1
|
Ni H, Hou X, Tian S, Liu C, Zhang G, Peng Y, Chen L, Wang J, Chen Q, Xin D. Insights into the Early Steps of the Symbiotic Interaction between Soybean ( Glycine max) and Sinorhizobium fredii Symbiosis Using Transcriptome, Small RNA, and Degradome Sequencing. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:17084-17098. [PMID: 39013023 PMCID: PMC11299180 DOI: 10.1021/acs.jafc.4c02312] [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: 03/14/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/18/2024]
Abstract
Symbiotic nitrogen fixation carried out by the soybean-rhizobia symbiosis increases soybean yield and reduces the amount of nitrogen fertilizer that has been applied. MicroRNAs (miRNAs) are crucial in plant growth and development, prompting an investigation into their role in the symbiotic interaction of soybean with partner rhizobia. Through integrated small RNA, transcriptome, and degradome sequencing analysis, 1215 known miRNAs, 314 of them conserved, and 187 novel miRNAs were identified, with 44 differentially expressed miRNAs in soybean roots inoculated with Sinorhizobium fredii HH103 and a ttsI mutant. The study unveiled that the known miRNA gma-MIR398a-p5 was downregulated in the presence of the ttsI mutation, while the target gene of gma-MIR398a-p5, Glyma.06G007500, associated with nitrogen metabolism, was upregulated. The results of this study offer insights for breeding high-efficiency nitrogen-fixing soybean varieties, enhancing crop yield and quality.
Collapse
Affiliation(s)
| | | | - Siyi Tian
- Key Laboratory of Soybean
Biology of the Chinese Ministry of Education, Key Laboratory of Soybean
Biology and Breeding, Genetics of Chinese Agriculture Ministry, College
of Agriculture, Northeast Agricultural University, Harbin 150036, China
| | - Chunyan Liu
- Key Laboratory of Soybean
Biology of the Chinese Ministry of Education, Key Laboratory of Soybean
Biology and Breeding, Genetics of Chinese Agriculture Ministry, College
of Agriculture, Northeast Agricultural University, Harbin 150036, China
| | - Guoqing Zhang
- Key Laboratory of Soybean
Biology of the Chinese Ministry of Education, Key Laboratory of Soybean
Biology and Breeding, Genetics of Chinese Agriculture Ministry, College
of Agriculture, Northeast Agricultural University, Harbin 150036, China
| | - Yang Peng
- Key Laboratory of Soybean
Biology of the Chinese Ministry of Education, Key Laboratory of Soybean
Biology and Breeding, Genetics of Chinese Agriculture Ministry, College
of Agriculture, Northeast Agricultural University, Harbin 150036, China
| | - Lin Chen
- Key Laboratory of Soybean
Biology of the Chinese Ministry of Education, Key Laboratory of Soybean
Biology and Breeding, Genetics of Chinese Agriculture Ministry, College
of Agriculture, Northeast Agricultural University, Harbin 150036, China
| | - Jinhui Wang
- Key Laboratory of Soybean
Biology of the Chinese Ministry of Education, Key Laboratory of Soybean
Biology and Breeding, Genetics of Chinese Agriculture Ministry, College
of Agriculture, Northeast Agricultural University, Harbin 150036, China
| | - Qingshan Chen
- Key Laboratory of Soybean
Biology of the Chinese Ministry of Education, Key Laboratory of Soybean
Biology and Breeding, Genetics of Chinese Agriculture Ministry, College
of Agriculture, Northeast Agricultural University, Harbin 150036, China
| | - Dawei Xin
- Key Laboratory of Soybean
Biology of the Chinese Ministry of Education, Key Laboratory of Soybean
Biology and Breeding, Genetics of Chinese Agriculture Ministry, College
of Agriculture, Northeast Agricultural University, Harbin 150036, China
| |
Collapse
|
2
|
Zhiyong S, Yaxuan G, Yuanyuan W, Xiang Y, Xu G, Zhenhong L, Jingping N, Jianping L, Zhenyu L. Nitrogen-fixing bacteria promote growth and bioactive components accumulation of Astragalus mongholicus by regulating plant metabolism and rhizosphere microbiota. BMC Microbiol 2024; 24:261. [PMID: 39004720 PMCID: PMC11247893 DOI: 10.1186/s12866-024-03409-y] [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: 01/20/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024] Open
Abstract
BACKGROUND The excessive application of chemical fertilizers in the cultivation of Astragalus mongholicus Bunge results in a reduction in the quality of the medicinal plant and compromises the sustainable productivity of the soil. PGPB inoculant is a hot topic in ecological agriculture research. In the cultivation of Astragalus mongholicus, the screened nitrogen-fixing bacteria can promote plant growth, however, whether it can promote the accumulation of main bioactive components remains unknown. In this study, mixed inoculants containing 5 strains of growth promoting bacteria (Rhizobium T16 , Sinorhizobium T21 , Bacillus J1 , Bacillus G4 and Arthrobacter J2) were used in the field experiment. The metabolic substances in