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Mukherjee A, Singh BN, Kaur S, Sharma M, Ferreira de Araújo AS, Pereira APDA, Morya R, Puopolo G, Melo VMM, Verma JP. Unearthing the power of microbes as plant microbiome for sustainable agriculture. Microbiol Res 2024; 286:127780. [PMID: 38970905 DOI: 10.1016/j.micres.2024.127780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 07/08/2024]
Abstract
In recent years, research into the complex interactions and crosstalk between plants and their associated microbiota, collectively known as the plant microbiome has revealed the pivotal role of microbial communities for promoting plant growth and health. Plants have evolved intricate relationships with a diverse array of microorganisms inhabiting their roots, leaves, and other plant tissues. This microbiota mainly includes bacteria, archaea, fungi, protozoans, and viruses, forming a dynamic and interconnected network within and around the plant. Through mutualistic or cooperative interactions, these microbes contribute to various aspects of plant health and development. The direct mechanisms of the plant microbiome include the enhancement of plant growth and development through nutrient acquisition. Microbes have the ability to solubilize essential minerals, fix atmospheric nitrogen, and convert organic matter into accessible forms, thereby augmenting the nutrient pool available to the plant. Additionally, the microbiome helps plants to withstand biotic and abiotic stresses, such as pathogen attacks and adverse environmental conditions, by priming the plant's immune responses, antagonizing phytopathogens, and improving stress tolerance. Furthermore, the plant microbiome plays a vital role in phytohormone regulation, facilitating hormonal balance within the plant. This regulation influences various growth processes, including root development, flowering, and fruiting. Microbial communities can also produce secondary metabolites, which directly or indirectly promote plant growth, development, and health. Understanding the functional potential of the plant microbiome has led to innovative agricultural practices, such as microbiome-based biofertilizers and biopesticides, which harness the power of beneficial microorganisms to enhance crop yields while reducing the dependency on chemical inputs. In the present review, we discuss and highlight research gaps regarding the plant microbiome and how the plant microbiome can be used as a source of single and synthetic bioinoculants for plant growth and health.
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Affiliation(s)
- Arpan Mukherjee
- Plant-Microbe Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Bansh Narayan Singh
- Plant-Microbe Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Simranjit Kaur
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753, Australia; Crop Research Centre, Oak Park, Carlow, Ireland
| | - Minaxi Sharma
- CARAH ASBL, Rue Pal Pastur 11, Ath 7800, Belgium; China Beacons of Excellence Research and Innovation Institute (CBI), University of Nottingham Ningbo China, Ningbo 315000, China
| | | | | | - Raj Morya
- Department of Civil and Environmental engineering, Yonsei University, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Gerardo Puopolo
- Center Agriculture Food Environment (C3A), University of Trento, Via Mach 1, San Michele all'Adige 38098, Italy; Research and Innovation center, Fondazione Edmund Mach, Via E. Mach 1, San Michelle all'Adige 38098, Italy
| | - Vânia Maria Maciel Melo
- Department of Biological Sciences, Faculty of Science, Federal University of Ceará, Pici, Fortaleza, Ceará 60020-181, Brazil
| | - Jay Prakash Verma
- Plant-Microbe Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India.
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Charakas C, Khokhani D. Expanded trade: tripartite interactions in the mycorrhizosphere. mSystems 2024; 9:e0135223. [PMID: 38837330 PMCID: PMC11265408 DOI: 10.1128/msystems.01352-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024] Open
Abstract
Interactions between arbuscular mycorrhizal fungi (AMF), plants, and the soil microbial community have the potential to increase the availability and uptake of phosphorus (P) and nitrogen (N) in agricultural systems. Nutrient exchange between plant roots, AMF, and the adjacent soil microbes occurs at the interface between roots colonized by mycorrhizal fungi and soil, referred to as the mycorrhizosphere. Research on the P exchange focuses on plant-AMF or AMF-microbe interactions, lacking a holistic view of P exchange between the plants, AMF, and other microbes. Recently, N exchange at both interfaces revealed the synergistic role of AMF and bacterial community in N uptake by the host plant. Here, we highlight work carried out on each interface and build upon it by emphasizing research involving all members of the tripartite network. Both nutrient systems are challenging to study due to the complex chemical and biological nature of the mycorrhizosphere. We discuss some of the effective methods to identify important nutrient processes and the tripartite members involved in these processes. The extrapolation of in vitro studies into the field is often fraught with contradiction and noise. Therefore, we also suggest some approaches that can potentially bridge the gap between laboratory-generated data and their extrapolation to the field, improving the applicability and contextual relevance of data within the field of mycorrhizosphere interactions. Overall, we argue that the research community needs to adopt a holistic tripartite approach and that we have the means to increase the applicability and accuracy of in vitro data in the field.
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Affiliation(s)
- Christos Charakas
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, Minnesota, USA
| | - Devanshi Khokhani
- Department of Plant Pathology, University of Minnesota, Twin Cities, Minnesota, USA
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3
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Wang T, Chen Q, Liang Q, Zhao Q, Lu X, Tian J, Guan Z, Liu C, Li J, Zhou M, Tian J, Liang C. Bacillus suppresses nitrogen efficiency of soybean-rhizobium symbiosis through regulation of nitrogen-related transcriptional and microbial patterns. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38963088 DOI: 10.1111/pce.15023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/21/2024] [Accepted: 06/21/2024] [Indexed: 07/05/2024]
Abstract
The regulation of legume-rhizobia symbiosis by microorganisms has obtained considerable interest in recent research, particularly in the common rhizobacteria Bacillus. However, few studies have provided detailed explanations regarding the regulatory mechanisms involved. Here, we investigated the effects of Bacillus (Bac.B) on Bradyrhizobium-soybean (Glycine max) symbiosis and elucidated the underlying ecological mechanisms. We found that two Bradyrhizobium strains (i.e. Bra.Q2 and Bra.D) isolated from nodules significantly promoted nitrogen (N) efficiency of soybean via facilitating nodule formation, thereby enhanced plant growth and yield. However, the intrusion of Bac.B caused a reverse shift in the synergistic efficiency of N2 fixation in the soybean-Bradyrhizobium symbiosis. Biofilm formation and naringenin may be importantin suppression of Bra.Q2 growth regulated by Bac.B. In addition, transcriptome and microbiome analyses revealed that Bra.Q2 and Bac.B might interact to regulateN transport and assimilation, thus influence the bacterial composition related to plant N nutrition in nodules. Also, the metabolisms of secondary metabolites and hormones associated with plant-microbe interaction and growth regulation were modulated by Bra.Q2 and Bac.B coinoculation. Collectively, we demonstrate that Bacillus negatively affects Bradyrhizobium-soybean symbiosis and modulate microbial interactions in the nodule. Our findings highlight a novel Bacillus-based regulation to improve N efficiency and sustainable agricultural development.
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Affiliation(s)
- Tianqi Wang
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Qianqian Chen
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Quan Liang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Qian Zhao
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Xing Lu
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Jihui Tian
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Zidi Guan
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Chang Liu
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Jifu Li
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Ming Zhou
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Jiang Tian
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Cuiyue Liang
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
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4
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Xu Y, Teng Y, Wang X, Wang H, Li Y, Ren W, Zhao L, Wei M, Luo Y. Biohydrogen utilization in legume-rhizobium symbiosis reveals a novel mechanism of accelerated tetrachlorobiphenyl transformation. BIORESOURCE TECHNOLOGY 2024; 404:130918. [PMID: 38823562 DOI: 10.1016/j.biortech.2024.130918] [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: 02/03/2024] [Revised: 05/23/2024] [Accepted: 05/30/2024] [Indexed: 06/03/2024]
Abstract
Symbiosis between Glycine max and Bradyrhizobium diazoefficiens were used as a model system to investigate whether biohydrogen utilization promotes the transformation of the tetrachlorobiphenyl PCB77. Both a H2 uptake-positive (Hup+) strain (wild type) and a Hup- strain (a hupL deletion mutant) were inoculated into soybean nodules. Compared with Hup- nodules, Hup+ nodules increased dechlorination significantly by 61.1 % and reduced the accumulation of PCB77 in nodules by 37.7 % (p < 0.05). After exposure to nickel, an enhancer of uptake hydrogenase, dechlorination increased significantly by 2.2-fold, and the accumulation of PCB77 in nodules decreased by 54.4 % (p < 0.05). Furthermore, the tetrachlorobiphenyl transformation in the soybean root nodules was mainly testified to be mediated by nitrate reductase (encoded by the gene NR) for tetrachlorobiphenyl dechlorination and biphenyl-2,3-diol 1,2-dioxygenase (bphC) for biphenyl degradation. This study demonstrates for the first time that biohydrogen utilization has a beneficial effect on tetrachlorobiphenyl biotransformation in a legume-rhizobium symbiosis.
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Affiliation(s)
- Yongfeng Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xiaomi Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongzhe Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanning Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjie Ren
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ling Zhao
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Wei
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Yongming Luo
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
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5
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Louisson Z, Gutiérrez-Ginés MJ, Taylor M, Buckley HL, Hermans SM, Lear G. Soil conditions are a more important determinant of microbial community composition and functional potential than neighboring plant diversity. iScience 2024; 27:110056. [PMID: 38883816 PMCID: PMC11176639 DOI: 10.1016/j.isci.2024.110056] [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: 12/04/2023] [Revised: 04/14/2024] [Accepted: 05/17/2024] [Indexed: 06/18/2024] Open
Abstract
Replanting is an important tool for ecological recovery. Management strategies, such as planting areas with monocultures or species mixtures, have implications for restoration success. We used 16S and ITS rRNA gene amplicon sequencing and shotgun metagenomics to assess how the diversity of neighboring tree species impacted soil bacterial and fungal communities, and their functional potential, within the root zone of mānuka (Leptospermum scoparium) trees. We compared data from monoculture and mixed tree species plots and confirmed that soil microbial taxonomic and functional community profiles significantly differed (p < 0.001). Compared to the diversity of neighboring tree species within the plot, soil environmental conditions and geographic distance was more important for structuring the microbial communities. The bacterial communities appeared more impacted by soil conditions, while the fungal communities displayed stronger spatial structuring, possibly due to wider bacterial dispersal. The different mechanisms structuring bacterial and fungal communities could have implications for ecological restoration outcomes.
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Affiliation(s)
- Ziva Louisson
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland 1010, New Zealand
| | - Maria J Gutiérrez-Ginés
- Institute of Environmental Science and Research Ltd., 27 Creyke Road, Ilam, Christchurch 8041, New Zealand
| | - Matthew Taylor
- Waikato Regional Council, 160 Ward St, Hamilton 3204, New Zealand
| | - Hannah L Buckley
- School of Science, Auckland University of Technology, 34 St Paul Street, Auckland 1010, New Zealand
| | - Syrie M Hermans
- School of Science, Auckland University of Technology, 34 St Paul Street, Auckland 1010, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland 1010, New Zealand
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6
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Chakraborty S, Venkataraman M, Infante V, Pfleger BF, Ané JM. Scripting a new dialogue between diazotrophs and crops. Trends Microbiol 2024; 32:577-589. [PMID: 37770375 PMCID: PMC10950843 DOI: 10.1016/j.tim.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 09/30/2023]
Abstract
Diazotrophs are bacteria and archaea that can reduce atmospheric dinitrogen (N2) into ammonium. Plant-diazotroph interactions have been explored for over a century as a nitrogen (N) source for crops to improve agricultural productivity and sustainability. This scientific quest has generated much information about the molecular mechanisms underlying the function, assembly, and regulation of nitrogenase, ammonium assimilation, and plant-diazotroph interactions. This review presents various approaches to manipulating N fixation activity, ammonium release by diazotrophs, and plant-diazotroph interactions. We discuss the research avenues explored in this area, propose potential future routes, emphasizing engineering at the metabolic level via biorthogonal signaling, and conclude by highlighting the importance of biocontrol measures and public acceptance.
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Affiliation(s)
- Sanhita Chakraborty
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA
| | - Maya Venkataraman
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, Madison, WI, USA
| | - Valentina Infante
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, Madison, WI, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA; Department of Agronomy, University of Wisconsin - Madison, Madison, WI, USA.
