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Sámano ML, Nanjareddy K, Arthikala MK. NIN-like proteins (NLPs) as crucial nitrate sensors: an overview of their roles in nitrogen signaling, symbiosis, abiotic stress, and beyond. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:1209-1223. [PMID: 39100871 PMCID: PMC11291829 DOI: 10.1007/s12298-024-01485-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 02/22/2024] [Accepted: 07/04/2024] [Indexed: 08/06/2024]
Abstract
Nitrogen is an essential macronutrient critical for plant growth and productivity. Plants have the capacity to uptake inorganic nitrate and ammonium, with nitrate playing a crucial role as a signaling molecule in various cellular processes. The availability of nitrate and the signaling pathways involved finely tune the processes of nitrate uptake and assimilation. NIN-like proteins (NLPs), a group of transcription factors belonging to the RWP-RK gene family, act as major nitrate sensors and are implicated in the primary nitrate response (PNR) within the nucleus of both non-leguminous and leguminous plants through their RWP-RK domains. In leguminous plants, NLPs are indispensable for the initiation and development of nitrogen-fixing nodules in symbiosis with rhizobia. Moreover, NLPs play pivotal roles in plant responses to abiotic stresses, including drought and cold. Recent studies have identified NLP homologs in oomycete pathogens, suggesting their potential involvement in pathogenesis and virulence. This review article delves into the conservation of RWP-RK genes, examining their significance and implications across different plant species. The focus lies on the role of NLPs as nitrate sensors, investigating their involvement in various processes, including rhizobial symbiosis in both leguminous and non-leguminous plants. Additionally, the multifaceted functions of NLPs in abiotic stress responses, developmental processes, and interactions with plant pathogens are explored. By comprehensively analyzing the role of NLPs in nitrate signaling and their broader implications for plant growth and development, this review sheds light on the intricate mechanisms underlying nitrogen sensing and signaling in various plant lineages.
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Affiliation(s)
- Mariana López Sámano
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (UNAM), 37689 León, Mexico
| | - Kalpana Nanjareddy
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (UNAM), 37689 León, Mexico
| | - Manoj-Kumar Arthikala
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (UNAM), 37689 León, Mexico
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2
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Bennett GM, Kwak Y, Maynard R. Endosymbioses Have Shaped the Evolution of Biological Diversity and Complexity Time and Time Again. Genome Biol Evol 2024; 16:evae112. [PMID: 38813885 PMCID: PMC11154151 DOI: 10.1093/gbe/evae112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 05/31/2024] Open
Abstract
Life on Earth comprises prokaryotes and a broad assemblage of endosymbioses. The pages of Molecular Biology and Evolution and Genome Biology and Evolution have provided an essential window into how these endosymbiotic interactions have evolved and shaped biological diversity. Here, we provide a current perspective on this knowledge by drawing on decades of revelatory research published in Molecular Biology and Evolution and Genome Biology and Evolution, and insights from the field at large. The accumulated work illustrates how endosymbioses provide hosts with novel phenotypes that allow them to transition between adaptive landscapes to access environmental resources. Such endosymbiotic relationships have shaped and reshaped life on Earth. The early serial establishment of mitochondria and chloroplasts through endosymbioses permitted massive upscaling of cellular energetics, multicellularity, and terrestrial planetary greening. These endosymbioses are also the foundation upon which all later ones are built, including everything from land-plant endosymbioses with fungi and bacteria to nutritional endosymbioses found in invertebrate animals. Common evolutionary mechanisms have shaped this broad range of interactions. Endosymbionts generally experience adaptive and stochastic genome streamlining, the extent of which depends on several key factors (e.g. mode of transmission). Hosts, in contrast, adapt complex mechanisms of resource exchange, cellular integration and regulation, and genetic support mechanisms to prop up degraded symbionts. However, there are significant differences between endosymbiotic interactions not only in how partners have evolved with each other but also in the scope of their influence on biological diversity. These differences are important considerations for predicting how endosymbioses will persist and adapt to a changing planet.
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Affiliation(s)
- Gordon M Bennett
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
- National Science Foundation Biological Integration Institute—INSITE, University of California, Merced, CA, USA
| | - Younghwan Kwak
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
- National Science Foundation Biological Integration Institute—INSITE, University of California, Merced, CA, USA
| | - Reo Maynard
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
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3
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Zhang Y, Fu Y, Xian W, Li X, Feng Y, Bu F, Shi Y, Chen S, van Velzen R, Battenberg K, Berry AM, Salgado MG, Liu H, Yi T, Fournier P, Alloisio N, Pujic P, Boubakri H, Schranz ME, Delaux PM, Wong GKS, Hocher V, Svistoonoff S, Gherbi H, Wang E, Kohlen W, Wall LG, Parniske M, Pawlowski K, Normand P, Doyle JJ, Cheng S. Comparative phylogenomics and phylotranscriptomics provide insights into the genetic complexity of nitrogen-fixing root-nodule symbiosis. PLANT COMMUNICATIONS 2024; 5:100671. [PMID: 37553834 PMCID: PMC10811378 DOI: 10.1016/j.xplc.2023.100671] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/10/2023] [Accepted: 08/03/2023] [Indexed: 08/10/2023]
Abstract
Plant root-nodule symbiosis (RNS) with mutualistic nitrogen-fixing bacteria is restricted to a single clade of angiosperms, the Nitrogen-Fixing Nodulation Clade (NFNC), and is best understood in the legume family. Nodulating species share many commonalities, explained either by divergence from a common ancestor over 100 million years ago or by convergence following independent origins over that same time period. Regardless, comparative analyses of diverse nodulation syndromes can provide insights into constraints on nodulation-what must be acquired or cannot be lost for a functional symbiosis-and the latitude for variation in the symbiosis. However, much remains to be learned about nodulation, especially outside of legumes. Here, we employed a large-scale phylogenomic analysis across 88 species, complemented by 151 RNA-seq libraries, to elucidate the evolution of RNS. Our phylogenomic analyses further emphasize the uniqueness of the transcription factor NIN as a master regulator of nodulation and identify key mutations that affect its function across the NFNC. Comparative transcriptomic assessment revealed nodule-specific upregulated genes across diverse nodulating plants, while also identifying nodule-specific and nitrogen-response genes. Approximately 70% of symbiosis-related genes are highly conserved in the four representative species, whereas defense-related and host-range restriction genes tend to be lineage specific. Our study also identified over 900 000 conserved non-coding elements (CNEs), over 300 000 of which are unique to sampled NFNC species. NFNC-specific CNEs are enriched with the active H3K9ac mark and are correlated with accessible chromatin regions, thus representing a pool of candidate regulatory elements for genes involved in RNS. Collectively, our results provide novel insights into the evolution of nodulation and lay a foundation for engineering of RNS traits in agriculturally important crops.
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Affiliation(s)
- Yu Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yuan Fu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenfei Xian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xiuli Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yong Feng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Fengjiao Bu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yan Shi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Shiyu Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Robin van Velzen
- Biosystematics Group, Department of Plant Sciences, Wageningen University, 6708PB Wageningen, the Netherlands
| | - Kai Battenberg
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Alison M Berry
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Marco G Salgado
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Hui Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road, Kunming 650201, China
| | - Tingshuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road, Kunming 650201, China
| | - Pascale Fournier
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Nicole Alloisio
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Petar Pujic
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Hasna Boubakri
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - M Eric Schranz
- Biosystematics Group, Department of Plant Sciences, Wageningen University, 6708PB Wageningen, the Netherlands
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet Tolosan, France
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Valerie Hocher
- French National Research Institute for Sustainable Development (IRD), UMR LSTM (IRD/CIRAD/INRAe/Montpellier University/Supagro)- Campus International Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Sergio Svistoonoff
- French National Research Institute for Sustainable Development (IRD), UMR LSTM (IRD/CIRAD/INRAe/Montpellier University/Supagro)- Campus International Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Hassen Gherbi
- French National Research Institute for Sustainable Development (IRD), UMR LSTM (IRD/CIRAD/INRAe/Montpellier University/Supagro)- Campus International Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai, China
| | - Wouter Kohlen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708PB Wageningen, the Netherlands
| | - Luis G Wall
- Laboratory of Biochemistry, Microbiology and Soil Biological Interactions, Department of Science and Technology, National University of Quilmes, CONICET, Bernal, Argentina
| | - Martin Parniske
- Faculty of Biology, Genetics, LMU Munich, Großhaderner Strasse 2-4, 82152 Martinsried, Germany
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Philippe Normand
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Jeffrey J Doyle
- School of Integrative Plant Science, Sections of Plant Biology and Plant Breeding & Genetics, Cornell University, Ithaca, NY 14853, USA.
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
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4
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Hlaváčková K, Šamaj J, Ovečka M. Cytoskeleton as a roadmap navigating rhizobia to establish symbiotic root nodulation in legumes. Biotechnol Adv 2023; 69:108263. [PMID: 37775072 DOI: 10.1016/j.biotechadv.2023.108263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/28/2023] [Accepted: 09/24/2023] [Indexed: 10/01/2023]
Abstract
Legumes enter into symbiotic associations with soil nitrogen-fixing rhizobia, culminating in the creation of new organs, root nodules. This complex process relies on chemical and physical interaction between legumes and rhizobia, including early signalling events informing the host legume plant of a potentially beneficial microbe and triggering the nodulation program. The great significance of this plant-microbe interaction rests upon conversion of atmospheric dinitrogen not accessible to plants into a biologically active form of ammonia available to plants. The plant cytoskeleton consists in a highly dynamic network and undergoes rapid remodelling upon sensing various developmental and environmental cues, including response to attachment, internalization, and accommodation of rhizobia in plant root and nodule cells. This dynamic nature is governed by cytoskeleton-associated proteins that modulate cytoskeletal behaviour depending on signal perception and transduction. Precisely localized cytoskeletal rearrangements are therefore essential for the uptake of rhizobia, their targeted delivery, and establishing beneficial root nodule symbiosis. This review summarizes current knowledge about rhizobia-dependent rearrangements and functions of the cytoskeleton in legume roots and nodules. General patterns and nodule type-, nodule stage-, and species-specific aspects of actin filaments and microtubules remodelling are discussed. Moreover, emerging evidence is provided about fine-tuning the root nodulation process through cytoskeleton-associated proteins. We also consider future perspectives on dynamic localization studies of the cytoskeleton during early symbiosis utilizing state of the art molecular and advanced microscopy approaches. Based on acquired detailed knowledge of the mutualistic interactions with microbes, these approaches could contribute to broader biotechnological crop improvement.
