1
|
Li R, Zarate D, Avila-Magaña V, Li J. Comparative transcriptomics revealed parallel evolution and innovation of photosymbiosis molecular mechanisms in a marine bivalve. Proc Biol Sci 2024; 291:20232408. [PMID: 38807516 DOI: 10.1098/rspb.2023.2408] [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: 10/27/2023] [Accepted: 04/05/2024] [Indexed: 05/30/2024] Open
Abstract
Photosymbioses between heterotrophic hosts and autotrophic symbionts are evolutionarily prevalent and ecologically significant. However, the molecular mechanisms behind such symbioses remain less elucidated, which hinders our understanding of their origin and adaptive evolution. This study compared gene expression patterns in a photosymbiotic bivalve (Fragum sueziense) and a closely related non-symbiotic species (Trigoniocardia granifera) under different light conditions to detect potential molecular pathways involved in mollusc photosymbiosis. We discovered that the presence of algal symbionts greatly impacted host gene expression in symbiont-containing tissues. We found that the host immune functions were suppressed under normal light compared with those in the dark. In addition, we found that cilia in the symbiont-containing tissues play important roles in symbiont regulation or photoreception. Interestingly, many potential photosymbiosis genes could not be annotated or do not exhibit orthologues in T. granifera transcriptomes, indicating unique molecular functions in photosymbiotic bivalves. Overall, we found both novel and known molecular mechanisms involved in animal-algal photosymbiosis within bivalves. Given that many of the molecular pathways are shared among distantly related host lineages, such as molluscs and cnidarians, it indicates that parallel and/or convergent evolution is instrumental in shaping host-symbiont interactions and responses in these organisms.
Collapse
Affiliation(s)
- Ruiqi Li
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, USA
- Museum of Natural History, University of Colorado Boulder, Boulder, USA
| | - Daniel Zarate
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, USA
- Museum of Natural History, University of Colorado Boulder, Boulder, USA
| | | | - Jingchun Li
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, USA
- Museum of Natural History, University of Colorado Boulder, Boulder, USA
| |
Collapse
|
2
|
Nzeyimana F, Onwonga RN, Ayuke FO, Chemining'wa GN, Nabahungu NL, Bigirimana J, Noella Josiane UK. Determination of abundance and symbiotic effectiveness of native rhizobia nodulating soybean and other legumes in Rwanda. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2024; 5:e10138. [PMID: 38505702 PMCID: PMC10949400 DOI: 10.1002/pei3.10138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 02/07/2024] [Accepted: 02/26/2024] [Indexed: 03/21/2024]
Abstract
Rhizobia diversity in the rhizosphere is one of the key promoters of biological nitrogen fixation between host legumes and microsymbionts, although related complex interaction may depend on various factors. This research was intended to assess the abundance of indigenous rhizobia isolates under various soil conditions, as well as their effectiveness to nodulate legumes such as soybeans. Factors such as soil properties and legume species influence the volume and symbiotic effectiveness of native rhizobia to nodulate crop legumes. To investigate the abundance of rhizobia isolates, legume crops were uprooted to obtain nodules for most probable number (MPN) determination of rhizobia isolates, and soybean (Glycine max.) was used to verify the presence of suitable and efficient rhizobia strains for nitrogen fixation. Soil samples were obtained from the holes out of which nodules were collected, and the laboratory analysis included pH, Mg, K, available P, organic C, Ca, and N to establish the correlation between the soil status and number of rhizobia isolates' cells. Significant variations (p-value <.05) were observed in the cell counts of Rhizobia isolates from Glycine max, Phaseolus vulgaris, Pisum sativum, and Vigna unguiculata, particularly when compared to Arachis hypogaea isolates under acidic conditions. Notably, Pisum sativum and Vigna unguiculata showed consistent performance across all pH conditions. The number of rhizobia isolates was found to be significantly linked to total N and P deficiencies (p < .05). It was also established that total N was dependent on the number of rhizobia cells and that there is a strong correlation between organic carbon and N content. This study highlights the crucial role of understanding and optimizing conditions for rhizobia nodulation in diverse soil environments, emphasizing its potential impact on enhancing biological nitrogen fixation in legumes.
Collapse
Affiliation(s)
- Felix Nzeyimana
- Faculty of AgricultureUniversity of NairobiNairobiKenya
- Rwanda Agriculture and Animal Resources Development Board (RAB)KigaliRwanda
| | | | - Fredrick O. Ayuke
- Faculty of AgricultureUniversity of NairobiNairobiKenya
- Rwanda Institute for Conservation Agriculture (RICA)GashoraRwanda
| | | | | | - Joseph Bigirimana
- Department of AgricultureUniversity of Technology and Art of ByumbaGicumbi‐Rwanda
| | - Umuhoza K. Noella Josiane
- College of Agriculture Animal Science and Veterinary Medicine, Crop Sciences DepartmentUniversity of RwandaKigaliRwanda
| |
Collapse
|
3
|
Syska C, Kiers A, Rancurel C, Bailly-Bechet M, Lipuma J, Alloing G, Garcia I, Dupont L. VapC10 toxin of the legume symbiont Sinorhizobium meliloti targets tRNASer and controls intracellular lifestyle. THE ISME JOURNAL 2024; 18:wrae015. [PMID: 38365913 PMCID: PMC10945364 DOI: 10.1093/ismejo/wrae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/05/2024] [Accepted: 01/25/2024] [Indexed: 02/18/2024]
Abstract
The soil bacterium Sinorhizobium meliloti can establish a nitrogen-fixing symbiosis with the model legume Medicago truncatula. The rhizobia induce the formation of a specialized root organ called nodule, where they differentiate into bacteroids and reduce atmospheric nitrogen into ammonia. Little is known on the mechanisms involved in nodule senescence onset and in bacteroid survival inside the infected plant cells. Although toxin-antitoxin (TA) systems have been shown to promote intracellular survival within host cells in human pathogenic bacteria, their role in symbiotic bacteria was rarely investigated. S. meliloti encodes several TA systems, mainly of the VapBC family. Here we present the functional characterization, through a multidisciplinary approach, of the VapBC10 TA system of S. meliloti. Following a mapping by overexpression of an RNase in Escherichia coli (MORE) RNA-seq analysis, we demonstrated that the VapC10 toxin is an RNase that cleaves the anticodon loop of two tRNASer. Thereafter, a bioinformatics approach was used to predict VapC10 targets in bacteroids. This analysis suggests that toxin activation triggers a specific proteome reprogramming that could limit nitrogen fixation capability and viability of bacteroids. Accordingly, a vapC10 mutant induces a delayed senescence in nodules, associated to an enhanced bacteroid survival. VapBC10 TA system could contribute to S. meliloti adaptation to symbiotic lifestyle, in response to plant nitrogen status.
Collapse
Affiliation(s)
- Camille Syska
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech (ISA), Sophia Antipolis 06903, France
| | - Aurélie Kiers
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech (ISA), Sophia Antipolis 06903, France
| | - Corinne Rancurel
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech (ISA), Sophia Antipolis 06903, France
| | - Marc Bailly-Bechet
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech (ISA), Sophia Antipolis 06903, France
| | | | - Geneviève Alloing
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech (ISA), Sophia Antipolis 06903, France
| | - Isabelle Garcia
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech (ISA), Sophia Antipolis 06903, France
| | - Laurence Dupont
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech (ISA), Sophia Antipolis 06903, France
| |
Collapse
|
4
|
Wang X, Qiu Z, Zhu W, Wang N, Bai M, Kuang H, Cai C, Zhong X, Kong F, Lü P, Guan Y. The NAC transcription factors SNAP1/2/3/4 are central regulators mediating high nitrogen responses in mature nodules of soybean. Nat Commun 2023; 14:4711. [PMID: 37543605 PMCID: PMC10404276 DOI: 10.1038/s41467-023-40392-w] [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: 12/10/2022] [Accepted: 07/26/2023] [Indexed: 08/07/2023] Open
Abstract
Legumes can utilize atmospheric nitrogen via symbiotic nitrogen fixation, but this process is inhibited by high soil inorganic nitrogen. So far, how high nitrogen inhibits N2 fixation in mature nodules is still poorly understood. Here we construct a co-expression network in soybean nodule and find that a dynamic and reversible transcriptional network underlies the high N inhibition of N2 fixation. Intriguingly, several NAC transcription factors (TFs), designated as Soybean Nitrogen Associated NAPs (SNAPs), are amongst the most connected hub TFs. The nodules of snap1/2/3/4 quadruple mutants show less sensitivity to the high nitrogen inhibition of nitrogenase activity and acceleration of senescence. Integrative analysis shows that these SNAP TFs largely influence the high nitrogen transcriptional response through direct regulation of a subnetwork of senescence-associated genes and transcriptional regulators. We propose that the SNAP-mediated transcriptional network may trigger nodule senescence in response to high nitrogen.