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7
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Tonelli D, Rosa L, Gabrielli P, Parente A, Contino F. Cost-competitive decentralized ammonia fertilizer production can increase food security. NATURE FOOD 2024; 5:469-479. [PMID: 38755344 PMCID: PMC11199140 DOI: 10.1038/s43016-024-00979-y] [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: 09/27/2023] [Accepted: 04/09/2024] [Indexed: 05/18/2024]
Abstract
The current centralized configuration of the ammonia industry makes the production of nitrogen fertilizers susceptible to the volatility of fossil fuel prices and involves complex supply chains with long-distance transport costs. An alternative consists of on-site decentralized ammonia production using small modular technologies, such as electric Haber-Bosch or electrocatalytic reduction. Here we evaluate the cost-competitiveness of producing low-carbon ammonia at the farm scale, from a solar agrivoltaic system, or using electricity from the grid, within a novel global fertilizer industry. Projected costs for decentralized ammonia production are compared with historical market prices from centralized production. We find that the cost-competitiveness of decentralized production relies on transport costs and supply chain disruptions. Taking both factors into account, decentralized production could achieve cost-competitiveness for up to 96% of the global ammonia demand by 2030. These results show the potential of decentralized ammonia technologies in revolutionizing the fertilizer industry, particularly in regions facing food insecurity.
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Affiliation(s)
- Davide Tonelli
- Institute of Mechanics, Materials and Civil Engineering, UCLouvain, Ottignies-Louvain-la-Neuve, Belgium.
- Aero-Thermo-Mechanics Department, ULB, Brussels, Belgium.
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA.
| | - Lorenzo Rosa
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA.
| | - Paolo Gabrielli
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA
- Institute of Energy and Process Engineering, ETH Zurich, Zurich, Switzerland
| | | | - Francesco Contino
- Institute of Mechanics, Materials and Civil Engineering, UCLouvain, Ottignies-Louvain-la-Neuve, Belgium
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8
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Xie CJ, Yao L, Tang R, Han S, Yang S, Alwathnani H, Rensing C, Liu GH, Zhou SG. Azotosporobacter soli gen. nov., sp. nov., a novel nitrogen-fixing bacterium isolated from paddy soil. Antonie Van Leeuwenhoek 2024; 117:79. [PMID: 38755437 DOI: 10.1007/s10482-024-01978-6] [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: 02/26/2024] [Accepted: 05/07/2024] [Indexed: 05/18/2024]
Abstract
A nitrogen-fixing strain designated SG130T was isolated from paddy soil in Fujian Province, China. Strain SG130T was Gram-staining-negative, rod-shaped, and strictly anaerobic. Strain SG130T showed the highest 16S rRNA gene sequence similarities with the type strains Dendrosporobacter quercicolus DSM 1736T (91.7%), Anaeroarcus burkinensis DSM 6283T (91.0%) and Anaerospora hongkongensis HKU 15T (90.9%). Furthermore, the phylogenetic and phylogenomic analysis also suggested strain SG130T clustered with members of the family Sporomusaceae and was distinguished from other genera within this family. Growth of strain SG130T was observed at 25-45 °C (optimum 30 °C), pH 6.0-9.5 (optimum 7.0) and 0-1% (w/v) NaCl (optimum 0.1%). The quinones were Q-8 and Q-9. The polar lipids were phosphatidylserine (PS), phosphatidylethanolamine (PE), glycolipid (GL), phospholipid (PL) and an unidentified lipid (UL). The major fatty acids (> 10%) were iso-C13:0 3OH (26.6%), iso-C17:1 (15.6%) and iso-C15:1 F (11.4%). The genomic DNA G + C content was 50.7%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain SG130T and the most closely related type strain D. quercicolus DSM 1736T (ANI 68.0% and dDDH 20.3%) were both below the cut-off level for species delineation. The average amino acid identity (AAI) between strain SG130T and the most closely related type strain D. quercicolus DSM 1736T was 63.2%, which was below the cut-off value for bacterial genus delineation (65%). Strain SG130T possessed core genes (nifHDK) involved in nitrogen fixation, and nitrogenase activity (106.38 μmol C2H4 g-1 protein h-1) was examined using the acetylene reduction assay. Based on the above results, strain SG130T is confirmed to represent a novel genus of the family Sporomusaceae, for which the name Azotosporobacter soli gen. nov., sp. nov. is proposed. The type strain is SG130T (= GDMCC 1.3312T = JCM 35641T).
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Affiliation(s)
- Cheng-Jie Xie
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, 350002, People's Republic of China
| | - Ling Yao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, 350002, People's Republic of China
| | - Rong Tang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou City, Guangdong Province, 510006, People's Republic of China
| | - Shuang Han
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, 350002, People's Republic of China
| | - Shang Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, 350002, People's Republic of China
| | - Hend Alwathnani
- Department of Botany and Microbiology, King Saud University, Riyadh, Saudi Arabia
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, 350002, People's Republic of China
| | - Guo-Hong Liu
- Institute of Resources, Environment and Soil Fertilizer, Fujian Academy of Agricultural Sciences, Fuzhou City, Fujian Province, 350003, People's Republic of China.
| | - Shun-Gui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, 350002, People's Republic of China.
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9
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Lewis NM, Kisgeropoulos EC, Lubner CE, Fixen KR. Characterization of ferredoxins involved in electron transfer pathways for nitrogen fixation implicates differences in electronic structure in tuning 2[4Fe4S] Fd activity. J Inorg Biochem 2024; 254:112521. [PMID: 38471286 DOI: 10.1016/j.jinorgbio.2024.112521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 03/03/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024]
Abstract
Ferredoxins (Fds) are small proteins which shuttle electrons to pathways like biological nitrogen fixation. Physical properties tune the reactivity of Fds with different pathways, but knowledge on how these properties can be manipulated to engineer new electron transfer pathways is lacking. Recently, we showed that an evolved strain of Rhodopseudomonas palustris uses a new electron transfer pathway for nitrogen fixation. This pathway involves a variant of the primary Fd of nitrogen fixation in R. palustris, Fer1, in which threonine at position 11 is substituted for isoleucine (Fer1T11I). To understand why this substitution in Fer1 enables more efficient electron transfer, we used in vivo and in vitro methods to characterize Fer1 and Fer1T11I. Electrochemical characterization revealed both Fer1 and Fer1T11I have similar redox transitions (-480 mV and - 550 mV), indicating the reduction potential was unaffected despite the proximity of T11 to an iron‑sulfur (FeS) cluster of Fer1. Additionally, disruption of hydrogen bonding around an FeS cluster in Fer1 by substituting threonine with alanine (T11A) or valine (T11V) did not increase nitrogenase activity, indicating that disruption of hydrogen bonding does not explain the difference in activity observed for Fer1T11I. Electron paramagnetic resonance spectroscopy studies revealed key differences in the electronic structure of Fer1 and Fer1T11I, which indicate changes to the high spin states and/or spin-spin coupling between the FeS clusters of Fer1. Our data implicates these electronic structure differences in facilitating electron flow and sets a foundation for further investigations to understand the connection between these properties and intermolecular electron transfer.
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Affiliation(s)
- Nathan M Lewis
- Department of Plant and Microbial Biology and the Biotechnology Institute, University of Minnesota, Minneapolis, MN, United States of America
| | | | - Carolyn E Lubner
- National Renewable Energy Laboratory, Golden, CO, United States of America.
| | - Kathryn R Fixen
- Department of Plant and Microbial Biology and the Biotechnology Institute, University of Minnesota, Minneapolis, MN, United States of America.
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10
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Mallikaarachchi KS, Huang JL, Madras S, Cuellar RA, Huang Z, Gega A, Rathnayaka-Mudiyanselage IW, Al-Husini N, Saldaña-Rivera N, Ma LH, Ng E, Chen JC, Schrader JM. Sinorhizobium meliloti BR-bodies promote fitness during host colonization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.05.588320. [PMID: 38617242 PMCID: PMC11014517 DOI: 10.1101/2024.04.05.588320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Biomolecular condensates, such as the nucleoli or P-bodies, are non-membrane-bound assemblies of proteins and nucleic acids that facilitate specific cellular processes. Like eukaryotic P-bodies, the recently discovered bacterial ribonucleoprotein bodies (BR-bodies) organize the mRNA decay machinery, yet the similarities in molecular and cellular functions across species have been poorly explored. Here, we examine the functions of BR-bodies in the nitrogen-fixing endosymbiont Sinorhizobium meliloti, which colonizes the roots of compatible legume plants. Assembly of BR-bodies into visible foci in S. meliloti cells requires the C-terminal intrinsically disordered region (IDR) of RNase E, and foci fusion is readily observed in vivo, suggesting they are liquid-like condensates that form via mRNA sequestration. Using Rif-seq to measure mRNA lifetimes, we found a global slowdown in mRNA decay in a mutant deficient in BR-bodies, indicating that compartmentalization of the degradation machinery promotes efficient mRNA turnover. While BR-bodies are constitutively present during exponential growth, the abundance of BR-bodies increases upon cell stress, whereby they promote stress resistance. Finally, using Medicago truncatula as host, we show that BR-bodies enhance competitiveness during colonization and appear to be required for effective symbiosis, as mutants without BR-bodies failed to stimulate plant growth. These results suggest that BR-bodies provide a fitness advantage for bacteria during infection, perhaps by enabling better resistance against the host immune response.
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Affiliation(s)
| | | | | | - Rodrigo A. Cuellar
- Department of Biology, San Francisco State University
- Current affiliation: University of Wisconsin, Madison
| | | | - Alisa Gega
- Department of Biological Sciences, Wayne State University
- Current affiliation: University of Toledo Medical School, Toledo
| | | | | | | | - Loi H. Ma
- Department of Biology, San Francisco State University
| | - Eric Ng
- Department of Biology, San Francisco State University
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11
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Qin H, Wang Z, Sha W, Song S, Qin F, Zhang W. Role of Plant-Growth-Promoting Rhizobacteria in Plant Machinery for Soil Heavy Metal Detoxification. Microorganisms 2024; 12:700. [PMID: 38674644 PMCID: PMC11052264 DOI: 10.3390/microorganisms12040700] [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: 02/23/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Heavy metals migrate easily and are difficult to degrade in the soil environment, which causes serious harm to the ecological environment and human health. Thus, soil heavy metal pollution has become one of the main environmental issues of global concern. Plant-growth-promoting rhizobacteria (PGPR) is a kind of microorganism that grows around the rhizosphere and can promote plant growth and increase crop yield. PGPR can change the bioavailability of heavy metals in the rhizosphere microenvironment, increase heavy metal uptake by phytoremediation plants, and enhance the phytoremediation efficiency of heavy-metal-contaminated soils. In recent years, the number of studies on the phytoremediation efficiency of heavy-metal-contaminated soil enhanced by PGPR has increased rapidly. This paper systematically reviews the mechanisms of PGPR that promote plant growth (including nitrogen fixation, phosphorus solubilization, potassium solubilization, iron solubilization, and plant hormone secretion) and the mechanisms of PGPR that enhance plant-heavy metal interactions (including chelation, the induction of systemic resistance, and the improvement of bioavailability). Future research on PGPR should address the challenges in heavy metal removal by PGPR-assisted phytoremediation.
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Affiliation(s)
| | | | | | | | - Fenju Qin
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Wenchao Zhang
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou 215009, China
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12
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Boo A, Toth T, Yu Q, Pfotenhauer A, Fields BD, Lenaghan SC, Stewart CN, Voigt CA. Synthetic microbe-to-plant communication channels. Nat Commun 2024; 15:1817. [PMID: 38418817 PMCID: PMC10901793 DOI: 10.1038/s41467-024-45897-6] [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: 02/10/2023] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
Plants and microbes communicate to collaborate to stop pests, scavenge nutrients, and react to environmental change. Microbiota consisting of thousands of species interact with each other and plants using a large chemical language that is interpreted by complex regulatory networks. In this work, we develop modular interkingdom communication channels, enabling bacteria to convey environmental stimuli to plants. We introduce a "sender device" in Pseudomonas putida and Klebsiella pneumoniae, that produces the small molecule p-coumaroyl-homoserine lactone (pC-HSL) when the output of a sensor or circuit turns on. This molecule triggers a "receiver device" in the plant to activate gene expression. We validate this system in Arabidopsis thaliana and Solanum tuberosum (potato) grown hydroponically and in soil, demonstrating its modularity by swapping bacteria that process different stimuli, including IPTG, aTc and arsenic. Programmable communication channels between bacteria and plants will enable microbial sentinels to transmit information to crops and provide the building blocks for designing artificial consortia.