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Affiliation(s)
- Kateřina Hlaváčková
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic.
| | - Jozef Šamaj
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic.
| | - Miroslav Ovečka
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic.
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5
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Abstract
Plants associate with nitrogen-fixing bacteria to secure nitrogen, which is generally the most limiting nutrient for plant growth. Endosymbiotic nitrogen-fixing associations are widespread among diverse plant lineages, ranging from microalgae to angiosperms, and are primarily one of three types: cyanobacterial, actinorhizal or rhizobial. The large overlap in the signaling pathways and infection components of arbuscular mycorrhizal, actinorhizal and rhizobial symbioses reflects their evolutionary relatedness. These beneficial associations are influenced by environmental factors and other microorganisms in the rhizosphere. In this review, we summarize the diversity of nitrogen-fixing symbioses, key signal transduction pathways and colonization mechanisms relevant to such interactions, and compare and contrast these interactions with arbuscular mycorrhizal associations from an evolutionary standpoint. Additionally, we highlight recent studies on environmental factors regulating nitrogen-fixing symbioses to provide insights into the adaptation of symbiotic plants to complex environments.
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Affiliation(s)
- Peng Xu
- National key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ertao Wang
- National key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; New Cornerstone Science Laboratory, Shenzhen 518054, China.
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6
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Li XR, Sun J, Albinsky D, Zarrabian D, Hull R, Lee T, Jarratt-Barnham E, Chiu CH, Jacobsen A, Soumpourou E, Albanese A, Kohlen W, Luginbuehl LH, Guillotin B, Lawrensen T, Lin H, Murray J, Wallington E, Harwood W, Choi J, Paszkowski U, Oldroyd GED. Nutrient regulation of lipochitooligosaccharide recognition in plants via NSP1 and NSP2. Nat Commun 2022; 13:6421. [PMID: 36307431 PMCID: PMC9616857 DOI: 10.1038/s41467-022-33908-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 10/07/2022] [Indexed: 12/25/2022] Open
Abstract
Many plants associate with arbuscular mycorrhizal fungi for nutrient acquisition, while legumes also associate with nitrogen-fixing rhizobial bacteria. Both associations rely on symbiosis signaling and here we show that cereals can perceive lipochitooligosaccharides (LCOs) for activation of symbiosis signaling, surprisingly including Nod factors produced by nitrogen-fixing bacteria. However, legumes show stringent perception of specifically decorated LCOs, that is absent in cereals. LCO perception in plants is activated by nutrient starvation, through transcriptional regulation of Nodulation Signaling Pathway (NSP)1 and NSP2. These transcription factors induce expression of an LCO receptor and act through the control of strigolactone biosynthesis and the karrikin-like receptor DWARF14-LIKE. We conclude that LCO production and perception is coordinately regulated by nutrient starvation to promote engagement with mycorrhizal fungi. Our work has implications for the use of both mycorrhizal and rhizobial associations for sustainable productivity in cereals.
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Affiliation(s)
- Xin-Ran Li
- grid.5335.00000000121885934Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR UK
| | - Jongho Sun
- grid.5335.00000000121885934Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR UK
| | - Doris Albinsky
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Darius Zarrabian
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Raphaella Hull
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Tak Lee
- grid.5335.00000000121885934Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR UK ,grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Edwin Jarratt-Barnham
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Chai Hao Chiu
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Amy Jacobsen
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Eleni Soumpourou
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Alessio Albanese
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Wouter Kohlen
- grid.4818.50000 0001 0791 5666Laboratory for Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Leonie H. Luginbuehl
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Bruno Guillotin
- grid.503344.50000 0004 0445 6769Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Castanet-Tolosan, France ,grid.137628.90000 0004 1936 8753Present Address: NYU-Center of Genomic and System Biology, 12 Waverly Place, New York, NY USA
| | - Tom Lawrensen
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Hui Lin
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Jeremy Murray
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Emma Wallington
- grid.17595.3f0000 0004 0383 6532NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Wendy Harwood
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Jeongmin Choi
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Uta Paszkowski
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Giles E. D. Oldroyd
- grid.5335.00000000121885934Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR UK ,grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
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7
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Gäbelein C, Reiter MA, Ernst C, Giger GH, Vorholt JA. Engineering Endosymbiotic Growth of E. coli in Mammalian Cells. ACS Synth Biol 2022; 11:3388-3396. [PMID: 36194551 PMCID: PMC9594318 DOI: 10.1021/acssynbio.2c00292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Endosymbioses are cellular mergers in which one cell lives within another cell and have led to major evolutionary transitions, most prominently to eukaryogenesis. Generation of synthetic endosymbioses aims to provide a defined starting point for studying fundamental processes in emerging endosymbiotic systems and enable the engineering of cells with novel properties. Here, we tested the potential of different bacteria for artificial endosymbiosis in mammalian cells. To this end, we adopted the fluidic force microscopy technology to inject diverse bacteria directly into the cytosol of HeLa cells and examined the endosymbiont-host interactions by real-time fluorescence microscopy. Among them, Escherichia coli grew exponentially within the cytoplasm, however, at a faster pace than its host cell. To slow down the intracellular growth of E. coli, we introduced auxotrophies in E. coli and demonstrated that the intracellular growth rate can be reduced by limiting the uptake of aromatic amino acids. In consequence, the survival of the endosymbiont-host pair was prolonged. The presented experimental framework enables studying endosymbiotic candidate systems at high temporal resolution and at the single cell level. Our work represents a starting point for engineering a stable, vertically inherited endosymbiosis.
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8
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Mathesius U. Are legumes different? Origins and consequences of evolving nitrogen fixing symbioses. JOURNAL OF PLANT PHYSIOLOGY 2022; 276:153765. [PMID: 35952452 DOI: 10.1016/j.jplph.2022.153765] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 05/14/2023]
Abstract
Nitrogen fixing symbioses between plants and bacteria are ancient and, while not numerous, are formed in diverse lineages of plants ranging from microalgae to angiosperms. One symbiosis stands out as the most widespread one is that between legumes and rhizobia, leading to the formation of nitrogen-fixing nodules. The legume family is one of the largest and most diverse group of plants and legumes have been used by humans since the beginning of agriculture, both as high nitrogen food, as well as pastures and rotation crops. One open question is whether their ability to form a nitrogen-fixing symbiosis has contributed to legumes' success, and whether legumes have any unique characteristics that have made them more diverse and widespread than other groups of plants. This review examines the evolutionary journey that has led to the diversification of legumes, in particular its nitrogen-fixing symbiosis, and asks four questions to investigate which legume traits might have contributed to their success: 1. In what ways do legumes differ from other plant groups that have evolved nitrogen-fixing symbioses? In order to answer this question, the characteristics of the symbioses, and efficiencies of nitrogen fixation are compared between different groups of nitrogen fixing plants. 2. Could certain unique features of legumes be a reason for their success? This section examines the manifestations and possible benefits of a nitrogen-rich 'lifestyle' in legumes. 3. If nitrogen fixation was a reason for such a success, why have some species lost the symbiosis? Formation of symbioses has trade-offs, and while these are less well known for non-legumes, there are known energetic and ecological reasons for loss of symbiotic potential in legumes. 4. What can we learn from the unique traits of legumes for future crop improvements? While exploiting some of the physiological properties of legumes could be used to improve legume breeding, our increasing molecular understanding of the essential regulators of root nodule symbioses raise hope of creating new nitrogen fixing symbioses in other crop species.
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Affiliation(s)
- Ulrike Mathesius
- Division of Plant Sciences, Research School of Biology, The Australian National University, 134 Linnaeus Way, Canberra, ACT, 2601, Australia.
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9
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Constitutive activation of a nuclear-localized calcium channel complex in Medicago truncatula. Proc Natl Acad Sci U S A 2022; 119:e2205920119. [PMID: 35972963 PMCID: PMC9407390 DOI: 10.1073/pnas.2205920119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nuclear Ca2+ oscillations allow symbiosis signaling, facilitating plant recognition of beneficial microsymbionts, nitrogen-fixing rhizobia, and nutrient-capturing arbuscular mycorrhizal fungi. Two classes of channels, DMI1 and CNGC15, in a complex on the nuclear membrane, coordinate symbiotic Ca2+ oscillations. However, the mechanism of Ca2+ signature generation is unknown. Here, we demonstrate spontaneous activation of this channel complex, through gain-of-function mutations in DMI1, leading to spontaneous nuclear Ca2+ oscillations and spontaneous nodulation, in a CNGC15-dependent manner. The mutations destabilize a hydrogen-bond or salt-bridge network between two RCK domains, with the resultant structural changes, alongside DMI1 cation permeability, activating the channel complex. This channel complex was reconstituted in human HEK293T cell lines, with the resultant calcium influx enhanced by autoactivated DMI1 and CNGC15s. Our results demonstrate the mode of activation of this nuclear channel complex, show that DMI1 and CNGC15 are sufficient to create oscillatory Ca2+ signals, and provide insights into its native mode of induction.
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10
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Fronk DC, Sachs JL. Symbiotic organs: the nexus of host-microbe evolution. Trends Ecol Evol 2022; 37:599-610. [PMID: 35393155 DOI: 10.1016/j.tree.2022.02.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/14/2022] [Accepted: 02/28/2022] [Indexed: 02/07/2023]
Abstract
Diverse plants and animals have evolved specialized structures to filter and house beneficial microbes. These symbiotic organs form crucial points of exchange between host and symbiont, are often shaped by both partners, and exhibit features that facilitate a suite of microbial services. While symbiotic organs exhibit varied function, morphology, and developmental plasticity, they share core features linked to the evolutionary maintenance of beneficial symbiosis. Moreover, these organs can have a significant role in altering the demographic forces that shape microbial genomes, driving population bottlenecks and horizontal gene transfer (HGT). To advance our understanding of these 'joint phenotypes' across varied systems, future research must consider the emergent forces that can shape symbiotic organs, including fitness feedbacks and conflicts between interacting genomes.
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Affiliation(s)
- David C Fronk
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA
| | - Joel L Sachs
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA; Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA; Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA.