the root tissues of Astragalus mongholicus were identified during the harvest period by non-targeted metabolomics method, and the differential metabolites between groups were identified by statistical analysis. Meanwhile, high-throughput sequencing was performed to analyze the changes of rhizosphere soil and endophytic microbial community structure after mixed microbial treatment. RESULTS The results of non-targeted metabolism indicated a significant increase in the levels of 26 metabolites after treatment including 13 flavonoids, 3 saponins and 10 other components. The contents of three plant hormones (abscisic acid, salicylic acid and spermidine) also increased after treatment, which presumed to play an important role in regulating plant growth and metabolism. Studies on endosphere and rhizosphere bacterial communities showed that Rhzobiaceae, Micromonosporaceae, and Hypomicrobiaceae in endophytic, and Oxalobactereae in rhizosphere were significantly increased after treatment. These findings suggest their potential importance in plant growth promotion and secondary metabolism regulation. CONCLUSIONS This finding provides a basis for developing nitrogen-fixing bacteria fertilizer and improving the ecological planting efficiency of Astragalus mongholicus.
Collapse
Affiliation(s)
- Shi Zhiyong
- College Of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Guo Yaxuan
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, 030006, China
| | - Wang Yuanyuan
- College Of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Yan Xiang
- College Of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Guo Xu
- College Of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Lei Zhenhong
- Shanxi Zhendong Pharmaceutical (China), Changzhi, 047000, China
| | - Niu Jingping
- College Of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Liang Jianping
- College Of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China.
- Shanxi Key Laboratory of Chinese Veterinary Medicine Modernization, Shanxi Agricultural University, Jinzhong, 030801, China.
| | - Li Zhenyu
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, 030006, China.
| |
Collapse
|
3
|
Deng JL, Zhao L, Wei H, Ye HX, Yang L, Sun L, Zhao Z, Murray JD, Liu CW. A deeply conserved amino acid required for VAPYRIN localization and function during legume-rhizobial symbiosis. THE NEW PHYTOLOGIST 2024; 243:14-22. [PMID: 38703001 DOI: 10.1111/nph.19779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/10/2024] [Indexed: 05/06/2024]
Affiliation(s)
- Jin-Li Deng
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Li Zhao
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Hong Wei
- The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Han-Xiao Ye
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Li Yang
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Linfeng Sun
- The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Zhong Zhao
- Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Jeremy D Murray
- National Key Laboratory of Plant Molecular Genetics, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Cheng-Wu Liu
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| |
Collapse
|
4
|
Kosmopoulos JC, Batstone-Doyle RT, Heath KD. Co-inoculation with novel nodule-inhabiting bacteria reduces the benefits of legume-rhizobium symbiosis. Can J Microbiol 2024; 70:275-288. [PMID: 38507780 DOI: 10.1139/cjm-2023-0209] [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] [Indexed: 03/22/2024]
Abstract
The ecologically and economically vital symbiosis between nitrogen-fixing rhizobia and leguminous plants is often thought of as a bi-partite interaction, yet studies increasingly show the prevalence of non-rhizobial endophytes (NREs) that occupy nodules alongside rhizobia. Yet, what impact these NREs have on plant or rhizobium fitness remains unclear. Here, we investigated four NRE strains found to naturally co-occupy nodules of the legume Medicago truncatula alongside Sinorhizobium meliloti in native soils. Our objectives were to (1) examine the direct and indirect effects of NREs on M. truncatula and S. meliloti fitness, and (2) determine whether NREs can re-colonize root and nodule tissues upon reinoculation. We identified one NRE strain (522) as a novel Paenibacillus species, another strain (717A) as a novel Bacillus species, and the other two (702A and 733B) as novel Pseudomonas species. Additionally, we found that two NREs (Bacillus 717A and Pseudomonas 733B) reduced the fitness benefits obtained from symbiosis for both partners, while the other two (522, 702A) had little effect. Lastly, we found that NREs were able to co-infect host tissues alongside S. meliloti. This study demonstrates that variation of NREs present in natural populations must be considered to better understand legume-rhizobium dynamics in soil communities.
