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Du B, Haensch R, Alfarraj S, Rennenberg H. Strategies of plants to overcome abiotic and biotic stresses. Biol Rev Camb Philos Soc 2024; 99:1524-1536. [PMID: 38561998 DOI: 10.1111/brv.13079] [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: 06/29/2023] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
In their environment, plants are exposed to a multitude of abiotic and biotic stresses that differ in intensity, duration and severity. As sessile organisms, they cannot escape these stresses, but instead have developed strategies to overcome them or to compensate for the consequences of stress exposure. Defence can take place at different levels and the mechanisms involved are thought to differ in efficiency across these levels. To minimise metabolic constraints and to reduce the costs of stress defence, plants prioritise first-line defence strategies in the apoplastic space, involving ascorbate, defensins and small peptides, as well as secondary metabolites, before cellular processes are affected. In addition, a large number of different symplastic mechanisms also provide efficient stress defence, including chemical antioxidants, antioxidative enzymes, secondary metabolites, defensins and other peptides as well as proteins. At both the symplastic and the apoplastic level of stress defence and compensation, a number of specialised transporters are thought to be involved in exchange across membranes that still have not been identified, and information on the regeneration of different defence compounds remains ambiguous. In addition, strategies to overcome and compensate for stress exposure operate not only at the cellular, but also at the organ and whole-plant levels, including stomatal regulation, and hypersensitive and systemic responses to prevent or reduce the spread of stress impacts within the plant. Defence can also take place at the ecosystem level by root exudation of signalling molecules and the emission of volatile organic compounds, either directly or indirectly into the rhizosphere and/or the aboveground atmosphere. The mechanisms by which plants control the production of these compounds and that mediate perception of stressful conditions are still not fully understood. Here we summarise plant defence strategies from the cellular to ecosystem level, discuss their advantages and disadvantages for plant growth and development, elucidate the current state of research on the transport and regeneration capacity of defence metabolites, and outline insufficiently explored questions for further investigation.
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Affiliation(s)
- Baoguo Du
- College of Life Science and Biotechnology, Ecological Security and Protection Key laboratory of Sichuan Province, Mianyang Normal University, Mianxing Road West 166, Mianyang, 621000, PR China
- Chair of Tree Physiology, Institute of Forest Sciences, University of Freiburg, Georges-Köhler-Allee 53, Freiburg, D-79110, Germany
| | - Robert Haensch
- Institute of Plant Biology, Technische Universität Braunschweig, Humboldtstr. 1, Braunschweig, D-38106, Germany
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, No. 2, Tiansheng Road, Beibei District, Chongqing, 400715, PR China
| | - Saleh Alfarraj
- King Saud University, PO Box 2455, Riyadh, 11451, Saudi Arabia
| | - Heinz Rennenberg
- Chair of Tree Physiology, Institute of Forest Sciences, University of Freiburg, Georges-Köhler-Allee 53, Freiburg, D-79110, Germany
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, No. 2, Tiansheng Road, Beibei District, Chongqing, 400715, PR China
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2
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Ghosh P, Chakraborty J. Exploring the role of symbiotic modifier peptidases in the legume - rhizobium symbiosis. Arch Microbiol 2024; 206:147. [PMID: 38462552 DOI: 10.1007/s00203-024-03920-w] [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: 11/21/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/12/2024]
Abstract
Legumes can establish a mutual association with soil-derived nitrogen-fixing bacteria called 'rhizobia' forming lateral root organs called root nodules. Rhizobia inside the root nodules get transformed into 'bacteroids' that can fix atmospheric nitrogen to ammonia for host plants in return for nutrients and shelter. A substantial 200 million tons of nitrogen is fixed annually through biological nitrogen fixation. Consequently, the symbiotic mechanism of nitrogen fixation is utilized worldwide for sustainable agriculture and plays a crucial role in the Earth's ecosystem. The development of effective nitrogen-fixing symbiosis between legumes and rhizobia is very specialized and requires coordinated signaling. A plethora of plant-derived nodule-specific cysteine-rich (NCR or NCR-like) peptides get actively involved in this complex and tightly regulated signaling process of symbiosis between some legumes of the IRLC (Inverted Repeat-Lacking Clade) and Dalbergioid clades and nitrogen-fixing rhizobia. Recent progress has been made in identifying two such peptidases that actively prevent bacterial differentiation, leading to symbiotic incompatibility. In this review, we outlined the functions of NCRs and two nitrogen-fixing blocking peptidases: HrrP (host range restriction peptidase) and SapA (symbiosis-associated peptidase A). SapA was identified through an overexpression screen from the Sinorhizobium meliloti 1021 core genome, whereas HrrP is inherited extra-chromosomally. Interestingly, both peptidases affect the symbiotic outcome by degrading the NCR peptides generated from the host plants. These NCR-degrading peptidases can shed light on symbiotic incompatibility, helping to elucidate the reasons behind the inefficiency of nitrogen fixation observed in certain groups of rhizobia with specific legumes.
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Affiliation(s)
- Prithwi Ghosh
- Department of Botany, Narajole Raj College, Vidyasagar University, Midnapore, 721211, India.
| | - Joydeep Chakraborty
- School of Plant Sciences and Food Security, Tel Aviv University, Tel-Aviv, Israel
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3
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Fan K, Wang Z, Sze CC, Niu Y, Wong FL, Li MW, Lam HM. MicroRNA 4407 modulates nodulation in soybean by repressing a root-specific ISOPENTENYLTRANSFERASE (GmIPT3). THE NEW PHYTOLOGIST 2023; 240:1034-1051. [PMID: 37653681 DOI: 10.1111/nph.19222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/28/2023] [Indexed: 09/02/2023]
Abstract
MicroRNAs (miRNAs) are important regulators of plant biological processes, including soybean nodulation. One miRNA, miR4407, was identified in soybean roots and nodules. However, the function of miR4407 in soybean is still unknown. MiR4407, unique to soybean, positively regulates lateral root emergence and root structures and represses a root-specific ISOPENTENYLTRANSFERASE (GmIPT3). By altering the expression of miR4407 and GmIPT3, we investigated the role of miR4407 in lateral root and nodule development. Both miR4407 and GmIPT3 are expressed in the inner root cortex and nodule primordia. Upon rhizobial inoculation, miR4407 was downregulated while GmIPT3 was upregulated. Overexpressing miR4407 reduced the number of nodules in transgenic soybean hairy roots while overexpressing the wild-type GmIPT3 or a miR4407-resistant GmIPT3 mutant (mGmIPT3) significantly increased the nodule number. The mechanism of miR4407 and GmIPT3 functions was also linked to autoregulation of nodulation (AON), where miR4407 overexpression repressed miR172c and activated its target, GmNNC1, turning on AON. Exogenous CK mimicked the effects of GmIPT3 overexpression on miR172c, supporting the notion that GmIPT3 regulates nodulation by enhancing root-derived CK. Overall, our data revealed a new miRNA-mediated regulatory mechanism of nodulation in soybean. MiR4407 showed a dual role in lateral root and nodule development.
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Affiliation(s)
- Kejing Fan
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Zhili Wang
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ching-Ching Sze
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yongchao Niu
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Fuk-Ling Wong
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Man-Wah Li
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hon-Ming Lam
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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4
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Rahman A, Manci M, Nadon C, Perez IA, Farsamin WF, Lampe MT, Le TH, Torres Martínez L, Weisberg AJ, Chang JH, Sachs JL. Competitive interference among rhizobia reduces benefits to hosts. Curr Biol 2023; 33:2988-3001.e4. [PMID: 37490853 DOI: 10.1016/j.cub.2023.06.081] [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: 01/23/2023] [Revised: 03/31/2023] [Accepted: 06/29/2023] [Indexed: 07/27/2023]
Abstract
The capacity of beneficial microbes to compete for host infection-and the ability of hosts to discriminate among them-introduces evolutionary conflict that is predicted to destabilize mutualism. We investigated fitness outcomes in associations between legumes and their symbiotic rhizobia to characterize fitness impacts of microbial competition. Diverse Bradyrhizobium strains varying in their capacity to fix nitrogen symbiotically with a common host plant, Acmispon strigosus, were tested in full-factorial coinoculation experiments involving 28 pairwise strain combinations. We analyzed the effects of interstrain competition and host discrimination on symbiotic-interaction outcomes by relativizing fitness proxies to clonally infected and uninfected controls. More than one thousand root nodules of coinoculated plants were genotyped to quantify strain occupancy, and the Bradyrhizobium strain genome sequences were analyzed to uncover the genetic bases of interstrain competition outcomes. Strikingly, interstrain competition favored a fast-growing, minimally beneficial rhizobia strain. Host benefits were significantly diminished in coinoculation treatments relative to expectations from clonally inoculated controls, consistent with competitive interference among rhizobia that reduced both nodulation and plant growth. Competition traits appear polygenic, linked with inter-strain allelopathic interactions in the rhizosphere. This study confirms that competition among strains can destabilize mutualism by favoring microbes that are superior in colonizing host tissues but provide minimal benefits to host plants. Moreover, our findings help resolve the paradox that despite efficient host control post infection, legumes nonetheless encounter rhizobia that vary in their nitrogen fixation.
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Affiliation(s)
- Arafat Rahman
- Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Max Manci
- Department of Microbiology & Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA
| | - Cassandra Nadon
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Ivan A Perez
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Warisha F Farsamin
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Matthew T Lampe
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Tram H Le
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Lorena Torres Martínez
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA; Department of Biology, St. Mary's College of Maryland, St. Mary's City, MD 20686, USA
| | - Alexandra J Weisberg
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Jeff H Chang
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Joel L Sachs
- Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA; Department of Microbiology & Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA; Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA.
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5
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Burghardt LT, diCenzo GC. The evolutionary ecology of rhizobia: multiple facets of competition before, during, and after symbiosis with legumes. Curr Opin Microbiol 2023; 72:102281. [PMID: 36848712 DOI: 10.1016/j.mib.2023.102281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 01/12/2023] [Accepted: 01/20/2023] [Indexed: 02/27/2023]
Abstract
Rhizobial bacteria have complex lifestyles that involve growth and survival in bulk soil, plant rhizospheres and rhizoplanes, legume infection threads, and mature and senescing legume nodules. In nature, rhizobia coexist and compete with many other rhizobial strains and species to form host associations. We review recent work defining competitive interactions across these environments. We highlight the use of sophisticated measurement tools and sequencing technologies to examine competition mechanisms in planta, and highlight environments (e.g. soil and senescing nodules) where we still know exceedingly little. We argue that moving toward an explicitly ecological framework (types of competition, resources, and genetic differentiation) will clarify the evolutionary ecology of these foundational organisms and open doors for engineering sustainable, beneficial associations with hosts.