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11
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Ladha JK, Peoples MB, Reddy PM, Biswas JC, Bennett A, Jat ML, Krupnik TJ. Biological nitrogen fixation and prospects for ecological intensification in cereal-based cropping systems. FIELD CROPS RESEARCH 2022; 283:108541. [PMID: 35782167 PMCID: PMC9133800 DOI: 10.1016/j.fcr.2022.108541] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 03/29/2022] [Accepted: 04/03/2022] [Indexed: 05/02/2023]
Abstract
The demand for nitrogen (N) for crop production increased rapidly from the middle of the twentieth century and is predicted to at least double by 2050 to satisfy the on-going improvements in productivity of major food crops such as wheat, rice and maize that underpin the staple diet of most of the world's population. The increased demand will need to be fulfilled by the two main sources of N supply - biological nitrogen (gas) (N2) fixation (BNF) and fertilizer N supplied through the Haber-Bosch processes. BNF provides many functional benefits for agroecosystems. It is a vital mechanism for replenishing the reservoirs of soil organic N and improving the availability of soil N to support crop growth while also assisting in efforts to lower negative environmental externalities than fertilizer N. In cereal-based cropping systems, legumes in symbiosis with rhizobia contribute the largest BNF input; however, diazotrophs involved in non-symbiotic associations with plants or present as free-living N2-fixers are ubiquitous and also provide an additional source of fixed N. This review presents the current knowledge of BNF by free-living, non-symbiotic and symbiotic diazotrophs in the global N cycle, examines global and regional estimates of contributions of BNF, and discusses possible strategies to enhance BNF for the prospective benefit of cereal N nutrition. We conclude by considering the challenges of introducing in planta BNF into cereals and reflect on the potential for BNF in both conventional and alternative crop management systems to encourage the ecological intensification of cereal and legume production.
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Affiliation(s)
- Jagdish K. Ladha
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Mark B. Peoples
- Commonwealth Scientific and Industrial Research Organisation, Canberra, Australia
| | | | | | - Alan Bennett
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Mangi L. Jat
- International Maize and Wheat Improvement Center, New Delhi, India
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12
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Shamseldin A. Future Outlook of Transferring Biological Nitrogen Fixation (BNF) to Cereals and Challenges to Retard Achieving this Dream. Curr Microbiol 2022; 79:171. [PMID: 35476236 DOI: 10.1007/s00284-022-02852-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 03/21/2022] [Indexed: 11/03/2022]
Abstract
BNF is a fascinating phenomenon which contributes to protect the nature from environmental pollution that can be happened as a result of heavy nitrogen applications. The importance of BNF is due to its supply of the agricultural lands with about 200 million tons of N annually. In this biological process, a specific group of bacteria collectively called rhizobia fix the atmospheric N in symbiosis with legumes called symbiotic nitrogen fixation and others (free living) fix nitrogen gas from the atmosphere termed asymbiotic. Several trials were done by scientists around the world to make cereals more benefited from nitrogen gas through different approaches. The first approach is to engineer cereals to form nodulated roots. Secondly is to transfer nif genes directly to cereals and fix N without Rhizobium partner. The other two approaches are maximizing the inoculation of cereals with both of diazotrophs or endophytes. Recently, scientists solved some challenges that entangle engineering cereals with nif genes directly and they confirmed the suitability of mitochondria and plastids as a suitable place for better biological function of nif genes expression in cereals. Fortunately, this article is confirming the success of scientists not only to transfer synthetic nitrogenase enzyme to Escherichia coli that gave 50% of its activity of expression, but also move it to plants as Nicotiana benthamiana. This mini review aims at explaining the future outlook of BNF and the challenges limiting its transfer to cereals and levels of success to make cereals self nitrogen fixing.
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Affiliation(s)
- Abdelaal Shamseldin
- Environmental Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications, New Borg El Arab, Alexandria, Egypt.
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13
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Role of Nodulation-Enhancing Rhizobacteria in the Promotion of Medicago sativa Development in Nutrient-Poor Soils. PLANTS 2022; 11:plants11091164. [PMID: 35567168 PMCID: PMC9099972 DOI: 10.3390/plants11091164] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/15/2022] [Accepted: 04/24/2022] [Indexed: 11/17/2022]
Abstract
Legumes are usually used as cover crops to improve soil quality due to the biological nitrogen fixation that occurs due to the interaction of legumes and rhizobia. This symbiosis can be used to recover degraded soils using legumes as pioneer plants. In this work, we screened for bacteria that improve the legume–rhizobia interaction in nutrient-poor soils. Fourteen phosphate solubilizer-strains were isolated, showing at least three out of the five tested plant growth promoting properties. Furthermore, cellulase, protease, pectinase, and chitinase activities were detected in three of the isolated strains. Pseudomonas sp. L1, Chryseobacterium soli L2, and Priestia megaterium L3 were selected to inoculate seeds and plants of Medicago sativa using a nutrient-poor soil as substrate under greenhouse conditions. The effects of the three bacteria individually and in consortium showed more vigorous plants with increased numbers of nodules and a higher nitrogen content than non-inoculated plants. Moreover, bacterial inoculation increased plants’ antioxidant activities and improved their development in nutrient-poor soils, suggesting an important role in the stress mechanisms of plants. In conclusion, the selected strains are nodulation-enhancing rhizobacteria that improve leguminous plants growth and nodulation in nutrient-poor soils and could be used by sustainable agriculture to promote plants’ development in degraded soils.
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14
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Rai A, Jha MN, Singh D, Thapa S, Chaurasia SK, Jha G. Detection of endophytic association between Aeschynomene nodulating Bradyrhizobium sp. and traditional Desariya rice roots under rice-Aeschynomene ecosystem of chaur land, Bihar, India. Biol Futur 2021; 73:95-105. [PMID: 34773605 DOI: 10.1007/s42977-021-00105-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 11/02/2021] [Indexed: 11/27/2022]
Abstract
Engineering diazotrophic rice having either an integral component of diazotrophic microbes or placing microbial origin nif gene to the rice plant is the dream of biotechnologist. Rice-Aeschynomene ecosystem of pristine chaur land provides a suitable niche to search Rhizobium endophytes in rice. Accordingly, the work was initiated to search suitable endophytic Rhizobium strain for artificial symbiosis within the roots of Desariya rice and its source through morphological, biochemical and molecular approaches. Detection of Acetylene reduction assay (ARA) activity in sterilized Desariya rice root confirmed the presence of putative diazotrophic endophytes in rice root. Isolates from Aeschynomene aspera L. nodulating and Desariya rice endophytic Rhizobium were evaluated for growth, IAA, morphological and biochemical features. Carbon profiling pattern of both these isolates indicated that Desariya rice endophytic Rhizobium has its similarity with Aeschynomene aspera L. nodulating Rhizobium. 16S rRNA gene sequencing confirmed the presence of endophytic Bradyrhizobium sp. in Desariya rice roots and its similarity with Aeschynomene aspera L. nodulating Bradyrhizobium. Desariya rice Bradyrhizobium may be an ideal candidate in the future for creating artificial symbiosis in rice due to its similarity with Aeschynomene aspera L. Bradyrhizobium.
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Affiliation(s)
- Abhilasha Rai
- Department of Microbiology, College of Basic Sciences and Humanities, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar, 848125, India
| | - Manindra Nath Jha
- Department of Microbiology, College of Basic Sciences and Humanities, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar, 848125, India
| | - Devendra Singh
- Department of Microbiology, College of Basic Sciences and Humanities, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar, 848125, India.
- ICAR-Central Arid Zone Research Institute, Jodhpur, Rajasthan, 342003, India.
| | - Shobit Thapa
- ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, MaunathBhanjan, Uttar Pradesh, 275103, India
| | - Sanjeet Kumar Chaurasia
- Department of Microbiology, College of Basic Sciences and Humanities, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar, 848125, India
| | - Gopaljee Jha
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
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15
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Priyadarshini P, Choudhury S, Tilgam J, Bharati A, Sreeshma N. Nitrogen fixing cereal: A rising hero towards meeting food security. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:912-920. [PMID: 34547550 DOI: 10.1016/j.plaphy.2021.09.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 09/05/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
Nitrogen serves as one of the primary components of major biomolecules and thus extends a significant contribution to crop growth and yield. But the inability of plants to utilize freely available atmospheric N2 makes the whole agricultural system dependent on chemical fertilizers, which incur significant input cost to supplement required quantities of nitrogen to crops. Only bacteria and archaea have been gifted with the power of drawing free N2 from air to convert them into NH3, which is one of the two utilizable forms of nitrogen taken up by plants. Legumes, the only family of crops, can engage themselves in symbiotic nitrogen fixation where they establish a mutualistic relationship with nitrogen-fixing bacteria and in turn, can waive off the necessity of adding nitrogen fertilizers. Sincere effort, therefore, has been undertaken to incorporate this capability of nitrogen-fixation into non-legume crops, especially cereals which make up a vital portion in the food basket. Biotechnological interventions have also played important role in providing nitrogen fixing trait to non-legumes. This review takes up an effort to look into and accumulate all the important updates to date regarding nitrogen-fixing non-legumes with a special focus on cereals, which is one of the most important future goals in the field of science in the present era.
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Affiliation(s)
- Parichita Priyadarshini
- ICAR-Crop Improvement Division, Indian Grassland and Fodder Research Institute, Jhansi, U.P., 284003, India
| | - Sharani Choudhury
- ICAR - National Institute for Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Jyotsana Tilgam
- ICAR- National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, U.P., 274103, India.
| | - Alka Bharati
- ICAR-Central Agroforestry Research Institute, Jhansi, U.P., 284003, India
| | - N Sreeshma
- ICAR - National Institute for Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
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16
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Furuta KM, Xiang L, Cui S, Yoshida S. Molecular dissection of haustorium development in Orobanchaceae parasitic plants. PLANT PHYSIOLOGY 2021; 186:1424-1434. [PMID: 33783524 PMCID: PMC8260117 DOI: 10.1093/plphys/kiab153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
Characterizing molecular aspects of haustorium development by parasitic plants in the Orobanchaceae family has identified hormone signaling/transport and specific genes as major players.
