1
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Wang Z, Fu X, Kuramae EE. Insight into farming native microbiome by bioinoculant in soil-plant system. Microbiol Res 2024; 285:127776. [PMID: 38820701 DOI: 10.1016/j.micres.2024.127776] [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: 02/12/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 06/02/2024]
Abstract
Applying beneficial microorganisms (BM) as bioinoculants presents a promising soil-amendment strategy while impacting the native microbiome, which jointly alters soil-plant performance. Leveraging the untapped potential of native microbiomes alongside bioinoculants may enable farmers to sustainably regulate soil-plant systems via natural bioresources. This review synthesizes literature on native microbiome responses to BMs and their interactive effects on soil and plant performance. We highlight that native microbiomes harbor both microbial "helpers" that can improve soil fertility and plant productivity, as well as "inhibitors" that hinder these benefits. To harness the full potential of resident microbiome, it is crucial to elucidate their intricate synergistic and antagonistic interplays with introduced BMs and clarify the conditions that facilitate durable BM-microbiome synergies. Hence, we indicate current challenges in predicting these complex microbial interactions and propose corresponding strategies for microbiome breeding via BM bioinoculant. Overall, fully realizing the potential of BMs requires clarifying their interactions with native soil microbiomes and judiciously engineering microbiome to harness helpful microbes already present within agroecosystems.
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Affiliation(s)
- Zhikang Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen 6708 PB, the Netherlands
| | - Xiangxiang Fu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China.
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen 6708 PB, the Netherlands; Ecology and biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, the Netherlands.
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2
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Kozaeva E, Eida AA, Gunady EF, Dangl JL, Conway JM, Brophy JA. Roots of synthetic ecology: microbes that foster plant resilience in the changing climate. Curr Opin Biotechnol 2024; 88:103172. [PMID: 39029405 DOI: 10.1016/j.copbio.2024.103172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/11/2024] [Accepted: 06/26/2024] [Indexed: 07/21/2024]
Abstract
Microbes orchestrate nearly all major biogeochemical processes. The ability to program their influence on plant growth and development is attractive for sustainable agriculture. However, the complexity of microbial ecosystems and our limited understanding of the mechanisms by which plants and microbes interact with each other and the environment make it challenging to use microbiomes to influence plant growth. Novel technologies at the intersection of microbial ecology, systems biology, and bioengineering provide new tools to probe the role of plant microbiomes across environments. Here, we summarize recent studies on plant and microbe responses to abiotic stresses, showcasing key molecules and micro-organisms that are important for plant health. We highlight opportunities to use synthetic microbial communities to understand the complexity of plant-microbial interactions and discuss future avenues of programming ecology to improve plant and ecosystem health.
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Affiliation(s)
- Ekaterina Kozaeva
- Department of Bioengineering, Stanford University, Stanford, CA, USA; Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Abdul Aziz Eida
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ella F Gunady
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Jeffery L Dangl
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jonathan M Conway
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.
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3
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Amenta ML, Vaccaro F, Varriale S, Sangaré JR, Defez R, Mengoni A, Bianco C. Cereals can trap endophytic bacteria with potential beneficial traits when grown ex-situ in harsh soils. FEMS Microbiol Ecol 2024; 100:fiae041. [PMID: 38544316 PMCID: PMC11009874 DOI: 10.1093/femsec/fiae041] [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: 08/18/2023] [Revised: 03/01/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024] Open
Abstract
Microbial communities associated with plants growing in harsh conditions, including salinity and water deficiency, have developed adaptive features which permit them to grow and survive under extreme environmental conditions. In the present study, an ex-situ plant trapping method has been applied to collect the culturable microbial diversity associated with the soil from harsh and remote areas. Oryza sativa cv. Baldo and Triticum durum Primadur plants were used as recruiters, while the soil surrounding the roots of Oryza glaberrima plants from remote regions of Mali (West Africa) was used as substrate for their growth. The endophytic communities recruited by the two plant species belonged to Proteobacteria and Firmicutes, and the dominant genera were Bacillus, Kosakonia, and Enterobacter. These endophytes were characterized by analyzing some of the most common plant growth promoting traits. Halotolerant, inorganic phosphate-solubilizing and N-fixing strains were found, and some of them simultaneously showing these three traits. We verified that 'Baldo' recruited mostly halotolerant and P-solubilizers endophytes, while the endophytes selected by 'Primadur' were mainly N-fixers. The applied ex-situ plant trapping method allowed to isolate endophytes with potential beneficial traits that could be applied for the improvement of rice and wheat growth under adverse environmental conditions.
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Affiliation(s)
- Maria Laura Amenta
- National Research Council, Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy
| | - Francesca Vaccaro
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Stefano Varriale
- National Research Council,
Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy
| | - Jean Rodrigue Sangaré
- Institut d'Economie Rurale (IER), Centre Régional de Recherche Agronomique (CRRA) de Sikasso, B.P: 16, Mali
| | - Roberto Defez
- National Research Council, Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Carmen Bianco
- National Research Council, Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy
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4
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Zeng Y, Wang M, Yu Y, Wang L, Cui L, Li C, Liu Y, Zheng Y. Rice N-biofertilization by inoculation with an engineered photosynthetic diazotroph. World J Microbiol Biotechnol 2024; 40:136. [PMID: 38499730 DOI: 10.1007/s11274-024-03956-6] [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: 01/05/2024] [Accepted: 03/13/2024] [Indexed: 03/20/2024]
Abstract
Photosynthetic diazotrophs expressing iron-only (Fe-only) nitrogenase can be developed into a promising biofertilizer, as it is independent on the molybdenum availability in the soil. However, the expression of Fe-only nitrogenase in diazotrophs is repressed by the fixed nitrogen of the soil, limiting the efficiency of nitrogen fixation in farmland with low ammonium concentrations that are inadequate for sustainable crop growth. Here, we succeeded in constitutively expressing the Fe-only nitrogenase even in the presence of ammonium by controlling the transcription of Fe-only nitrogenase gene cluster (anfHDGK) with the transcriptional activator of Mo nitrogenase (NifA*) in several different ways, indicating that the engineered NifA* strains can be used as promising chassis cells for efficient expression of different types of nitrogenases. When applied as a biofertilizer, the engineered Rhodopseudomonas palustris effectively stimulated rice growth, contributing to the reduced use of chemical fertilizer and the development of sustainable agriculture.
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Affiliation(s)
- Yan Zeng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Mengmei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunkai Yu
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, 161006, China
| | - Lida Wang
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, 161006, China
| | - Lingwei Cui
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chang Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
- College of Agriculture, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Ying Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Yanning Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China.