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Affiliation(s)
- Alice Boo
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Tyler Toth
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Qiguo Yu
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Alexander Pfotenhauer
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Brandon D Fields
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Scott C Lenaghan
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - C Neal Stewart
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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13
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Li S, Yan L, Zhang W, Yi C, Haider S, Wang C, Liu Y, Shi L, Xu F, Ding G. Nitrate alleviates ammonium toxicity in Brassica napus by coordinating rhizosphere and cell pH and ammonium assimilation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:786-804. [PMID: 37955989 DOI: 10.1111/tpj.16529] [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: 07/07/2022] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023]
Abstract
In natural and agricultural situations, ammonium (NH 4 + ) is a preferred nitrogen (N) source for plants, but excessive amounts can be hazardous to them, known asNH 4 + toxicity. Nitrate (NO 3 - ) has long been recognized to reduceNH 4 + toxicity. However, little is known about Brassica napus, a major oil crop that is sensitive to highNH 4 + . Here, we found thatNO 3 - can mitigateNH 4 + toxicity by balancing rhizosphere and intracellular pH and accelerating ammonium assimilation in B. napus.NO 3 - increased the uptake ofNO 3 - andNH 4 + under highNH 4 + circumstances by triggering the expression ofNO 3 - andNH 4 + transporters, whileNO 3 - and H+ efflux from the cytoplasm to the apoplast was enhanced by promoting the expression ofNO 3 - efflux transporters and genes encoding plasma membrane H+ -ATPase. In addition,NO 3 - increased pH in the cytosol, vacuole, and rhizosphere, and down-regulated genes induced by acid stress. Root glutamine synthetase (GS) activity was elevated byNO 3 - under highNH 4 + conditions to enhance the assimilation ofNH 4 + into amino acids, thereby reducingNH 4 + accumulation and translocation to shoot in rapeseed. In addition, root GS activity was highly dependent on the environmental pH.NO 3 - might induce metabolites involved in amino acid biosynthesis and malate metabolism in the tricarboxylic acid cycle, and inhibit phenylpropanoid metabolism to mitigateNH 4 + toxicity. Collectively, our results indicate thatNO 3 - balances both rhizosphere and intracellular pH via effectiveNO 3 - transmembrane cycling, acceleratesNH 4 + assimilation, and up-regulates malate metabolism to mitigateNH 4 + toxicity in oilseed rape.
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Affiliation(s)
- Shuang Li
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lei Yan
- Institute of Biomedical Engineering, College of Life Science, Qingdao University, Qingdao, 266071, China
| | - Wen Zhang
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ceng Yi
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sharjeel Haider
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chuang Wang
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yu Liu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Lei Shi
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fangsen Xu
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangda Ding
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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14
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Williamson G, Harris T, Bizior A, Hoskisson PA, Pritchard L, Javelle A. Biological ammonium transporters: evolution and diversification. FEBS J 2024. [PMID: 38265636 DOI: 10.1111/febs.17059] [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: 09/26/2023] [Revised: 12/14/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024]
Abstract
Although ammonium is the preferred nitrogen source for microbes and plants, in animal cells it is a toxic product of nitrogen metabolism that needs to be excreted. Thus, ammonium movement across biological membranes, whether for uptake or excretion, is a fundamental and ubiquitous biological process catalysed by the superfamily of the Amt/Mep/Rh transporters. A remarkable feature of the Amt/Mep/Rh family is that they are ubiquitous and, despite sharing low amino acid sequence identity, are highly structurally conserved. Despite sharing a common structure, these proteins have become involved in a diverse range of physiological process spanning all domains of life, with reports describing their involvement in diverse biological processes being published regularly. In this context, we exhaustively present their range of biological roles across the domains of life and after explore current hypotheses concerning their evolution to help to understand how and why the conserved structure fulfils diverse physiological functions.
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Affiliation(s)
- Gordon Williamson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Thomas Harris
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Adriana Bizior
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Paul Alan Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Leighton Pritchard
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Arnaud Javelle
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
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15
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Sun Y, Shi M, Wang D, Gong Y, Sha Q, Lv P, Yang J, Chu P, Guo S. Research progress on the roles of actin-depolymerizing factor in plant stress responses. FRONTIERS IN PLANT SCIENCE 2023; 14:1278311. [PMID: 38034575 PMCID: PMC10687421 DOI: 10.3389/fpls.2023.1278311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023]
Abstract
Actin-depolymerizing factors (ADFs) are highly conserved small-molecule actin-binding proteins found throughout eukaryotic cells. In land plants, ADFs form a small gene family that displays functional redundancy despite variations among its individual members. ADF can bind to actin monomers or polymerized microfilaments and regulate dynamic changes in the cytoskeletal framework through specialized biochemical activities, such as severing, depolymerizing, and bundling. The involvement of ADFs in modulating the microfilaments' dynamic changes has significant implications for various physiological processes, including plant growth, development, and stress response. The current body of research has greatly advanced our comprehension of the involvement of ADFs in the regulation of plant responses to both biotic and abiotic stresses, particularly with respect to the molecular regulatory mechanisms that govern ADF activity during the transmission of stress signals. Stress has the capacity to directly modify the transcription levels of ADF genes, as well as indirectly regulate their expression through transcription factors such as MYB, C-repeat binding factors, ABF, and 14-3-3 proteins. Furthermore, apart from their role in regulating actin dynamics, ADFs possess the ability to modulate the stress response by influencing downstream genes associated with pathogen resistance and abiotic stress response. This paper provides a comprehensive overview of the current advancements in plant ADF gene research and suggests that the identification of plant ADF family genes across a broader spectrum, thorough analysis of ADF gene regulation in stress resistance of plants, and manipulation of ADF genes through genome-editing techniques to enhance plant stress resistance are crucial avenues for future investigation in this field.
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16
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Wang X, Sun T, Yan S, Chen S, Zhang Y. Sediment microbial community characteristics in sea cucumber restocking area. MARINE ENVIRONMENTAL RESEARCH 2023; 192:106233. [PMID: 37866200 DOI: 10.1016/j.marenvres.2023.106233] [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: 07/08/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 10/24/2023]
Abstract
Variations of microbial species and functional composition in coastal sediment are usually taken as the results of the provision of supplementary nutrients affected by human activities. However, responses of microbiome stability to restocking biological resources remain less understood in coastal benthic systems without nutrient supplements. Here, combined with metagenomics and microbiome co-occurrence networks, the composition, function, and community stability of microbes were evaluated in a coastal area where sea cucumbers (Apostichopus japonicus) restocked after six months. Also, the physicochemical characteristics of sediments and bottom water were analyzed. We found the total organic carbon, total nitrogen, and total phosphorus of sediment did not change significantly in the restocking area after six months, whereas the concentration of dissolved inorganic nitrogen in bottom water increased significantly. Moreover, the relative abundance of Nitrospina at the class level was increased significantly in the restocking area. Also, enzymes related to nitrate reduction and nitrous oxide reductase were increased in the restocking area. Of note, stock enhancement of sea cucumbers altered associations between bacteria rather than their composition. The elimination of negative associations and reduction of the potential keystone taxa in the restocking area indicated destabilized bacterial communities. Our work may contribute to elucidating the response of microbial stability to stock enhancement. This finding also suggests that microbial community stability can be considered as an indicator of ecological risk under the influence of stock enhancement.
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Affiliation(s)
- Xiaoling Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Tao Sun
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China.
| | - Shengjun Yan
- National Marine Environmental Monitoring Center, Dalian, 116021, China
| | - Shangyi Chen
- Comprehensive Administrative Law Enforcement Bureau, Qingdao, 266011, China
| | - Yue Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
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17
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Zhang J, Wang N, Li S, Wang J, Feng Y, Wang E, Li Y, Yang T, Chen W. The Effect of Different Rhizobial Symbionts on the Composition and Diversity of Rhizosphere Microorganisms of Chickpea in Different Soils. PLANTS (BASEL, SWITZERLAND) 2023; 12:3421. [PMID: 37836161 PMCID: PMC10575130 DOI: 10.3390/plants12193421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND Chickpea (Cicer arietinum L.) is currently the third most important legume crop in the world. It could form root nodules with its symbiotic rhizobia in soils and perform bio-nitrogen fixation. Mesorhizobium ciceri is a prevalent species in the world, except China, where Mesorhizobium muleiense is the main species associated with chickpea. There were significant differences in the competitive ability between M. ciceri and M. muleiense in sterilized and unsterilized soils collected from Xinjiang, China, where chickpea has been grown long term. In unsterilized soils, M. muleiense was more competitive than M. ciceri, while in sterilized soils, the opposite was the case. In addition, the competitive ability of M. ciceri in soils of new areas of chickpea cultivation was significantly higher than that of M. muleiense. It was speculated that there might be some biological factors in Xinjiang soils of China that could differentially affect the competitive nodulation of these two chickpea rhizobia. To address this question, we compared the composition and diversity of microorganisms in the rhizosphere of chickpea inoculated separately with the above two rhizobial species in soils from old and new chickpea-producing regions. RESULTS Chickpea rhizosphere microbial diversity and composition varied in different areas and were affected significantly due to rhizobial inoculation. In general, eight dominant phyla with 34 dominant genera and 10 dominant phyla with 47 dominant genera were detected in the rhizosphere of chickpea grown in soils of Xinjiang and of the new zones, respectively, with the inoculated rhizobia. Proteobacteria and Actinobacteria were dominant at the phylum level in the rhizosphere of all soils. Pseudomonas appeared significantly enriched after inoculation with M. muleiense in soils from Xinjiang, a phenomenon not found in the new areas of chickpea cultivation, demonstrating that Pseudomonas might be the key biological factor affecting the competitive colonization of M. muleiense and M. ciceri there. CONCLUSIONS Different chickpea rhizobial inoculations of M. muleiense and M. ciceri affected the rhizosphere microbial composition in different sampling soils from different chickpea planting areas. Through high throughput sequencing and statistical analysis, it could be found that Pseudomonas might be the key microorganism influencing the competitive nodulation of different chickpea rhizobia in different soils, as it is the dominant non-rhizobia community in Xinjiang rhizosphere soils, but not in other areas.
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Affiliation(s)
- Junjie Zhang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
- Collaborative Innovation Center for Food Production and Safety of Henan Province, Zhengzhou 450002, China
| | - Nan Wang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Shuo Li
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Jingqi Wang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Yufeng Feng
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de Mexico C.P. 11340, Mexico
| | - Youguo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Tao Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenfeng Chen
- College of Biological Sciences, Rhizobium Research Center, China Agricultural University, Beijing 100193, China
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18
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Louisson Z, Ranjard L, Buckley HL, Case BS, Lear G. Soil bacterial community composition is more stable in kiwifruit orchards relative to phyllosphere communities over time. ENVIRONMENTAL MICROBIOME 2023; 18:71. [PMID: 37620948 PMCID: PMC10463660 DOI: 10.1186/s40793-023-00526-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023]
Abstract
BACKGROUND Soil and phyllosphere (leaves and fruit) microbes play critical roles in the productivity and health of crops. However, microbial community dynamics are currently understudied in orchards, with a limited number incorporating temporal monitoring. We used 16S rRNA gene amplicon sequencing to investigate bacterial community temporal dynamics and community assembly processes on the leaves and fruit, and in the soil of 12 kiwifruit orchards across a cropping season in New Zealand. RESULTS Community composition significantly differed (P < 0.001) among the three sample types. However, the communities in the phyllosphere substrates more closely resembled each other, relative to the communities in the soil. There was more temporal stability in the soil bacterial community composition, relative to the communities residing on the leaves and fruit, and low similarity between the belowground and aboveground communities. Bacteria in the soil were more influenced by deterministic processes, while stochastic processes were more important for community assembly in the phyllosphere. CONCLUSIONS The higher temporal variability and the stochastic nature of the community assembly processes observed in the phyllosphere communities highlights why predicting the responsiveness of phyllosphere communities to environmental change, or the likelihood of pathogen invasion, can be challenging. The relative temporal stability and the influence of deterministic selection on soil microbial communities suggests a greater potential for their prediction and reliable manipulation.