Collapse
Affiliation(s)
- James C Kosmopoulos
- School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, WI, USA
| | - Rebecca T Batstone-Doyle
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Katy D Heath
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| |
Collapse
|
5
|
Ali R, Chaluvadi SR, Wang X, Hazzouri KM, Sudalaimuthuasari N, Rafi M, Al-Nuaimi M, Sasi S, Antepenko E, Bennetzen JL, Amiri KMA. Microbiome properties in the root nodules of Prosopis cineraria, a leguminous desert tree. Microbiol Spectr 2024; 12:e0361723. [PMID: 38624222 PMCID: PMC11237379 DOI: 10.1128/spectrum.03617-23] [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: 10/09/2023] [Accepted: 03/14/2024] [Indexed: 04/17/2024] Open
Abstract
We conducted a comprehensive analysis of the total microbiome and transcriptionally active microbiome communities in the roots and root nodules of Prosopis cineraria, an important leguminous tree in arid regions of many Asian countries. Mature P. cineraria trees growing in the desert did not exhibit any detected root nodules. However, we observed root nodules on the roots of P. cineraria growing on a desert farm and on young plants growing in a growth chamber, when inoculated with rhizosphere soil, including with rhizosphere soil from near desert tree roots that had no nodules. Compared to nearby soil, non-nodulated roots were enriched with Actinobacteria (e.g., Actinophytocola sp.), whereas root nodules sampled from the desert farm and growth chamber had abundant Alphaproteobacteria (e.g., Ensifer sp.). These nodules yielded many microbes in addition to such nitrogen-fixing bacteria as Ensifer and Sinorhizobium species. Significant differences exist in the composition and abundance of microbial isolates between the nodule surface and the nodule endosphere. Shotgun metagenome analysis of nodule endospheres revealed that the root nodules comprised over 90% bacterial DNA, whereas metatranscriptome analysis showed that the plant produces vastly more transcripts than the microbes in these nodules. Control inoculations demonstrated that four out of six Rhizobium, Agrobacterium, or Ensifer isolates purified from P. cineraria nodules produced nodules in the roots of P. cineraria seedlings under greenhouse conditions. The best nodulation was achieved when seedlings were inoculated with a mixture of those bacterial strains. Though root nodulation could be achieved under water stress conditions, nodule number and nodule biomass increased with copious water availability. .IMPORTANCEMicrobial communities were investigated in roots and root nodules of Prosopis cineraria, a leguminous tree species in arid Asian regions that is responsible for exceptionally important contributions to soil fertility in these dramatically dry locations. Soil removed from regions near nodule-free roots on these mature plants contained an abundance of bacteria with the genetic ability to generate nodules and fix nitrogen but did not normally nodulate in their native rhizosphere environment, suggesting a very different co-evolved relationship than that observed for herbaceous legumes. The relative over-expression of the low-gene-density plant DNA compared to the bacterial DNA in the nodules was also unexpected, indicating a very powerful induction of host genetic contributions within the nodule. Finally, the water dependence of nodulation in inoculated seedlings suggested a possible link between early seedling growth (before a deep root system can be developed) and the early development of nitrogen-fixing capability.
Collapse
Affiliation(s)
- Rashid Ali
- Mitrix Bio., Inc., Farmington, Connecticut, USA
| | | | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - Khaled M. Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, UAE
| | | | - Mohammed Rafi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, UAE
| | - Mariam Al-Nuaimi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, UAE
| | - Shina Sasi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, UAE
| | - Eric Antepenko
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | | | - Khaled M. A. Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, UAE
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, UAE
| |
Collapse
|
6
|
Gao JP, Liang W, Liu CW, Xie F, Murray JD. Unraveling the rhizobial infection thread. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2235-2245. [PMID: 38262702 DOI: 10.1093/jxb/erae017] [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: 10/20/2023] [Accepted: 01/23/2024] [Indexed: 01/25/2024]
Abstract
Most legumes can form an endosymbiotic association with soil bacteria called rhizobia, which colonize specialized root structures called nodules where they fix nitrogen. To colonize nodule cells, rhizobia must first traverse the epidermis and outer cortical cell layers of the root. In most legumes, this involves formation of the infection thread, an intracellular structure that becomes colonized by rhizobia, guiding their passage through the outer cell layers of the root and into the newly formed nodule cells. In this brief review, we recount the early research milestones relating to the rhizobial infection thread and highlight two relatively recent advances in the symbiotic infection mechanism, the eukaryotically conserved 'MYB-AUR1-MAP' mitotic module, which links cytokinesis mechanisms to intracellular infection, and the discovery of the 'infectosome' complex, which guides infection thread growth. We also discuss the potential intertwining of the two modules and the hypothesis that cytokinesis served as a foundation for intracellular infection of symbiotic microbes.