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Nshimiyimana JB, Zhao K, Wang W, Kong W. Diazotrophic abundance and community structure associated with three meadow plants on the Qinghai-Tibet Plateau. Front Microbiol 2024; 14:1292860. [PMID: 38260880 PMCID: PMC10801153 DOI: 10.3389/fmicb.2023.1292860] [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: 09/12/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Symbiotic diazotrophs form associations with legumes and substantially fix nitrogen into soils. However, grasslands on the Qinghai-Tibet Plateau are dominated by non-legume plants, such as Kobresia tibetica. Herein, we investigated the diazotrophic abundance, composition, and community structure in the soils and roots of three plants, non-legume K. tibetica and Kobresia humilis and the legume Oxytropis ochrocephala, using molecular methods targeting nifH gene. Diazotrophs were abundantly observed in both bulk and rhizosphere soils, as well as in roots of all three plants, but their abundance varied with plant type and soil. In both bulk and rhizosphere soils, K. tibetica showed the highest diazotroph abundance, whereas K. humilis had the lowest. In roots, O. ochrocephala and K. humilis showed the highest and the lowest diazotroph abundance, respectively. The bulk and rhizosphere soils exhibited similar diazotrophic community structure in both O. ochrocephala and K. tibetica, but were substantially distinct from the roots in both plants. Interestingly, the root diazotrophic community structures in legume O. ochrocephala and non-legume K. tibetica were similar. Diazotrophs in bulk and rhizosphere soils were more diverse than those in the roots of three plants. Rhizosphere soils of K. humilis were dominated by Actinobacteria, while rhizosphere soils and roots of K. tibetica were dominated by Verrumicrobia and Proteobacteria. The O. ochrocephala root diazotrophs were dominated by Alphaproteobacteria. These findings indicate that free-living diazotrophs abundantly and diversely occur in grassland soils dominated by non-legume plants, suggesting that these diazotrophs may play important roles in fixing nitrogen into soils on the plateau.
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Affiliation(s)
- Jean Bosco Nshimiyimana
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- Department of Life and Geography Sciences, Qinghai Normal University, Xining, China
| | - Kang Zhao
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- Department of Life and Geography Sciences, Qinghai Normal University, Xining, China
| | - Wenying Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization in Qinghai Tibet Plateau, Xining, China
| | - Weidong Kong
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- Department of Life and Geography Sciences, Qinghai Normal University, Xining, China
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6
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Venkataraman M, Yñigez-Gutierrez A, Infante V, MacIntyre A, Fernandes-Júnior PI, Ané JM, Pfleger B. Synthetic Biology Toolbox for Nitrogen-Fixing Soil Microbes. ACS Synth Biol 2023; 12:3623-3634. [PMID: 37988619 PMCID: PMC10754042 DOI: 10.1021/acssynbio.3c00414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
The soil environment adjacent to plant roots, termed the rhizosphere, is home to a wide variety of microorganisms that can significantly affect the physiology of nearby plants. Microbes in the rhizosphere can provide nutrients, secrete signaling compounds, and inhibit pathogens. These processes could be manipulated with synthetic biology to enhance the agricultural performance of crops grown for food, energy, or environmental remediation, if methods can be implemented in these nonmodel microbes. A common first step for domesticating nonmodel organisms is the development of a set of genetic engineering tools, termed a synthetic biology toolbox. A toolbox comprises transformation protocols, replicating vectors, genome engineering (e.g., CRISPR/Cas9), constitutive and inducible promoter systems, and other gene expression control elements. This work validated synthetic biology toolboxes in three nitrogen-fixing soil bacteria: Azotobacter vinelandii, Stutzerimonas stutzeri (Pseudomonas stutzeri), and a new isolate of Klebsiella variicola. All three organisms were amenable to transformation and reporter protein expression, with several functional inducible systems available for each organism. S. stutzeri and K. variicola showed more reliable plasmid-based expression, resulting in successful Cas9 recombineering to create scarless deletions and insertions. Using these tools, we generated mutants with inducible nitrogenase activity and introduced heterologous genes to produce resorcinol products with relevant biological activity in the rhizosphere.
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Affiliation(s)
- Maya Venkataraman
- Department of Chemical and Biological Engineering, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Audrey Yñigez-Gutierrez
- Department of Chemical and Biological Engineering, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Valentina Infante
- Department of Bacteriology, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - April MacIntyre
- Department of Bacteriology, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Valent BioSciences, Libertyville, Illinois 60048, United States
| | - Paulo Ivan Fernandes-Júnior
- Department of Bacteriology, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Brazilian Agricultural Research Corporation (Embrapa), Tropical Semi-Arid Research Center (Embrapa Semiárido), Petrolina, Pernambuco 56302-970, Brazil
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Microbiology Doctoral Training Program, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Brian Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Microbiology Doctoral Training Program, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
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7
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Li X, Liu Y, Wang Z, Yang C, Zhang R, Luo Y, Ma Y, Deng Y. Microbiome analysis and biocontrol bacteria isolation from rhizosphere soils associated with different sugarcane root rot severity. Front Bioeng Biotechnol 2022; 10:1062351. [PMID: 36588942 PMCID: PMC9802638 DOI: 10.3389/fbioe.2022.1062351] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
To explore the causal pathogen and the correlated rhizosphere soil microecology of sugarcane root rot, we sampled the sugarcane root materials displaying different disease severity, and the corresponding rhizosphere soil, for systematic root phenotype and microbial population analyses. We found that with increased level of disease severity reflected by above-ground parts of sugarcane, the total root length, total root surface area and total volume were significantly reduced, accompanied with changes in the microbial population diversity and structure in rhizosphere soil. Fungal community richness was significantly lower in the rhizosphere soil samples from mildly diseased plant than that from either healthy plant, or severely diseased plant. Particularly, we noticed that a peculiar decrease of potential pathogenic fungi in rhizosphere soil, including genera Fusarium, Talaromyces and Neocosmospora, with increased level of disease severity. As for bacterial community, Firmicutes was found to be of the highest level, while Acidobacteria and Chloroflexi of the lowest level, in rhizosphere soil from healthy plant compared to that from diseased plant of different severity. FUNGuild prediction showed that the proportion of saprophytic fungi was higher in the rhizosphere soil of healthy plants, while the proportion of pathogenic fungi was higher in the rhizosphere soil of diseased plants. By co-occurrence network analysis we demonstrated the Bacillus and Burkholderia were in a strong interaction with Fusarium pathogen(s). Consistently, the biocontrol and/or growth-promoting bacteria isolated from the rhizosphere soil were mostly (6 out of 7) belonging to Bacillus and Burkholderia species. By confrontation culture and pot experiments, we verified the biocontrol and/or growth-promoting property of the isolated bacterial strains. Overall, we demonstrated a clear correlation between sugarcane root rot severity and rhizosphere soil microbiome composition and function, and identified several promising biocontrol bacteria strains with strong disease suppression effect and growth-promoting properties.