Collapse
Affiliation(s)
- Xin Wang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Zhimin Qiu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenjun Zhu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Nan Wang
- School of Life Sciences, Inner Mongolia University, Hohhot, 010000, China
| | - Mengyan Bai
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huaqin Kuang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Chenlin Cai
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Xiangbin Zhong
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Fanjiang Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Peitao Lü
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
| | - Yuefeng Guan
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China.
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Tang R, Tan H, Dai Y, Li L, Huang Y, Yao H, Cai Y, Yu G. Application of antimicrobial peptides in plant protection: making use of the overlooked merits. FRONTIERS IN PLANT SCIENCE 2023; 14:1139539. [PMID: 37538059 PMCID: PMC10394246 DOI: 10.3389/fpls.2023.1139539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 04/07/2023] [Indexed: 08/05/2023]
Abstract
Pathogen infection is one of the major causes of yield loss in the crop field. The rapid increase of antimicrobial resistance in plant pathogens has urged researchers to develop both new pesticides and management strategies for plant protection. The antimicrobial peptides (AMPs) showed potential on eliminating plant pathogenic fungi and bacteria. Here, we first summarize several overlooked advantages and merits of AMPs, which includes the steep dose-response relations, fast killing ability, broad synergism, slow resistance selection. We then discuss the possible application of AMPs for plant protection with above merits, and highlight how AMPs can be incorporated into a more efficient integrated management system that both increases the crop yield and reduce resistance evolution of pathogens.
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Nitrogen-Fixing Symbiotic Paraburkholderia Species: Current Knowledge and Future Perspectives. NITROGEN 2023. [DOI: 10.3390/nitrogen4010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
A century after the discovery of rhizobia, the first Beta-proteobacteria species (beta-rhizobia) were isolated from legume nodules in South Africa and South America. Since then, numerous species belonging to the Burkholderiaceae family have been isolated. The presence of a highly branching lineage of nodulation genes in beta-rhizobia suggests a long symbiotic history. In this review, we focus on the beta-rhizobial genus Paraburkholderia, which includes two main groups: the South American mimosoid-nodulating Paraburkholderia and the South African predominantly papilionoid-nodulating Paraburkholderia. Here, we discuss the latest knowledge on Paraburkholderia nitrogen-fixing symbionts in each step of the symbiosis, from their survival in the soil, through the first contact with the legumes until the formation of an efficient nitrogen-fixing symbiosis in root nodules. Special attention is given to the strain P. phymatum STM815T that exhibits extraordinary features, such as the ability to: (i) enter into symbiosis with more than 50 legume species, including the agriculturally important common bean, (ii) outcompete other rhizobial species for nodulation of several legumes, and (iii) endure stressful soil conditions (e.g., high salt concentration and low pH) and high temperatures.
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Quides KW, Lee Y, Hur T, Atamian HS. Evaluation of qPCR to Detect Shifts in Population Composition of the Rhizobial Symbiont Mesorhizobium japonicum during Serial in Planta Transfers. BIOLOGY 2023; 12:biology12020277. [PMID: 36829553 PMCID: PMC9953586 DOI: 10.3390/biology12020277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/25/2023] [Accepted: 01/31/2023] [Indexed: 02/12/2023]
Abstract
Microbial symbionts range from mutualistic to commensal to antagonistic. While these roles are distinct in their outcome, they are also fluid in a changing environment. Here, we used the Lotus japonicus-Mesorhizobium japonicum symbiosis to investigate short-term and long-term shifts in population abundance using an effective, fast, and low-cost tracking methodology for M. japonicum. We use quantitative polymerase chain reaction (qPCR) to track previously generated signature-tagged M. japonicum mutants targeting the Tn5 transposon insertion and the flanking gene. We used a highly beneficial wild type and moderately beneficial and non-beneficial mutants of M. japonicum sp. nov. to demonstrate the specificity of these primers to estimate the relative abundance of each genotype within individual nodules and after serial transfers to new hosts. For the moderate and non-beneficial genotypes, qPCR allowed us to differentiate genotypes that are phenotypically indistinguishable and investigate host control with suboptimal symbionts. We consistently found the wild type increasing in the proportion of the population, but our data suggest a potential reproductive trade-off between the moderate and non-beneficial genotypes. The multi-generation framework we used, coupled with qPCR, can easily be scaled up to track dozens of M. japonicum mutants simultaneously. Moreover, these mutants can be used to explore M. japonicum genotype abundance in the presence of a complex soil community.
Collapse
Affiliation(s)
- Kenjiro W. Quides
- Biological Sciences Program, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
| | - Yoobeen Lee
- Biological Sciences Program, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
| | - Teresa Hur
- Biological Sciences Program, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
| | - Hagop S. Atamian
- Biological Sciences Program, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
- Correspondence:
| |
Collapse
|
11
|
Wang J, Cao X, Wang C, Chen F, Feng Y, Yue L, Wang Z, Xing B. Fe-Based Nanomaterial-Induced Root Nodulation Is Modulated by Flavonoids to Improve Soybean ( Glycine max) Growth and Quality. ACS NANO 2022; 16:21047-21062. [PMID: 36479882 DOI: 10.1021/acsnano.2c08753] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Innovative technology to increase efficient nitrogen (N) use while avoiding environmental damages is needed because of the increasing food demand of the rapidly growing global population. Soybean (Glycine max) has evolved a complex symbiosis with N-fixing bacteria that forms nodules to fix N. Herein, foliar application of 10 mg L-1 Fe7(PO4)6 and Fe3O4 nanomaterials (NMs) (Fe-based NMs) promoted soybean growth and root nodulation, thus improving the yield and quality over that of the unexposed control, EDTA-control, and 1 and 5 mg L-1 NMs. Mechanistically, flavonoids, key signaling molecules at the initial signaling steps in nodulation, were increased by more than 20% upon exposure to 10 mg L-1 Fe-based NMs, due to enhanced key enzyme (phenylalanine ammonia-lyase, PAL) activity and up-regulation of flavonoid biosynthetic genes (GmPAL, GmC4H, Gm4CL, and GmCHS). Accumulated flavonoids were secreted to the rhizosphere, recruiting rhizobia for colonization. Fe7(PO4)6 NMs increased Allorhizobium by 87.3%, and Fe3O4 NMs increased Allorhizobium and Mesorhizobium by 142.2% and 34.9%, leading to increased root nodules by 50.0% and 35.4% over the unexposed control, respectively. Leghemoglobin content was also noticeably improved by 8.2-46.5% upon Fe-based NMs. The higher levels of nodule number and leghemoglobin content resulted in enhanced N content by 15.5-181.2% during the whole growth period. Finally, the yield (pod number and grain biomass) and quality (flavonoids, soluble protein, and elemental nutrients) were significantly increased more than 14% by Fe-based NMs. Our study provides an effective nanoenabled strategy for inducing root nodules to increase N use efficiency, and then both yield and quality of soybean.
Collapse
Affiliation(s)
- Jing Wang
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Xuesong Cao
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Chuanxi Wang
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Feiran Chen
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Yan Feng
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Le Yue
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, Massachusetts 01003, United States
| |
Collapse
|
12
|
Genome-Wide Association Studies across Environmental and Genetic Contexts Reveal Complex Genetic Architecture of Symbiotic Extended Phenotypes. mBio 2022; 13:e0182322. [PMID: 36286519 PMCID: PMC9765617 DOI: 10.1128/mbio.01823-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A goal of modern biology is to develop the genotype-phenotype (G→P) map, a predictive understanding of how genomic information generates trait variation that forms the basis of both natural and managed communities. As microbiome research advances, however, it has become clear that many of these traits are symbiotic extended phenotypes, being governed by genetic variation encoded not only by the host's own genome, but also by the genomes of myriad cryptic symbionts. Building a reliable G→P map therefore requires accounting for the multitude of interacting genes and even genomes involved in symbiosis. Here, we use naturally occurring genetic variation in 191 strains of the model microbial symbiont Sinorhizobium meliloti paired with two genotypes of the host Medicago truncatula in four genome-wide association studies (GWAS) to determine the genomic architecture of a key symbiotic extended phenotype-partner quality, or the fitness benefit conferred to a host by a particular symbiont genotype, within and across environmental contexts and host genotypes. We define three novel categories of loci in rhizobium genomes that must be accounted for if we want to build a reliable G→P map of partner quality; namely, (i) loci whose identities depend on the environment, (ii) those that depend on the host genotype with which rhizobia interact, and (iii) universal loci that are likely important in all or most environments. IMPORTANCE Given the rapid rise of research on how microbiomes can be harnessed to improve host health, understanding the contribution of microbial genetic variation to host phenotypic variation is pressing, and will better enable us to predict the evolution of (and select more precisely for) symbiotic extended phenotypes that impact host health. We uncover extensive context-dependency in both the identity and functions of symbiont loci that control host growth, which makes predicting the genes and pathways important for determining symbiotic outcomes under different conditions more challenging. Despite this context-dependency, we also resolve a core set of universal loci that are likely important in all or most environments, and thus, serve as excellent targets both for genetic engineering and future coevolutionary studies of symbiosis.