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Affiliation(s)
- Ziva Louisson
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland, 1010, New Zealand.
| | - Louis Ranjard
- PlantTech Research Institute, 29 Grey St, Tauranga, 3011, New Zealand
| | - Hannah L Buckley
- School of Science, Auckland University of Technology, 34 St Paul Street, Auckland, 1010, New Zealand
| | - Bradley S Case
- School of Science, Auckland University of Technology, 34 St Paul Street, Auckland, 1010, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland, 1010, New Zealand
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19
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Yu H, Xiao A, Wu J, Li H, Duan Y, Chen Q, Zhu H, Cao Y. GmNAC039 and GmNAC018 activate the expression of cysteine protease genes to promote soybean nodule senescence. THE PLANT CELL 2023; 35:2929-2951. [PMID: 37177994 PMCID: PMC10396383 DOI: 10.1093/plcell/koad129] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 04/03/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023]
Abstract
Root nodules are major sources of nitrogen for soybean (Glycine max (L.) Merr.) growth, development, production, and seed quality. Symbiotic nitrogen fixation is time-limited, as the root nodule senesces during the reproductive stage of plant development, specifically during seed development. Nodule senescence is characterized by the induction of senescence-related genes, such as papain-like cysteine proteases (CYPs), which ultimately leads to the degradation of both bacteroids and plant cells. However, how nodule senescence-related genes are activated in soybean is unknown. Here, we identified 2 paralogous NAC transcription factors, GmNAC039 and GmNAC018, as master regulators of nodule senescence. Overexpression of either gene induced soybean nodule senescence with increased cell death as detected using a TUNEL assay, whereas their knockout delayed senescence and increased nitrogenase activity. Transcriptome analysis and nCUT&Tag-qPCR assays revealed that GmNAC039 directly binds to the core motif CAC(A)A and activates the expression of 4 GmCYP genes (GmCYP35, GmCYP37, GmCYP39, and GmCYP45). Similar to GmNAC039 and GmNAC018, overexpression or knockout of GmCYP genes in nodules resulted in precocious or delayed senescence, respectively. These data provide essential insights into the regulatory mechanisms of nodule senescence, in which GmNAC039 and GmNAC018 directly activate the expression of GmCYP genes to promote nodule senescence.
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Affiliation(s)
- Haixiang Yu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Aifang Xiao
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jiashan Wu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Haoxing Li
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yan Duan
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Qingshan Chen
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, Heilongjiang 150038, China
| | - Hui Zhu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yangrong Cao
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
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20
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Dunn MF, Becerra-Rivera VA. The Biosynthesis and Functions of Polyamines in the Interaction of Plant Growth-Promoting Rhizobacteria with Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:2671. [PMID: 37514285 PMCID: PMC10385936 DOI: 10.3390/plants12142671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/12/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023]
Abstract
Plant growth-promoting rhizobacteria (PGPR) are members of the plant rhizomicrobiome that enhance plant growth and stress resistance by increasing nutrient availability to the plant, producing phytohormones or other secondary metabolites, stimulating plant defense responses against abiotic stresses and pathogens, or fixing nitrogen. The use of PGPR to increase crop yield with minimal environmental impact is a sustainable and readily applicable replacement for a portion of chemical fertilizer and pesticides required for the growth of high-yielding varieties. Increased plant health and productivity have long been gained by applying PGPR as commercial inoculants to crops, although with uneven results. The establishment of plant-PGPR relationships requires the exchange of chemical signals and nutrients between the partners, and polyamines (PAs) are an important class of compounds that act as physiological effectors and signal molecules in plant-microbe interactions. In this review, we focus on the role of PAs in interactions between PGPR and plants. We describe the basic ecology of PGPR and the production and function of PAs in them and the plants with which they interact. We examine the metabolism and the roles of PAs in PGPR and plants individually and during their interaction with one another. Lastly, we describe some directions for future research.
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Affiliation(s)
- Michael F Dunn
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Víctor A Becerra-Rivera
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
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21
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Resendiz-Nava CN, Alonso-Onofre F, Silva-Rojas HV, Rebollar-Alviter A, Rivera-Pastrana DM, Stasiewicz MJ, Nava GM, Mercado-Silva EM. Tomato Plant Microbiota under Conventional and Organic Fertilization Regimes in a Soilless Culture System. Microorganisms 2023; 11:1633. [PMID: 37512805 PMCID: PMC10383152 DOI: 10.3390/microorganisms11071633] [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: 05/18/2023] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Tomato is the main vegetable cultivated under soilless culture systems (SCSs); production of organic tomato under SCSs has increased due to consumer demands for healthier and environmentally friendly vegetables. However, organic tomato production under SCSs has been associated with low crop performance and fruit quality defects. These agricultural deficiencies could be linked to alterations in tomato plant microbiota; nonetheless, this issue has not been sufficiently addressed. Thus, the main goal of the present study was to characterize the rhizosphere and phyllosphere of tomato plants cultivated under conventional and organic SCSs. To accomplish this goal, tomato plants grown in commercial greenhouses under conventional or organic SCSs were tested at 8, 26, and 44 weeks after seedling transplantation. Substrate (n = 24), root (n = 24), and fruit (n = 24) composite samples were subjected to DNA extraction and high-throughput 16S rRNA gene sequencing. The present study revealed that the tomato core microbiota was predominantly constituted by Proteobacteria, Actinobacteria, and Firmicutes. Remarkably, six bacterial families, Bacillaceae, Microbacteriaceae, Nocardioidaceae, Pseudomonadaceae, Rhodobacteraceae, and Sphingomonadaceae, were shared among all substrate, rhizosphere, and fruit samples. Importantly, it was shown that plants under organic SCSs undergo a dysbiosis characterized by significant changes in the relative abundance of Bradyrhizobiaceae, Caulobacteraceae, Chitinophagaceae, Enterobacteriaceae, Erythrobacteraceae, Flavobacteriaceae, Nocardioidaceae, Rhodobacteraceae, and Streptomycetaceae. These results suggest that microbial alterations in substrates, roots, and fruits could be potential factors in contributing to the crop performance and fruit quality deficiencies observed in organic SCSs.
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Affiliation(s)
- Carolina N Resendiz-Nava
- Facultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Queretaro 76010, Queretaro, Mexico
| | | | - Hilda V Silva-Rojas
- Posgrado en Recursos Geneticos y Productividad, Produccion de Semillas, Colegio de Postgraduados, Km 36.5 Carretera Mexico-Texcoco, Texcoco 56264, Mexico
| | - Angel Rebollar-Alviter
- Centro Regional Morelia, Universidad Autonoma de Chapingo, Morelia 58170, Michoacan, Mexico
| | - Dulce M Rivera-Pastrana
- Facultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Queretaro 76010, Queretaro, Mexico
| | - Matthew J Stasiewicz
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, 1302W Pennsylvania Ave, Urbana, IL 61801, USA
| | - Gerardo M Nava
- Facultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Queretaro 76010, Queretaro, Mexico
| | - Edmundo M Mercado-Silva
- Facultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Queretaro 76010, Queretaro, Mexico
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22
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Alleman AB, Peters JW. Mechanisms for Generating Low Potential Electrons across the Metabolic Diversity of Nitrogen-Fixing Bacteria. Appl Environ Microbiol 2023; 89:e0037823. [PMID: 37154716 PMCID: PMC10231201 DOI: 10.1128/aem.00378-23] [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: 05/10/2023] Open
Abstract
The availability of fixed nitrogen is a limiting factor in the net primary production of all ecosystems. Diazotrophs overcome this limit through the conversion of atmospheric dinitrogen to ammonia. Diazotrophs are phylogenetically diverse bacteria and archaea that exhibit a wide range of lifestyles and metabolisms, including obligate anaerobes and aerobes that generate energy through heterotrophic or autotrophic metabolisms. Despite the diversity of metabolisms, all diazotrophs use the same enzyme, nitrogenase, to reduce N2. Nitrogenase is an O2-sensitive enzyme that requires a high amount of energy in the form of ATP and low potential electrons carried by ferredoxin (Fd) or flavodoxin (Fld). This review summarizes how the diverse metabolisms of diazotrophs utilize different enzymes to generate low potential reducing equivalents for nitrogenase catalysis. These enzymes include substrate-level Fd oxidoreductases, hydrogenases, photosystem I or other light-driven reaction centers, electron bifurcating Fix complexes, proton motive force-driven Rnf complexes, and Fd:NAD(P)H oxidoreductases. Each of these enzymes is critical for generating low potential electrons while simultaneously integrating the native metabolism to balance nitrogenase's overall energy needs. Understanding the diversity of electron transport systems to nitrogenase in various diazotrophs will be essential to guide future engineering strategies aimed at expanding the contributions of biological nitrogen fixation in agriculture.
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Affiliation(s)
- Alexander B. Alleman
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - John W. Peters
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
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23
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Xu Y, Teng Y, Wang X, Ren W, Zhao L, Luo Y, Christie P, Greening C. Endogenous biohydrogen from a rhizobium-legume association drives microbial biodegradation of polychlorinated biphenyl in contaminated soil. ENVIRONMENT INTERNATIONAL 2023; 176:107962. [PMID: 37196568 DOI: 10.1016/j.envint.2023.107962] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/11/2023] [Accepted: 05/04/2023] [Indexed: 05/19/2023]
Abstract
Endogenous hydrogen (H2) is produced through rhizobium-legume associations in terrestrial ecosystems worldwide through dinitrogen fixation. In turn, this gas may alter rhizosphere microbial community structure and modulate biogeochemical cycles. However, very little is understood about the role that this H2 leaking to the rhizosphere plays in shaping the persistent organic pollutants degrading microbes in contaminated soils. Here, we combined DNA-stable isotope probing (DNA-SIP) with metagenomics to explore how endogenous H2 from the symbiotic rhizobium-alfalfa association drives the microbial biodegradation of tetrachlorobiphenyl PCB 77 in a contaminated soil. The results showed that PCB77 biodegradation efficiency increased significantly in soils treated with endogenous H2. Based on metagenomes of 13C-enriched DNA fractions, endogenous H2 selected bacteria harboring PCB degradation genes. Functional gene annotation allowed the reconstruction of several complete pathways for PCB catabolism, with different taxa conducting successive metabolic steps of PCB metabolism. The enrichment through endogenous H2 of hydrogenotrophic Pseudomonas and Magnetospirillum encoding biphenyl oxidation genes drove PCB biodegradation. This study proves that endogenous H2 is a significant energy source for active PCB-degrading communities and suggests that elevated H2 can influence the microbial ecology and biogeochemistry of the legume rhizosphere.
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Affiliation(s)
- Yongfeng Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Xiaomi Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Wenjie Ren
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Ling Zhao
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yongming Luo
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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24
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Sim JXF, Drigo B, Doolette CL, Vasileiadis S, Donner E, Karpouzas DG, Lombi E. Repeated applications of fipronil, propyzamide and flutriafol affect soil microbial functions and community composition: A laboratory-to-field assessment. CHEMOSPHERE 2023; 331:138850. [PMID: 37146771 DOI: 10.1016/j.chemosphere.2023.138850] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/07/2023]
Abstract
Pesticides play an important role in conventional agriculture by controlling pests, weeds, and plant diseases. However, repeated applications of pesticides may have long lasting effects on non-target microorganisms. Most studies have investigated the short-term effects of pesticides on soil microbial communities at the laboratory scale. Here, we assessed the ecotoxicological impact of fipronil (insecticide), propyzamide (herbicide) and flutriafol (fungicide) on (i) soil microbial enzymatic activities, (ii) potential nitrification, (iii) abundance of the fungal and bacterial community and key functional genes (nifH, amoA, chiA, cbhl and phosphatase) and (iii) diversity of bacteria, fungi, ammonia oxidizing bacteria (AOB) and archaea (AOA) after repeated pesticide applications in laboratory and field experiments. Our results showed that repeated applications of propyzamide and flutriafol affected the soil microbial community structure in the field and had significant inhibitory effects on enzymatic activities. The abundances of soil microbiota affected by pesticides recovered to levels similar to the control following a second application, suggesting that they might be able to recover from the pesticide effects. However, the persistent pesticide inhibitory effects on soil enzymatic activities suggests that the ability of the microbial community to cope with the repeated application was not accompanied by functional recovery. Overall, our results suggest that repeated pesticide applications may influence soil health and microbial functionalities and that more information should be collected to inform risk-based policy development.
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Affiliation(s)
- Jowenna X F Sim
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia.
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Casey L Doolette
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Sotirios Vasileiadis
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Larissa, Viopolis, 41500, Greece
| | - Erica Donner
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Dimitrios G Karpouzas
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Larissa, Viopolis, 41500, Greece
| | - Enzo Lombi
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia
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25
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Bathe U, Leong BJ, Van Gelder K, Barbier GG, Henry CS, Amthor JS, Hanson AD. Respiratory energy demands and scope for demand expansion and destruction. PLANT PHYSIOLOGY 2023; 191:2093-2103. [PMID: 36271857 PMCID: PMC10069906 DOI: 10.1093/plphys/kiac493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
Nonphotosynthetic plant metabolic processes are powered by respiratory energy, a limited resource that metabolic engineers—like plants themselves—must manage prudently.
