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Jones EM, Marken JP, Silver PA. Synthetic microbiology in sustainability applications. Nat Rev Microbiol 2024; 22:345-359. [PMID: 38253793 DOI: 10.1038/s41579-023-01007-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2023] [Indexed: 01/24/2024]
Abstract
Microorganisms are a promising means to address many societal sustainability challenges owing to their ability to thrive in diverse environments and interface with the microscale chemical world via diverse metabolic capacities. Synthetic biology can engineer microorganisms by rewiring their regulatory networks or introducing new functionalities, enhancing their utility for target applications. In this Review, we provide a broad, high-level overview of various research efforts addressing sustainability challenges through synthetic biology, emphasizing foundational microbiological research questions that can accelerate the development of these efforts. We introduce an organizational framework that categorizes these efforts along three domains - factory, farm and field - that are defined by the extent to which the engineered microorganisms interface with the natural external environment. Different application areas within the same domain share many fundamental challenges, highlighting productive opportunities for cross-disciplinary collaborations between researchers working in historically disparate fields.
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Affiliation(s)
- Ethan M Jones
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - John P Marken
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Resnick Sustainability Institute, California Institute of Technology, Pasadena, CA, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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2
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Lim SR, Lee SJ. Multiplex CRISPR-Cas Genome Editing: Next-Generation Microbial Strain Engineering. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38744727 DOI: 10.1021/acs.jafc.4c01650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Genome editing is a crucial technology for obtaining desired phenotypes in a variety of species, ranging from microbes to plants, animals, and humans. With the advent of CRISPR-Cas technology, it has become possible to edit the intended sequence by modifying the target recognition sequence in guide RNA (gRNA). By expressing multiple gRNAs simultaneously, it is possible to edit multiple targets at the same time, allowing for the simultaneous introduction of various functions into the cell. This can significantly reduce the time and cost of obtaining engineered microbial strains for specific traits. In this review, we investigate the resolution of multiplex genome editing and its application in engineering microorganisms, including bacteria and yeast. Furthermore, we examine how recent advancements in artificial intelligence technology could assist in microbial genome editing and engineering. Based on these insights, we present our perspectives on the future evolution and potential impact of multiplex genome editing technologies in the agriculture and food industry.
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Affiliation(s)
- Se Ra Lim
- Department of Systems Biotechnology and Institute of Microbiomics, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Sang Jun Lee
- Department of Systems Biotechnology and Institute of Microbiomics, Chung-Ang University, Anseong 17546, Republic of Korea
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3
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Liang X, Ishfaq S, Liu Y, Jijakli MH, Zhou X, Yang X, Guo W. Identification and genomic insights into a strain of Bacillus velezensis with phytopathogen-inhibiting and plant growth-promoting properties. Microbiol Res 2024; 285:127745. [PMID: 38733724 DOI: 10.1016/j.micres.2024.127745] [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: 11/20/2023] [Revised: 04/27/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024]
Abstract
The use of biological agents offers a sustainable alternative to chemical control in managing plant diseases. In this study, Bacillus velezensis IFST-221 was isolated from the rhizosphere of a healthy maize plant amidst a population showing severe disease symptoms. The investigation demonstrated a broad-spectrum antagonistic activity of IFST-221 against eight species of pathogenic ascomycetes and oomycetes, suggesting its potential utility in combating plant diseases like maize ear rot and cotton Verticillium wilt. Additionally, our study unveiled that IFST-221 has demonstrated significant plant growth-promoting properties, particularly in maize, cotton, tomato, and broccoli seedlings. This growth promotion was linked to its ability to produce indole-3-acetic acid, nitrogen fixation, phosphate and potassium solubilization, and biofilm formation in laboratory conditions. A complete genome sequencing of IFST-221 yielded a genome size of 3.858 M bp and a GC content of 46.71%. The genome analysis identified 3659 protein-coding genes, among which were nine secondary metabolite clusters with known antimicrobial properties. Additionally, three unknown compounds with potentially novel properties were also predicted from the genomic data. Genome mining also identified several key genes associated with plant growth regulation, colonization, and biofilm formation. These findings provide a compelling case for the application of B. velezensis IFST-221 in agricultural practices. The isolate's combined capabilities of plant growth promotion and antagonistic activity against common plant pathogens suggest its promise as an integrated biological agent in disease management and plant productivity enhancement.
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Affiliation(s)
- Xiaoyan Liang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing 100193, China; Gembloux Agro-Bio Tech, Liege University, Laboratory of Integrated and Urban Plant Pathology, Passage des déportés 2, Gembloux 5030, Belgium
| | - Shumila Ishfaq
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Yang Liu
- School of Food Science and Engineering, Foshan University/National Technical Center (Foshan) for Quality Control of Famous and Special Agricultural Products (CAQS-GAP-KZZX043)/Guangdong Key Laboratory of Food Intelligent Manufacturing, Foshan, Guangdong 528231, China
| | - M Haissam Jijakli
- Gembloux Agro-Bio Tech, Liege University, Laboratory of Integrated and Urban Plant Pathology, Passage des déportés 2, Gembloux 5030, Belgium
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiuling Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Wei Guo
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing 100193, China.
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Xiong C, K. Singh B, Zhu YG, Hu HW, Li PP, Han YL, Han LL, Zhang QB, Wang JT, Liu SY, Wu CF, Ge AH, Zhang LM, He JZ. Microbial species pool-mediated diazotrophic community assembly in crop microbiomes during plant development. mSystems 2024; 9:e0105523. [PMID: 38501864 PMCID: PMC11019923 DOI: 10.1128/msystems.01055-23] [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: 10/02/2023] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Plant-associated diazotrophs strongly relate to plant nitrogen (N) supply and growth. However, our knowledge of diazotrophic community assembly and microbial N metabolism in plant microbiomes is largely limited. Here we examined the assembly and temporal dynamics of diazotrophic communities across multiple compartments (soils, epiphytic and endophytic niches of root and leaf, and grain) of three cereal crops (maize, wheat, and barley) and identified the potential N-cycling pathways in phylloplane microbiomes. Our results demonstrated that the microbial species pool, influenced by site-specific environmental factors (e.g., edaphic factors), had a stronger effect than host selection (i.e., plant species and developmental stage) in shaping diazotrophic communities across the soil-plant continuum. Crop diazotrophic communities were dominated by a few taxa (~0.7% of diazotrophic phylotypes) which were mainly affiliated with Methylobacterium, Azospirillum, Bradyrhizobium, and Rhizobium. Furthermore, eight dominant taxa belonging to Azospirillum and Methylobacterium were identified as keystone diazotrophic taxa for three crops and were potentially associated with microbial network stability and crop yields. Metagenomic binning recovered 58 metagenome-assembled genomes (MAGs) from the phylloplane, and the majority of them were identified as novel species (37 MAGs) and harbored genes potentially related to multiple N metabolism processes (e.g., nitrate reduction). Notably, for the first time, a high-quality MAG harboring genes involved in the complete denitrification process was recovered in the phylloplane and showed high identity to Pseudomonas mendocina. Overall, these findings significantly expand our understanding of ecological drivers of crop diazotrophs and provide new insights into the potential microbial N metabolism in the phyllosphere.IMPORTANCEPlants harbor diverse nitrogen-fixing microorganisms (i.e., diazotrophic communities) in both belowground and aboveground tissues, which play a vital role in plant nitrogen supply and growth promotion. Understanding the assembly and temporal dynamics of crop diazotrophic communities is a prerequisite for harnessing them to promote plant growth. In this study, we show that the site-specific microbial species pool largely shapes the structure of diazotrophic communities in the leaves and roots of three cereal crops. We further identify keystone diazotrophic taxa in crop microbiomes and characterize potential microbial N metabolism pathways in the phyllosphere, which provides essential information for developing microbiome-based tools in future sustainable agricultural production.
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Affiliation(s)
- Chao Xiong
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Pei-Pei Li
- College of Resource and Environmental Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yan-Lai Han
- College of Resource and Environmental Sciences, Henan Agricultural University, Zhengzhou, China
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qin-Bing Zhang
- Soil and Fertilizer Station of Qilin District, Qujing, Yunnan Province, China
| | - Jun-Tao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia
| | - Si-Yi Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chuan-Fa Wu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resource and Environmental Sciences, Henan Agricultural University, Zhengzhou, China
| | - An-Hui Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
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Kashiwagi FM, Wendler Miranda B, Maltempi de Souza E, Müller-Santos M. The naringenin-dependent regulator FdeR can be applied as a NIMPLY gate controlled by naringenin and arabinose. Synth Biol (Oxf) 2024; 9:ysae001. [PMID: 38249314 PMCID: PMC10799723 DOI: 10.1093/synbio/ysae001] [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: 07/10/2023] [Revised: 12/07/2023] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
The FdeR regulator has been reported as a transcriptional activator dependent on the interaction with naringenin. Previously, FdeR and its cognate promoter were used to construct naringenin-sensitive sensors, though no correlation was associated between the FdeR level of expression and outputs. Therefore, to understand this correlation, we constructed a circuit with FdeR expression adjusted by the arabinose concentration through an AraC-PBAD system and the FdeR-regulated promoter controlling the expression of GFP. We observed a significant reduction in the activity of the target promoter by increasing FdeR expression, indicating that although FdeR has been primarily classified as a transcriptional activator, it also represses transcription. Leveraging the bifunctional feature of FdeR, acting as both transcriptional activator and repressor, we demonstrated that this genetic circuit, when previously switched on by naringenin, can be switched off by inducing an increased FdeR expression level. This engineered system functioned as a NIMPLY gate, effectively decreasing GFP expression by 50% when arabinose was added without removing naringenin from the medium. Exploiting FdeR versatility, this study demonstrates an innovative application of this transcriptional factor for developing novel NIMPLY gates activated by a molecule with low toxicity and nutraceutical properties that may be important for several applications. Graphical Abstract.
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Affiliation(s)
- Fernanda Miyuki Kashiwagi
- Postgraduate Program in Science (Biochemistry), Department of Biochemistry and Molecular Biology, Nitrogen Fixation Laboratory, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Brenno Wendler Miranda
- Postgraduate Program in Science (Biochemistry), Department of Biochemistry and Molecular Biology, Nitrogen Fixation Laboratory, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Emanuel Maltempi de Souza
- Postgraduate Program in Science (Biochemistry), Department of Biochemistry and Molecular Biology, Nitrogen Fixation Laboratory, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Marcelo Müller-Santos
- Postgraduate Program in Science (Biochemistry), Department of Biochemistry and Molecular Biology, Nitrogen Fixation Laboratory, Federal University of Paraná (UFPR), Curitiba, Brazil
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Custer GF, Mealor BA, Fowers B, van Diepen LTA. Soil microbiome analysis supports claims of ineffectiveness of Pseudomonas fluorescens D7 as a biocontrol agent of Bromus tectorum. Microbiol Spectr 2024; 12:e0177123. [PMID: 38051051 PMCID: PMC10782950 DOI: 10.1128/spectrum.01771-23] [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: 04/28/2023] [Accepted: 10/29/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Cheatgrass is one of North America's most problematic invasive species. Invasion by this annual grass alters ecosystem structure and function and has proven very challenging to remove with traditional approaches. Commercially available bioherbicides, like P. fluorescens D7, are applied with the goal of providing lasting control from a single application. However, experimental results suggest that this bioherbicide has limited efficacy under field conditions. Potential explanations for variable efficacy include a failure of this bioherbicide to establish in the soil microbiome. However, to our knowledge, no data exist to support or refute this hypothesis. Here, we use a deep-sequencing approach to better understand the effects of this bioherbicide on the soil microbiome and screen for P. fluorescens at 18 months post-application.