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Affiliation(s)
- Kaori Miyashima Furuta
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Lei Xiang
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Songkui Cui
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Satoko Yoshida
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
- JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan
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17
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Sheoran S, Kumar S, Kumar P, Meena RS, Rakshit S. Nitrogen fixation in maize: breeding opportunities. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1263-1280. [PMID: 33677701 DOI: 10.1007/s00122-021-03791-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/06/2021] [Indexed: 06/12/2023]
Abstract
Maize (Zea mays L.) is a highly versatile crop with huge demand of nitrogen (N) for its growth and development. N is the most essential macronutrient for crop production. Despite being the highest abundant element in the atmosphere (~ 78%), it is scarcely available for plant growth. To fulfil the N demand, commercial agriculture is largely dependent on synthetic fertilizers. Excessive dependence on inorganic fertilizers has created extensive ecological as well as economic problems worldwide. Hence, for a sustainable solution to nitrogenous fertilizer use, development of biological nitrogen fixation (BNF) in cereals will be the best alternative. BNF is a well-known mechanism in legumes where diazotrophs convert atmospheric nitrogen (N≡N) to plant-available form, ammonium (NH4+). From many decades, researchers have dreamt to develop a similar symbiotic partnership as in legumes to the cereal crops. A large number of endophytic diazotrophs have been found associated with maize. Elucidation of the genetic and molecular aspects of their interaction will open up new avenues to introgress BNF in maize breeding. With the advanced understanding of N-fixation process, researchers are at a juncture of breeding and engineering this symbiotic relationships in cereals. Different breeding, genetic engineering, omics, gene editing, and synthetic biology approaches will be discussed in this review to make BNF a reality in cereals. It will help to provide a road map to develop/improve the BNF in maize to an advance step for the sustainable production system to achieve the food and nutritional security.
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Affiliation(s)
- Seema Sheoran
- ICAR-Indian Institute of Maize Research, PAU Campus, Ludhiana, 1410 04, India
| | - Sandeep Kumar
- ICAR-Indian Institute of Pulses Research, Regional Station, Phanda, Bhopal, 462 030, India
| | - Pradeep Kumar
- ICAR-Indian Institute of Maize Research, PAU Campus, Ludhiana, 1410 04, India
| | - Ram Swaroop Meena
- Department of Agronomy, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221 005, India
| | - Sujay Rakshit
- ICAR-Indian Institute of Maize Research, PAU Campus, Ludhiana, 1410 04, India.
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18
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Tsiknia M, Tsikou D, Papadopoulou KK, Ehaliotis C. Multi-species relationships in legume roots: From pairwise legume-symbiont interactions to the plant - microbiome - soil continuum. FEMS Microbiol Ecol 2021; 97:5957530. [PMID: 33155054 DOI: 10.1093/femsec/fiaa222] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 11/03/2020] [Indexed: 01/02/2023] Open
Abstract
Mutualistic relationships of legume plants with, either bacteria (like rhizobia) or fungi (like arbuscular mycorrhizal fungi), have been investigated intensively, usually as bi-partite interactions. However, diverse symbiotic interactions take place simultaneously or sequentially under field conditions. Their collective, but not additive, contribution to plant growth and performance remains hard to predict, and appears to be furthermore affected by crop species and genotype, non-symbiotic microbial interactions and environmental variables. The challenge is: (i) to unravel the complex overlapping mechanisms that operate between the microbial symbionts as well as between them, their hosts and the rhizosphere (ii) to understand the dynamics of the respective mechanisms in evolutionary and ecological terms. The target for agriculture, food security and the environment, is to use this insight as a solid basis for developing new integrated technologies, practices and strategies for the efficient use of beneficial microbes in legumes and other plants. We review recent advances in our understanding of the symbiotic interactions in legumes roots brought about with the aid of molecular and bioinformatics tools. We go through single symbiont-host interactions, proceed to tripartite symbiont-host interactions, appraise interactions of symbiotic and associative microbiomes with plants in the root-rhizoplane-soil continuum of habitats and end up by examining attempts to validate community ecology principles in the legume-microbe-soil biosystem.
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Affiliation(s)
- Myrto Tsiknia
- Soils and Soil Chemistry Lab, Department of Natural Resources and Agricultural Engineering, Agricultural University of Athens, Iera Odos 75 st., Athens 11855, Greece
| | - Daniela Tsikou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Kalliope K Papadopoulou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Constantinos Ehaliotis
- Soils and Soil Chemistry Lab, Department of Natural Resources and Agricultural Engineering, Agricultural University of Athens, Iera Odos 75 st., Athens 11855, Greece
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19
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Quides KW, Salaheldine F, Jariwala R, Sachs JL. Dysregulation of host-control causes interspecific conflict over host investment into symbiotic organs. Evolution 2021; 75:1189-1200. [PMID: 33521949 DOI: 10.1111/evo.14173] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 10/31/2020] [Accepted: 01/08/2021] [Indexed: 12/14/2022]
Abstract
Microbial mutualists provide substantial benefits to hosts that feed back to enhance the fitness of the associated microbes. In many systems, beneficial microbes colonize symbiotic organs, specialized host structures that house symbionts and mediate resources exchanged between parties. Mutualisms are characterized by net benefits exchanged among members of different species, however, inequalities in the magnitude of these exchanges could result in evolutionary conflict, destabilizing the mutualism. We investigated joint fitness effects of root nodule formation, the symbiotic organ of legumes that house nitrogen-fixing rhizobia in planta. We quantified host and symbiont fitness parameters dependent on the number of nodules formed using near-isogenic Lotus japonicus and Mesorhizobium loti mutants, respectively. Empirically estimated fitness functions suggest that legume and rhizobia fitness is aligned as the number of nodules formed increases from zero until the host optimum is reached, a point where aligned fitness interests shift to diverging fitness interests between host and symbiont. However, fitness conflict was only inferred when analyzing wild-type hosts along with their mutants dysregulated for control over nodule formation. These data demonstrate that to avoid conflict, hosts must tightly regulate investment into symbiotic organs maximizing their benefit to cost ratio of associating with microbes.
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Affiliation(s)
- Kenjiro W Quides
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, California, 92521, USA.,Current Institution: Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Fathi Salaheldine
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, California, 92521, USA
| | - Ruchi Jariwala
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, California, 92521, USA
| | - Joel L Sachs
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, California, 92521, USA.,Institute for Integrative Genome Biology, University of California, Riverside, California, USA
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20
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Okuma N, Kawaguchi M. Systemic Optimization of Legume Nodulation: A Shoot-Derived Regulator, miR2111. FRONTIERS IN PLANT SCIENCE 2021; 12:682486. [PMID: 34335652 PMCID: PMC8321092 DOI: 10.3389/fpls.2021.682486] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/24/2021] [Indexed: 05/15/2023]
Abstract
Long-distance signaling between the shoot and roots of land plants plays a crucial role in ensuring their growth and development in a fluctuating environment, such as with soil nutrient deficiencies. MicroRNAs (miRNAs) are considered to contribute to such environmental adaptation via long-distance signaling since several miRNAs are transported between the shoot and roots in response to various soil nutrient changes. Leguminous plants adopt a shoot-mediated long-distance signaling system to maintain their mutualism with symbiotic nitrogen-fixing rhizobia by optimizing the number of symbiotic organs and root nodules. Recently, the involvement and importance of shoot-derived miR2111 in regulating nodule numbers have become evident. Shoot-derived miR2111 can systemically enhance rhizobial infection, and its accumulation is quickly suppressed in response to rhizobial inoculation and high-concentration nitrate application. In this mini-review, we briefly summarize the recent progress on the systemic optimization of nodulation in response to external environments, with a focus on systemic regulation via miR2111.
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Affiliation(s)
- Nao Okuma
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, School of Life Sciences, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan
- *Correspondence: Nao Okuma,
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, School of Life Sciences, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan
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21
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Valverde-Barrantes OJ, Maherali H, Baraloto C, Blackwood CB. Independent evolutionary changes in fine-root traits among main clades during the diversification of seed plants. THE NEW PHYTOLOGIST 2020; 228:541-553. [PMID: 32535912 DOI: 10.1111/nph.16729] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
Changes in fine-root morphology are typically associated with transitions from the ancestral arbuscular mycorrhizal (AM) to the alternative ectomycorrhizal (ECM) or nonmycorrhizal (NM) associations. However, the modifications in root morphology may also coincide with new modifications in leaf hydraulics and growth habit during angiosperm diversification. These hypotheses have not been evaluated concurrently, and this limits our understanding of the causes of fine-root evolution. To explore the evolution of fine-root systems, we assembled a 600+ species database to reconstruct historical changes in seed plants over time. We utilise ancestral reconstruction approaches together with phylogenetically informed comparative analyses to test whether changes in fine-root traits were most strongly associated with mycorrhizal affiliation, leaf hydraulics or growth form. Our findings showed significant shifts in root diameter, specific root length and root tissue density as angiosperms diversified, largely independent from leaf changes or mycorrhizal affiliation. Growth form was the only factor associated with fine-root traits in statistical models including mycorrhizal association and leaf venation, suggesting substantial modifications in fine-root morphology during transitions from woody to nonwoody habits. Divergences in fine-root systems were crucial in the evolution of seed plant lineages, with important implications for ecological processes in terrestrial ecosystems.
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Affiliation(s)
- Oscar J Valverde-Barrantes
- International Center for Tropical Biodiversity, Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA
| | - Hafiz Maherali
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Christopher Baraloto
- International Center for Tropical Biodiversity, Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA
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22
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Harris JM, Pawlowski K, Mathesius U. Editorial: Evolution of Signaling in Plant Symbioses. FRONTIERS IN PLANT SCIENCE 2020; 11:456. [PMID: 32411157 PMCID: PMC7198894 DOI: 10.3389/fpls.2020.00456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/27/2020] [Indexed: 05/29/2023]
Affiliation(s)
- Jeanne Marie Harris
- Department of Plant Biology, University of Vermont, Burlington, VT, United States
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Ulrike Mathesius
- Division of Plant Sciences, Research School of Biology, Australian National University, Canberra, ACT, Australia
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23
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Oldroyd GED, Leyser O. A plant's diet, surviving in a variable nutrient environment. Science 2020; 368:368/6486/eaba0196. [PMID: 32241923 DOI: 10.1126/science.aba0196] [Citation(s) in RCA: 169] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/14/2020] [Indexed: 12/19/2022]
Abstract
As primary producers, plants rely on a large aboveground surface area to collect carbon dioxide and sunlight and a large underground surface area to collect the water and mineral nutrients needed to support their growth and development. Accessibility of the essential nutrients nitrogen (N) and phosphorus (P) in the soil is affected by many factors that create a variable spatiotemporal landscape of their availability both at the local and global scale. Plants optimize uptake of the N and P available through modifications to their growth and development and engagement with microorganisms that facilitate their capture. The sensing of these nutrients, as well as the perception of overall nutrient status, shapes the plant's response to its nutrient environment, coordinating its development with microbial engagement to optimize N and P capture and regulate overall plant growth.