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Affiliation(s)
| | | | | | | | - Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Jeffrey S Amthor
- Northern Arizona University Center for Ecosystem Science and Society, Flagstaff, Arizona 86011, USA
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26
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Ahmed N, Ishfaq M, Ali G. Genetic engineering for enhanced biological nitrogen fixation in cereal crops. Trends Biotechnol 2023; 41:473-475. [PMID: 36344382 DOI: 10.1016/j.tibtech.2022.10.006] [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: 10/12/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
Enhancing biological nitrogen (N) fixation in cereal crops has been a long-sought objective. Recently, Yan et al. identified plant compounds that induce biofilm production of diazotrophic bacteria and then performed genetic engineering in order to improve nitrogen fixation in rice plants. These findings hold promise for sustainable agriculture.
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Affiliation(s)
- Nasim Ahmed
- Agricultural Biotechnological Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan; Department of Biotechnology, The University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan.
| | - Muhammad Ishfaq
- Department of Agronomy, The University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Ghazanfar Ali
- Department of Biotechnology, The University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
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27
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Guo K, Yang J, Yu N, Luo L, Wang E. Biological nitrogen fixation in cereal crops: Progress, strategies, and perspectives. PLANT COMMUNICATIONS 2023; 4:100499. [PMID: 36447432 PMCID: PMC10030364 DOI: 10.1016/j.xplc.2022.100499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/07/2022] [Accepted: 11/28/2022] [Indexed: 05/04/2023]
Abstract
Nitrogen is abundant in the atmosphere but is generally the most limiting nutrient for plants. The inability of many crop plants, such as cereals, to directly utilize freely available atmospheric nitrogen gas means that their growth and production often rely heavily on the application of chemical fertilizers, which leads to greenhouse gas emissions and the eutrophication of water. By contrast, legumes gain access to nitrogen through symbiotic association with rhizobia. These bacteria convert nitrogen gas into biologically available ammonia in nodules through a process termed symbiotic biological nitrogen fixation, which plays a decisive role in ecosystem functioning. Engineering cereal crops that can fix nitrogen like legumes or associate with nitrogen-fixing microbiomes could help to avoid the problems caused by the overuse of synthetic nitrogen fertilizer. With the development of synthetic biology, various efforts have been undertaken with the aim of creating so-called "N-self-fertilizing" crops capable of performing autonomous nitrogen fixation to avoid the need for chemical fertilizers. In this review, we briefly summarize the history and current status of engineering N-self-fertilizing crops. We also propose several potential biotechnological approaches for incorporating biological nitrogen fixation capacity into non-legume plants.
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Affiliation(s)
- Kaiyan Guo
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jun Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Nan Yu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Li Luo
- School of Life Sciences, Shanghai Key Laboratory of Bioenergy Crops, Shanghai University, Shanghai 200444, China.
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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28
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Alam I, Zhang H, Du H, Rehman NU, Manghwar H, Lei X, Batool K, Ge L. Bioengineering Techniques to Improve Nitrogen Transformation and Utilization: Implications for Nitrogen Use Efficiency and Future Sustainable Crop Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:3921-3938. [PMID: 36842151 DOI: 10.1021/acs.jafc.2c08051] [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: 06/18/2023]
Abstract
Nitrogen (N) is crucial for plant growth and development, especially in physiological and biochemical processes such as component of different proteins, enzymes, nucleic acids, and plant growth regulators. Six categories, such as transporters, nitrate absorption, signal molecules, amino acid biosynthesis, transcription factors, and miscellaneous genes, broadly encompass the genes regulating NUE in various cereal crops. Herein, we outline detailed research on bioengineering modifications of N metabolism to improve the different crop yields and biomass. We emphasize effective and precise molecular approaches and technologies, including N transporters, transgenics, omics, etc., which are opening up fascinating opportunities for a complete analysis of the molecular elements that contribute to NUE. Moreover, the detection of various types of N compounds and associated signaling pathways within plant organs have been discussed. Finally, we highlight the broader impacts of increasing NUE in crops, crucial for better agricultural yield and in the greater context of global climate change.
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Affiliation(s)
- Intikhab Alam
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- College of Life Sciences, SCAU, Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Hanyin Zhang
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Huan Du
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- College of Life Sciences, SCAU, Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Naveed Ur Rehman
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Hakim Manghwar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, SCAU, Guangzhou 510642, China
| | - Xiao Lei
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Khadija Batool
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liangfa Ge
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
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29
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Martin Del Campo JS, Rigsbee J, Bueno Batista M, Mus F, Rubio LM, Einsle O, Peters JW, Dixon R, Dean DR, Dos Santos PC. Overview of physiological, biochemical, and regulatory aspects of nitrogen fixation in Azotobacter vinelandii. Crit Rev Biochem Mol Biol 2023; 57:492-538. [PMID: 36877487 DOI: 10.1080/10409238.2023.2181309] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Understanding how Nature accomplishes the reduction of inert nitrogen gas to form metabolically tractable ammonia at ambient temperature and pressure has challenged scientists for more than a century. Such an understanding is a key aspect toward accomplishing the transfer of the genetic determinants of biological nitrogen fixation to crop plants as well as for the development of improved synthetic catalysts based on the biological mechanism. Over the past 30 years, the free-living nitrogen-fixing bacterium Azotobacter vinelandii emerged as a preferred model organism for mechanistic, structural, genetic, and physiological studies aimed at understanding biological nitrogen fixation. This review provides a contemporary overview of these studies and places them within the context of their historical development.
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Affiliation(s)
| | - Jack Rigsbee
- Department of Chemistry, Wake Forest University, Winston-Salem, NC, USA
| | | | - Florence Mus
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Spain
| | - Oliver Einsle
- Department of Biochemistry, University of Freiburg, Freiburg, Germany
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Dennis R Dean
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
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30
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Lace B, Su C, Invernot Perez D, Rodriguez-Franco M, Vernié T, Batzenschlager M, Egli S, Liu CW, Ott T. RPG acts as a central determinant for infectosome formation and cellular polarization during intracellular rhizobial infections. eLife 2023; 12:80741. [PMID: 36856086 PMCID: PMC9991063 DOI: 10.7554/elife.80741] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 02/21/2023] [Indexed: 03/02/2023] Open
Abstract
Host-controlled intracellular accommodation of nitrogen-fixing bacteria is essential for the establishment of a functional Root Nodule Symbiosis (RNS). In many host plants, this occurs via transcellular tubular structures (infection threads - ITs) that extend across cell layers via polar tip-growth. Comparative phylogenomic studies have identified RPG (RHIZOBIUM-DIRECTED POLAR GROWTH) among the critical genetic determinants for bacterial infection. In Medicago truncatula, RPG is required for effective IT progression within root hairs but the cellular and molecular function of the encoded protein remains elusive. Here, we show that RPG resides in the protein complex formed by the core endosymbiotic components VAPYRIN (VPY) and LUMPY INFECTION (LIN) required for IT polar growth, co-localizes with both VPY and LIN in IT tip- and perinuclear-associated puncta of M. truncatula root hairs undergoing infection and is necessary for VPY recruitment into these structures. Fluorescence Lifetime Imaging Microscopy (FLIM) of phosphoinositide species during bacterial infection revealed that functional RPG is required to sustain strong membrane polarization at the advancing tip of the IT. In addition, loss of RPG functionality alters the cytoskeleton-mediated connectivity between the IT tip and the nucleus and affects the polar secretion of the cell wall modifying enzyme NODULE PECTATE LYASE (NPL). Our results integrate RPG into a core host machinery required to support symbiont accommodation, suggesting that its occurrence in plant host genomes is essential to co-opt a multimeric protein module committed to endosymbiosis to sustain IT-mediated bacterial infection.
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Affiliation(s)
- Beatrice Lace
- University of Freiburg, Faculty of BiologyFreiburgGermany
| | - Chao Su
- University of Freiburg, Faculty of BiologyFreiburgGermany
| | | | | | - Tatiana Vernié
- LRSV, Université de Toulouse, CNRS, UPS, INP ToulouseCastanet-TolosanFrance
| | | | - Sabrina Egli
- University of Freiburg, Faculty of BiologyFreiburgGermany
| | - Cheng-Wu Liu
- School of Life Sciences, Division of Life Sciences and Medicine, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of ChinaHefeiChina
| | - Thomas Ott
- University of Freiburg, Faculty of BiologyFreiburgGermany
- CIBSS – Centre of Integrative Biological Signalling Studies, University of FreiburgFreiburgGermany
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31
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Boersma PJ, Lagugné-Labarthet F, McDowell T, Macfie SM. Silver nanoparticles inhibit nitrogen fixation in soybean (Glycine max) root nodules. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:32014-32031. [PMID: 36456673 DOI: 10.1007/s11356-022-24446-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Antimicrobial silver nanoparticles (AgNPs) are popular in consumer and industrial products, leading to increasing concentrations in the environment. We tested whether exposure to AgNPs could be detrimental to a microbe, its host plant, and their symbiotic relationship. When subjected to 10 µg/mL AgNPs, growth of Bradyrhizobium japonicum USDA 110 was halted. Axenic nitrogen-fertilized Glycine max seedlings were unaffected by 2.5 µg/mL of 30 nm AgNPs, but growth was inhibited with the same dose of 16 nm AgNPs. With 2.5 µg/mL AgNPs, biomass of inoculated plants was 50% of the control. Bacteroids were not found in nodules on plants treated with 2.5 µg/mL AgNPs and plants given 0.5-2.5 µg/mL AgNPs had 40-65% decreased nitrogen fixation. In conclusion, AgNPs not only interfere with general plant and bacterial growth but also inhibit nodule development and bacterial nitrogen fixation. We should be mindful of not releasing AgNPs to the environment or to agricultural land.
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Affiliation(s)
- Paul J Boersma
- Department of Biology, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - François Lagugné-Labarthet
- Department of Chemistry, University of Western Ontario, London, ON, N6A 3K7, Canada
- Centre for Advanced Material and Biomaterial Research (CAMBR), University of Western Ontario, London, ON, N6A 3K7, Canada
| | - Tim McDowell
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford St., London, ON, N5V 4T3, Canada
| | - Sheila M Macfie
- Department of Biology, University of Western Ontario, London, ON, N6A 5B7, Canada.
- Centre for Advanced Material and Biomaterial Research (CAMBR), University of Western Ontario, London, ON, N6A 3K7, Canada.
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32
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Bennett EM, Murray JW, Isalan M. Engineering Nitrogenases for Synthetic Nitrogen Fixation: From Pathway Engineering to Directed Evolution. BIODESIGN RESEARCH 2023; 5:0005. [PMID: 37849466 PMCID: PMC10521693 DOI: 10.34133/bdr.0005] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 12/24/2022] [Indexed: 10/19/2023] Open
Abstract
Globally, agriculture depends on industrial nitrogen fertilizer to improve crop growth. Fertilizer production consumes fossil fuels and contributes to environmental nitrogen pollution. A potential solution would be to harness nitrogenases-enzymes capable of converting atmospheric nitrogen N2 to NH3 in ambient conditions. It is therefore a major goal of synthetic biology to engineer functional nitrogenases into crop plants, or bacteria that form symbiotic relationships with crops, to support growth and reduce dependence on industrially produced fertilizer. This review paper highlights recent work toward understanding the functional requirements for nitrogenase expression and manipulating nitrogenase gene expression in heterologous hosts to improve activity and oxygen tolerance and potentially to engineer synthetic symbiotic relationships with plants.
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Affiliation(s)
- Emily M. Bennett
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - James W. Murray
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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33
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Eckardt NA, Ainsworth EA, Bahuguna RN, Broadley MR, Busch W, Carpita NC, Castrillo G, Chory J, DeHaan LR, Duarte CM, Henry A, Jagadish SVK, Langdale JA, Leakey ADB, Liao JC, Lu KJ, McCann MC, McKay JK, Odeny DA, Jorge de Oliveira E, Platten JD, Rabbi I, Rim EY, Ronald PC, Salt DE, Shigenaga AM, Wang E, Wolfe M, Zhang X. Climate change challenges, plant science solutions. THE PLANT CELL 2023; 35:24-66. [PMID: 36222573 PMCID: PMC9806663 DOI: 10.1093/plcell/koac303] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g. heat, drought, salt stress, flooding, disease outbreaks) and engineering efficient carbon-capturing and carbon-sequestering plants. Here, we present examples of research being conducted in these areas and discuss challenges and open questions as a call to action for the plant science community.