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Affiliation(s)
- Xinyang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Yue Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Laboratory of Crop Physiology and Field Ecology, Northwest A&F University, Yangling, China
| | - Ziting Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Chenglong Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Runzhi Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Yibao Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Yuming Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Yizhen Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China,*Correspondence: Yizhen Deng,
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8
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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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9
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Lv F, Zhan Y, Lu W, Ke X, Shao Y, Ma Y, Zheng J, Yang Z, Jiang S, Shang L, Ma Y, Cheng L, Elmerich C, Yan Y, Lin M. Regulation of hierarchical carbon substrate utilization, nitrogen fixation, and root colonization by the Hfq/Crc/CrcZY genes in Pseudomonas stutzeri. iScience 2022; 25:105663. [PMID: 36505936 PMCID: PMC9730152 DOI: 10.1016/j.isci.2022.105663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/08/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Bacteria of the genus Pseudomonas consume preferred carbon substrates in nearly reverse order to that of enterobacteria, and this process is controlled by RNA-binding translational repressors and regulatory ncRNA antagonists. However, their roles in microbe-plant interactions and the underlying mechanisms remain uncertain. Here we show that root-associated diazotrophic Pseudomonas stutzeri A1501 preferentially catabolizes succinate, followed by the less favorable substrate citrate, and ultimately glucose. Furthermore, the Hfq/Crc/CrcZY regulatory system orchestrates this preference and contributes to optimal nitrogenase activity and efficient root colonization. Hfq has a central role in this regulatory network through different mechanisms of action, including repressing the translation of substrate-specific catabolic genes, activating the nitrogenase gene nifH posttranscriptionally, and exerting a positive effect on the transcription of an exopolysaccharide gene cluster. Our results illustrate an Hfq-mediated mechanism linking carbon metabolism to nitrogen fixation and root colonization, which may confer rhizobacteria competitive advantages in rhizosphere environments.
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Affiliation(s)
- Fanyang Lv
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuhua Zhan
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Lu
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiubin Ke
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yahui Shao
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yiyuan Ma
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Juan Zheng
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhimin Yang
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shanshan Jiang
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liguo Shang
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yao Ma
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | | | - Yongliang Yan
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China,Corresponding author
| | - Min Lin
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China,Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China,Corresponding author
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10
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Klimasmith IM, Kent AD. Micromanaging the nitrogen cycle in agroecosystems. Trends Microbiol 2022; 30:1045-1055. [PMID: 35618540 DOI: 10.1016/j.tim.2022.04.006] [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: 12/16/2021] [Revised: 03/29/2022] [Accepted: 04/29/2022] [Indexed: 01/13/2023]
Abstract
While large inputs of synthetic nitrogen fertilizers enable our current rate of crop production and feed a growing global population, these fertilizers come at a heavy environmental cost. Driven by microbial processes, excess applied nitrogen is lost from agroecosystems as nitrate and nitrous oxide (N2O) contaminating aquatic ecosystems and contributing to climate change. Interest in nitrogen-fixing microorganisms as an alternative to synthetic fertilizers is rapidly accelerating. Microbial inoculants offer the promise of a sustainable and affordable source of nitrogen, but the impact of inoculants on nitrogen dynamics at an ecosystem level is not fully understood. This review synthesizes recent studies on microbial inoculants as tools for nutrient management and considers the ramifications of inoculants for nitrogen transformations beyond fixation.
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Affiliation(s)
- Isaac M Klimasmith
- Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Angela D Kent
- Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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11
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Pankievicz VCS, Delaux PM, Infante V, Hirsch HH, Rajasekar S, Zamora P, Jayaraman D, Calderon CI, Bennett A, Ané JM. Nitrogen fixation and mucilage production on maize aerial roots is controlled by aerial root development and border cell functions. FRONTIERS IN PLANT SCIENCE 2022; 13:977056. [PMID: 36275546 PMCID: PMC9583020 DOI: 10.3389/fpls.2022.977056] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Exploring natural diversity for biological nitrogen fixation in maize and its progenitors is a promising approach to reducing our dependence on synthetic fertilizer and enhancing the sustainability of our cropping systems. We have shown previously that maize accessions from the Sierra Mixe can support a nitrogen-fixing community in the mucilage produced by their abundant aerial roots and obtain a significant fraction of their nitrogen from the air through these associations. In this study, we demonstrate that mucilage production depends on root cap and border cells sensing water, as observed in underground roots. The diameter of aerial roots correlates with the volume of mucilage produced and the nitrogenase activity supported by each root. Young aerial roots produce more mucilage than older ones, probably due to their root cap's integrity and their ability to produce border cells. Transcriptome analysis on aerial roots at two different growth stages before and after mucilage production confirmed the expression of genes involved in polysaccharide synthesis and degradation. Genes related to nitrogen uptake and assimilation were up-regulated upon water exposure. Altogether, our findings suggest that in addition to the number of nodes with aerial roots reported previously, the diameter of aerial roots and abundance of border cells, polysaccharide synthesis and degradation, and nitrogen uptake are critical factors to ensure efficient nitrogen fixation in maize aerial roots.
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Affiliation(s)
| | - Pierre-Marc Delaux
- Department of Bacteriology and Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | - Valentina Infante
- Department of Bacteriology and Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | - Hayley H. Hirsch
- Department of Bacteriology and Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | - Shanmugam Rajasekar
- Department of Bacteriology and Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | - Pablo Zamora
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Dhileepkumar Jayaraman
- Department of Bacteriology and Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Alan Bennett
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Jean-Michel Ané
- Department of Bacteriology and Agronomy, University of Wisconsin-Madison, Madison, WI, United States
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12
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Ladha JK, Peoples MB, Reddy PM, Biswas JC, Bennett A, Jat ML, Krupnik TJ. Biological nitrogen fixation and prospects for ecological intensification in cereal-based cropping systems. FIELD CROPS RESEARCH 2022; 283:108541. [PMID: 35782167 PMCID: PMC9133800 DOI: 10.1016/j.fcr.2022.108541] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 03/29/2022] [Accepted: 04/03/2022] [Indexed: 05/02/2023]
Abstract
The demand for nitrogen (N) for crop production increased rapidly from the middle of the twentieth century and is predicted to at least double by 2050 to satisfy the on-going improvements in productivity of major food crops such as wheat, rice and maize that underpin the staple diet of most of the world's population. The increased demand will need to be fulfilled by the two main sources of N supply - biological nitrogen (gas) (N2) fixation (BNF) and fertilizer N supplied through the Haber-Bosch processes. BNF provides many functional benefits for agroecosystems. It is a vital mechanism for replenishing the reservoirs of soil organic N and improving the availability of soil N to support crop growth while also assisting in efforts to lower negative environmental externalities than fertilizer N. In cereal-based cropping systems, legumes in symbiosis with rhizobia contribute the largest BNF input; however, diazotrophs involved in non-symbiotic associations with plants or present as free-living N2-fixers are ubiquitous and also provide an additional source of fixed N. This review presents the current knowledge of BNF by free-living, non-symbiotic and symbiotic diazotrophs in the global N cycle, examines global and regional estimates of contributions of BNF, and discusses possible strategies to enhance BNF for the prospective benefit of cereal N nutrition. We conclude by considering the challenges of introducing in planta BNF into cereals and reflect on the potential for BNF in both conventional and alternative crop management systems to encourage the ecological intensification of cereal and legume production.