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Affiliation(s)
- Giles E D Oldroyd
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK. .,Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge CB3 0LE, UK
| | - Ottoline Leyser
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
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Konkolewska A, Piechalak A, Ciszewska L, Antos-Krzemińska N, Skrzypczak T, Hanć A, Sitko K, Małkowski E, Barałkiewicz D, Małecka A. Combined use of companion planting and PGPR for the assisted phytoextraction of trace metals (Zn, Pb, Cd). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:13809-13825. [PMID: 32034599 PMCID: PMC7162837 DOI: 10.1007/s11356-020-07885-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 01/27/2020] [Indexed: 05/20/2023]
Abstract
Biomass production and metal accumulation in plant tissue (bioconcentration) are two critical factors limiting the phytoextraction rate. Metal translocation to aboveground organs should be accounted for as the third most important factor, as harvesting of the plant roots is usually economically disadvantageous. These three parameters could be potentially increased with the use of companion planting, a well-known agricultural technique, and inoculation with plant growth-promoting bacteria (PGPB). The aim of the study was to determine whether intercropping and inoculation with endophytic PGPB (Burkholderia phytofirmans PsJNT) can increase the efficiency of phytoextraction of Zn, Pb, and Cd. The study was conducted on Brassica juncea (L.) Czern. "Małopolska" grown in a monoculture or co-planted with Zea mays L. "Codimon" and Medicago sativa L. "Sanditi." Results show that companion planting and inoculation with rhizobacteria can increase the efficiency of metal phytoextraction, mainly by increasing the yield of dry biomass and the survival rate of plants grown on contaminated soil. We have shown that the simultaneous planting of B. juncea with M. sativa and inoculation with PGPB were the most efficient variants of assisted phytoextraction reaching a recovery of 95% Zn, 90% Cd, and on average about 160% Pb compared with control B. juncea plants grown in monoculture.
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Affiliation(s)
- Agnieszka Konkolewska
- Department of Biochemistry, Adam Mickiewicz University in Poznan, Uniwersytet Poznanski 6 Street, 61-614, Poznan, Poland.
| | - Aneta Piechalak
- Laboratory of Genome Biology, Adam Mickiewicz University in Poznan, Uniwersytet Poznanski 6 Street, 61-614, Poznan, Poland
| | - Liliana Ciszewska
- Laboratory of RNA Biochemistry, Adam Mickiewicz University in Poznan, Uniwersytet Poznanski 6 Street, 61-614, Poznan, Poland
| | - Nina Antos-Krzemińska
- Department of Bioenergetics, Adam Mickiewicz University in Poznan, Uniwersytet Poznanski 6 Street, 61-614, Poznan, Poland
| | - Tomasz Skrzypczak
- Institute of Biology and Human Evolutionary, Adam Mickiewicz University in Poznan, Uniwersytet Poznanski 6 Street, 61-614, Poznan, Poland
| | - Anetta Hanć
- Department of Trace Analysis, Faculty Chemistry, Adam Mickiewicz University in Poznań, Uniwersytet Poznanski 8 Street, 61-614, Poznan, Poland
| | - Krzysztof Sitko
- Faculty of Natural Sciences, University of Silesia in Katowice, 40-032, Katowice, Poland
| | - Eugeniusz Małkowski
- Faculty of Natural Sciences, University of Silesia in Katowice, 40-032, Katowice, Poland
| | - Danuta Barałkiewicz
- Department of Trace Analysis, Faculty Chemistry, Adam Mickiewicz University in Poznań, Uniwersytet Poznanski 8 Street, 61-614, Poznan, Poland
| | - Arleta Małecka
- Laboratory of Biotechnology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, Uniwersytet Poznanski 6 Street, 61-614, Poznan, Poland.
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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: 78] [Impact Index Per Article: 15.6] [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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Wu Z, Wang M, Yang S, Chen S, Chen X, Liu C, Wang S, Wang H, Zhang B, Liu H, Qin R, Wang X. A global coexpression network of soybean genes gives insights into the evolution of nodulation in nonlegumes and legumes. THE NEW PHYTOLOGIST 2019; 223:2104-2119. [PMID: 30977533 DOI: 10.1111/nph.15845] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
Abstract
A coexpression network is a powerful tool for revealing genes' relationship with many biological processes. Mass transcriptomic and genomic data from different plant species provide the foundation for understanding the evolution of nodulation across the Viridiplantae at a systematic level. We used weighted coexpression network analysis (WGCNA) to mine a nodule-related module (NRM) in Glycine max. Comparative genomic analysis of 78 green plant species revealed that NRM genes are recruited from different evolutionary nodes along with gene duplication events. A set of core coexpressed genes within legumes may play vital roles in regulating nodule environments essential for nitrogen fixation, including oxygen concentrations, sulfur transport, and iron homeostasis (such as GmCHY). The regulation of these genes occurred mainly at the transcription level, although some of them, such as sulfate transporters, may also undergo positive selection at protein level. We revealed that ancient orthologs and duplication events before the origin of legumes were preadapted for symbiosis. Conserved coregulated genes found within legumes paved the way for nodule formation and nitrogen fixation. These findings provide significant insights into the evolution of nodulation and indicate promising candidates for identifying other key components of legume nodulation and nitrogen fixation.
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Affiliation(s)
- Zhihua Wu
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, South-Central University for Nationalities, Wuhan, Hubei Province, 430074, China
| | - Meirong Wang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Siyu Yang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Shengcai Chen
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Xu Chen
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Chang Liu
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Shixiang Wang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Haijiao Wang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Bao Zhang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, South-Central University for Nationalities, Wuhan, Hubei Province, 430074, China
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, South-Central University for Nationalities, Wuhan, Hubei Province, 430074, China
| | - Xuelu Wang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
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Pucciariello C, Boscari A, Tagliani A, Brouquisse R, Perata P. Exploring Legume-Rhizobia Symbiotic Models for Waterlogging Tolerance. FRONTIERS IN PLANT SCIENCE 2019; 10:578. [PMID: 31156662 PMCID: PMC6530402 DOI: 10.3389/fpls.2019.00578] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 04/18/2019] [Indexed: 06/09/2023]
Abstract
Unexpected and increasingly frequent extreme precipitation events result in soil flooding or waterlogging. Legumes have the capacity to establish a symbiotic relationship with endosymbiotic atmospheric dinitrogen-fixing rhizobia, thus contributing to natural nitrogen soil enrichment and reducing the need for chemical fertilization. The impact of waterlogging on nitrogen fixation and legume productivity needs to be considered for crop improvement. This review focuses on the legumes-rhizobia symbiotic models. We aim to summarize the mechanisms underlying symbiosis establishment, nodule development and functioning under waterlogging. The mechanisms of oxygen sensing of the host plant and symbiotic partner are considered in view of recent scientific advances.
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Affiliation(s)
- Chiara Pucciariello
- PlantLab, Institute of Life Sciences, Sant’Anna School of Advanced Studies, Pisa, Italy
| | - Alexandre Boscari
- Institut Sophia Agrobiotech, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Côte d’Azur, Nice, France
| | - Andrea Tagliani
- PlantLab, Institute of Life Sciences, Sant’Anna School of Advanced Studies, Pisa, Italy
| | - Renaud Brouquisse
- Institut Sophia Agrobiotech, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Côte d’Azur, Nice, France
| | - Pierdomenico Perata
- PlantLab, Institute of Life Sciences, Sant’Anna School of Advanced Studies, Pisa, Italy
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Harman GE, Uphoff N. Symbiotic Root-Endophytic Soil Microbes Improve Crop Productivity and Provide Environmental Benefits. SCIENTIFICA 2019; 2019:9106395. [PMID: 31065398 PMCID: PMC6466867 DOI: 10.1155/2019/9106395] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/05/2019] [Indexed: 05/02/2023]
Abstract
Plants should not be regarded as entities unto themselves, but as the visible part of plant-microbe complexes which are best understood as "holobiomes." Some microorganisms when given the opportunity to inhabit plant roots become root symbionts. Such root colonization by symbiotic microbes can raise crop yields by promoting the growth of both shoots and roots, by enhancing uptake, fixation, and/or more efficient use of nutrients, by improving plants' resistance to pests, diseases, and abiotic stresses that include drought, salt, and other environmental conditions, and by enhancing plants' capacity for photosynthesis. We refer plant-microbe associations with these capabilities that have been purposefully established as enhanced plant holobiomes (EPHs). Here, we consider four groups of phylogenetically distinct and distant symbiotic endophytes: (1) Rhizobiaceae bacteria; (2) plant-obligate arbuscular mycorrhizal fungi (AMF); (3) selected endophytic strains of fungi in the genus Trichoderma; and (4) fungi in the Sebicales order, specifically Piriformospora indica. Although these exhibit quite different "lifestyles" when inhabiting plants, all induce beneficial systemic changes in plants' gene expression that are surprisingly similar. For example, all induce gene expression that produces proteins which detoxify reactive oxygen species (ROS). ROS are increased by environmental stresses on plants or by overexcitation of photosynthetic pigments. Gene overexpression results in a cellular environment where ROS levels are controlled and made more compatible with plants' metabolic processes. EPHs also frequently exhibit increased rates of photosynthesis that contribute to greater plant growth and other capabilities. Soil organic matter (SOM) is augmented when plant root growth is increased and roots remain in the soil. The combination of enhanced photosynthesis, increasing sequestration of CO2 from the air, and elevation of SOM removes C from the atmosphere and stores it in the soil. Reductions in global greenhouse gas levels can be accelerated by incentives for carbon farming and carbon cap-and-trade programs that reward such climate-friendly agriculture. The development and spread of EPHs as part of such initiatives has potential both to enhance farm productivity and incomes and to decelerate global warming.