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Affiliation(s)
- Gordon F. Custer
- Department of Ecosystem Science and Management, University of Wyoming, Laramie, Wyoming, USA
- Program in Ecology, University of Wyoming, Laramie, Wyoming, USA
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
- The One Health Microbiome Center, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Brian A. Mealor
- Department of Plant Sciences, University of Wyoming, Laramie, Wyoming, USA
- Sheridan Research and Extension Center, Sheridan, Wyoming, USA
- Institute for Managing Annual Grasses Invading Natural Ecosystems, Sheridan, Wyoming, USA
| | - Beth Fowers
- Department of Plant Sciences, University of Wyoming, Laramie, Wyoming, USA
- Sheridan Research and Extension Center, Sheridan, Wyoming, USA
- Institute for Managing Annual Grasses Invading Natural Ecosystems, Sheridan, Wyoming, USA
| | - Linda T. A. van Diepen
- Department of Ecosystem Science and Management, University of Wyoming, Laramie, Wyoming, USA
- Program in Ecology, University of Wyoming, Laramie, Wyoming, USA
- Institute for Managing Annual Grasses Invading Natural Ecosystems, Sheridan, Wyoming, USA
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7
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Shi Z, Yang M, Li K, Yang L, Yang L. Influence of cultivation duration on microbial taxa aggregation in Panax ginseng soils across ecological niches. Front Microbiol 2024; 14:1284191. [PMID: 38282744 PMCID: PMC10813202 DOI: 10.3389/fmicb.2023.1284191] [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: 08/29/2023] [Accepted: 12/22/2023] [Indexed: 01/30/2024] Open
Abstract
Introduction Microbial communities are crucial for plant health and productivity. However, the influence of cultivation age on the ecological processes in assembling plant microbiomes at various ecological niches remains unclear. Methods We selected 12 samples from ginseng farmlands with different cultivation years (N4: 4 years old, N6: 6 years old). We used soil physicochemical properties, enzyme activities, and high-throughput sequencing (16S rDNA and ITS) to examine the rhizoplane (RP), rhizosphere (RS), and bulk soil (BS). Results Our results indicated that cultivation years significantly affect the soil microbiome's diversity and community composition across different ecological niches. The BS microbiome experienced the largest effect, while the RS experienced the smallest. N6 showed a greater impact than N4. This effect was more pronounced on the fungal communities than the bacterial communities of various ecological niches and can be closely related to the soil's physicochemical properties. In N4 soils, we observed an upward trend in both the number of ASVs (amplicon sequence variations) and the diversity of soil microbial taxa across various ecological niches. In N4RP, the bacteria Sphingomonas, known for degrading toxic soil compounds, was present. All ecological niches in N4 showed significant enrichment of Tetracladium fungi, positively associated with crop yield (N4RP at 6.41%, N4RS at 11.31%, and N4BS at 3.45%). In N6 soils, we noted a stark decline in fungal diversity within the BS, with a 57.5% reduction in ASVs. Moreover, Sphingomonas was abundantly present in N6RS and N6BS soils. The relative abundance of the pathogen-inhibiting fungus Exophiala in N6RP and N6RS reached 34.18% and 13.71%, respectively, marking increases of 4.9-fold and 7.7-fold. Additionally, another pathogeninhibiting fungus, Humicola, showed significant enrichment in N6BS, with a 7.5-fold increase. The phenolic acid-producing fungus Pseudogymnoascus in N6RP, N6RS, and N6BS showed increases of 2.41-fold, 2.55-fold, and 4.32-fold, respectively. We hypothesize that functional genes related to the metabolism of terpenoids and polyketides, as well as signaling molecules and interactions, regulate soil microbial taxa in ginseng from different cultivation years. Discussion In conclusion, our study enhances understanding of plant-microbe interactions and aids the sustainable development of medicinal plants, particularly by addressing ginseng succession disorder.
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Affiliation(s)
| | | | | | - Li Yang
- Cultivation Base of State Key Laboratory for Ecological Restoration and Ecosystem Management, College of Traditional Chinese Medicine, Jilin Agricultural University, Changchun, China
| | - Limin Yang
- Cultivation Base of State Key Laboratory for Ecological Restoration and Ecosystem Management, College of Traditional Chinese Medicine, Jilin Agricultural University, Changchun, China
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Guo Z, Qin Y, Lv J, Wang X, Ye T, Dong X, Du N, Zhang T, Piao F, Dong H, Shen S. High red/far-red ratio promotes root colonization of Serratia plymuthica A21-4 in tomato by root exudates-stimulated chemotaxis and biofilm formation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108245. [PMID: 38064903 DOI: 10.1016/j.plaphy.2023.108245] [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: 07/29/2023] [Revised: 11/08/2023] [Accepted: 11/27/2023] [Indexed: 02/15/2024]
Abstract
Effective colonization on plant roots is a prerequisite for plant growth promoting rhizobacterias (PGPR) to exert beneficial activities. Light is essential for plant growth, development and stress response. However, how light modulates root colonization of PGPR remains unclear. Here, we found that high red/far red (R/FR) light promoted and low R/FR light inhibited the colonization and growth enhancement of Serratia plymuthica A21-4 (S. plymuthica A21-4) on tomato, respectively. Non-targeted metabolomic analysis of root exudates collected from different R/FR ratio treated tomato seedlings with or without S. plymuthica A21-4 inoculation by UPLC-MS/MS showed that 64 primary metabolites in high R/FR light-grown plants significantly increased compared with those determined for low R/FR light-grown plants. Among them, 7 amino acids, 1 organic acid and 1 sugar obviously induced the chemotaxis and biofilm formation of S. plymuthica A21-4 compared to the control. Furthermore, exogenous addition of five artificial root exudate compontents (leucine, methionine, glutamine, 6-aminocaproic acid and melezitose) regained and further increased the colonization ability and growth promoting ability of S. plymuthica A21-4 on tomato under low R/FR light and high R/FR light, respectively, indicating their involvement in high R/FR light-regulated the interaction of tomato root and S. plymuthica A21-4. Taken together, our results, for the first time, clearly demonstrate that high R/FR light-induced root exudates play a key role in chemotaxis, biofilm formation and root colonization of S. plymuthica A21-4. This study can help promote the combined application of light supplementation and PGPR to facilitate crop growth and health in green agricultural production.
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Affiliation(s)
- Zhixin Guo
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China; International Joint Laboratory of Henan Horticultural Crop Biology, Henan Provincial Facility Horticulture Engineering Technology Research Center, Zhengzhou, 450046, PR China
| | - Yanping Qin
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Jingli Lv
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Xiaojie Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Ting Ye
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Xiaoxing Dong
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Nanshan Du
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Tao Zhang
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Fengzhi Piao
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Han Dong
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China; International Joint Laboratory of Henan Horticultural Crop Biology, Henan Provincial Facility Horticulture Engineering Technology Research Center, Zhengzhou, 450046, PR China.
| | - Shunshan Shen
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450046, PR China.
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Burz SD, Causevic S, Dal Co A, Dmitrijeva M, Engel P, Garrido-Sanz D, Greub G, Hapfelmeier S, Hardt WD, Hatzimanikatis V, Heiman CM, Herzog MKM, Hockenberry A, Keel C, Keppler A, Lee SJ, Luneau J, Malfertheiner L, Mitri S, Ngyuen B, Oftadeh O, Pacheco AR, Peaudecerf F, Resch G, Ruscheweyh HJ, Sahin A, Sanders IR, Slack E, Sunagawa S, Tackmann J, Tecon R, Ugolini GS, Vacheron J, van der Meer JR, Vayena E, Vonaesch P, Vorholt JA. From microbiome composition to functional engineering, one step at a time. Microbiol Mol Biol Rev 2023; 87:e0006323. [PMID: 37947420 PMCID: PMC10732080 DOI: 10.1128/mmbr.00063-23] [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] [Indexed: 11/12/2023] Open
Abstract
SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.
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Affiliation(s)
- Sebastian Dan Burz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Senka Causevic
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Alma Dal Co
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Marija Dmitrijeva
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institut de microbiologie, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | | | | | - Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | | | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Soon-Jae Lee
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Julien Luneau
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Bidong Ngyuen
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Omid Oftadeh
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | | | | | - Grégory Resch
- Center for Research and Innovation in Clinical Pharmaceutical Sciences, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | - Asli Sahin
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Ian R. Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Emma Slack
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | | | - Janko Tackmann
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Robin Tecon
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Evangelia Vayena
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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Chen Y, Fu W, Xiao H, Zhai Y, Luo Y, Wang Y, Liu Z, Li Q, Huang J. A Review on Rhizosphere Microbiota of Tea Plant ( Camellia sinensis L): Recent Insights and Future Perspectives. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19165-19188. [PMID: 38019642 DOI: 10.1021/acs.jafc.3c02423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Rhizosphere microbial colonization of the tea plant provides many beneficial functions for the host, But the factors that influence the composition of these rhizosphere microbes and their functions are still unknown. In order to explore the interaction between tea plants and rhizosphere microorganisms, we summarized the current studies. First, the review integrated the known rhizosphere microbial communities of tea tree, including bacteria, fungi, and arbuscular mycorrhizal fungi. Then, various factors affecting tea rhizosphere microorganisms were studied, including: endogenous factors, environmental factors, and agronomic practices. Finally, the functions of rhizosphere microorganisms were analyzed, including (a) promoting the growth and quality of tea trees, (b) alleviating biotic and abiotic stresses, and (c) improving soil fertility. Finally, we highlight the gaps in knowledge of tea rhizosphere microorganisms and the future direction of development. In summary, understanding rhizosphere microbial interactions with tea plants is key to promoting the growth, development, and sustainable productivity of tea plants.
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Affiliation(s)
- Yixin Chen
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China
- Collaborative Innovation Centre of Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Wenjie Fu
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China
- Collaborative Innovation Centre of Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Han Xiao
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China
- Collaborative Innovation Centre of Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Yuke Zhai
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China
- National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, P.R. China
| | - Yu Luo
- Institute of Soil and Water Resources and Environmental Sciences, Zhejiang University, Hangzhou, Zhejiang 3100058, P.R. China
| | - Yingzi Wang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China
- Collaborative Innovation Centre of Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Zhonghua Liu
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China
- Collaborative Innovation Centre of Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, China
- National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, P.R. China
| | - Qin Li
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China
- Collaborative Innovation Centre of Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, China
- National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, P.R. China
- Institute of Soil and Water Resources and Environmental Sciences, Zhejiang University, Hangzhou, Zhejiang 3100058, P.R. China
| | - Jianan Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China
- Collaborative Innovation Centre of Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, China
- National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, P.R. China
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11
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Williamson J, Matthews AC, Raymond B. Competition and co-association, but not phosphorous availability, shape the benefits of phosphate-solubilizing root bacteria for maize ( Zea mays). Access Microbiol 2023; 5:000543.v3. [PMID: 38188242 PMCID: PMC10765048 DOI: 10.1099/acmi.0.000543.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 11/16/2023] [Indexed: 01/09/2024] Open
Abstract
Predicting the conditions under which rhizobacteria benefit plant growth remains challenging. Here we tested the hypothesis that benefits from inoculation with phosphate-solubilizing rhizobacteria will depend upon two environmental conditions: phosphate availability and competition between bacteria. We used maize-associated rhizobacteria with varying phosphate solubilization ability in experiments in soil, sterilized soil and gnotobiotic microcosms under conditions of varying orthophosphate availability, while we manipulated the intensity of competition by varying the number of isolates in plant inocula. Growth promotion by microbes did not depend on phosphate availability but was affected by interactions between inoculants: the beneficial effects of one Serratia isolate were only detectable when plants were inoculated with a single strain and the beneficial effects of a competition-sensitive Rhizobium was only detectable in sterilized soil or in microcosms inoculated with single strains. Moreover, microcosm experiments suggested that facilitation of a parasitic isolate, not competitive interactions between bacteria, prevented plants from gaining benefits from a potential mutualist. Competition and facilitation affected colonization of plants in microcosms but growth promotion by Serratia was more affected by inoculation treatment than culturable densities on roots. Experimental manipulation of seed inocula can reveal whether plant growth stimulation is robust with respect to competition, as well as the ecological strategies of different rhizobacteria. From an applied perspective, phosphate solubilization may not provide the mechanism for bacterial growth promotion but may indicate mutualistic potential due to phylogenetic associations. Importantly, benefits to plants are vulnerable to interactions between rhizobacteria and may not persist in mixed inoculations.
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Affiliation(s)
- Joseph Williamson
- Department of Life Sciences, Silwood Park campus, Imperial College London, Ascot, SL5 7PY, UK
- Centre for Biodiversity and Environment Research, Department of Genetics, University College London, Gower St, London, WC1E 6BT, UK
| | - Andrew Charles Matthews
- Department of Life Sciences, Silwood Park campus, Imperial College London, Ascot, SL5 7PY, UK
- College of Life and Environmental Sciences, Penryn campus, University of Exeter, Penryn, TR10 9FE, UK
| | - Ben Raymond
- Department of Life Sciences, Silwood Park campus, Imperial College London, Ascot, SL5 7PY, UK
- College of Life and Environmental Sciences, Penryn campus, University of Exeter, Penryn, TR10 9FE, UK
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12
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Zhou Y, Yang Z, Liu J, Li X, Wang X, Dai C, Zhang T, Carrión VJ, Wei Z, Cao F, Delgado-Baquerizo M, Li X. Crop rotation and native microbiome inoculation restore soil capacity to suppress a root disease. Nat Commun 2023; 14:8126. [PMID: 38065941 PMCID: PMC10709580 DOI: 10.1038/s41467-023-43926-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
It is widely known that some soils have strong levels of disease suppression and prevent the establishment of pathogens in the rhizosphere of plants. However, what soils are better suppressing disease, and how management can help us to boost disease suppression remain unclear. Here, we used field, greenhouse and laboratory experiments to investigate the effect of management (monocropping and rotation) on the capacity of rhizosphere microbiomes in suppressing peanut root rot disease. Compared with crop rotations, monocropping resulted in microbial assemblies that were less effective in suppressing root rot diseases. Further, the depletion of key rhizosphere taxa in monocropping, which were at a disadvantage in the competition for limited exudates resources, reduced capacity to protect plants against pathogen invasion. However, the supplementation of depleted strains restored rhizosphere resistance to pathogen. Taken together, our findings highlight the role of native soil microbes in fighting disease and supporting plant health, and indicate the potential of using microbial inocula to regenerate the natural capacity of soil to fight disease.