Collapse
|
13
|
de Faria SM, Ringelberg JJ, Gross E, Koenen EJM, Cardoso D, Ametsitsi GKD, Akomatey J, Maluk M, Tak N, Gehlot HS, Wright KM, Teaumroong N, Songwattana P, de Lima HC, Prin Y, Zartman CE, Sprent JI, Ardley J, Hughes CE, James EK. The innovation of the symbiosome has enhanced the evolutionary stability of nitrogen fixation in legumes. THE NEW PHYTOLOGIST 2022; 235:2365-2377. [PMID: 35901264 PMCID: PMC9541511 DOI: 10.1111/nph.18321] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/31/2022] [Indexed: 05/12/2023]
Abstract
Nitrogen-fixing symbiosis is globally important in ecosystem functioning and agriculture, yet the evolutionary history of nodulation remains the focus of considerable debate. Recent evidence suggesting a single origin of nodulation followed by massive parallel evolutionary losses raises questions about why a few lineages in the N2 -fixing clade retained nodulation and diversified as stable nodulators, while most did not. Within legumes, nodulation is restricted to the two most diverse subfamilies, Papilionoideae and Caesalpinioideae, which show stable retention of nodulation across their core clades. We characterize two nodule anatomy types across 128 species in 56 of the 152 genera of the legume subfamily Caesalpinioideae: fixation thread nodules (FTs), where nitrogen-fixing bacteroids are retained within the apoplast in modified infection threads, and symbiosomes, where rhizobia are symplastically internalized in the host cell cytoplasm within membrane-bound symbiosomes (SYMs). Using a robust phylogenomic tree based on 997 genes from 147 Caesalpinioideae genera, we show that losses of nodulation are more prevalent in lineages with FTs than those with SYMs. We propose that evolution of the symbiosome allows for a more intimate and enduring symbiosis through tighter compartmentalization of their rhizobial microsymbionts, resulting in greater evolutionary stability of nodulation across this species-rich pantropical legume clade.
Collapse
Affiliation(s)
- Sergio M. de Faria
- Embrapa Agrobiologia465 km 07, SeropédicaRio de JaneiroBR23891‐000Brazil
| | - Jens J. Ringelberg
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
| | - Eduardo Gross
- Departamento de Ciências Agrárias e AmbientaisUniversidade Estadual de Santa Cruz (UESC)IlhéusBA45662‐900Brazil
| | - Erik J. M. Koenen
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
| | - Domingos Cardoso
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN‐TREE)Instituto de Biologia, Universidade Federal de Bahia (UFBA)Rua Barão de Jeremoabo, s.n., OndinaSalvador40170‐115BABrazil
| | | | - John Akomatey
- CSIR‐Forestry Research Institute of GhanaFUMESUAPO Box UP 63 KNUSTKumasiGhana
| | - Marta Maluk
- The James Hutton InstituteInvergowrieDundeeDD2 5DAUK
| | - Nisha Tak
- Department of Botany, BNF and Microbial Genomics Lab.Center of Advanced Study, Jai Narain Vyas UniversityJodhpur342001RajasthanIndia
| | - Hukam S. Gehlot
- Department of Botany, BNF and Microbial Genomics Lab.Center of Advanced Study, Jai Narain Vyas UniversityJodhpur342001RajasthanIndia
| | | | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural TechnologySuranaree University of TechnologyNakhonratchasima30000Thailand
| | - Pongpan Songwattana
- School of Biotechnology, Institute of Agricultural TechnologySuranaree University of TechnologyNakhonratchasima30000Thailand
| | - Haroldo C. de Lima
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro (JBRJ/MMA)Rua Pacheco Leão 915Rio de Janeiro22460‐030RJBrazil
- Instituto Nacional da Mata Atlântica (INMA‐MCTI)Av. José Ruschi 4Santa Teresa29650‐000ESBrazil
| | - Yves Prin
- CIRAD, UMR LSTMCampus de Baillarguet34398Montpellier Cedex 5France
| | - Charles E. Zartman
- Departamento de BiodiversidadeInstituto Nacional de Pesquisas da Amazônia (INPA)Av. André Araújo Aleixo, Caixa Postal 478Manaus69060‐001AMBrazil
| | - Janet I. Sprent
- Division of Plant SciencesUniversity of Dundee at The James Hutton InstituteInvergowrieDundeeDD2 5DAUK
| | - Julie Ardley
- College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWA6150Australia
| | - Colin E. Hughes
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
| | - Euan K. James
- The James Hutton InstituteInvergowrieDundeeDD2 5DAUK
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Epstein B, Burghardt LT, Heath KD, Grillo MA, Kostanecki A, Hämälä T, Young ND, Tiffin P. Combining GWAS and population genomic analyses to characterize coevolution in a legume-rhizobia symbiosis. Mol Ecol 2022. [PMID: 35793264 DOI: 10.1111/mec.16602] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/03/2022] [Accepted: 07/04/2022] [Indexed: 11/28/2022]
Abstract
The mutualism between legumes and rhizobia is clearly the product of past coevolution. However, the nature of ongoing evolution between these partners is less clear. To characterize the nature of recent coevolution between legumes and rhizobia, we used population genomic analysis to characterize selection on functionally annotated symbiosis genes as well as on symbiosis gene candidates identified through a two-species association analysis. For the association analysis, we inoculated each of 202 accessions of the legume host Medicago truncatula with a community of 88 Sinorhizobia (Ensifer) meliloti strains. Multistrain inoculation, which better reflects the ecological reality of rhizobial selection in nature than single-strain inoculation, allows strains to compete for nodulation opportunities and host resources and for hosts to preferentially form nodules and provide resources to some strains. We found extensive host by symbiont, that is, genotype-by-genotype, effects on rhizobial fitness and some annotated rhizobial genes bear signatures of recent positive selection. However, neither genes responsible for this variation nor annotated host symbiosis genes are enriched for signatures of either positive or balancing selection. This result suggests that stabilizing selection dominates selection acting on symbiotic traits and that variation in these traits is under mutation-selection balance. Consistent with the lack of positive selection acting on host genes, we found that among-host variation in growth was similar whether plants were grown with rhizobia or N-fertilizer, suggesting that the symbiosis may not be a major driver of variation in plant growth in multistrain contexts.
Collapse
Affiliation(s)
- Brendan Epstein
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Liana T Burghardt
- Department of Plant Sciences, The University of Pennsylvania, University Park, Pennsylvania, USA
| | - Katy D Heath
- Department of Plant Biology, University of Illinois, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
| | - Michael A Grillo
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Adam Kostanecki
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Tuomas Hämälä
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA.,School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Nevin D Young
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA.,Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| |
Collapse
|
16
|
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.
Collapse
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.
| |
Collapse
|
17
|
Nett RS, Bender KS, Peters RJ. Production of the plant hormone gibberellin by rhizobia increases host legume nodule size. THE ISME JOURNAL 2022; 16:1809-1817. [PMID: 35414717 PMCID: PMC9213532 DOI: 10.1038/s41396-022-01236-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 03/26/2022] [Accepted: 03/31/2022] [Indexed: 12/11/2022]
Abstract
Plant-associated microbes have evolved the ability to independently produce gibberellin (GA) phytohormones as a mechanism to influence their host. Indeed, GA was first discovered as a metabolite from the fungal rice pathogen Gibberella fujikuroi, which uses it as a virulence factor. Though some bacterial plant pathogens similarly use GA to promote infection, symbiotic nitrogen-fixing bacteria (rhizobia), which inhabit the root nodules of legumes, also can produce GA, suggesting a role in symbiosis. The bacterial GA biosynthetic operon has been identified, but in rhizobia this typically no longer encodes the final metabolic gene (cyp115), so that these symbionts can only produce the penultimate intermediate GA9. Here, we demonstrate that soybean (Glycine max) expresses functional GA 3-oxidases (GA3ox) within its nodules, which have the capability to convert GA9 produced by the enclosed rhizobial symbiont Bradyrhizobium diazoefficiens to bioactive GA4. This rhizobia-derived GA is demonstrated to cause an increase in nodule size and decrease in the number of nodules. The increase in individual nodule size correlates to greater numbers of bacterial progeny within a nodule, thereby providing a selective advantage to rhizobia that produce GA during the rhizobia-legume symbiosis. The expression of GA3ox in nodules and resultant nodulation effects of the GA product suggests that soybean has co-opted control of bioactive GA production, and thus nodule size, for its own benefit. Thus, our results suggest rhizobial GA biosynthesis has coevolved with host plant metabolism for cooperative production of a phytohormone that influences nodulation in a mutually beneficial manner.