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Affiliation(s)
- Liana T Burghardt
- The Pennsylvania State University, Department of Plant Science, University Park, PA 16802, United States; The Pennsylvania State University, Ecology Graduate Program, University Park, PA 16802, United States.
| | - George C diCenzo
- Queen's University, Department of Biology, Kingston, ON K7L 3N6, Canada
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6
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Jardinaud MF, Carrere S, Gourion B, Gamas P. Symbiotic Nodule Development and Efficiency in the Medicago truncatula Mtefd-1 Mutant Is Highly Dependent on Sinorhizobium Strains. PLANT & CELL PHYSIOLOGY 2023; 64:27-42. [PMID: 36151948 DOI: 10.1093/pcp/pcac134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Symbiotic nitrogen fixation (SNF) can play a key role in agroecosystems to reduce the negative impact of nitrogen fertilizers. Its efficiency is strongly affected by the combination of bacterial and plant genotypes, but the mechanisms responsible for the differences in the efficiency of rhizobium strains are not well documented. In Medicago truncatula, SNF has been mostly studied using model systems, such as M. truncatula A17 in interaction with Sinorhizobium meliloti Sm2011. Here we analyzed both the wild-type (wt) A17 and the Mtefd-1 mutant in interaction with five S. meliloti and two Sinorhizobium medicae strains. ETHYLENE RESPONSE FACTOR REQUIRED FOR NODULE DIFFERENTIATION (MtEFD) encodes a transcription factor, which contributes to the control of nodule number and differentiation in M. truncatula. We found that, in contrast to Sm2011, four strains induce functional (Fix+) nodules in Mtefd-1, although less efficient for SNF than in wt A17. In contrast, the Mtefd-1 hypernodulation phenotype is not strain-dependent. We compared the plant nodule transcriptomes in response to SmBL225C, a highly efficient strain with A17, versus Sm2011, in wt and Mtefd-1 backgrounds. This revealed faster nodule development with SmBL225C and early nodule senescence with Sm2011. These RNA sequencing analyses allowed us to identify candidate plant factors that could drive the differential nodule phenotype. In conclusion, this work shows the value of having a set of rhizobium strains to fully evaluate the biological importance of a plant symbiotic gene.
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Affiliation(s)
- Marie-Françoise Jardinaud
- LIPME, INRAE, CNRS, Université de Toulouse, 24 Chemin de Borde Rouge, Auzeville-Tolosane 31320, France
| | - Sebastien Carrere
- LIPME, INRAE, CNRS, Université de Toulouse, 24 Chemin de Borde Rouge, Auzeville-Tolosane 31320, France
| | - Benjamin Gourion
- LIPME, INRAE, CNRS, Université de Toulouse, 24 Chemin de Borde Rouge, Auzeville-Tolosane 31320, France
| | - Pascal Gamas
- LIPME, INRAE, CNRS, Université de Toulouse, 24 Chemin de Borde Rouge, Auzeville-Tolosane 31320, France
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7
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Competitiveness and Phylogenetic Relationship of Rhizobial Strains with Different Symbiotic Efficiency in Trifolium repens: Conversion of Parasitic into Non-Parasitic Rhizobia by Natural Symbiotic Gene Transfer. BIOLOGY 2023; 12:biology12020243. [PMID: 36829520 PMCID: PMC9953144 DOI: 10.3390/biology12020243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 02/09/2023]
Abstract
In Uruguayan soils, populations of native and naturalized rhizobia nodulate white clover. These populations include efficient rhizobia but also parasitic strains, which compete for nodule occupancy and hinder optimal nitrogen fixation by the grassland. Nodulation competitiveness assays using gusA-tagged strains proved a high nodule occupancy by the inoculant strain U204, but this was lower than the strains with intermediate efficiencies, U268 and U1116. Clover biomass production only decreased when the parasitic strain UP3 was in a 99:1 ratio with U204, but not when UP3 was at equal or lower numbers than U204. Based on phylogenetic analyses, strains with different efficiencies did not cluster together, and U1116 grouped with the parasitic strains. Our results suggest symbiotic gene transfer from an effective strain to U1116, thereby improving its symbiotic efficiency. Genome sequencing of U268 and U204 strains allowed us to assign them to species Rhizobium redzepovicii, the first report of this species nodulating clover, and Rhizobium leguminosarun, respectively. We also report the presence of hrrP- and sapA-like genes in the genomes of WSM597, U204, and U268 strains, which are related to symbiotic efficiency in rhizobia. Interestingly, we report here chromosomally located hrrP-like genes.
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8
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Legumes Regulate Symbiosis with Rhizobia via Their Innate Immune System. Int J Mol Sci 2023; 24:ijms24032800. [PMID: 36769110 PMCID: PMC9917363 DOI: 10.3390/ijms24032800] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 02/05/2023] Open
Abstract
Plant roots are constantly exposed to a diverse microbiota of pathogens and mutualistic partners. The host's immune system is an essential component for its survival, enabling it to monitor nearby microbes for potential threats and respond with a defence response when required. Current research suggests that the plant immune system has also been employed in the legume-rhizobia symbiosis as a means of monitoring different rhizobia strains and that successful rhizobia have evolved to overcome this system to infect the roots and initiate nodulation. With clear implications for host-specificity, the immune system has the potential to be an important target for engineering versatile crops for effective nodulation in the field. However, current knowledge of the interacting components governing this pathway is limited, and further research is required to build on what is currently known to improve our understanding. This review provides a general overview of the plant immune system's role in nodulation. With a focus on the cycles of microbe-associated molecular pattern-triggered immunity (MTI) and effector-triggered immunity (ETI), we highlight key molecular players and recent findings while addressing the current knowledge gaps in this area.
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9
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Adaptive Evolution of Rhizobial Symbiosis beyond Horizontal Gene Transfer: From Genome Innovation to Regulation Reconstruction. Genes (Basel) 2023; 14:genes14020274. [PMID: 36833201 PMCID: PMC9957244 DOI: 10.3390/genes14020274] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
There are ubiquitous variations in symbiotic performance of different rhizobial strains associated with the same legume host in agricultural practices. This is due to polymorphisms of symbiosis genes and/or largely unexplored variations in integration efficiency of symbiotic function. Here, we reviewed cumulative evidence on integration mechanisms of symbiosis genes. Experimental evolution, in concert with reverse genetic studies based on pangenomics, suggests that gain of the same circuit of key symbiosis genes through horizontal gene transfer is necessary but sometimes insufficient for bacteria to establish an effective symbiosis with legumes. An intact genomic background of the recipient may not support the proper expression or functioning of newly acquired key symbiosis genes. Further adaptive evolution, through genome innovation and reconstruction of regulation networks, may confer the recipient of nascent nodulation and nitrogen fixation ability. Other accessory genes, either co-transferred with key symbiosis genes or stochastically transferred, may provide the recipient with additional adaptability in ever-fluctuating host and soil niches. Successful integrations of these accessory genes with the rewired core network, regarding both symbiotic and edaphic fitness, can optimize symbiotic efficiency in various natural and agricultural ecosystems. This progress also sheds light on the development of elite rhizobial inoculants using synthetic biology procedures.
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10
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Zorin EA, Kliukova MS, Afonin AM, Gribchenko ES, Gordon ML, Sulima AS, Zhernakov AI, Kulaeva OA, Romanyuk DA, Kusakin PG, Tsyganova AV, Tsyganov VE, Tikhonovich IA, Zhukov VA. A variable gene family encoding nodule-specific cysteine-rich peptides in pea ( Pisum sativum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:884726. [PMID: 36186063 PMCID: PMC9515463 DOI: 10.3389/fpls.2022.884726] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
Various legume plants form root nodules in which symbiotic bacteria (rhizobia) fix atmospheric nitrogen after differentiation into a symbiotic form named bacteroids. In some legume species, bacteroid differentiation is promoted by defensin-like nodule-specific cysteine-rich (NCR) peptides. NCR peptides have best been studied in the model legume Medicago truncatula Gaertn., while in many other legumes relevant information is still fragmentary. Here, we characterize the NCR gene family in pea (Pisum sativum L.) using genomic and transcriptomic data. We found 360 genes encoding NCR peptides that are expressed in nodules. The sequences of pea NCR genes and putative peptides are highly variable and differ significantly from NCR sequences of M. truncatula. Indeed, only one pair of orthologs (PsNCR47-MtNCR312) has been identified. The NCR genes in the pea genome are located in clusters, and the expression patterns of NCR genes from one cluster tend to be similar. These data support the idea of independent evolution of NCR genes by duplication and diversification in related legume species. We also described spatiotemporal expression profiles of NCRs and identified specific transcription factor (TF) binding sites in promoters of "early" and "late" NCR genes. Further, we studied the expression of NCR genes in nodules of Fix- mutants and predicted potential regulators of NCR gene expression, one among them being the TF ERN1 involved in the early steps of nodule organogenesis. In general, this study contributes to understanding the functions of NCRs in legume nodules and contributes to understanding the diversity and potential antibiotic properties of pea nodule-specific antimicrobial molecules.
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Affiliation(s)
- Evgeny A. Zorin
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Marina S. Kliukova
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Alexey M. Afonin
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Emma S. Gribchenko
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Mikhail L. Gordon
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Anton S. Sulima
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | | | - Olga A. Kulaeva
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Daria A. Romanyuk
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Pyotr G. Kusakin
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Anna V. Tsyganova
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Viktor E. Tsyganov
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Igor A. Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Vladimir A. Zhukov
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
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11
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Batstone RT, Burghardt LT, Heath KD. Phenotypic and genomic signatures of interspecies cooperation and conflict in naturally occurring isolates of a model plant symbiont. Proc Biol Sci 2022; 289:20220477. [PMID: 35858063 PMCID: PMC9277234 DOI: 10.1098/rspb.2022.0477] [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: 12/25/2022] Open
Abstract
Given the need to predict the outcomes of (co)evolution in host-associated microbiomes, whether microbial and host fitnesses tend to trade-off, generating conflict, remains a pressing question. Examining the relationships between host and microbe fitness proxies at both the phenotypic and genomic levels can illuminate the mechanisms underlying interspecies cooperation and conflict. We examined naturally occurring genetic variation in 191 strains of the model microbial symbiont Sinorhizobium meliloti, paired with each of two host Medicago truncatula genotypes in single- or multi-strain experiments to determine how multiple proxies of microbial and host fitness were related to one another and test key predictions about mutualism evolution at the genomic scale, while also addressing the challenge of measuring microbial fitness. We found little evidence for interspecies fitness conflict; loci tended to have concordant effects on both microbe and host fitnesses, even in environments with multiple co-occurring strains. Our results emphasize the importance of quantifying microbial relative fitness for understanding microbiome evolution and thus harnessing microbiomes to improve host fitness. Additionally, we find that mutualistic coevolution between hosts and microbes acts to maintain, rather than erode, genetic diversity, potentially explaining why variation in mutualism traits persists in nature.