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Affiliation(s)
- Jagdish K. Ladha
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Mark B. Peoples
- Commonwealth Scientific and Industrial Research Organisation, Canberra, Australia
| | | | | | - Alan Bennett
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Mangi L. Jat
- International Maize and Wheat Improvement Center, New Delhi, India
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13
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Pathania N, Kumar A, Sharma P, Kaur A, Sharma S, Jain R. Harnessing rhizobacteria to fulfil inter-linked nutrient dependency on soil and alleviate stresses in plants. J Appl Microbiol 2022; 133:2694-2716. [PMID: 35656999 DOI: 10.1111/jam.15649] [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: 03/09/2022] [Revised: 05/12/2022] [Accepted: 05/31/2022] [Indexed: 11/27/2022]
Abstract
Plant rhizo-microbiome comprises of complex microbial communities that colonizes at the interphase of plant roots and soil. Plant-growth-promoting rhizobacteria (PGPR) in the rhizosphere provides important ecosystem services ranging from release of essential nutrients for enhancing soil quality and improving plant health to imparting protection to plants against rising biotic and abiotic stresses. Hence, PGPR serve as restoring agents to rejuvenate soil health and mediate plant fitness in the facet of changing climate. Though, it is evident that nutrients availability in soil are managed through inter-linked mechanisms, how PGPR expediate these processes remain less recognized. Promising results of PGPR inoculation on plant growth are continually reported in controlled environmental conditions, however, their field application often fails due to competition with native microbiota and low colonization efficiency in roots. The development of highly efficient and smart bacterial synthetic communities by integrating bacterial ecological and genetic features provides better opportunities for successful inoculant formulations. This review provides an overview of the inter-play between nutrient availability and disease suppression governed by rhizobacteria in soil followed by the role of synthetic bacterial communities in developing efficient microbial inoculants. Moreover, an outlook on the beneficial activities of rhizobacteria in modifying soil characteristics to sustainably boost agroecosystem functioning is also provided.
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Affiliation(s)
- Neemisha Pathania
- Department of Soil Science, Punjab Agricultural University, Ludhiana, Punjab 141004, India
| | - Arun Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
| | - Poonam Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab 141004, India
| | - Avneet Kaur
- Department of Soil Science, Punjab Agricultural University, Ludhiana, Punjab 141004, India
| | - Sandeep Sharma
- Department of Soil Science, Punjab Agricultural University, Ludhiana, Punjab 141004, India
| | - Rahul Jain
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
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14
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Helal DS, El-Khawas H, Elsayed TR. Molecular characterization of endophytic and ectophytic plant growth promoting bacteria isolated from tomato plants (Solanum lycopersicum L.) grown in different soil types. J Genet Eng Biotechnol 2022; 20:79. [PMID: 35608711 PMCID: PMC9130443 DOI: 10.1186/s43141-022-00361-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 05/02/2022] [Indexed: 11/24/2022]
Abstract
Background Successful rhizosphere colonization by plant growth promoting rhizobacteria (PGPR) is of crucial importance to perform the desired plant growth promoting activities. Since rhizocompetence is a dynamic process influenced by surrounding environmental conditions. In the present study, we hypothesized that bacterial isolates obtained from different tomato plant microhabitats (balk soil, rhizosphere, endorhiza, phyllosphere, and endoshoot) grown in different soils (sand, clay, and peat moss) will show different rhizocompetence abilities. Results To evaluate this hypothesis, bacterial isolates were obtained from different plant microhabitats and screened for their phosphate solubilizing and nitrogen fixing activates. BOX-PCR fingerprint profiles showed high genotypic diversity among the tested isolates and that same genotypes were shared between different soils and/or plant microhabitats. 16S rRNA gene sequences of 25 PGP isolates, representing different plant spheres and soil types, were affiliated to eight genera: Enterobacter, Paraburkholderia, Klebsiella, Bacillus, Paenibacillus, Stenotrophomonas, Pseudomonas, and Kosakonia. The rhizocompetence of each isolate was evaluated in the rhizosphere of tomato plants grown on a mixture of the three soils. Different genotypes of the same bacterial species displayed different rhizocompetence potentials. However, isolates obtained from the above-ground parts of the plant showed high rhizocompetence. In addition, biological control-related genes, ituD and srfC, were detected in the obtained spore forming bacterial isolates. Conclusion This study evaluates, for the first time, the relationship between plant microhabitat and the rhizocompetence ability in tomato rhizosphere. The results indicated that soil type and plant sphere can influence both the genotypic diversity and rhizocompetence ability of the same bacterial species. Bacterial isolates obtained in this study are promising to be used as an environmentally friendly substitution of chemical fertilizers. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-022-00361-0.
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Affiliation(s)
- Donia S Helal
- Department of Agricultural Microbiology, Faculty of Agriculture, Cairo University, Cairo, Egypt
| | - Hussein El-Khawas
- Department of Agricultural Microbiology, Faculty of Agriculture, Cairo University, Cairo, Egypt
| | - Tarek R Elsayed
- Department of Agricultural Microbiology, Faculty of Agriculture, Cairo University, Cairo, Egypt.