Collapse
Affiliation(s)
- Jin-Peng Gao
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wenjie Liang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Cheng-Wu Liu
- School of Life Sciences, Division of Life Sciences and Medicine, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei 230026, China
| | - Fang Xie
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jeremy D Murray
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- John Innes Centre, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Norwich Research Park, Norwich NR4 7UH, UK
| |
Collapse
|
7
|
Harnpicharnchai P, Siriarchawatana P, Mayteeworakoon S, Ingsrisawang L, Likhitrattanapisal S, Eurwilaichitr L, Ingsriswang S. Interplay of xenobiotic-degrading and antibiotic-resistant microorganisms among the microbiome found in the air, handrail, and floor of the subway station. ENVIRONMENTAL RESEARCH 2024; 247:118269. [PMID: 38246293 DOI: 10.1016/j.envres.2024.118269] [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: 10/30/2023] [Revised: 01/11/2024] [Accepted: 01/18/2024] [Indexed: 01/23/2024]
Abstract
Investigating the quality of the subway environment, especially regarding antibiotic resistance genes (ARGs) and xenobiotics, conveys ecological and health impacts. In this study, compositions and relations of microorganisms harboring ARGs and xenobiotic degradation and metabolism genes (XDGs) in the Sukhumvit subway station (MRT-SKV) in Bangkok was assessed by analyzing the taxonomic and genetic diversity of the microbiome in the air and on the surfaces of floor and handrail. The major bacteria in the MRT-SKV (including Moraxella, which was abundant in the bioaerosol and handrail samples, and Staphylococcus, which was abundant in the bioaerosol samples) were found to contain both ARGs and XDGs. The co-abundance correlation network revealed notable relationships among bacteria harboring antibiotic resistance genes (ARGs) and xenobiotic degradation genes (XDGs). Significant associations were observed between ARGs linked to glycopeptide and fluoroquinolone resistance and genes associated with benzoate, styrene, and atrazine degradation pathways, as well as between ARGs related to cephamycin, cephalosporin, and MLS resistance and XDGs associated with the cytochrome P450-dependent drug metabolism pathway. These correlations suggested that selective pressure exerted by certain xenobiotics and antibiotics can simultaneously affect both ARGs and XDGs in the environment and should favor correlations and co-survival among ARG- and XDG-containing bacteria in the environments. The correlations may occur via shared mechanisms of resistance to both xenobiotics and antibiotics. Finally, different correlation pairs were seen in different niches (air, handrail, floor) of the subway environment or different geolocations. Thus, the relationship between ARG and XDG pairs most likely depends on the unique characteristics of the niches and on the prominent types of xenobiotics and antibiotics in the subway environment. The results indicated that interactions and connections between microbial communities can impact how they function. These microorganisms can have profound effects on accumulation of xenobiotics and ARGs in the MRT-SKV.
Collapse
Affiliation(s)
- Piyanun Harnpicharnchai
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand
| | - Paopit Siriarchawatana
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand
| | - Sermsiri Mayteeworakoon
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand
| | - Lily Ingsrisawang
- Department of Statistics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Somsak Likhitrattanapisal
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand
| | - Lily Eurwilaichitr
- National Energy Technology Center, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand
| | - Supawadee Ingsriswang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand.
| |
Collapse
|
8
|
Li Y, Liu Q, Zhang DX, Zhang ZY, Xu A, Jiang YL, Chen ZC. Metal nutrition and transport in the process of symbiotic nitrogen fixation. PLANT COMMUNICATIONS 2024; 5:100829. [PMID: 38303509 PMCID: PMC11009365 DOI: 10.1016/j.xplc.2024.100829] [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: 09/28/2023] [Revised: 01/14/2024] [Accepted: 01/26/2024] [Indexed: 02/03/2024]
Abstract
Symbiotic nitrogen fixation (SNF) facilitated by the interaction between legumes and rhizobia is a well-documented and eco-friendly alternative to chemical nitrogen fertilizers. Host plants obtain fixed nitrogen from rhizobia by providing carbon and mineral nutrients. These mineral nutrients, which are mostly in the form of metal ions, are implicated in various stages of the SNF process. This review describes the functional roles played by metal ions in nodule formation and nitrogen fixation and specifically addresses their transport mechanisms and associated transporters within root nodules. Future research directions and potential strategies for enhancing SNF efficiency are also discussed.