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Moreau D, Bardgett RD, Finlay RD, Jones DL, Philippot L. A plant perspective on nitrogen cycling in the rhizosphere. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13303] [Citation(s) in RCA: 159] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Delphine Moreau
- Agroécologie, AgroSup Dijon INRA, Université Bourgogne Franche‐Comté Dijon France
| | - Richard D. Bardgett
- School of Earth and Environmental Sciences The University of Manchester Manchester UK
| | - Roger D. Finlay
- Department of Forest Mycology and Plant Pathology Uppsala Biocenter, Swedish University of Agricultural Sciences Uppsala Sweden
| | - David L. Jones
- Environment Centre Wales Bangor University Gwynedd UK
- UWA School of Agriculture and Environment University of Western Australia Crawley Western Australia Australia
| | - Laurent Philippot
- Agroécologie, AgroSup Dijon INRA, Université Bourgogne Franche‐Comté Dijon France
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Abstract
Animal–microbe associations are critical drivers of evolutionary innovation, yet the origin of specialized symbiotic organs remains largely unexplored. We analyzed the genome of Euprymna scolopes, a model cephalopod, and observed large-scale genomic reorganizations compared with the ancestral bilaterian genome. We report distinct evolutionary signatures within the two symbiotic organs of E. scolopes, the light organ (LO) and the accessory nidamental gland (ANG). The LO evolved through subfunctionalization of genes expressed in the eye, indicating a deep evolutionary link between these organs. Alternatively, the ANG was enriched in novel, species-specific orphan genes suggesting these two tissues originated via different evolutionary strategies. These analyses represent the first genomic insights into the evolution of multiple symbiotic organs within a single animal host. Microbes have been critical drivers of evolutionary innovation in animals. To understand the processes that influence the origin of specialized symbiotic organs, we report the sequencing and analysis of the genome of Euprymna scolopes, a model cephalopod with richly characterized host–microbe interactions. We identified large-scale genomic reorganization shared between E. scolopes and Octopus bimaculoides and posit that this reorganization has contributed to the evolution of cephalopod complexity. To reveal genomic signatures of host–symbiont interactions, we focused on two specialized organs of E. scolopes: the light organ, which harbors a monoculture of Vibrio fischeri, and the accessory nidamental gland (ANG), a reproductive organ containing a bacterial consortium. Our findings suggest that the two symbiotic organs within E. scolopes originated by different evolutionary mechanisms. Transcripts expressed in these microbe-associated tissues displayed their own unique signatures in both coding sequences and the surrounding regulatory regions. Compared with other tissues, the light organ showed an abundance of genes associated with immunity and mediating light, whereas the ANG was enriched in orphan genes known only from E. scolopes. Together, these analyses provide evidence for different patterns of genomic evolution of symbiotic organs within a single host.
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31
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Gifford I, Battenberg K, Vaniya A, Wilson A, Tian L, Fiehn O, Berry AM. Distinctive Patterns of Flavonoid Biosynthesis in Roots and Nodules of Datisca glomerata and Medicago spp. Revealed by Metabolomic and Gene Expression Profiles. FRONTIERS IN PLANT SCIENCE 2018; 9:1463. [PMID: 30364174 PMCID: PMC6192435 DOI: 10.3389/fpls.2018.01463] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 09/14/2018] [Indexed: 05/08/2023]
Abstract
Plants within the Nitrogen-fixing Clade (NFC) of Angiosperms form root nodule symbioses with nitrogen-fixing bacteria. Actinorhizal plants (in Cucurbitales, Fagales, Rosales) form symbioses with the actinobacteria Frankia while legumes (Fabales) form symbioses with proteobacterial rhizobia. Flavonoids, secondary metabolites of the phenylpropanoid pathway, have been shown to play major roles in legume root nodule symbioses: as signal molecules that in turn trigger rhizobial nodulation initiation signals and acting as polar auxin transport inhibitors, enabling a key step in nodule organogenesis. To explore a potentially broader role for flavonoids in root nodule symbioses across the NFC, we combined metabolomic and transcriptomic analyses of roots and nodules of the actinorhizal host Datisca glomerata and legumes of the genus Medicago. Patterns of biosynthetic pathways were inferred from flavonoid metabolite profiles and phenylpropanoid gene expression patterns in the two hosts to identify similarities and differences. Similar classes of flavonoids were represented in both hosts, and an increase in flavonoids generally in the nodules was observed, with differences in flavonoids prominent in each host. While both hosts produced derivatives of naringenin, the metabolite profile in D. glomerata indicated an emphasis on the pinocembrin biosynthetic pathway, and an abundance of flavonols with potential roles in symbiosis. Additionally, the gene expression profile indicated a decrease in expression in the lignin/monolignol pathway. In Medicago sativa, by contrast, isoflavonoids were highly abundant featuring more diverse and derived isoflavonoids than D. glomerata. Gene expression patterns supported these differences in metabolic pathways, especially evident in a difference in expression of cinnamic acid 4-hydroxylase (C4H), which was expressed at substantially lower levels in D. glomerata than in a Medicago truncatula transcriptome where it was highly expressed. C4H is a major rate-limiting step in phenylpropanoid biosynthesis that separates the pinocembrin pathway from the lignin/monolignol and naringenin-based flavonoid branches. Shikimate O-hydroxycinnamoyltransferase, the link between flavonoid biosynthesis and the lignin/monolignol pathway, was also expressed at much lower levels in D. glomerata than in M. truncatula. Our results indicate (a) a likely major role for flavonoids in actinorhizal nodules, and (b) differences in metabolic flux in flavonoid and phenylpropanoid biosynthesis between the different hosts in symbiosis.
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Affiliation(s)
- Isaac Gifford
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Kai Battenberg
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Arpana Vaniya
- West Coast Metabolomics Center, University of California, Davis, Davis, CA, United States
| | - Alex Wilson
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Li Tian
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, Davis, CA, United States
| | - Alison M. Berry
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
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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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Prihatna C, Larkan NJ, Barbetti MJ, Barker SJ. Tomato CYCLOPS/IPD3 is required for mycorrhizal symbiosis but not tolerance to Fusarium wilt in mycorrhiza-deficient tomato mutant rmc. MYCORRHIZA 2018; 28:495-507. [PMID: 29948410 DOI: 10.1007/s00572-018-0842-z] [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: 02/22/2018] [Accepted: 05/31/2018] [Indexed: 06/08/2023]
Abstract
Mycorrhizal symbiosis requires several common symbiosis genes including CYCLOPS/IPD3. The reduced mycorrhizal colonisation (rmc) tomato mutant has a deletion of five genes including CYCLOPS/IPD3, and rmc is more susceptible to Fusarium wilt than its wild-type parental line. This study investigated the genetic defects leading to both fungal interaction phenotypes and whether these were separable. Complementation was performed in rmc to test the requirement for CYCLOPS/IPD3 in mycorrhiza formation and Fusarium wilt tolerance. Promoter analysis via GFP expression in roots was conducted to determine the role of native regulatory elements in the proper functioning of CYCLOPS/IPD3. CYCLOPS/IPD3 regulated by its native promoter, but not a 2×35S promoter, restores mycorrhizal association in rmc. GFP regulated by the 2×35S promoter is not expressed in epidermal cells of roots, indicating that expression of CYCLOPS/IPD3 in these cells is required for colonisation by the fungi utilised in this research. CYCLOPS/IPD3 did not restore Fusarium wilt tolerance, however, showing that the genetic requirements for mycorrhizal association and Fusarium wilt tolerance are different. Our results confirm the expected role of CYCLOPS/IPD3 in mycorrhizal symbiosis and suggest that Fusarium tolerance is conferred by one of the other four genes affected by the deletion.
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Affiliation(s)
- Cahya Prihatna
- School of Agriculture and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia.
- PT Wilmar Benih Indonesia, Jalan Jababeka X Blok F No. 9, Bekasi, Jawa Barat, 17530, Indonesia.
| | | | - Martin John Barbetti
- School of Agriculture and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
- The UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Susan Jane Barker
- School of Agriculture and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
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Palakurty SX, Stinchcombe JR, Afkhami ME. Cooperation and coexpression: How coexpression networks shift in response to multiple mutualists. Mol Ecol 2018. [DOI: 10.1111/mec.14550] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
| | - John R. Stinchcombe
- Department of Ecology and Evolutionary Biology University of Toronto Toronto ON Canada
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35
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Ossler JN, Heath KD. Shared Genes but Not Shared Genetic Variation: Legume Colonization by Two Belowground Symbionts. Am Nat 2018. [DOI: 10.1086/695829] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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36
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Flores AC, Via VD, Savy V, Villagra UM, Zanetti ME, Blanco F. Comparative phylogenetic and expression analysis of small GTPases families in legume and non-legume plants. PLANT SIGNALING & BEHAVIOR 2018; 13:e1432956. [PMID: 29452030 PMCID: PMC5846509 DOI: 10.1080/15592324.2018.1432956] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 01/22/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND Small monomeric GTPases act as molecular switches in several processes that involve polar cell growth, participating mainly in vesicle trafficking and cytoskeleton rearrangements. This gene superfamily has largely expanded in plants through evolution as compared with other Kingdoms, leading to the suggestion that members of each subfamily might have acquired new functions associated to plant-specific processes. Legume plants engage in a nitrogen-fixing symbiotic interaction with rhizobia in a process that involves polar growth processes associated with the infection throughout the root hair. To get insight into the evolution of small GTPases associated with this process, we use a comparative genomic approach to establish differences in the Ras GTPase superfamily between legume and non-legume plants. RESULTS Phylogenetic analyses did not show clear differences in the organization of the different subfamilies of small GTPases between plants that engage or not in nodule symbiosis. Protein alignments revealed a strong conservation at the sequence level of small GTPases previously linked to nodulation by functional genetics. Interestingly, one Rab and three Rop proteins showed conserved amino acid substitutions in legumes, but these changes do not alter the predicted conformational structure of these proteins. Although the steady-state levels of most small GTPases do not change in response to rhizobia, we identified a subset of Rab, Rop and Arf genes whose transcript levels are modulated during the symbiotic interaction, including their spatial distribution along the indeterminate nodule. CONCLUSIONS This study provides a comprehensive study of the small GTPase superfamily in several plant species. The genetic program associated to root nodule symbiosis includes small GTPases to fulfill specific functions during infection and formation of the symbiosomes. These GTPases seems to have been recruited from members that were already present in common ancestors with plants as distant as monocots since we failed to detect asymmetric evolution in any of the subfamily trees. Expression analyses identified a number of legume members that can have undergone neo- or sub-functionalization associated to the spatio-temporal transcriptional control during the onset of the symbiotic interaction.