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Affiliation(s)
- Yanyan Zhou
- State Key Laboratory of Tree Genetics and Breeding, College of Ecology and Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhen Yang
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Jinguang Liu
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xudong Li
- State Key Laboratory of Tree Genetics and Breeding, College of Ecology and Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Xingxiang Wang
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- Ecological Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan, 335211, China
| | - Chuanchao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Taolin Zhang
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- Ecological Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan, 335211, China
| | - Víctor J Carrión
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM) UMA-CSIC, 29010, Málaga, Spain
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Zhong Wei
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fuliang Cao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Xiaogang Li
- State Key Laboratory of Tree Genetics and Breeding, College of Ecology and Environment, Nanjing Forestry University, Nanjing, 210037, China.
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
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13
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Jiménez‐Guerrero I, López‐Baena FJ, Borrero‐de Acuña JM, Pérez‐Montaño F. Membrane vesicle engineering with "à la carte" bacterial-immunogenic molecules for organism-free plant vaccination. Microb Biotechnol 2023; 16:2223-2235. [PMID: 37530752 PMCID: PMC10686165 DOI: 10.1111/1751-7915.14323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/13/2023] [Accepted: 07/18/2023] [Indexed: 08/03/2023] Open
Abstract
The United Nations heralds a world population exponential increase exceeding 9.7 billion by 2050. This poses the challenge of covering the nutritional needs of an overpopulated world by the hand of preserving the environment. Extensive agriculture practices harnessed the employment of fertilizers and pesticides to boost crop productivity and prevent economic and harvest yield losses attributed to plagues and diseases. Unfortunately, the concomitant hazardous effects stemmed from such agriculture techniques are cumbersome, that is, biodiversity loss, soils and waters contaminations, and human and animal poisoning. Hence, the so-called 'green agriculture' research revolves around designing novel biopesticides and plant growth-promoting bio-agents to the end of curbing the detrimental effects. In this field, microbe-plant interactions studies offer multiple possibilities for reshaping the plant holobiont physiology to its benefit. Along these lines, bacterial extracellular membrane vesicles emerge as an appealing molecular tool to capitalize on. These nanoparticles convey a manifold of molecules that mediate intricate bacteria-plant interactions including plant immunomodulation. Herein, we bring into the spotlight bacterial extracellular membrane vesicle engineering to encase immunomodulatory effectors into their cargo for their application as biocontrol agents. The overarching goal is achieving plant priming by deploying its innate immune responses thereby preventing upcoming infections.
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14
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Chen C, Zhao YY, Wang D, Ren YH, Liu HL, Tian Y, Geng YF, Tang YR, Chen XF. Effects of nanoscale zinc oxide treatment on growth, rhizosphere microbiota, and metabolism of Aconitum carmichaelii. PeerJ 2023; 11:e16177. [PMID: 37868063 PMCID: PMC10590109 DOI: 10.7717/peerj.16177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/04/2023] [Indexed: 10/24/2023] Open
Abstract
Trace elements play a crucial role in the growth and bioactive substance content of medicinal plants, but their utilization efficiency in soil is often low. In this study, soil and Aconitum carmichaelii samples were collected and measured from 22 different locations, followed by an analysis of the relationship between trace elements and the yield and alkaloid content of the plants. The results indicated a significant positive correlation between zinc, trace elements in the soil, and the yield and alkaloid content of A. carmichaelii. Subsequent treatment of A. carmichaelii with both bulk zinc oxide (ZnO) and zinc oxide nanoparticles (ZnO NPs) demonstrated that the use of ZnO NPs significantly enhanced plant growth and monoester-type alkaloid content. To elucidate the underlying mechanisms responsible for these effects, metabolomic analysis was performed, resulting in the identification of 38 differentially expressed metabolites in eight metabolic pathways between the two treatments. Additionally, significant differences were observed in the rhizosphere bacterial communities, with Bacteroidota and Actinobacteriota identified as valuable biomarkers for ZnO NP treatment. Covariation analysis further revealed significant correlations between specific microbial communities and metabolite expression levels. These findings provide compelling evidence that nanoscale zinc exhibits much higher utilization efficiency compared to traditional zinc fertilizer.
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Affiliation(s)
- Cun Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
- College of Chemistry and Life Science, Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, Sichuan, China
| | - Yu-yang Zhao
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Duo Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Ying-hong Ren
- College of Chemistry and Life Science, Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, Sichuan, China
| | - Hong-ling Liu
- College of Chemistry and Life Science, Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, Sichuan, China
| | - Ye Tian
- Sichuan Jianengda Panxi Pharmaceutical Co. LTD, Xichang, Sichuan, China
| | - Yue-fei Geng
- Sichuan Jianengda Panxi Pharmaceutical Co. LTD, Xichang, Sichuan, China
| | - Ying-rui Tang
- College of Chemistry and Life Science, Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, Sichuan, China
| | - Xing-fu Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
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15
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Garrido-Sanz D, Čaušević S, Vacheron J, Heiman CM, Sentchilo V, van der Meer JR, Keel C. Changes in structure and assembly of a species-rich soil natural community with contrasting nutrient availability upon establishment of a plant-beneficial Pseudomonas in the wheat rhizosphere. MICROBIOME 2023; 11:214. [PMID: 37770950 PMCID: PMC10540321 DOI: 10.1186/s40168-023-01660-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/31/2023] [Indexed: 09/30/2023]
Abstract
BACKGROUND Plant-beneficial bacterial inoculants are of great interest in agriculture as they have the potential to promote plant growth and health. However, the inoculation of the rhizosphere microbiome often results in a suboptimal or transient colonization, which is due to a variety of factors that influence the fate of the inoculant. To better understand the fate of plant-beneficial inoculants in complex rhizosphere microbiomes, composed by hundreds of genotypes and multifactorial selection mechanisms, controlled studies with high-complexity soil microbiomes are needed. RESULTS We analysed early compositional changes in a taxa-rich natural soil bacterial community under both exponential nutrient-rich and stationary nutrient-limited growth conditions (i.e. growing and stable communities, respectively) following inoculation with the plant-beneficial bacterium Pseudomonas protegens in a bulk soil or a wheat rhizosphere environment. P. protegens successfully established under all conditions tested and was more abundant in the rhizosphere of the stable community. Nutrient availability was a major factor driving microbiome composition and structure as well as the underlying assembly processes. While access to nutrients resulted in communities assembled mainly by homogeneous selection, stochastic processes dominated under the nutrient-deprived conditions. We also observed an increased rhizosphere selection effect under nutrient-limited conditions, resulting in a higher number of amplicon sequence variants (ASVs) whose relative abundance was enriched. The inoculation with P. protegens produced discrete changes, some of which involved other Pseudomonas. Direct competition between Pseudomonas strains partially failed to replicate the observed differences in the microbiome and pointed to a more complex interaction network. CONCLUSIONS The results of this study show that nutrient availability is a major driving force of microbiome composition, structure and diversity in both the bulk soil and the wheat rhizosphere and determines the assembly processes that govern early microbiome development. The successful establishment of the inoculant was facilitated by the wheat rhizosphere and produced discrete changes among other members of the microbiome. Direct competition between Pseudomonas strains only partially explained the microbiome changes, indicating that indirect interactions or spatial distribution in the rhizosphere or soil interface may be crucial for the survival of certain bacteria. Video Abstract.
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Affiliation(s)
- Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland.
| | - Senka Čaušević
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Clara M Heiman
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland.
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16
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Mazoyon C, Catterou M, Alahmad A, Mongelard G, Guénin S, Sarazin V, Dubois F, Duclercq J. Sphingomonas sediminicola Dae20 Is a Highly Promising Beneficial Bacteria for Crop Biostimulation Due to Its Positive Effects on Plant Growth and Development. Microorganisms 2023; 11:2061. [PMID: 37630621 PMCID: PMC10459697 DOI: 10.3390/microorganisms11082061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Current agricultural practices rely heavily on synthetic fertilizers, which not only consume a lot of energy but also disrupt the ecological balance. The overuse of synthetic fertilizers has led to soil degradation. In a more sustainable approach, alternative methods based on biological interactions, such as plant growth-promoting bacteria (PGPRs), are being explored. PGPRs, which include both symbiotic and free-living bacteria, form mutualistic relationships with plants by enhancing nutrient availability, producing growth regulators, and regulating stress responses. This study investigated the potential of Sphingomonas sediminicola Dae20, an α-Proteobacteria species commonly found in the rhizosphere, as a beneficial PGPR. We observed that S. sediminicola Dae20 stimulated the root system and growth of three different plant species in the Brassicaceae family, including Arabidopsis thaliana, mustard, and rapeseed. The bacterium produced auxin, nitric oxide, siderophores and showed ACC deaminase activity. In addition to activating an auxin response in the plant, S. sediminicola Dae20 exhibited the ability to modulate other plant hormones, such as abscisic acid, jasmonic acid and salicylic acid, which are critical for plant development and defense responses. This study highlights the multifunctional properties of S. sediminicola Dae20 as a promising PGPR and underscores the importance of identifying effective and versatile beneficial bacteria to improve plant nutrition and promote sustainable agricultural practices.
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Affiliation(s)
- Candice Mazoyon
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France; (C.M.); (M.C.); (A.A.); (F.D.)
| | - Manuella Catterou
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France; (C.M.); (M.C.); (A.A.); (F.D.)
| | - Abdelrahman Alahmad
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France; (C.M.); (M.C.); (A.A.); (F.D.)
- Agroécologie, Hydrogéochimie, Milieux et Ressources (AGHYLE, UP2018.C101) UniLaSalle Rouen, SFR NORVEGE FED 4277, 76130 Mont-Saint Aignan, France
| | - Gaëlle Mongelard
- Centre de Ressources Régionales en Biologie Moléculaire (CRRBM), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France; (G.M.); (S.G.)
| | - Stéphanie Guénin
- Centre de Ressources Régionales en Biologie Moléculaire (CRRBM), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France; (G.M.); (S.G.)
| | | | - Fréderic Dubois
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France; (C.M.); (M.C.); (A.A.); (F.D.)
| | - Jérôme Duclercq
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France; (C.M.); (M.C.); (A.A.); (F.D.)
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17
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Lozo J, Ristović N, Kungulovski G, Jovanović Ž, Rakić T, Stanković S, Radović S. Rhizosphere microbiomes of resurrection plants Ramonda serbica and R. nathaliae: comparative analysis and search for bacteria mitigating drought stress in wheat (Triticum aestivum L.). World J Microbiol Biotechnol 2023; 39:256. [PMID: 37474779 DOI: 10.1007/s11274-023-03702-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/12/2023] [Indexed: 07/22/2023]
Abstract
Rhizosphere microbial communities play an important role in maintaining the health and productivity of the plant host. The rhizobacteria Pseudomonas putida P2 of Ramonda serbica and Bacillus cereus P5 of R. nathaliae were selected for treatment of the Belija wheat cultivar because of their plant growth-promoting (PGP) properties. Compared to the non-treated drought-stressed plants, the plants treated with rhizobacteria showed increased activity of the two major antioxidant enzymes, superoxide dismutase, and ascorbate peroxidase. Plants treated with the B. cereus P5 strain exhibited higher proline content under drought stress, suggesting that proline accumulation depends on the relative water content (RWC) status of the plants studied. Inoculation of wheat seeds with the P. putida P2 strain improved water status by increasing RWC and alleviating oxidative stress by reducing H2O2 and malondialdehyde concentrations in plants exposed to severe drought, possibly also helping plants to overcome drought through its 1-aminocyclopropane-1-carboxylic acid deaminase activity. Analysis of data from Next Generation sequencing (NGS) revealed that the dominant bacterial taxa in the rhizosphere of resurrection plants R. serbica and R. nathaliae were extremophilic, thermotolerant, Vicinamibacter silvestris, Chthoniobacter flavus, and Gaiella occulta. From the fungi detected Penicillium was the most abundant in both samples, while Fusarium and Mucor were present only in the rhizosphere of R. serbica and the entomopathogenic fungi Metarhizium, and Tolypocladiumu only in the rhizosphere of R. nathaliae. The fungal communities varied among plants, suggesting a stronger environmental influence than plant species. Our study demonstrates the importance of in vivo experiments to confirm the properties of PGP bacteria and indicates that the rhizosphere of resurrection plants is a valuable source of unique microorganisms that can be used to improve the drought stress tolerance of crops.