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15
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Laveilhé A, Fochesato S, Lalaouna D, Heulin T, Achouak W. Phytobeneficial traits of rhizobacteria under the control of multiple molecular dialogues. Microb Biotechnol 2022; 15:2083-2096. [PMID: 35502577 PMCID: PMC9249325 DOI: 10.1111/1751-7915.14023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 02/14/2022] [Accepted: 02/14/2022] [Indexed: 11/29/2022] Open
Abstract
Pseudomonads play crucial roles in plant growth promotion and control of plant diseases. However, under natural conditions, other microorganisms competing for the same nutrient resources in the rhizosphere may exert negative control over their phytobeneficial characteristics. We assessed the expression of phytobeneficial genes involved in biocontrol, biostimulation and iron regulation such as, phlD, hcnA, acdS, and iron‐small regulatory RNAs prrF1 and prrF2 in Pseudomonas brassicacearum co‐cultivated with three phytopathogenic fungi, and two rhizobacteria in the presence or absence of Brassica napus, and in relation to iron availability. We found that the antifungal activity of P. brassicacearum depends mostly on the production of DAPG and not on HCN whose production is suppressed by fungi. We have also shown that the two‐competing bacterial strains modulate the plant growth promotion activity of P. brassicacearum by modifying the expression of phlD, hcnA and acdS according to iron availability. Overall, it allows us to better understand the complexity of the multiple molecular dialogues that take place underground between microorganisms and between plants and its rhizosphere microbiota and to show that synergy in favour of phytobeneficial gene expression may exist between different bacterial species. We assessed the expression of phytobeneficial genes, phlD, hcnA and acdS, and iron‐small regulatory RNAs prrF1 and prrF2 in Pseudomonas brassicacearum co‐cultivated with three phytopathogenic fungi, and two rhizobacteria in the presence or absence of Brassica napus, and in relation to iron availability. Our study illustrates that interkingdom and interspecies interactions in addition to external factors may affect the success of introduced beneficial microorganisms by modulating the expression of phytobeneficial genes.
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Affiliation(s)
- Arnaud Laveilhé
- Lab Microbial Ecology of the Rhizosphere (LEMiRE), CEA, CNRS, BIAM, Aix Marseille Univ, Saint-Paul-Lez-Durance, F-13108, France
| | - Sylvain Fochesato
- Lab Microbial Ecology of the Rhizosphere (LEMiRE), CEA, CNRS, BIAM, Aix Marseille Univ, Saint-Paul-Lez-Durance, F-13108, France
| | - David Lalaouna
- ARN UPR 9002, Université de Strasbourg, CNRS, Strasbourg, F-67000, France
| | - Thierry Heulin
- Lab Microbial Ecology of the Rhizosphere (LEMiRE), CEA, CNRS, BIAM, Aix Marseille Univ, Saint-Paul-Lez-Durance, F-13108, France
| | - Wafa Achouak
- Lab Microbial Ecology of the Rhizosphere (LEMiRE), CEA, CNRS, BIAM, Aix Marseille Univ, Saint-Paul-Lez-Durance, F-13108, France
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16
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Gao G, Zhang Y, Niu S, Chen Y, Wang S, Anwar N, Chen S, Li G, Ma T. Reclassification of Enterobacter sp. FY-07 as Kosakonia oryzendophytica FY-07 and Its Potential to Promote Plant Growth. Microorganisms 2022; 10:microorganisms10030575. [PMID: 35336150 PMCID: PMC8951479 DOI: 10.3390/microorganisms10030575] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/01/2022] [Accepted: 03/01/2022] [Indexed: 02/04/2023] Open
Abstract
Precise classification of bacteria facilitates prediction of their ecological niche. The genus Enterobacter includes pathogens of plants and animals but also beneficial bacteria that may require reclassification. Here, we propose reclassification of Enterobacter FY-07 (FY-07), a strain that has many plant-growth-promoting traits and produces bacterial cellulose (BC), to the Kosakonia genera. To re-examine the taxonomic position of FY-07, a polyphasic approach including 16S rRNA gene sequence analysis, ATP synthase β subunit (atpD) gene sequence analysis, DNA gyrase (gyrB) gene sequence analysis, initiation translation factor 2 (infB) gene sequence analysis, RNA polymerase β subunit (rpoB) gene sequence analysis, determination of DNA G + C content, average nucleotide identity based on BLAST, in silico DNA–DNA hybridization and analysis of phenotypic features was applied. This polyphasic analysis suggested that Enterobacter sp. FY-07 should be reclassified as Kosakonia oryzendophytica FY-07. In addition, the potential of FY-07 to promote plant growth was also investigated by detecting related traits and the colonization of FY-07 in rice roots.
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Affiliation(s)
- Ge Gao
- Key Laboratory of Molecular Microbiology and Technology, College of Life Sciences, Nankai University, Ministry of Education, Tianjin 300071, China; (G.G.); (Y.Z.); (S.N.); (Y.C.); (S.W.); (N.A.); (S.C.)
| | - Yan Zhang
- Key Laboratory of Molecular Microbiology and Technology, College of Life Sciences, Nankai University, Ministry of Education, Tianjin 300071, China; (G.G.); (Y.Z.); (S.N.); (Y.C.); (S.W.); (N.A.); (S.C.)
| | - Shaofang Niu
- Key Laboratory of Molecular Microbiology and Technology, College of Life Sciences, Nankai University, Ministry of Education, Tianjin 300071, China; (G.G.); (Y.Z.); (S.N.); (Y.C.); (S.W.); (N.A.); (S.C.)
| | - Yu Chen
- Key Laboratory of Molecular Microbiology and Technology, College of Life Sciences, Nankai University, Ministry of Education, Tianjin 300071, China; (G.G.); (Y.Z.); (S.N.); (Y.C.); (S.W.); (N.A.); (S.C.)
| | - Shaojing Wang
- Key Laboratory of Molecular Microbiology and Technology, College of Life Sciences, Nankai University, Ministry of Education, Tianjin 300071, China; (G.G.); (Y.Z.); (S.N.); (Y.C.); (S.W.); (N.A.); (S.C.)
| | - Nusratgul Anwar
- Key Laboratory of Molecular Microbiology and Technology, College of Life Sciences, Nankai University, Ministry of Education, Tianjin 300071, China; (G.G.); (Y.Z.); (S.N.); (Y.C.); (S.W.); (N.A.); (S.C.)
| | - Shuai Chen
- Key Laboratory of Molecular Microbiology and Technology, College of Life Sciences, Nankai University, Ministry of Education, Tianjin 300071, China; (G.G.); (Y.Z.); (S.N.); (Y.C.); (S.W.); (N.A.); (S.C.)
| | - Guoqiang Li
- Key Laboratory of Molecular Microbiology and Technology, College of Life Sciences, Nankai University, Ministry of Education, Tianjin 300071, China; (G.G.); (Y.Z.); (S.N.); (Y.C.); (S.W.); (N.A.); (S.C.)
- Tianjin Engineering Technology Center of Green Manufacturing Biobased Materials, Tianjin 300071, China
- Correspondence: (G.L.); (T.M.); Tel./Fax: +86-22-2350-8870 (T.M.)
| | - Ting Ma
- Key Laboratory of Molecular Microbiology and Technology, College of Life Sciences, Nankai University, Ministry of Education, Tianjin 300071, China; (G.G.); (Y.Z.); (S.N.); (Y.C.); (S.W.); (N.A.); (S.C.)
