151
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Huisman R, Geurts R. A Roadmap toward Engineered Nitrogen-Fixing Nodule Symbiosis. PLANT COMMUNICATIONS 2020; 1:100019. [PMID: 33404552 PMCID: PMC7748023 DOI: 10.1016/j.xplc.2019.100019] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/06/2019] [Accepted: 12/27/2019] [Indexed: 05/26/2023]
Abstract
In the late 19th century, it was discovered that legumes can establish a root nodule endosymbiosis with nitrogen-fixing rhizobia. Soon after, the question was raised whether it is possible to transfer this trait to non-leguminous crops. In the past century, an ever-increasing amount of knowledge provided unique insights into the cellular, molecular, and genetic processes controlling this endosymbiosis. In addition, recent phylogenomic studies uncovered several genes that evolved to function specifically to control nodule formation and bacterial infection. However, despite this massive body of knowledge, the long-standing objective to engineer the nitrogen-fixing nodulation trait on non-leguminous crop plants has not been achieved yet. In this review, the unsolved questions and engineering strategies toward nitrogen-fixing nodulation in non-legume plants are discussed and highlighted.
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Affiliation(s)
- Rik Huisman
- Wageningen University, Department of Plant Sciences, Laboratory of Molecular Biology, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Rene Geurts
- Wageningen University, Department of Plant Sciences, Laboratory of Molecular Biology, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
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152
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Current Progress in Nitrogen Fixing Plants and Microbiome Research. PLANTS 2020; 9:plants9010097. [PMID: 31940996 PMCID: PMC7020401 DOI: 10.3390/plants9010097] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/02/2020] [Accepted: 01/08/2020] [Indexed: 01/10/2023]
Abstract
In agroecosystems, nitrogen is one of the major nutrients limiting plant growth. To meet the increased nitrogen demand in agriculture, synthetic fertilizers have been used extensively in the latter part of the twentieth century, which have led to environmental challenges such as nitrate pollution. Biological nitrogen fixation (BNF) in plants is an essential mechanism for sustainable agricultural production and healthy ecosystem functioning. BNF by legumes and associative, endosymbiotic, and endophytic nitrogen fixation in non-legumes play major roles in reducing the use of synthetic nitrogen fertilizer in agriculture, increased plant nutrient content, and soil health reclamation. This review discusses the process of nitrogen-fixation in plants, nodule formation, the genes involved in plant-rhizobia interaction, and nitrogen-fixing legume and non-legume plants. This review also elaborates on current research efforts involved in transferring nitrogen-fixing mechanisms from legumes to non-legumes, especially to economically important crops such as rice, maize, and wheat at the molecular level and relevant other techniques involving the manipulation of soil microbiome for plant benefits in the non-legume root environment.
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153
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Del Valle I, Webster TM, Cheng HY, Thies JE, Kessler A, Miller MK, Ball ZT, MacKenzie KR, Masiello CA, Silberg JJ, Lehmann J. Soil organic matter attenuates the efficacy of flavonoid-based plant-microbe communication. SCIENCE ADVANCES 2020; 6:eaax8254. [PMID: 32064339 PMCID: PMC6989149 DOI: 10.1126/sciadv.aax8254] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 11/22/2019] [Indexed: 05/07/2023]
Abstract
Plant-microbe interactions are mediated by signaling compounds that control vital plant functions, such as nodulation, defense, and allelopathy. While interruption of signaling is typically attributed to biological processes, potential abiotic controls remain less studied. Here, we show that higher organic carbon (OC) contents in soils repress flavonoid signals by up to 70%. Furthermore, the magnitude of repression is differentially dependent on the chemical structure of the signaling molecule, the availability of metal ions, and the source of the plant-derived OC. Up to 63% of the signaling repression occurs between dissolved OC and flavonoids rather than through flavonoid sorption to particulate OC. In plant experiments, OC interrupts the signaling between a legume and a nitrogen-fixing microbial symbiont, resulting in a 75% decrease in nodule formation. Our results suggest that soil OC decreases the lifetime of flavonoids underlying plant-microbe interactions.
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Affiliation(s)
- Ilenne Del Valle
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, 6100 Main Street, MS 180, Houston, TX 77005, USA
- Corresponding author. (I.D.V.); (T.M.W.)
| | - Tara M. Webster
- Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
- Corresponding author. (I.D.V.); (T.M.W.)
| | - Hsiao-Ying Cheng
- Department of Bioengineering, Rice University, 6100 Main Street, MS 142, Houston, TX 77005, USA
| | - Janice E. Thies
- Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
- Atkinson Center for a Sustainable Future, Cornell University, Ithaca, NY 14853, USA
| | - André Kessler
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Mary Kaitlyn Miller
- Department of Chemistry, Rice University, 6100 Main Street, MS 60, Houston, TX 77005, USA
| | - Zachary T. Ball
- Department of Chemistry, Rice University, 6100 Main Street, MS 60, Houston, TX 77005, USA
| | - Kevin R. MacKenzie
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Caroline A. Masiello
- Department of Chemistry, Rice University, 6100 Main Street, MS 60, Houston, TX 77005, USA
- Department of Earth, Environmental and Planetary Sciences, Rice University, MS 126, Houston, TX 77005, USA
- Department of BioSciences, Rice University, 6100 Main Street, MS 140, Houston, TX 77005, USA
| | - Jonathan J. Silberg
- Department of Bioengineering, Rice University, 6100 Main Street, MS 142, Houston, TX 77005, USA
- Department of BioSciences, Rice University, 6100 Main Street, MS 140, Houston, TX 77005, USA
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, MS 362, Houston, TX 77005, USA
| | - Johannes Lehmann
- Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
- Atkinson Center for a Sustainable Future, Cornell University, Ithaca, NY 14853, USA
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154
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Nag P, Shriti S, Das S. Microbiological strategies for enhancing biological nitrogen fixation in nonlegumes. J Appl Microbiol 2020; 129:186-198. [PMID: 31858682 DOI: 10.1111/jam.14557] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/12/2019] [Accepted: 12/16/2019] [Indexed: 01/17/2023]
Abstract
In an agro-ecosystem, industrially produced nitrogenous fertilizers are the principal sources of nitrogen for plant growth; unfortunately these also serve as the leading sources of pollution. Hence, it becomes imperative to find pollution-free methods of providing nitrogen to crop plants. A diverse group of free-living, plant associative and symbiotic prokaryotes are able to perform biological nitrogen fixation (BNF). BNF is a two component process involving the nitrogen fixing diazotrophs and the host plant. Symbiotic nitrogen fixation is most efficient as it can fix nitrogen inside the nodule formed on the roots of the plant; delivering nitrogen directly to the host. However, most of the important crop plants are nonleguminous and are unable to form symbiotic associations. In this context, the plant associative and endophytic diazotrophs assume importance. BNF in nonlegumes can be encouraged either through the transfer of BNF traits from legumes or by elevating the nitrogen fixing capacity of the associative and endophytic diazotrophs. In this review we discuss mainly the microbiological strategies which may be used in nonleguminous crops for enhancement of BNF.
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Affiliation(s)
- P Nag
- Division of Plant Biology, Bose Institute, Kolkata, West Bengal, India
| | - S Shriti
- Division of Plant Biology, Bose Institute, Kolkata, West Bengal, India
| | - S Das
- Division of Plant Biology, Bose Institute, Kolkata, West Bengal, India
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155
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Reinprecht Y, Schram L, Marsolais F, Smith TH, Hill B, Pauls KP. Effects of Nitrogen Application on Nitrogen Fixation in Common Bean Production. FRONTIERS IN PLANT SCIENCE 2020; 11:1172. [PMID: 32849727 PMCID: PMC7424037 DOI: 10.3389/fpls.2020.01172] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/20/2020] [Indexed: 05/13/2023]
Abstract
The nitrogen fixing ability of common bean (Phaseolus vulgaris L.) in association with rhizobia is often characterized as poor compared to other legumes, and nitrogen fertilizers are commonly used in bean production to achieve high yields, which in general inhibits nitrogen fixation. In addition, plants cannot take up all the nitrogen applied to the soil as a fertilizer leading to runoff and groundwater contamination. The overall objective of this work is to reduce use of nitrogen fertilizer in common bean production. This would be a major advance in profitability for the common bean industry in Canada and would significantly improve the ecological footprint of the crop. In the current work, 22 bean genotypes [including recombinant inbred lines (RILs) from the Mist × Sanilac population and a non-nodulating mutant (R99)] were screened for their capacity to fix atmospheric nitrogen under four nitrogen regimes. The genotypes were evaluated in replicated field trials on N-poor soils over three years for the percent nitrogen derived from atmosphere (%Ndfa), yield, and a number of yield-related traits. Bean genotypes differed for all analyzed traits, and the level of nitrogen significantly affected most of the traits, including %Ndfa and yield in all three years. In contrast, application of rhizobia significantly affected only few traits, and the effect was inconsistent among the years. Nitrogen application reduced symbiotic nitrogen fixation (SNF) to various degrees in different bean genotypes. This variation suggests that SNF in common bean can be improved through breeding and selection for the ability of bean genotypes to fix nitrogen in the presence of reduced fertilizer levels. Moreover, genotypes like RIL_38, RIL_119, and RIL_131, being both high yielding and good nitrogen fixers, have potential for simultaneous improvement of both traits. However, breeding advancement might be slow due to an inconsistent correlation between these traits.
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Affiliation(s)
- Yarmilla Reinprecht
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
- *Correspondence: Yarmilla Reinprecht,
| | - Lyndsay Schram
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Frédéric Marsolais
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Thomas H. Smith
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Brett Hill
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Karl Peter Pauls
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
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156
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Sahruzaini NA, Rejab NA, Harikrishna JA, Khairul Ikram NK, Ismail I, Kugan HM, Cheng A. Pulse Crop Genetics for a Sustainable Future: Where We Are Now and Where We Should Be Heading. FRONTIERS IN PLANT SCIENCE 2020; 11:531. [PMID: 32431724 PMCID: PMC7212832 DOI: 10.3389/fpls.2020.00531] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/07/2020] [Indexed: 05/12/2023]
Abstract
The last decade has witnessed dramatic changes in global food consumption patterns mainly because of population growth and economic development. Food substitutions for healthier eating, such as swapping regular servings of meat for protein-rich crops, is an emerging diet trend that may shape the future of food systems and the environment worldwide. To meet the erratic consumer demand in a rapidly changing world where resources become increasingly scarce due largely to anthropogenic activity, the need to develop crops that benefit both human health and the environment has become urgent. Legumes are often considered to be affordable plant-based sources of dietary proteins. Growing legumes provides significant benefits to cropping systems and the environment because of their natural ability to perform symbiotic nitrogen fixation, which enhances both soil fertility and water-use efficiency. In recent years, the focus in legume research has seen a transition from merely improving economically important species such as soybeans to increasingly turning attention to some promising underutilized species whose genetic resources hold the potential to address global challenges such as food security and climate change. Pulse crops have gained in popularity as an affordable source of food or feed; in fact, the United Nations designated 2016 as the International Year of Pulses, proclaiming their critical role in enhancing global food security. Given that many studies have been conducted on numerous underutilized pulse crops across the world, we provide a systematic review of the related literature to identify gaps and opportunities in pulse crop genetics research. We then discuss plausible strategies for developing and using pulse crops to strengthen food and nutrition security in the face of climate and anthropogenic changes.