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Affiliation(s)
- Rebecca T. Batstone
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
| | - Liana T. Burghardt
- Department of Plant Science, The Pennsylvania State University, 103 Tyson Building, University Park, PA, 16802 USA
| | - Katy D. Heath
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 286 Morrill Hall, 505 South Goodwin Avenue, Urbana, IL 61801, USA
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12
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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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13
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Ferreira EGC, Gomes DF, Delai CV, Barreiros MAB, Grange L, Rodrigues EP, Henning LMM, Barcellos FG, Hungria M. Revealing potential functions of hypothetical proteins induced by genistein in the symbiosis island of Bradyrhizobium japonicum commercial strain SEMIA 5079 (= CPAC 15). BMC Microbiol 2022; 22:122. [PMID: 35513812 PMCID: PMC9069715 DOI: 10.1186/s12866-022-02527-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/11/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Bradyrhizobium japonicum strain SEMIA 5079 (= CPAC 15) is a nitrogen-fixing symbiont of soybean broadly used in commercial inoculants in Brazil. Its genome has about 50% of hypothetical (HP) protein-coding genes, many in the symbiosis island, raising questions about their putative role on the biological nitrogen fixation (BNF) process. This study aimed to infer functional roles to 15 HP genes localized in the symbiosis island of SEMIA 5079, and to analyze their expression in the presence of a nod-gene inducer. RESULTS A workflow of bioinformatics tools/databases was established and allowed the functional annotation of the HP genes. Most were enzymes, including transferases in the biosynthetic pathways of cobalamin, amino acids and secondary metabolites that may help in saprophytic ability and stress tolerance, and hydrolases, that may be important for competitiveness, plant infection, and stress tolerance. Putative roles for other enzymes and transporters identified are discussed. Some HP proteins were specific to the genus Bradyrhizobium, others to specific host legumes, and the analysis of orthologues helped to predict roles in BNF. CONCLUSIONS All 15 HP genes were induced by genistein and high induction was confirmed in five of them, suggesting major roles in the BNF process.
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Affiliation(s)
- Everton Geraldo Capote Ferreira
- Londrina State University (UEL), Celso Garcia Cid Road (PR 445), km 380, CEP 86057-970 Londrina, PR Brazil
- Embrapa Soja, Rodovia Carlos João Strass, C.P. 231, CEP 86001-970 Londrina, PR Brazil
| | | | - Caroline Vanzzo Delai
- Federal University of Paraná (UFPR), Estrada dos Pioneiros 2153, CEP 85950-000 Palotina, PR Brazil
| | | | - Luciana Grange
- Federal University of Paraná (UFPR), Estrada dos Pioneiros 2153, CEP 85950-000 Palotina, PR Brazil
| | - Elisete Pains Rodrigues
- Londrina State University (UEL), Celso Garcia Cid Road (PR 445), km 380, CEP 86057-970 Londrina, PR Brazil
| | | | - Fernando Gomes Barcellos
- Londrina State University (UEL), Celso Garcia Cid Road (PR 445), km 380, CEP 86057-970 Londrina, PR Brazil
| | - Mariangela Hungria
- Londrina State University (UEL), Celso Garcia Cid Road (PR 445), km 380, CEP 86057-970 Londrina, PR Brazil
- Embrapa Soja, Rodovia Carlos João Strass, C.P. 231, CEP 86001-970 Londrina, PR Brazil
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14
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Wendlandt CE, Roberts M, Nguyen KT, Graham ML, Lopez Z, Helliwell EE, Friesen ML, Griffitts JS, Price P, Porter SS. Negotiating mutualism: A locus for exploitation by rhizobia has a broad effect size distribution and context-dependent effects on legume hosts. J Evol Biol 2022; 35:844-854. [PMID: 35506571 PMCID: PMC9325427 DOI: 10.1111/jeb.14011] [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] [Received: 12/07/2021] [Revised: 03/07/2022] [Accepted: 04/02/2022] [Indexed: 01/02/2023]
Abstract
In mutualisms, variation at genes determining partner fitness provides the raw material upon which coevolutionary selection acts, setting the dynamics and pace of coevolution. However, we know little about variation in the effects of genes that underlie symbiotic fitness in natural mutualist populations. In some species of legumes that form root nodule symbioses with nitrogen‐fixing rhizobial bacteria, hosts secrete nodule‐specific cysteine‐rich (NCR) peptides that cause rhizobia to differentiate in the nodule environment. However, rhizobia can cleave NCR peptides through the expression of genes like the plasmid‐borne Host range restriction peptidase (hrrP), whose product degrades specific NCR peptides. Although hrrP activity can confer host exploitation by depressing host fitness and enhancing symbiont fitness, the effects of hrrP on symbiosis phenotypes depend strongly on the genotypes of the interacting partners. However, the effects of hrrP have yet to be characterised in a natural population context, so its contribution to variation in wild mutualist populations is unknown. To understand the distribution of effects of hrrP in wild rhizobia, we measured mutualism phenotypes conferred by hrrP in 12 wild Ensifer medicae strains. To evaluate context dependency of hrrP effects, we compared hrrP effects across two Medicago polymorpha host genotypes and across two experimental years for five E. medicae strains. We show for the first time in a natural population context that hrrP has a wide distribution of effect sizes for many mutualism traits, ranging from strongly positive to strongly negative. Furthermore, we show that hrrP effect size varies across host genotypes and experiment years, suggesting that researchers should be cautious about extrapolating the role of genes in natural populations from controlled laboratory studies of single genetic variants.
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Affiliation(s)
- Camille E Wendlandt
- School of Biological Sciences, Washington State University, Vancouver, Washington, USA
| | - Miles Roberts
- School of Biological Sciences, Washington State University, Vancouver, Washington, USA
| | - Kyle T Nguyen
- School of Biological Sciences, Washington State University, Vancouver, Washington, USA
| | - Marion L Graham
- Biology Department, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Zoie Lopez
- School of Biological Sciences, Washington State University, Vancouver, Washington, USA
| | - Emily E Helliwell
- School of Biological Sciences, Washington State University, Vancouver, Washington, USA
| | - Maren L Friesen
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA.,Department of Crop & Soil Sciences, Washington State University, Pullman, Washington, USA
| | - Joel S Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Paul Price
- Biology Department, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Stephanie S Porter
- School of Biological Sciences, Washington State University, Vancouver, Washington, USA
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15
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Wang T, Balla B, Kovács S, Kereszt A. Varietas Delectat: Exploring Natural Variations in Nitrogen-Fixing Symbiosis Research. FRONTIERS IN PLANT SCIENCE 2022; 13:856187. [PMID: 35481136 PMCID: PMC9037385 DOI: 10.3389/fpls.2022.856187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
The nitrogen-fixing symbiosis between leguminous plants and soil bacteria collectively called rhizobia plays an important role in the global nitrogen cycle and is an essential component of sustainable agriculture. Genetic determinants directing the development and functioning of the interaction have been identified with the help of a very limited number of model plants and bacterial strains. Most of the information obtained from the study of model systems could be validated on crop plants and their partners. The investigation of soybean cultivars and different rhizobia, however, has revealed the existence of ineffective interactions between otherwise effective partners that resemble gene-for-gene interactions described for pathogenic systems. Since then, incompatible interactions between natural isolates of model plants, called ecotypes, and different bacterial partner strains have been reported. Moreover, diverse phenotypes of both bacterial mutants on different host plants and plant mutants with different bacterial strains have been described. Identification of the genetic factors behind the phenotypic differences did already and will reveal novel functions of known genes/proteins, the role of certain proteins in some interactions, and the fine regulation of the steps during nodule development.
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Affiliation(s)
- Ting Wang
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
- Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | - Benedikta Balla
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
- Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | - Szilárd Kovács
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
| | - Attila Kereszt
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
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16
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Cangioli L, Vaccaro F, Fini M, Mengoni A, Fagorzi C. Scent of a Symbiont: The Personalized Genetic Relationships of Rhizobium—Plant Interaction. Int J Mol Sci 2022; 23:ijms23063358. [PMID: 35328782 PMCID: PMC8954435 DOI: 10.3390/ijms23063358] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 01/24/2023] Open
Abstract
Many molecular signals are exchanged between rhizobia and host legume plants, some of which are crucial for symbiosis to take place, while others are modifiers of the interaction, which have great importance in the competition with the soil microbiota and in the genotype-specific perception of host plants. Here, we review recent findings on strain-specific and host genotype-specific interactions between rhizobia and legumes, discussing the molecular actors (genes, gene products and metabolites) which play a role in the establishment of symbiosis, and highlighting the need for research including the other components of the soil (micro)biota, which could be crucial in developing rational-based strategies for bioinoculants and synthetic communities’ assemblage.
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17
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Klein M, Stewart JD, Porter SS, Weedon JT, Kiers ET. Evolution of manipulative microbial behaviors in the rhizosphere. Evol Appl 2022; 15:1521-1536. [DOI: 10.1111/eva.13333] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 01/01/2023] Open
Affiliation(s)
- Malin Klein
- Department of Ecological Science Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Justin D. Stewart
- Department of Ecological Science Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Stephanie S. Porter
- School of Biological Sciences Washington State University Vancouver Washington USA
| | - James T. Weedon
- Department of Ecological Science Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - E. Toby Kiers
- Department of Ecological Science Vrije Universiteit Amsterdam Amsterdam The Netherlands
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18
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Basile LA, Lepek VC. Legume-rhizobium dance: an agricultural tool that could be improved? Microb Biotechnol 2021; 14:1897-1917. [PMID: 34318611 PMCID: PMC8449669 DOI: 10.1111/1751-7915.13906] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 12/29/2022] Open
Abstract
The specific interaction between rhizobia and legume roots leads to the development of a highly regulated process called nodulation, by which the atmospheric nitrogen is converted into an assimilable plant nutrient. This capacity is the basis for the use of bacterial inoculants for field crop cultivation. Legume plants have acquired tools that allow the entry of compatible bacteria. Likewise, plants can impose sanctions against the maintenance of nodules occupied by rhizobia with low nitrogen-fixing capacity. At the same time, bacteria must overcome different obstacles posed first by the environment and then by the legume. The present review describes the mechanisms involved in the regulation of the entire legume-rhizobium symbiotic process and the strategies and tools of bacteria for reaching the nitrogen-fixing state inside the nodule. Also, we revised different approaches to improve the nodulation process for a better crop yield.