- Tianjin Engineering Technology Center of Green Manufacturing Biobased Materials, Tianjin 300071, China
- Correspondence: (G.L.); (T.M.); Tel./Fax: +86-22-2350-8870 (T.M.)
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17
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Lips D. Fuelling the future of sustainable sugar fermentation across generations. ENGINEERING BIOLOGY 2022; 6:3-16. [PMID: 36968555 PMCID: PMC9995162 DOI: 10.1049/enb2.12017] [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: 10/08/2021] [Revised: 11/15/2021] [Accepted: 11/21/2021] [Indexed: 11/20/2022] Open
Abstract
Biomanufacturing in the form of industrial sugar fermentation is moving beyond pharmaceuticals and biofuels into chemicals, materials, and food ingredients. As the production scale of these increasingly consumer-facing applications expands over the next decades, considerations regarding the environmental impact of the renewable biomass feedstocks used to extract fermentable sugars will become more important. Sugars derived from first-generation biomass in the form of, for example, corn and sugarcane are easily accessible and support high-yield fermentation processes, but are associated with the environmental impacts of industrial agriculture, land use, and competition with other applications in food and feed. Fermentable sugars can also be extracted from second- and third-generation feedstocks in the form of lignocellulose and macroalgae, respectively, potentially overcoming some of these concerns. Doing so, however, comes with various challenges, including the need for more extensive pretreatment processes and the fermentation of mixed and unconventional sugars. In this review, we provide a broad overview of these three generations of biomass feedstocks, outlining their challenges and prospects for fuelling the industrial fermentation industry throughout the 21st century.
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18
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Bi 2S 3 quantum dots in situ grown on MoS 2 nanoflowers: An efficient electron-rich interface for photoelectrochemical N 2 reduction. J Colloid Interface Sci 2021; 611:294-305. [PMID: 34954605 DOI: 10.1016/j.jcis.2021.12.096] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 12/27/2022]
Abstract
Photoelectrocatalysis is considered a green, environmentally friendly, sustainable technology for NH3 synthesis. However, the low efficiency of ammonia synthesis is currently the primary problem in photoelectrochemical nitrogen reduction reactions (PEC NRR). Herein, a nanocomposite BQD/MS developed through the in-situ growth of Bi2S3 quantum dots (BQD) on MoS2 (MS) nanoflowers was demonstrated as an efficient PEC NRR catalyst. Experimental results showed that the strong interaction between BQD and MS modulated the interfacial charge distribution and increased the electron density on the MS side. Meanwhile, the excellent structure of BQD/MS promoted the effective migration of photogenerated electrons from excited BQD to the MS surface. The electron-rich MS reaction interface was conducive to cleaving the stable NN bond and improving the N2 reduction performance. As a result, the prepared BQD/15MS photocathode obtained an excellent Faradaic efficiency of 33.2% and an NH3 yield of 18.5 μg h-1 mg-1, which was about three times that of bare MS.
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19
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Wen A, Havens KL, Bloch SE, Shah N, Higgins DA, Davis-Richardson AG, Sharon J, Rezaei F, Mohiti-Asli M, Johnson A, Abud G, Ane JM, Maeda J, Infante V, Gottlieb SS, Lorigan JG, Williams L, Horton A, McKellar M, Soriano D, Caron Z, Elzinga H, Graham A, Clark R, Mak SM, Stupin L, Robinson A, Hubbard N, Broglie R, Tamsir A, Temme K. Enabling Biological Nitrogen Fixation for Cereal Crops in Fertilized Fields. ACS Synth Biol 2021; 10:3264-3277. [PMID: 34851109 DOI: 10.1021/acssynbio.1c00049] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Agricultural productivity relies on synthetic nitrogen fertilizers, yet half of that reactive nitrogen is lost to the environment. There is an urgent need for alternative nitrogen solutions to reduce the water pollution, ozone depletion, atmospheric particulate formation, and global greenhouse gas emissions associated with synthetic nitrogen fertilizer use. One such solution is biological nitrogen fixation (BNF), a component of the complex natural nitrogen cycle. BNF application to commercial agriculture is currently limited by fertilizer use and plant type. This paper describes the identification, development, and deployment of the first microbial product optimized using synthetic biology tools to enable BNF for corn (Zea mays) in fertilized fields, demonstrating the successful, safe commercialization of root-associated diazotrophs and realizing the potential of BNF to replace and reduce synthetic nitrogen fertilizer use in production agriculture. Derived from a wild nitrogen-fixing microbe isolated from agricultural soils, Klebsiella variicola 137-1036 ("Kv137-1036") retains the capacity of the parent strain to colonize corn roots while increasing nitrogen fixation activity 122-fold in nitrogen-rich environments. This technical milestone was then commercialized in less than half of the time of a traditional biological product, with robust biosafety evaluations and product formulations contributing to consumer confidence and ease of use. Tested in multi-year, multi-site field trial experiments throughout the U.S. Corn Belt, fields grown with Kv137-1036 exhibited both higher yields (0.35 ± 0.092 t/ha ± SE or 5.2 ± 1.4 bushels/acre ± SE) and reduced within-field yield variance by 25% in 2018 and 8% in 2019 compared to fields fertilized with synthetic nitrogen fertilizers alone. These results demonstrate the capacity of a broad-acre BNF product to fix nitrogen for corn in field conditions with reliable agronomic benefits.
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Affiliation(s)
- Amy Wen
- Pivot Bio, Berkeley, California 94710, United States
| | | | - Sarah E. Bloch
- Morrison & Foerster LLP, San Francisco, California 94105, United States
| | - Neal Shah
- Pivot Bio, Berkeley, California 94710, United States
| | | | | | - Judee Sharon
- University of Minnesota─Twin Cities, Minneapolis, Minnesota 55401, United States
| | | | | | | | - Gabriel Abud
- Tempo Automation, San Francisco, California 94103, United States
| | - Jean-Michel Ane
- University of Minnesota─Twin Cities, Minneapolis, Minnesota 55401, United States
| | - Junko Maeda
- University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Valentina Infante
- University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | | | | | | | - Alana Horton
- Pivot Bio, Berkeley, California 94710, United States
| | | | | | - Zoe Caron
- Pivot Bio, Berkeley, California 94710, United States
| | | | - Ashley Graham
- Olema Oncology, San Francisco, California 94107, United States
| | | | - San-Ming Mak
- Pivot Bio, Berkeley, California 94710, United States
| | - Laura Stupin
- Pivot Bio, Berkeley, California 94710, United States
| | | | | | | | - Alvin Tamsir
- Pivot Bio, Berkeley, California 94710, United States
| | - Karsten Temme
- Pivot Bio, Berkeley, California 94710, United States
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20
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Connolly JA, Harcombe WR, Smanski MJ, Kinkel LL, Takano E, Breitling R. Harnessing intercellular signals to engineer the soil microbiome. Nat Prod Rep 2021; 39:311-324. [PMID: 34850800 DOI: 10.1039/d1np00034a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: Focus on 2015 to 2020Plant and soil microbiomes consist of diverse communities of organisms from across kingdoms and can profoundly affect plant growth and health. Natural product-based intercellular signals govern important interactions between microbiome members that ultimately regulate their beneficial or harmful impacts on the plant. Exploiting these evolved signalling circuits to engineer microbiomes towards beneficial interactions with crops is an attractive goal. There are few reports thus far of engineering the intercellular signalling of microbiomes, but this article argues that it represents a tremendous opportunity for advancing the field of microbiome engineering. This could be achieved through the selection of synergistic consortia in combination with genetic engineering of signal pathways to realise an optimised microbiome.