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Affiliation(s)
- Nurul Amylia Sahruzaini
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Nur Ardiyana Rejab
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Jennifer Ann Harikrishna
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Nur Kusaira Khairul Ikram
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Ismanizan Ismail
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Hazel Marie Kugan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Acga Cheng
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- *Correspondence: Acga Cheng,
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157
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Medicago-Sinorhizobium-Ralstonia Co-infection Reveals Legume Nodules as Pathogen Confined Infection Sites Developing Weak Defenses. Curr Biol 2020; 30:351-358.e4. [DOI: 10.1016/j.cub.2019.11.066] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/02/2019] [Accepted: 11/21/2019] [Indexed: 11/20/2022]
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158
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Isolation and Proto-cooperation of Pseudomonas putida TS 18 from Water Calyx Fluid of Spathodea campanulata P. Beauv. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.4.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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159
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Aerobic nitrogen-fixing bacteria for hydrogen and ammonium production: current state and perspectives. Appl Microbiol Biotechnol 2019; 104:1383-1399. [PMID: 31879824 DOI: 10.1007/s00253-019-10210-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/16/2019] [Accepted: 10/20/2019] [Indexed: 10/25/2022]
Abstract
Biological nitrogen fixation (BNF) is accomplished through the action of the oxygen-sensitive enzyme nitrogenase. One unique caveat of this reaction is the inclusion of hydrogen gas (H2) evolution as a requirement of the reaction mechanism. In the absence of nitrogen gas as a substrate, nitrogenase will reduce available protons to become a directional ATP-dependent hydrogenase. Aerobic nitrogen-fixing microbes are of particular interest, because these organisms have evolved to perform these reactions with oxygen-sensitive enzymes in an environment surrounded by oxygen. The ability to maintain a functioning nitrogenase in aerobic conditions facilitates the application of these organisms under conditions where most anaerobic nitrogen fixers are excluded. In recent years, questions related to the potential yields of the nitrogenase-derived products ammonium and H2 have grown more approachable to experimentation based on efforts to construct increasingly more complicated strains of aerobic nitrogen fixers such as the obligate aerobe Azotobacter vinelandii. This mini-review provides perspectives of recent and historical efforts to understand and quantify the yields of ammonium and H2 that can be obtained through the model aerobe A. vinelandii, and outstanding questions that remain to be answered to fully realize the potential of nitrogenase in these applications with model aerobic bacteria.
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160
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Ryu MH, Zhang J, Toth T, Khokhani D, Geddes BA, Mus F, Garcia-Costas A, Peters JW, Poole PS, Ané JM, Voigt CA. Control of nitrogen fixation in bacteria that associate with cereals. Nat Microbiol 2019; 5:314-330. [DOI: 10.1038/s41564-019-0631-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 11/04/2019] [Indexed: 12/23/2022]
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161
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Pankievicz VCS, Irving TB, Maia LGS, Ané JM. Are we there yet? The long walk towards the development of efficient symbiotic associations between nitrogen-fixing bacteria and non-leguminous crops. BMC Biol 2019; 17:99. [PMID: 31796086 PMCID: PMC6889567 DOI: 10.1186/s12915-019-0710-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 10/18/2019] [Indexed: 01/09/2023] Open
Abstract
Nitrogen is an essential element of life, and nitrogen availability often limits crop yields. Since the Green Revolution, massive amounts of synthetic nitrogen fertilizers have been produced from atmospheric nitrogen and natural gas, threatening the sustainability of global food production and degrading the environment. There is a need for alternative means of bringing nitrogen to crops, and taking greater advantage of biological nitrogen fixation seems a logical option. Legumes are used in most cropping systems around the world because of the nitrogen-fixing symbiosis with rhizobia. However, the world's three major cereal crops-rice, wheat, and maize-do not associate with rhizobia. In this review, we will survey how genetic approaches in rhizobia and their legume hosts allowed tremendous progress in understanding the molecular mechanisms controlling root nodule symbioses, and how this knowledge paves the way for engineering such associations in non-legume crops. We will also discuss challenges in bringing these systems into the field and how they can be surmounted by interdisciplinary collaborations between synthetic biologists, microbiologists, plant biologists, breeders, agronomists, and policymakers.
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Affiliation(s)
| | - Thomas B Irving
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Lucas G S Maia
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Jean-Michel Ané
- Department of Agronomy, University of Wisconsin, Madison, WI, USA.
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA.
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162
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Díaz-Pereira E, Marín Sanleandro P, Asencio AD. Effects of drought and water pulses on microbial functionality and the role of Cyanoprokaryota in the rhizospheres of gypsophytes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 691:919-932. [PMID: 31326815 DOI: 10.1016/j.scitotenv.2019.07.145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 06/10/2023]
Abstract
In the rhizospheres of three gypsophytes and in non-rhizospheric soil, two samplings were carried out - the first during a summer drought and the second during spring - to detect the responses to the availability of water in the soil. Urease and protease showed higher values after the drought whereas β-glucosidase was highest in the spring. This pattern was the same for all the rhizospheres tested. However, the arylsulfatase and alkaline phosphatase did not change. Surprising results were obtained when water retention and water loss were studied, with the highest values being obtained for the dry season due to the association of Cyanoprokaryota with the rhizospheres. The results are also explained by two water pulses that occurred before the samplings. Several parameters, whose values changed markedly due to the microbiological activation just after the drought and water pulses, are proposed as indicators of this activation: microbial biomass carbon and basal respiration rate, together with urease and protease. However, it was the dehydrogenase activity in spring that best reflected the microbiology associated with the carbon cycle, together with β-glucosidase. The interrelationships between carbon and nitrogen were shown through the indices: water soluble nitrogen and water soluble carbon. We propose three functional adaptation mechanisms of these plants associated with the Cyanoprokaryota in their rhizospheres and related to the water availability as determined by drought and water pulse effects. Herniaria fruticosa is a pioneer with the greatest diversity of Cyanoprokaryota, in both summer and spring (10 species and 11 species, respectively), and with high-medium abundance (5-30%). Teucrium balthazaris exhibits an intermediate strategy, with greater diversity of Cyanoprokaryota in spring (7 species) and predominance of high-medium abundance (5-30%). Finally, Helianthemum squamatum has lower diversity, with one species in summer (with low abundance, <5%) and no species in spring.
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Affiliation(s)
- E Díaz-Pereira
- Soil and Water Conservation Research Group (CEBAS-CSIC), E-30100 Murcia, Spain.
| | - P Marín Sanleandro
- University of Murcia, Faculty of Chemistry, Department of Agricultural Chemistry, Geology and Pedology, E-30100 Murcia, Spain.
| | - A D Asencio
- University Miguel Hernández of Elche, Department of Applied Biology, E-03202 Elche, Spain.
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163
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Wang X, Hsu C, Dubeux JCB, Mackowiak C, Blount A, Han X, Liao H. Effects of rhizoma peanut cultivars ( Arachis glabrata Benth.) on the soil bacterial diversity and predicted function in nitrogen fixation. Ecol Evol 2019; 9:12676-12687. [PMID: 31788206 PMCID: PMC6875664 DOI: 10.1002/ece3.5735] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/25/2022] Open
Abstract
There is a growing awareness of the importance of soil microorganisms in agricultural management practices. Currently, much less is known about whether different crop cultivar has an effect on the taxonomic structure and diversity, and specific functions of soil bacterial communities. Here, we examined the changes of the diversity and composition and enzyme-encoding nitrogenase genes in a long-term field experiment with seven different rhizoma peanut cultivars in southeastern USA, coupling high-throughput 16S rRNA gene sequencing and the sequence-based function prediction with Tax4Fun. Of the 32 phyla detected (Proteobacteria class), 13 were dominant: Acidobacteria, Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Bacteroidetes, Verrucomicrobia, Gammaproteobacteria, Deltaproteobacteria, Gemmatimonadetes, Firmicutes, Nitrospirae, Chloroflexi, and Planctomycetes (relative abundance >1%). We found no evidence that the diversity and composition of bacterial communities were significantly different among different cultivars, but the abundance of some dominant bacterial groups that have N-fixation potentials (at broad or fine taxonomic level) and predicted abundances of some enzyme-encoding nitrogenase genes showed significant across-cultivar differences. The nitrogenase genes were notably abundant in Florigraze and Latitude soils while remarkably lower in Arbook and UF_TITO soils when compared with other cultivars, indicating different nitrogen fixation potentials among different cultivars. The findings also suggest that the abundance of certain bacterial taxa and the specific function bacteria perform in ecosystems can have an inherent association. Our study is helpful to understand how microbiological responses and feedback to different plant genotypes through the variation in structure and function of their communities in the rhizosphere.
