ricardo A. Chávez Montes
- Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Science Department, Texas Tech University, Lubbock, TX, United States
| | - Luis Herrera-Estrella
- Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Science Department, Texas Tech University, Lubbock, TX, United States
- Unidad de Genomica Avanzada/Langebio, Centro de Investigacion y de Estudios Avanzados, Irapuato, Guanajuato, Mexico
| | - Damar Lopez-Arredondo
- Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Science Department, Texas Tech University, Lubbock, TX, United States
| |
Collapse
|
12
|
Shi H, Yang J, Li Q, PinChu C, Song Z, Yang H, Luo Y, Liu C, Fan W. Diversity and correlation analysis of different root exudates on the regulation of microbial structure and function in soil planted with Panax notoginseng. Front Microbiol 2023; 14:1282689. [PMID: 38125568 PMCID: PMC10731274 DOI: 10.3389/fmicb.2023.1282689] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/17/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction Specific interactions between root exudates and soil microorganisms has been proposed as one of the reasons accounting for the continuous cropping obstacle (CCO) of Panax notoginseng. However, rotation of other crops on soils planted with P. notoginseng (SPP) did not show CCO, suggesting that root exudates of different crops differentially regulate soil microorganisms in SPP. Methods Here, we investigated the microbial community structure and specific interaction mechanisms of the root exudates of the four plant species, P. notoginseng (Pn), Zea mays (Zm), Nicotiana tabacum (Nt) and Perilla frutescens (Pf), in SPP by static soil culture experiment. Results The results showed that the chemical diversity of root exudates varied significantly among the four plant species. Pn had the highest number of unique root exudates, followed by Nt, Zm and Pf. Terpenoids, flavonoids, alkaloids and phenolic acids were the most abundant differentially accumulated metabolites (DAMs) in Pn, Nt, Zm and Pf, respectively. However, lipids were the most abundant common DAMs among Zm Nt and Pf. Pn root exudates decreased the relative abundance of bacteria, but increased that of fungi. While specific DAMs in Pn enriched Phenylobacterium_zucineum, Sphingobium_yanoikuyae, Ophiostoma_ulmi and functional pathways of Nucleotide excision repair, Streptomycin biosynthesis, Cell cycle-Caulobacter and Glycolysis/Gluconeogenesis, it inhibited Paraburkholderia _caledonica and Ralstonia_pickettii. However, common DAMs in Zm, Nt and Pf had opposite effects. Moreover, common DAMs in Zm, Nt and Pf enriched Ralstonia_pseudosolanacearum and functional pathway of Xylene degradation; unique DAMs in Zm enriched Talaromyces_purcureogeneus, while inhibiting Fusarium_tricinctum and functional pathways of Nucleotide excision repair and Alanine, aspartate and glutamate metabolism; unique DAMs in Pf enriched Synchytrium_taraxaci. Discussion The core strains identified that interact with different root exudates will provide key clues for regulation of soil microorganisms in P. notoginseng cultivation to alleviate CCO.
Collapse
Affiliation(s)
- Huineng Shi
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Jianli Yang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
| | - Qi Li
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Cier PinChu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Zhanhua Song
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Honglei Yang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Yu Luo
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Chunlan Liu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Wei Fan
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
| |
Collapse
|
13
|
Low KE, Tingley JP, Klassen L, King ML, Xing X, Watt C, Hoover SER, Gorzelak M, Abbott DW. Carbohydrate flow through agricultural ecosystems: Implications for synthesis and microbial conversion of carbohydrates. Biotechnol Adv 2023; 69:108245. [PMID: 37652144 DOI: 10.1016/j.biotechadv.2023.108245] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/10/2023] [Accepted: 08/25/2023] [Indexed: 09/02/2023]
Abstract
Carbohydrates are chemically and structurally diverse biomolecules, serving numerous and varied roles in agricultural ecosystems. Crops and horticulture products are inherent sources of carbohydrates that are consumed by humans and non-human animals alike; however carbohydrates are also present in other agricultural materials, such as soil and compost, human and animal tissues, milk and dairy products, and honey. The biosynthesis, modification, and flow of carbohydrates within and between agricultural ecosystems is intimately related with microbial communities that colonize and thrive within these environments. Recent advances in -omics techniques have ushered in a new era for microbial ecology by illuminating the functional potential for carbohydrate metabolism encoded within microbial genomes, while agricultural glycomics is providing fresh perspective on carbohydrate-microbe interactions and how they influence the flow of functionalized carbon. Indeed, carbohydrates and carbohydrate-active enzymes are interventions with unrealized potential for improving carbon sequestration, soil fertility and stability, developing alternatives to antimicrobials, and circular production systems. In this manner, glycomics represents a new frontier for carbohydrate-based biotechnological solutions for agricultural systems facing escalating challenges, such as the changing climate.
Collapse
Affiliation(s)
- Kristin E Low
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Jeffrey P Tingley
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Leeann Klassen
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Marissa L King
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Xiaohui Xing
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Caitlin Watt
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Shelley E R Hoover
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Monika Gorzelak
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - D Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada.
| |
Collapse
|
14
|
Swift JF, Migicovsky Z, Trello GE, Miller AJ. Grapevine bacterial communities display compartment-specific dynamics over space and time within the Central Valley of California. ENVIRONMENTAL MICROBIOME 2023; 18:84. [PMID: 37996903 PMCID: PMC10668525 DOI: 10.1186/s40793-023-00539-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
BACKGROUND Plant organs (compartments) host distinct microbiota which shift in response to variation in both development and climate. Grapevines are woody perennial crops that are clonally propagated and cultivated across vast geographic areas, and as such, their microbial communities may also reflect site-specific influences. These site-specific influences along with microbial differences across sites compose 'terroir', the environmental influence on wine produced in a given region. Commercial grapevines are typically composed of a genetically distinct root (rootstock) grafted to a shoot system (scion) which adds an additional layer of complexity via genome-to-genome interactions. RESULTS To understand spatial and temporal patterns of bacterial diversity in grafted grapevines, we used 16S rRNA amplicon sequencing to quantify soil and compartment microbiota (berries, leaves, and roots) for grafted grapevines in commercial vineyards across three counties in the Central Valley of California over two successive growing seasons. Community composition revealed compartment-specific dynamics. Roots assembled site-specific bacterial communities that reflected rootstock genotype and environment influences, whereas bacterial communities of leaves and berries displayed associations with time. CONCLUSIONS These results provide further evidence of a microbial terroir within the grapevine root systems but also reveal that the microbiota of above-ground compartments are only weakly associated with the local soil microbiome in the Central Valley of California.
Collapse
Affiliation(s)
- Joel F Swift
- Department of Biology, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO, 63103, USA.
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA.
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, 66045, USA.
| | - Zoë Migicovsky
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
- Department of Biology, Acadia University, Wolfville, NS, B4P 2R6, Canada
| | - Grace E Trello
- Department of Biology, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO, 63103, USA
| | - Allison J Miller
- Department of Biology, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO, 63103, USA.
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA.
| |
Collapse
|
15
|
Delamare J, Brunel-Muguet S, Boukerb AM, Bressan M, Dumas L, Firmin S, Leroy F, Morvan-Bertrand A, Prigent-Combaret C, Personeni E. Impact of PGPR inoculation on root morphological traits and root exudation in rapeseed and camelina: interactions with heat stress. PHYSIOLOGIA PLANTARUM 2023; 175:e14058. [PMID: 38148195 DOI: 10.1111/ppl.14058] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 12/28/2023]
Abstract
Root exudation is involved in the recruitment of beneficial microorganisms by trophic relationships and/or signalling pathways. Among beneficial microorganisms, Plant Growth-Promoting Rhizobacteria (PGPR) are known to improve plant growth and stress resistance. These interactions are of particular importance for species that do not interact with mycorrhizal fungi, such as rapeseed (Brassica napus L.) and camelina (Camelina sativa (L.) Crantz). However, heat stress is known to have a quantitative and qualitative impact on root exudation and could affect the interactions between plants and PGPR. We aimed to analyse the effects of PGPR inoculation on root morphology and exudation in rapeseed and camelina at the reproductive stage. The modulation of the effects of these interactions under heat stress was also investigated. The plants were inoculated twice at the reproductive stage with two different Pseudomonas species and were exposed to heat stress after the second inoculation. In non-stressing conditions, after bacterial inoculation, rapeseed and camelina exhibited two contrasting behaviours in C root allocation. While rapeseed plants seemed to suffer from the interactions with the bacteria, camelina plants appeared to control the relationship with the PGPR by modifying the composition of their root exudates. Under heat stress, the plant-PGPR interaction was unbalanced for rapeseed, for which the C allocation strategy is mainly driven by the C cost from the bacteria. Alternatively, camelina plants prioritized C allocation for their own above-ground development. This work opens up new perspectives for understanding plant-PGPR interactions, especially in an abiotic stress context.
Collapse
Affiliation(s)
- Jérémy Delamare
- UNICAEN, INRAE, UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, Esplanade de la Paix, CS14032, Normandie Université, Caen Cedex 5, France
| | - Sophie Brunel-Muguet
- UNICAEN, INRAE, UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, Esplanade de la Paix, CS14032, Normandie Université, Caen Cedex 5, France
| | - Amine M Boukerb
- CBSA UR4312, Univ Rouen Normandie, Unité de Recherche Communication Bactérienne et Stratégies Anti-infectieuses, Évreux, France
| | | | - Lucien Dumas
- UNICAEN, INRAE, UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, Esplanade de la Paix, CS14032, Normandie Université, Caen Cedex 5, France
| | | | | | - Annette Morvan-Bertrand
- UNICAEN, INRAE, UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, Esplanade de la Paix, CS14032, Normandie Université, Caen Cedex 5, France
| | - Claire Prigent-Combaret
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 Novembre 1918, Université de Lyon, Villeurbanne, France
| | - Emmanuelle Personeni
- UNICAEN, INRAE, UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, Esplanade de la Paix, CS14032, Normandie Université, Caen Cedex 5, France
| |
Collapse
|
16
|
de Barros Dantas LL, Eldridge BM, Dorling J, Dekeya R, Lynch DA, Dodd AN. Circadian regulation of metabolism across photosynthetic organisms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:650-668. [PMID: 37531328 PMCID: PMC10953457 DOI: 10.1111/tpj.16405] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 08/04/2023]
Abstract
Circadian regulation produces a biological measure of time within cells. The daily cycle in the availability of light for photosynthesis causes dramatic changes in biochemical processes in photosynthetic organisms, with the circadian clock having crucial roles in adaptation to these fluctuating conditions. Correct alignment between the circadian clock and environmental day-night cycles maximizes plant productivity through its regulation of metabolism. Therefore, the processes that integrate circadian regulation with metabolism are key to understanding how the circadian clock contributes to plant productivity. This forms an important part of exploiting knowledge of circadian regulation to enhance sustainable crop production. Here, we examine the roles of circadian regulation in metabolic processes in source and sink organ structures of Arabidopsis. We also evaluate possible roles for circadian regulation in root exudation processes that deposit carbon into the soil, and the nature of the rhythmic interactions between plants and their associated microbial communities. Finally, we examine shared and differing aspects of the circadian regulation of metabolism between Arabidopsis and other model photosynthetic organisms, and between circadian control of metabolism in photosynthetic and non-photosynthetic organisms. This synthesis identifies a variety of future research topics, including a focus on metabolic processes that underlie biotic interactions within ecosystems.