Collapse
Affiliation(s)
- Ryan S Nett
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Kelly S Bender
- Department of Microbiology, Southern Illinois University, Carbondale, IL, USA
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA.
| |
Collapse
|
18
|
Wang L, Rengel Z, Zhang K, Jin K, Lyu Y, Zhang L, Cheng L, Zhang F, Shen J. Ensuring future food security and resource sustainability: insights into the rhizosphere. iScience 2022; 25:104168. [PMID: 35434553 PMCID: PMC9010633 DOI: 10.1016/j.isci.2022.104168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Feeding the world’s growing population requires continuously increasing crop yields with less fertilizers and agrochemicals on limited land. Focusing on plant belowground traits, especially root-soil-microbe interactions, holds a great promise for overcoming this challenge. The belowground root-soil-microbe interactions are complex and involve a range of physical, chemical, and biological processes that influence nutrient-use efficiency, plant growth and health. Understanding, predicting, and manipulating these rhizosphere processes will enable us to harness the relevant interactions to improve plant productivity and nutrient-use efficiency. Here, we review the recent progress and challenges in root-soil-microbe interactions. We also highlight how root-soil-microbe interactions could be manipulated to ensure food security and resource sustainability in a changing global climate, with an emphasis on reducing our dependence on fertilizers and agrochemicals.
Collapse
Affiliation(s)
- Liyang Wang
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
| | - Zed Rengel
- Soil Science & Plant Nutrition, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia.,Institute for Adriatic Crops and Karst Reclamation, Split 21000, Croatia
| | - Kai Zhang
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
| | - Kemo Jin
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
| | - Yang Lyu
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
| | - Lin Zhang
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
| | - Lingyun Cheng
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
| | - Fusuo Zhang
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
| | - Jianbo Shen
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
| |
Collapse
|
19
|
Plant-Microbe Interaction in Sustainable Agriculture: The Factors That May Influence the Efficacy of PGPM Application. SUSTAINABILITY 2022. [DOI: 10.3390/su14042253] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The indiscriminate use of chemical fertilizers and pesticides has caused considerable environmental damage over the years. However, the growing demand for food in the coming years and decades requires the use of increasingly productive and efficient agriculture. Several studies carried out in recent years have shown how the application of plant growth-promoting microbes (PGPMs) can be a valid substitute for chemical industry products and represent a valid eco-friendly alternative. However, because of the complexity of interactions created with the numerous biotic and abiotic factors (i.e., environment, soil, interactions between microorganisms, etc.), the different formulates often show variable effects. In this review, we analyze the main factors that influence the effectiveness of PGPM applications and some of the applications that make them a useful tool for agroecological transition.
Collapse
|
20
|
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
| |
Collapse
|
21
|
Ortiz-Barbosa GS, Torres-Martínez L, Manci A, Neal S, Soubra T, Khairi F, Trinh J, Cardenas P, Sachs JL. No disruption of rhizobial symbiosis during early stages of cowpea domestication. Evolution 2022; 76:496-511. [PMID: 35014694 DOI: 10.1111/evo.14424] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/15/2021] [Accepted: 11/26/2021] [Indexed: 11/26/2022]
Abstract
Modern agriculture intensely selects aboveground plant structures, while often neglecting belowground features, and evolutionary tradeoffs between these traits are predicted to disrupt host control over microbiota. Moreover, drift, inbreeding, and relaxed selection for symbiosis in crops might degrade plant mechanisms that support beneficial microbes. We studied the impact of domestication on the nitrogen fixing symbiosis between cowpea and root-nodulating Bradyrhizobium. We combined genome-wide analyses with a greenhouse inoculation study to investigate genomic diversity, heritability, and symbiosis trait variation among wild and early-domesticated cowpea genotypes. Cowpeas experienced modest decreases in genome-wide diversity during early domestication. Nonetheless, domesticated cowpeas responded efficiently to variation in symbiotic effectiveness, by forming more root nodules with nitrogen-fixing rhizobia and sanctioning non-fixing strains. Domesticated populations invested a larger proportion of host tissues into root nodules than wild cowpeas. Unlike soybean and wheat, cowpea showed no compelling evidence for degradation of symbiosis during domestication. Domesticated cowpeas experienced a less severe bottleneck than these crops and the low nutrient conditions in Africa where cowpea landraces were developed likely favored plant genotypes that gain substantial benefits from symbiosis. Breeders have largely neglected symbiosis traits, but artificial selection for improved plant responses to microbiota could increase plant performance and sustainability. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- G S Ortiz-Barbosa
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA
| | - L Torres-Martínez
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, CA
| | - A Manci
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA
| | - S Neal
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, CA
| | - T Soubra
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, CA
| | - F Khairi
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, CA
| | - J Trinh
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, CA
| | - P Cardenas
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, CA
| | - J L Sachs
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA.,Department of Evolution Ecology and Organismal Biology, University of California, Riverside, CA.,Institute of Integrative Genome Biology, University of California, Riverside, CA
| |
Collapse
|
22
|
Putra R, Vandegeer RK, Karan S, Powell JR, Hartley SE, Johnson SN. Silicon enrichment alters functional traits in legumes depending on plant genotype and symbiosis with nitrogen‐fixing bacteria. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13912] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Rocky Putra
- Hawkesbury Institute for the Environment Western Sydney University Richmond NSW Australia
| | - Rebecca K. Vandegeer
- Hawkesbury Institute for the Environment Western Sydney University Richmond NSW Australia
| | - Shawan Karan
- Technical Support Services and Mass Spectrometry Facility Western Sydney University Campbelltown NSW Australia
| | - Jeff R. Powell
- Hawkesbury Institute for the Environment Western Sydney University Richmond NSW Australia
| | - Susan E. Hartley
- Department of Biology York Environmental Sustainability Institute University of York York UK
- Department of Animal and Plant Sciences University of Sheffield Sheffield UK
| | - Scott N. Johnson
- Hawkesbury Institute for the Environment Western Sydney University Richmond NSW Australia
| |
Collapse
|
23
|
Scheiner SM, Barfield M, Holt RD. Do I build or do I move? Adaptation by habitat construction versus habitat choice. Evolution 2021; 76:414-428. [PMID: 34534361 DOI: 10.1111/evo.14355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/30/2021] [Accepted: 09/10/2021] [Indexed: 01/20/2023]
Abstract
Trait adaptation to a heterogeneous environment can occur through six modes: genetic differentiation of those traits, a jack-of-all-trades phenotypic uniformity, diversified bet-hedging, phenotypic plasticity, habitat choice, and habitat construction. A key question is what circumstances favor one mode over another, and how they might interact if a system can express more than one mode at a time. We examined the joint evolution of habitat choice and habitat construction using individual-based simulations. We manipulated when during the life cycle construction occurred and the fitness value of construction. We found that for our model habitat construction was nearly always favored over habitat choice, especially if construction happened after dispersal. Because of the ways that the various modes of adaptation interact with each other, there is no simple answer as to which will be favored; it depends on details of the biology and ecology of a given system.
Collapse
Affiliation(s)
- Samuel M Scheiner
- Division of Environmental Biology, National Science Foundation, Arlington, Virginia, 22230
| | - Michael Barfield
- Department of Biology, University of Florida, Gainesville, Florida, 32611
| | - Robert D Holt
- Department of Biology, University of Florida, Gainesville, Florida, 32611
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
McCutcheon JP. The Genomics and Cell Biology of Host-Beneficial Intracellular Infections. Annu Rev Cell Dev Biol 2021; 37:115-142. [PMID: 34242059 DOI: 10.1146/annurev-cellbio-120219-024122] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microbes gain access to eukaryotic cells as food for bacteria-grazing protists, for host protection by microbe-killing immune cells, or for microbial benefit when pathogens enter host cells to replicate. But microbes can also gain access to a host cell and become an important-often required-beneficial partner. The oldest beneficial microbial infections are the ancient eukaryotic organelles now called the mitochondrion and plastid. But numerous other host-beneficial intracellular infections occur throughout eukaryotes. Here I review the genomics and cell biology of these interactions with a focus on intracellular bacteria. The genomes of host-beneficial intracellular bacteria have features that span a previously unfilled gap between pathogens and organelles. Host cell adaptations to allow the intracellular persistence of beneficial bacteria are found along with evidence for the microbial manipulation of host cells, but the cellular mechanisms of beneficial bacterial infections are not well understood. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- John P McCutcheon
- Biodesign Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA;
| |
Collapse
|
26
|
Schulte CCM, Borah K, Wheatley RM, Terpolilli JJ, Saalbach G, Crang N, de Groot DH, Ratcliffe RG, Kruger NJ, Papachristodoulou A, Poole PS. Metabolic control of nitrogen fixation in rhizobium-legume symbioses. SCIENCE ADVANCES 2021; 7:7/31/eabh2433. [PMID: 34330708 PMCID: PMC8324050 DOI: 10.1126/sciadv.abh2433] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/14/2021] [Indexed: 05/16/2023]
Abstract
Rhizobia induce nodule formation on legume roots and differentiate into bacteroids, which catabolize plant-derived dicarboxylates to reduce atmospheric N2 into ammonia. Despite the agricultural importance of this symbiosis, the mechanisms that govern carbon and nitrogen allocation in bacteroids and promote ammonia secretion to the plant are largely unknown. Using a metabolic model derived from genome-scale datasets, we show that carbon polymer synthesis and alanine secretion by bacteroids facilitate redox balance in microaerobic nodules. Catabolism of dicarboxylates induces not only a higher oxygen demand but also a higher NADH/NAD+ ratio than sugars. Modeling and 13C metabolic flux analysis indicate that oxygen limitation restricts the decarboxylating arm of the tricarboxylic acid cycle, which limits ammonia assimilation into glutamate. By tightly controlling oxygen supply and providing dicarboxylates as the energy and electron source donors for N2 fixation, legumes promote ammonia secretion by bacteroids. This is a defining feature of rhizobium-legume symbioses.