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Affiliation(s)
- Jelena Lozo
- Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, 11000, Serbia.
- Faculty of Biology, Centre for biological control and plant growth promotion, University of Belgrade, Belgrade, Serbia.
| | - Nemanja Ristović
- Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, 11000, Serbia
| | | | - Živko Jovanović
- Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, 11000, Serbia
| | - Tamara Rakić
- Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, 11000, Serbia
| | - Slaviša Stanković
- Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, 11000, Serbia
- Faculty of Biology, Centre for biological control and plant growth promotion, University of Belgrade, Belgrade, Serbia
| | - Svetlana Radović
- Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, 11000, Serbia
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18
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Shi A, Hu Y, Zhang X, Zhou D, Xu J, Rensing C, Zhang L, Xing S, Ni W, Yang W. Biochar loaded with bacteria enhanced Cd/Zn phytoextraction by facilitating plant growth and shaping rhizospheric microbial community. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 327:121559. [PMID: 37023890 DOI: 10.1016/j.envpol.2023.121559] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/22/2023] [Accepted: 04/02/2023] [Indexed: 06/19/2023]
Abstract
Biochar and metal-tolerant bacteria have been widely used in the remediation of heavy metal contaminated soil. However, the synergistic effect of biochar-functional microbes on phytoextraction by hyperaccumulators remains unclear. In this study, the heavy metal-tolerant strain Burkholderia contaminans ZCC was selected and loaded on biochar to produce biochar-resistant bacterial material (BM), and the effects of BM on Cd/Zn phytoextraction by Sedum alfredii Hance and rhizospheric microbial community were explored. The results showed that, BM application significantly enhanced the Cd and Zn accumulation of S. alfredii by 230.13% and 381.27%, respectively. Meanwhile, BM alleviated metal toxicity of S. alfredii by reducing oxidative damage and increasing chlorophyll and antioxidant enzyme activity. High-throughput sequencing revealed that BM significantly improved soil bacterial and fungal diversity, and increased the abundance of genera with plant growth promoting and metal solubilizing functions such as Gemmatimonas, Dyella and Pseudarthrobacter. Co-occurrence network analysis showed that BM significantly increased the complexity of the rhizospheric bacterial and fungal network. Structural equation model analysis revealed that soil chemistry property, enzyme activity and microbial diversity contributed directly or indirectly to Cd and Zn extraction by S. alfredii. Overall, our results suggested that biochar- B. contaminans ZCC was able to enhance the growth and Cd/Zn accumulation by S. alfredii. This study enhanced our understanding on the hyperaccumulator-biochar-functional microbe interactions, and provided a feasible strategy for promoting the phytoextraction efficiency of heavy metal contaminated soils.
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Affiliation(s)
- An Shi
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ying Hu
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiao Zhang
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dan Zhou
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Junlong Xu
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Christopher Rensing
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liming Zhang
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shihe Xing
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wuzhong Ni
- College of Environment and Resources, Zhejiang University, Hangzhou, 310058, China
| | - Wenhao Yang
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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19
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Ali M, Cybulska J, Frąc M, Zdunek A. Application of polysaccharides for the encapsulation of beneficial microorganisms for agricultural purposes: A review. Int J Biol Macromol 2023; 244:125366. [PMID: 37327939 DOI: 10.1016/j.ijbiomac.2023.125366] [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: 01/03/2023] [Revised: 05/25/2023] [Accepted: 06/11/2023] [Indexed: 06/18/2023]
Abstract
Intensive farming practices have increased the consumption of chemical-based pesticides and fertilizers thereby creating health issues for humans and animals and also causing a deterioration in the natural ecosystem. The promotion of biomaterials synthesis could potentially lead to the replacement of synthetic products and improve soil fertility, protect plants from pathogen attacks, and enhance the productivity of the agricultural sector resulting in less environmental pollution. Microbial bioengineering involving the use and improvement of encapsulation using polysaccharides has the required potential to address environmental issues and promote green chemistry. This article describes various encapsulation techniques and polysaccharides which have an immense applicable capability to encapsulate microbial cells. The review elucidates the factors that may result in a reduced viable cell count during encapsulation, particularly using the spray drying method, where a high temperature is required to dry the suspension, this may damage the microbial cells. The environmental advantage of the application of polysaccharides as carriers of beneficial microorganisms, which do not pose a risk for soil due to their full biodegradability, was also shown. The encapsulated microbial cells may assist in addressing certain environmental problems such as ameliorating the unfavourable effects of plant pests and pathogens, and promoting agricultural sustainability.
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Affiliation(s)
- Mohsin Ali
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Justyna Cybulska
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland.
| | - Madgalena Frąc
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Artur Zdunek
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
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20
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Liu H, Huang H, Liang K, Lin K, Shangguan Y, Xu H. Characterization of a cadmium-resistant functional bacteria (Burkholderia sp. SRB-1) and mechanism analysis at physiochemical and genetic level. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27824-2. [PMID: 37269515 DOI: 10.1007/s11356-023-27824-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 05/18/2023] [Indexed: 06/05/2023]
Abstract
In this study, the capacity of cadmium (Cd)-resistant plant growth-promoting bacteria (PGPB) Burkholderia sp. SRB-1 (SRB-1) and its mechanisms were explored through morphological characterizations, biochemical response, plant growth-promoting traits, and functional gene expression patterns. The results showed that SRB-1 was an excellent Cd-resistant bacteria (MIC was 420 mg L-1), and its maximum Cd removal rate reached 72.25%. Biosorption was the main removal method of Cd for SRB-1, preventing intracellular Cd accumulation and maintaining cellular metabolism. Various functional groups on the cell wall were involved in Cd binding, which deposited as CdS and CdCO3 on the cell surface according to XPS analysis and might be critical for reducing Cd physiochemical toxicity. Furthermore, metals exporting (zntA, czcA, czcB, czcC), detoxification (dsbA, cysM), and antioxidation (katE, katG, SOD1) related genes were annotated in the SRB-1 genome. The results of Cd distribution and antioxidative enzyme activity in SRB-1 also illustrated that Cd2+ efflux and antioxidative response were the main intracellular Cd-resistant mechanisms. These conclusions were further verified by qRT-PCR analysis. Overall, the strategies of extracellular biosorption, cation efflux, and intracellular detoxification jointly build the Cd-resistant system, which invested Burkholderia sp. SRB-1 with potential for bioremediation in heavily Cd-contaminated environmental sites.
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Affiliation(s)
- Huakang Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065, Sichuan, People's Republic of China
| | - Huayan Huang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065, Sichuan, People's Republic of China
| | - Ke Liang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065, Sichuan, People's Republic of China
| | - Kangkai Lin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065, Sichuan, People's Republic of China
| | - Yuxian Shangguan
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Heng Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065, Sichuan, People's Republic of China.
- Key Laboratory of Environment Protection, Soil Ecological Protection and Pollution Control, Sichuan University & Department of Ecology and Environment of Sichuan, Chengdu, 610065, Sichuan, People's Republic of China.
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21
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Oliva G, Vigliotta G, Terzaghi M, Guarino F, Cicatelli A, Montagnoli A, Castiglione S. Counteracting action of Bacillus stratosphericus and Staphylococcus succinus strains against deleterious salt effects on Zea mays L. Front Microbiol 2023; 14:1171980. [PMID: 37303788 PMCID: PMC10248413 DOI: 10.3389/fmicb.2023.1171980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/02/2023] [Indexed: 06/13/2023] Open
Abstract
The salinization of soil is the process of progressive accumulation of salts such as sulfates, sodium, or chlorides into the soil. The increased level of salt has significant effects on glycophyte plants, such as rice, maize, and wheat, which are staple foods for the world's population. Consequently, it is important to develop biotechnologies that improve crops and clean up the soil. Among other remediation methods, there is an environmentally friendly approach to ameliorate the cultivation of glycophyte plants in saline soil, namely, the use of microorganisms tolerant to salt with growth-promoting features. Plant growth-promoting rhizobacteria (PGPR) can improve plant growth by colonizing their roots and playing a vital role in helping plants to establish and grow in nutrient-deficient conditions. Our research aimed to test in vivo halotolerant PGPR, isolated and characterized in vitro in a previous study conducted in our laboratory, inoculating them on maize seedlings to improve their growth in the presence of sodium chloride. The bacterial inoculation was performed using the seed-coating method, and the produced effects were evaluated by morphometric analysis, quantization of ion contents (sodium, potassium), produced biomass, both for epigeal (shoot) and hypogeal (root) organs, and by measuring salt-induced oxidative damage. The results showed an increase in biomass and sodium tolerance and even a reduction of oxidative stress in seedlings pretreated with a PGPR bacterial consortium (Staphylococcus succinus + Bacillus stratosphericus) over the control. Moreover, we observed that salt reduces growth and alters root system traits of maize seedlings, while bacterial treatment improves plant growth and partially restores the root architecture system in saline stress conditions. Therefore, the PGPR seed-coating or seedling treatment could be an effective strategy to enhance sustainable agriculture in saline soils due to the protection of the plants from their inhibitory effect.
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Affiliation(s)
- Gianmaria Oliva
- Department of Chemistry and Biology “A. Zambelli”, University of Salerno, Fisciano, SA, Italy
| | - Giovanni Vigliotta
- Department of Chemistry and Biology “A. Zambelli”, University of Salerno, Fisciano, SA, Italy
| | - Mattia Terzaghi
- Department of Chemistry and Biology “A. Zambelli”, University of Salerno, Fisciano, SA, Italy
- Department of Biosciences, Biotechnologies and Environment, University of Bari “Aldo Moro”, Bari, BA, Italy
| | - Francesco Guarino
- Department of Chemistry and Biology “A. Zambelli”, University of Salerno, Fisciano, SA, Italy
| | - Angela Cicatelli
- Department of Chemistry and Biology “A. Zambelli”, University of Salerno, Fisciano, SA, Italy
| | - Antonio Montagnoli
- Department of Biotechnologies and Life Sciences (DBSV), University of Insubria, Varese, Italy
| | - Stefano Castiglione
- Department of Chemistry and Biology “A. Zambelli”, University of Salerno, Fisciano, SA, Italy
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22
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Li C, Jia Z, Zhang S, Li T, Ma S, Cheng X, Chen M, Nie H, Zhai L, Zhang B, Liu X, Zhang J, Müller C. The positive effects of mineral-solubilizing microbial inoculants on asymbiotic nitrogen fixation of abandoned mine soils are driven by keystone phylotype. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 882:163663. [PMID: 37094687 DOI: 10.1016/j.scitotenv.2023.163663] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/03/2023] [Accepted: 04/18/2023] [Indexed: 05/03/2023]
Abstract
Toward the restoration of the increasing numbers of abandoned mines across China, external-soil spray seeding technologies have become more extensively utilized. However, considerable challenges remain that seriously hamper the effectiveness of these technologies, such as inadequate nutrient availability for plants. Previous studies have shown that mineral-solubilizing microbial inoculants can increase the nodules of legumes. However, their effects on symbiotic nitrogen fixation (SNF), asymbiotic nitrogen fixation (ANF), and diazotrophic communities remain unknown. Further, research into the application of functional microorganisms for the restoration of abandoned mines has been conducted either in greenhouses, or their application in the field has been too brief. Thus, we established a four-year field experiment in an abandoned mine and quantified the SNF, ANF, and diazotrophic communities. To the best of our knowledge, this study is the first to describe the long-term application of specific functional microorganisms for the remediation of abandoned mine sites in the field. We revealed that mineral-solubilizing microbial inoculants significantly increased the soil ANF rate and SNF content. There was no significant correlation between the diazotrophic alpha diversity and soil ANF rate; however, there were strong positive associations between the relative abundance and biodiversity of keystone phylotype (module #5) within ecological clusters and the ANF rate. Molecular ecological networks indicated that microbial inoculants increased network complexity and stability. Moreover, the inoculants significantly enhanced the deterministic ratio of diazotrophic communities. Furthermore, homogeneous selection predominantly mediated the assembly of soil diazotrophic communities. It was concluded that mineral-solubilizing microorganisms played a critical role in maintaining and enhancing nitrogen, which offers a new solution with great potential for the restoration of ecosystems at abandoned mine sites.
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Affiliation(s)
- Chong Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China; Institute of Plant Ecology, Justus-Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany.
| | - Zhaohui Jia
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China.
| | - Shuifeng Zhang
- Faculty of Information Technology, Nanjing Forest Police College, Nanjing 210000, China.
| | - Tao Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China.
| | - Shilin Ma
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China.
| | - Xuefei Cheng
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China.
| | - Meiling Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China.
| | - Hui Nie
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China.
| | - Lu Zhai
- Department of Natural Resource Ecology and Management, Oklahoma State University, Stillwater, OK 74078, USA; Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA.
| | - Bo Zhang
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA.
| | - Xin Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China.
| | - Jinchi Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China.
| | - Christoph Müller
- Institute of Plant Ecology, Justus-Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany; School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin, Ireland; Liebig Centre for Agroecology and Climate Impact Research, Justus Liebig University, Germany.