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Affiliation(s)
- Ana Claudia Flores
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
| | - Virginia Dalla Via
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
| | - Virginia Savy
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
| | - Ulises Mancini Villagra
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
| | - María Eugenia Zanetti
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
| | - Flavio Blanco
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
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37
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Coba de la Peña T, Fedorova E, Pueyo JJ, Lucas MM. The Symbiosome: Legume and Rhizobia Co-evolution toward a Nitrogen-Fixing Organelle? FRONTIERS IN PLANT SCIENCE 2018; 8:2229. [PMID: 29403508 PMCID: PMC5786577 DOI: 10.3389/fpls.2017.02229] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 12/19/2017] [Indexed: 05/21/2023]
Abstract
In legume nodules, symbiosomes containing endosymbiotic rhizobial bacteria act as temporary plant organelles that are responsible for nitrogen fixation, these bacteria develop mutual metabolic dependence with the host legume. In most legumes, the rhizobia infect post-mitotic cells that have lost their ability to divide, although in some nodules cells do maintain their mitotic capacity after infection. Here, we review what is currently known about legume symbiosomes from an evolutionary and developmental perspective, and in the context of the different interactions between diazotroph bacteria and eukaryotes. As a result, it can be concluded that the symbiosome possesses organelle-like characteristics due to its metabolic behavior, the composite origin and differentiation of its membrane, the retargeting of host cell proteins, the control of microsymbiont proliferation and differentiation by the host legume, and the cytoskeletal dynamics and symbiosome segregation during the division of rhizobia-infected cells. Different degrees of symbiosome evolution can be defined, specifically in relation to rhizobial infection and to the different types of nodule. Thus, our current understanding of the symbiosome suggests that it might be considered a nitrogen-fixing link in organelle evolution and that the distinct types of legume symbiosomes could represent different evolutionary stages toward the generation of a nitrogen-fixing organelle.
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Affiliation(s)
- Teodoro Coba de la Peña
- Instituto de Ciencias Agrarias ICA-CSIC, Madrid, Spain
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), La Serena, Chile
| | - Elena Fedorova
- Instituto de Ciencias Agrarias ICA-CSIC, Madrid, Spain
- K. A. Timiryazev Institute of Plant Physiology, Russian Academy of Science, Moscow, Russia
| | - José J Pueyo
- Instituto de Ciencias Agrarias ICA-CSIC, Madrid, Spain
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38
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Burks D, Azad R, Wen J, Dickstein R. The Medicago truncatula Genome: Genomic Data Availability. Methods Mol Biol 2018; 1822:39-59. [PMID: 30043295 DOI: 10.1007/978-1-4939-8633-0_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Medicago truncatula emerged in 1990 as a model for legumes, comprising the third largest land plant family. Most legumes form symbiotic nitrogen-fixing root nodules with compatible soil bacteria and thus are important contributors to the global nitrogen cycle and sustainable agriculture. Legumes and legume products are important sources for human and animal protein as well as for edible and industrial oils. In the years since M. truncatula was chosen as a legume model, many genetic, genomic, and molecular resources have become available, including reference quality genome sequences for two widely used genotypes. Accessibility of genomic data is important for many different types of studies with M. truncatula as well as for research involving crop and forage legumes. In this chapter, we discuss strategies to obtain archived M. truncatula genomic data originally deposited into custom databases that are no longer maintained but are now accessible in general databases. We also review key current genomic databases that are specific to M. truncatula as well as those that contain M. truncatula data in addition to data from other plants.
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Affiliation(s)
- David Burks
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Rajeev Azad
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA.,Department of Mathematics, University of North Texas, Denton, TX, USA
| | | | - Rebecca Dickstein
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA.
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39
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Li H, Chen M, Duan L, Zhang T, Cao Y, Zhang Z. Domain Swap Approach Reveals the Critical Roles of Different Domains of SYMRK in Root Nodule Symbiosis in Lotus japonicus. FRONTIERS IN PLANT SCIENCE 2018; 9:697. [PMID: 29988452 PMCID: PMC6024595 DOI: 10.3389/fpls.2018.00697] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/07/2018] [Indexed: 05/13/2023]
Abstract
Symbiosis receptor kinase (SYMRK) is a cell membrane-localized protein kinase containing extracellular malectin-like domain (MLD) and leucine-rich repeat (LRR) domains, which is critically required for both root nodule symbiosis (RNS) and arbuscular mycorrhizal symbiosis (AMS). SYMRK is widely distributed in the genomes of different plant species; however, the contribution of different domains of SYMRK and its homologs from other plant species to RNS is largely unclear. In this study, SYMRK and its homologs from three typical plant species including Medicago truncatula (for both RNS and AMS), Oryza sativa (for AMS but not RNS), and Arabidopsis thaliana (for neither RNS or AMS) were investigated using domain swap approach in response to rhizobia in Lotus japonicus. Full-length SYMRK from rice and Medicago but not from Arabidopsis could complement Lotus symrk-409 mutant plants to contribute RNS. The chimeric protein with the extracellular domain (ED) of LjSYMRK and cytoplasmic domains (CD) of SYMRK from both Medicago and rice but not Arabidopsis could contribute to RNS in Lotus, suggesting that the CD of SYMRK is required for symbiotic signaling. The chimeric receptors containing the CD of LjSYMRK (SYMRKCD) and the EDs of MtDMI2 (MtDMI2ED), OsSYMRK (OsSYMRKED), AtSYMRK (AtSYMRKED), NFR1 (NFR1ED), and NFR5 (NFR5ED) could complement Lotus symrk-409 mutant plants to develop nodules. However, MtDMI2 could partially complement Lotus symrk-409 mutants to form both effective nodules and ineffective bumps, which is similar to the complementation results from MtDMI2ED-LjSYMRKCD and LjSYMRKGDLC in Lotus symrk-409 mutants, suggesting that ED of SYMRK has a very fine-tune regulation for RNS in Lotus. The deletion of either MLD or LRR on SYMRKGDLC (a mutant version of SYMRK with GDPC motif replaced by GDLC) could contribute to RNS when overexpressed in Lotus symrk-409 mutants, suggesting that MLD and LRR domains might work together to be involved in symbiotic signaling and the LRR domain might play a negative role in LjSYMRKGDLC-mediated RNS. By mutagenizing the conserved amino acids on LRR domain, five serine residues were found to be required for the function of LjSYMRKGDLC in RNS. These finding precisely refine the molecular mechanisms of SYMRK function in symbiotic signaling in L. japonicus.
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40
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De Cuyper C, Goormachtig S. Strigolactones in the Rhizosphere: Friend or Foe? MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:683-690. [PMID: 28598262 DOI: 10.1094/mpmi-02-17-0051-cr] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Strigolactones are well-known endogenous plant hormones that play a major role in planta by influencing different physiological processes. Moreover, ex planta, strigolactones are important signaling molecules in root exudates and function as host detection cues to launch mutualistic interactions with arbuscular mycorrhizal fungi in the rhizosphere. However, parasitic plants belonging to the Orobanchaceae family hijacked this communication system to stimulate their seed germination when in close proximity to the roots of a suitable host. As a result, the secretion of strigolactones by the plant can have both favorable and detrimental outcomes. Here, we discuss these dual positive and negative effects of strigolactones and we provide a detailed overview on the role of these molecules in the complex dialogs between plants and different organisms in the rhizosphere.
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Affiliation(s)
- Carolien De Cuyper
- Department of Plant Biotechnology and Bioinformatics, Ghent University, and Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, and Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
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41
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Harrison TL, Wood CW, Heath KD, Stinchcombe JR. Geographically structured genetic variation in the
Medicago lupulina
–
Ensifer
mutualism. Evolution 2017; 71:1787-1801. [DOI: 10.1111/evo.13268] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 04/08/2017] [Accepted: 04/15/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Tia L. Harrison
- Department of Ecology and Evolutionary BiologyUniversity of Toronto 25 Willcocks Street Toronto Ontario Canada M5S 3B2
| | - Corlett W. Wood
- Department of Ecology and Evolutionary BiologyUniversity of Toronto 25 Willcocks Street Toronto Ontario Canada M5S 3B2
| | - Katy D. Heath
- Department of Plant BiologyUniversity of Illinois 505 S. Goodwin Avenue Urbana Illinois 61801
| | - John R. Stinchcombe
- Department of Ecology and Evolutionary BiologyUniversity of Toronto 25 Willcocks Street Toronto Ontario Canada M5S 3B2
- Centre for Genome Evolution and FunctionUniversity of Toronto 25 Willcocks Street Toronto Ontario Canada M5S 3B2
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42
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Ibáñez F, Wall L, Fabra A. Starting points in plant-bacteria nitrogen-fixing symbioses: intercellular invasion of the roots. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1905-1918. [PMID: 27756807 DOI: 10.1093/jxb/erw387] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Agricultural practices contribute to climate change by releasing greenhouse gases such as nitrous oxide that are mainly derived from nitrogen fertilizers. Therefore, understanding biological nitrogen fixation in farming systems is beneficial to agriculture and environmental preservation. In this context, a better grasp of nitrogen-fixing systems and nitrogen-fixing bacteria-plant associations will contribute to the optimization of these biological processes. Legumes and actinorhizal plants can engage in a symbiotic interaction with nitrogen-fixing rhizobia or actinomycetes, resulting in the formation of specialized root nodules. The legume-rhizobia interaction is mediated by a complex molecular signal exchange, where recognition of different bacterial determinants activates the nodulation program in the plant. To invade plants roots, bacteria follow different routes, which are determined by the host plant. Entrance via root hairs is probably the best understood. Alternatively, entry via intercellular invasion has been observed in many legumes. Although there are common features shared by intercellular infection mechanisms, differences are observed in the site of root invasion and bacterial spread on the cortex reaching and infecting a susceptible cell to form a nodule. This review focuses on intercellular bacterial invasion of roots observed in the Fabaceae and considers, within an evolutionary context, the different variants, distribution and molecular determinants involved. Intercellular invasion of actinorhizal plants and Parasponia is also discussed.
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Affiliation(s)
- Fernando Ibáñez
- Departamento de Ciencias Naturales, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Luis Wall
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
| | - Adriana Fabra
- Departamento de Ciencias Naturales, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
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43
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Dombrowski JE, Hollenbeck VG, Martin RC. Isolation and Identification of Bacterial Endophytes from Grasses along the Oregon Coast. ACTA ACUST UNITED AC 2017. [DOI: 10.4236/ajps.2017.83040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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44
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Saha C, Mukherjee G, Agarwal-Banka P, Seal A. A consortium of non-rhizobial endophytic microbes from Typha angustifolia functions as probiotic in rice and improves nitrogen metabolism. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18:938-946. [PMID: 27453497 DOI: 10.1111/plb.12485] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 07/19/2016] [Indexed: 06/06/2023]
Abstract
Endophytic microbes isolated from plants growing in nutrient-deficient environments often possess properties that improve nutrition of agriculturally important plants. A consortium of non-rhizobial endophytic microbes isolated from a macrophyte Typha angustifolia growing in the marginal wetlands associated with a Uranium mine was characterized for their beneficial effect on rice and the mechanisms of growth promotion were investigated. The microbes were identified and characterized for their potential plant growth promoting (PGP) properties. Effect of these microbes on nitrogen (N)-metabolism of rice was tested as Typha endophytes were predominantly (N)-fixing. Relative N-use efficiency and expression of genes involved in N-uptake and assimilation were investigated in treated plants. Evidence of horizontal gene transfer (HGT) of dinitrogen reductase gene was observed within the consortium from a Pseudomonas stutzeri strain. The consortium behaved as plant probiotic and showed substantial growth benefits to Typha, their natural host as well as to rice. Typha endophytes colonized rice endosphere significantly increasing biomass, shoot length and chlorophyll content in rice plants both under N-sufficient and N-deficient conditions. N-uptake and assimilation genes were upregulated in plants treated with the endophytes even after three weeks post infection. Our results suggested, HGT of nitrogen-fixation trait to be highly prevalent among endophytes isolated from nutrient-poor habitats of the uranium mine. A long-term nitrogen deficiency response in the treated plants was elicited by the consortium improving N-uptake, assimilation and relative N-use efficiency of rice plants. This appeared to be at least one of the main strategies of plant growth promotion.