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Affiliation(s)
- Jack A Connolly
- Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, Faculty of Science and Engineering, School of Natural Sciences, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.
| | - William R Harcombe
- BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, MN55108, USA.,Department of Evolution, and Behaviour, University of Minnesota, Twin-Cities Saint Paul, MN55108, USA
| | - Michael J Smanski
- BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, MN55108, USA.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Twin-Cities, Saint Paul, MN55108, USA
| | - Linda L Kinkel
- BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, MN55108, USA.,Department of Plant Pathology, University of Minnesota, Twin-Cities, Saint Paul, MN 55108, USA
| | - Eriko Takano
- Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, Faculty of Science and Engineering, School of Natural Sciences, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, Faculty of Science and Engineering, School of Natural Sciences, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.
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21
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Li J, Pan H, Yang H, Wang C, Liu H, Zhou H, Li P, Li C, Lu X, Tian Y. Rhamnolipid Enhances the Nitrogen Fixation Activity of Azotobacter chroococcum by Influencing Lysine Succinylation. Front Microbiol 2021; 12:697963. [PMID: 34394039 PMCID: PMC8360865 DOI: 10.3389/fmicb.2021.697963] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/28/2021] [Indexed: 11/23/2022] Open
Abstract
The enhancement of nitrogen fixation activity of diazotrophs is essential for safe crop production. Lysine succinylation (KSuc) is widely present in eukaryotes and prokaryotes and regulates various biological process. However, knowledge of the extent of KSuc in nitrogen fixation of Azotobacter chroococcum is scarce. In this study, we found that 250 mg/l of rhamnolipid (RL) significantly increased the nitrogen fixation activity of A. chroococcum by 39%, as compared with the control. Real-time quantitative reverse transcription PCR (qRT-PCR) confirmed that RL could remarkably increase the transcript levels of nifA and nifHDK genes. In addition, a global KSuc of A. chroococcum was profiled using a 4D label-free quantitative proteomic approach. In total, 5,008 KSuc sites were identified on 1,376 succinylated proteins. Bioinformatics analysis showed that the addition of RL influence on the KSuc level, and the succinylated proteins were involved in various metabolic processes, particularly enriched in oxidative phosphorylation, tricarboxylic acid cycle (TCA) cycle, and nitrogen metabolism. Meanwhile, multiple succinylation sites on MoFe protein (NifDK) may influence nitrogenase activity. These results would provide an experimental basis for the regulation of biological nitrogen fixation with KSuc and shed new light on the mechanistic study of nitrogen fixation.
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Affiliation(s)
- Jin Li
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Hu Pan
- Institute of Agricultural Product Quality Standard and Testing Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Hui Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Chong Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Huhu Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Hui Zhou
- College of Food Science and Technology, Hunan Agricultural University, Changsha, China
| | - Peiwang Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
| | - Changzhu Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
| | - Xiangyang Lu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Yun Tian
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
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22
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Agoussar A, Yergeau E. Engineering the plant microbiota in the context of the theory of ecological communities. Curr Opin Biotechnol 2021; 70:220-225. [PMID: 34217124 DOI: 10.1016/j.copbio.2021.06.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 06/09/2021] [Accepted: 06/14/2021] [Indexed: 10/21/2022]
Abstract
Crop-associated microorganisms are known to have a determining influence on crop growth and resistance to stresses. Indeed, microorganisms can deter pathogens, reduce stress levels, improve nutrition, and stimulate growth. However, the microbial communities associated with a plant are rarely optimal for agricultural needs. But how can we engineer crops-associated microbial communities? An interesting framework to address this question is the theory of ecological communities that stipulates four processes by which communities can change: 1) selection, 2) dispersal, 3) speciation and 4) ecological drift. Of these, speciation and dispersal can result in the addition of new species to the plant microbiota, whereas selection and drift can lead to the loss of species. We believe that if these mechanisms are sufficiently understood, they could be harnessed to purposefully engineer the crop microbiota. Here, we will discuss the recent efforts to modify the phenotype of plants that are aligned with these ecological processes.
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Affiliation(s)
- Asmaâ Agoussar
- Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada
| | - Etienne Yergeau
- Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada.
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23
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Bueno Batista M, Brett P, Appia-Ayme C, Wang YP, Dixon R. Disrupting hierarchical control of nitrogen fixation enables carbon-dependent regulation of ammonia excretion in soil diazotrophs. PLoS Genet 2021; 17:e1009617. [PMID: 34111137 PMCID: PMC8219145 DOI: 10.1371/journal.pgen.1009617] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/22/2021] [Accepted: 05/23/2021] [Indexed: 12/14/2022] Open
Abstract
The energetic requirements for biological nitrogen fixation necessitate stringent regulation of this process in response to diverse environmental constraints. To ensure that the nitrogen fixation machinery is expressed only under appropriate physiological conditions, the dedicated NifL-NifA regulatory system, prevalent in Proteobacteria, plays a crucial role in integrating signals of the oxygen, carbon and nitrogen status to control transcription of nitrogen fixation (nif) genes. Greater understanding of the intricate molecular mechanisms driving transcriptional control of nif genes may provide a blueprint for engineering diazotrophs that associate with cereals. In this study, we investigated the properties of a single amino acid substitution in NifA, (NifA-E356K) which disrupts the hierarchy of nif regulation in response to carbon and nitrogen status in Azotobacter vinelandii. The NifA-E356K substitution enabled overexpression of nitrogenase in the presence of excess fixed nitrogen and release of ammonia outside the cell. However, both of these properties were conditional upon the nature of the carbon source. Our studies reveal that the uncoupling of nitrogen fixation from its assimilation is likely to result from feedback regulation of glutamine synthetase, allowing surplus fixed nitrogen to be excreted. Reciprocal substitutions in NifA from other Proteobacteria yielded similar properties to the A. vinelandii counterpart, suggesting that this variant protein may facilitate engineering of carbon source-dependent ammonia excretion amongst diverse members of this family.