Collapse
Affiliation(s)
- Carolin C M Schulte
- Department of Plant Sciences, University of Oxford, Oxford, UK
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Khushboo Borah
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | | | | | | | - Nick Crang
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Daan H de Groot
- Systems Biology Lab, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | | | | | | | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, UK.
- John Innes Centre, Norwich Research Park, Norwich, UK
| |
Collapse
|
27
|
Quides KW, Weisberg AJ, Trinh J, Salaheldine F, Cardenas P, Lee HH, Jariwala R, Chang JH, Sachs JL. Experimental evolution can enhance benefits of rhizobia to novel legume hosts. Proc Biol Sci 2021; 288:20210812. [PMID: 34034525 PMCID: PMC8150021 DOI: 10.1098/rspb.2021.0812] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Legumes preferentially associate with and reward beneficial rhizobia in root nodules, but the processes by which rhizobia evolve to provide benefits to novel hosts remain poorly understood. Using cycles of in planta and in vitro evolution, we experimentally simulated lifestyles where rhizobia repeatedly interact with novel plant genotypes with which they initially provide negligible benefits. Using a full-factorial replicated design, we independently evolved two rhizobia strains in associations with each of two Lotus japonicus genotypes that vary in regulation of nodule formation. We evaluated phenotypic evolution of rhizobia by quantifying fitness, growth effects and histological features on hosts, and molecular evolution via genome resequencing. Rhizobia evolved enhanced host benefits and caused changes in nodule development in one of the four host–symbiont combinations, that appeared to be driven by reduced costs during symbiosis, rather than increased nitrogen fixation. Descendant populations included genetic changes that could alter rhizobial infection or proliferation in host tissues, but lack of evidence for fixation of these mutations weakens the results. Evolution of enhanced rhizobial benefits occurred only in a subset of experiments, suggesting a role for host–symbiont genotype interactions in mediating the evolution of enhanced benefits from symbionts.
Collapse
Affiliation(s)
- 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
| | - Jerry Trinh
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Fathi Salaheldine
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Paola Cardenas
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Hsu-Han Lee
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Ruchi Jariwala
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Joel L Sachs
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA.,Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA.,Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| |
Collapse
|
28
|
Root endophyte-enhanced peanut-rhizobia interaction is associated with regulation of root exudates. Microbiol Res 2021; 250:126765. [PMID: 34049186 DOI: 10.1016/j.micres.2021.126765] [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: 11/07/2020] [Accepted: 04/03/2021] [Indexed: 12/21/2022]
Abstract
Root exudates play a crucial role in the symbiosis between leguminous plants and rhizobia. Our previous studies have shown that a fungal endophyte Phomopsis liquidambaris promotes peanut-rhizobia nodulation and nitrogen fixation, but the underlying mechanism are largely unknown. Here, we explore the role of peanut root exudates in Ph. liquidambaris-mediated nodulation enhancement. We first collected root exudates from Ph. liquidambaris-inoculated and un-inoculated peanuts and determined their effects on rhizobial growth, biofilm formation, chemotaxis, nodC gene expression, and peanut nodulation. Our results found a positive effect of Ph. liquidambaris-inoculated root exudates on these characteristics of rhizobia. Next, we compared the root exudates profile of Ph. liquidambaris-inoculated and un-inoculated plants and found that Ph. liquidambaris altered the concentrations of phenolic acids, flavonoids, organic acids and amino acids in root exudates. Furthermore, the rhizobial chemotaxis, growth and biofilm formation in response to the changed compounds at different concentrations showed that all of the test compounds induced rhizobial chemotactic behavior, and organic acids (citric acid and oxalic acid) and amino acid (glutamate, glycine and glutamine) at higher concentrations increased rhizobial growth and biofilm formation. Collectively, our results suggest that root exudates alterations contribute to Ph. liquidambaris-mediated peanut-rhizobia nodulation enhancement.
Collapse
|
29
|
Scheiner SM, Barfield M, Holt RD. The evolution of habitat construction with and without phenotypic plasticity. Evolution 2021; 75:1650-1664. [PMID: 33826145 DOI: 10.1111/evo.14226] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 03/16/2021] [Accepted: 03/20/2021] [Indexed: 12/24/2022]
Abstract
Habitat construction and phenotypic plasticity are alternative responses to variable environments. We explored evolution along an environmental gradient of habitat construction alone and in combination with phenotypic plasticity using individual-based simulations that manipulated the fitness benefit of construction and whether construction maintained or eliminated that gradient. Construction was favored when its benefits were more likely to flow to the immediate offspring of the constructing individuals. Habitat construction and phenotypic plasticity traded off against each other or plasticity was selected against, depending on how the optimum environment varied and with the fitness value of construction. When selection favored differences in the amount of construction along the environmental gradient, genetic differentiation for habitat construction increased as the fitness value of construction increased. The degree to which each adaptive response was likely to evolve also depended on the precise ordering of life history events. Adaptive habitat construction does not always occur and may be selected against.
Collapse
Affiliation(s)
- Samuel M Scheiner
- Division of Environmental Biology, National Science Foundation, Alexandria, VA, 22230
| | - Michael Barfield
- Department of Biology, University of Florida, Gainesville, FL, 32611
| | - Robert D Holt
- Department of Biology, University of Florida, Gainesville, FL, 32611
| |
Collapse
|
30
|
Torres-Martínez L, Porter SS, Wendlandt C, Purcell J, Ortiz-Barbosa G, Rothschild J, Lampe M, Warisha F, Le T, Weisberg AJ, Chang JH, Sachs JL. Evolution of specialization in a plant-microbial mutualism is explained by the oscillation theory of speciation. Evolution 2021; 75:1070-1086. [PMID: 33782951 DOI: 10.1111/evo.14222] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 02/18/2021] [Accepted: 03/14/2021] [Indexed: 12/11/2022]
Abstract
Specialization in mutualisms is thought to be a major driver of diversification, but few studies have explored how novel specialization evolves, or its relation to the evolution of other niche axes. A fundamental question is whether generalist interactions evolve to become more specialized (i.e., oscillation hypothesis) or if partner switches evolve without any change in niche breadth (i.e., musical chairs hypothesis). We examined alternative models for the evolution of specialization by estimating the mutualistic, climatic, and edaphic niche breadths of sister plant species, combining phylogenetic, environmental, and experimental data on Acmispon strigosus and Acmispon wrangelianus genotypes across their overlapping ranges in California. We found that specialization along all three niche axes was asymmetric across species, such that the species with broader climatic and edaphic niches, Acmispon strigosus, was also able to gain benefit from and invest in associating with a broader set of microbial mutualists. Our data are consistent with the oscillation model of specialization, and a parallel narrowing of the edaphic, climatic, and mutualistic dimensions of the host species niche. Our findings provide novel evidence that the evolution of specialization in mutualism is accompanied by specialization in other niche dimensions.