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Affiliation(s)
- Laura A. Basile
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo A. Ugalde”Universidad Nacional de San Martín (IIB‐UNSAM‐CONICET)Av. 25 de Mayo y Francia, Gral. San Martín, Provincia de Buenos AiresBuenos AiresB1650HMPArgentina
| | - Viviana C. Lepek
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo A. Ugalde”Universidad Nacional de San Martín (IIB‐UNSAM‐CONICET)Av. 25 de Mayo y Francia, Gral. San Martín, Provincia de Buenos AiresBuenos AiresB1650HMPArgentina
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19
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Ghosh P, Adolphsen KN, Yurgel SN, Kahn ML. Sinorhizobium medicae WSM419 Genes That Improve Symbiosis between Sinorhizobium meliloti Rm1021 and Medicago truncatula Jemalong A17 and in Other Symbiosis Systems. Appl Environ Microbiol 2021; 87:e0300420. [PMID: 33990306 PMCID: PMC8276806 DOI: 10.1128/aem.03004-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 05/10/2021] [Indexed: 11/20/2022] Open
Abstract
Some soil bacteria, called rhizobia, can interact symbiotically with legumes, in which they form nodules on the plant roots, where they can reduce atmospheric dinitrogen to ammonia, a form of nitrogen that can be used by growing plants. Rhizobium-plant combinations can differ in how successful this symbiosis is: for example, Sinorhizobium meliloti Rm1021 forms a relatively ineffective symbiosis with Medicago truncatula Jemalong A17, but Sinorhizobium medicae WSM419 is able to support more vigorous plant growth. Using proteomic data from free-living and symbiotic S. medicae WSM419, we previously identified a subset of proteins that were not closely related to any S. meliloti Rm1021 proteins and speculated that adding one or more of these proteins to S. meliloti Rm1021 would increase its effectiveness on M. truncatula A17. Three genes, Smed_3503, Smed_5985, and Smed_6456, were cloned into S. meliloti Rm1021 downstream of the E. coli lacZ promoter. Strains with these genes increased nodulation and improved plant growth, individually and in combination with one another. Smed_3503, renamed iseA (increased symbiotic effectiveness), had the largest impact, increasing M. truncatula biomass by 61%. iseA homologs were present in all currently sequenced S. medicae strains but were infrequent in other Sinorhizobium isolates. Rhizobium leguminosarum bv. viciae 3841 containing iseA led to more nodules on pea and lentil. Split-root experiments with M. truncatula A17 indicated that S. meliloti Rm1021 carrying the S. medicae iseA is less sensitive to plant-induced resistance to rhizobial infection, suggesting an interaction with the plant's regulation of nodule formation. IMPORTANCE Legume symbiosis with rhizobia is highly specific. Rhizobia that can nodulate and fix nitrogen on one legume species are often unable to associate with a different species. The interaction can be more subtle. Symbiotically enhanced growth of the host plant can differ substantially when nodules are formed by different rhizobial isolates of a species, much like disease severity can differ when conspecific isolates of pathogenic bacteria infect different cultivars. Much is known about bacterial genes essential for a productive symbiosis, but less is understood about genes that marginally improve performance. We used a proteomic strategy to identify Sinorhizobium genes that contribute to plant growth differences that are seen when two different strains nodulate M. truncatula A17. These genes could also alter the symbiosis between R. leguminosarum bv. viciae 3841 and pea or lentil, suggesting that this approach identifies new genes that may more generally contribute to symbiotic productivity.
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Affiliation(s)
- Prithwi Ghosh
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Katie N. Adolphsen
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
- School of Molecular Biosciences, Washington State University, Pullman, Washington, USA
| | - Svetlana N. Yurgel
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Michael L. Kahn
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
- School of Molecular Biosciences, Washington State University, Pullman, Washington, USA
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20
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A conserved rhizobial peptidase that interacts with host-derived symbiotic peptides. Sci Rep 2021; 11:11779. [PMID: 34083727 PMCID: PMC8175422 DOI: 10.1038/s41598-021-91394-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 05/24/2021] [Indexed: 02/07/2023] Open
Abstract
In the Medicago truncatula-Sinorhizobium meliloti symbiosis, chemical signaling initiates rhizobial infection of root nodule tissue, where a large portion of the bacteria are endocytosed into root nodule cells to function in nitrogen-fixing organelles. These intracellular bacteria are subjected to an arsenal of plant-derived nodule-specific cysteine-rich (NCR) peptides, which induce the physiological changes that accompany nitrogen fixation. NCR peptides drive these intracellular bacteria toward terminal differentiation. The bacterial peptidase HrrP was previously shown to degrade host-derived NCR peptides and give the bacterial symbionts greater fitness at the expense of host fitness. The hrrP gene is found in roughly 10% of Sinorhizobium isolates, as it is carried on an accessory plasmid. The objective of the present study is to identify peptidase genes in the core genome of S. meliloti that modulate symbiotic outcome in a manner similar to the accessory hrrP gene. In an overexpression screen of annotated peptidase genes, we identified one such symbiosis-associated peptidase (sap) gene, sapA (SMc00451). When overexpressed, sapA leads to a significant decrease in plant fitness. Its promoter is active in root nodules, with only weak expression evident under free-living conditions. The SapA enzyme can degrade a broad range of NCR peptides in vitro.
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21
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Bradyrhizobium diazoefficiens USDA110 Nodulation of Aeschynomene afraspera Is Associated with Atypical Terminal Bacteroid Differentiation and Suboptimal Symbiotic Efficiency. mSystems 2021; 6:6/3/e01237-20. [PMID: 33975972 PMCID: PMC8125078 DOI: 10.1128/msystems.01237-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Legume-rhizobium symbiosis is a major ecological process in the nitrogen cycle, responsible for the main input of fixed nitrogen into the biosphere. The efficiency of this symbiosis relies on the coevolution of the partners. Legume plants can form root organs called nodules where they house intracellular symbiotic rhizobium bacteria. Within nodule cells, rhizobia differentiate into bacteroids, which fix nitrogen for the benefit of the plant. Depending on the combination of host plants and rhizobial strains, the output of rhizobium-legume interactions varies from nonfixing associations to symbioses that are highly beneficial for the plant. Bradyrhizobium diazoefficiens USDA110 was isolated as a soybean symbiont, but it can also establish a functional symbiotic interaction with Aeschynomene afraspera. In contrast to soybean, A. afraspera triggers terminal bacteroid differentiation, a process involving bacterial cell elongation, polyploidy, and increased membrane permeability, leading to a loss of bacterial viability while plants increase their symbiotic benefit. A combination of plant metabolomics, bacterial proteomics, and transcriptomics along with cytological analyses were used to study the physiology of USDA110 bacteroids in these two host plants. We show that USDA110 establishes a poorly efficient symbiosis with A. afraspera despite the full activation of the bacterial symbiotic program. We found molecular signatures of high levels of stress in A. afraspera bacteroids, whereas those of terminal bacteroid differentiation were only partially activated. Finally, we show that in A. afraspera, USDA110 bacteroids undergo atypical terminal differentiation hallmarked by the disconnection of the canonical features of this process. This study pinpoints how a rhizobium strain can adapt its physiology to a new host and cope with terminal differentiation when it did not coevolve with such a host. IMPORTANCE Legume-rhizobium symbiosis is a major ecological process in the nitrogen cycle, responsible for the main input of fixed nitrogen into the biosphere. The efficiency of this symbiosis relies on the coevolution of the partners. Some, but not all, legume plants optimize their return on investment in the symbiosis by imposing on their microsymbionts a terminal differentiation program that increases their symbiotic efficiency but imposes a high level of stress and drastically reduces their viability. We combined multi-omics with physiological analyses to show that the symbiotic couple formed by Bradyrhizobium diazoefficiens USDA110 and Aeschynomene afraspera, in which the host and symbiont did not evolve together, is functional but displays a low symbiotic efficiency associated with a disconnection of terminal bacteroid differentiation features.
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22
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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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23
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Wendlandt CE, Helliwell E, Roberts M, Nguyen KT, Friesen ML, von Wettberg E, Price P, Griffitts JS, Porter SS. Decreased coevolutionary potential and increased symbiont fecundity during the biological invasion of a legume-rhizobium mutualism. Evolution 2021; 75:731-747. [PMID: 33433925 DOI: 10.1111/evo.14164] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/08/2020] [Accepted: 12/07/2020] [Indexed: 12/20/2022]
Abstract
Although most invasive species engage in mutualism, we know little about how mutualism evolves as partners colonize novel environments. Selection on cooperation and standing genetic variation for mutualism traits may differ between a mutualism's invaded and native ranges, which could alter cooperation and coevolutionary dynamics. To test for such differences, we compare mutualism traits between invaded- and native-range host-symbiont genotype combinations of the weedy legume, Medicago polymorpha, and its nitrogen-fixing rhizobium symbiont, Ensifer medicae, which have coinvaded North America. We find that mutualism benefits for plants are indistinguishable between invaded- and native-range symbioses. However, rhizobia gain greater fitness from invaded-range mutualisms than from native-range mutualisms, and this enhancement of symbiont fecundity could increase the mutualism's spread by increasing symbiont availability during plant colonization. Furthermore, mutualism traits in invaded-range symbioses show lower genetic variance and a simpler partitioning of genetic variance between host and symbiont sources, compared to native-range symbioses. This suggests that biological invasion has reduced mutualists' potential to respond to coevolutionary selection. Additionally, rhizobia bearing a locus (hrrP) that can enhance symbiotic fitness have more exploitative phenotypes in invaded-range than in native-range symbioses. These findings highlight the impacts of biological invasion on the evolution of mutualistic interactions.
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Affiliation(s)
- Camille E Wendlandt
- School of Biological Sciences, Washington State University, Vancouver, Washington
| | - Emily Helliwell
- School of Biological Sciences, Washington State University, Vancouver, Washington
| | - Miles Roberts
- School of Biological Sciences, Washington State University, Vancouver, Washington
| | - Kyle T Nguyen
- School of Biological Sciences, Washington State University, Vancouver, Washington
| | - Maren L Friesen
- Department of Plant Pathology, Department of Crop and Soil Sciences, Washington State University, Pullman, Washington
| | - Eric von Wettberg
- Department of Plant and Soil Science, Gund Institute for the Environment, University of Vermont, Burlington, Vermont
| | - Paul Price
- Department of Biology, Eastern Michigan University, Ypsilanti, Michigan
| | - Joel S Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah
| | - Stephanie S Porter
- School of Biological Sciences, Washington State University, Vancouver, Washington
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24
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Walker L, Lagunas B, Gifford ML. Determinants of Host Range Specificity in Legume-Rhizobia Symbiosis. Front Microbiol 2020; 11:585749. [PMID: 33329456 PMCID: PMC7728800 DOI: 10.3389/fmicb.2020.585749] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/06/2020] [Indexed: 01/24/2023] Open
Abstract
Leguminous plants possess the almost unique ability to enter symbiosis with soil-resident, nitrogen fixing bacteria called rhizobia. During this symbiosis, the bacteria physically colonize specialized organs on the roots of the host plant called nodules, where they reduce atmospheric nitrogen into forms that can be assimilated by the host plant and receive photosynthates in return. In order for nodule development to occur, there is extensive chemical cross-talk between both parties during the formative stages of the symbiosis. The vast majority of the legume family are capable of forming root nodules and typically rhizobia are only able to fix nitrogen within the context of this symbiotic association. However, many legume species only enter productive symbiosis with a few, or even single rhizobial species or strains, and vice-versa. Permitting symbiosis with only rhizobial strains that will be able to fix nitrogen with high efficiency is a crucial strategy for the host plant to prevent cheating by rhizobia. This selectivity is enforced at all stages of the symbiosis, with partner choice beginning during the initial communication between the plant and rhizobia. However, it can also be influenced even once nitrogen-fixing nodules have developed on the root. This review sets out current knowledge about the molecular mechanisms employed by both parties to influence host range during legume-rhizobia symbiosis.