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Affiliation(s)
| | - Paul Brett
- Department of Metabolic Biology, John Innes Centre, Norwich, United Kingdom
| | - Corinne Appia-Ayme
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Yi-Ping Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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24
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Goyal RK, Schmidt MA, Hynes MF. Molecular Biology in the Improvement of Biological Nitrogen Fixation by Rhizobia and Extending the Scope to Cereals. Microorganisms 2021; 9:microorganisms9010125. [PMID: 33430332 PMCID: PMC7825764 DOI: 10.3390/microorganisms9010125] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 12/29/2020] [Accepted: 01/06/2021] [Indexed: 11/16/2022] Open
Abstract
The contribution of biological nitrogen fixation to the total N requirement of food and feed crops diminished in importance with the advent of synthetic N fertilizers, which fueled the “green revolution”. Despite being environmentally unfriendly, the synthetic versions gained prominence primarily due to their low cost, and the fact that most important staple crops never evolved symbiotic associations with bacteria. In the recent past, advances in our knowledge of symbiosis and nitrogen fixation and the development and application of recombinant DNA technology have created opportunities that could help increase the share of symbiotically-driven nitrogen in global consumption. With the availability of molecular biology tools, rapid improvements in symbiotic characteristics of rhizobial strains became possible. Further, the technology allowed probing the possibility of establishing a symbiotic dialogue between rhizobia and cereals. Because the evolutionary process did not forge a symbiotic relationship with the latter, the potential of molecular manipulations has been tested to incorporate a functional mechanism of nitrogen reduction independent of microbes. In this review, we discuss various strategies applied to improve rhizobial strains for higher nitrogen fixation efficiency, more competitiveness and enhanced fitness under unfavorable environments. The challenges and progress made towards nitrogen self-sufficiency of cereals are also reviewed. An approach to integrate the genetically modified elite rhizobia strains in crop production systems is highlighted.
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Affiliation(s)
- Ravinder K. Goyal
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB T4L 1W1, Canada;
- Correspondence:
| | - Maria Augusta Schmidt
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB T4L 1W1, Canada;
- Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada;
| | - Michael F. Hynes
- Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada;
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25
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Danielson N, McKay S, Bloom P, Dunn J, Jakel N, Bauer T, Hannon J, Jewett MC, Shanks B. Industrial Biotechnology—An Industry at an Inflection Point. Ind Biotechnol (New Rochelle N Y) 2020. [DOI: 10.1089/ind.2020.29230.nda] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Sarah McKay
- National Corn Growers Association, St. Charles, MO, USA
| | - Paul Bloom
- Archer Daniels Midland Co., Decatur, IL, USA
| | - Jennifer Dunn
- Northwestern University, Evanston, IL, USA
- Northwestern Argonne Institute of Science and Engineering, Evanston, IL, USA
| | - Neal Jakel
- Fluid Quip Technologies, Cedar Rapids, IA, USA
| | | | | | - Michael C. Jewett
- Northwestern University, Evanston, IL, USA
- Northwestern Argonne Institute of Science and Engineering, Evanston, IL, USA
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26
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Ke J, Wang B, Yoshikuni Y. Microbiome Engineering: Synthetic Biology of Plant-Associated Microbiomes in Sustainable Agriculture. Trends Biotechnol 2020; 39:244-261. [PMID: 32800605 DOI: 10.1016/j.tibtech.2020.07.008] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 12/28/2022]
Abstract
To support an ever-increasing population, modern agriculture faces numerous challenges that pose major threats to global food and energy security. Plant-associated microbes, with their many plant growth-promoting (PGP) traits, have enormous potential in helping to solve these challenges. However, the results of their use in agriculture have been variable, probably because of poor colonization. Phytomicrobiome engineering is an emerging field of synthetic biology that may offer ways to alleviate this limitation. This review highlights recent advances in both bottom-up and top-down approaches to engineering non-model bacteria and microbiomes to promote beneficial plant-microbe interactions, as well as advances in strategies to evaluate these interactions. Biosafety, biosecurity, and biocontainment strategies to address the environmental concerns associated with field use of synthetic microbes are also discussed.
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Affiliation(s)
- Jing Ke
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Bing Wang
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yasuo Yoshikuni
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Global Institution for Collaborative Research and Education, Hokkaido University, Hokkaido 060-8589, Japan.
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27
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Park Y, Espah Borujeni A, Gorochowski TE, Shin J, Voigt CA. Precision design of stable genetic circuits carried in highly-insulated E. coli genomic landing pads. Mol Syst Biol 2020; 16:e9584. [PMID: 32812710 PMCID: PMC7436927 DOI: 10.15252/msb.20209584] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 07/07/2020] [Accepted: 07/22/2020] [Indexed: 01/02/2023] Open
Abstract
Genetic circuits have many applications, from guiding living therapeutics to ordering process in a bioreactor, but to be useful they have to be genetically stable and not hinder the host. Encoding circuits in the genome reduces burden, but this decreases performance and can interfere with native transcription. We have designed genomic landing pads in Escherichia coli at high-expression sites, flanked by ultrastrong double terminators. DNA payloads >8 kb are targeted to the landing pads using phage integrases. One landing pad is dedicated to carrying a sensor array, and two are used to carry genetic circuits. NOT/NOR gates based on repressors are optimized for the genome and characterized in the landing pads. These data are used, in conjunction with design automation software (Cello 2.0), to design circuits that perform quantitatively as predicted. These circuits require fourfold less RNA polymerase than when carried on a plasmid and are stable for weeks in a recA+ strain without selection. This approach enables the design of synthetic regulatory networks to guide cells in environments or for applications where plasmid use is infeasible.
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Affiliation(s)
- Yongjin Park
- Synthetic Biology CenterDepartment of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Amin Espah Borujeni
- Synthetic Biology CenterDepartment of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Thomas E Gorochowski
- Synthetic Biology CenterDepartment of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Broad Institute of MIT and HarvardCambridgeMAUSA
| | - Jonghyeon Shin
- Synthetic Biology CenterDepartment of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Christopher A Voigt
- Synthetic Biology CenterDepartment of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Broad Institute of MIT and HarvardCambridgeMAUSA
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28
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Xu G, Takahashi H. Improving nitrogen use efficiency: from cells to plant systems. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4359-4364. [PMID: 32710784 DOI: 10.1093/jxb/eraa309] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Affiliation(s)
- Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- China MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing, China
| | - Hideki Takahashi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, USA
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