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Affiliation(s)
- Xiao‐Bo Wang
- North Florida Research and Education CenterUniversity of FloridaQuincyFLUSA
- Erguna Forest‐Steppe Ecotone Research StationInstitute of Applied EcologyChinese Academy of SciencesShenyangChina
- Key Laboratory of Vegetation EcologyMinistry of EducationNortheast Normal UniversityChangchunChina
| | - Chih‐Ming Hsu
- North Florida Research and Education CenterUniversity of FloridaQuincyFLUSA
| | - José C. B. Dubeux
- North Florida Research and Education CenterUniversity of FloridaMariannaFLUSA
| | - Cheryl Mackowiak
- North Florida Research and Education CenterUniversity of FloridaQuincyFLUSA
| | - Ann Blount
- North Florida Research and Education CenterUniversity of FloridaMariannaFLUSA
| | - Xing‐Guo Han
- Erguna Forest‐Steppe Ecotone Research StationInstitute of Applied EcologyChinese Academy of SciencesShenyangChina
- Institute of BotanyChinese Academy of SciencesBeijingChina
| | - Hui‐Ling Liao
- North Florida Research and Education CenterUniversity of FloridaQuincyFLUSA
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164
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Kumawat KC, Sharma P, Singh I, Sirari A, Gill BS. Co-existence of Leclercia adecarboxylata (LSE-1) and Bradyrhizobium sp. (LSBR-3) in nodule niche for multifaceted effects and profitability in soybean production. World J Microbiol Biotechnol 2019; 35:172. [PMID: 31673798 DOI: 10.1007/s11274-019-2752-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 10/18/2019] [Indexed: 01/06/2023]
Abstract
The present study was designed with the objective of improving growth and nodulation of soybean [Glycine max (L.) Merill] with co-inoculation of native Bradyrhizobium sp. (LSBR-3) (KF906140) and non-rhizobial nodule endophytic diazotroph Leclercia adecarboxylata (LSE-1) (KX925974) with multifunctional plant growth promoting (PGP) traits in cereal based cropping system (Rice-Wheat). A total of 40 endophytic bacteria from cultivated and wild sp. of soybean were screened for multifarious PGP traits and pathogenicity test. Based on PGP traits, antagonistic activities and bio-safety test; L. adecarboxylata (LSE-1) was identified with 16 S rRNA gene sequencing along with the presence of nifH (nitrogen fixation) and ipdc (IAA production) genes. Dual inoculant LSE-1 and LSBR-3 increased indole acetic acid (IAA), P & Zn-solubilization, 1-aminocyclopropane-1-carboxylate deaminase (ACCD) activity, siderophore, biofilm formation and exo-polysaccharides in contrast to single inoculation treatment. Further, assessment of dual inoculant LSBR-3 + LSE-1 improved growth parameters, nodulation, soil enzymes activities, nutrient accumulation and yield as compared to single as well as un-inoculated control treatment under field conditions. Single inoculant LSBR-3 improved yield by 8.84% over control. Further, enhancement of 4.15% grain yield was noticed with LSBR-3 + LSE-1 over LSBR-3 alone treatment. Application of LSBR-3 + LSE-1 gave superior B:C ratio (1.29) and additional income approximately 116 USD ha-1 in contrast to control treatment. The present results thus, is the first report of novel endophytic diazotroph L. adecarboxylata (LSE-1) as PGPR from Indian conditions particularly in Punjab region for exploiting as potential PGPR along with Bradyrhizobium sp. (LSBR-3) in soybean.
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Affiliation(s)
- K C Kumawat
- Department of Microbiology, Punjab Agricultural University, Ludhiana, 141004, India.
| | - Poonam Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, India
| | - Inderjeet Singh
- Department of Microbiology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Asmita Sirari
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, India
| | - B S Gill
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, India
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165
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Abstract
Rhizobia are α- and β-proteobacteria that form a symbiotic partnership with legumes, fixing atmospheric dinitrogen to ammonia and providing it to the plant. Oxygen regulation is key in this symbiosis. Fixation is performed by an oxygen-intolerant nitrogenase enzyme but requires respiration to meet its high energy demands. To satisfy these opposing constraints the symbiotic partners cooperate intimately, employing a variety of mechanisms to regulate and respond to oxygen concentration. During symbiosis rhizobia undergo significant changes in gene expression to differentiate into nitrogen-fixing bacteroids. Legumes host these bacteroids in specialized root organs called nodules. These generate a near-anoxic environment using an oxygen diffusion barrier, oxygen-binding leghemoglobin and control of mitochondria localization. Rhizobia sense oxygen using multiple interconnected systems which enable a finely-tuned response to the wide range of oxygen concentrations they experience when transitioning from soil to nodules. The oxygen-sensing FixL-FixJ and hybrid FixL-FxkR two-component systems activate at relatively high oxygen concentration and regulate fixK transcription. FixK activates the fixNOQP and fixGHIS operons producing a high-affinity terminal oxidase required for bacterial respiration in the microaerobic nodule. Additionally or alternatively, some rhizobia regulate expression of these operons by FnrN, an FNR-like oxygen-sensing protein. The final stage of symbiotic establishment is activated by the NifA protein, regulated by oxygen at both the transcriptional and protein level. A cross-species comparison of these systems highlights differences in their roles and interconnections but reveals common regulatory patterns and themes. Future work is needed to establish the complete regulon of these systems and identify other regulatory signals.
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Affiliation(s)
- Paul J Rutten
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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166
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Wein T, Romero Picazo D, Blow F, Woehle C, Jami E, Reusch TB, Martin WF, Dagan T. Currency, Exchange, and Inheritance in the Evolution of Symbiosis. Trends Microbiol 2019; 27:836-849. [DOI: 10.1016/j.tim.2019.05.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/19/2019] [Accepted: 05/30/2019] [Indexed: 12/28/2022]
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167
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Gifford I, Vance S, Nguyen G, Berry AM. A Stable Genetic Transformation System and Implications of the Type IV Restriction System in the Nitrogen-Fixing Plant Endosymbiont Frankia alni ACN14a. Front Microbiol 2019; 10:2230. [PMID: 31608043 PMCID: PMC6769113 DOI: 10.3389/fmicb.2019.02230] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 09/11/2019] [Indexed: 12/26/2022] Open
Abstract
Genus Frankia is comprised primarily of nitrogen-fixing actinobacteria that form root nodule symbioses with a group of hosts known as the actinorhizal plants. These plants are evolutionarily closely related to the legumes that are nodulated by the rhizobia. Both host groups utilize homologs of nodulation genes for root-nodule symbiosis, derived from common plant ancestors. The corresponding endosymbionts, Frankia and the rhizobia, however, are distantly related groups of bacteria, leading to questions about their symbiotic mechanisms and evolutionary history. To date, a stable system of electrotransformation has been lacking in Frankia despite numerous attempts by research groups worldwide. We have identified type IV methyl-directed restriction systems, highly-expressed in a range of actinobacteria, as a likely barrier to Frankia transformation. Here we report the successful electrotransformation of the model strain F. alni ACN14a with an unmethylated, broad host-range replicating plasmid, expressing chloramphenicol-resistance for selection and GFP as a marker of gene expression. This system circumvented the type IV restriction barrier and allowed the stable maintenance of the plasmid. During nitrogen limitation, Frankia differentiates into two cell types: the vegetative hyphae and nitrogen-fixing vesicles. When the expression of egfp under the control of the nif gene cluster promoter was localized using fluorescence imaging, the expression of nitrogen fixation in nitrogen-limited culture was localized in Frankia vesicles but not in hyphae. The ability to separate gene expression patterns between Frankia hyphae and vesicles will enable deeper comparisons of molecular signaling and metabolic exchange between Frankia-actinorhizal and rhizobia-legume symbioses to be made, and may broaden potential applications in agriculture. Further downstream applications are possible, including gene knock-outs and complementation, to open up a range of experiments in Frankia and its symbioses. Additionally, in the transcriptome of F. alni ACN14a, type IV restriction enzymes were highly expressed in nitrogen-replete culture but their expression strongly decreased during symbiosis. The down-regulation of type IV restriction enzymes in symbiosis suggests that horizontal gene transfer may occur more frequently inside the nodule, with possible new implications for the evolution of Frankia.
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Affiliation(s)
- Isaac Gifford
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
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168
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Andreozzi A, Prieto P, Mercado-Blanco J, Monaco S, Zampieri E, Romano S, Valè G, Defez R, Bianco C. Efficient colonization of the endophytes Herbaspirillum huttiense RCA24 and Enterobacter cloacae RCA25 influences the physiological parameters of Oryza sativa L. cv. Baldo rice. Environ Microbiol 2019; 21:3489-3504. [PMID: 31106946 DOI: 10.1111/1462-2920.14688] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 05/15/2019] [Accepted: 05/17/2019] [Indexed: 11/26/2022]
Abstract
Several important bacterial characteristics, such as biological nitrogen fixation, phosphate solubilization, 1-aminocyclopropane-1-carboxylate deaminase activity and production of siderophores and phytohormones, can be assessed as plant growth promotion traits. Our aim was to evaluate the effects of nitrogen fixing and indole-3-acetic acid (IAA) producing endophytes in two Oryza sativa cultivars (Baldo and Vialone Nano). Three bacteria, Herbaspirillum huttiense RCA24, Enterobacter asburiae RCA23 and Staphylococcus sp. 377, producing different IAA levels, were tested for their ability to enhance nifH gene expression and nitrogenase activity in Enterobacter cloacae RCA25. Results showed that H. huttiense RCA24 performed best. Improvement in nitrogen fixation and changes in physiological parameters such as chlorophyll, nitrogen content and shoot dry weight were observed for plants co-inoculated with strains RCA25 and RCA24 in a 10:1 ratio. Based on confocal laser scanning microscopy analysis, strain RCA24 was the best colonizer of the root interior and the only IAA producer located in the same root niche occupied by RCA25 cells. This work shows that the choice of a bio-inoculum having the right composition is one of the key aspects to be considered for the inoculation of a specific host plant cultivar with microbial consortia.
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Affiliation(s)
- Anna Andreozzi
- Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy
| | - Pilar Prieto
- Departamento de Mejora Genética, Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Campus 'Alameda del Obispo', Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Jesús Mercado-Blanco
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Campus 'Alameda del Obispo', Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Stefano Monaco
- CREA - CI, Research Centre for Cereal and Industrial Crops, 13100, Vercelli, Italy
| | - Elisa Zampieri
- CREA - CI, Research Centre for Cereal and Industrial Crops, 13100, Vercelli, Italy
| | - Silvia Romano
- Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy
| | - Gianpiero Valè
- DiSIT, Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Piazza San Eusebio 5, I-13100 Vercelli, Italy
| | - Roberto Defez
- Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy
| | - Carmen Bianco
- Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy
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169
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Lee TK, Han I, Kim MS, Seong HJ, Kim JS, Sul WJ. Characterization of a nifH-Harboring Bacterial Community in the Soil-Limited Gotjawal Forest. Front Microbiol 2019; 10:1858. [PMID: 31456776 PMCID: PMC6700220 DOI: 10.3389/fmicb.2019.01858] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/29/2019] [Indexed: 11/13/2022] Open
Abstract
Using a high-throughput metagenomic approach, we evaluated nifH-harboring bacterial communities and their assembly in the Gotjawal forest, which was naturally formed on basalt rocks with thin layer of soil. Significant differences in soil properties and community structure were observed in comparison with similar communities in various habitats, including other lava-formed forests (on Jeju Island and in Hawaii) and in regions with high humidity (Florida) or low temperatures (Alaska). nifH-harboring bacterial communities were found to assemble along gradients of environmental factors, particularly cation-exchange capacity. Unlike in other regions, in the Gotjawal forest, Paenibacillus and Clostridium, which belong to the phylum Firmicutes, were present in significantly higher proportion than in other regions. Network analysis suggested that much fewer co-occurrence relationships occurred in the Gotjawal forest than in other lava-formed forests. Our results indicate that the unique nifH-harboring bacterial community and its assembly in the Gotjawal forest are due to its distinctive soil properties, which has implications for microbial interactions and functional potentials.