Collapse
Affiliation(s)
| | - Bethany M. Eldridge
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Jack Dorling
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Richard Dekeya
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Deirdre A. Lynch
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Antony N. Dodd
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Tani A, Masuda S, Fujitani Y, Iga T, Haruna Y, Kikuchi S, Shuaile W, Lv H, Katayama S, Yurimoto H, Sakai Y, Kato J. Metabolism-linked methylotaxis sensors responsible for plant colonization in Methylobacterium aquaticum strain 22A. Front Microbiol 2023; 14:1258452. [PMID: 37901831 PMCID: PMC10613068 DOI: 10.3389/fmicb.2023.1258452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/02/2023] [Indexed: 10/31/2023] Open
Abstract
Motile bacteria take a competitive advantage in colonization of plant surfaces to establish beneficial associations that eventually support plant health. Plant exudates serve not only as primary growth substrates for bacteria but also as bacterial chemotaxis attractants. A number of plant-derived compounds and corresponding chemotaxis sensors have been documented, however, the sensors for methanol, one of the major volatile compounds released by plants, have not been identified. Methylobacterium species are ubiquitous plant surface-symbiotic, methylotrophic bacteria. A plant-growth promoting bacterium, M. aquaticum strain 22A exhibits chemotaxis toward methanol (methylotaxis). Its genome encodes 52 methyl-accepting chemotaxis proteins (MCPs), among which we identified three MCPs (methylotaxis proteins, MtpA, MtpB, and MtpC) responsible for methylotaxis. The triple gene mutant of the MCPs exhibited no methylotaxis, slower gathering to plant tissues, and less efficient colonization on plants than the wild type, suggesting that the methylotaxis mediates initiation of plant-Methylobacterium symbiosis and engages in proliferation on plants. To examine how these MCPs are operating methylotaxis, we generated multiple gene knockouts of the MCPs, and Ca2+-dependent MxaFI and lanthanide (Ln3+)-dependent XoxF methanol dehydrogenases (MDHs), whose expression is regulated by the presence of Ln3+. MtpA was found to be a cytosolic sensor that conducts formaldehyde taxis (formtaxis), as well as methylotaxis when MDHs generate formaldehyde. MtpB contained a dCache domain and exhibited differential cellular localization in response to La3+. MtpB expression was induced by La3+, and its activity required XoxF1. MtpC exhibited typical cell pole localization, required MxaFI activity, and was regulated under MxbDM that is also required for MxaF expression. Strain 22A methylotaxis is realized by three independent MCPs, two of which monitor methanol oxidation by Ln3+-regulated MDHs, and one of which monitors the common methanol oxidation product, formaldehyde. We propose that methanol metabolism-linked chemotaxis is the key factor for the efficient colonization of Methylobacterium on plants.
Collapse
Affiliation(s)
- Akio Tani
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Sachiko Masuda
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
- Japan Science and Technology Agency, Advanced Low Carbon Technology Research and Development Program (JST ALCA), Kawaguchi, Japan
| | - Yoshiko Fujitani
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Toshiki Iga
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Yuuki Haruna
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Shiho Kikuchi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Wang Shuaile
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Haoxin Lv
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Shiori Katayama
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hiroya Yurimoto
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yasuyoshi Sakai
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Junichi Kato
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| |
Collapse
|
19
|
Benmrid B, Ghoulam C, Zeroual Y, Kouisni L, Bargaz A. Bioinoculants as a means of increasing crop tolerance to drought and phosphorus deficiency in legume-cereal intercropping systems. Commun Biol 2023; 6:1016. [PMID: 37803170 PMCID: PMC10558546 DOI: 10.1038/s42003-023-05399-5] [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: 05/12/2023] [Accepted: 09/28/2023] [Indexed: 10/08/2023] Open
Abstract
Ensuring plant resilience to drought and phosphorus (P) stresses is crucial to support global food security. The phytobiome, shaped by selective pressures, harbors stress-adapted microorganisms that confer host benefits like enhanced growth and stress tolerance. Intercropping systems also offer benefits through facilitative interactions, improving plant growth in water- and P-deficient soils. Application of microbial consortia can boost the benefits of intercropping, although questions remain about the establishment, persistence, and legacy effects within resident soil microbiomes. Understanding microbe- and plant-microbe dynamics in drought-prone soils is key. This review highlights the beneficial effects of rhizobacterial consortia-based inoculants in legume-cereal intercropping systems, discusses challenges, proposes a roadmap for development of P-solubilizing drought-adapted consortia, and identifies research gaps in crop-microbe interactions.
Collapse
Affiliation(s)
- Bouchra Benmrid
- Plant-Microbe Interactions Laboratory, AgroBiosciences Program, College for Sustainable Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir, 43150, Morocco.
| | - Cherki Ghoulam
- Plant-Microbe Interactions Laboratory, AgroBiosciences Program, College for Sustainable Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir, 43150, Morocco
- Agrobiotechnology & Bioengineering Center, Research Unit CNRST labeled, Cadi Ayyad University, Faculty of Sciences and Techniques, 40000, Marrakech, Morocco
| | - Youssef Zeroual
- Situation Innovation - OCP Group, Jorf Lasfar, 24025, Morocco
| | - Lamfeddal Kouisni
- African Sustainable Agriculture Research Institute, Mohammed VI Polytechnic University, Laayoune, Morocco
| | - Adnane Bargaz
- Plant-Microbe Interactions Laboratory, AgroBiosciences Program, College for Sustainable Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir, 43150, Morocco.
| |
Collapse
|
20
|
Yeruva DK, S VM. Electrogenic engineered flow through tri-phasic wetland system for azo dye treatment: Microbial dynamics and functional metagenomics. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 334:122107. [PMID: 37369299 DOI: 10.1016/j.envpol.2023.122107] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 06/12/2023] [Accepted: 06/24/2023] [Indexed: 06/29/2023]
Abstract
Electrogenic engineered flow through tri-phasic wetland (EEFW) system based on nature-based ecological principles was studied by integrating successive biological microenvironments. The potential mechanism of the plant root-based microbial community and its functional diversity with the influence of plant-microbe-electrode synergism towards dye degradation was evaluated. The EEFW system was operated at three varied dye loads of 10, 25 and 50 mg L-1, where the results from the cumulative outlets revealed a maximum dye removal efficiency of 96%, 96.5% and 93%, respectively. Microbial community analysis depicted synergistic dependence on the plant-microbe-electrode interactions, influencing their functional diversity and metabolism towards detoxification of pollutants. The core microbial taxa enriched against the microenvironment variation were mostly associated with carbon and dye removal viz., Desulfomonile tiedjei and Rhodopseudomonas palustris in Tank 1 and Chloroflexi bacterium and Steroidobacter denitrificans in Tank 2. The degradation of polycyclic aromatic hydrocarbons, chloroalkane/chloroalkene, nitrotoluene, bisphenol, caprolactam and 1,1,1-trichloro-2,2-bis(4-chlorophenyl) ethane (DDT) were observed to be predominant in Tank 1. EEFW system could be one of the option for utilizing nature-based processes for the treatment of wastewater by self-induced bioelectrogenesis to augment process efficiency.
Collapse
Affiliation(s)
- Dileep Kumar Yeruva
- Bioengineering and Environmental Science Lab, Department of Energy and Environmental Engineering, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, 500 007, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Venkata Mohan S
- Bioengineering and Environmental Science Lab, Department of Energy and Environmental Engineering, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, 500 007, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India.
| |
Collapse
|
21
|
Zhao X, Li J, Zhang D, Jiang L, Wang Y, Hu B, Wang S, Dai Y, Luo C, Zhang G. Unveiling the novel role of ryegrass rhizospheric metabolites in benzo[a]pyrene biodegradation. ENVIRONMENT INTERNATIONAL 2023; 180:108215. [PMID: 37741005 DOI: 10.1016/j.envint.2023.108215] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 09/11/2023] [Accepted: 09/15/2023] [Indexed: 09/25/2023]
Abstract
Rhizoremediation is a promising remediation technology for the removal of soil persistent organic pollutants (POPs), especially benzo[a]pyrene (BaP). However, our understanding of the associations among rhizospheric soil metabolites, functional microorganisms, and POPs degradation in different plant growth stages is limited. We combined stable-isotope probing (SIP), high-throughput sequencing, and metabolomics to analyze changes in rhizospheric soil metabolites, functional microbes, and BaP biodegradation in the early growth stages (tillering, jointing) and later stage (booting) of ryegrass. Microbial community structures differed significantly among growth stages. Metabolisms such as benzenoids and carboxylic acids tended to be enriched in the early growth stage, while lipids and organic heterocyclic compounds dominated in the later stage. From SIP, eight BaP-degrading microbes were identified, and most of which such as Ilumatobacter and Singulisphaera were first linked with BaP biodegradation. Notably, the relationship between the differential metabolites and BaP degradation efficiency further suggested that BaP-degrading microbes might metabolize BaP directly to produce benzenoid metabolites (3-hydroxybenzo[a]pyrene), or utilize benzenoids (phyllodulcin) to stimulate the co-metabolism of BaP in early growth stage; some lipids and organic acids, e.g. 1-aminocyclopropane-1-carboxylic acid, might provide nutrients for the degraders to promote BaP metabolism in later stage. Accordingly, we determined that certain rhizospheric metabolites might regulate the rhizospheric microbial communities at different growth stages, and shift the composition and diversity of BaP-degrading bacteria, thereby enhancing in situ BaP degradation. Our study sheds light on POPs rhizoremediation mechanisms in petroleum-contaminated soils.
Collapse
Affiliation(s)
- Xuan Zhao
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; College of Architecture and Civil Engineering, Kunming University, Kunming 650214, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jibing Li
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun 130021, China
| | - Longfei Jiang
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
| | - Yujie Wang
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Beibei Hu
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Shuang Wang
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yeliang Dai
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China.