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Affiliation(s)
- Liam Walker
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Beatriz Lagunas
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Miriam L Gifford
- School of Life Sciences, University of Warwick, Coventry, United Kingdom.,Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, United Kingdom
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25
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Yang LL, Jiang Z, Li Y, Wang ET, Zhi XY. Plasmids Related to the Symbiotic Nitrogen Fixation Are Not Only Cooperated Functionally but Also May Have Evolved over a Time Span in Family Rhizobiaceae. Genome Biol Evol 2020; 12:2002-2014. [PMID: 32687170 PMCID: PMC7719263 DOI: 10.1093/gbe/evaa152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2020] [Indexed: 12/17/2022] Open
Abstract
Rhizobia are soil bacteria capable of forming symbiotic nitrogen-fixing nodules associated with leguminous plants. In fast-growing legume-nodulating rhizobia, such as the species in the family Rhizobiaceae, the symbiotic plasmid is the main genetic basis for nitrogen-fixing symbiosis, and is susceptible to horizontal gene transfer. To further understand the symbioses evolution in Rhizobiaceae, we analyzed the pan-genome of this family based on 92 genomes of type/reference strains and reconstructed its phylogeny using a phylogenomics approach. Intriguingly, although the genetic expansion that occurred in chromosomal regions was the main reason for the high proportion of low-frequency flexible gene families in the pan-genome, gene gain events associated with accessory plasmids introduced more genes into the genomes of nitrogen-fixing species. For symbiotic plasmids, although horizontal gene transfer frequently occurred, transfer may be impeded by, such as, the host’s physical isolation and soil conditions, even among phylogenetically close species. During coevolution with leguminous hosts, the plasmid system, including accessory and symbiotic plasmids, may have evolved over a time span, and provided rhizobial species with the ability to adapt to various environmental conditions and helped them achieve nitrogen fixation. These findings provide new insights into the phylogeny of Rhizobiaceae and advance our understanding of the evolution of symbiotic nitrogen fixation.
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Affiliation(s)
- Ling-Ling Yang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, PR China
| | - Zhao Jiang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, PR China
| | - Yan Li
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, PR China
| | - En-Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City D.F., México
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, PR China
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Lindström K, Mousavi SA. Effectiveness of nitrogen fixation in rhizobia. Microb Biotechnol 2020; 13:1314-1335. [PMID: 31797528 PMCID: PMC7415380 DOI: 10.1111/1751-7915.13517] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 12/01/2022] Open
Abstract
Biological nitrogen fixation in rhizobia occurs primarily in root or stem nodules and is induced by the bacteria present in legume plants. This symbiotic process has fascinated researchers for over a century, and the positive effects of legumes on soils and their food and feed value have been recognized for thousands of years. Symbiotic nitrogen fixation uses solar energy to reduce the inert N2 gas to ammonia at normal temperature and pressure, and is thus today, especially, important for sustainable food production. Increased productivity through improved effectiveness of the process is seen as a major research and development goal. The interaction between rhizobia and their legume hosts has thus been dissected at agronomic, plant physiological, microbiological and molecular levels to produce ample information about processes involved, but identification of major bottlenecks regarding efficiency of nitrogen fixation has proven to be complex. We review processes and results that contributed to the current understanding of this fascinating system, with focus on effectiveness of nitrogen fixation in rhizobia.
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Affiliation(s)
- Kristina Lindström
- Faculty of Biological and Environmental Sciences and Helsinki Institute of Sustainability Science (HELSUS)University of HelsinkiFI‐00014HelsinkiFinland
| | - Seyed Abdollah Mousavi
- Faculty of Biological and Environmental Sciences and Helsinki Institute of Sustainability Science (HELSUS)University of HelsinkiFI‐00014HelsinkiFinland
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Chomicki G, Werner GDA, West SA, Kiers ET. Compartmentalization drives the evolution of symbiotic cooperation. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190602. [PMID: 32772665 DOI: 10.1098/rstb.2019.0602] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Across the tree of life, hosts have evolved mechanisms to control and mediate interactions with symbiotic partners. We suggest that the evolution of physical structures that allow hosts to spatially separate symbionts, termed compartmentalization, is a common mechanism used by hosts. Such compartmentalization allows hosts to: (i) isolate symbionts and control their reproduction; (ii) reward cooperative symbionts and punish or stop interactions with non-cooperative symbionts; and (iii) reduce direct conflict among different symbionts strains in a single host. Compartmentalization has allowed hosts to increase the benefits that they obtain from symbiotic partners across a diversity of interactions, including legumes and rhizobia, plants and fungi, squid and Vibrio, insects and nutrient provisioning bacteria, plants and insects, and the human microbiome. In cases where compartmentalization has not evolved, we ask why not. We argue that when partners interact in a competitive hierarchy, or when hosts engage in partnerships which are less costly, compartmentalization is less likely to evolve. We conclude that compartmentalization is key to understanding the evolution of symbiotic cooperation. This article is part of the theme issue 'The role of the microbiome in host evolution'.
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Affiliation(s)
- Guillaume Chomicki
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Gijsbert D A Werner
- Department of Zoology, University of Oxford, Zoology Research and Administration Building, 11a Mansfield Road, Oxford OX1 3SZ, UK.,Netherlands Scientific Council for Government Policy, Buitenhof 34, 2513 AH Den Haag, The Netherlands
| | - Stuart A West
- Department of Zoology, University of Oxford, Zoology Research and Administration Building, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - E Toby Kiers
- Department of Ecological Science, VU University, Amsterdam, The Netherlands
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Kang W, Jiang Z, Chen Y, Wu F, Liu C, Wang H, Shi S, Zhang XX. Plant transcriptome analysis reveals specific molecular interactions between alfalfa and its rhizobial symbionts below the species level. BMC PLANT BIOLOGY 2020; 20:293. [PMID: 32590947 PMCID: PMC7318466 DOI: 10.1186/s12870-020-02503-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 06/18/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND Leguminous plants alter patterns of gene expression in response to symbiotic colonization and infection by their cognate rhizobial bacteria, but the extent of the transcriptomic response has rarely been examined below the species level. Here we describe the identification of 12 rhizobial biotypes of Ensifer meliloti, which form nitrogen-fixing nodules in the roots of alfalfa (Medicago sativa L.), followed by a comparative RNA-seq analysis of four alfalfa cultivars each inoculated with two E. meliloti strains varying in symbiotic performance and phylogenetic relatedness. RESULTS Rhizobial biotypes were identified on the basis of their symbiotic performance, particularly shoot dry weight. Differentially expressed genes (DEGs) and metabolic pathways were determined by comparing the RNA-seq data with that of the uninoculated control plant. Significant differences were found between DEGs generated in each cultivar with the inoculation of two rhizobial strains in comparison (P < 0.01). A total of 8111 genes was differentially expressed, representing ~ 17.1% of the M. sativa genome. The proportion of DEGs ranges from 0.5 to 12.2% for each alfalfa cultivar. Interestingly, genes with predicted roles in flavonoid biosynthesis and plant-pathogen interaction (NBS-LRR) were identified as the most significant DEGs. Other DEGs include Medsa002106 and genes encoding nodulins and NCR peptides whose expression is specifically induced during the development of nitrogen-fixing nodules. More importantly, strong significant positive correlations were observed between plant transcriptomes (DEGs and KEGG pathways) and phylogenetic distances between the two rhizobial inoculants. CONCLUSIONS Alfalfa expresses significantly distinct sets of genes in response to infection by different rhizobial strains at the below-species levels (i.e. biotype or strain). Candidate genes underlying the specific interactions include Medsa002106 and those encoding nodulins and NCR peptides and proteins in the NBS-LRR family.
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Affiliation(s)
- Wenjuan Kang
- College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
- School of Natural and Computational Sciences, Massey University at Albany, Auckland, 0745, New Zealand
| | - Zhehao Jiang
- College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yonggang Chen
- College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Fang Wu
- College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Chang Liu
- College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Haifang Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Shangli Shi
- College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China.
- Key Laboratory of Grassland Ecosystem of the Chinese Ministry of Education, Lanzhou, 730070, China.
| | - Xue-Xian Zhang
- School of Natural and Computational Sciences, Massey University at Albany, Auckland, 0745, New Zealand
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29
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Lima RM, Kylarová S, Mergaert P, Kondorosi É. Unexplored Arsenals of Legume Peptides With Potential for Their Applications in Medicine and Agriculture. Front Microbiol 2020; 11:1307. [PMID: 32625188 PMCID: PMC7314904 DOI: 10.3389/fmicb.2020.01307] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 05/22/2020] [Indexed: 12/13/2022] Open
Abstract
During endosymbiosis, bacteria live intracellularly in the symbiotic organ of their host. The host controls the proliferation of endosymbionts and prevents their spread to other tissues and organs. In Rhizobium-legume symbiosis the major host effectors are secreted nodule-specific cysteine-rich (NCR) peptides, produced exclusively in the symbiotic cells. NCRs have evolved in the Inverted Repeat Lacking Clade (IRLC) of the Leguminosae family. They are secreted peptides that mediate terminal differentiation of the endosymbionts, forming polyploid, non-cultivable cells with increased membrane permeability. NCRs form an extremely large family of peptides, which have four or six conserved cysteines but otherwise highly diverse amino acid sequences, resulting in a wide variety of anionic, neutral and cationic peptides. In vitro, many synthetic NCRs have strong antimicrobial activities against both Gram-negative and Gram-positive bacteria, including the ESKAPE strains and pathogenic fungi. The spectra and minimal bactericidal and anti-fungal concentrations of NCRs differ, indicating that, in addition to their charge, the amino acid composition and sequence also play important roles in their antimicrobial activity. NCRs attack the bacteria and fungi at the cell envelope and membrane as well as intracellularly, forming interactions with multiple essential cellular machineries. NCR-like peptides with similar symbiotic functions as the NCRs also exist in other branches of the Leguminosae family. Thus, legumes provide countless and so far unexplored sources of symbiotic peptides representing an enormous resource of pharmacologically interesting molecules.