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Affiliation(s)
- Tae Kwon Lee
- Department of Environmental Engineering, Yonsei University, Wonju, South Korea
| | - Il Han
- Department of Environmental Engineering, Yonsei University, Wonju, South Korea
| | - Min Sung Kim
- Department of Environmental Engineering, Yonsei University, Wonju, South Korea
| | - Hoon Je Seong
- Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea
| | - Jong-Shik Kim
- Marine Industry Research Institute for East Sea Rim, Uljin, South Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea
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170
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Perin G, Yunus IS, Valton M, Alobwede E, Jones PR. Sunlight-driven recycling to increase nutrient use-efficiency in agriculture. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101554] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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171
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Burén S, Rubio LM. State of the art in eukaryotic nitrogenase engineering. FEMS Microbiol Lett 2019; 365:4733273. [PMID: 29240940 PMCID: PMC5812491 DOI: 10.1093/femsle/fnx274] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/11/2017] [Indexed: 12/27/2022] Open
Abstract
Improving the ability of plants and plant-associated organisms to fix and assimilate atmospheric nitrogen has inspired plant biotechnologists for decades, not only to alleviate negative effects on nature from increased use and availability of reactive nitrogen, but also because of apparent economic benefits and opportunities. The combination of recent advances in synthetic biology and increased knowledge about the biochemistry and biosynthesis of the nitrogenase enzyme has made the seemingly remote and for long unreachable dream more possible. In this review, we will discuss strategies how this could be accomplished using biotechnology, with a special focus on recent progress on engineering plants to express its own nitrogenase.
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Affiliation(s)
- Stefan Burén
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223-Pozuelo de Alarcón, Madrid, Spain
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223-Pozuelo de Alarcón, Madrid, Spain
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172
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Li H, Zhao Q, Huang H. Current states and challenges of salt-affected soil remediation by cyanobacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 669:258-272. [PMID: 30878933 DOI: 10.1016/j.scitotenv.2019.03.104] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/23/2019] [Accepted: 03/07/2019] [Indexed: 06/09/2023]
Abstract
Natural and human activities lead to soil degradation and soil salinization. The decrease of farmlands threatens food security. There are approximately 1 billion ha salt-affected soils all over of world, which can be made available resources after chemical, physical and biological remediation. Nostoc, Anabaena and other cyanobacterial species have outstanding capabilities, such as the ability to fix nitrogen from the air, produce an extracellular matrix and produce compatible solutes. The remediation of salt-affected soil is a complex and difficult task. During the past years, much new research has been conducted that shows that cyanobacteria are effective for salt-affected soil remediation in laboratory studies and field trials. The related mechanisms for both salt tolerance and salt-affected soil remediation were also evaluated from the perspective of biochemistry, molecular biology and systems biology. The effect of cyanobacteria on salt-affected soil is related to nitrogen fixation and other mechanisms. There are complicated interactions among cyanobacteria, bacteria, fungi and the soil. The interaction between cyanobacteria and salt-tolerant plants should be considered if the cyanobacterium is utilized to improve the soil fertility in addition to performing soil remediation. It is critical to re-establish the micro-ecology in salt-affected soils and improve the salt affected soil remediation efficiency. The first challenge is the selection of suitable cyanobacterial strain. The co-culture of cyanobacteria and bacteria is also potential approach. The cultivation of cyanobacteria on a large scale should be optimized to improve productivity and decrease cost. The development of bio-remediating agents for salt-affected soil remediation also relies on other technical problems, such as harvesting and contamination control. The application of cyanobacteria in salt-affected soil remediation will reconstruct green agriculture and promote the sustainable development of human society.
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Affiliation(s)
- Han Li
- School of Pharmaceutical Science, Nanjing Tech University, No. 30 Puzhu South Road, Nanjing 211816, People's Republic of China
| | - Quanyu Zhao
- School of Pharmaceutical Science, Nanjing Tech University, No. 30 Puzhu South Road, Nanjing 211816, People's Republic of China.
| | - He Huang
- School of Pharmaceutical Science, Nanjing Tech University, No. 30 Puzhu South Road, Nanjing 211816, People's Republic of China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), People's Republic of China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, No. 5 Xinmofan Road, Nanjing 210009, People's Republic of China
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173
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Klepa MS, Ferraz Helene LC, O’Hara G, Hungria M. Bradyrhizobium agreste sp. nov., Bradyrhizobium glycinis sp. nov. and Bradyrhizobium diversitatis sp. nov., isolated from a biodiversity hotspot of the genus Glycine in Western Australia. Int J Syst Evol Microbiol 2019; 71:004742. [PMID: 33709900 PMCID: PMC8375429 DOI: 10.1099/ijsem.0.004742] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/19/2021] [Indexed: 01/16/2023] Open
Abstract
Strains of the genus Bradyrhizobium associated with agronomically important crops such as soybean (Glycine max) are increasingly studied; however, information about symbionts of wild Glycine species is scarce. Australia is a genetic centre of wild Glycine species and we performed a polyphasic analysis of three Bradyrhizobium strains-CNPSo 4010T, CNPSo 4016T, and CNPSo 4019T-trapped from Western Australian soils with Glycine clandestina, Glycine tabacina and Glycine max, respectively. The phylogenetic tree of the 16S rRNA gene clustered all strains into the Bradyrhizobium japonicum superclade; strains CNPSo 4010T and CNPSo 4016T had Bradyrhizobium yuanmingense CCBAU 10071T as the closest species, whereas strain CNPSo 4019T was closer to Bradyrhizobium liaoningense LMG 18230T. The multilocus sequence analysis (MLSA) with five housekeeping genes-dnaK, glnII, gyrB, recA and rpoB-confirmed the same clusters as the 16S rRNA phylogeny, but indicated low similarity to described species, with nucleotide identities ranging from 93.6 to 97.6% of similarity. Considering the genomes of the three strains, the average nucleotide identity and digital DNA-DNA hybridization values were lower than 94.97 and 59.80 %, respectively, with the closest species. In the nodC phylogeny, strains CNPSo 4010T and CNPSo 4019T grouped with Bradyrhizobium zhanjiangense and Bradyrhizobium ganzhouense, respectively, while strain CNPSo 4016T was positioned separately from the all symbiotic Bradyrhizobium species. Other genomic (BOX-PCR), phenotypic and symbiotic properties were evaluated and corroborated with the description of three new lineages of Bradyrhizobium. We propose the names of Bradyrhizobium agreste sp. nov. for CNPSo 4010T (=WSM 4802T=LMG 31645T) isolated from Glycine clandestina, Bradyrhizobium glycinis sp. nov. for CNPSo 4016T (=WSM 4801T=LMG 31649T) isolated from Glycine tabacina and Bradyrhizobium diversitatis sp. nov. for CNPSo 4019T (=WSM 4799T=LMG 31650T) isolated from G. max.
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Affiliation(s)
- Milena Serenato Klepa
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, Distrito Federal, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970, Londrina, Paraná, Brazil
| | - Luisa Caroline Ferraz Helene
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, Distrito Federal, Brazil
| | - Graham O’Hara
- Centre for Rhizobium Studies (CRS), Murdoch University 90 South St. Murdoch, WA, Australia
| | - Mariangela Hungria
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, Distrito Federal, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970, Londrina, Paraná, Brazil
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174
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Miri M, Janakirama P, Huebert T, Ross L, McDowell T, Orosz K, Markmann K, Szczyglowski K. Inside out: root cortex-localized LHK1 cytokinin receptor limits epidermal infection of Lotus japonicus roots by Mesorhizobium loti. THE NEW PHYTOLOGIST 2019; 222:1523-1537. [PMID: 30636324 DOI: 10.1111/nph.15683] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 01/03/2019] [Indexed: 05/27/2023]
Abstract
During Lotus japonicus-Mesorhizobium loti symbiosis, the LOTUS HISTIDINE KINASE1 (LHK1) cytokinin receptor regulates both the initiation of nodule formation and the scope of root infection. However, the exact spatiotemporal mechanism by which this receptor exerts its symbiotic functions has remained elusive. In this study, we performed cell type-specific complementation experiments in the hyperinfected lhk1-1 mutant background, targeting LHK1 to either the root epidermis or the root cortex. We also utilized various genetic backgrounds to characterize expression of several genes regulating symbiotic infection. We show here that expression of LHK1 in the root cortex is required and sufficient to regulate both nodule formation and epidermal infections. The LHK1-dependent signalling that restricts subsequent infection events is triggered before initial cell divisions for nodule primordium formation. We also demonstrate that AHK4, the Arabidopsis orthologue of LHK1, is able to regulate M. loti infection in L. japonicus, suggesting that an endogenous cytokinin receptor could be sufficient for engineering nitrogen-fixing root nodule symbiosis in nonlegumes. Our data provide experimental evidence for the existence of an LHK1-dependent root cortex-to-epidermis feedback mechanism regulating rhizobial infection. This root-localized regulatory module functionally links with the systemic autoregulation of nodulation (AON) to maintain the homeostasis of symbiotic infection.
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Affiliation(s)
- Mandana Miri
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, ON, N6A 5BF, Canada
| | - Preetam Janakirama
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, N5V 4T3, Canada
| | - Terry Huebert
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, N5V 4T3, Canada
| | - Loretta Ross
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, N5V 4T3, Canada
| | - Tim McDowell
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, N5V 4T3, Canada
| | - Kathleen Orosz
- Fanshawe College, 1001 Fanshawe College Boulevard, London, ON, N5Y 5R6, Canada
| | - Katharina Markmann
- The Center for Plant Molecular Biology, Tübingen University, 72076, Tübingen, Germany
| | - Krzysztof Szczyglowski
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, ON, N6A 5BF, Canada
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175
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Manipulating nitrogen regulation in diazotrophic bacteria for agronomic benefit. Biochem Soc Trans 2019; 47:603-614. [PMID: 30936245 PMCID: PMC6490700 DOI: 10.1042/bst20180342] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 11/29/2022]
Abstract
Biological nitrogen fixation (BNF) is controlled by intricate regulatory mechanisms to ensure that fixed nitrogen is readily assimilated into biomass and not released to the environment. Understanding the complex regulatory circuits that couple nitrogen fixation to ammonium assimilation is a prerequisite for engineering diazotrophic strains that can potentially supply fixed nitrogen to non-legume crops. In this review, we explore how the current knowledge of nitrogen metabolism and BNF regulation may allow strategies for genetic manipulation of diazotrophs for ammonia excretion and provide a contribution towards solving the nitrogen crisis.