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23
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Rincón-Molina CI, Ruíz-Valdiviezo VM, Rincón-Rosales R, Flores Félix JD. Editorial: Plant growth-promoting bacteria as a key tool for future agriculture: Agronomic, molecular and omics approaches. Front Microbiol 2023; 14:1168891. [PMID: 37007460 PMCID: PMC10064123 DOI: 10.3389/fmicb.2023.1168891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 03/07/2023] [Indexed: 03/19/2023] Open
Affiliation(s)
| | | | - Reiner Rincón-Rosales
- Instituto Tecnológico de Tuxtla Gutiérrez/Tecnológico Nacional de Mexico, Tuxtla Gutiérrez, Mexico
| | - José David Flores Félix
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
- *Correspondence: José David Flores Félix
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24
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Zhang Y, Cheng Z, Li Q, Dai Q, Hu J. Responses of rhizosphere bacterial communities in newly reclaimed mudflat paddies to rice genotype and nitrogen fertilizer rate. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:38761-38774. [PMID: 36586025 DOI: 10.1007/s11356-022-25020-2] [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: 07/25/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
The rhizosphere microbiome plays a vital role in crop growth and adaptation. However, the effects of rice genotype, nitrogen (N) fertilization, and their interactions on the rhizosphere bacterial communities in low fertility soil remain poorly understood. In this study, a two-factor field experiment was performed in newly reclaimed mudflat paddies characterized by poor fertility to analyze bacterial communities in the rhizosphere of Yongyou 2640 (japonica/indica hybrid rice, JIH) and Huaidao No.5 (japonica conventional rice, JC) under different N fertilizer rates. Results showed that genotype, followed by N fertilizer rate, was the primary factor affecting rhizobacteria diversity. Rhizobacteria diversity was higher in JIH than in JC and that of JIH and JC did not significantly change overall as N fertilizer rates but increased and decreased at N fertilizer rates of over 300 kg N ha-1, respectively. The inconsistent response was probably attributed to the difference in the increase of ammonium and/or nitrate in the rhizosphere of JIH and JC. Genotype explained approximately 26% of the variation in rhizosphere bacterial communities. Rhizosphere bacterial communities with N fertilizer rates of over 300 kg N ha-1 were more dissimilar to those without N fertilization relative to those with N fertilizer rates of below 300 kg N ha-1, which was mainly attributed to changes in the concentration of ammonium and/or nitrate. The relative abundances of some potential beneficial genera such as Salinimicrobium, Salegentibacter, Gillisia, and Anaerolinea in the rhizosphere of JC and Salegentibacter, Lysobacter, Nocardioides, and Pontibacter in the rhizosphere of JIH were increased under N fertilizer rates of less than 300 kg N ha-1 and positively correlated with rice yields, which indicate that changes in bacterial communities caused by N fertilization might be strongly associated with the improvement of rice yield. Overall, rhizosphere bacterial communities were more sensitive to genotype in newly reclaimed mudflat paddies and showed a consistent response to N fertilizer rates.
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Affiliation(s)
- Yang Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, China
- Key Laboratory of Arable Land Quality Monitoring and Evaluation, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou, 225127, China
| | - Zhandou Cheng
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, China
| | - Qing Li
- Jiangsu Key Laboratory of Crop Genetic and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, 225009, China
| | - Qigen Dai
- Jiangsu Key Laboratory of Crop Genetic and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, 225009, China.
| | - Jian Hu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, China
- Key Laboratory of Arable Land Quality Monitoring and Evaluation, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou, 225127, China
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25
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Ahmed A, He P, He P, Wu Y, He Y, Munir S. Environmental effect of agriculture-related manufactured nano-objects on soil microbial communities. ENVIRONMENT INTERNATIONAL 2023; 173:107819. [PMID: 36842382 DOI: 10.1016/j.envint.2023.107819] [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: 10/21/2022] [Revised: 01/30/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Agriculture-related manufactured nano-objects (MNOs) can revolutionize the crop production and help to achieve sustainable development goals. MNOs with diverse physico-chemical properties and ability to encapsulate and deliver active ingredients in controlled, targeted and stimuli responsive manner can enhance the efficiency while minimizing collateral damage to non-target organisms and environment. Application of MNOs in the form of nanopesticides and nanofertilizers is known to affect soil microbial communities both positively and negatively, but detailed studies with varying dose, type and environmental conditions are scarce. Therefore, it is imperative to understand the complex mechanisms and factors which shape the MNOs-microbial interactions through integrating state of the art technologies including omics (transcriptomics, metabolomics, and proteomics), artificial intelligence, and statistical frameworks. Lastly, we propose the idea of MNOs-mediated manipulation of soil microbiome to modify the soil microbial communities for improved microbial services. These microbial services, if harnessed appropriately, can revolutionize modern agriculture and help in achieving sustainable development goals.
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Affiliation(s)
- Ayesha Ahmed
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Pengfei He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Pengbo He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Yixin Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Yueqiu He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China.
| | - Shahzad Munir
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China.
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26
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Seasonal activities of the phyllosphere microbiome of perennial crops. Nat Commun 2023; 14:1039. [PMID: 36823152 PMCID: PMC9950430 DOI: 10.1038/s41467-023-36515-y] [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: 11/08/2022] [Accepted: 02/03/2023] [Indexed: 02/25/2023] Open
Abstract
Understanding the interactions between plants and microorganisms can inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on replicated plots of field-grown switchgrass and miscanthus, and to quantify their activities over two growing seasons for switchgrass. We use metagenome and metatranscriptome sequencing and curate 40 medium- and high-quality metagenome-assembled-genomes (MAGs). We find that classes represented by these MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) are active in the late season, and upregulate transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase. Stress-associated pathways are expressed for most MAGs, suggesting engagement with the host environment. We also detect seasonally activated biosynthetic pathways for terpenes and various non-ribosomal peptide pathways that are poorly annotated. Our findings support that leaf-associated bacterial populations are seasonally dynamic and responsive to host cues.
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27
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Cheng Z, Zheng Q, Shi J, He Y, Yang X, Huang X, Wu L, Xu J. Metagenomic and machine learning-aided identification of biomarkers driving distinctive Cd accumulation features in the root-associated microbiome of two rice cultivars. ISME COMMUNICATIONS 2023; 3:14. [PMID: 36813851 PMCID: PMC9947119 DOI: 10.1038/s43705-023-00213-z] [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: 06/14/2022] [Revised: 01/03/2023] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
Developing low-cadmium (Cd) rice cultivars has emerged as a promising avenue for food safety in Cd-contaminated farmlands. The root-associated microbiomes of rice have been shown to enhance rice growth and alleviate Cd stress. However, the microbial taxon-specific Cd resistance mechanisms underlying different Cd accumulation characteristics between different rice cultivars remain largely unknown. This study compared low-Cd cultivar XS14 and hybrid rice cultivar YY17 for Cd accumulation with five soil amendments. The results showed that XS14 was characterized by more variable community structures and stable co-occurrence networks in the soil-root continuum compared to YY17. The stronger stochastic processes in assembly of the XS14 (~25%) rhizosphere community than that of YY17 (~12%) suggested XS14 may have higher resistance to changes in soil properties. Microbial co-occurrence networks and machine learning models jointly identified keystone indicator microbiota, such as Desulfobacteria in XS14 and Nitrospiraceae in YY17. Meanwhile, genes involved in sulfur cycling and nitrogen cycling were observed among the root-associated microbiome of these two cultivars, respectively. Microbiomes in the rhizosphere and root of XS14 showed a higher diversity in functioning, with the significant enrichment of functional genes related to amino acid and carbohydrate transport and metabolism, and sulfur cycling. Our findings revealed differences and similarities in the microbial communities associated with two rice cultivars, as well as bacterial biomarkers predictive of Cd-accumulation capacity. Thus, we provide new insights into taxon-specific recruitment strategies of two rice cultivars under Cd stress and highlight the utility of biomarkers in offering clues for enhancing crop resilience to Cd stresses in the future.
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Affiliation(s)
- Zhongyi Cheng
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Qiang Zheng
- Department of Mathematics and Theories, Peng Cheng Laboratory, Shenzhen, 518000, China
| | - Jiachun Shi
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China.
| | - Yan He
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Xueling Yang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Xiaowei Huang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Laosheng Wu
- Department of Environmental Sciences, University of California, Riverside, CA, 92521, USA
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
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28
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Fu S, Deng Y, Zou K, Zhang S, Duan Z, Wu X, Zhou J, Li S, Liu X, Liang Y. Dynamic variation of Paris polyphylla root-associated microbiome assembly with planting years. PLANTA 2023; 257:61. [PMID: 36808254 DOI: 10.1007/s00425-023-04074-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
P. polyphylla selectively enriches beneficial microorganisms to help their growth. Paris polyphylla (P. polyphylla) is an important perennial plant for Chinese traditional medicine. Uncovering the interaction between P. polyphylla and the related microorganisms would help to utilize and cultivate P. polyphylla. However, studies focusing on P. polyphylla and related microbes are scarce, especially on the assembly mechanisms and dynamics of the P. polyphylla microbiome. High-throughput sequencing of the 16S rRNA genes was implemented to investigate the diversity, community assembly process and molecular ecological network of the bacterial communities in three root compartments (bulk soil, rhizosphere, and root endosphere) across three years. Our results demonstrated that the composition and assembly process of the microbial community in different compartments varied greatly and were strongly affected by planting years. Bacterial diversity was reduced from bulk soils to rhizosphere soils to root endosphere and varied over time. Microorganisms benefit to plants was selectively enriched in P. polyphylla roots as was its core microbiome, including Pseudomonas, Rhizobium, Steroidobacter, Sphingobium and Agrobacterium. The network's complexity and the proportion of stochasticity in the community assembly process increased. Besides, nitrogen metabolism, carbon metabolism, phosphonate and phosphinate metabolism genes in bulk soils increased over time. These findings suggest that P. polyphylla exerts a selective effect to enrich the beneficial microorganisms and proves the sequential increasing selection pressure with P. polyphylla growth. Our work adds to the understanding of the dynamic processes of plant-associated microbial community assembly, guides the selection and application timing of P. polyphylla-associated microbial inoculants and is vital for sustainable agriculture.
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Affiliation(s)
- Shaodong Fu
- School of Resource Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Yan Deng
- Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Kai Zou
- College of Advanced Materials Engineering, Jiaxing Nanhu University, Jiaxing, Zhejiang, China
| | - Shuangfei Zhang
- School of Resource Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Zhenchun Duan
- School of Resource Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Xinhong Wu
- School of Resource Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Jin Zhou
- School of Resource Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Shihui Li
- School of Resource Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Xueduan Liu
- School of Resource Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Yili Liang
- School of Resource Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China.
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Tang F, Li Q, Yue J, Ge F, Li F, Liu Y, Zhang D, Tian J. Penicillium oxalicum augments soil lead immobilization by affecting indigenous microbial community structure and inorganic phosphate solubilization potential during microbial-induced phosphate precipitation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 319:120953. [PMID: 36584858 DOI: 10.1016/j.envpol.2022.120953] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/18/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Phosphate-solubilizing microorganisms (PSMs) are critically important for increasing soil phosphate (P) and decreasing lead (Pb) bioavailability during microbial-induced phosphate precipitation (MIPP). However, their relative contributions to the indigenous soil microbial communities and P-cycling genes during the MIPP process remain unclear. In this study, inoculation of the PSM P. oxalicum in hydroxyapatite-cultured and Pb-contaminated soil increased soil phosphatase activities, available P (AP) concentrations and reduced available Pb levels. Metagenomics revealed a 3.9-44.0% increase in the abundance of P-cycling genes by P. oxalicum inoculation. No P-cycling genes were assigned to Penicillium. While P. oxalicum increased the complexity of microbial community co-occurrence networks, and improved the directly interrelationships between Penicillium and genera containing P-cycling gene. These results suggesting that P. oxalicum obviously positively affected the regulation of indigenous P-cycling functional communities during the MIPP process. Inorganic P solubilization genes (gcd, ppa, and ppx) have been shown to affect soil AP, suggesting that inorganic P solubilization is the major driver of Pb immobilization improvement following P. oxalicum inoculation. These results enhance our understanding of the significant ecological role of PSMs in governing soil P-cycling and alleviating Pb2+ biotoxicity during the MIPP process.