Collapse
Affiliation(s)
- Lorena Torres-Martínez
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California, 92521
| | - Stephanie S Porter
- School of Biological Sciences, Washington State University, Vancouver, Washington, 98686, United States of America
| | - Camille Wendlandt
- School of Biological Sciences, Washington State University, Vancouver, Washington, 98686, United States of America
| | - Jessica Purcell
- Department of Entomology, University of California, Riverside, California, 92521, United States of America
| | - Gabriel Ortiz-Barbosa
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, 92521, United States of America
| | - Jacob Rothschild
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California, 92521
| | - Mathew Lampe
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California, 92521
| | - Farsamin Warisha
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California, 92521
| | - Tram Le
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California, 92521
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, United States of America
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, United States of America
| | - Joel L Sachs
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California, 92521.,Department of Microbiology and Plant Pathology, University of California, Riverside, California, 92521, United States of America.,Institute of Integrative Genome Biology, University of California, Riverside, California, 92521, United States of America
| |
Collapse
|
31
|
Saidi S, Cherif-Silini H, Chenari Bouket A, Silini A, Eshelli M, Luptakova L, Alenezi FN, Belbahri L. Improvement of Medicago sativa Crops Productivity by the Co-inoculation of Sinorhizobium meliloti-Actinobacteria Under Salt Stress. Curr Microbiol 2021; 78:1344-1357. [PMID: 33646380 PMCID: PMC7997840 DOI: 10.1007/s00284-021-02394-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 02/07/2021] [Indexed: 01/22/2023]
Abstract
Biotic and abiotic stresses are severely limiting plant production and productivity. Of notable importance is salt stress that not only limits plant growth and survival, but affects the soil fertility and threatens agricultural ecosystems sustainability. The problem is exacerbated in fragile arid and semi-arid areas where high evaporation, low precipitation and the use of salty water for irrigation is accelerating soil salinization. Legumes, considered very nutritious foods for people and providing essential nutrients for ecosystems are a fundamental element of sustainable agriculture. They can restore soil health by their ability to fix nitrogen in a symbiotic interaction with the rhizobia of the soil. However, salt stress is severely limiting productivity and nitrogen fixation ability in legumes. Plant growth-promoting rhizobacteria (PGPR) and mainly actinobacteria promote plant growth by producing phytohormones, siderophores, antibiotics and antifungal compounds, solubilizing phosphate and providing antagonism to phytopathogenic microorganisms. In addition, actinobacteria have beneficial effects on nodulation and growth of legumes. In this study, actinobacteria isolated from different niches and having PGP activities were used in co-inoculation experiments with rhizobia in Medicago sativa plants rhizosphere submitted to salt stress. The results indicate that drought- and salinity-tolerant Actinobacteria with multiple PGP traits can potentially increase alfalfa growth under saline conditions, in the presence or absence of symbiotic rhizobial bacteria. Actinobacteria discovered in this study can, therefore, be suitable biofertilizers in the formulation of agricultural products improving plant development, health and productivity in saline soils, a necessary alternative for modern agriculture and sustainable development.
Collapse
Affiliation(s)
- Samira Saidi
- Laboratory of Applied Microbiology, Department of Microbiology, Faculty of Natural and Life Sciences, University Ferhat Abbas Setif, Sétif, Algeria
| | - Hafsa Cherif-Silini
- Laboratory of Applied Microbiology, Department of Microbiology, Faculty of Natural and Life Sciences, University Ferhat Abbas Setif, Sétif, Algeria
| | - Ali Chenari Bouket
- Plant Protection Research Department, East Azarbaijan Agricultural and Natural Resources Research and Education Center, AREEO, Tabriz, Iran
| | - Allaoua Silini
- Laboratory of Applied Microbiology, Department of Microbiology, Faculty of Natural and Life Sciences, University Ferhat Abbas Setif, Sétif, Algeria
| | - Manal Eshelli
- Food Science and Technology Department, Faculty of Agriculture, University of Tripoli, Tripoli, Libya
| | - Lenka Luptakova
- Department of Biology and Genetics, Institute of Biology, Zoology and Radiobiology, University of Veterinary Medicine and Pharmacy, Kosice, Slovakia
| | - Faizah N Alenezi
- Department of Environmental Technology Management, College of Life Sciences, Kuwait University, Safat, Kuwait
| | - Lassaad Belbahri
- NextBiotech, 98 Rue Ali Belhouane, Agareb, Tunisia.
- Laboratory of Soil Biology, University of Neuchatel, Neuchâtel, Switzerland.
| |
Collapse
|
32
|
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.
Collapse
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
| |
Collapse
|
33
|
Abstract
Rhizobia are a phylogenetically diverse group of soil bacteria that engage in mutualistic interactions with legume plants. Although specifics of the symbioses differ between strains and plants, all symbioses ultimately result in the formation of specialized root nodule organs which host the nitrogen-fixing microsymbionts called bacteroids. Inside nodules, bacteroids encounter unique conditions that necessitate global reprogramming of physiological processes and rerouting of their metabolism. Decades of research have addressed these questions using genetics, omics approaches, and more recently computational modelling. Here we discuss the common adaptations of rhizobia to the nodule environment that define the core principles of bacteroid functioning. All bacteroids are growth-arrested and perform energy-intensive nitrogen fixation fueled by plant-provided C4-dicarboxylates at nanomolar oxygen levels. At the same time, bacteroids are subject to host control and sanctioning that ultimately determine their fitness and have fundamental importance for the evolution of a stable mutualistic relationship.
Collapse
|
34
|
O'Brien AM, Jack CN, Friesen ML, Frederickson ME. Whose trait is it anyways? Coevolution of joint phenotypes and genetic architecture in mutualisms. Proc Biol Sci 2021; 288:20202483. [PMID: 33434463 DOI: 10.1098/rspb.2020.2483] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Evolutionary biologists typically envision a trait's genetic basis and fitness effects occurring within a single species. However, traits can be determined by and have fitness consequences for interacting species, thus evolving in multiple genomes. This is especially likely in mutualisms, where species exchange fitness benefits and can associate over long periods of time. Partners may experience evolutionary conflict over the value of a multi-genomic trait, but such conflicts may be ameliorated by mutualism's positive fitness feedbacks. Here, we develop a simulation model of a host-microbe mutualism to explore the evolution of a multi-genomic trait. Coevolutionary outcomes depend on whether hosts and microbes have similar or different optimal trait values, strengths of selection and fitness feedbacks. We show that genome-wide association studies can map joint traits to loci in multiple genomes and describe how fitness conflict and fitness feedback generate different multi-genomic architectures with distinct signals around segregating loci. Partner fitnesses can be positively correlated even when partners are in conflict over the value of a multi-genomic trait, and conflict can generate strong mutualistic dependency. While fitness alignment facilitates rapid adaptation to a new optimum, conflict maintains genetic variation and evolvability, with implications for applied microbiome science.
Collapse
Affiliation(s)
- Anna M O'Brien
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Chandra N Jack
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | - Maren L Friesen
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA.,Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA
| | - Megan E Frederickson
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| |
Collapse
|
35
|
Ochieno DMW, Karoney EM, Muge EK, Nyaboga EN, Baraza DL, Shibairo SI, Naluyange V. Rhizobium-Linked Nutritional and Phytochemical Changes Under Multitrophic Functional Contexts in Sustainable Food Systems. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2020.604396] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Rhizobia are bacteria that exhibit both endophytic and free-living lifestyles. Endophytic rhizobial strains are widely known to infect leguminous host plants, while some do infect non-legumes. Infection of leguminous roots often results in the formation of root nodules. Associations between rhizobia and host plants may result in beneficial or non-beneficial effects. Such effects are linked to various biochemical changes that have far-reaching implications on relationships between host plants and the dependent multitrophic biodiversity. This paper explores relationships that exist between rhizobia and various plant species. Emphasis is on nutritional and phytochemical changes that occur in rhizobial host plants, and how such changes affect diverse consumers at different trophic levels. The purpose of this paper is to bring into context various aspects of such interactions that could improve knowledge on the application of rhizobia in different fields. The relevance of rhizobia in sustainable food systems is addressed in context.
Collapse
|
36
|
Burghardt LT. Evolving together, evolving apart: measuring the fitness of rhizobial bacteria in and out of symbiosis with leguminous plants. THE NEW PHYTOLOGIST 2020; 228:28-34. [PMID: 31276218 DOI: 10.1111/nph.16045] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/20/2019] [Indexed: 05/11/2023]
Abstract
Most plant-microbe interactions are facultative, with microbes experiencing temporally and spatially variable selection. How this variation affects microbial evolution is poorly understood. Given its tractability and ecological and agricultural importance, the legume-rhizobia nitrogen-fixing symbiosis is a powerful model for identifying traits and genes underlying bacterial fitness. New technologies allow high-throughput measurement of the relative fitness of bacterial mutants, strains and species in mixed inocula in the host, rhizosphere and soil environments. I consider how host genetic variation (G × G), other environmental factors (G × E), and host life-cycle variation may contribute to the maintenance of genetic variation and adaptive trajectories of rhizobia - and, potentially, other facultative symbionts. Lastly, I place these findings in the context of developing beneficial inoculants in a changing climate.
Collapse
Affiliation(s)
- Liana T Burghardt
- Department of Plant and Microbial Biology, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St Paul, MN, 55108, USA
| |
Collapse
|
37
|
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: 37] [Impact Index Per Article: 9.3] [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'.