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176
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Bashandy SR, Abd‐Alla MH, Bagy MMK. Biological Nitrogen Fixation and Biofertilizers as Ideal Potential Solutions for Sustainable Agriculture. INTEGRATING GREEN CHEMISTRY AND SUSTAINABLE ENGINEERING 2019:343-396. [DOI: 10.1002/9781119509868.ch12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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177
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Rajakovich LJ, Pandelia ME, Mitchell AJ, Chang WC, Zhang B, Boal AK, Krebs C, Bollinger JM. A New Microbial Pathway for Organophosphonate Degradation Catalyzed by Two Previously Misannotated Non-Heme-Iron Oxygenases. Biochemistry 2019; 58:1627-1647. [PMID: 30789718 PMCID: PMC6503667 DOI: 10.1021/acs.biochem.9b00044] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The assignment of biochemical functions to hypothetical proteins is challenged by functional diversification within many protein structural superfamilies. This diversification, which is particularly common for metalloenzymes, renders functional annotations that are founded solely on sequence and domain similarities unreliable and often erroneous. Definitive biochemical characterization to delineate functional subgroups within these superfamilies will aid in improving bioinformatic approaches for functional annotation. We describe here the structural and functional characterization of two non-heme-iron oxygenases, TmpA and TmpB, which are encoded by a genomically clustered pair of genes found in more than 350 species of bacteria. TmpA and TmpB are functional homologues of a pair of enzymes (PhnY and PhnZ) that degrade 2-aminoethylphosphonate but instead act on its naturally occurring, quaternary ammonium analogue, 2-(trimethylammonio)ethylphosphonate (TMAEP). TmpA, an iron(II)- and 2-(oxo)glutarate-dependent oxygenase misannotated as a γ-butyrobetaine (γbb) hydroxylase, shows no activity toward γbb but efficiently hydroxylates TMAEP. The product, ( R)-1-hydroxy-2-(trimethylammonio)ethylphosphonate [( R)-OH-TMAEP], then serves as the substrate for the second enzyme, TmpB. By contrast to its purported phosphohydrolytic activity, TmpB is an HD-domain oxygenase that uses a mixed-valent diiron cofactor to enact oxidative cleavage of the C-P bond of its substrate, yielding glycine betaine and phosphate. The high specificities of TmpA and TmpB for their N-trimethylated substrates suggest that they have evolved specifically to degrade TMAEP, which was not previously known to be subject to microbial catabolism. This study thus adds to the growing list of known pathways through which microbes break down organophosphonates to harvest phosphorus, carbon, and nitrogen in nutrient-limited niches.
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Affiliation(s)
- Lauren J. Rajakovich
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Maria-Eirini Pandelia
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Andrew J. Mitchell
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Wei-chen Chang
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Bo Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: REG Life Sciences, LLC, South San Francisco, California 94080
| | - Amie K. Boal
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - J. Martin Bollinger
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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178
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Piché-Choquette S, Constant P. Molecular Hydrogen, a Neglected Key Driver of Soil Biogeochemical Processes. Appl Environ Microbiol 2019; 85:e02418-18. [PMID: 30658976 PMCID: PMC6414374 DOI: 10.1128/aem.02418-18] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The atmosphere of the early Earth is hypothesized to have been rich in reducing gases such as hydrogen (H2). H2 has been proposed as the first electron donor leading to ATP synthesis due to its ubiquity throughout the biosphere as well as its ability to easily diffuse through microbial cells and its low activation energy requirement. Even today, hydrogenase enzymes enabling the production and oxidation of H2 are found in thousands of genomes spanning the three domains of life across aquatic, terrestrial, and even host-associated ecosystems. Even though H2 has already been proposed as a universal growth and maintenance energy source, its potential contribution as a driver of biogeochemical cycles has received little attention. Here, we bridge this knowledge gap by providing an overview of the classification, distribution, and physiological role of hydrogenases. Distribution of these enzymes in various microbial functional groups and recent experimental evidence are finally integrated to support the hypothesis that H2-oxidizing microbes are keystone species driving C cycling along O2 concentration gradients found in H2-rich soil ecosystems. In conclusion, we suggest focusing on the metabolic flexibility of H2-oxidizing microbes by combining community-level and individual-level approaches aiming to decipher the impact of H2 on C cycling and the C-cycling potential of H2-oxidizing microbes, via both culture-dependent and culture-independent methods, to give us more insight into the role of H2 as a driver of biogeochemical processes.
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179
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To Fix or Not To Fix: Controls on Free-Living Nitrogen Fixation in the Rhizosphere. Appl Environ Microbiol 2019; 85:AEM.02546-18. [PMID: 30658971 DOI: 10.1128/aem.02546-18] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Free-living nitrogen fixation (FLNF) in the rhizosphere, or N fixation by heterotrophic bacteria living on/near root surfaces, is ubiquitous and a significant source of N in some terrestrial systems. FLNF is also of interest in crop production as an alternative to chemical fertilizer, potentially reducing production costs and ameliorating negative environmental impacts of fertilizer N additions. Despite this interest, a mechanistic understanding of controls (e.g., carbon, oxygen, nitrogen, and nutrient availability) on FLNF in the rhizosphere is lacking but necessary. FLNF is distinct from and occurs under more diverse and dynamic conditions than symbiotic N fixation; therefore, predicting FLNF rates and understanding controls on FLNF has proven difficult. This has led to large gaps in our understanding of FLNF, and studies aimed at identifying controls on FLNF are needed. Here, we provide a mechanistic overview of FLNF, including how various controls may influence FLNF in the rhizosphere in comparison with symbiotic N fixation occurring in plant nodules where environmental conditions are moderated by the plant. We apply this knowledge to a real-world example, the bioenergy crop switchgrass (Panicum virgatum), to provide context of how FLNF may function in a managed system. We also highlight future challenges to assessing FLNF and understanding how FLNF functions in the environment and significantly contributes to plant N availability and productivity.
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180
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Iacopino S, Jurinovich S, Cupellini L, Piccinini L, Cardarelli F, Perata P, Mennucci B, Giuntoli B, Licausi F. A Synthetic Oxygen Sensor for Plants Based on Animal Hypoxia Signaling. PLANT PHYSIOLOGY 2019; 179:986-1000. [PMID: 30459266 PMCID: PMC6393790 DOI: 10.1104/pp.18.01003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/08/2018] [Indexed: 05/21/2023]
Abstract
Due to the involvement of oxygen in many essential metabolic reactions, all living organisms have developed molecular systems that allow adaptive physiological and metabolic transitions depending on oxygen availability. In mammals, the expression of hypoxia-response genes is controlled by the heterodimeric Hypoxia-Inducible Factor. The activity of this transcriptional regulator is linked mainly to the oxygen-dependent hydroxylation of conserved proline residues in its α-subunit, carried out by prolyl-hydroxylases, and subsequent ubiquitination via the E3 ligase von Hippel-Lindau tumor suppressor, which targets Hypoxia-Inducible Factor-α to the proteasome. By exploiting bioengineered versions of this mammalian oxygen sensor, we designed and optimized a synthetic device that drives gene expression in an oxygen-dependent fashion in plants. Transient assays in Arabidopsis (Arabidopsis thaliana) mesophyll protoplasts indicated that a combination of the yeast Gal4/upstream activating sequence system and the mammalian oxygen sensor machinery can be used effectively to engineer a modular, oxygen-inducible transcriptional regulator. This synthetic device also was shown to be selectively controlled by oxygen in whole plants when its components were expressed stably in Arabidopsis seedlings. We envision the exploitation of our genetically encoded controllers to generate plants able to switch gene expression selectively depending on oxygen availability, thereby providing a proof of concept for the potential of synthetic biology to assist agricultural practices in environments with variable oxygen provision.
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Affiliation(s)
- Sergio Iacopino
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa 56127, Italy
| | | | | | - Luca Piccinini
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa 56127, Italy
| | - Francesco Cardarelli
- National Enterprise for nanoScience and nanoTechnology, Scuola Normale Superiore, Pisa 56126, Italy
| | | | | | - Beatrice Giuntoli
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa 56127, Italy
- Biology Department, Università di Pisa, Pisa 56126, Italy
| | - Francesco Licausi
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa 56127, Italy
- Biology Department, Università di Pisa, Pisa 56126, Italy
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181
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Schnurbusch T. Wheat and barley biology: Towards new frontiers. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:198-203. [PMID: 30694021 DOI: 10.1111/jipb.12782] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Thorsten Schnurbusch
- Independent HEISENBERG-Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
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182
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Abstract
With the likelihood that changes in global climate will adversely affect the soil C reservoir in the northern circumpolar permafrost zone, an understanding of the potential role of diazotrophic communities in enhancing biological N2 fixation, which constrains both plant production and microbial decomposition in tundra soils, is important in elucidating the responses of soil microbial communities to global climate change. A recent study showed that the composition of the diazotrophic community in a tundra soil exhibited no change under a short-term (1.5-year) winter warming experiment. However, it remains crucial to examine whether the lack of diazotrophic community responses to warming is persistent over a longer time period as a possibly important mechanism in stabilizing tundra soil C. Through a detailed characterization of the effects of winter warming on diazotrophic communities, we showed that a long-term (5-year) winter warming substantially enhanced diazotrophic abundance and altered community composition, though soil depth had a stronger influence on diazotrophic community composition than warming. These changes were best explained by changes in soil moisture, soil thaw duration, and plant biomass. These results provide crucial insights into the potential factors that may impact future C and N availability in tundra regions. Tundra ecosystems are typically carbon (C) rich but nitrogen (N) limited. Since biological N2 fixation is the major source of biologically available N, the soil N2-fixing (i.e., diazotrophic) community serves as an essential N supplier to the tundra ecosystem. Recent climate warming has induced deeper permafrost thaw and adversely affected C sequestration, which is modulated by N availability. Therefore, it is crucial to examine the responses of diazotrophic communities to warming across the depths of tundra soils. Herein, we carried out one of the deepest sequencing efforts of nitrogenase gene (nifH) to investigate how 5 years of experimental winter warming affects Alaskan soil diazotrophic community composition and abundance spanning both the organic and mineral layers. Although soil depth had a stronger influence on diazotrophic community composition than warming, warming significantly (P < 0.05) enhanced diazotrophic abundance by 86.3% and aboveground plant biomass by 25.2%. Diazotrophic composition in the middle and lower organic layers, detected by nifH sequencing and a microarray-based tool (GeoChip), was markedly altered, with an increase of α-diversity. Changes in diazotrophic abundance and composition significantly correlated with soil moisture, soil thaw duration, and plant biomass, as shown by structural equation modeling analyses. Therefore, more abundant diazotrophic communities induced by warming may potentially serve as an important mechanism for supplementing biologically available N in this tundra ecosystem.
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183
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Teng Y, Xu Y, Wang X, Christie P. Function of Biohydrogen Metabolism and Related Microbial Communities in Environmental Bioremediation. Front Microbiol 2019; 10:106. [PMID: 30837956 PMCID: PMC6383490 DOI: 10.3389/fmicb.2019.00106] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/17/2019] [Indexed: 01/30/2023] Open
Abstract
Hydrogen (H2) metabolism has attracted considerable interest because the activities of H2-producing and consuming microbes shape the global H2 cycle and may have vital relationships with the global cycling of other elements. There are many pathways of microbial H2 emission and consumption which may affect the structure and function of microbial communities. A wide range of microbial groups employ H2 as an electron donor to catalyze the reduction of pollutants such as organohalides, azo compounds, and trace metals. Syntrophy coupled mutualistic interaction between H2-producing and H2-consuming microorganisms can transfer H2 and be accompanied by the removal of toxic compounds. Moreover, hydrogenases have been gradually recognized to have a key role in the progress of pollutant degradation. This paper reviews recent advances in elucidating role of H2 metabolism involved in syntrophy and hydrogenases in environmental bioremediation. Further investigations should focus on the application of bioenergy in bioremediation to make microbiological H2 metabolism a promising remediation strategy.