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Affiliation(s)
| | - Elizabeth A Ainsworth
- USDA ARS Global Change and Photosynthesis Research Unit, Urbana, Illinois 61801, USA
| | - Rajeev N Bahuguna
- Centre for Advanced Studies on Climate Change, Dr Rajendra Prasad Central Agricultural University, Samastipur 848125, Bihar, India
| | - Martin R Broadley
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Nicholas C Carpita
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Gabriel Castrillo
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Joanne Chory
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | | | - Carlos M Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Amelia Henry
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - S V Krishna Jagadish
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas 79410, USA
| | - Jane A Langdale
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Andrew D B Leakey
- Department of Plant Biology, Department of Crop Sciences, and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Illinois 61801, USA
| | - James C Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Kuan-Jen Lu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Maureen C McCann
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - John K McKay
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Damaris A Odeny
- The International Crops Research Institute for the Semi-Arid Tropics–Eastern and Southern Africa, Gigiri 39063-00623, Nairobi, Kenya
| | | | - J Damien Platten
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - Ismail Rabbi
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
| | - Ellen Youngsoo Rim
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Pamela C Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
- Innovative Genomics Institute, Berkeley, California 94704, USA
| | - David E Salt
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alexandra M Shigenaga
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Marnin Wolfe
- Auburn University, Dept. of Crop Soil and Environmental Sciences, College of Agriculture, Auburn, Alabama 36849, USA
| | - Xiaowei Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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Chemla Y, Dorfan Y, Yannai A, Meng D, Cao P, Glaven S, Gordon DB, Elbaz J, Voigt CA. Parallel engineering of environmental bacteria and performance over years under jungle-simulated conditions. PLoS One 2022; 17:e0278471. [PMID: 36516154 PMCID: PMC9750038 DOI: 10.1371/journal.pone.0278471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 11/15/2022] [Indexed: 12/15/2022] Open
Abstract
Engineered bacteria could perform many functions in the environment, for example, to remediate pollutants, deliver nutrients to crops or act as in-field biosensors. Model organisms can be unreliable in the field, but selecting an isolate from the thousands that naturally live there and genetically manipulating them to carry the desired function is a slow and uninformed process. Here, we demonstrate the parallel engineering of isolates from environmental samples by using the broad-host-range XPORT conjugation system (Bacillus subtilis mini-ICEBs1) to transfer a genetic payload to many isolates in parallel. Bacillus and Lysinibacillus species were obtained from seven soil and water samples from different locations in Israel. XPORT successfully transferred a genetic function (reporter expression) into 25 of these isolates. They were then screened to identify the best-performing chassis based on the expression level, doubling time, functional stability in soil, and environmentally-relevant traits of its closest annotated reference species, such as the ability to sporulate and temperature tolerance. From this library, we selected Bacillus frigoritolerans A3E1, re-introduced it to soil, and measured function and genetic stability in a contained environment that replicates jungle conditions. After 21 months of storage, the engineered bacteria were viable, could perform their function, and did not accumulate disruptive mutations.
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Affiliation(s)
- Yonatan Chemla
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Yuval Dorfan
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Adi Yannai
- School of Molecular Cell Biology & Biotechnology, Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Dechuan Meng
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Paul Cao
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Sarah Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States of America
| | - D. Benjamin Gordon
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Johann Elbaz
- School of Molecular Cell Biology & Biotechnology, Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Christopher A. Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail:
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Guardiola-Márquez CE, Santos-Ramírez MT, Segura-Jiménez ME, Figueroa-Montes ML, Jacobo-Velázquez DA. Fighting Obesity-Related Micronutrient Deficiencies through Biofortification of Agri-Food Crops with Sustainable Fertilization Practices. PLANTS (BASEL, SWITZERLAND) 2022; 11:3477. [PMID: 36559589 PMCID: PMC9784404 DOI: 10.3390/plants11243477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/03/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Obesity is a critical medical condition worldwide that is increasingly involved with nutritional derangements associated with micronutrient deficiencies, including iron, zinc, calcium, magnesium, selenium, and vitamins A, C, D, and E. Nutritional deficiencies in obesity are mainly caused by poor-quality diets, higher nutrient requirements, alterations in micronutrient metabolism, and invasive obesity treatments. The current conventional agricultural system is designed for intensive food production, focusing on food quantity rather than food quality, consuming excessive agricultural inputs, and producing nutrient-deficient foods, thus generating severe health and environmental problems; agricultural food products may worsen obesity-related malnutrition. Therefore, modern agriculture is adopting new biofortification technologies to combat micronutrient deficiencies and improve agricultural productivity and sustainability. Biofertilization and nanofertilization practices are increasingly used due to their efficiency, safety, and reduced environmental impact. Biofertilizers are preparations of PGP-microorganisms that promote plant growth by influencing plant metabolism and improving the nutrient uptake, and nanofertilizers consist of synthesized nanoparticles with unique physicochemical properties that are capable of increasing plant nutrition and enriching agricultural products. This review presents the current micronutrient deficiencies associated with obesity, the modern unsustainable agri-food system contributing to obesity progression, and the development of bio- and nanofertilizers capable of biofortifying agri-food crops with micronutrients commonly deficient in patients with obesity.
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Affiliation(s)
| | - María Teresa Santos-Ramírez
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Ave. General Ramon Corona 2514, Zapopan 45138, Jalisco, Mexico
| | - M. Eugenia Segura-Jiménez
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Ave. General Ramon Corona 2514, Zapopan 45138, Jalisco, Mexico
| | - Melina Lizeth Figueroa-Montes
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Ave. General Ramon Corona 2514, Zapopan 45138, Jalisco, Mexico
| | - Daniel A. Jacobo-Velázquez
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Ave. General Ramon Corona 2514, Zapopan 45138, Jalisco, Mexico
- Tecnologico de Monterrey, The Institute for Obesity Research, Ave. General Ramon Corona 2514, Zapopan 45201, Jalisco, Mexico
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Li Q, Zhang H, Song Y, Wang M, Hua C, Li Y, Chen S, Dixon R, Li J. Alanine synthesized by alanine dehydrogenase enables ammonium-tolerant nitrogen fixation in Paenibacillus sabinae T27. Proc Natl Acad Sci U S A 2022; 119:e2215855119. [PMID: 36459643 PMCID: PMC9894248 DOI: 10.1073/pnas.2215855119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/08/2022] [Indexed: 12/04/2022] Open
Abstract
Most diazotrophs fix nitrogen only under nitrogen-limiting conditions, for example, in the presence of relatively low concentrations of NH4+ (0 to 2 mM). However, Paenibacillus sabinae T27 exhibits an unusual pattern of nitrogen regulation of nitrogen fixation, since although nitrogenase activities are high under nitrogen-limiting conditions (0 to 3 mM NH4+) and are repressed under conditions of nitrogen sufficiency (4 to 30 mM NH4+), nitrogenase activity is reestablished when very high levels of NH4+ (30 to 300 mM) are present in the medium. To further understand this pattern of nitrogen fixation regulation, we carried out transcriptome analyses of P. sabinae T27 in response to increasing ammonium concentrations. As anticipated, the nif genes were highly expressed, either in the absence of fixed nitrogen or in the presence of a high concentration of NH4+ (100 mM), but were subject to negative feedback regulation at an intermediate concentration of NH4+ (10 mM). Among the differentially expressed genes, ald1, encoding alanine dehydrogenase (ADH1), was highly expressed in the presence of a high level of NH4+ (100 mM). Mutation and complementation experiments revealed that ald1 is required for nitrogen fixation at high ammonium concentrations. We demonstrate that alanine, synthesized by ADH1 from pyruvate and NH4+, inhibits GS activity, leading to a low intracellular glutamine concentration that prevents feedback inhibition of GS and mimics nitrogen limitation, enabling activation of nif transcription by the nitrogen-responsive regulator GlnR in the presence of high levels of extracellular ammonium.
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Affiliation(s)
- Qin Li
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing100193, People’s Republic of China
| | - Haowei Zhang
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing100193, People’s Republic of China
| | - Yi Song
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing100193, People’s Republic of China
| | - Minyang Wang
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing100193, People’s Republic of China
| | - Chongchong Hua
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing100193, People’s Republic of China
| | - Yashi Li
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing100193, People’s Republic of China
| | - Sanfeng Chen
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing100193, People’s Republic of China
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, NorwichNR4 7UH, United Kingdom
| | - Jilun Li
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing100193, People’s Republic of China
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Patra D, Mandal S. Non-rhizobia are the alternative sustainable solution for growth and development of the nonlegume plants. Biotechnol Genet Eng Rev 2022:1-30. [PMID: 36471635 DOI: 10.1080/02648725.2022.2152623] [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: 08/20/2022] [Accepted: 11/13/2022] [Indexed: 12/12/2022]
Abstract
The major research focus for biological nitrogen fixation (BNF) has mostly been on typical rhizobia with legumes. But the newly identified non-rhizobial bacteria, both individually or in combination could also be an alternative for nitrogen supplementation in both legumes and nonlegume plants. Although about 90% of BNF is derived from a legume - rhizobia symbiosis, the non-legumes specially the cereals lack canonical nitrogen fixation system through root-nodule organogenesis. The non-rhizobia may colonize in the rhizosphere or present in endophytic/associative nature. The non-rhizobia are well known for facilitating plant growth through their potential to alleviate various stresses (salt, drought, and pathogens), acquisition of minerals (P, K, etc.), or by producing phytohormones. Bacterial symbiosis in non-legumes represents by the Gram-positive Frankia having a major contribution in overall fortification of usable nitrogenous material in soil where they are associated with their hosts. This review discusses the recent updates on the diversity and association of the non-rhizobial species and their impact on the growth and productivity of their host plants with particular emphasis on major economically important cereal plants. The future application possibilities of non-rhizobia for soil fertility and plant growth enhancement for sustainable agriculture have been discussed.
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Affiliation(s)
- Dipanwita Patra
- Department of Microbiology, University of Calcutta, Kolkata, India
| | - Sukhendu Mandal
- Department of Microbiology, University of Calcutta, Kolkata, India
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Khan AR, Mustafa A, Hyder S, Valipour M, Rizvi ZF, Gondal AS, Yousuf Z, Iqbal R, Daraz U. Bacillus spp. as Bioagents: Uses and Application for Sustainable Agriculture. BIOLOGY 2022; 11:biology11121763. [PMID: 36552272 PMCID: PMC9775066 DOI: 10.3390/biology11121763] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
Food security will be a substantial issue in the near future due to the expeditiously growing global population. The current trend in the agriculture industry entails the extravagant use of synthesized pesticides and fertilizers, making sustainability a difficult challenge. Land degradation, lower production, and vulnerability to both abiotic and biotic stresses are problems caused by the usage of these pesticides and fertilizers. The major goal of sustainable agriculture is to ameliorate productivity and reduce pests and disease prevalence to such a degree that prevents large-scale damage to crops. Agriculture is a composite interrelation among plants, microbes, and soil. Plant microbes play a major role in growth promotion and improve soil fertility as well. Bacillus spp. produces an extensive range of bio-chemicals that assist in plant disease control, promote plant development, and make them suitable for agricultural uses. Bacillus spp. support plant growth by N fixation, P and K solubilization, and phytohormone synthesis, in addition to being the most propitious biocontrol agent. Moreover, Bacilli excrete extracellular metabolites, including antibiotics, lytic enzymes, and siderophores, and demonstrate antagonistic activity against phytopathogens. Bacillus spp. boosts plant resistance toward pathogens by inducing systemic resistance (ISR). The most effective microbial insecticide against insects and pests in agriculture is Bacillus thuringiensis (Bt). Additionally, the incorporation of toxin genes in genetically modified crops increases resistance to insects and pests. There is a constant increase in the identified Bacillus species as potential biocontrol agents. Moreover, they have been involved in the biosynthesis of metallic nanoparticles. The main objective of this review article is to display the uses and application of Bacillus specie as a promising biopesticide in sustainable agriculture. Bacillus spp. strains that are antagonistic and promote plant yield attributes could be valuable in developing novel formulations to lead the way toward sustainable agriculture.