Collapse
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
| |
Collapse
|
38
|
Younginger BS, Friesen ML. Connecting signals and benefits through partner choice in plant-microbe interactions. FEMS Microbiol Lett 2020; 366:5626345. [PMID: 31730203 DOI: 10.1093/femsle/fnz217] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 10/17/2019] [Indexed: 12/20/2022] Open
Abstract
Stabilizing mechanisms in plant-microbe symbioses are critical to maintaining beneficial functions, with two main classes: host sanctions and partner choice. Sanctions are currently presumed to be more effective and widespread, based on the idea that microbes rapidly evolve cheating while retaining signals matching cooperative strains. However, hosts that effectively discriminate among a pool of compatible symbionts would gain a significant fitness advantage. Using the well-characterized legume-rhizobium symbiosis as a model, we evaluate the evidence for partner choice in the context of the growing field of genomics. Empirical studies that rely upon bacteria varying only in nitrogen-fixation ability ignore host-symbiont signaling and frequently conclude that partner choice is not a robust stabilizing mechanism. Here, we argue that partner choice is an overlooked mechanism of mutualism stability and emphasize that plants need not use the microbial services provided a priori to discriminate among suitable partners. Additionally, we present a model that shows that partner choice signaling increases symbiont and host fitness in the absence of sanctions. Finally, we call for a renewed focus on elucidating the signaling mechanisms that are critical to partner choice while further aiming to understand their evolutionary dynamics in nature.
Collapse
Affiliation(s)
- Brett S Younginger
- Department of Plant Pathology, Washington State University, PO Box 646430, 345 Johnson Hall, Pullman, WA 99164, USA
| | - Maren L Friesen
- Department of Plant Pathology, Washington State University, PO Box 646430, 345 Johnson Hall, Pullman, WA 99164, USA.,Department of Crop and Soil Sciences, Washington State University, PO Box 646420, 115 Johnson Hall, Pullman, WA 99164, USA
| |
Collapse
|
39
|
Batstone RT, Peters MAE, Simonsen AK, Stinchcombe JR, Frederickson ME. Environmental variation impacts trait expression and selection in the legume-rhizobium symbiosis. AMERICAN JOURNAL OF BOTANY 2020; 107:195-208. [PMID: 32064599 DOI: 10.1002/ajb2.1432] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 11/04/2019] [Indexed: 05/22/2023]
Abstract
PREMISE The ecological outcomes of mutualism are well known to shift across abiotic or biotic environments, but few studies have addressed how different environments impact evolutionary responses, including the intensity of selection on and the expression of genetic variance in key mutualism-related traits. METHODS We planted 30 maternal lines of the legume Medicago lupulina in four field common gardens and compared our measures of selection on and genetic variance in nodulation, a key trait reflecting legume investment in the symbiosis, with those from a previous greenhouse experiment using the same 30 M. lupulina lines. RESULTS We found that both the mean and genetic variance for nodulation were much greater in the greenhouse than in the field and that the form of selection on nodulation significantly differed across environments. We also found significant genotype-by-environment (G × E) effects for fitness-related traits that were generated by differences in the rank order of plant lines among environments. CONCLUSIONS Overall, our results suggest that the expression of genotypic variation and selection on nodulation differ across environments. In the field, significant rank-order changes for plant fitness potentially help maintain genetic variation in natural populations, even in the face of directional or stabilizing selection.
Collapse
Affiliation(s)
- Rebecca T Batstone
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
- Carl Woese Institute for Genomic Biology, University of Illinois at Champaign-Urbana, Urbana, IL, 61801, USA
| | - Madeline A E Peters
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Anna K Simonsen
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
- Koffler Scientific Reserve, University of Toronto, King, ON, L7B 1K5, Canada
| | - Megan E Frederickson
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| |
Collapse
|
40
|
Heath KD, Podowski JC, Heniff S, Klinger CR, Burke PV, Weese DJ, Yang WH, Lau JA. Light availability and rhizobium variation interactively mediate the outcomes of legume-rhizobium symbiosis. AMERICAN JOURNAL OF BOTANY 2020; 107:229-238. [PMID: 32072629 DOI: 10.1002/ajb2.1435] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 12/08/2019] [Indexed: 05/22/2023]
Abstract
PREMISE Nutrients, light, water, and temperature are key factors limiting the growth of individual plants in nature. Mutualistic interactions between plants and microbes often mediate resource limitation for both partners. In the mutualism between legumes and rhizobia, plants provide rhizobia with carbon in exchange for fixed nitrogen. Because partner quality in mutualisms is genotype-dependent, within-species genetic variation is expected to alter the responses of mutualists to changes in the resource environment. Here we ask whether partner quality variation in rhizobia mediates the response of host plants to changing light availability, and conversely, whether light alters the expression of partner quality variation. METHODS We inoculated clover hosts with 11 strains of Rhizobium leguminosarum that differed in partner quality, grew plants under either ambient or low light conditions in the greenhouse, and measured plant growth, nodule traits, and foliar nutrient composition. RESULTS Light availability and rhizobium inoculum interactively determined plant growth, and variation in rhizobium partner quality was more apparent in ambient light. CONCLUSIONS Our results suggest that variation in the costs and benefits of rhizobium symbionts mediate host responses to light availability and that rhizobium strain variation might more important in higher-light environments. Our work adds to a growing appreciation for the role of microbial intraspecific and interspecific diversity in mediating extended phenotypes in their hosts and suggests an important role for light availability in the ecology and evolution of legume-rhizobium symbiosis.
Collapse
Affiliation(s)
- Katy D Heath
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S. Goodwin Ave., Urbana, IL, 61801, USA
| | - Justin C Podowski
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S. Goodwin Ave., Urbana, IL, 61801, USA
| | - Stephanie Heniff
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S. Goodwin Ave., Urbana, IL, 61801, USA
| | - Christie R Klinger
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S. Goodwin Ave., Urbana, IL, 61801, USA
| | - Patricia V Burke
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S. Goodwin Ave., Urbana, IL, 61801, USA
| | - Dylan J Weese
- Department of Biology, St. Ambrose University, Davenport, IA, 52803, USA
| | - Wendy H Yang
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S. Goodwin Ave., Urbana, IL, 61801, USA
| | - Jennifer A Lau
- W. K. Kellogg Biological Station and Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| |
Collapse
|
41
|
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.
Collapse
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
| |
Collapse
|
42
|
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.
Collapse
|
43
|
Lucke M, Correa MG, Levy A. The Role of Secretion Systems, Effectors, and Secondary Metabolites of Beneficial Rhizobacteria in Interactions With Plants and Microbes. FRONTIERS IN PLANT SCIENCE 2020; 11:589416. [PMID: 33240304 PMCID: PMC7680756 DOI: 10.3389/fpls.2020.589416] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/14/2020] [Indexed: 05/05/2023]
Abstract
Beneficial rhizobacteria dwell in plant roots and promote plant growth, development, and resistance to various stress types. In recent years there have been large-scale efforts to culture root-associated bacteria and sequence their genomes to uncover novel beneficial microbes. However, only a few strains of rhizobacteria from the large pool of soil microbes have been studied at the molecular level. This review focuses on the molecular basis underlying the phenotypes of three beneficial microbe groups; (1) plant-growth promoting rhizobacteria (PGPR), (2) root nodulating bacteria (RNB), and (3) biocontrol agents (BCAs). We focus on bacterial proteins and secondary metabolites that mediate known phenotypes within and around plants, and the mechanisms used to secrete these. We highlight the necessity for a better understanding of bacterial genes responsible for beneficial plant traits, which can be used for targeted gene-centered and molecule-centered discovery and deployment of novel beneficial rhizobacteria.