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Affiliation(s)
- Fei Tang
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan 411105, PR China
| | - Qiqiang Li
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan 411105, PR China
| | - Jiaru Yue
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan 411105, PR China
| | - Fei Ge
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan 411105, PR China
| | - Feng Li
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan 411105, PR China
| | - Yun Liu
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan 411105, PR China
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun 130021, PR China; Key Laboratory of Groundwater Resources and Environment Ministry of Education, Jilin University, Changchun 130021, PR China
| | - Jiang Tian
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan 411105, PR China.
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30
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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.
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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
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Haskett TL, Geddes BA, Paramasivan P, Green P, Chitnavis S, Mendes MD, Jorrín B, Knights HE, Bastholm TR, Ramsay JP, Oldroyd GED, Poole PS. Rhizopine biosensors for plant-dependent control of bacterial gene expression. Environ Microbiol 2023; 25:383-396. [PMID: 36428208 PMCID: PMC10107442 DOI: 10.1111/1462-2920.16288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022]
Abstract
Engineering signalling between plants and microbes could be exploited to establish host-specificity between plant-growth-promoting bacteria and target crops in the environment. We previously engineered rhizopine-signalling circuitry facilitating exclusive signalling between rhizopine-producing (RhiP) plants and model bacterial strains. Here, we conduct an in-depth analysis of rhizopine-inducible expression in bacteria. We characterize two rhizopine-inducible promoters and explore the bacterial host-range of rhizopine biosensor plasmids. By tuning the expression of rhizopine uptake genes, we also construct a new biosensor plasmid pSIR05 that has minimal impact on host cell growth in vitro and exhibits markedly improved stability of expression in situ on RhiP barley roots compared to the previously described biosensor plasmid pSIR02. We demonstrate that a sub-population of Azorhizobium caulinodans cells carrying pSIR05 can sense rhizopine and activate gene expression when colonizing RhiP barley roots. However, these bacteria were mildly defective for colonization of RhiP barley roots compared to the wild-type parent strain. This work provides advancement towards establishing more robust plant-dependent control of bacterial gene expression and highlights the key challenges remaining to achieve this goal.
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Affiliation(s)
| | - Barney A Geddes
- Department of Plant Sciences, University of Oxford, Oxford, UK
- Department of Microbiological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | | | - Patrick Green
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Samir Chitnavis
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Marta D Mendes
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Beatriz Jorrín
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | | | - Tahlia R Bastholm
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, Western Australia, Australia
| | - Joshua P Ramsay
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, Western Australia, Australia
| | - Giles E D Oldroyd
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Crop Science Centre, University of Cambridge, Cambridge, UK
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, UK
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32
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Plant Growth-Promoting Bacteria (PGPB) with Biofilm-Forming Ability: A Multifaceted Agent for Sustainable Agriculture. DIVERSITY 2023. [DOI: 10.3390/d15010112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Plant growth-promoting bacteria (PGPB) enhance plant growth, as well as protect plants from several biotic and abiotic stresses through a variety of mechanisms. Therefore, the exploitation of PGPB in agriculture is feasible as it offers sustainable and eco-friendly approaches to maintaining soil health while increasing crop productivity. The vital key of PGPB application in agriculture is its effectiveness in colonizing plant roots and the phyllosphere, and in developing a protective umbrella through the formation of microcolonies and biofilms. Biofilms offer several benefits to PGPB, such as enhancing resistance to adverse environmental conditions, protecting against pathogens, improving the acquisition of nutrients released in the plant environment, and facilitating beneficial bacteria–plant interactions. Therefore, bacterial biofilms can successfully compete with other microorganisms found on plant surfaces. In addition, plant-associated PGPB biofilms are capable of protecting colonization sites, cycling nutrients, enhancing pathogen defenses, and increasing tolerance to abiotic stresses, thereby increasing agricultural productivity and crop yields. This review highlights the role of biofilms in bacterial colonization of plant surfaces and the strategies used by biofilm-forming PGPB. Moreover, the factors influencing PGPB biofilm formation at plant root and shoot interfaces are critically discussed. This will pave the role of PGPB biofilms in developing bacterial formulations and addressing the challenges related to their efficacy and competence in agriculture for sustainability.
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Li Q, Yang X, Li J, Li M, Li C, Yao T. In-depth characterization of phytase-producing plant growth promotion bacteria isolated in alpine grassland of Qinghai-Tibetan Plateau. Front Microbiol 2023; 13:1019383. [PMID: 36687657 PMCID: PMC9846362 DOI: 10.3389/fmicb.2022.1019383] [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: 08/15/2022] [Accepted: 11/30/2022] [Indexed: 01/05/2023] Open
Abstract
The use of plant growth promoting bacteria (PGPB) express phytase (myo-inositol hexakisphosphate phosphohydrolase) capable of hydrolyzing inositol phosphate in soil was a sustainable approach to supply available phosphorus (P) to plants. A total of 73 bacterial isolates with extracellular phytase activity were selected from seven dominant grass species rhizosphere in alpine grassland of Qinghai-Tibetan Plateau. Then, the plant growth promoting (PGP) traits of candidate bacteria were screened by qualitative and quantitative methods, including organic/inorganic Phosphorus solubilization (P. solubilization), plant hormones (PHs) production, nitrogen fixation, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity and antimicrobial activity. Further experiment were conducted to test their growth promoting effect on Lolium perenne L. under P-limitation. Our results indicated that these bacteria as members of phyla Proteobacteria (90.41%) and Actinobacteria (9.59%) were related to 16 different genera. The isolates of Pseudomonas species showed the highest isolates number (36) and average values of phytase activity (0.267 ± 0.012 U mL-1), and showed a multiple of PGP traits, which was a great candidate for PGPBs. In addition, six strains were positive in phytase gene (β-propeller phytase, bpp) amplification, which significantly increased the shoot length, shoot/root fresh weight, root average diameter and root system phytase activity of Lolium perenne L. under P-limitation, and the expression of phytase gene (bppP) in root system were verified by qPCR. Finally, the PHY101 gene encoding phytase from Pseudomonas mandelii GS10-1 was cloned, sequenced, and recombinantly expressed in Escherichia coli. Biochemical characterization demonstrated that the recombinant phytase PHY101 revealed the highest activity at pH 6 and 40°C temperature. In particular, more than 60% of activity was retained at a low temperature of 15°C. This study demonstrates the opportunity for commercialization of the phytase-producing PGPB to developing localized microbial inoculants and engineering rhizobacteria for sustainable use in alpine grasslands.
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Wang Z, Yang T, Mei X, Wang N, Li X, Yang Q, Dong C, Jiang G, Lin J, Xu Y, Shen Q, Jousset A, Banerjee S. Bio-Organic Fertilizer Promotes Pear Yield by Shaping the Rhizosphere Microbiome Composition and Functions. Microbiol Spectr 2022; 10:e0357222. [PMID: 36453930 PMCID: PMC9769518 DOI: 10.1128/spectrum.03572-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022] Open
Abstract
Bio-organic fertilizers (BOF) containing both organic amendments and beneficial microorganisms have been consistently shown to improve soils fertility and yield. However, the exact mechanisms which link amendments and yields remain disputed, and the complexity of bio-organic fertilizers may work in parallel in several ways. BOF may directly improve yield by replenishing soil nutrients or introducing beneficial microbial genes or indirectly by altering the soil microbiome to enrich native beneficial microorganisms. In this work, we aim to disentangle the relative contributions of direct and indirect effects on pear yield. We treated pear trees with either chemical fertilizer or organic fertilizer with/without the plant-beneficial bacterium Bacillus velezensis SQR9. We then assessed, in detail, soil physicochemical and biological properties (metagenome sequencing) as well as pear yield. We then evaluated the relative importance of direct and indirect effects of soil amendments on pear yield. Both organic treatments increased plant yield by up to 20%, with the addition of bacteria tripling the increase driven by organic fertilizer alone. This increase could be linked to alterations in soil physicochemical properties, bacterial community function, and metabolism. Supplementation of organic fertilizer SQR9 increased rhizosphere microbiome richness and functional diversity. Fertilizer-sensitive microbes and functions responded as whole guilds. Pear yield was most positively associated with the Mitsuaria- and Actinoplanes-dominated ecological clusters and with gene clusters involved in ion transport and secondary metabolite biosynthesis. Together, these results suggested that bio-organic fertilizers mainly act indirectly on plant yield by creating soil chemical properties which promote a plant-beneficial microbiome. IMPORTANCE Bio-organic fertilization is a widely used, eco-friendly, sustainable approach to increasing plant productivity in the agriculture and fruit industries. However, it remains unclear whether the promotion of fruit productivity is related to specific changes in microbial inoculants, the resident microbiome, and/or the physicochemical properties of rhizosphere soils. We found that bio-organic fertilizers alter soil chemical properties, thus manipulating specific microbial taxa and functions within the rhizosphere microbiome of pear plants to promote yield. Our work unveils the ecological mechanisms which underlie the beneficial impacts of bio-organic fertilizers on yield promotion in fruit orchards, which may help in the design of more efficient biofertilizers to promote sustainable fruit production.
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Affiliation(s)
- Zhonghua Wang
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Key Laboratory of Plant immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - Tianjie Yang
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Key Laboratory of Plant immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Xinlan Mei
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Key Laboratory of Plant immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Ningqi Wang
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Key Laboratory of Plant immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Xiaogang Li
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - Qingsong Yang
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - Caixia Dong
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Key Laboratory of Plant immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Gaofei Jiang
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Key Laboratory of Plant immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Jing Lin
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - Yangchun Xu
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Key Laboratory of Plant immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Qirong Shen
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Key Laboratory of Plant immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Alexandre Jousset
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Key Laboratory of Plant immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, North Dakota, USA
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35
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Nakayasu M, Takamatsu K, Yazaki K, Sugiyama A. Plant specialized metabolites in the rhizosphere of tomatoes: secretion and effects on microorganisms. Biosci Biotechnol Biochem 2022; 87:13-20. [PMID: 36373409 DOI: 10.1093/bbb/zbac181] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022]
Abstract
Plants interact with microorganisms in the phyllosphere and rhizosphere. Here the roots exude plant specialized metabolites (PSMs) that have diverse biological and ecological functions. Recent reports have shown that these PSMs influence the rhizosphere microbiome, which is essential for the plant's growth and health. This review summarizes several specialized metabolites secreted into the rhizosphere of the tomato plant (Solanum lycopersicum), which is an important model species for plant research and a commercial crop. In this review, we focused on the effects of such plant metabolites on plant-microbe interactions. We also reviewed recent studies on improving the growth of tomatoes by analyzing and reconstructing the rhizosphere microbiome and discussed the challenges to be addressed in establishing sustainable agriculture.
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Affiliation(s)
- Masaru Nakayasu
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - Kyoko Takamatsu
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - Kazufumi Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, Japan
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36
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Xiong C, Lu Y. Microbiomes in agroecosystem: Diversity, function and assembly mechanisms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:833-849. [PMID: 36184075 DOI: 10.1111/1758-2229.13126] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Soils are a main repository of biodiversity harbouring immense diversity of microbial species that plays a central role in fundamental ecological processes and acts as the seed bank for emergence of the plant microbiome in cropland ecosystems. Crop-associated microbiomes play an important role in shaping plant performance, which includes but not limited to nutrient uptake, disease resistance, and abiotic stress tolerance. Although our understanding of structure and function of soil and plant microbiomes has been rapidly advancing, most of our knowledge comes from ecosystems in natural environment. In this review, we present an overview of the current knowledge of diversity and function of microbial communities along the soil-plant continuum in agroecosystems. To characterize the ecological mechanisms for community assembly of soil and crop microbiomes, we explore how crop host and environmental factors such as plant species and developmental stage, pathogen invasion, and land management shape microbiome structure, microbial co-occurrence patterns, and crop-microbiome interactions. Particularly, the relative importance of deterministic and stochastic processes in microbial community assembly is illustrated under different environmental conditions, and potential sources and keystone taxa of the crop microbiome are described. Finally, we highlight a few important questions and perspectives in future crop microbiome research.
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Affiliation(s)
- Chao Xiong
- College of Urban and Environmental Sciences, Peking University, Beijing, People's Republic of China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, People's Republic of China
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37
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Halvorsen TM, Ricci DP, Park DM, Jiao Y, Yung MC. Comparison of Kill Switch Toxins in Plant-Beneficial Pseudomonas fluorescens Reveals Drivers of Lethality, Stability, and Escape. ACS Synth Biol 2022; 11:3785-3796. [PMID: 36346907 DOI: 10.1021/acssynbio.2c00386] [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: 11/09/2022]
Abstract
Kill switches provide a biocontainment strategy in which unwanted growth of an engineered microorganism is prevented by expression of a toxin gene. A major challenge in kill switch engineering is balancing evolutionary stability with robust cell killing activity in application relevant host strains. Understanding host-specific containment dynamics and modes of failure helps to develop potent yet stable kill switches. To guide the design of robust kill switches in the agriculturally relevant strain Pseudomonas fluorescens SBW25, we present a comparison of lethality, stability, and genetic escape of eight different toxic effectors in the presence of their cognate inactivators (i.e., toxin-antitoxin modules, polymorphic exotoxin-immunity systems, restriction endonuclease-methyltransferase pair). We find that cell killing capacity and evolutionary stability are inversely correlated and dependent on the level of protection provided by the inactivator gene. Decreasing the proteolytic stability of the inactivator protein can increase cell killing capacity, but at the cost of long-term circuit stability. By comparing toxins within the same genetic context, we determine that modes of genetic escape increase with circuit complexity and are driven by toxin activity, the protective capacity of the inactivator, and the presence of mutation-prone sequences within the circuit. Collectively, the results of our study reveal that circuit complexity, toxin choice, inactivator stability, and DNA sequence design are powerful drivers of kill switch stability and valuable targets for optimization of biocontainment systems.