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
| |
Collapse
|
22
|
Li J, Yang C, Jousset A, Yang K, Wang X, Xu Z, Yang T, Mei X, Zhong Z, Xu Y, Shen Q, Friman VP, Wei Z. Engineering multifunctional rhizosphere probiotics using consortia of Bacillus amyloliquefaciens transposon insertion mutants. eLife 2023; 12:e90726. [PMID: 37706503 PMCID: PMC10519709 DOI: 10.7554/elife.90726] [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: 07/04/2023] [Accepted: 09/13/2023] [Indexed: 09/15/2023] Open
Abstract
While bacterial diversity is beneficial for the functioning of rhizosphere microbiomes, multi-species bioinoculants often fail to promote plant growth. One potential reason for this is that competition between different species of inoculated consortia members creates conflicts for their survival and functioning. To circumvent this, we used transposon insertion mutagenesis to increase the functional diversity within Bacillus amyloliquefaciens bacterial species and tested if we could improve plant growth promotion by assembling consortia of highly clonal but phenotypically dissimilar mutants. While most insertion mutations were harmful, some significantly improved B. amyloliquefaciens plant growth promotion traits relative to the wild-type strain. Eight phenotypically distinct mutants were selected to test if their functioning could be improved by applying them as multifunctional consortia. We found that B. amyloliquefaciens consortium richness correlated positively with plant root colonization and protection from Ralstonia solanacearum phytopathogenic bacterium. Crucially, 8-mutant consortium consisting of phenotypically dissimilar mutants performed better than randomly assembled 8-mutant consortia, suggesting that improvements were likely driven by consortia multifunctionality instead of consortia richness. Together, our results suggest that increasing intra-species phenotypic diversity could be an effective way to improve probiotic consortium functioning and plant growth promotion in agricultural systems.
Collapse
Affiliation(s)
- Jingxuan Li
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Chunlan Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Alexandre Jousset
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Keming Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Xiaofang Wang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Zhihui Xu
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Tianjie Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Xinlan Mei
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Zengtao Zhong
- College of Life Science, Nanjing Agricultural UniversityNanjingChina
| | - Yangchun Xu
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Qirong Shen
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Ville-Petri Friman
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
- Department of Microbiology, University of HelsinkiHelsinkiFinland
| | - Zhong Wei
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| |
Collapse
|
23
|
Aizi T, Lijuan L, Lihua L, Wei L, Jiamei Q. Comparative analysis of microbial community structure in different times of Panax ginseng Rhizosphere microbiome and soil properties under larch forest. BMC Genom Data 2023; 24:51. [PMID: 37710149 PMCID: PMC10500862 DOI: 10.1186/s12863-023-01154-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023] Open
Abstract
BACKGROUND Panax ginseng cultivated under the forest is popular because its shape and effective ingredients are similar to wild ginseng. The growth of P. ginseng in the larch forest is generally better than in the broad-leaved forest, and the incidence rate of diseases is low. Therefore, the selection of forest species is one of the basic factors in the successful cropping of P. ginseng. METHODS Illumina HiSeq high-throughput sequencing was used to analyze the 16S rRNA/ITS gene sequence of P. ginseng rhizosphere soil under larch forest to study the rhizosphere microbiome's diversity and community composition structure. RESULTS The species classification and richness of rhizosphere bacterial and fungal communities in the same-aged P. ginseng were similar. Consistent with the soil system of commonly cultivated crops, Proteobacteria, Actinobacteriota, Acidobacteriota, Verrucomicrobiota, Chloroflexi, and Basidiomycota, Ascomycota were the dominant phylum of bacteria and fungi, respectively. Compared with the soil without planting P. ginseng, the diversity of microorganisms and community structure of continuous planting for 2 years, 5 years, and 18 years of P. ginseng rhizosphere soil had little change. The accumulation levels of Ilyonectria, Fusarium, Gibberella, and Cylindrocarpon were not significantly increased with planting P. ginseng and the increased age of cropping P. ginseng. CONCLUSIONS The results of this study showed that the soil function of the larch forest was good, which provided a theoretical basis for the land selection and soil improvement of cultivating P. ginseng under the larch forest.
Collapse
Affiliation(s)
- Tong Aizi
- Key Laboratory of Evaluation and Application of Changbai Mountain Biological Germplasm Resources of Jilin Province, College of Life Science, Tonghua Normal University, Tonghua, 134002, China
| | - Liu Lijuan
- Key Laboratory of Evaluation and Application of Changbai Mountain Biological Germplasm Resources of Jilin Province, College of Life Science, Tonghua Normal University, Tonghua, 134002, China
| | - Liu Lihua
- Key Laboratory of Evaluation and Application of Changbai Mountain Biological Germplasm Resources of Jilin Province, College of Life Science, Tonghua Normal University, Tonghua, 134002, China
| | - Liu Wei
- Key Laboratory of Evaluation and Application of Changbai Mountain Biological Germplasm Resources of Jilin Province, College of Life Science, Tonghua Normal University, Tonghua, 134002, China
| | - Qin Jiamei
- Key Laboratory of Evaluation and Application of Changbai Mountain Biological Germplasm Resources of Jilin Province, College of Life Science, Tonghua Normal University, Tonghua, 134002, China.
| |
Collapse
|
24
|
Wang B, Lin Y, Yu W, Xia Q, Ali A, Wei F, Dai C, Zhang J, Cai Z, Zhao J. The loss of microbial autotoxin degradation functions is associated with the decline of beneficial bacterial agents induced by phenolic acids. Microbiol Spectr 2023; 11:e0338022. [PMID: 37698393 PMCID: PMC10581185 DOI: 10.1128/spectrum.03380-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 07/07/2023] [Indexed: 09/13/2023] Open
Abstract
Continuous cultivation of medicinal plants can disrupt the rhizosphere's microbial community. There is still a need to know about the beneficial bacterial community, their putative drivers, and the potential functions they may have. This study used different growth years of Sanqi ginseng (Panax notoginseng) with root rot to look at the beneficial microbial community structure, the function of microbial carbon source utilization, and the function of rhizosphere soil metabolism. The beneficial bacterial community changed and the relative abundance of beneficial agents was suppressed significantly with the successive Sanqi ginseng plantings. The carbon source utilization capacity and diversity increased significantly, whereas three autotoxin degradation-related pathways (biosynthesis of other secondary metabolites, metabolism of terpenoids and polyketides, and xenobiotics biodegradation and metabolism) were downregulated considerably with planting year extended. The changes in the beneficial agents were driven by the shifts in phenolic acid profiles, and the decline of beneficial microbes led to the loss of microbial autotoxin degradation functions. Overall, these results provide insight into beneficial microbes, microbial functions, phenolic acids, and their interactions, and these findings are essential for maintaining healthy and sustainable cultivation of Sanqi ginseng. IMPORTANCE Sanqi ginseng is a valuable perennial Chinese herb with various benefits for human health. However, continuous cultivation causes a high incidence of root rot disease, which leads to decreased yield and serious economic losses and ultimately impedes the sustainable development of Chinese medicine production. The significance of this study is to reveal the pattern of changes in beneficial bacteria and their related functions in root rot diseased rhizosphere with the successive planting years of Sanqi ginseng. This study found that the decline of beneficial bacterial agents mediated by phenolic acid profiles appears to be associated with the loss of microbial autotoxin degradation functions. This result may have new implications for deciphering the causes of Sanqi ginseng's continuous cropping obstacles.
Collapse
Affiliation(s)
- Baoying Wang
- School of Geography, Nanjing Normal University, Nanjing, China
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yulan Lin
- School of Geography, Nanjing Normal University, Nanjing, China
| | - Wenhao Yu
- School of Geography, Nanjing Normal University, Nanjing, China
| | - Qing Xia
- School of Geography, Nanjing Normal University, Nanjing, China
| | - Ahmad Ali
- School of Geography, Nanjing Normal University, Nanjing, China
| | - Fugang Wei
- Miaoxiang Sanqi Technology Co., Ltd., Wenshan, China
| | - Chuanchao Dai
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jinbo Zhang
- School of Geography, Nanjing Normal University, Nanjing, China
- Jiangsu Engineering Research Center for Soil Utilization & Sustainable Agriculture, Nanjing, China
| | - Zucong Cai
- School of Geography, Nanjing Normal University, Nanjing, China
- Jiangsu Engineering Research Center for Soil Utilization & Sustainable Agriculture, Nanjing, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
| | - Jun Zhao
- School of Geography, Nanjing Normal University, Nanjing, China
- Jiangsu Engineering Research Center for Soil Utilization & Sustainable Agriculture, Nanjing, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
| |
Collapse
|
25
|
Xu A, Liu C, Zhao S, Song Z, Sun H. Dynamic distribution of Massilia spp. in sewage, substrate, plant rhizosphere/phyllosphere and air of constructed wetland ecosystem. Front Microbiol 2023; 14:1211649. [PMID: 37577432 PMCID: PMC10413979 DOI: 10.3389/fmicb.2023.1211649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction Massilia bacteria are widely distributed and have various ecological functions. Preliminary studies have shown that Massilia is the dominant species in constructed wetland ecosystems, but its species composition and distribution in constructed wetlands are still unclear. Methods In this paper, the in-house-designed primers were used to construct a 16S rDNA clone library of Massilia. The RFLP sequence analysis method was used to analyze the diversity of Massilia clone library and the composition of Massilia in sewage, substrate, plant rhizosphere, plant phyllosphere and air in a constructed wetland sewage treatment system. Redundancy analysis (RDA) and canonical correspondence analysis (CCA) were used to analyze the correlation between environmental factors and the population characteristics of Massilia in the corresponding environment. The dominant species of Massilia were analyzed for differences. Results The results showed that the 16S rDNA clone library in primer 5 worked well. According to the clone library diversity index analysis, the richness of Massilia varied significantly in different environments in different seasons, where the overall summer and autumn richness was higher than that in the spring and winter. The relative abundance of 5 Massilia in the constructed wetland ecosystem was greater than 1% in all samples, which were M. alkalitolerans, M. albidiflava, M. aurea, M. brevitalea, and M. timonae. The seasonal variation of dominant genera was significantly correlated with environmental factors in constructed wetlands. Discussion The above results indicated that the species of Massilia were abundant and widely distributed in the constructed wetland ecosystem, and there were significant seasonal differences. In addition, the Massilia clone library of constructed wetland was constructed for the first time in this study and the valuable data of Massilia community structure were provided, which was conducive to the further study of microbial community in constructed wetland.