Collapse
|
44
|
Favero VO, Carvalho RH, Motta VM, Leite ABC, Coelho MRR, Xavier GR, Rumjanek NG, Urquiaga S. Bradyrhizobium as the Only Rhizobial Inhabitant of Mung Bean ( Vigna radiata) Nodules in Tropical Soils: A Strategy Based on Microbiome for Improving Biological Nitrogen Fixation Using Bio-Products. FRONTIERS IN PLANT SCIENCE 2020; 11:602645. [PMID: 33510747 PMCID: PMC7835340 DOI: 10.3389/fpls.2020.602645] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/14/2020] [Indexed: 05/07/2023]
Abstract
The mung bean has a great potential under tropical conditions given its high content of grain protein. Additionally, its ability to benefit from biological nitrogen fixation (BNF) through association with native rhizobia inhabiting nodule microbiome provides most of the nitrogen independence on fertilizers. Soil microbial communities which are influenced by biogeographical factors and soil properties, represent a source of rhizobacteria capable of stimulating plant growth. The objective of this study is to support selection of beneficial bacteria that form positive interactions with mung bean plants cultivated in tropical soils, as part of a seed inoculation program for increasing grain yield based on the BNF and other mechanisms. Two mung bean genotypes (Camaleão and Esmeralda) were cultivated in 10 soil samples. Nodule microbiome was characterized by next-generation sequencing using Illumina MiSeq 16S rRNA. More than 99% of nodule sequences showed similarity with Bradyrhizobium genus, the only rhizobial present in nodules in our study. Higher bacterial diversity of soil samples collected in agribusiness areas (MW_MT-I, II or III) was associated with Esmeralda genotype, while an organic agroecosystem soil sample (SE_RJ-V) showed the highest bacterial diversity independent of genotype. Furthermore, OTUs close to Bradyrhizobium elkanii have dominated in all soil samples, except in the sample from the organic agroecosystem, where just B. japonicum was present. Bacterial community of mung bean nodules is mainly influenced by soil pH, K, Ca, and P. Besides a difference on nodule colonization by OTU sequences close to the Pseudomonas genus regarding the two genotypes was detected too. Although representing a small rate, around 0.1% of the total, Pseudomonas OTUs were only retrieved from nodules of Esmeralda genotype, suggesting a different trait regarding specificity between macro- and micro-symbionts. The microbiome analysis will guide the next steps in the development of an inoculant for mung bean aiming to promote plant growth and grain yield, composed either by an efficient Bradyrhizobium strain on its own or co-inoculated with a Pseudomonas strain. Considering the results achieved, the assessment of microbial ecology parameters is a potent coadjuvant capable to accelerate the inoculant development process and to improve the benefits to the crop by soil microorganisms.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Norma Gouvêa Rumjanek
- Embrapa Agrobiology, Seropédica, Rio de Janeiro, Brazil
- *Correspondence: Norma Gouvêa Rumjanek,
| | | |
Collapse
|
45
|
White PJ. Root traits benefitting crop production in environments with limited water and nutrient availability. ANNALS OF BOTANY 2019; 124:mcz162. [PMID: 31599920 PMCID: PMC6881216 DOI: 10.1093/aob/mcz162] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/04/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Breeding for advantageous root traits will play a fundamental role in improving the efficiency of water and nutrient acquisition, closing yield gaps, and underpinning the "Evergreen Revolution" that must match crop production with human demand. SCOPE This preface provides an overview of a Special Issue of Annals of Botany on "Root traits benefitting crop production in environments with limited water and nutrient availability". The first papers in the Special Issue examine how breeding for reduced shoot stature and greater harvest index during the Green Revolution affected root system architecture. It is observed that reduced plant height and root architecture are inherited independently and can be improved simultaneously to increase the acquisition and utilisation of carbon, water and mineral nutrients. These insights are followed by papers examining beneficial root traits for resource acquisition in environments with limited water or nutrient availability, such as deep rooting, control of hydraulic conductivity, formation of aerenchyma, proliferation of lateral roots and root hairs, foraging of nutrient-rich patches, manipulation of rhizosphere pH and the exudation of low molecular weight organic solutes. The Special Issue concludes with papers exploring the interactions of plant roots and microorganisms, highlighting the need for plants to control the symbiotic relationships between mycorrhizal fungi and rhizobia to achieve maximal growth, and the roles of plants and microbes in the modification and development of soils.
Collapse
Affiliation(s)
- Philip J White
- Ecological Science Group, The James Hutton Institute, Invergowrie, Dundee, UK
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Distinguished Scientist Fellowship Program, King Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
46
|
Guerrieri A, Dong L, Bouwmeester HJ. Role and exploitation of underground chemical signaling in plants. PEST MANAGEMENT SCIENCE 2019; 75:2455-2463. [PMID: 31166074 PMCID: PMC6771575 DOI: 10.1002/ps.5507] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/01/2019] [Accepted: 06/01/2019] [Indexed: 05/09/2023]
Abstract
The soil ecosystem is composed of a mixture of living organisms and non-living matter as well as the complex interactions between them. In the past 100 years or so, agricultural soil ecosystems have been strongly affected by agricultural practices such as tillage and the use of pesticides and fertilizers, which strongly affect soil nutrient composition, pH and biodiversity. In modern pest management, however, the focus is gradually shifting from crop production through agricultural practices to soil ecosystem protection. In this review we discuss how the underground chemical signals secreted by plant roots play a role in keeping the soil ecosystem in balance and how they affect plant fitness by shaping the root biome, increasing nutrient availability, promoting symbiosis, and attracting beneficial organisms and repelling harmful ones, including other plants. We review a number of fascinating cases, such as signaling molecules with dual, positive and negative, functions and bacterial quorum sensing mimicking molecules. Finally, examples of how these compounds can be exploited in modern pest management are reviewed, and the prospects for future developments discussed. © 2019 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Collapse
Affiliation(s)
- Alessandra Guerrieri
- Plant Hormone Biology GroupSwammerdam Institute for Life Sciences (SILS), University of AmsterdamAmsterdamthe Netherlands
| | - Lemeng Dong
- Plant Hormone Biology GroupSwammerdam Institute for Life Sciences (SILS), University of AmsterdamAmsterdamthe Netherlands
| | - Harro J Bouwmeester
- Plant Hormone Biology GroupSwammerdam Institute for Life Sciences (SILS), University of AmsterdamAmsterdamthe Netherlands
| |
Collapse
|
47
|
Burghardt LT, Epstein B, Tiffin P. Legacy of prior host and soil selection on rhizobial fitness in planta. Evolution 2019; 73:2013-2023. [PMID: 31334838 DOI: 10.1111/evo.13807] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 01/03/2023]
Abstract
Measuring selection acting on microbial populations in natural or even seminatural environments is challenging because many microbial populations experience variable selection. The majority of rhizobial bacteria are found in the soil. However, they also live symbiotically inside nodules of legume hosts and each nodule can release thousands of daughter cells back into the soil. We tested how past selection (i.e., legacies) by two plant genotypes and by the soil alone affected selection and genetic diversity within a population of 101 strains of Ensifer meliloti. We also identified allelic variants most strongly associated with soil- and host-dependent fitness. In addition to imposing direct selection on rhizobia populations, soil and host environments had lasting effects across host generations. Host presence and genotype during the legacy period explained 22% and 12% of the variance in the strain composition of nodule communities in the second cohort, respectively. Although strains with high host fitness in the legacy cohort tended to be enriched in the second cohort, the diversity of the strain community was greater when the second cohort was preceded by host rather than soil legacies. Our results indicate the potential importance of soil selection driving the evolution of these plant-associated microbes.
Collapse
Affiliation(s)
- Liana T Burghardt
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, 55108
| | - Brendan Epstein
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, 55108
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, 55108
| |
Collapse
|
48
|
Microbial associations enabling nitrogen acquisition in plants. Curr Opin Microbiol 2019; 49:83-89. [DOI: 10.1016/j.mib.2019.10.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/03/2019] [Accepted: 10/11/2019] [Indexed: 01/29/2023]
|
49
|
Das DR, Horváth B, Kundu A, Kaló P, DasGupta M. Functional conservation of CYCLOPS in crack entry legume Arachis hypogaea. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 281:232-241. [PMID: 30824056 DOI: 10.1016/j.plantsci.2018.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/05/2018] [Accepted: 12/07/2018] [Indexed: 06/09/2023]
Abstract
Root nodule symbiosis in legumes is established following interaction of compatible rhizobia that activates an array of genes, commonly known as symbiotic-pathway, resulting in nodule development. In model legumes, bacterial entry mainly occurs through infection thread involving the expression of transcription factor CYCLOPS/IPD3. Here we show the functional analysis of AhCYCLOPS in Arachis hypogaea where bacteria invade roots through epidermal cracks. Exploiting significant cross-species domain conservation, trans-complementation experiments involving ectopic expression of AhCYCLOPS in transgenic hairy-roots of Medicago truncatula ipd3 mutants resulted in functional complementation of Medicago nodules. Moreover, native promoter of AhCYCLOPS was sufficient for this cross-species complementation irrespective of the different modes of infection of roots by rhizobia and nodule ontology. To unravel the role of AhCYCLOPS during 'crack-entry' nodulation in A. hypogaea, RNAi of AhCYCLOPS was performed which resulted in delayed nodule inception followed by drastic reduction in nodule number on transgenic hairy-roots. The infection zone of a significant number of RNAi nodules showed presence of infected cells with enlarged nucleus and rod shaped undifferentiated bacteria. Expression analysis showed downregulation of several nodulation responsible effectors endorsing the compromised condition of RNAi roots. Together, the results indicated that AhCYCLOPS plays an important role in A. hypogaea nodule development.
Collapse
Affiliation(s)
- Debapriya Rajlakshmi Das
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Beatrix Horváth
- Agricultural Biotechnology Institute, NARIC, Szent-Györgyi Albert u. 4, Gödöllő, Hungary
| | - Anindya Kundu
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Péter Kaló
- Agricultural Biotechnology Institute, NARIC, Szent-Györgyi Albert u. 4, Gödöllő, Hungary
| | - Maitrayee DasGupta
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
| |
Collapse
|
50
|
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
| |
Collapse
|