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Affiliation(s)
- Rui M Lima
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Salome Kylarová
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Peter Mergaert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Éva Kondorosi
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
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30
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Chiu CH, Paszkowski U. Receptor-Like Kinases Sustain Symbiotic Scrutiny. PLANT PHYSIOLOGY 2020; 182:1597-1612. [PMID: 32054781 PMCID: PMC7140970 DOI: 10.1104/pp.19.01341] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/25/2020] [Indexed: 05/04/2023]
Abstract
Plant receptor-like kinases (RLKs) control the initiation, development, and maintenance of symbioses with beneficial mycorrhizal fungi and nitrogen-fixing bacteria. Carbohydrate perception activates symbiosis signaling via Lysin-motif RLKs and subsequently the common symbiosis signaling pathway. As the receptors activated are often also immune receptors in multiple species, exactly how carbohydrate identities avoid immune activation and drive symbiotic outcome is still not fully understood. This may involve the coincident detection of additional signaling molecules that provide specificity. Because of the metabolic costs of supporting symbionts, the level of symbiosis development is fine-tuned by a range of local and mobile signals that are activated by various RLKs. Beyond early, precontact symbiotic signaling, signal exchanges ensue throughout infection, nutrient exchange, and turnover of symbiosis. Here, we review the latest understanding of plant symbiosis signaling from the perspective of RLK-mediated pathways.
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Affiliation(s)
- Chai Hao Chiu
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Uta Paszkowski
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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31
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Roy P, Achom M, Wilkinson H, Lagunas B, Gifford ML. Symbiotic Outcome Modified by the Diversification from 7 to over 700 Nodule-Specific Cysteine-Rich Peptides. Genes (Basel) 2020; 11:E348. [PMID: 32218172 PMCID: PMC7230169 DOI: 10.3390/genes11040348] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/11/2020] [Accepted: 03/22/2020] [Indexed: 12/31/2022] Open
Abstract
Legume-rhizobium symbiosis represents one of the most successfully co-evolved mutualisms. Within nodules, the bacterial cells undergo distinct metabolic and morphological changes and differentiate into nitrogen-fixing bacteroids. Legumes in the inverted repeat lacking clade (IRLC) employ an array of defensin-like small secreted peptides (SSPs), known as nodule-specific cysteine-rich (NCR) peptides, to regulate bacteroid differentiation and activity. While most NCRs exhibit bactericidal effects in vitro, studies confirm that inside nodules they target the bacterial cell cycle and other cellular pathways to control and extend rhizobial differentiation into an irreversible (or terminal) state where the host gains control over bacteroids. While NCRs are well established as positive regulators of effective symbiosis, more recent findings also suggest that NCRs affect partner compatibility. The extent of bacterial differentiation has been linked to species-specific size and complexity of the NCR gene family that varies even among closely related species, suggesting a more recent origin of NCRs followed by rapid expansion in certain species. NCRs have diversified functionally, as well as in their expression patterns and responsiveness, likely driving further functional specialisation. In this review, we evaluate the functions of NCR peptides and their role as a driving force underlying the outcome of rhizobial symbiosis, where the plant is able to determine the outcome of rhizobial interaction in a temporal and spatial manner.
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Affiliation(s)
- Proyash Roy
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK; (P.R.); (M.A.); (H.W.); (B.L.)
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka 1205, Bangladesh
| | - Mingkee Achom
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK; (P.R.); (M.A.); (H.W.); (B.L.)
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, NY 14853, USA
| | - Helen Wilkinson
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK; (P.R.); (M.A.); (H.W.); (B.L.)
| | - Beatriz Lagunas
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK; (P.R.); (M.A.); (H.W.); (B.L.)
| | - Miriam L. Gifford
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK; (P.R.); (M.A.); (H.W.); (B.L.)
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32
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Grman E, Allen J, Galloway E, McBride J, Bauer JT, Price PA. Inoculation with remnant prairie soils increased the growth of three native prairie legumes but not necessarily their associations with beneficial soil microbes. Restor Ecol 2020. [DOI: 10.1111/rec.13126] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Emily Grman
- Department of Biology Eastern Michigan University 441 Mark Jefferson Science Complex Ypsilanti MI 48197 U.S.A
| | - Jamie Allen
- Department of Biology Eastern Michigan University 441 Mark Jefferson Science Complex Ypsilanti MI 48197 U.S.A
| | - Emily Galloway
- Department of Biology Eastern Michigan University 441 Mark Jefferson Science Complex Ypsilanti MI 48197 U.S.A
| | - Justin McBride
- Department of Biology Eastern Michigan University 441 Mark Jefferson Science Complex Ypsilanti MI 48197 U.S.A
| | - Jonathan T. Bauer
- Department of Biology Miami University 212 Pearson Hall Oxford OH 45056 U.S.A
- Institute for the Environment and Sustainability Miami University 118 Shideler Hall Oxford OH 45056 U.S.A
| | - Paul A. Price
- Department of Biology Eastern Michigan University 441 Mark Jefferson Science Complex Ypsilanti MI 48197 U.S.A
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33
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Gano-Cohen KA, Wendlandt CE, Al Moussawi K, Stokes PJ, Quides KW, Weisberg AJ, Chang JH, Sachs JL. Recurrent mutualism breakdown events in a legume rhizobia metapopulation. Proc Biol Sci 2020; 287:20192549. [PMID: 31992172 DOI: 10.1098/rspb.2019.2549] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Bacterial mutualists generate major fitness benefits for eukaryotes, reshaping the host phenotype and its interactions with the environment. Yet, microbial mutualist populations are predicted to generate mutants that defect from providing costly services to hosts while maintaining the capacity to exploit host resources. Here, we examined the mutualist service of symbiotic nitrogen fixation in a metapopulation of root-nodulating Bradyrhizobium spp. that associate with the native legume Acmispon strigosus. We quantified mutualism traits of 85 Bradyrhizobium isolates gathered from a 700 km transect in California spanning 10 sampled A. strigosus populations. We clonally inoculated each Bradyrhizobium isolate onto A. strigosus hosts and quantified nodulation capacity and net effects of infection, including host growth and isotopic nitrogen concentration. Six Bradyrhizobium isolates from five populations were categorized as ineffective because they formed nodules but did not enhance host growth via nitrogen fixation. Six additional isolates from three populations failed to form root nodules. Phylogenetic reconstruction inferred two types of mutualism breakdown, including three to four independent losses of effectiveness and five losses of nodulation capacity on A. strigosus. The evolutionary and genomic drivers of these mutualism breakdown events remain poorly understood.
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Affiliation(s)
- Kelsey A Gano-Cohen
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA
| | - Camille E Wendlandt
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Khadija Al Moussawi
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, CA, USA
| | - Peter J Stokes
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Kenjiro W Quides
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, CA, USA
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Joel L Sachs
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA.,Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.,Department of Evolution Ecology and Organismal Biology, University of California, Riverside, CA, USA.,Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
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34
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The rhizobial autotransporter determines the symbiotic nitrogen fixation activity of Lotus japonicus in a host-specific manner. Proc Natl Acad Sci U S A 2020; 117:1806-1815. [PMID: 31900357 DOI: 10.1073/pnas.1913349117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Leguminous plants establish endosymbiotic associations with rhizobia and form root nodules in which the rhizobia fix atmospheric nitrogen. The host plant and intracellular rhizobia strictly control this symbiotic nitrogen fixation. We recently reported a Lotus japonicus Fix- mutant, apn1 (aspartic peptidase nodule-induced 1), that impairs symbiotic nitrogen fixation. APN1 encodes a nodule-specific aspartic peptidase involved in the Fix- phenotype in a rhizobial strain-specific manner. This host-strain specificity implies that some molecular interactions between host plant APN1 and rhizobial factors are required, although the biological function of APN1 in nodules and the mechanisms governing the interactions are unknown. To clarify how rhizobial factors are involved in strain-specific nitrogen fixation, we explored transposon mutants of Mesorhizobium loti strain TONO, which normally form Fix- nodules on apn1 roots, and identified TONO mutants that formed Fix+ nodules on apn1 The identified causal gene encodes an autotransporter, part of a protein secretion system of Gram-negative bacteria. Expression of the autotransporter gene in M. loti strain MAFF3030399, which normally forms Fix+ nodules on apn1 roots, resulted in Fix- nodules. The autotransporter of TONO functions to secrete a part of its own protein (a passenger domain) into extracellular spaces, and the recombinant APN1 protein cleaved the passenger protein in vitro. The M. loti autotransporter showed the activity to induce the genes involved in nodule senescence in a dose-dependent manner. Therefore, we conclude that the nodule-specific aspartic peptidase, APN1, suppresses negative effects of the rhizobial autotransporter in order to maintain effective symbiotic nitrogen fixation in root nodules.
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35
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Syska C, Brouquisse R, Alloing G, Pauly N, Frendo P, Bosseno M, Dupont L, Boscari A. Molecular Weapons Contribute to Intracellular Rhizobia Accommodation Within Legume Host Cell. FRONTIERS IN PLANT SCIENCE 2019; 10:1496. [PMID: 31850013 PMCID: PMC6902015 DOI: 10.3389/fpls.2019.01496] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/28/2019] [Indexed: 06/10/2023]
Abstract
The interaction between legumes and bacteria of rhizobia type results in a beneficial symbiotic relationship characterized by the formation of new root organs, called nodules. Within these nodules the bacteria, released in plant cells, differentiate into bacteroids and fix atmospheric nitrogen through the nitrogenase activity. This mutualistic interaction has evolved sophisticated signaling networks to allow rhizobia entry, colonization, bacteroid differentiation and persistence in nodules. Nodule cysteine rich (NCR) peptides, reactive oxygen species (ROS), reactive nitrogen species (RNS), and toxin-antitoxin (TA) modules produced by the host plants or bacterial microsymbionts have a major role in the control of the symbiotic interaction. These molecules described as weapons in pathogenic interactions have evolved to participate to the intracellular bacteroid accommodation by escaping control of plant innate immunity and adapt the functioning of the nitrogen-fixation to environmental signalling cues.