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Affiliation(s)
- Aimen Razzaq Khan
- Department of Botany, Government College Women University Sialkot, Sialkot 51310, Pakistan
| | - Adeena Mustafa
- Department of Botany, Government College Women University Sialkot, Sialkot 51310, Pakistan
| | - Sajjad Hyder
- Department of Botany, Government College Women University Sialkot, Sialkot 51310, Pakistan
- Correspondence: (S.H.); (M.V.)
| | - Mohammad Valipour
- Department of Engineering and Engineering Technology, Metropolitan State University of Denver, Denver, CO 80217, USA
- Correspondence: (S.H.); (M.V.)
| | - Zarrin Fatima Rizvi
- Department of Botany, Government College Women University Sialkot, Sialkot 51310, Pakistan
| | - Amjad Shahzad Gondal
- Department of Plant Pathology, Bahauddin Zakariya University Multan, Multan 60000, Pakistan
| | - Zubaida Yousuf
- Department of Botany, Lahore College for Women University, Lahore 54000, Pakistan
| | - Rashid Iqbal
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Umar Daraz
- State Key Laboratory of Grassland Agroecosystem, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
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Ribeiro IDA, Bach E, Passaglia LMP. Alternative nitrogenase of Paenibacillus sonchi genomovar Riograndensis: An insight in the origin of Fe-nitrogenase in the Paenibacillaceae family. Mol Phylogenet Evol 2022; 177:107624. [PMID: 36084857 DOI: 10.1016/j.ympev.2022.107624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 07/26/2022] [Accepted: 08/29/2022] [Indexed: 11/25/2022]
Abstract
Paenibacillus sonchi genomovar Riograndensis is a nitrogen-fixing bacteria isolated from wheat that displays diverse plant growth-promoting abilities. Beyond conventional Mo-nitrogenase, this organism also harbors an alternative Fe-nitrogenase, whose many aspects related to regulation, physiology, and evolution remain to be elucidated. In this work, the origins of this alternative system were investigated, exploring the distribution and diversification of nitrogenases in the Panibacillaceae family. Our analysis showed that diazotrophs represent 17% of Paenibacillaceae genomes, of these, only 14.4% (2.5% of all Paenibacillaceae genomes) also contained Fe or V- nitrogenases. Diverse nif-like sequences were also described, occurring mainly in genomes that also harbor the alternative systems. The analysis of genomes containing Fe-nitrogenase showed a conserved cluster of nifEN anfHDGK across three genera: Gorillibacterium, Fontibacillus, and Paenibacillus. A phylogeny of anfHDGK separated the Fe-nitrogenases into three main groups. Our analysis suggested that Fe-nitrogenase was acquired by the ancestral lineage of Fontibacillus, Gorillibacterium, and Paenibacillus genera via horizontal gene transfer (HGT), and further events of transfer and gene loss marked the evolution of this alternative nitrogenase in these groups. The species phylogeny of N-fixing Paenibacillaceae separated the diazotrophs into five clades, one of these containing all occurrences of strains harboring alternative nitrogenases in the Paenibacillus genus. The pangenome of this clade is open and composed of more than 96% of accessory genes. Diverse functional categories were enriched in the flexible genome, including functions related to replication and repair. The latter involved diverse genes related to HGT, suggesting that such events may have an important role in the evolution of diazotrophic Paenibacillus. This study provided an insight into the organization, distribution, and evolution of alternative nitrogenase genes in Paenibacillaceae, considering different genomic aspects.
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Affiliation(s)
- Igor Daniel Alves Ribeiro
- Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil
| | - Evelise Bach
- Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil.
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40
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Katz E, Knapp A, Lensink M, Keller CK, Stefani J, Li JJ, Shane E, Tuermer-Lee K, Bloom AJ, Kliebenstein DJ. Genetic variation underlying differential ammonium and nitrate responses in Arabidopsis thaliana. THE PLANT CELL 2022; 34:4696-4713. [PMID: 36130068 PMCID: PMC9709984 DOI: 10.1093/plcell/koac279] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
Nitrogen is an essential element required for plant growth and productivity. Understanding the mechanisms and natural genetic variation underlying nitrogen use in plants will facilitate the engineering of plant nitrogen use to maximize crop productivity while minimizing environmental costs. To understand the scope of natural variation that may influence nitrogen use, we grew 1,135 Arabidopsis thaliana natural genotypes on two nitrogen sources, nitrate and ammonium, and measured both developmental and defense metabolite traits. By using different environments and focusing on multiple traits, we identified a wide array of different nitrogen responses. These responses are associated with numerous genes, most of which were not previously associated with nitrogen responses. Only a small portion of these genes appear to be shared between environments or traits, while most are predominantly specific to a developmental or defense trait under a specific nitrogen source. Finally, by using a large population, we were able to identify unique nitrogen responses, such as preferring ammonium or nitrate, which appear to be generated by combinations of loci rather than a few large-effect loci. This suggests that it may be possible to obtain novel phenotypes in complex nitrogen responses by manipulating sets of genes with small effects rather than solely focusing on large-effect single gene manipulations.
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Affiliation(s)
- Ella Katz
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
| | - Anna Knapp
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
| | - Mariele Lensink
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
- Integrative Genetics and Genomics Graduate Group, University of California Davis, Davis, California 95616, USA
| | - Caroline Kaley Keller
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
- Plant Biology Graduate Group, University of California Davis, Davis, California 95616, USA
| | - Jordan Stefani
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
| | - Jia-Jie Li
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
| | - Emily Shane
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
| | - Kaelyn Tuermer-Lee
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
| | - Arnold J Bloom
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
- DynaMo Center of Excellence, University of Copenhagen, 1165 Copenhagen, Denmark
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41
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Luo G, Najafi J, Correia PMP, Trinh MDL, Chapman EA, Østerberg JT, Thomsen HC, Pedas PR, Larson S, Gao C, Poland J, Knudsen S, DeHaan L, Palmgren M. Accelerated Domestication of New Crops: Yield is Key. PLANT & CELL PHYSIOLOGY 2022; 63:1624-1640. [PMID: 35583202 PMCID: PMC9680862 DOI: 10.1093/pcp/pcac065] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/17/2022] [Accepted: 05/17/2022] [Indexed: 05/05/2023]
Abstract
Sustainable agriculture in the future will depend on crops that are tolerant to biotic and abiotic stresses, require minimal input of water and nutrients and can be cultivated with a minimal carbon footprint. Wild plants that fulfill these requirements abound in nature but are typically low yielding. Thus, replacing current high-yielding crops with less productive but resilient species will require the intractable trade-off of increasing land area under cultivation to produce the same yield. Cultivating more land reduces natural resources, reduces biodiversity and increases our carbon footprint. Sustainable intensification can be achieved by increasing the yield of underutilized or wild plant species that are already resilient, but achieving this goal by conventional breeding programs may be a long-term prospect. De novo domestication of orphan or crop wild relatives using mutagenesis is an alternative and fast approach to achieve resilient crops with high yields. With new precise molecular techniques, it should be possible to reach economically sustainable yields in a much shorter period of time than ever before in the history of agriculture.
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Affiliation(s)
| | | | | | | | | | | | | | - Pai Rosager Pedas
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V DK-1799, Denmark
| | - Steve Larson
- US Department of Agriculture (USDA), USDA–ARS Forage & Range Research Lab, Utah State University Logan, Logan, UT 84322, USA
| | - Caixia Gao
- Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jesse Poland
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Makkah 23955, Saudi Arabia
| | - Søren Knudsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V DK-1799, Denmark
| | - Lee DeHaan
- The Land Institute, Salina, KS 67401, USA
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Guo H, He X, Zhang H, Tan R, Yang J, Xu F, Wang S, Yang C, Ding G. Physiological Responses of Cigar Tobacco Crop to Nitrogen Deficiency and Genome-Wide Characterization of the NtNPF Family Genes. PLANTS (BASEL, SWITZERLAND) 2022; 11:3064. [PMID: 36432793 PMCID: PMC9697317 DOI: 10.3390/plants11223064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/02/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
Tobacco prefers nitrate as a nitrogen (N) source. However, little is known about the molecular components responsible for nitrate uptake and the physiological responses of cigar tobacco to N deficiency. In this study, a total of 117 nitrate transporter 1 (NRT1) and peptide transporter (PTR) family (NPF) genes were comprehensively identified and systematically characterized in the whole tobacco genome. The NtNPF members showed significant genetic diversity within and across subfamilies but showed conservation between subfamilies. The NtNPF genes are dispersed unevenly across the chromosomes. The phylogenetic analysis revealed that eight subfamilies of NtNPF genes are tightly grouped with their orthologues in Arabidopsis. The promoter regions of the NtNPF genes had extensive cis-regulatory elements. Twelve core NtNPF genes, which were strongly induced by N limitation, were identified based on the RNA-seq data. Furthermore, N deprivation severely impaired plant growth of two cigar tobaccos, and CX26 may be more sensitive to N deficiency than CX14. Moreover, 12 hub genes respond differently to N deficiency between the two cultivars, indicating the vital roles in regulating N uptake and transport in cigar tobacco. The findings here contribute towards a better knowledge of the NtNPF genes and lay the foundation for further functional analysis of cigar tobacco.
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Affiliation(s)
- Hao Guo
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuyou He
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Zhang
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Ronglei Tan
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinpeng Yang
- Tobacco Research Institute of Hubei Province, Wuhan 430030, China
| | - Fangsen Xu
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Sheliang Wang
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunlei Yang
- Tobacco Research Institute of Hubei Province, Wuhan 430030, China
| | - Guangda Ding
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
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Huang X, Zeng Z, Chen Z, Tong X, Jiang J, He C, Xiang T. Deciphering the potential of a plant growth promoting endophyte Rhizobium sp. WYJ-E13, and functional annotation of the genes involved in the metabolic pathway. Front Microbiol 2022; 13:1035167. [PMID: 36406393 PMCID: PMC9671153 DOI: 10.3389/fmicb.2022.1035167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/17/2022] [Indexed: 09/24/2023] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) are well-acknowledged root endophytic bacteria used for plant growth promotion. However, which metabolites produced by PGPR could promote plant growth remains unclear. Additionally, which genes are responsible for plant growth-promoting traits is also not elucidated. Thus, as comprehensive understanding of the mechanism of endophyte in growth promotion is limited, this study aimed to determine the metabolites and genes involved in plant growth-promotion. We isolated an endophytic Rhizobium sp. WYJ-E13 strain from the roots of Curcuma wenyujin Y.H. Chen et C. Ling, a perennial herb and medicinal plant. The tissue culture experiment showed its plant growth-promoting ability. The bacterium colonization in the root was confirmed by scanning electron microscopy and paraffin sectioning. Furthermore, it was noted that the WYJ-E13 strain produced cytokinin, anthranilic acid, and L-phenylalanine by metabolome analysis. Whole-genome analysis of the strain showed that it consists of a circular chromosome of 4,350,227 bp with an overall GC content of 60.34%, of a 2,149,667 bp plasmid1 with 59.86% GC, and of a 406,180 bp plasmid2 with 58.05% GC. Genome annotation identified 4,349 putative protein-coding genes, 51 tRNAs, and 9 rRNAs. The CDSs number allocated to the Kyoto Encyclopedia of Genes and Genomes, Gene Ontology, and Clusters of Orthologous Genes databases were 2027, 3,175 and 3,849, respectively. Comparative genome analysis displayed that Rhizobium sp. WYJ-E13 possesses the collinear region among three species: Rhizobium acidisoli FH23, Rhizobium gallicum R602 and Rhizobium phaseoli R650. We recognized a total set of genes that are possibly related to plant growth promotion, including genes involved in nitrogen metabolism (nifU, gltA, gltB, gltD, glnA, glnD), hormone production (trp ABCDEFS), sulfur metabolism (cysD, cysE, cysK, cysN), phosphate metabolism (pstA, pstC, phoB, phoH, phoU), and root colonization. Collectively, these findings revealed the roles of WYJ-E13 strain in plant growth-promotion. To the best of our knowledge, this was the first study using whole-genome sequencing for Rhizobium sp. WYJ-E13 associated with C. wenyujin. WYJ-E13 strain has a high potential to be used as Curcuma biofertilizer for sustainable agriculture.
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Affiliation(s)
- Xiaoping Huang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou, China
| | - Zhanghui Zeng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou, China
| | - Zhehao Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou, China
| | - Xiaxiu Tong
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Jie Jiang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Chenjing He
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Taihe Xiang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou, China
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Álvarez C, Brenes-Álvarez M, Molina-Heredia FP, Mariscal V. Quantitative Proteomics at Early Stages of the Symbiotic Interaction Between Oryza sativa and Nostoc punctiforme Reveals Novel Proteins Involved in the Symbiotic Crosstalk. PLANT & CELL PHYSIOLOGY 2022; 63:1433-1445. [PMID: 35373828 PMCID: PMC9620832 DOI: 10.1093/pcp/pcac043] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/22/2022] [Accepted: 04/09/2022] [Indexed: 06/14/2023]
Abstract
Symbiosis between cyanobacteria and plants is considered pivotal for biological nitrogen deposition in terrestrial ecosystems. Despite extensive knowledge of the ecology of plant-cyanobacterium symbioses, little is known about the molecular mechanisms involved in recognition between partners. Here, we conducted a quantitative sequential window acquisition of all theoretical fragment ion spectra mass spectrometry pipeline to analyze protein changes in Oryza sativa and Nostoc punctiforme during early events of symbiosis. We found differentially expressed proteins in both organisms linked to several biological functions, including signal transduction, adhesion, defense-related proteins and cell wall modification. In N. punctiforme we found increased expression of 62 proteins that have been previously described in other Nostoc-plant symbioses, reinforcing the robustness of our study. Our findings reveal new proteins activated in the early stages of the Nostoc-Oryza symbiosis that might be important for the recognition between the plant and the host. Oryza mutants in genes in the common symbiosis signaling pathway (CSSP) show reduced colonization efficiency, providing first insights on the involvement of the CSSP for the accommodation of N. punctiforme inside the plant cells. This information may have long-term implications for a greater understanding of the symbiotic interaction between Nostoc and land plants.