Collapse
Affiliation(s)
- Ailing Xu
- School of Environmental and Municipal Engineering, Qingdao Technological University, Qingdao, Shandong, China
| | - Congcong Liu
- School of Environmental and Municipal Engineering, Qingdao Technological University, Qingdao, Shandong, China
| | - Shuke Zhao
- Qingdao sub-Center, Shandong Water Transfer Project Operation and Maintenance Center, Qingdao, Shandong, China
| | - Zhiwen Song
- School of Environmental and Municipal Engineering, Qingdao Technological University, Qingdao, Shandong, China
| | - Hui Sun
- Qingdao sub-Center, Shandong Water Transfer Project Operation and Maintenance Center, Qingdao, Shandong, China
| |
Collapse
|
26
|
Hu G, Wang Y, Blake C, Nordgaard M, Liu X, Wang B, Kovács ÁT. Parallel genetic adaptation of Bacillus subtilis to different plant species. Microb Genom 2023; 9:mgen001064. [PMID: 37466402 PMCID: PMC10438812 DOI: 10.1099/mgen.0.001064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
Plant growth-promoting rhizobacteria benefit plants by stimulating their growth or protecting them against phytopathogens. Rhizobacteria must colonize and persist on plant roots to exert their benefits. However, little is known regarding the processes by which rhizobacteria adapt to different plant species, or behave under alternating host plant regimes. Here, we used experimental evolution and whole-population whole-genome sequencing to analyse how Bacillus subtilis evolves on Arabidopsis thaliana and tomato seedlings, and under an alternating host plant regime, in a static hydroponic setup. We observed parallel evolution across multiple levels of biological organization in all conditions, which was greatest for the two heterogeneous, multi-resource, spatially structured environments at the genetic level. Species-specific adaptation at the genetic level was also observed, possibly caused by the selection stress imposed by different host plants. Furthermore, a trade-off between motility and biofilm development was supported by mutational changes in motility- and biofilm-related genes. Finally, we identified several condition-specific and common targeted genes in different environments by comparing three different B. subtilis biofilm adaptation settings. The results demonstrate a common evolutionary pattern when B. subtilis is adapting to the plant rhizosphere in similar conditions, and reveal differences in genetic mechanisms between different host plants. These findings will likely support strain improvements for sustainable agriculture.
Collapse
Affiliation(s)
- Guohai Hu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, PR China
- BGI-Shenzhen, Shenzhen 518083, PR China
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Yue Wang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, PR China
- BGI-Shenzhen, Shenzhen 518083, PR China
- BGI-Beijing, Beijing 102601, PR China
| | - Christopher Blake
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Mathilde Nordgaard
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Xin Liu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, PR China
- BGI-Shenzhen, Shenzhen 518083, PR China
- BGI-Beijing, Beijing 102601, PR China
| | - Bo Wang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, PR China
- BGI-Shenzhen, Shenzhen 518083, PR China
- Shenzhen Key Laboratory of Environmental Microbial Genomics and Application, BGI Shenzhen, 518083 Shenzhen, PR China
| | - Ákos T. Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800 Lyngby, Denmark
- Institute of Biology Leiden, Leiden University, 2333BE Leiden, Netherlands
| |
Collapse
|
27
|
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.
Collapse
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
| |
Collapse
|
28
|
Chen P, Yu K, He Y. The dynamics and transmission of antibiotic resistance associated with plant microbiomes. ENVIRONMENT INTERNATIONAL 2023; 176:107986. [PMID: 37257204 DOI: 10.1016/j.envint.2023.107986] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/17/2023] [Accepted: 05/17/2023] [Indexed: 06/02/2023]
Abstract
Antibiotic resistance genes (ARGs) have been widely found and studied in soil and water environments. However, the propagation of ARGs in plant microbiomes has attracted insufficient attention. Plant microbiomes, especially the rhizosphere microorganisms, are closely connected with water, soil, and air, which allows ARGs to spread widely in ecosystems and pose a threat to human health after entering the human body with bacteria. Therefore, it is necessary to deeply understand and explore the dynamics and the transmission of ARGs in rhizosphere microorganisms and endophytes of plants. In this review, the transmission and influencing factors of ARGs in the microorganisms associated with plants, especially the influence of root exudates on plant microbiomes, are analyzed. Notably, the role of intrinsic genes of plants in determining root exudates and their potential effects on ARGs are proposed and analyzed. The important role of phyllosphere microorganisms and endophytes in the transmission of ARGs and co-resistance of antibiotics and other substances are also emphasized. The proliferation and transmission of ARGs associated with plant microbiomes addressed in this review is conducive to revealing the fate of ARGs in plant microorganisms and alleviating ARG pollution.
Collapse
Affiliation(s)
- Ping Chen
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Kaifeng Yu
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yiliang He
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
| |
Collapse
|
29
|
Town JR, Dumonceaux T, Tidemann B, Helgason BL. Crop rotation significantly influences the composition of soil, rhizosphere, and root microbiota in canola (Brassica napus L.). ENVIRONMENTAL MICROBIOME 2023; 18:40. [PMID: 37161618 PMCID: PMC10169384 DOI: 10.1186/s40793-023-00495-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/19/2023] [Indexed: 05/11/2023]
Abstract
BACKGROUND Crop rotation is an agronomic practice that is known to enhance productivity and yield, and decrease pest and disease pressure. Economic and other factors have increased the frequency of certain crops, including canola, with unknown effects on the below ground microbial communities that impact plant health and performance. This study investigated the effect of 12 years of crop rotation including canola-wheat; canola-pea-barley; and unrotated canola across three geographic sites in Western Canada with diverse soil types and environmental conditions. To provide data on mature, established crop rotation strategies, root exudate profiles, soil nutrient fluxes, and bacterial and fungal microbial community profiles were determined at the flowering stage in the final two (canola) years of the 12-year rotations. RESULTS After 12 years of rotation, nutrient fluxes were affected in the soil in an inconsistent manner, with K, NO3, Mg, Ca, P, and Fe fluxes variably impacted by rotation depending on the year and site of sampling. As expected, rotation positively influenced yield and oil content, and decreased disease pressure from Leptosphaeria and Alternaria. In two of the three sites, root exudate profiles were significantly influenced by crop rotation. Bacterial soil, root, and rhizosphere communities were less impacted by crop rotation than the fungal communities. Fungal sequences that were associated with specific rotation strategies were identified in the bulk soil, and included known fungal pathogens in the canola-only strategy. Two closely related fungal sequences identified as Olpidium brassicae were extremely abundant at all sites in both years. One of these sequences was observed uniquely at a single site and was significantly associated with monocropped canola; moreover, its abundance correlated negatively with yield in both years. CONCLUSIONS Long-term canola monoculture affected root exudate profiles and soil nutrient fluxes differently in the three geographic locations. Bacterial communities were less impacted by rotation compared to the fungal communities, which consistently exhibited changes in composition in all ecological niches at all sites, in both years. Fungal sequences identified as O. brassicae were highly abundant at all sites, one of which was strongly associated with canola monoculture. Soil management decisions should include consideration of the effects on the microbial ecosystems associated with the plants in order to inform best management practices.
Collapse
Affiliation(s)
- Jennifer R Town
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, SK, Canada.
| | - Tim Dumonceaux
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, SK, Canada
| | - Breanne Tidemann
- Agriculture and Agri-Food Canada, Lacombe Research and Development Centre, Lacombe, AB, Canada
| | - Bobbi L Helgason
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, SK, Canada
- Department of Soil Science, University of Saskatchewan, Saskatoon, SK, Canada
| |
Collapse
|
30
|
Quiza L, Tremblay J, Pagé AP, Greer CW, Pozniak CJ, Li R, Haug B, Hemmingsen SM, St-Arnaud M, Yergeau E. The effect of wheat genotype on the microbiome is more evident in roots and varies through time. ISME COMMUNICATIONS 2023; 3:32. [PMID: 37076737 PMCID: PMC10115884 DOI: 10.1038/s43705-023-00238-4] [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: 10/22/2022] [Revised: 03/27/2023] [Accepted: 04/04/2023] [Indexed: 04/21/2023]
Abstract
Crop breeding has traditionally ignored the plant-associated microbial communities. Considering the interactions between plant genotype and associated microbiota is of value since different genotypes of the same crop often harbor distinct microbial communities which can influence the plant phenotype. However, recent studies have reported contrasting results, which led us to hypothesize that the effect of genotype is constrained by growth stages, sampling year and plant compartment. To test this hypothesis, we sampled bulk soil, rhizosphere soil and roots of 10 field-grown wheat genotypes, twice per year, for 4 years. DNA was extracted and regions of the bacterial 16 S rRNA and CPN60 genes and the fungal ITS region were amplified and sequenced. The effect of genotype was highly contingent on the time of sampling and on the plant compartment sampled. Only for a few sampling dates, were the microbial communities significantly different across genotypes. The effect of genotype was most often significant for root microbial communities. The three marker genes used provided a highly coherent picture of the effect of genotype. Taken together, our results confirm that microbial communities in the plant environment strongly vary across compartments, growth stages, and years, and that this can mask the effect of genotype.
Collapse
Affiliation(s)
- Liliana Quiza
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, QC, Canada
| | - Julien Tremblay
- Energy, Mining, and Environment Research Centre, National Research Council Canada, Montréal, QC, Canada
| | - Antoine P Pagé
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Charles W Greer
- Energy, Mining, and Environment Research Centre, National Research Council Canada, Montréal, QC, Canada
| | | | - Rong Li
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Brenda Haug
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Sean M Hemmingsen
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Marc St-Arnaud
- Institut de recherche en biologie végétale, Université de Montréal and Jardin botanique de Montréal, 4101 rue Sherbrooke E., Montréal, QC, Canada
| | - Etienne Yergeau
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, QC, Canada.
| |
Collapse
|
31
|
McRose D, Li J, Newman D. The chemical ecology of coumarins and phenazines affects iron acquisition by pseudomonads. Proc Natl Acad Sci U S A 2023; 120:e2217951120. [PMID: 36996105 PMCID: PMC10083548 DOI: 10.1073/pnas.2217951120] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/27/2023] [Indexed: 03/31/2023] Open
Abstract
Secondary metabolites are important facilitators of plant-microbe interactions in the rhizosphere, contributing to communication, competition, and nutrient acquisition. However, at first glance, the rhizosphere seems full of metabolites with overlapping functions, and we have a limited understanding of basic principles governing metabolite use. Increasing access to the essential nutrient iron is one important, but seemingly redundant role performed by both plant and microbial Redox-Active Metabolites (RAMs). We used coumarins, RAMs made by the model plant Arabidopsis thaliana, and phenazines, RAMs made by soil-dwelling pseudomonads, to ask whether plant and microbial RAMs might each have distinct functions under different environmental conditions. We show that variations in oxygen and pH lead to predictable differences in the capacity of coumarins vs phenazines to increase the growth of iron-limited pseudomonads and that these effects depend on whether pseudomonads are grown on glucose, succinate, or pyruvate: carbon sources commonly found in root exudates. Our results are explained by the chemical reactivities of these metabolites and the redox state of phenazines as altered by microbial metabolism. This work shows that variations in the chemical microenvironment can profoundly affect secondary metabolite function and suggests plants may tune the utility of microbial secondary metabolites by altering the carbon released in root exudates. Together, these findings suggest that RAM diversity may be less overwhelming when viewed through a chemical ecological lens: Distinct molecules can be expected to be more or less important to certain ecosystem functions, such as iron acquisition, depending on the local chemical microenvironments in which they reside.