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Affiliation(s)
- Tiffany M Halvorsen
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, California 94550, United States
| | - Dante P Ricci
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, California 94550, United States
| | - Dan M Park
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, California 94550, United States
| | - Yongqin Jiao
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, California 94550, United States
| | - Mimi C Yung
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, California 94550, United States
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38
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NG CWW, YAN WH, TSIM KWK, SO PS, XIA YT, TO CT. Effects of Bacillus subtilis and Pseudomonas fluorescens as the soil amendment. Heliyon 2022; 8:e11674. [PMID: 36439778 PMCID: PMC9691937 DOI: 10.1016/j.heliyon.2022.e11674] [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: 07/14/2022] [Revised: 10/08/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
Abstract
The application of soil beneficial bacteria (SBB) in agriculture is steadily increasing as it provides a promising way to replace chemical fertilisers and other supplements. Although the role of SBB as a biofertiliser is well understood, little is known about the response of soil physiochemical properties via the change in soil enzymatic activities with SBB growth. In this study, sterilised bulk soil was inoculated with Bacillus subtilis (BS) and Pseudomonas fluorescens (PF), which exhibit excellent characteristics in vitro for potentially improving soil quality. It is found that the contents of bioavailable nitrogen and ammonium in soil inoculated with SBB increased significantly, up to 34% and 57% relative to a control. This resulted from the enhancement of soil urease activity with BS and PF treatments by approximately 90% and 70%, respectively. The increased soil urease activity can be explained by the increased microorganism activity evident from the larger population size of BS (0.78–0.97 CFU mL−1/CFU mL−1) than PF (0.55–0.79 CFU mL−1/CFU mL−1) (p < 0.05). Results of principal component analysis also reinforce the interaction apparent in the significant relationship between soil urease activity and microbial biomass carbon (p < 0.05). Therefore, it can be concluded that the enhancement of soil enzymatic activities induced bulk soil fertility upregulation because of bacterial growth. These results demonstrate the application of SBB to be a promising strategy for bulk soil amendment, particularly nutrient restoration.
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Affiliation(s)
- Charles Wang Wai NG
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
| | - Wen Hui YAN
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
- Corresponding author.
| | - Karl Wah Keung TSIM
- Division of Life Science and Centre for Chinese Medicine, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
| | - Pui San SO
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
| | - Yi Teng XIA
- Division of Life Science and Centre for Chinese Medicine, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
| | - Chun Ting TO
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
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Pantigoso HA, Newberger D, Vivanco JM. The rhizosphere microbiome: Plant-microbial interactions for resource acquisition. J Appl Microbiol 2022; 133:2864-2876. [PMID: 36648151 PMCID: PMC9796772 DOI: 10.1111/jam.15686] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 06/16/2022] [Accepted: 06/22/2022] [Indexed: 01/21/2023]
Abstract
While horticulture tools and methods have been extensively developed to improve the management of crops, systems to harness the rhizosphere microbiome to benefit plant crops are still in development. Plants and microbes have been coevolving for several millennia, conferring fitness advantages that expand the plant's own genetic potential. These beneficial associations allow the plants to cope with abiotic stresses such as nutrient deficiency across a wide range of soils and growing conditions. Plants achieve these benefits by selectively recruiting microbes using root exudates, positively impacting their nutrition, health and overall productivity. Advanced knowledge of the interplay between root exudates and microbiome alteration in response to plant nutrient status, and the underlying mechanisms there of, will allow the development of technologies to increase crop yield. This review summarizes current knowledge and perspectives on plant-microbial interactions for resource acquisition and discusses promising advances for manipulating rhizosphere microbiomes and root exudation.
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Affiliation(s)
- Hugo A. Pantigoso
- Center for Root and Rhizosphere Biology, Department of Horticulture and Landscape ArchitectureColorado State UniversityFort CollinsColorado80523‐1173United States
| | - Derek Newberger
- Center for Root and Rhizosphere Biology, Department of Horticulture and Landscape ArchitectureColorado State UniversityFort CollinsColorado80523‐1173United States
| | - Jorge M. Vivanco
- Center for Root and Rhizosphere Biology, Department of Horticulture and Landscape ArchitectureColorado State UniversityFort CollinsColorado80523‐1173United States
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Chen X, Yang F, Bai C, Shi Q, Hu S, Tang X, Peng L, Ding H. Bacillus velezensis Strain GUMT319 Reshapes Soil Microbiome Biodiversity and Increases Grape Yields. BIOLOGY 2022; 11:biology11101486. [PMID: 36290389 PMCID: PMC9598471 DOI: 10.3390/biology11101486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/09/2022] [Accepted: 10/10/2022] [Indexed: 11/18/2022]
Abstract
Bacillus velezensis strain GUMT319 is a rhizobacteria biocontrol agent that can control tobacco black shank disease. We took GUMT319 as a biological fertilizer on Vitis vinifera L. The test group was treated with GUMT319 for one year and the control group had a water treatment. Yields of GUMT319-treated grape groups were significantly increased compared to the controls. The average length and width of single grape fruit, weight of 100 grape fruits, the sugar/acid ratio, and the content of vitamin C were all increased in the GUMT319-treated grape group. The pH of the soil was higher and the contents of alkaline hydrolyzable nitrogen and available potassium were significantly lower in the GUMT319-treated groups than the controls. The soil microbial community composition was evaluated by 16S rDNA high-throughput sequencing, and the Shannon index and Simpson index all showed that soil microbes were more abundant in the GUMT319-treated group. These results indicate that GUMT319 is not only a biocontrol agent, but also a plant growth-promoting rihizobacteria. It can increase the yield of grape by altering the physical and chemical properties and the microbial community composition of the soil.
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Affiliation(s)
- Xiangru Chen
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Fang Yang
- Sino Green Agri-Biotech Co., Ltd., Beijing 102101, China
| | - Chunwei Bai
- Tonghe Zhiyuan (Beijing) Environmental Protection Technology Co., Ltd., Beijing 100036, China
| | - Qianrui Shi
- Liangshan Yi Autonomous Prefecture Bureau of Agriculture and Rural Affairs, Xichang 615000, China
| | - Shan Hu
- College of Tobacco Science, Guizhou University, Guiyang 550025, China
| | - Xianying Tang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Lijuan Peng
- College of Tobacco Science, Guizhou University, Guiyang 550025, China
| | - Haixia Ding
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China
- Correspondence:
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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.
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Affiliation(s)
| | - José R. Dinneny
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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Wang C, Ji Y, Cao X, Yue L, Chen F, Li J, Yang H, Wang Z, Xing B. Carbon Dots Improve Nitrogen Bioavailability to Promote the Growth and Nutritional Quality of Soybeans under Drought Stress. ACS NANO 2022; 16:12415-12424. [PMID: 35946591 DOI: 10.1021/acsnano.2c03591] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The inefficient utilization of nitrogen (N) in soil and drought stress seriously threatens agricultural and food production. Herein, soil application of carbon dots (CDs, 5 mg kg-1) promoted the growth and nutritional quality of soybeans by improving N bioavailability, which was beneficial to alleviate the economic losses caused by drought stress. Soil application of CDs enhanced the N-fixing ability of nodules, regulated rhizosphere processes, and ultimately enhanced N and water uptake in soybeans under drought stress. Compared to control (drought stress), the application of CDs under drought stress enhanced soybean nitrogenase activity by 8.6% and increased N content in soybean shoots and roots by 18.5% and 14.8%, respectively. CDs in soil promoted the secretion of root exudates (e.g., organic acids, fatty acids, and polyketides) and regulated beneficial microbial communities (e.g., Proteobacteria, Acidobacteria, Gemmatimonadetes, and Actinobacteria), thus enhancing the N release from soil. Besides, compared to control, the expression of GmNRT, GmAMT, GmLB, and GmAQP genes in roots were upregulated by 1.2-, 1.8-, 2.7-, and 2.3-fold respectively, implying enhanced N transport and water uptake. Furthermore, the proteins, fatty acids, and amino acids in soybean grains were improved by 3.4%, 6.9%, and 17.3%, respectively, as a result of improved N bioavailability. Therefore, CD-enabled agriculture is promising for improving the drought tolerance and quality of soybeans, which is of significance for food security in facing the crisis of global climate change.
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Affiliation(s)
- Chuanxi Wang
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Yahui Ji
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Xuesong Cao
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Le Yue
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Feiran Chen
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Jing Li
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Hanyue Yang
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, Massachusetts 01003, United States
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Zhu L, Huang J, Lu X, Zhou C. Development of plant systemic resistance by beneficial rhizobacteria: Recognition, initiation, elicitation and regulation. FRONTIERS IN PLANT SCIENCE 2022; 13:952397. [PMID: 36017257 PMCID: PMC9396261 DOI: 10.3389/fpls.2022.952397] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
A plant growing in nature is not an individual, but it holds an intricate community of plants and microbes with relatively stable partnerships. The microbial community has recently been demonstrated to be closely linked with plants since their earliest evolution, to help early land plants adapt to environmental threats. Mounting evidence has indicated that plants can release diverse kinds of signal molecules to attract beneficial bacteria for mediating the activities of their genetics and biochemistry. Several rhizobacterial strains can promote plant growth and enhance the ability of plants to withstand pathogenic attacks causing various diseases and loss in crop productivity. Beneficial rhizobacteria are generally called as plant growth-promoting rhizobacteria (PGPR) that induce systemic resistance (ISR) against pathogen infection. These ISR-eliciting microbes can mediate the morphological, physiological and molecular responses of plants. In the last decade, the mechanisms of microbial signals, plant receptors, and hormone signaling pathways involved in the process of PGPR-induced ISR in plants have been well investigated. In this review, plant recognition, microbial elicitors, and the related pathways during plant-microbe interactions are discussed, with highlights on the roles of root hair-specific syntaxins and small RNAs in the regulation of the PGPR-induced ISR in plants.
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Affiliation(s)
- Lin Zhu
- Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture and Rural Affairs, Anhui Science and Technology University, Bengbu, China
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jiameng Huang
- Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture and Rural Affairs, Anhui Science and Technology University, Bengbu, China
| | - Xiaoming Lu
- Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture and Rural Affairs, Anhui Science and Technology University, Bengbu, China
| | - Cheng Zhou
- Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture and Rural Affairs, Anhui Science and Technology University, Bengbu, China
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
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Díaz M, Bach T, González Anta G, Agaras B, Wibberg D, Noguera F, Canciani W, Valverde C. Agronomic efficiency and genome mining analysis of the wheat-biostimulant rhizospheric bacterium Pseudomonas pergaminensis sp. nov. strain 1008 T. FRONTIERS IN PLANT SCIENCE 2022; 13:894985. [PMID: 35968096 PMCID: PMC9369656 DOI: 10.3389/fpls.2022.894985] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Pseudomonas sp. strain 1008 was isolated from the rhizosphere of field grown wheat plants at the tillering stage in an agricultural plot near Pergamino city, Argentina. Based on its in vitro phosphate solubilizing capacity and the production of IAA, strain 1008 was formulated as an inoculant for bacterization of wheat seeds and subjected to multiple field assays within the period 2010-2017. Pseudomonas sp. strain 1008 showed a robust positive impact on the grain yield (+8% on average) across a number of campaigns, soil properties, seed genotypes, and with no significant influence of the simultaneous seed treatment with a fungicide, strongly supporting the use of this biostimulant bacterium as an agricultural input for promoting the yield of wheat. Full genome sequencing revealed that strain 1008 has the capacity to access a number of sources of inorganic and organic phosphorus, to compete for iron scavenging, to produce auxin, 2,3-butanediol and acetoin, and to metabolize GABA. Additionally, the genome of strain 1008 harbors several loci related to rhizosphere competitiveness, but it is devoid of biosynthetic gene clusters for production of typical secondary metabolites of biocontrol representatives of the Pseudomonas genus. Finally, the phylogenomic, phenotypic, and chemotaxonomic comparative analysis of strain 1008 with related taxa strongly suggests that this wheat rhizospheric biostimulant isolate is a representative of a novel species within the genus Pseudomonas, for which the name Pseudomonas pergaminensis sp. nov. (type strain 1008T = DSM 113453T = ATCC TSD-287T) is proposed.