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Affiliation(s)
- Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yongfeng Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaomi Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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184
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diCenzo GC, Zamani M, Checcucci A, Fondi M, Griffitts JS, Finan TM, Mengoni A. Multidisciplinary approaches for studying rhizobium–legume symbioses. Can J Microbiol 2019; 65:1-33. [DOI: 10.1139/cjm-2018-0377] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The rhizobium–legume symbiosis is a major source of fixed nitrogen (ammonia) in the biosphere. The potential for this process to increase agricultural yield while reducing the reliance on nitrogen-based fertilizers has generated interest in understanding and manipulating this process. For decades, rhizobium research has benefited from the use of leading techniques from a very broad set of fields, including population genetics, molecular genetics, genomics, and systems biology. In this review, we summarize many of the research strategies that have been employed in the study of rhizobia and the unique knowledge gained from these diverse tools, with a focus on genome- and systems-level approaches. We then describe ongoing synthetic biology approaches aimed at improving existing symbioses or engineering completely new symbiotic interactions. The review concludes with our perspective of the future directions and challenges of the field, with an emphasis on how the application of a multidisciplinary approach and the development of new methods will be necessary to ensure successful biotechnological manipulation of the symbiosis.
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Affiliation(s)
- George C. diCenzo
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Maryam Zamani
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alice Checcucci
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Marco Fondi
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Joel S. Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Turlough M. Finan
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
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185
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Methods for Detecting Biocontrol and Plant Growth-Promoting Traits in Rhizobacteria. METHODS IN RHIZOSPHERE BIOLOGY RESEARCH 2019. [DOI: 10.1007/978-981-13-5767-1_8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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186
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Stambulska UY, Bayliak MM. Legume-Rhizobium Symbiosis: Secondary Metabolites, Free Radical Processes, and Effects of Heavy Metals. BIOACTIVE MOLECULES IN FOOD 2019. [DOI: 10.1007/978-3-319-76887-8_43-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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187
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McGuiness PN, Reid JB, Foo E. The Role of Gibberellins and Brassinosteroids in Nodulation and Arbuscular Mycorrhizal Associations. FRONTIERS IN PLANT SCIENCE 2019; 10:269. [PMID: 30930916 PMCID: PMC6429038 DOI: 10.3389/fpls.2019.00269] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 02/19/2019] [Indexed: 05/20/2023]
Abstract
Plant hormones play key roles in nodulation and arbuscular mycorrhizal (AM) associations. These two agriculturally and ecologically important symbioses enable plants to gain access to nutrients, in particular, nitrogen in the case of nodulation and phosphorous in the case of AM. Work over the past few decades has revealed how symbioses with nitrogen-fixing rhizobia, restricted almost exclusively to legumes, evolved in part from ancient AM symbioses formed by more than 80% of land plants. Although overlapping, these symbiotic programs also have important differences, including the de novo development of a new organ found only in nodulation. One emerging area of research is the role of two plant hormone groups, the gibberellins (GAs) and brassinosteroids (BRs), in the development and maintenance of these symbioses. In this review, we compare and contrast the roles of these hormones in the two symbioses, including potential interactions with other hormones. This not only focuses on legumes, most of which can host both symbionts, but also examines the role of these in AM development in non-legumes. GA acts by suppressing DELLA, and this regulatory module acts to negatively influence both rhizobial and mycorrhizal infection but appears to promote nodule organogenesis. While an overall positive role for BRs in nodulation and AM has been suggested by studies using mutants disrupted in BR biosynthesis or response, application studies indicate that BR may play a more complex role in nodulation. Given the nature of these symbioses, with events regulated both spatially and temporally, future studies should examine in more detail how GAs and BRs may influence precise events during these symbioses, including interactions with other hormone groups.
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188
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Demtröder L, Narberhaus F, Masepohl B. Coordinated regulation of nitrogen fixation and molybdate transport by molybdenum. Mol Microbiol 2018; 111:17-30. [PMID: 30325563 DOI: 10.1111/mmi.14152] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2018] [Indexed: 12/01/2022]
Abstract
Biological nitrogen fixation, the reduction of chemically inert dinitrogen to bioavailable ammonia, is a central process in the global nitrogen cycle highly relevant for life on earth. N2 reduction to NH3 is catalyzed by nitrogenases exclusively synthesized by diazotrophic prokaryotes. All diazotrophs have a molybdenum nitrogenase containing the unique iron-molybdenum cofactor FeMoco. In addition, some diazotrophs encode one or two alternative Mo-free nitrogenases that are less efficient at reducing N2 than Mo-nitrogenase. To permit biogenesis of Mo-nitrogenase and other molybdoenzymes when Mo is scarce, bacteria synthesize the high-affinity molybdate transporter ModABC. Generally, Mo supports expression of Mo-nitrogenase genes, while it represses production of Mo-free nitrogenases and ModABC. Since all three nitrogenases and ModABC can reach very high levels at suitable Mo concentrations, tight Mo-mediated control saves considerable resources and energy. This review outlines the similarities and differences in Mo-responsive regulation of nitrogen fixation and molybdate transport in diverse diazotrophs.
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Affiliation(s)
- Lisa Demtröder
- Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | | | - Bernd Masepohl
- Microbial Biology, Ruhr University Bochum, Bochum, Germany
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189
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Dhanushkodi R, Matthew C, McManus MT, Dijkwel PP. Drought-induced senescence of Medicago truncatula nodules involves serpin and ferritin to control proteolytic activity and iron levels. THE NEW PHYTOLOGIST 2018; 220:196-208. [PMID: 29974467 DOI: 10.1111/nph.15298] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 05/20/2018] [Indexed: 05/09/2023]
Abstract
Drought is a major constraint for legume growth and yield. Senescence of nitrogen-fixing nodules is one of the early drought responses and may cause nutrient stress in addition to water stress in legumes. For nodule senescence to function as part of a drought-survival strategy, we propose that the intrinsically destructive senescence process must be tightly regulated. Medicago truncatula protease inhibitor and iron scavenger-encoding genes, possibly involved in controlling nodule senescence, were identified. RNA interference (RNAi) lines were constructed in which expression of a serpin or ferritins was knocked down. Both wild-type and RNAi lines were subjected to drought stress and nodule activity and plant physiological responses were measured. Drought caused M. truncatula to initiate nodule senescence before plant growth was affected and before an increase in papain-like proteolytic activity and free iron levels was apparent. Knock-down expression of serpin6 and ferritins caused increased protease activity, free iron levels, early nodule senescence and reduced plant growth. The results suggest that M. truncatula nodule-expressed serpin6 and ferritins mediate ordered drought-induced senescence by regulating papain-like cysteine protease activity and free iron levels. This strategy may allow the drought-stressed plants to benefit maximally from residual nitrogen fixation and nutrient recovery resulting from break down of macromolecules.
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Affiliation(s)
- Ramadoss Dhanushkodi
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - Cory Matthew
- Institute of Agriculture and Environment, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - Michael T McManus
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - Paul P Dijkwel
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
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190
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Suyal DC, Kumar S, Joshi D, Soni R, Goel R. Quantitative proteomics of psychotrophic diazotroph in response to nitrogen deficiency and cold stress. J Proteomics 2018; 187:235-242. [PMID: 30092381 DOI: 10.1016/j.jprot.2018.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 07/20/2018] [Accepted: 08/04/2018] [Indexed: 12/11/2022]
Abstract
Effective protocols and novel biomarkers are the need of this hour to screen potential cold adapted diazotrophs for sustainable mountain agricultural plans. LC-MS/MS based gel less quantitative proteomics was employed to investigate the metabolic response of Himalayan cold adapted diazotroph Pseudomonas palleroniana N26 (JN055435) for nitrogen deficiency and cold stress. More than 5000 proteins were identified, and 125 of them showed significant difference with a 2-fold or greater change (p < .05) between normal and stress conditions, including 29 up-regulated proteins and 35 down-regulated proteins. Expression of nifA, nifL, nifH, nifB, nifD, and nifK during N2 fixing conditions reveals that nitrogenase system was successfully activated. Further, 8% of the upregulated proteins showed similarity with uncharacterized proteins of several nitrogen fixing genera which suggests their in-depth investigation. Additionally, as per earlier studies, cowN was differentially expressed under nitrogen fixing conditions; thereby, confirming its potential to be a potent biomarker for monitoring the nitrogen fixation in cold niches. BIOLOGICAL SIGNIFICANCE Understanding of nitrogenase expression and regulation is essential to employ potential diazotrophs under diverse ecological niches to achieve agricultural as well as environmental sustainability. The molecular mechanisms of cold adapted diazotrophy are still unaddressed. In this scenario, present study, besides characterizing diazotrophic proteins, is helpful in identifying the protein(s) or a biomarker viz. CowN to facilitate the monitoring of nitrogen fixation in cold niches. To the best of our knowledge, this is the first gel-less quantitative free-living diazotrophic proteome study using label free mass spectrometry having high mass accuracy in both MS and MS/MS scans. It enriches the diazotrophic proteome database and will complement the other "omics" technologies for improved crop protection and sustainability strategies.
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Affiliation(s)
- Deep Chandra Suyal
- Department of Microbiology, College of Basic Sciences and Humanities, G.B.Pant University of Agriculture and Technology, Pantnagar 263145, Uttarakhand, India
| | - Saurabh Kumar
- Department of Microbiology, College of Basic Sciences and Humanities, G.B.Pant University of Agriculture and Technology, Pantnagar 263145, Uttarakhand, India
| | - Divya Joshi
- Department of Microbiology, College of Basic Sciences and Humanities, G.B.Pant University of Agriculture and Technology, Pantnagar 263145, Uttarakhand, India
| | - Ravindra Soni
- Department of Agricultural Microbiology, College of Agriculture, Indira Gandhi Krishi Viswavidyalaya, Raipur, C.G., India
| | - Reeta Goel
- Department of Microbiology, College of Basic Sciences and Humanities, G.B.Pant University of Agriculture and Technology, Pantnagar 263145, Uttarakhand, India.