Collapse
Affiliation(s)
- Darcy L. McRose
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Jinyang Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
| | - Dianne K. Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| |
Collapse
|
32
|
Yu J, Niu Y, You Y, Cox CJ, Barrett RL, Trias-Blasi A, Guo J, Wen J, Lu L, Chen Z. Integrated phylogenomic analyses unveil reticulate evolution in Parthenocissus (Vitaceae), highlighting speciation dynamics in the Himalayan-Hengduan Mountains. THE NEW PHYTOLOGIST 2023; 236:1140-1153. [PMID: 36305244 DOI: 10.1111/nph.18289] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/22/2022] [Indexed: 05/20/2023]
Abstract
Hybridization caused by frequent environmental changes can lead both to species diversification (speciation) and to speciation reversal (despeciation), but the latter has rarely been demonstrated. Parthenocissus, a genus with its trifoliolate lineage in the Himalayan-Hengduan Mountains (HHM) region showing perplexing phylogenetic relationships, provides an opportunity for investigating speciation dynamics based on integrated evidence. We investigated phylogenetic discordance and reticulate evolution in Parthenocissus based on rigorous analyses of plastome and transcriptome data. We focused on reticulations in the trifoliolate lineage in the HHM region using a population-level genome resequencing dataset, incorporating evidence from morphology, distribution, and elevation. Comprehensive analyses confirmed multiple introgressions within Parthenocissus in a robust temporal-spatial framework. Around the HHM region, at least three hybridization hot spots were identified, one of which showed evidence of ongoing speciation reversal. We present a solid case study using an integrative methodological approach to investigate reticulate evolutionary history and its underlying mechanisms in plants. It demonstrates an example of speciation reversal through frequent hybridizations in the HHM region, which provides new perspectives on speciation dynamics in mountainous areas with strong topographic and environmental heterogeneity.
Collapse
Affiliation(s)
- Jinren Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanting Niu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Botanical Garden, Beijing, 100093, China
| | - Yichen You
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cymon J Cox
- Centro de Ciências do Mar, Universidade do Algarve, Gambelas, Faro, 8005-319, Portugal
| | - Russell L Barrett
- National Herbarium of New South Wales, Australian Botanic Garden, Locked Bag 6002, Mount Annan, 2567, NSW, Australia
| | | | - Jing Guo
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC-166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Limin Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhiduan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| |
Collapse
|
33
|
Moomin A, Russell WR, Knott RM, Scobbie L, Mensah KB, Adu-Gyamfi PKT, Duthie SJ. Season, storage and extraction method impact on the phytochemical profile of Terminalia ivorensis. BMC PLANT BIOLOGY 2023; 23:162. [PMID: 36964494 PMCID: PMC10039578 DOI: 10.1186/s12870-023-04144-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Terminalia ivorensis (TI) is used in West African ethnomedicine for the treatment of conditions including ulcers, malaria and wounds. Despite its widespread use, the phytochemical profile of TI remains largely undetermined. This research investigated the effects of extraction method, season, and storage conditions on the phytochemical composition of TI to contribute towards understanding the potential benefits. METHODS TI bark was collected in September 2014, September 2018 and February 2018 during the rainy or dry seasons in Eastern Region, Ghana. Samples were extracted sequentially with organic solvents (petroleum ether, chloroform, ethyl acetate and ethanol) or using water (traditional). Metabolites were identified by liquid chromatography-mass spectrometry/mass spectrometry and compared statistically by ANOVA. RESULTS A total of 82 different phytochemicals were identified across all samples. A greater yield of the major phytochemicals (44%, p < 0.05) was obtained by water as compared with organic extraction. There was also a higher concentration of metabolites present in cold (63%, p < 0.05) compared with hot water extraction. A significantly (p < 0.05) higher number of phytochemicals were identified from TI collected in the dry (85%) compared to the rainy season (69%). TI bark stored for four years retained 84% of the major phytochemicals. CONCLUSION This work provides important information on composition and how this is modified by growing conditions, storage and method of extraction informing progress on the development of TI as a prophylactic formulation or medicine.
Collapse
Affiliation(s)
- Aliu Moomin
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, AB10 7GJ UK
- University of Aberdeen, Rowett Institute, Foresterhill Campus, Ashgrove Road West, Scotland, AB25 2ZD UK
| | - Wendy R. Russell
- University of Aberdeen, Rowett Institute, Foresterhill Campus, Ashgrove Road West, Scotland, AB25 2ZD UK
| | - Rachel M. Knott
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, AB10 7GJ UK
| | - Lorraine Scobbie
- University of Aberdeen, Rowett Institute, Foresterhill Campus, Ashgrove Road West, Scotland, AB25 2ZD UK
| | - Kwesi Boadu Mensah
- Department of Pharmacology, Faculty of Pharmacy and Pharmaceutical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Paa Kofi Tawiah Adu-Gyamfi
- Faculty of Health and Allied Sciences, Department of Nursing and Midwifery, Pentecost University College, Accra, Ghana
| | - Susan J. Duthie
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, AB10 7GJ UK
| |
Collapse
|
34
|
Miao Y, Zhang X, Zhang G, Feng Z, Pei J, Liu C, Huang L. From guest to host: parasite Cistanche deserticola shapes and dominates bacterial and fungal community structure and network complexity. ENVIRONMENTAL MICROBIOME 2023; 18:11. [PMID: 36814319 PMCID: PMC9945605 DOI: 10.1186/s40793-023-00471-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Rhizosphere and plant microbiota are assumed to play an essential role in deciding the well-being of hosts, but effects of parasites on their host microbiota have been rarely studied. Also, the characteristics of the rhizosphere and root microbiota of parasites and hosts under parasitism is relatively unknown. In this study, we used Cistanche deserticola and Haloxylon ammodendron from cultivated populations as our model parasites and host plants, respectively. We collected samples from BULK soil (BULK), rhizosphere soil of H. ammodendron not parasitized (NCD) and parasitized (RHA) to study how the parasite influenced the rhizosphere microbiota of the host. We also collected samples from the rhizosphere soil and roots of C. deserticola (RCD and ECD) and Haloxylon ammodendron (RHA and EHA) to explore the difference between the microbiota of the parasite and its host under parasitism. RESULTS The parasite reduced the compositional and co-occurrence network complexities of bacterial and fungal microbiota of RHA. Additionally, the parasite increased the proportion of stochastic processes mainly belonging to dispersal limitation in the bacterial microbiota of RHA. Based on the PCoA ordinations and permutational multivariate analysis of variance, the dissimilarity between microbiota of C. deserticola and H. ammodendron were rarely evident (bacteria, R2 = 0.29971; fungi, R2 = 0.15631). Interestingly, four hub nodes of H. ammodendron in endosphere fungal microbiota were identified, while one hub node of C. deserticola in endosphere fungal microbiota was identified. It indicated that H. ammodendron played a predominant role in the co-occurrence network of endosphere fungal microbiota. Source model of plant microbiome suggested the potential source percentage from the parasite to the host (bacteria: 52.1%; fungi: 16.7%) was lower than host-to-parasite (bacteria: 76.5%; fungi: 34.3%), illustrating that microbial communication was bidirectional, mainly from the host to the parasite. CONCLUSIONS Collectively, our results suggested that the parasite C. deserticola shaped the diversity, composition, co-occurrence network, and community assembly mechanisms of the rhizosphere microbiota of H. ammodendron. Additionally, the microbiota of C. deserticola and H. ammodendron were highly similar and shared. Our findings on parasite and host microbiota provided a novel line of evidence supporting the influence of parasites on the microbiota of their hosts.
Collapse
Affiliation(s)
- Yujing Miao
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Xinke Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Guoshuai Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Zhan Feng
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
- Jiangxi University of Traditional Chinese Medicine, Nanchang, 330000, Jiangxi, China
| | - Jin Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, Sichuan, China
| | - Chang Liu
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Linfang Huang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
| |
Collapse
|
35
|
Poupin MJ, Ledger T, Roselló-Móra R, González B. The Arabidopsis holobiont: a (re)source of insights to understand the amazing world of plant-microbe interactions. ENVIRONMENTAL MICROBIOME 2023; 18:9. [PMID: 36803555 PMCID: PMC9938593 DOI: 10.1186/s40793-023-00466-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
As holobiont, a plant is intrinsically connected to its microbiomes. However, some characteristics of these microbiomes, such as their taxonomic composition, biological and evolutionary role, and especially the drivers that shape them, are not entirely elucidated. Reports on the microbiota of Arabidopsis thaliana first appeared more than ten years ago. However, there is still a lack of a comprehensive understanding of the vast amount of information that has been generated using this holobiont. The main goal of this review was to perform an in-depth, exhaustive, and systematic analysis of the literature regarding the Arabidopsis-microbiome interaction. A core microbiota was identified as composed of a few bacterial and non-bacterial taxa. The soil (and, to a lesser degree, air) were detected as primary microorganism sources. From the plant perspective, the species, ecotype, circadian cycle, developmental stage, environmental responses, and the exudation of metabolites were crucial factors shaping the plant-microbe interaction. From the microbial perspective, the microbe-microbe interactions, the type of microorganisms belonging to the microbiota (i.e., beneficial or detrimental), and the microbial metabolic responses were also key drivers. The underlying mechanisms are just beginning to be unveiled, but relevant future research needs were identified. Thus, this review provides valuable information and novel analyses that will shed light to deepen our understanding of this plant holobiont and its interaction with the environment.
Collapse
Affiliation(s)
- M J Poupin
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, 7941169, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - T Ledger
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, 7941169, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - R Roselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), Illes Balears, Majorca, Spain
| | - B González
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, 7941169, Santiago, Chile.
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile.