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Affiliation(s)
- Consolación Álvarez
- *Corresponding authors: Vicente Mariscal, E-mail, ; Consolación Álvarez, E-mail,
| | - Manuel Brenes-Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, cicCartuja, Américo Vespucio 49, Seville 41092, Spain
| | - Fernando P Molina-Heredia
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, cicCartuja, Américo Vespucio 49, Seville 41092, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes s/n, Seville 41012, Spain
| | - Vicente Mariscal
- *Corresponding authors: Vicente Mariscal, E-mail, ; Consolación Álvarez, E-mail,
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Baysal C, Burén S, He W, Jiang X, Capell T, Rubio LM, Christou P. Functional expression of the nitrogenase Fe protein in transgenic rice. Commun Biol 2022; 5:1006. [PMID: 36198910 PMCID: PMC9534833 DOI: 10.1038/s42003-022-03921-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/30/2022] [Indexed: 11/24/2022] Open
Abstract
Engineering cereals to express functional nitrogenase is a long-term goal of plant biotechnology and would permit partial or total replacement of synthetic N fertilizers by metabolization of atmospheric N2. Developing this technology is hindered by the genetic and biochemical complexity of nitrogenase biosynthesis. Nitrogenase and many of the accessory proteins involved in its assembly and function are O2 sensitive and only sparingly soluble in non-native hosts. We generated transgenic rice plants expressing the nitrogenase structural component, Fe protein (NifH), which carries a [4Fe-4S] cluster in its active form. NifH from Hydrogenobacter thermophilus was targeted to mitochondria together with the putative peptidyl prolyl cis-trans isomerase NifM from Azotobacter vinelandii to assist in NifH polypeptide folding. The isolated NifH was partially active in electron transfer to the MoFe protein nitrogenase component (NifDK) and in the biosynthesis of the nitrogenase iron-molybdenum cofactor (FeMo-co), two fundamental roles for NifH in N2 fixation. NifH functionality was, however, limited by poor [4Fe-4S] cluster occupancy, highlighting the importance of in vivo [Fe-S] cluster insertion and stability to achieve biological N2 fixation in planta. Nevertheless, the expression and activity of a nitrogenase component in rice plants represents the first major step to engineer functional nitrogenase in cereal crops.
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Affiliation(s)
- Can Baysal
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN, USA
| | - Stefan Burén
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - Wenshu He
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain
| | - Xi Jiang
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - Teresa Capell
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón (Madrid), Spain.
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain.
| | - Paul Christou
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain.
- ICREA, Catalan Institute for Research and Advanced Studies, Passeig Lluís Companys 23, 08010, Barcelona, Spain.
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Chatterjee P, Schafran P, Li FW, Meeks JC. Nostoc Talks Back: Temporal Patterns of Differential Gene Expression During Establishment of Anthoceros-Nostoc Symbiosis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:917-932. [PMID: 35802132 DOI: 10.1094/mpmi-05-22-0101-r] [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: 06/15/2023]
Abstract
Endosymbiotic associations between hornworts and nitrogen-fixing cyanobacteria form when the plant is limited for combined nitrogen (N). We generated RNA-seq data to examine temporal gene expression patterns during the culturing of N-starved Anthoceros punctatus in the absence and the presence of symbiotic cyanobacterium Nostoc punctiforme. In symbiont-free A. punctatus gametophytes, N starvation caused downregulation of chlorophyll content and chlorophyll fluorescence characteristics as well as transcription of photosynthesis-related genes. This downregulation was reversed in A. punctatus cocultured with N. punctiforme, corresponding to the provision by the symbiont of N2-derived NH4+, which commenced within 5 days of coculture and reached a maximum by 14 days. We also observed transient increases in transcription of ammonium and nitrate transporters in a N. punctiforme-dependent manner as well as that of a SWEET transporter that was initially independent of N2-derived NH4+. The temporal patterns of differential gene expression indicated that N. punctiforme transmits signals that impact gene expression to A. punctatus both prior to and after its provision of fixed N. This study is the first illustrating the temporal patterns of gene expression during establishment of an endosymbiotic nitrogen-fixing association in this monophyletic evolutionary lineage of land plants. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Poulami Chatterjee
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, U.S.A
| | - Peter Schafran
- Boyce Thompson Institute, Ithaca, NY 14853, U.S.A
- Plant Biology Section, Cornell University, Ithaca, NY 14953, U.S.A
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY 14853, U.S.A
- Plant Biology Section, Cornell University, Ithaca, NY 14953, U.S.A
| | - John C Meeks
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, U.S.A
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Trinchera A, Migliore M, Warren Raffa D, Ommeslag S, Debode J, Shanmugam S, Dane S, Babry J, Kivijarvi P, Kristensen HL, Lepse L, Salo T, Campanelli G, Willekens K. Can multi-cropping affect soil microbial stoichiometry and functional diversity, decreasing potential soil-borne pathogens? A study on European organic vegetable cropping systems. FRONTIERS IN PLANT SCIENCE 2022; 13:952910. [PMID: 36237499 PMCID: PMC9552534 DOI: 10.3389/fpls.2022.952910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Crop diversification in spatial and temporal patterns can optimize the synchronization of nutrients plant demand and availability in soils, as plant diversity and soil microbial communities are the main drivers of biogeochemical C and nutrient cycling. The introduction of multi-cropping in organic vegetable production can represent a key strategy to ensure efficient complementation mediated by soil microbiota, including beneficial mycorrhizal fungi. This study shows the effect of the introduction of multi-cropping in five European organic vegetable systems (South-West: Italy; North-West: Denmark and Belgium; North-East: Finland and Latvia) on: (i) soil physicochemical parameters; (ii) soil microbial biomass stoichiometry; (iii) crop root mycorrhization; (iv) bacterial and fungal diversity and composition in crop rhizosphere; (v) relative abundance of selected fungal pathogens species. In each site, three cropping systems were considered: (1) crop 1-monocropping; (2) crop 2-monocropping; (3) crop 1-crop 2-intercropping or strip cropping. Results showed that, just before harvest, multi-cropping can increase soil microbial biomass amount and shape microbial community toward a predominance of some bacteria or fungi phyla, in the function of soil nutrient availability. We mainly observed a selection effect of crop type on rhizosphere microbiota. Particularly, Bacteroidetes and Mortierellomycota relative abundances in rhizosphere soil resulted in suitable ecological indicators of the positive effect of plant diversity in field, the first ones attesting an improved C and P cycles in soil and the second ones a reduced soil pathogens' pressure. Plant diversity also increased the root mycorrhizal colonization between the intercropped crops that, when properly selected, can also reduce the relative abundance of potential soil-borne pathogens, with a positive effect on crop productivity in long term.
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Affiliation(s)
- Alessandra Trinchera
- Council for Agricultural Research and Economics-Research Centre for Agriculture and Environment, Rome, Italy
| | - Melania Migliore
- Council for Agricultural Research and Economics-Research Centre for Agriculture and Environment, Rome, Italy
| | - Dylan Warren Raffa
- Council for Agricultural Research and Economics-Research Centre for Agriculture and Environment, Rome, Italy
| | - Sarah Ommeslag
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Jane Debode
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | | | - Sandra Dane
- Latvian Institute of Horticulture, LatHort, Dobeles Novads, Latvia
| | | | - Pirjo Kivijarvi
- LUKE (FI) Natural Resources Institute Finland, Helsinki, Finland
| | | | - Liga Lepse
- Latvian Institute of Horticulture, LatHort, Dobeles Novads, Latvia
| | - Tapio Salo
- LUKE (FI) Natural Resources Institute Finland, Helsinki, Finland
| | - Gabriele Campanelli
- Council for Agricultural Research and Economics-Research Centre for Vegetable and Ornamental Crops, Monsampolo del Tronto, Italy
| | - Koen Willekens
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
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Chan C. Progress in Salicylic Acid-Dependent Signaling for Growth–Defense Trade-Off. Cells 2022; 11:cells11192985. [PMID: 36230947 PMCID: PMC9563428 DOI: 10.3390/cells11192985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 11/21/2022] Open
Abstract
One grand challenge for studying plant biotic and abiotic stress responses is to optimize plant growth and plasticity under variable environmental constraints, which in the long run benefits agricultural production. However, efforts in promoting plant immunity are often accompanied by compromised morphological “syndromes” such as growth retardation, sterility, and reduced yield. Such a trade-off is dictated by complex signaling driven by secondary messengers and phytohormones. Salicylic acid (SA) is a well-known phytohormone essential for basal immunity and systemic acquired resistance. Interestingly, recent updates suggest that external environmental cues, nutrient status, developmental stages, primary metabolism, and breeding strategies attribute an additional layer of control over SA-dependent signaling, and, hence, plant performance against pathogens. In this review, these external and internal factors are summarized, focusing on their specific roles on SA biosynthesis and downstream signaling leading to immunity. A few considerations and future opportunities are highlighted to improve plant fitness with minimal growth compensation.
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Affiliation(s)
- Ching Chan
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
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49
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Draft Genome Sequences of Three Nitrogen-Fixing Strains Isolated from Soil Cooled for Growing Temperate Root Crops in a Tropical Climate. Microbiol Resour Announc 2022; 11:e0050122. [PMID: 36000856 PMCID: PMC9476910 DOI: 10.1128/mra.00501-22] [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] [Indexed: 11/20/2022] Open
Abstract
Nitrogen-fixing bacteria can form a symbiotic relationship with several members of the major plant groups and with fungi. Here, we present the draft genome sequences of three nitrogen-fixing strains isolated from soil cooled for growing temperate root crops in a tropical climate.
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50
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Mathesius U. Are legumes different? Origins and consequences of evolving nitrogen fixing symbioses. JOURNAL OF PLANT PHYSIOLOGY 2022; 276:153765. [PMID: 35952452 DOI: 10.1016/j.jplph.2022.153765] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 05/14/2023]
Abstract
Nitrogen fixing symbioses between plants and bacteria are ancient and, while not numerous, are formed in diverse lineages of plants ranging from microalgae to angiosperms. One symbiosis stands out as the most widespread one is that between legumes and rhizobia, leading to the formation of nitrogen-fixing nodules. The legume family is one of the largest and most diverse group of plants and legumes have been used by humans since the beginning of agriculture, both as high nitrogen food, as well as pastures and rotation crops. One open question is whether their ability to form a nitrogen-fixing symbiosis has contributed to legumes' success, and whether legumes have any unique characteristics that have made them more diverse and widespread than other groups of plants. This review examines the evolutionary journey that has led to the diversification of legumes, in particular its nitrogen-fixing symbiosis, and asks four questions to investigate which legume traits might have contributed to their success: 1. In what ways do legumes differ from other plant groups that have evolved nitrogen-fixing symbioses? In order to answer this question, the characteristics of the symbioses, and efficiencies of nitrogen fixation are compared between different groups of nitrogen fixing plants. 2. Could certain unique features of legumes be a reason for their success? This section examines the manifestations and possible benefits of a nitrogen-rich 'lifestyle' in legumes. 3. If nitrogen fixation was a reason for such a success, why have some species lost the symbiosis? Formation of symbioses has trade-offs, and while these are less well known for non-legumes, there are known energetic and ecological reasons for loss of symbiotic potential in legumes. 4. What can we learn from the unique traits of legumes for future crop improvements? While exploiting some of the physiological properties of legumes could be used to improve legume breeding, our increasing molecular understanding of the essential regulators of root nodule symbioses raise hope of creating new nitrogen fixing symbioses in other crop species.
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Affiliation(s)
- Ulrike Mathesius
- Division of Plant Sciences, Research School of Biology, The Australian National University, 134 Linnaeus Way, Canberra, ACT, 2601, Australia.
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