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Affiliation(s)
- Camille Syska
- Université Côte d’Azur, INRA, CNRS, ISA, Sophia Antipolis, France
| | | | | | - Nicolas Pauly
- Laboratoire des Interactions Plantes-Microorganismes, INRA, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Pierre Frendo
- Université Côte d’Azur, INRA, CNRS, ISA, Sophia Antipolis, France
| | - Marc Bosseno
- Université Côte d’Azur, INRA, CNRS, ISA, Sophia Antipolis, France
| | - Laurence Dupont
- Université Côte d’Azur, INRA, CNRS, ISA, Sophia Antipolis, France
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36
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Benezech C, Doudement M, Gourion B. Legumes tolerance to rhizobia is not always observed and not always deserved. Cell Microbiol 2019; 22:e13124. [DOI: 10.1111/cmi.13124] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/03/2019] [Accepted: 09/05/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Claire Benezech
- LIPM, Université de Toulouse, INRA, CNRS Castanet‐Tolosan France
| | - Maëva Doudement
- LIPM, Université de Toulouse, INRA, CNRS Castanet‐Tolosan France
| | - Benjamin Gourion
- LIPM, Université de Toulouse, INRA, CNRS Castanet‐Tolosan France
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37
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Mergaert P. Role of antimicrobial peptides in controlling symbiotic bacterial populations. Nat Prod Rep 2019; 35:336-356. [PMID: 29393944 DOI: 10.1039/c7np00056a] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Covering: up to 2018 Antimicrobial peptides (AMPs) have been known for well over three decades as crucial mediators of the innate immune response in animals and plants, where they are involved in the killing of infecting microbes. However, AMPs have now also been found to be produced by eukaryotic hosts during symbiotic interactions with bacteria. These symbiotic AMPs target the symbionts and therefore have a more subtle biological role: not eliminating the microbial symbiont population but rather keeping it in check. The arsenal of AMPs and the symbionts' adaptations to resist them are in a careful balance, which contributes to the establishment of the host-microbe homeostasis. Although in many cases the biological roles of symbiotic AMPs remain elusive, for a number of symbiotic interactions, precise functions have been assigned or proposed to the AMPs, which are discussed here. The microbiota living on epithelia in animals, from the most primitive ones to the mammals, are challenged by a cocktail of AMPs that determine the specific composition of the bacterial community as well as its spatial organization. In the symbiosis of legume plants with nitrogen-fixing rhizobium bacteria, the host deploys an extremely large panel of AMPs - called nodule-specific cysteine-rich (NCR) peptides - that drive the bacteria into a terminally differentiated state and manipulate the symbiont physiology to maximize the benefit for the host. The NCR peptides are used as tools to enslave the bacterial symbionts, limiting their reproduction but keeping them metabolically active for nitrogen fixation. In the nutritional symbiotic interactions of insects and protists that have vertically transmitted bacterial symbionts with reduced genomes, symbiotic AMPs could facilitate the integration of the endosymbiont and host metabolism by favouring the flow of metabolites across the symbiont membrane through membrane permeabilization.
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Affiliation(s)
- P Mergaert
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.
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38
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Gao M, Benge A, Wu TJ, Javier R. Use of Plasmid pVMG to Make Transcriptional ß-Glucuronidase Reporter Gene Fusions in the Rhizobium Genome for Monitoring the Expression of Rhizobial Genes In Vivo. Biol Proced Online 2019; 21:8. [PMID: 31073281 PMCID: PMC6498626 DOI: 10.1186/s12575-019-0096-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 04/25/2019] [Indexed: 11/29/2022] Open
Abstract
Background The soil bacterium Sinorhizobium meliloti and its allies are important nitrogen-fixing bacterial symbionts that cause N2-fixing nodules on the roots of legumes. Chromosomal ß-glucuronidase gene (uidA) transcriptional fusions are frequently used to monitor the expression of bacterial genes during the symbiosis. However, the construction of the fusions is laborious. Results The narrow-host-range, fusion selective plasmid pVMG was constructed and used as a vector for the construction of chromosomal uidA transcriptional fusions in the S. meliloti genome. Translation termination codons were added in all three reading frames upstream of the promoterless uidA in this vector to ensure transcriptional fusions. pVMG replicated to high copy number in Escherichia coli, offering advantages for the isolation of fusion-containing plasmids and the restriction analysis. Genomic locations of uidA fusions were verified in a simple PCR experiment. All these helps reduce the sample processing time and efforts. As a demonstration of its usefulness, the N-acyl homoserine lactone (AHL) signal synthase gene promoter was fused to uidA and shown to be expressed by S. meliloti in the senescence zone of the nodule on the host plant, M. truncatula. This indicates the presence of AHL signals at the late stages of symbiosis. Conclusions A simple, pVMG-based method for construction of chromosomal uidA transcriptional fusions has been successfully used in the model rhizobium S. meliloti. It is also applicable for other rhizobial strains. Electronic supplementary material The online version of this article (10.1186/s12575-019-0096-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mengsheng Gao
- Soil and Water Sciences Department, Cancer and Genetics Research Complex, University of Florida-Institute of Food and Agricultural Sciences, Room 330E, Gainesville, 32610 USA
| | - Anne Benge
- Soil and Water Sciences Department, Cancer and Genetics Research Complex, University of Florida-Institute of Food and Agricultural Sciences, Room 330E, Gainesville, 32610 USA
| | - Tai-Jung Wu
- Soil and Water Sciences Department, Cancer and Genetics Research Complex, University of Florida-Institute of Food and Agricultural Sciences, Room 330E, Gainesville, 32610 USA
| | - Regina Javier
- Soil and Water Sciences Department, Cancer and Genetics Research Complex, University of Florida-Institute of Food and Agricultural Sciences, Room 330E, Gainesville, 32610 USA
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Sathoff AE, Samac DA. Antibacterial Activity of Plant Defensins. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:507-514. [PMID: 30501455 DOI: 10.1094/mpmi-08-18-0229-cr] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Plant defensins are antimicrobial host defense peptides expressed in all higher plants. Performing a significant role in plant innate immunity, plant defensins display potent activity against a wide range of pathogens. Vertebrate and invertebrate defensins have well-characterized antibacterial activity, but plant defensins are commonly considered to display antimicrobial activity against only fungi. In this review, we highlight the often-overlooked antibacterial activity of plant defensins. Also, we illustrate methods to evaluate defensins for antibacterial activity and describe the current advances in uncovering their antibacterial modes of action.
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Affiliation(s)
- Andrew E Sathoff
- 1 Department of Plant Pathology, 1991 Upper Buford Circle, University of Minnesota, St. Paul, MN, 55108, U.S.A.; and
| | - Deborah A Samac
- 1 Department of Plant Pathology, 1991 Upper Buford Circle, University of Minnesota, St. Paul, MN, 55108, U.S.A.; and
- 2 USDA-ARS, Plant Science Research Unit, 1991 Upper Buford Circle, St. Paul, MN 55108, U.S.A
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Gano‐Cohen KA, Wendlandt CE, Stokes PJ, Blanton MA, Quides KW, Zomorrodian A, Adinata ES, Sachs JL. Interspecific conflict and the evolution of ineffective rhizobia. Ecol Lett 2019; 22:914-924. [DOI: 10.1111/ele.13247] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/07/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Kelsey A. Gano‐Cohen
- Department of Microbiology and Plant Pathology University of California Riverside CA USA
- Department of Evolution Ecology & Organismal Biology University of California Riverside CA USA
| | - Camille E. Wendlandt
- Department of Evolution Ecology & Organismal Biology University of California Riverside CA USA
- Department of Botany and Plant Sciences University of California Riverside CA USA
| | - Peter J. Stokes
- Department of Evolution Ecology & Organismal Biology University of California Riverside CA USA
| | - Mia A. Blanton
- Department of Evolution Ecology & Organismal Biology University of California Riverside CA USA
| | - Kenjiro W. Quides
- Department of Evolution Ecology & Organismal Biology University of California Riverside CA USA
| | - Avissa Zomorrodian
- Department of Evolution Ecology & Organismal Biology University of California Riverside CA USA
| | - Eunice S. Adinata
- Department of Evolution Ecology & Organismal Biology University of California Riverside CA USA
| | - Joel L. Sachs
- Department of Microbiology and Plant Pathology University of California Riverside CA USA
- Department of Evolution Ecology & Organismal Biology University of California Riverside CA USA
- Department of Botany and Plant Sciences University of California Riverside CA USA
- Institute for Integrative Genome Biology University of California Riverside CA USA
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Pfeilmeier S, George J, Morel A, Roy S, Smoker M, Stransfeld L, Downie JA, Peeters N, Malone JG, Zipfel C. Expression of the Arabidopsis thaliana immune receptor EFR in Medicago truncatula reduces infection by a root pathogenic bacterium, but not nitrogen-fixing rhizobial symbiosis. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:569-579. [PMID: 30120864 PMCID: PMC6381793 DOI: 10.1111/pbi.12999] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 07/11/2018] [Accepted: 08/13/2018] [Indexed: 05/12/2023]
Abstract
Interfamily transfer of plant pattern recognition receptors (PRRs) represents a promising biotechnological approach to engineer broad-spectrum, and potentially durable, disease resistance in crops. It is however unclear whether new recognition specificities to given pathogen-associated molecular patterns (PAMPs) affect the interaction of the recipient plant with beneficial microbes. To test this in a direct reductionist approach, we transferred the Brassicaceae-specific PRR ELONGATION FACTOR-THERMO UNSTABLE RECEPTOR (EFR), conferring recognition of the bacterial EF-Tu protein, from Arabidopsis thaliana to the legume Medicago truncatula. Constitutive EFR expression led to EFR accumulation and activation of immune responses upon treatment with the EF-Tu-derived elf18 peptide in leaves and roots. The interaction of M. truncatula with the bacterial symbiont Sinorhizobium meliloti is characterized by the formation of root nodules that fix atmospheric nitrogen. Although nodule numbers were slightly reduced at an early stage of the infection in EFR-Medicago when compared to control lines, nodulation was similar in all lines at later stages. Furthermore, nodule colonization by rhizobia, and nitrogen fixation were not compromised by EFR expression. Importantly, the M. truncatula lines expressing EFR were substantially more resistant to the root bacterial pathogen Ralstonia solanacearum. Our data suggest that the transfer of EFR to M. truncatula does not impede root nodule symbiosis, but has a positive impact on disease resistance against a bacterial pathogen. In addition, our results indicate that Rhizobium can either avoid PAMP recognition during the infection process, or is able to actively suppress immune signaling.