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile.
| |
Collapse
|
36
|
Wang L, Liu J, Zhang M, Wu T, Chai B. Ecological Processes of Bacterial and Fungal Communities Associated with Typha orientalis Roots in Wetlands Were Distinct during Plant Development. Microbiol Spectr 2023; 11:e0505122. [PMID: 36688664 PMCID: PMC9927475 DOI: 10.1128/spectrum.05051-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/20/2022] [Indexed: 01/24/2023] Open
Abstract
Root-associated microbiomes are essential for the ecological function of the root system. However, their assembly mechanisms in wetland are poorly understood. In this study, we explored and compared the ecological processes of bacterial and fungal communities in water, bulk soil, rhizosphere soil, and root endosphere niches for 3 developmental stages of Typha orientalis at different wetland sites, and assessed the potential functions of root endosphere microbiomes with function prediction. Our findings suggest that the microbial diversity, composition, and interaction networks along the water-soil-plant continuum are shaped predominantly by compartment niche and developmental stage, rather than by wetland site. Source tracking analysis indicated that T. orientalis' root endosphere is derived primarily from the rhizosphere soil (bacteria 39.9%, fungi 27.3%) and water (bacteria 18.9%, fungi 19.1%) niches. In addition, we found that the assembly of bacterial communities is driven primarily by deterministic processes and fungal communities by stochastic processes. The interaction network among microbes varies at different developmental stages of T. orientalis, and is accompanied by changes in microbial keystone taxa. The functional prediction data supports the distribution pattern of the bacterial and fungal microbiomes, which have different ecological roles at different plant developmental stages, where more beneficial bacterial taxa are observed in the root endosphere in the early stages, but more saprophytic fungi in the late stages. Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities and have significant implications for the future applications of plant microbiomes in the wetland ecosystem. IMPORTANCE Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities, and have significant implications for the future applications of plant microbiomes in the wetland ecosystem.
Collapse
Affiliation(s)
- Lixiao Wang
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan, China
| | - Jinxian Liu
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan, China
| | - Meiting Zhang
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan, China
| | - Tiehang Wu
- Department of Biology, Georgia Southern University, Statesboro, Georgia, USA
| | - Baofeng Chai
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan, China
| |
Collapse
|
37
|
Olanbiwoninu A, Popoola B. Biofilms and their impact on the food industry. Saudi J Biol Sci 2023; 30:103523. [PMID: 36568412 PMCID: PMC9772555 DOI: 10.1016/j.sjbs.2022.103523] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 11/02/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022] Open
Abstract
Biofilm could be defined as a complex communities of microorganisms seen affixed to surfaces, they form clusters without sticking to any surface and buried firmly in an extracellular matrix (ECM). This matrix is formed by microorganisms in the formation of either extracellular polymeric substances (EPSS) or extracellular polymer. Many reviews have addressed the negative consequences of biofilm production in the food industry, among which we talk about biofilms being responsible for spoilage microorganisms and foodborne pathogens such as Listeria monocytogenes, Bacillus cereus etc. These contamination could be linked to biofilms presence in the processing plant. Although researches have tried conferring solutions to these challenges in the food industry, however, in this review we have tried to focus on the positive impact of biofilms formed in the food industry. It is critically expedient while trying to find the solution to the challenges of biofilm in the food industry to develop and give a major focus on the advantages and positive impact biofilm has in the food industry, which has been greatly neglected. Hence in this article, we have highlighted some positive impacts of biofilms formed in the food industry, like enhancing plant health and productivity of food products, as an agent of water and wastewater treatment in the food industry, as a tool in reducing the amount of excess sludge in the wastewater treatment plant. The development of edible biofilms, fermented food products and the production of biodegradable food packaging are also part of biofilms beneficial roles in the food industries.
Collapse
|
38
|
Li P, Ye S, Chen J, Wang L, Li Y, Ge L, Wu G, Song L, Wang C, Sun Y, Wang J, Pan A, Quan Z, Wu Y. Combined metagenomic and metabolomic analyses reveal that Bt rice planting alters soil C-N metabolism. ISME COMMUNICATIONS 2023; 3:4. [PMID: 36690796 PMCID: PMC9870860 DOI: 10.1038/s43705-023-00217-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 01/04/2023] [Accepted: 01/13/2023] [Indexed: 01/25/2023]
Abstract
The environmental impacts of genetically modified (GM) plants remain a controversial global issue. To address these issues, comprehensive environmental risk assessments of GM plants is critical for the sustainable development and application of transgenic technology. In this paper, significant differences were not observed between microbial metagenomic and metabolomic profiles in surface waters of the Bt rice (T1C-1, the transgenic line) and non-Bt cultivars (Minghui 63 (the isogenic line) and Zhonghua 11 (the conventional japonica cultivar)). In contrast, differences in these profiles were apparent in the rhizospheres. T1C-1 planting increased soil microbiome diversity and network stability, but did not significantly alter the abundances of potential probiotic or phytopathogenic microorganisms compared with Minghui 63 and Zhonghua 11, which revealed no adverse effects of T1C-1 on soil microbial communities. T1C-1 planting could significantly alter soil C and N, probably via the regulation of the abundances of enzymes related to soil C and N cycling. In addition, integrated multi-omic analysis of root exudate metabolomes and soil microbiomes showed that the abundances of various metabolites released as root exudates were significantly correlated with subsets of microbial populations including the Acidobacteria, Actinobacteria, Chloroflexi, and Gemmatimonadetes that were differentially abundant in T1C-1 and Mnghui 63 soils. Finally, the potential for T1C-1-associated root metabolites to exert growth effects on T1C-1-associated species was experimentally validated by analysis of bacterial cultures, revealing that Bt rice planting could selectively modulate specific root microbiota. Overall, this study indicate that Bt rice can directly modulate rhizosphere microbiome assemblages by altering the metabolic compositions of root exudates that then alters soil metabolite profiles and physiochemical properties. This study unveils the mechanistic associations of Bt plant-microorganism-environment, which provides comprehensive insights into the potential ecological impacts of GM plants.
Collapse
Affiliation(s)
- Peng Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China.
- Shanghai Co-Elite Agricultural Sci-Tech (Group) Co., Ltd, 201106, Shanghai, China.
| | - Shuifeng Ye
- College of Life Sciences, Shangrao Normal University, 334001, Shangrao, China
| | - Jun Chen
- East China University of Technology, 330013, Nanchang, China
| | - Luyao Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Yujie Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Lei Ge
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Guogan Wu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Lili Song
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Cui Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Yu Sun
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Jinbin Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Aihu Pan
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Zhexue Quan
- School of Life Sciences, Fudan University, 200433, Shanghai, China.
| | - Yunfei Wu
- The College of Bioscience and Biotechnology, Yangzhou University, 225009, Yangzhou, China.
| |
Collapse
|
39
|
Tan Y, Wang J, He Y, Yu X, Chen S, Penttinen P, Liu S, Yang Y, Zhao K, Zou L. Organic Fertilizers Shape Soil Microbial Communities and Increase Soil Amino Acid Metabolites Content in a Blueberry Orchard. MICROBIAL ECOLOGY 2023; 85:232-246. [PMID: 35064809 DOI: 10.1007/s00248-022-01960-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
The decline in soil nutrients is becoming a major concern of soil degradation. The possibility of using organic waste as a soil additive to increase nutrients and essential components is significant in soil quality protection and waste management. The aim of this study was to investigate the effects of composted spent mushroom substrate (MS), giant panda feces (PF), and cattle manure (CM) as organic fertilizers in soil microbial communities and metabolites in blueberry orchard in China, which were measured by using high-throughput sequencing and gas chromatography-mass spectrometry (GC-MS)-based metabolomics. Altogether, 45.66% of the bacterial operational taxonomic units (OTUs) and 9.08% of the fungal OTUs were detected in all treatments. Principal coordinates analysis demonstrated that the bacterial and fungal communities in MS and PF treatments were similar, whereas the communities in the not-organic fertilized control (CK) were significantly different from those in the organic fertilizer treatments. Proteobacteria, Acidobacteria, and Bacteroidetes were the dominant bacterial phyla, and Basidiomycota, Ascomycota, and Mortierellomycota the dominant fungal phyla. Redundancy analysis indicated that pH and available potassium were the main factors determining the composition of microbial communities. The fungal genera Postia, Cephalotrichum, and Thermomyces increased in organic fertilizer treatments, and likely promoted the degradation of organic fertilizers into low molecular-weight metabolites (e.g., amino acids). PCA and PLS-DA models showed that the metabolites in CK were different from those in the other three treatments, and those in CM were clearly different from those in MS and PF. Co-occurrence network analysis showed that several taxa correlated positively with amino acid contents. The results of this study provide new insights into organic waste reutilization and new directions for further studies.
Collapse
Affiliation(s)
- Yulan Tan
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jing Wang
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yongguo He
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, the China Conservation and Research Center for the Giant Panda (CCRCGP), Dujiangyan, 611830, China
| | - Xiumei Yu
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Shujuan Chen
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China
| | - Petri Penttinen
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Shuliang Liu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China
| | - Yong Yang
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China
| | - Ke Zhao
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
- Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu Sichuan, 611130, China.
| | - Likou Zou
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
- Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu Sichuan, 611130, China.
| |
Collapse
|
40
|
Hartman MD, Burnham M, Parton WJ, Finzi A, DeLucia EH, Yang WH. In silico evaluation of plant nitrification suppression effects on agroecosystem nitrogen loss. Ecosphere 2022. [DOI: 10.1002/ecs2.4292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022] Open
Affiliation(s)
- Melannie D. Hartman
- Center for Advanced Bioenergy and Bioproducts Innovation, Natural Resource Ecology Laboratory Colorado State University Fort Collins Colorado USA
| | - Mark Burnham
- Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois at Urbana‐Champaign Urbana Illinois USA
| | - William J. Parton
- Center for Advanced Bioenergy and Bioproducts Innovation, Natural Resource Ecology Laboratory Colorado State University Fort Collins Colorado USA
| | - Adrien Finzi
- Center for Advanced Bioenergy and Bioproducts Innovation, Department of Biology Boston University Boston Massachusetts USA
| | - Evan H. DeLucia
- Center for Advanced Bioenergy and Bioproducts Innovation, Institute for Sustainability, Energy, and Environment, Department of Plant Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
| | - Wendy H. Yang
- Center for Advanced Bioenergy and Bioproducts Innovation, Institute for Sustainability, Energy, and Environment, Department of Plant Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
- Center for Advanced Bioenergy and Bioproducts Innovation, Institute for Sustainability, Energy, and Environment, Department of Geology University of Illinois at Urbana‐Champaign Urbana Illinois USA
| |
Collapse
|
41
|
Hestrin R, Kan M, Lafler M, Wollard J, Kimbrel JA, Ray P, Blazewicz SJ, Stuart R, Craven K, Firestone M, Nuccio EE, Pett-Ridge J. Plant-associated fungi support bacterial resilience following water limitation. THE ISME JOURNAL 2022; 16:2752-2762. [PMID: 36085516 PMCID: PMC9666503 DOI: 10.1038/s41396-022-01308-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 08/01/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
Drought disrupts soil microbial activity and many biogeochemical processes. Although plant-associated fungi can support plant performance and nutrient cycling during drought, their effects on nearby drought-exposed soil microbial communities are not well resolved. We used H218O quantitative stable isotope probing (qSIP) and 16S rRNA gene profiling to investigate bacterial community dynamics following water limitation in the hyphospheres of two distinct fungal lineages (Rhizophagus irregularis and Serendipita bescii) grown with the bioenergy model grass Panicum hallii. In uninoculated soil, a history of water limitation resulted in significantly lower bacterial growth potential and growth efficiency, as well as lower diversity in the actively growing bacterial community. In contrast, both fungal lineages had a protective effect on hyphosphere bacterial communities exposed to water limitation: bacterial growth potential, growth efficiency, and the diversity of the actively growing bacterial community were not suppressed by a history of water limitation in soils inoculated with either fungus. Despite their similar effects at the community level, the two fungal lineages did elicit different taxon-specific responses, and bacterial growth potential was greater in R. irregularis compared to S. bescii-inoculated soils. Several of the bacterial taxa that responded positively to fungal inocula belong to lineages that are considered drought susceptible. Overall, H218O qSIP highlighted treatment effects on bacterial community structure that were less pronounced using traditional 16S rRNA gene profiling. Together, these results indicate that fungal-bacterial synergies may support bacterial resilience to moisture limitation.