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191
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Becker M, Patz S, Becker Y, Berger B, Drungowski M, Bunk B, Overmann J, Spröer C, Reetz J, Tchuisseu Tchakounte GV, Ruppel S. Comparative Genomics Reveal a Flagellar System, a Type VI Secretion System and Plant Growth-Promoting Gene Clusters Unique to the Endophytic Bacterium Kosakonia radicincitans. Front Microbiol 2018; 9:1997. [PMID: 30214433 PMCID: PMC6125372 DOI: 10.3389/fmicb.2018.01997] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 08/08/2018] [Indexed: 01/04/2023] Open
Abstract
The recent worldwide discovery of plant growth-promoting (PGP) Kosakonia radicincitans in a large variety of crop plants suggests that this species confers significant influence on plants, both in terms of yield increase and product quality improvement. We provide a comparative genome analysis which helps to unravel the genetic basis for K. radicincitans' motility, competitiveness and plant growth-promoting capacities. We discovered that K. radicincitans carries multiple copies of complex gene clusters, among them two flagellar systems and three type VI secretion systems (T6SSs). We speculate that host invasion may be facilitated by different flagella, and bacterial competitor suppression by effector proteins ejected via T6SSs. We found a large plasmid in K. radicincitans DSM 16656T, the species type strain, that confers the potential to exploit plant-derived carbon sources. We propose that multiple copies of complex gene clusters in K. radicincitans are metabolically expensive but provide competitive advantage over other bacterial strains in nutrient-rich environments. The comparison of the DSM 16656T genome to genomes of other genera of enteric plant growth-promoting bacteria (PGPB) exhibits traits unique to DSM 16656T and K. radicincitans, respectively, and traits shared between genera. We used the output of the in silico analysis for predicting the purpose of genomic features unique to K. radicincitans and performed microarray, PhyloChip, and microscopical analyses to gain deeper insight into the interaction of DSM 16656T, plants and associated microbiota. The comparative genome analysis will facilitate the future search for promising candidates of PGPB for sustainable crop production.
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Affiliation(s)
- Matthias Becker
- Leibniz Institute of Vegetable and Ornamental Crops, Grossbeeren, Germany
| | - Sascha Patz
- Leibniz Institute of Vegetable and Ornamental Crops, Grossbeeren, Germany.,Algorithms in Bioinformatics, Center for Bioinformatics, University of Tübingen, Tübingen, Germany
| | - Yvonne Becker
- Leibniz Institute of Vegetable and Ornamental Crops, Grossbeeren, Germany.,Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institute-Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Beatrice Berger
- Leibniz Institute of Vegetable and Ornamental Crops, Grossbeeren, Germany.,Institute for National and International Plant Health, Julius Kühn-Institute-Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Mario Drungowski
- Leibniz Institute of Vegetable and Ornamental Crops, Grossbeeren, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jochen Reetz
- Federal Institute for Risk Assessment, Berlin, Germany
| | | | - Silke Ruppel
- Leibniz Institute of Vegetable and Ornamental Crops, Grossbeeren, Germany
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192
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Harke MJ, Frischkorn KR, Haley ST, Aylward FO, Zehr JP, Dyhrman ST. Periodic and coordinated gene expression between a diazotroph and its diatom host. ISME JOURNAL 2018; 13:118-131. [PMID: 30116042 DOI: 10.1038/s41396-018-0262-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/28/2018] [Accepted: 07/28/2018] [Indexed: 01/30/2023]
Abstract
In the surface ocean, light fuels photosynthetic carbon fixation of phytoplankton, playing a critical role in ecosystem processes including carbon export to the deep sea. In oligotrophic oceans, diatom-diazotroph associations (DDAs) play a keystone role in ecosystem function because diazotrophs can provide otherwise scarce biologically available nitrogen to the diatom host, fueling growth and subsequent carbon sequestration. Despite their importance, relatively little is known about the nature of these associations in situ. Here we used metatranscriptomic sequencing of surface samples from the North Pacific Subtropical Gyre (NPSG) to reconstruct patterns of gene expression for the diazotrophic symbiont Richelia and we examined how these patterns were integrated with those of the diatom host over day-night transitions. Richelia exhibited significant diel signals for genes related to photosynthesis, N2 fixation, and resource acquisition, among other processes. N2 fixation genes were significantly co-expressed with host nitrogen uptake and metabolism, as well as potential genes involved in carbon transport, which may underpin the exchange of nitrogen and carbon within this association. Patterns of expression suggested cell division was integrated between the host and symbiont across the diel cycle. Collectively these data suggest that symbiont-host physiological ecology is strongly interconnected in the NPSG.
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Affiliation(s)
- Matthew J Harke
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Columbia University, Palisades, NY, USA
| | - Kyle R Frischkorn
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Columbia University, Palisades, NY, USA.,Department of Earth and Environmental Sciences, Columbia University, New York, NY, USA
| | - Sheean T Haley
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Columbia University, Palisades, NY, USA
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | | | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Columbia University, Palisades, NY, USA. .,Department of Earth and Environmental Sciences, Columbia University, New York, NY, USA.
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Rosenblueth M, Ormeño-Orrillo E, López-López A, Rogel MA, Reyes-Hernández BJ, Martínez-Romero JC, Reddy PM, Martínez-Romero E. Nitrogen Fixation in Cereals. Front Microbiol 2018; 9:1794. [PMID: 30140262 PMCID: PMC6095057 DOI: 10.3389/fmicb.2018.01794] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 07/17/2018] [Indexed: 01/30/2023] Open
Abstract
Cereals such as maize, rice, wheat and sorghum are the most important crops for human nutrition. Like other plants, cereals associate with diverse bacteria (including nitrogen-fixing bacteria called diazotrophs) and fungi. As large amounts of chemical fertilizers are used in cereals, it has always been desirable to promote biological nitrogen fixation in such crops. The quest for nitrogen fixation in cereals started long ago with the isolation of nitrogen-fixing bacteria from different plants. The sources of diazotrophs in cereals may be seeds, soils, and even irrigation water and diazotrophs have been found on roots or as endophytes. Recently, culture-independent molecular approaches have revealed that some rhizobia are found in cereal plants and that bacterial nitrogenase genes are expressed in plants. Since the levels of nitrogen-fixation attained with nitrogen-fixing bacteria in cereals are not high enough to support the plant’s needs and never as good as those obtained with chemical fertilizers or with rhizobium in symbiosis with legumes, it has been the aim of different studies to increase nitrogen-fixation in cereals. In many cases, these efforts have not been successful. However, new diazotroph mutants with enhanced capabilities to excrete ammonium are being successfully used to promote plant growth as commensal bacteria. In addition, there are ambitious projects supported by different funding agencies that are trying to genetically modify maize and other cereals to enhance diazotroph colonization or to fix nitrogen or to form nodules with nitrogen-fixing symbiotic rhizobia.
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Affiliation(s)
- Mónica Rosenblueth
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ernesto Ormeño-Orrillo
- Laboratorio de Ecología Microbiana y Biotecnología, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
| | - Aline López-López
- Centro de Investigación en Genética y Ambiente, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Marco A Rogel
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | | | - Pallavolu M Reddy
- The Energy and Resources Institute, India Habitat Centre, New Delhi, India
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194
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Van Deynze A, Zamora P, Delaux PM, Heitmann C, Jayaraman D, Rajasekar S, Graham D, Maeda J, Gibson D, Schwartz KD, Berry AM, Bhatnagar S, Jospin G, Darling A, Jeannotte R, Lopez J, Weimer BC, Eisen JA, Shapiro HY, Ané JM, Bennett AB. Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota. PLoS Biol 2018; 16:e2006352. [PMID: 30086128 PMCID: PMC6080747 DOI: 10.1371/journal.pbio.2006352] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 07/03/2018] [Indexed: 12/19/2022] Open
Abstract
Plants are associated with a complex microbiota that contributes to nutrient acquisition, plant growth, and plant defense. Nitrogen-fixing microbial associations are efficient and well characterized in legumes but are limited in cereals, including maize. We studied an indigenous landrace of maize grown in nitrogen-depleted soils in the Sierra Mixe region of Oaxaca, Mexico. This landrace is characterized by the extensive development of aerial roots that secrete a carbohydrate-rich mucilage. Analysis of the mucilage microbiota indicated that it was enriched in taxa for which many known species are diazotrophic, was enriched for homologs of genes encoding nitrogenase subunits, and harbored active nitrogenase activity as assessed by acetylene reduction and 15N2 incorporation assays. Field experiments in Sierra Mixe using 15N natural abundance or 15N-enrichment assessments over 5 years indicated that atmospheric nitrogen fixation contributed 29%–82% of the nitrogen nutrition of Sierra Mixe maize. Nitrogen is an essential nutrient for plants, and for many nonlegume crops, the requirement for nitrogen is primarily met by the use of inorganic fertilizers. These fertilizers are produced from fossil fuel by energy-intensive processes that are estimated to use 1% to 2% of the total global energy supply and produce an equivalent share of greenhouse gases. Because maize (Zea mays L.) is a significant recipient of nitrogen fertilization, a research goal for decades has been to identify or engineer mechanisms for biological fixation of atmospheric nitrogen in association with this crop. We hypothesized that isolated indigenous landraces of maize grown using traditional practices with little or no fertilizer might have evolved strategies to improve plant performance under low-nitrogen nutrient conditions. Here, we show that for one such maize landrace grown in nitrogen-depleted fields near Oaxaca, Mexico, 29%–82% of the plant nitrogen is derived from atmospheric nitrogen. High levels of nitrogen fixation are supported, at least in part, by the abundant production of a sugar-rich mucilage associated with aerial roots that provides a home to a complex nitrogen-fixing microbiome.