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Affiliation(s)
- C Saha
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, India
| | - G Mukherjee
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, India
| | | | - A Seal
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, India.
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45
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Doyle JJ. Chasing unicorns: Nodulation origins and the paradox of novelty. AMERICAN JOURNAL OF BOTANY 2016; 103:1865-1868. [PMID: 27756731 DOI: 10.3732/ajb.1600260] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 08/31/2016] [Indexed: 05/25/2023]
Affiliation(s)
- Jeff J Doyle
- School of Integrative Plant Science, Section of Plant Breeding & Genetics and Section of Plant Biology, 240 Emerson Hall, Cornell University, Ithaca, New York 14853 USA
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46
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Wang C, Yu H, Luo L, Duan L, Cai L, He X, Wen J, Mysore KS, Li G, Xiao A, Duanmu D, Cao Y, Hong Z, Zhang Z. NODULES WITH ACTIVATED DEFENSE 1 is required for maintenance of rhizobial endosymbiosis in Medicago truncatula. THE NEW PHYTOLOGIST 2016; 212:176-91. [PMID: 27245091 DOI: 10.1111/nph.14017] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 04/13/2016] [Indexed: 05/27/2023]
Abstract
The symbiotic interaction between legume plants and rhizobia results in the formation of root nodules, in which symbiotic plant cells host and harbor thousands of nitrogen-fixing rhizobia. Here, a Medicago truncatula nodules with activated defense 1 (nad1) mutant was identified using reverse genetics methods. The mutant phenotype was characterized using cell and molecular biology approaches. An RNA-sequencing technique was used to analyze the transcriptomic reprogramming of nad1 mutant nodules. In the nad1 mutant plants, rhizobial infection and propagation in infection threads are normal, whereas rhizobia and their symbiotic plant cells become necrotic immediately after rhizobia are released from infection threads into symbiotic cells of nodules. Defense-associated responses were detected in nad1 nodules. NAD1 is specifically present in root nodule symbiosis plants with the exception of Morus notabilis, and the transcript is highly induced in nodules. NAD1 encodes a small uncharacterized protein with two predicted transmembrane helices and is localized at the endoplasmic reticulum. Our data demonstrate a positive role for NAD1 in the maintenance of rhizobial endosymbiosis during nodulation.
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Affiliation(s)
- Chao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haixiang Yu
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Li Luo
- Shanghai Key Lab of Bio-energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Liujian Duan
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liuyang Cai
- National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xinxing He
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiangqi Wen
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Kirankumar S Mysore
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Aifang Xiao
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Deqiang Duanmu
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yangrong Cao
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zonglie Hong
- Department of Plant, Soil and Entomological Sciences and Program of Microbiology, Molecular Biology and Biochemistry, University of Idaho, Moscow, ID, 83844, USA
| | - Zhongming Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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47
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Afkhami ME, Stinchcombe JR. Multiple mutualist effects on genomewide expression in the tripartite association between
Medicago truncatula,
nitrogen‐fixing bacteria and mycorrhizal fungi. Mol Ecol 2016; 25:4946-62. [DOI: 10.1111/mec.13809] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 08/05/2016] [Accepted: 08/11/2016] [Indexed: 01/25/2023]
Affiliation(s)
- Michelle E. Afkhami
- Department of Biology University of Miami 1301 Memorial Dr. #215 Coral Gables FL 33146 USA
- Department of Ecology and Evolutionary Biology University of Toronto 25 Willcocks St. Toronto ON Canada M5S 3B2
| | - John R. Stinchcombe
- Department of Ecology and Evolutionary Biology University of Toronto 25 Willcocks St. Toronto ON Canada M5S 3B2
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48
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Granqvist E, Sun J, Op den Camp R, Pujic P, Hill L, Normand P, Morris RJ, Downie JA, Geurts R, Oldroyd GED. Bacterial-induced calcium oscillations are common to nitrogen-fixing associations of nodulating legumes and nonlegumes. THE NEW PHYTOLOGIST 2015; 207:551-8. [PMID: 26010117 PMCID: PMC4736677 DOI: 10.1111/nph.13464] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 03/25/2015] [Indexed: 05/03/2023]
Abstract
Plants that form root-nodule symbioses are within a monophyletic 'nitrogen-fixing' clade and associated signalling processes are shared with the arbuscular mycorrhizal symbiosis. Central to symbiotic signalling are nuclear-associated oscillations in calcium ions (Ca(2+) ), occurring in the root hairs of several legume species in response to the rhizobial Nod factor signal. In this study we expanded the species analysed for activation of Ca(2+) oscillations, including nonleguminous species within the nitrogen-fixing clade. We showed that Ca(2+) oscillations are a common feature of legumes in their association with rhizobia, while Cercis, a non-nodulating legume, does not show Ca(2+) oscillations in response to Nod factors from Sinorhizobium fredii NGR234. Parasponia andersonii, a nonlegume that can associate with rhizobia, showed Nod factor-induced calcium oscillations to S. fredii NGR234 Nod factors, but its non-nodulating sister species, Trema tomentosa, did not. Also within the nitrogen-fixing clade are actinorhizal species that associate with Frankia bacteria and we showed that Alnus glutinosa induces Ca(2+) oscillations in root hairs in response to exudates from Frankia alni, but not to S. fredii NGR234 Nod factors. We conclude that the ability to mount Ca(2+) oscillations in response to symbiotic bacteria is a common feature of nodulating species within the nitrogen-fixing clade.
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Affiliation(s)
| | - Jongho Sun
- John Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Rik Op den Camp
- Department of Plant ScienceLaboratory of Molecular BiologyWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Petar Pujic
- Ecologie MicrobienneCentre National de la Recherche Scientifique UMR 5557Université Lyon IUniversité LyonVilleurbanneFrance
| | - Lionel Hill
- John Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Philippe Normand
- Ecologie MicrobienneCentre National de la Recherche Scientifique UMR 5557Université Lyon IUniversité LyonVilleurbanneFrance
| | | | | | - Rene Geurts
- Department of Plant ScienceLaboratory of Molecular BiologyWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
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49
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Djordjevic MA, Mohd-Radzman NA, Imin N. Small-peptide signals that control root nodule number, development, and symbiosis. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5171-81. [PMID: 26249310 DOI: 10.1093/jxb/erv357] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Many legumes have the capacity to enter into a symbiotic association with soil bacteria generically called 'rhizobia' that results in the formation of new lateral organs on roots called nodules within which the rhizobia fix atmospheric nitrogen (N). Up to 200 million tonnes of N per annum is fixed by this association. Therefore, this symbiosis plays an integral role in the N cycle and is exploited in agriculture to support the sustainable fixation of N for cropping and animal production in developing and developed nations. Root nodulation is an expendable developmental process and competency for nodulation is coupled to low-N conditions. Both nodule initiation and development is suppressed under high-N conditions. Although root nodule formation enables sufficient N to be fixed for legumes to grow under N-deficient conditions, the carbon cost is high and nodule number is tightly regulated by local and systemic mechanisms. How legumes co-ordinate nodule formation with the other main organs of nutrient acquisition, lateral roots, is not fully understood. Independent mechanisms appear to regulate lateral roots and nodules under low- and high-N regimes. Recently, several signalling peptides have been implicated in the local and systemic regulation of nodule and lateral root formation. Other peptide classes control the symbiotic interaction of rhizobia with the host. This review focuses on the roles played by signalling peptides during the early stages of root nodule formation, in the control of nodule number, and in the establishment of symbiosis. Here, we highlight the latest findings and the gaps in our understanding of these processes.
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Affiliation(s)
- Michael A Djordjevic
- Division of Plant Sciences, Research School of Biology, College of Medicine, Biology and the Environment, The Australian National University, Canberra ACT 2601, Australia
| | - Nadiatul A Mohd-Radzman
- Division of Plant Sciences, Research School of Biology, College of Medicine, Biology and the Environment, The Australian National University, Canberra ACT 2601, Australia
| | - Nijat Imin
- Division of Plant Sciences, Research School of Biology, College of Medicine, Biology and the Environment, The Australian National University, Canberra ACT 2601, Australia
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Delaux PM, Radhakrishnan G, Oldroyd G. Tracing the evolutionary path to nitrogen-fixing crops. CURRENT OPINION IN PLANT BIOLOGY 2015; 26:95-99. [PMID: 26123396 DOI: 10.1016/j.pbi.2015.06.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 05/01/2015] [Accepted: 06/02/2015] [Indexed: 06/04/2023]
Abstract
Nitrogen-fixing symbioses between plants and bacteria are restricted to a few plant lineages. The plant partner benefits from these associations by gaining access to the pool of atmospheric nitrogen. By contrast, other plant species, including all cereals, rely only on the scarce nitrogen present in the soil and what they can glean from associative bacteria. Global cereal yields from conventional agriculture are dependent on the application of massive levels of chemical fertilisers. Engineering nitrogen-fixing symbioses into cereal crops could in part mitigate the economic and ecological impacts caused by the overuse of fertilisers and provide better global parity in crop yields. Comparative phylogenetics and phylogenomics are powerful tools to identify genetic and genomic innovations behind key plant traits. In this review we highlight recent discoveries made using such approaches and we discuss how these approaches could be used to help direct the engineering of nitrogen-fixing symbioses into cereals.
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Affiliation(s)
- Pierre-Marc Delaux
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom.
| | - Guru Radhakrishnan
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Giles Oldroyd
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom.
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