Collapse
Affiliation(s)
- Rachel Hestrin
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA.
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, USA.
| | - Megan Kan
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA
| | - Marissa Lafler
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA
| | - Jessica Wollard
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA
| | - Jeffrey A Kimbrel
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA
| | - Prasun Ray
- Department of Natural Resources, University of Maryland Eastern Shore, Princess Anne, MD, USA
- Plant Biology Division, Noble Research Institute, Ardmore, OK, USA
| | - Steven J Blazewicz
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA
| | - Rhona Stuart
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA
| | - Kelly Craven
- Plant Biology Division, Noble Research Institute, Ardmore, OK, USA
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA
| | - Mary Firestone
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA
| | - Erin E Nuccio
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA.
- Life & Environmental Sciences Department, University of California Merced, Merced, CA, USA.
| |
Collapse
|
42
|
Chen JM, Feng WM, Yan H, Liu P, Zhou GS, Guo S, Yu G, Duan JA. Explore the interaction between root metabolism and rhizosphere microbiota during the growth of Angelica sinensis. FRONTIERS IN PLANT SCIENCE 2022; 13:1005711. [PMID: 36420035 PMCID: PMC9676459 DOI: 10.3389/fpls.2022.1005711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Angelica sinensis is a medicinal plant widely used to treat multiple diseases in Asia and Europe, which contains numerous active components with therapeutic value. The interaction between root and rhizosphere microorganisms is crucial for the growth and quality formation of medicinal plants. But the micro-plant-metabolite regulation patterns for A. sinensis remain largely undetermined. Here, we collected roots and rhizosphere soils from A. sinensis in seedling stage (M) and picking stage (G), respectively cultivated for one year and two years, generated metabolite for roots, microbiota data for rhizospheres, and conducted a comprehensive analysis. Changes in metabolic and microbial communities of A.sinensis over growth were distinct. The composition of rhizosphere microbes in G was dominated by proteobacteria, which had a strong correlation with the synthesis of organic acids, while in M was dominated by Actinobacteria, which had a strong correlation with the synthesis of phthalide and other organoheterocyclic compounds, flavonoids, amines, and fatty acid. Additionally, co-occurrence network analysis identified that Arthrobacter was found to be strongly correlated with the accumulation of senkyunolide A and n-butylidenephthalide. JGI 0001001.H03 was found to be strongly correlated with the accumulation of chlorogenic acid. Based on rhizosphere microorganisms, this study investigated the correlation between root metabolism and rhizosphere microbiota of A. sinensis at different growth stages in traditional geoherb region, which could provide references for exploring the quality formation mechanism of A. sinensis in the future.
Collapse
Affiliation(s)
| | | | - Hui Yan
- *Correspondence: Hui Yan, ; Pei Liu, ; Jin-Ao Duan,
| | - Pei Liu
- *Correspondence: Hui Yan, ; Pei Liu, ; Jin-Ao Duan,
| | | | | | | | - Jin-Ao Duan
- *Correspondence: Hui Yan, ; Pei Liu, ; Jin-Ao Duan,
| |
Collapse
|
43
|
Metabolite Production in Alkanna tinctoria Links Plant Development with the Recruitment of Individual Members of Microbiome Thriving at the Root-Soil Interface. mSystems 2022; 7:e0045122. [PMID: 36069453 PMCID: PMC9601132 DOI: 10.1128/msystems.00451-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Plants are naturally associated with diverse microbial communities, which play significant roles in plant performance, such as growth promotion or fending off pathogens. The roots of Alkanna tinctoria L. are rich in naphthoquinones, particularly the medicinally used enantiomers alkannin and shikonin and their derivatives. Former studies already have shown that microorganisms may modulate plant metabolism. To further investigate the potential interaction between A. tinctoria and associated microorganisms, we performed a greenhouse experiment in which A. tinctoria plants were grown in the presence of three distinct soil microbiomes. At four defined plant developmental stages, we made an in-depth assessment of bacterial and fungal root-associated microbiomes as well as all extracted primary and secondary metabolite content of root material. Our results showed that the plant developmental stage was the most important driver influencing the plant metabolite content, revealing peak contents of alkannin/shikonin derivatives at the fruiting stage. Plant root microbial diversity was influenced both by bulk soil origin and to a small extent by the developmental stage. The performed correlation analyses and cooccurrence networks on the measured metabolite content and the abundance of individual bacterial and fungal taxa suggested a dynamic and at times positive or negative relationship between root-associated microorganisms and root metabolism. In particular, the bacterial genera Labrys and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium as well as four species of the fungal genus Penicillium were found to be positively correlated with higher content of alkannins. IMPORTANCE Previous studies have shown that individual, isolated microorganisms may influence secondary metabolism of plants and induce or stimulate the production of medicinally relevant secondary metabolism. Here, we analyzed the microbiome-metabolome linkage of the medicinal plant Alkanna tinctoria, which is known to produce valuable compounds, particularly the naphthoquinones alkannin and shikonin and their derivatives. A detailed bacterial and fungal microbiome and metabolome analysis of A. tinctoria roots revealed that the plant developmental stage influenced root metabolite production, whereas soil inoculants from three different geographical origins in which plants were grown shaped root-associated microbiota. Metabolomes of plant roots of the same developmental stage across different soils were highly similar, pinpointing to plant maturity as the primary driver of secondary metabolite production. Correlation and network analyses identified bacterial and fungal taxa showing a positive relationship between root-associated microorganisms and root metabolism. In particular, the bacterial genera Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium and Labrys as well as the fungal species of genus Penicillium were found to be positively correlated with higher content of alkannins.
Collapse
|
44
|
Hamdan MF, Karlson CKS, Teoh EY, Lau SE, Tan BC. Genome Editing for Sustainable Crop Improvement and Mitigation of Biotic and Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2022. [PMID: 36235491 DOI: 10.1007/s44187-022-00009-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Climate change poses a serious threat to global agricultural activity and food production. Plant genome editing technologies have been widely used to develop crop varieties with superior qualities or can tolerate adverse environmental conditions. Unlike conventional breeding techniques (e.g., selective breeding and mutation breeding), modern genome editing tools offer more targeted and specific alterations of the plant genome and could significantly speed up the progress of developing crops with desired traits, such as higher yield and/or stronger resilience to the changing environment. In this review, we discuss the current development and future applications of genome editing technologies in mitigating the impacts of biotic and abiotic stresses on agriculture. We focus specifically on the CRISPR/Cas system, which has been the center of attention in the last few years as a revolutionary genome-editing tool in various species. We also conducted a bibliographic analysis on CRISPR-related papers published from 2012 to 2021 (10 years) to identify trends and potential in the CRISPR/Cas-related plant research. In addition, this review article outlines the current shortcomings and challenges of employing genome editing technologies in agriculture with notes on future prospective. We believe combining conventional and more innovative technologies in agriculture would be the key to optimizing crop improvement beyond the limitations of traditional agricultural practices.
Collapse
Affiliation(s)
- Mohd Fadhli Hamdan
- Centre for Research in Biotechnology for Agriculture, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Chou Khai Soong Karlson
- Centre for Research in Biotechnology for Agriculture, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Ee Yang Teoh
- Centre for Research in Biotechnology for Agriculture, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Su-Ee Lau
- Centre for Research in Biotechnology for Agriculture, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Boon Chin Tan
- Centre for Research in Biotechnology for Agriculture, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| |
Collapse
|
45
|
Sugars and Jasmonic Acid Concentration in Root Exudates Affect Maize Rhizosphere Bacterial Communities. Appl Environ Microbiol 2022; 88:e0097122. [PMID: 36073926 PMCID: PMC9499034 DOI: 10.1128/aem.00971-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Root exudates contribute to shaping the root-associated microbiomes, but it is unclear which of the many exudate compounds are important in this process. Here, we focused on understanding the influence of sugars and jasmonic acid (JA) concentrations in maize root exudates on the rhizobacterial communities. Twelve maize genotypes were identified with variable concentrations of sugars and JA based on a screening of 240 maize genotypes grown in a semihydroponic system. These twelve maize genotypes were grown in a replicated field experiment in which samples were collected at three maize developmental stages. The 16S rRNA gene (V4 region) was amplified and sequenced. Sugars and JA concentrations from rhizosphere soils were also quantified. The results indicated that the maize genotypic variability in sugars and JA concentration in root exudates, measured in the semihydroponic system, significantly affected the rhizosphere bacterial community composition at multiple stages plant development. In contrast, the root endosphere and bulk soil bacterial communities were only affected at specific growth stages. Sugars and JA concentration as quantified in rhizosphere soil samples confirmed that these two compounds affected the rhizobacterial communities at all developmental stages analyzed. The effects of specific sugars on the composition of the rhizobacterial communities were also measured, with larger effects of sucrose at earlier developmental stages and trehalose at later developmental stages. Our results indicate that JA and sugars are important root exudate compounds that influence the composition of the maize rhizobacterial communities. IMPORTANCE Roots secrete exudates that are important in interactions with soil microbes that promote plant growth and health. However, the exact chemical compounds in root exudates that participate in these interactions are not fully known. Here, we investigated whether sugars and the phytohormone jasmonic acid influence the composition of the rhizobacterial communities of maize, which is an important crop for food, feed, and energy. Our results revealed that both compounds contribute to the assemblage of rhizobacterial communities at different maize developmental stages. Knowledge about the specific compounds in root exudates that contribute to shape the rhizobiome will be important for future strategies to develop sustainable agricultural practices that are less dependent on agrochemicals.