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Affiliation(s)
- Allen Van Deynze
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Pablo Zamora
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Pierre-Marc Delaux
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Cristobal Heitmann
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Dhileepkumar Jayaraman
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Shanmugam Rajasekar
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Danielle Graham
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Junko Maeda
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Donald Gibson
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Kevin D. Schwartz
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Alison M. Berry
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Srijak Bhatnagar
- Genome Center, University of California, Davis, California, United States of America
| | - Guillaume Jospin
- Genome Center, University of California, Davis, California, United States of America
| | - Aaron Darling
- Genome Center, University of California, Davis, California, United States of America
| | - Richard Jeannotte
- Department of Population Health and Reproduction, University of California, Davis, California, United States of America
| | - Javier Lopez
- Instituto Tecnológico del Valle de Oaxaca, Oaxaca, Mexico
| | - Bart C. Weimer
- Department of Population Health and Reproduction, University of California, Davis, California, United States of America
| | - Jonathan A. Eisen
- Genome Center, University of California, Davis, California, United States of America
| | - Howard-Yana Shapiro
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Mars, Incorporated, McLean, Virginia, United States of America
| | - Jean-Michel Ané
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Alan B. Bennett
- Department of Plant Sciences, University of California, Davis, California, United States of America
- * E-mail:
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195
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Lade SB, Román C, Cueto-Ginzo AI, Serrano L, Sin E, Achón MA, Medina V. Host-specific proteomic and growth analysis of maize and tomato seedlings inoculated with Azospirillum brasilense Sp7. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 129:381-393. [PMID: 29945074 DOI: 10.1016/j.plaphy.2018.06.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/16/2018] [Accepted: 06/16/2018] [Indexed: 05/26/2023]
Abstract
Azospirillum brasilense Sp7 (Sp7) is a diazotrophic, free-living plant growth-promoting rhizobacterium (PGPR) that is increasingly used for its ability to reduce stress and improve nutrient uptake by plants. To test the hypothesis that Sp7 interacts differently with the primary metabolism in C3 and C4 plants, differential proteomics were employed to study weekly protein expression in Sp7-treated maize (Zea mays cv. B73) and tomato (Solanum lycopersicum cv. Boludo) seedlings. Plant and root growth parameters were also monitored. Protein changes were most striking at the four-leaf stage (T1) for both species. Proteins related to metabolism and redox homeostasis were most abundant in tomato at T1, but later, plants experienced inhibited Calvin-Benson (CB) cycle and chloroplast development, indicating that photosynthetic proteins were damaged by reactive oxygen species (ROS). In maize, Sp7 first increased ROS-scavenging enzymes and decreased those related to metabolism, which ultimately reduced photoinhibition at later sampling times. Overall, the early interaction with maize is more complex and beneficial because the photosynthetic aparatus is protected by the C4 mechanism, thereby improving the interaction of the PGPR with maize. Better seedling emergence and vigor were observed in inoculated maize compared to tomato. This study provides an integrated perspective on the Sp7 strain-specific interactions with young C3 and C4 plants to modulate primary metabolism and photosynthesis.
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Affiliation(s)
- Sarah Boyd Lade
- Department of Plant Production and Forestry Science, University of Lleida - Agrotecnio Center, Lleida, Spain.
| | - Carla Román
- Department of Plant Production and Forestry Science, University of Lleida - Agrotecnio Center, Lleida, Spain
| | - Ana Isabel Cueto-Ginzo
- Department of Plant Production and Forestry Science, University of Lleida - Agrotecnio Center, Lleida, Spain
| | - Luis Serrano
- Department of Plant Production and Forestry Science, University of Lleida - Agrotecnio Center, Lleida, Spain
| | - Ester Sin
- Department of Plant Production and Forestry Science, University of Lleida - Agrotecnio Center, Lleida, Spain
| | - Maria Angels Achón
- Department of Plant Production and Forestry Science, University of Lleida - Agrotecnio Center, Lleida, Spain
| | - Vicente Medina
- Department of Plant Production and Forestry Science, University of Lleida - Agrotecnio Center, Lleida, Spain
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196
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Global investigation of an engineered nitrogen-fixing Escherichia coli strain reveals regulatory coupling between host and heterologous nitrogen-fixation genes. Sci Rep 2018; 8:10928. [PMID: 30026566 PMCID: PMC6053447 DOI: 10.1038/s41598-018-29204-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 07/06/2018] [Indexed: 11/08/2022] Open
Abstract
Transfer of nitrogen fixation (nif) genes from diazotrophs to amenable heterologous hosts is of increasing interest to genetically engineer nitrogen fixation. However, how the non-diazotrophic host maximizes opportunities to fine-tune the acquired capacity for nitrogen fixation has not been fully explored. In this study, a global investigation of an engineered nitrogen-fixing Escherichia coli strain EN-01 harboring a heterologous nif island from Pseudomonas stutzeri was performed via transcriptomics and proteomics analyses. A total of 1156 genes and 206 discriminative proteins were found to be significantly altered when cells were incubated under nitrogen-fixation conditions. Pathways for regulation, metabolic flux and oxygen protection to nitrogenase were particularly discussed. An NtrC-dependent regulatory coupling between E. coli nitrogen regulation system and nif genes was established. Additionally, pentose phosphate pathway was proposed to serve as the primary route for glucose catabolism and energy supply to nitrogenase. Meanwhile, HPLC analysis indicated that organic acids produced by EN-01 might have negative effects on nitrogenase activity. This study provides a global view of the complex network underlying the acquired nif genes in the recombinant E. coli and also provides clues for the optimization and redesign of robust nitrogen-fixing organisms to improve nitrogenase efficiency by overcoming regulatory or metabolic obstacles.
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197
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Garcia J, Kao-Kniffin J. Microbial Group Dynamics in Plant Rhizospheres and Their Implications on Nutrient Cycling. Front Microbiol 2018; 9:1516. [PMID: 30050510 PMCID: PMC6050453 DOI: 10.3389/fmicb.2018.01516] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/18/2018] [Indexed: 12/20/2022] Open
Abstract
Plant rhizospheres encompass a dynamic zone of interactions between microorganisms and their respective plant hosts. For decades, researchers have worked to understand how these complex interactions influence different aspects of plant growth, development, and evolution. Studies of plant-microbial interactions in the root zone have typically focused on the effect of single microbial species or strains on a plant host. These studies, however, provide only a snapshot of the complex interactions that occur in the rhizosphere, leaving researchers with a limited understanding of how the complex microbiome influences the biology of the plant host. To better understand how rhizosphere interactions influence plant growth and development, novel frameworks and research methodologies could be implemented. In this perspective, we propose applying concepts in evolutionary biology to microbiome experiments for improved understanding of group-to-group and community-level microbial interactions influencing soil nutrient cycling. We also put forth simple experimental designs utilizing -omics techniques that can reveal important changes in the rhizosphere impacting the plant host. A greater focus on the components of complexity of the microbiome and how these impact plant host biology could yield more insight into previously unexplored aspects of host-microbe biology relevant to crop production and protection.
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Affiliation(s)
| | - Jenny Kao-Kniffin
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
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198
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The Multiplanetary Future of Plant Synthetic Biology. Genes (Basel) 2018; 9:genes9070348. [PMID: 29996548 PMCID: PMC6071031 DOI: 10.3390/genes9070348] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/06/2018] [Accepted: 07/09/2018] [Indexed: 11/24/2022] Open
Abstract
The interest in human space journeys to distant planets and moons has been re-ignited in recent times and there are ongoing plans for sending the first manned missions to Mars in the near future. In addition to generating oxygen, fixing carbon, and recycling waste and water, plants could play a critical role in producing food and biomass feedstock for the microbial manufacture of materials, chemicals, and medicines in long-term interplanetary outposts. However, because life on Earth evolved under the conditions of the terrestrial biosphere, plants will not perform optimally in different planetary habitats. The construction or transportation of plant growth facilities and the availability of resources, such as sunlight and liquid water, may also be limiting factors, and would thus impose additional challenges to efficient farming in an extraterrestrial destination. Using the framework of the forthcoming human missions to Mars, here we discuss a series of bioengineering endeavors that will enable us to take full advantage of plants in the context of a Martian greenhouse. We also propose a roadmap for research on adapting life to Mars and outline our opinion that synthetic biology efforts towards this goal will contribute to solving some of the main agricultural and industrial challenges here on Earth.
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199
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Adams MA, Buchmann N, Sprent J, Buckley TN, Turnbull TL. Crops, Nitrogen, Water: Are Legumes Friend, Foe, or Misunderstood Ally? TRENDS IN PLANT SCIENCE 2018; 23:539-550. [PMID: 29559299 DOI: 10.1016/j.tplants.2018.02.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 02/19/2018] [Accepted: 02/23/2018] [Indexed: 06/08/2023]
Abstract
Biological nitrogen fixation (BNF) by crop legumes reduces demand for industrial nitrogen fixation (INF). Nonetheless, rates of BNF in agriculture remain low, with strong negative feedback to BNF from reactive soil nitrogen (N) and drought. We show that breeding for yield has resulted in strong relationships between photosynthesis and leaf N in non-leguminous crops, whereas grain legumes show strong relations between leaf N and water use efficiency (WUE). We contrast these understandings with other studies that draw attention to the water costs of grain legume crops, and their potential for polluting the biosphere with N. We propose that breeding grain legumes for reduced stomatal conductance can increase WUE without compromising production or BNF. Legume crops remain a better bet than relying on INF.
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Affiliation(s)
- Mark A Adams
- Swinburne University, PO Box 218, Hawthorn, VIC 3122, Australia; Centre for Carbon Water and Food, The University of Sydney, 380 Werombi Road, Camden, NSW 2480, Australia.
| | - Nina Buchmann
- ETH Zurich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Janet Sprent
- Division of Plant Sciences, University of Dundee at JHI, Invergowrie, Dundee, DD2 5DA, UK
| | - Thomas N Buckley
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Tarryn L Turnbull
- Centre for Carbon Water and Food, The University of Sydney, 380 Werombi Road, Camden, NSW 2480, Australia
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200
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Hürter AL, Fort S, Cottaz S, Hedrich R, Geiger D, Roelfsema MRG. Mycorrhizal lipochitinoligosaccharides (LCOs) depolarize root hairs of Medicago truncatula. PLoS One 2018; 13:e0198126. [PMID: 29851976 PMCID: PMC5979017 DOI: 10.1371/journal.pone.0198126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 05/14/2018] [Indexed: 11/24/2022] Open
Abstract
Arbuscular Mycorrhiza and Root Nodule Symbiosis are symbiotic interactions with a high benefit for plant growth and crop production. Thus, it is of great interest to understand the developmental process of these symbioses in detail. We analysed very early symbiotic responses of Medicago truncatula root hair cells, by stimulation with lipochitinoligosaccharides specific for the induction of nodules (Nod-LCOs), or the interaction with mycorrhiza (Myc-LCOs). Intracellular micro electrodes were used, in combination with Ca2+ sensitive reporter dyes, to study the relations between cytosolic Ca2+ signals and membrane potential changes. We found that sulfated Myc- as well as Nod-LCOs initiate a membrane depolarization, which depends on the chemical composition of these signaling molecules, as well as the genotype of the plants that were studied. A successive application of sulfated Myc-LCOs and Nod-LCOs resulted only in a single transient depolarization, indicating that Myc-LCOs can repress plasma membrane responses to Nod-LCOs. In contrast to current models, the Nod-LCO-induced depolarization precedes changes in the cytosolic Ca2+ level of root hair cells. The Nod-LCO induced membrane depolarization thus is most likely independent of cytosolic Ca2+ signals and nuclear Ca2+ spiking.
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Affiliation(s)
- Anna-Lena Hürter
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, Würzburg University, Würzburg, Germany
| | - Sébastien Fort
- University Grenoble Alpes, CNRS, CERMAV, Grenoble, France
| | - Sylvain Cottaz
- University Grenoble Alpes, CNRS, CERMAV, Grenoble, France
| | - Rainer Hedrich
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, Würzburg University, Würzburg, Germany
| | - Dietmar Geiger
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, Würzburg University, Würzburg, Germany
| | - M. Rob G. Roelfsema
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, Würzburg University, Würzburg, Germany
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