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Affiliation(s)
- Sebastian Pfeilmeier
- The Sainsbury LaboratoryNorwich Research ParkNorwichUK
- John Innes CentreNorwich Research ParkNorwichUK
- Present address:
Institute of MicrobiologyDepartment of BiologyETH ZurichZurich8093Switzerland
| | | | - Arry Morel
- INRALaboratoire des Interactions Plantes Micro‐organismes (LIPM)UMR441Castanet‐TolosanFrance
- CNRSLaboratoire des Interactions Plantes Micro‐organismes (LIPM)UMR2594Castanet‐TolosanFrance
| | - Sonali Roy
- John Innes CentreNorwich Research ParkNorwichUK
- Present address:
Noble Research InstituteArdmoreOKUSA
| | | | - Lena Stransfeld
- The Sainsbury LaboratoryNorwich Research ParkNorwichUK
- Institute of Plant and Microbial Biology & Zurich‐Basel Plant Science CenterUniversity of ZurichZurichSwitzerland
| | | | - Nemo Peeters
- INRALaboratoire des Interactions Plantes Micro‐organismes (LIPM)UMR441Castanet‐TolosanFrance
- CNRSLaboratoire des Interactions Plantes Micro‐organismes (LIPM)UMR2594Castanet‐TolosanFrance
| | - Jacob G. Malone
- John Innes CentreNorwich Research ParkNorwichUK
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | - Cyril Zipfel
- The Sainsbury LaboratoryNorwich Research ParkNorwichUK
- Institute of Plant and Microbial Biology & Zurich‐Basel Plant Science CenterUniversity of ZurichZurichSwitzerland
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diCenzo GC, Zamani M, Checcucci A, Fondi M, Griffitts JS, Finan TM, Mengoni A. Multidisciplinary approaches for studying rhizobium–legume symbioses. Can J Microbiol 2019; 65:1-33. [DOI: 10.1139/cjm-2018-0377] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The rhizobium–legume symbiosis is a major source of fixed nitrogen (ammonia) in the biosphere. The potential for this process to increase agricultural yield while reducing the reliance on nitrogen-based fertilizers has generated interest in understanding and manipulating this process. For decades, rhizobium research has benefited from the use of leading techniques from a very broad set of fields, including population genetics, molecular genetics, genomics, and systems biology. In this review, we summarize many of the research strategies that have been employed in the study of rhizobia and the unique knowledge gained from these diverse tools, with a focus on genome- and systems-level approaches. We then describe ongoing synthetic biology approaches aimed at improving existing symbioses or engineering completely new symbiotic interactions. The review concludes with our perspective of the future directions and challenges of the field, with an emphasis on how the application of a multidisciplinary approach and the development of new methods will be necessary to ensure successful biotechnological manipulation of the symbiosis.
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Affiliation(s)
- George C. diCenzo
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Maryam Zamani
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alice Checcucci
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Marco Fondi
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Joel S. Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Turlough M. Finan
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
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Berrabah F, Ratet P, Gourion B. Legume Nodules: Massive Infection in the Absence of Defense Induction. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:35-44. [PMID: 30252618 DOI: 10.1094/mpmi-07-18-0205-fi] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Plants of the legume family host massive intracellular bacterial populations in the tissues of specialized organs, the nodules. In these organs, the bacteria, named rhizobia, can fix atmospheric nitrogen and transfer it to the plant. This special metabolic skill provides to the legumes an advantage when they grow on nitrogen-scarce substrates. While packed with rhizobia, the nodule cells remain alive, metabolically active, and do not develop defense reactions. Here, we review our knowledge on the control of plant immunity during the rhizobia-legume symbiosis. We present the results of an evolutionary process that selected both divergence of microbial-associated molecular motifs and active suppressors of immunity on the rhizobial side and, on the legume side, active mechanisms that contribute to suppression of immunity.
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Affiliation(s)
- Fathi Berrabah
- 1 Laboratory of Exploration and Valorization of Steppic Ecosystems, Faculty of Nature and Life Sciences, University of Ziane Achour, 17000 Djelfa, Algeria
| | - Pascal Ratet
- 2 Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France
- 3 Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France; and
| | - Benjamin Gourion
- 4 LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
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Sachs JL, Quides KW, Wendlandt CE. Legumes versus rhizobia: a model for ongoing conflict in symbiosis. THE NEW PHYTOLOGIST 2018; 219:1199-1206. [PMID: 29845625 DOI: 10.1111/nph.15222] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/04/2018] [Indexed: 05/21/2023]
Abstract
Contents Summary 1199 I. Introduction 1199 II. Selecting beneficial symbionts: one problem, many solutions 1200 III. Control and conflict over legume nodulation 1201 IV. Control and conflict over nodule growth and senescence 1204 V. Conclusion 1204 Acknowledgements 1205 References 1205 SUMMARY: The legume-rhizobia association is a powerful model of the limits of host control over microbes. Legumes regulate the formation of root nodules that house nitrogen-fixing rhizobia and adjust investment into nodule development and growth. However, the range of fitness outcomes in these traits reveals intense conflicts of interest between the partners. New work that we review and synthesize here shows that legumes have evolved varied mechanisms of control over symbionts, but that host control is often subverted by rhizobia. An outcome of this conflict is that both legumes and rhizobia have evolved numerous traits that can improve their own short-term fitness in this interaction, but little evidence exists for any net improvement in the joint trait of nitrogen fixation.
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Affiliation(s)
- Joel L Sachs
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, CA, 92521, USA
- Department of Botany & Plant Sciences, University of California, Riverside, CA, 92521, USA
- Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Kenjiro W Quides
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Camille E Wendlandt
- Department of Botany & Plant Sciences, University of California, Riverside, CA, 92521, USA
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45
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Chizhevskaya EP, Naidenova EA, Onishchuk OP, Andronov EE, Simarov BV. The Melanin Biosynthesis Gene from the CA15-1 Strain of Alfalfa Nodule Bacteria: Molecular Analysis and Phylogeny. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418080045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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46
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Stonoha-Arther C, Wang D. Tough love: accommodating intracellular bacteria through directed secretion of antimicrobial peptides during the nitrogen-fixing symbiosis. CURRENT OPINION IN PLANT BIOLOGY 2018; 44:155-163. [PMID: 29778978 DOI: 10.1016/j.pbi.2018.04.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 04/20/2018] [Accepted: 04/28/2018] [Indexed: 06/08/2023]
Abstract
The symbiosis formed by nitrogen-fixing bacteria with plant hosts mainly in the legume family involves a very intimate interaction. Within the symbiotic organ (the nodule) the bacteria are fully internalized by the host cell to become an intracellular organelle surrounded by a host-derived membrane. This arrangement is probably necessary for the efficient provision of energy and the sequestration of free oxygen molecules, two conditions required for sustained nitrogen fixation. Recent advances made in model legume species, such as Medicago truncatula, are beginning to uncover the genetic components allowing rhizobia to access the host cytoplasm and establish chronic intracellular infections without overt detrimental effects. It is now known that the rhizobial compartment in M. truncatula cells, the symbiosome, retains some features of the extracellular space as the target for a redirected host protein secretory pathway. A set of vesicle trafficking proteins function specifically in symbiotic cells to ensure the faithful delivery of secretory proteins to the intracellular bacteria, or bacteroid. This system is co-opted from the more ancient association with arbuscular mycorrhizal fungi found in most land plants, highlighting the evolutionary origin of the legume-rhizobia symbiosis. In some legume lineages, this heightened capability to process secretory proteins is needed to deliver a large number of symbiosis-specific antimicrobial peptides to the bacteria. Known as NCR peptides, these molecules transform bacteroids into a state of terminal differentiation, where the microbe loses its ability to proliferate outside their host. Numbering in their hundreds, these peptides manipulate various aspects of rhizobial biology, and affect the outcome of this symbiosis in complex ways. The extreme size of the NCR peptide family seems to be the result of an evolutionary conflict between the two partners to extract maximum benefit from each other.
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Affiliation(s)
| | - Dong Wang
- Plant Biology Graduate Program, University of Massachusetts Amherst, MA 01003, USA; Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, MA 01003, USA.
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Masson-Boivin C, Sachs JL. Symbiotic nitrogen fixation by rhizobia-the roots of a success story. CURRENT OPINION IN PLANT BIOLOGY 2018; 44:7-15. [PMID: 29289792 DOI: 10.1016/j.pbi.2017.12.001] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/12/2017] [Accepted: 12/13/2017] [Indexed: 05/12/2023]
Abstract
By evolving the dual capacity of intracellular survival and symbiotic nitrogen fixation in legumes, rhizobia have achieved an ecological and evolutionary success that has reshaped our biosphere. Despite complex challenges, including a dual lifestyle of intracellular infection separated by a free-living phase in soil, rhizobial symbiosis has spread horizontally to hundreds of bacterial species and geographically throughout the globe. This symbiosis has also persisted and been reshaped through millions of years of history. Here, we summarize recent advances in our understanding of the molecular mechanisms, ecological settings, and evolutionary pathways that are collectively responsible for this symbiotic success story. We offer predictions of how this symbiosis can evolve under new influences and for the benefit of a burgeoning human population.
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Affiliation(s)
| | - Joel L Sachs
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, CA, USA
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48
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Gourion B, Alunni B. Strain-Specific Symbiotic Genes: A New Level of Control in the Intracellular Accommodation of Rhizobia Within Legume Nodule Cells. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:287-288. [PMID: 29337641 DOI: 10.1094/mpmi-01-18-0010-le] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This is a short commentary on the article by Wang et al. published in MPMI Vol. 31, No. 2, pages 240-248.
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Affiliation(s)
- Benjamin Gourion
- 1 LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France; and
| | - Benoit Alunni
- 2 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
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49
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Clúa J, Roda C, Zanetti ME, Blanco FA. Compatibility between Legumes and Rhizobia for the Establishment of a Successful Nitrogen-Fixing Symbiosis. Genes (Basel) 2018; 9:E125. [PMID: 29495432 PMCID: PMC5867846 DOI: 10.3390/genes9030125] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 01/24/2018] [Accepted: 02/08/2018] [Indexed: 12/14/2022] Open
Abstract
The root nodule symbiosis established between legumes and rhizobia is an exquisite biological interaction responsible for fixing a significant amount of nitrogen in terrestrial ecosystems. The success of this interaction depends on the recognition of the right partner by the plant within the richest microbial ecosystems on Earth, the soil. Recent metagenomic studies of the soil biome have revealed its complexity, which includes microorganisms that affect plant fitness and growth in a beneficial, harmful, or neutral manner. In this complex scenario, understanding the molecular mechanisms by which legumes recognize and discriminate rhizobia from pathogens, but also between distinct rhizobia species and strains that differ in their symbiotic performance, is a considerable challenge. In this work, we will review how plants are able to recognize and select symbiotic partners from a vast diversity of surrounding bacteria. We will also analyze recent advances that contribute to understand changes in plant gene expression associated with the outcome of the symbiotic interaction. These aspects of nitrogen-fixing symbiosis should contribute to translate the knowledge generated in basic laboratory research into biotechnological advances to improve the efficiency of the nitrogen-fixing symbiosis in agronomic systems.
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Affiliation(s)
- Joaquín Clúa
- 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, 1900-La Plata, Argentina.
| | - Carla Roda
- 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, 1900-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, 1900-La Plata, Argentina.
| | - Flavio A 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, 1900-La Plata, Argentina.
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Abstract
Rhizobia are some of the best-studied plant microbiota. These oligotrophic Alphaproteobacteria or Betaproteobacteria form symbioses with their legume hosts. Rhizobia must exist in soil and compete with other members of the microbiota before infecting legumes and forming N2-fixing bacteroids. These dramatic lifestyle and developmental changes are underpinned by large genomes and even more complex pan-genomes, which encompass the whole population and are subject to rapid genetic exchange. The ability to respond to plant signals and chemoattractants and to colonize nutrient-rich roots are crucial for the competitive success of these bacteria. The availability of a large body of genomic, physiological, biochemical and ecological studies makes rhizobia unique models for investigating community interactions and plant colonization.
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