Collapse
|
46
|
Cillero JI, Henríquez PA, Ledger TW, Ruz GA, González B. Individual competence predominates over host nutritional status in Arabidopsis root exudate-mediated bacterial enrichment in a combination of four Burkholderiaceae species. BMC Microbiol 2022; 22:218. [PMID: 36114465 PMCID: PMC9482264 DOI: 10.1186/s12866-022-02633-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 08/31/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Rhizosphere microorganisms play a crucial role in plant health and development. Plant root exudates (PRE) are a complex mixture of organic molecules and provide nutritional and signaling information to rhizosphere microorganisms. Burkholderiaceae species are non-abundant in the rhizosphere but exhibit a wide range of plant-growth-promoting and plant-health-protection effects. Most of these plant-associated microorganisms have been studied in isolation under laboratory conditions, whereas in nature, they interact in competition or cooperation with each other. To improve our understanding of the factors driving growth dynamics of low-abundant bacterial species in the rhizosphere, we hypothesized that the growth and survival of four Burkholderiaceae strains (Paraburkholderia phytofirmans PsJN, Cupriavidus metallidurans CH34, C. pinatubonensis JMP134 and C. taiwanensis LMG19424) in Arabidopsis thaliana PRE is affected by the presence of each other.
Results
Differential growth abilities of each strain were found depending on plant age and whether PRE was obtained after growth on N limitation conditions. The best-adapted strain to grow in PRE was P. phytofirmans PsJN, with C. pinatubonensis JMP134 growing better than the other two Cupriavidus strains. Individual strain behavior changed when they succeeded in combinations. Clustering analysis showed that the 4-member co-culture grouped with one of the best-adapted strains, either P. phytofirmans PsJN or C. pinatubonensis JMP134, depending on the PRE used. Sequential transference experiments showed that the behavior of the 4-member co-culture relies on the type of PRE provided for growth.
Conclusions
The results suggest that individual strain behavior changed when they grew in combinations of two, three, or four members, and those changes are determined first by the inherent characteristics of each strain and secondly by the environment.
Collapse
|
47
|
Wen T, Yu GH, Hong WD, Yuan J, Niu GQ, Xie PH, Sun FS, Guo LD, Kuzyakov Y, Shen QR. Root exudate chemistry affects soil carbon mobilization via microbial community reassembly. FUNDAMENTAL RESEARCH 2022; 2:697-707. [PMID: 38933120 PMCID: PMC11197519 DOI: 10.1016/j.fmre.2021.12.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 11/20/2022] Open
Abstract
Plant roots are one of the major mediators that allocate carbon captured from the atmosphere to soils as rhizodeposits, including root exudates. Although rhizodeposition regulates both microbial activity and the biogeochemical cycling of nutrients, the effects of particular exudate species on soil carbon fluxes and key rhizosphere microorganisms remain unclear. By combining high-throughput sequencing, q-PCR, and NanoSIMS analyses, we characterized the bacterial community structure, quantified total bacteria depending on root exudate chemistry, and analyzed the consequences on the mobility of mineral-protected carbon. Using well-controlled incubation experiments, we showed that the three most abundant groups of root exudates (amino acids, carboxylic acids, and sugars) have contrasting effects on the release of dissolved organic carbon (DOC) and bioavailable Fe in an Ultisol through the disruption of organo-mineral associations and the alteration of bacterial communities, thus priming organic matter decomposition in the rhizosphere. High resolution (down to 50 nm) NanoSIMS images of mineral particles indicated that iron and silicon co-localized significantly more organic carbon following amino acid inputs than treatments without exudates or with carboxylic acids. The application of sugar strongly reduced microbial diversity without impacting soil carbon mobilization. Carboxylic acids increased the prevalence of Actinobacteria and facilitated carbon mobilization, whereas amino acid addition increased the abundances of Proteobacteria that prevented DOC release. In summary, root exudate functions are defined by their chemical composition that regulates bacterial community composition and, consequently, the biogeochemical cycling of carbon in the rhizosphere.
Collapse
Affiliation(s)
- Tao Wen
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Guang-Hui Yu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University Tianjin Bohai Rim Coastal Earth Critical Zone National Observation and Research Station, Tianjin 300072, China
| | - Wen-Dan Hong
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Yuan
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Guo-Qing Niu
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Peng-Hao Xie
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Fu-Sheng Sun
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University Tianjin Bohai Rim Coastal Earth Critical Zone National Observation and Research Station, Tianjin 300072, China
| | - Lao-Dong Guo
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, 600 E Greenfield Ave., Milwaukee, WI 53204, United States
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Göttingen, Göttingen 37073, Germany
- Agro-Technological Institute, Peoples Friendship University of Russia (RUDN University), Moscow 117198, Russia
| | - Qi-Rong Shen
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
48
|
Dundas CM, Dinneny JR. Genetic Circuit Design in Rhizobacteria. BIODESIGN RESEARCH 2022; 2022:9858049. [PMID: 37850138 PMCID: PMC10521742 DOI: 10.34133/2022/9858049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/31/2022] [Indexed: 10/19/2023] Open
Abstract
Genetically engineered plants hold enormous promise for tackling global food security and agricultural sustainability challenges. However, construction of plant-based genetic circuitry is constrained by a lack of well-characterized genetic parts and circuit design rules. In contrast, advances in bacterial synthetic biology have yielded a wealth of sensors, actuators, and other tools that can be used to build bacterial circuitry. As root-colonizing bacteria (rhizobacteria) exert substantial influence over plant health and growth, genetic circuit design in these microorganisms can be used to indirectly engineer plants and accelerate the design-build-test-learn cycle. Here, we outline genetic parts and best practices for designing rhizobacterial circuits, with an emphasis on sensors, actuators, and chassis species that can be used to monitor/control rhizosphere and plant processes.
Collapse
Affiliation(s)
| | - José R. Dinneny
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
49
|
Dhamale T, Saha BK, Papade SE, Singh S, Phale PS. A unique global metabolic trait of Pseudomonas bharatica CSV86 T: metabolism of aromatics over simple carbon sources and co-metabolism with organic acids. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35925665 DOI: 10.1099/mic.0.001206] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Hierarchical utilization of substrate by microbes (utilization of simple carbon sources prior to complex ones) poses a major limitation to the efficient remediation of aromatic pollutants. Aromatic compounds, being complex and reduced in nature, appear to be a deferred choice as the carbon source in the presence of a plethora of simple organic compounds in the environment. The soil bacterium Pseudomonas bharatica CSV86T displays a unique carbon source utilization hierarchy. It preferentially utilizes aromatics over glucose and co-metabolizes them with succinate or pyruvate (Basu et al., 2006, Applied and Environmental Microbiology, 72 : 22226-2230). In the present study, the substrate utilization hierarchy for strain CSV86T was tested for additional simple carbon sources such as glycerol, acetate, and tri-carboxylic acid (TCA) cycle intermediates like α-ketoglutarate and fumarate. When grown on a mixture of aromatics (benzoate or naphthalene) plus glycerol, the strain displayed a diauxic growth profile with significantly high activity of aromatic utilization enzymes (catechol 1,2- or 2,3-dioxygenase, respectively) in the first-log phase. This suggests utilization of aromatics in the first-log phase followed by glycerol in the second-log phase. On a mixture of an aromatic plus organic acid (acetate, α-ketoglutarate or fumarate), the strain displayed a monoauxic growth profile, indicating co-metabolism. Interestingly, the presence of glycerol, acetate, α-ketoglutarate or fumarate does not repress metabolism/utilization of the aromatic. Thus, the substrate utilization hierarchy of strain CSV86T is aromatics=organic acids>glucose/glycerol, which is unique as compared to other Pseudomonas species, where degradation of aromatics is repressed by glycerol, glucose, acetate or organic acids, including TCA cycle intermediates. This novel substrate utilization hierarchy appears to be a global metabolic phenomenon in strain CSV86T, thus implying it to be an ideal host for metabolic engineering as well as for its potential application in bioremediation.
Collapse
Affiliation(s)
- Tushar Dhamale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
| | - Braja Kishor Saha
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
| | - Sandesh E Papade
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
| | - Srushti Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India.,Present address: Presently affiliated to TCR Therapeutics, Inc., 100 Binney Street, Cambridge, MA 02142, USA
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
| |
Collapse
|
50
|
A Drying-Rewetting Cycle Imposes More Important Shifts on Soil Microbial Communities than Does Reduced Precipitation. mSystems 2022; 7:e0024722. [PMID: 35762785 PMCID: PMC9426475 DOI: 10.1128/msystems.00247-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Global changes will result in altered precipitation patterns, among which the increasing frequency of drought events has the highest deleterious potential for agriculture. Soil microbes have shown some promise to help crops adapt to drought events, but it is uncertain how crop-associated microorganisms will respond to altered precipitation patterns. To investigate this matter, we conducted a field experiment where we seeded two wheat cultivars (one resistant to water stress and the other sensitive) that were subjected to four precipitation exclusion (PE) regimes (0%, 25%, 50%, and 75% exclusion). These cultivars were sampled seven times (every 2 weeks, from May to August) within one growing season to investigate short-term microbiome responses to altered precipitation regimes and seasonality using 16S rRNA gene and internal transcribed spacer (ITS) region amplicon sequencing. One of the most striking features of the data set was the dramatic shift in microbial community diversity, structure, and composition together with a doubling of the relative abundance of the archaeal ammonia oxidizer genus Nitrososphaera following an important drying-rewetting event. Comparatively small but significant effects of PE and wheat cultivar on microbial community diversity, composition, and structure were observed. Taken together, our results demonstrate an uneven response of microbial taxa to decreasing soil water content, which was dwarfed by drying-rewetting events, to which soil bacteria and archaea were more sensitive than fungi. Importantly, our study showed that an increase in drying-rewetting cycles will cause larger shifts in soil microbial communities than a decrease in total precipitation, suggesting that under climate changes, the distribution of precipitation will be more important than small variations in the total quantity of precipitation. IMPORTANCE Climate change will have a profound effect on the precipitation patterns of global terrestrial ecosystems. Seasonal and interannual uneven distributions of precipitation will lead to increasing frequencies and intensities of extreme drought and rainfall events, which will affect crop productivity and nutrient contents in various agroecosystems. However, we still lack knowledge about the responses of soil microbial communities to reduced precipitation and drying-rewetting events in agroecosystems. Our results demonstrated an uneven response of the soil microbiome and a dramatic shift in microbial community diversity and structure to a significant drying-rewetting event with a large increase in the relative abundance of archaeal ammonia oxidizers. These findings highlight the larger importance of rewetting of dry soils on microbial communities, as compared to decreased precipitation, with potential for changes in the soil nitrogen cycling.
Collapse
|