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Affiliation(s)
- Marisa Díaz
- Rizobacter Argentina S.A., Buenos Aires, Argentina
| | - Teresa Bach
- Rizobacter Argentina S.A., Buenos Aires, Argentina
| | - Gustavo González Anta
- Escuela de Ciencias Agrarias, Exactas y Naturales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires (UNNOBA), Buenos Aires, Argentina
- Departamento de Ciencias Naturales y Exactas, Universidad Nacional de San Antonio de Areco (UNSAdA), Buenos Aires, Argentina
- Indrasa Biotecnología S.A., Córdoba, Argentina
| | - Betina Agaras
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Universidad Nacional de Quilmes-CONICET, Buenos Aires, Argentina
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | | | | | - Claudio Valverde
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Universidad Nacional de Quilmes-CONICET, Buenos Aires, Argentina
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Orozco-Mosqueda MDC, Fadiji AE, Babalola OO, Glick BR, Santoyo G. Rhizobiome engineering: Unveiling complex rhizosphere interactions to enhance plant growth and health. Microbiol Res 2022; 263:127137. [PMID: 35905581 DOI: 10.1016/j.micres.2022.127137] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/17/2022] [Accepted: 07/13/2022] [Indexed: 12/13/2022]
Abstract
Crop plants are affected by a series of inhibitory environmental and biotic factors that decrease their growth and production. To counteract these adverse effects, plants work together with the microorganisms that inhabit their rhizosphere, which is part of the soil influenced by root exudates. The rhizosphere is a microecosystem where a series of complex interactions takes place between the resident microorganisms (rhizobiome) and plant roots. Therefore, this study analyzes the dynamics of plant-rhizobiome communication, the role of exudates (diffusible and volatile) as a factor in stimulating a diverse rhizobiome, and the differences between rhizobiomes of domesticated crops and wild plants. The study also analyzes different strategies to decipher the rhizobiome through both classical cultivation techniques and the so-called "omics" sciences. In addition, the rhizosphere engineering concept and the two general strategies to manipulate the rhizobiome, i.e., top down and bottom up engineering have been revisited. In addition, recent studies on the effects on the indigenous rhizobiome of inoculating plants with foreign strains, the impact on the endobiome, and the collateral effects on plant crops are discussed. Finally, understanding of the complex rhizosphere interactions and the biological repercussions of rhizobiome engineering as essential steps for improving plant growth and health is proposed, including under adverse conditions.
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Affiliation(s)
| | - Ayomide Emmanuel Fadiji
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich 58030, Mexico.
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Li Z, Zheng Y, Li Y, Cheng X, Huang S, Yang X, Qin Y. Genotype-Specific Recruitment of Rhizosphere Bacteria From Sandy Loam Soil for Growth Promotion of Cucumis sativus var. hardwickii. Front Microbiol 2022; 13:910644. [PMID: 35832804 PMCID: PMC9271904 DOI: 10.3389/fmicb.2022.910644] [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: 04/01/2022] [Accepted: 05/11/2022] [Indexed: 11/16/2022] Open
Abstract
The composition and structure of the rhizosphere microbiome is affected by many factors, including soil type, genotype, and cultivation time of the plant. However, the interaction mechanisms among these factors are largely unclear. We use culture-independent 16S rRNA amplicon sequencing to investigate the rhizosphere bacterial composition and the structure of cultivated cucumber Xintaimici (XT) and wild-type cucumber Cucumis sativus var. hardwickii (HD) in four kinds of soils. We found that soil type, cultivation time, and genotype affected the composition and structure of cucumber rhizosphere bacterial communities. Notably, HD showed better physiological features in sandy soil and sandy loam soil than it did in black soil and farm soil at 50 days post-sowing, which was due to its stronger recruitment ability to Nitrospira, Nocardioides, Bacillus, and Gaiella in sandy soil, and more Tumebacillus, Nitrospira, and Paenibacillus in sandy loam soil. Meanwhile, we also found that HD showed a better recruiting capacity for these bacterial genera than XT in both sandy soil and sandy loam soil. Functional predictions indicated that these bacteria might have had stronger root colonization ability and then promoted the growth of cucumbers by enhancing nitrogen metabolism and active metabolite secretion. In this study, our findings provided a better insight into the relationship between cucumber phenotype, genotype, and the rhizosphere bacterial community, which will offer valuable theoretical references for rhizosphere microbiota studies and its future application in agriculture.
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Affiliation(s)
- Zeyang Li
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingying Zheng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yansu Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xu Cheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- *Correspondence: Sanwen Huang,
| | - Xueyong Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Xueyong Yang,
| | - Yuxuan Qin
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Yuxuan Qin,
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Control of nitrogen fixation and ammonia excretion in Azorhizobium caulinodans. PLoS Genet 2022; 18:e1010276. [PMID: 35727841 PMCID: PMC9249168 DOI: 10.1371/journal.pgen.1010276] [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: 03/24/2022] [Revised: 07/01/2022] [Accepted: 05/26/2022] [Indexed: 11/19/2022] Open
Abstract
Due to the costly energy demands of nitrogen (N) fixation, diazotrophic bacteria have evolved complex regulatory networks that permit expression of the catalyst nitrogenase only under conditions of N starvation, whereas the same condition stimulates upregulation of high-affinity ammonia (NH3) assimilation by glutamine synthetase (GS), preventing excess release of excess NH3 for plants. Diazotrophic bacteria can be engineered to excrete NH3 by interference with GS, however control is required to minimise growth penalties and prevent unintended provision of NH3 to non-target plants. Here, we tested two strategies to control GS regulation and NH3 excretion in our model cereal symbiont Azorhizobium caulinodans AcLP, a derivative of ORS571. We first attempted to recapitulate previous work where mutation of both PII homologues glnB and glnK stimulated GS shutdown but found that one of these genes was essential for growth. Secondly, we expressed unidirectional adenylyl transferases (uATs) in a ΔglnE mutant of AcLP which permitted strong GS shutdown and excretion of NH3 derived from N2 fixation and completely alleviated negative feedback regulation on nitrogenase expression. We placed a uAT allele under control of the NifA-dependent promoter PnifH, permitting GS shutdown and NH3 excretion specifically under microaerobic conditions, the same cue that initiates N2 fixation, then deleted nifA and transferred a rhizopine nifAL94Q/D95Q-rpoN controller plasmid into this strain, permitting coupled rhizopine-dependent activation of N2 fixation and NH3 excretion. This highly sophisticated and multi-layered control circuitry brings us a step closer to the development of a "synthetic symbioses” where N2 fixation and NH3 excretion could be specifically activated in diazotrophic bacteria colonising transgenic rhizopine producing cereals, targeting delivery of fixed N to the crop while preventing interaction with non-target plants. Inoculation of cereal crops with associative diazotrophic bacteria that convert atmospheric nitrogen (N2) into ammonia (NH3) could be used to sustainably improve delivery of nitrogen to crops. However, due to the costly energy demands of N2 fixation, bacteria restrict excess production of NH3 and release to the plants. Diazotrophs can be engineered for excess NH3 production and release, however genetic control is required to minimise growth penalties and prevent unintended provision of NH3 to non-target weed species. Here, we engineer coupled control of N2 fixation and NH3 release in response to the signalling molecule rhizopine supplemented in vitro. This control circuitry represents a prototype for the future development of a “synthetic symbiosis” where bacterial N2 fixation and NH3 excretion could be specifically activated following colonisation of transgenic rhizopine producing cereals in the field, minimising bacterial energy requirements and preventing provision of NH3 to non-target plants.
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48
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Microbiome engineering for sustainable agriculture: using synthetic biology to enhance nitrogen metabolism in plant-associated microbes. Curr Opin Microbiol 2022; 68:102172. [PMID: 35717707 DOI: 10.1016/j.mib.2022.102172] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/14/2022] [Accepted: 05/16/2022] [Indexed: 11/23/2022]
Abstract
Plants benefit from symbiotic relationships with their microbiomes. Modifying these microbiomes to further promote plant growth and improve stress tolerance in crops is a promising strategy. However, such efforts have had limited success, perhaps because the original microbiomes quickly re-establish. Since the complex biological networks involved are little understood, progress through conventional means is time-consuming. Synthetic biology, with its practical successes in multiple industries, could speed up this research considerably. Some fascinating candidates for production by synthetic microbiomes are organic nitrogen metabolites and related pyridoxal-5'-phosphate-dependent enzymes, which have pivotal roles in microbe-microbe and plant-microbe interactions. This review summarizes recent studies of these metabolites and enzymes and discusses prospective synthetic biology platforms for sustainable agriculture.
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Moore JAM, Abraham PE, Michener J, Muchero W, Cregger M. Ecosystem consequences of introducing plant growth promoting rhizobacteria to managed systems and potential legacy effects. THE NEW PHYTOLOGIST 2022; 234:1914-1918. [PMID: 35098533 PMCID: PMC9314638 DOI: 10.1111/nph.18010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/23/2022] [Indexed: 05/19/2023]
Abstract
The rapidly growing industry of crop biostimulants leverages the application of plant growth promoting rhizobacteria (PGPR) to promote plant growth and health. However, introducing nonnative rhizobacteria may impact other aspects of ecosystem functioning and have legacy effects; these potential consequences are largely unexplored. Nontarget consequences of PGPR may include changes in resident microbiomes, nutrient cycling, pollinator services, functioning of other herbivores, disease suppression, and organic matter persistence. Importantly, we lack knowledge of whether these ecosystem effects may manifest in adjacent ecosystems. The introduced PGPR can leave a functional legacy whether they persist in the community or not. Legacy effects include shifts in resident microbiomes and their temporal dynamics, horizontal transfer of genes from the PGPR to resident taxa, and changes in resident functional groups and interaction networks. Ecosystem functions may be affected by legacies PGPR leave following niche construction, such as when PGPR alter soil pH that in turn alters biogeochemical cycling rates. Here, we highlight new research directions to elucidate how introduced PGPR impact resident microbiomes and ecosystem functions and their capacity for legacy effects.
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Affiliation(s)
- Jessica A. M. Moore
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37830USA
| | - Paul E. Abraham
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37830USA
| | - Joshua K. Michener
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37830USA
| | - Wellington Muchero
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37830USA
| | - Melissa A. Cregger
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37830USA
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Zhu Y, Xiong C, Wei Z, Chen Q, Ma B, Zhou S, Tan J, Zhang L, Cui H, Duan G. Impacts of global change on the phyllosphere microbiome. THE NEW PHYTOLOGIST 2022; 234:1977-1986. [PMID: 34921429 PMCID: PMC9306672 DOI: 10.1111/nph.17928] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/08/2021] [Indexed: 05/21/2023]
Abstract
Plants form complex interaction networks with diverse microbiomes in the environment, and the intricate interplay between plants and their associated microbiomes can greatly influence ecosystem processes and functions. The phyllosphere, the aerial part of the plant, provides a unique habitat for diverse microbes, and in return the phyllosphere microbiome greatly affects plant performance. As an open system, the phyllosphere is subjected to environmental perturbations, including global change, which will impact the crosstalk between plants and their microbiomes. In this review, we aim to provide a synthesis of current knowledge of the complex interactions between plants and the phyllosphere microbiome under global changes and to identify future priority areas of research on this topic.
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Affiliation(s)
- Yong‐Guan Zhu
- Key Laboratory of Urban Environment and HealthInstitute of Urban EnvironmentChinese Academy of SciencesXiamen361021China
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - Chao Xiong
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - Zhong Wei
- Key Laboratory of Plant ImmunityJiangsu Provincial Key Laboratory for Organic Solid Waste UtilizationJiangsu Collaborative Innovation Center for Solid Organic Waste Resource UtilizationNational Engineering Research Center for Organic‐Based FertilizersNanjing Agricultural UniversityWeigang, Nanjing210095China
| | - Qing‐Lin Chen
- Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVic3010Australia
| | - Bin Ma
- Zhejiang Provincial Key Laboratory of Agricultural Resources and EnvironmentCollege of Environmental and Natural Resource SciencesZhejiang UniversityHangzhou310058China
- Hangzhou Innovation CenterZhejiang UniversityHangzhou311200China
| | - Shu‐Yi‐Dan Zhou
- Key Laboratory of Urban Environment and HealthInstitute of Urban EnvironmentChinese Academy of SciencesXiamen361021China
| | - Jiaqi Tan
- Department of Biological SciencesLouisiana State UniversityBaton RougeLA70803USA
| | - Li‐Mei Zhang
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - Hui‐Ling Cui
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - Gui‐Lan Duan
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
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