Collapse
Affiliation(s)
- Yuan Li
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qian Liu
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dan-Xun Zhang
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhuo-Yan Zhang
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ao Xu
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan-Long Jiang
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhi-Chang Chen
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| |
Collapse
|
9
|
Aroney STN, Pini F, Kessler C, Poole PS, Sánchez-Cañizares C. The motility and chemosensory systems of Rhizobium leguminosarum, their role in symbiosis, and link to PTS Ntr regulation. Environ Microbiol 2024; 26:e16570. [PMID: 38216524 DOI: 10.1111/1462-2920.16570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Motility and chemotaxis are crucial processes for soil bacteria and plant-microbe interactions. This applies to the symbiotic bacterium Rhizobium leguminosarum, where motility is driven by flagella rotation controlled by two chemotaxis systems, Che1 and Che2. The Che1 cluster is particularly important in free-living motility prior to the establishment of the symbiosis, with a che1 mutant delayed in nodulation and reduced in nodulation competitiveness. The Che2 system alters bacteroid development and nodule maturation. In this work, we also identified 27 putative chemoreceptors encoded in the R. leguminosarum bv. viciae 3841 genome and characterized its motility in different growth conditions. We describe a metabolism-based taxis system in rhizobia that acts at high concentrations of dicarboxylates to halt motility independent of chemotaxis. Finally, we show how PTSNtr influences cell motility, with PTSNtr mutants exhibiting reduced swimming in different media. Motility is restored by the active forms of the PTSNtr output regulatory proteins, unphosphorylated ManX and phosphorylated PtsN. Overall, this work shows how rhizobia typify soil bacteria by having a high number of chemoreceptors and highlights the importance of the motility and chemotaxis mechanisms in a free-living cell in the rhizosphere, and at different stages of the symbiosis.
Collapse
Affiliation(s)
| | | | - Celia Kessler
- Department of Biology, University of Oxford, Oxford, UK
| | | | | |
Collapse
|
10
|
Zhang X, Lan T, Jiang H, Ye K, Dai Z. Bacterial community driven nitrogen cycling in coastal sediments of intertidal transition zone. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168299. [PMID: 37926266 DOI: 10.1016/j.scitotenv.2023.168299] [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: 08/01/2023] [Revised: 10/14/2023] [Accepted: 11/01/2023] [Indexed: 11/07/2023]
Abstract
Microorganisms inhabiting in coastal sediments significantly affect the nitrogen cycling in coastal waters and ecosystems. However, the bacterial community that related to the key active nitrogen transformation processes in intertidal transition zone are still not understood. Across a long flat intertidal zone at depths from 0 to 3 m in Daya Bay, China, the bacterial communities in sediments and their driven nitrogen cycling potential were evaluated with environmental factors and 16S rRNA sequencing. The results showed that the intertidal zone is a divide for environmental factors as pH, salinity and C/N ratio, instead of an average shift from freshwater to salt water. At the same time, the environmental factors influenced the abundance of bacterial community related to nitrogen cycling. Across the intertidal zone, the dominant nitrogen transformation processes were different. At the high tide and middle tide sites, the primary nitrogen cycling process was nitrification that worked with Nitrosomonadaceae, Nitrospiraceae, 0319-6A21, and wb1-A12. At the low tide sites, nitrogen fixation was the dominant function conducted by Bradyrhizobiaceae. The reduction of nitrate was carried out with the help of Xanthomonadales but relatively weak in all sampling sites especially for low tide sites. This was mostly because the richness and evenness of bacterial community were the lowest at the low tide sites. Meanwhile, the pH, Cl-, salinity, NH4+, NO3- and C/N ratio were the important factors that shaped the composition of local bacterial community. Further, the nonmetric multidimensional scaling results indicated that there were significant statistical differences in the composition of bacterial community among samples at different layers. The dominant nitrogen cycling processes in coastal sediments at different tide levels were revealed in this study, which offered an extended concept of nitrogen transformation along the groundwater discharge path in the intertidal transition zone. The distributions and compositions of bacterial communities and predicted functions provided a new insight for coastal environment and ecosystem management.
Collapse
Affiliation(s)
- Xiaoying Zhang
- Institute of Intelligent Simulation and Early Warning for Subsurface Environment, Jilin University, Changchun 130026, China; College of Construction Engineering, Jilin University, Changchun 130026, China
| | - Tianshan Lan
- Institute of Intelligent Simulation and Early Warning for Subsurface Environment, Jilin University, Changchun 130026, China.
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Kexin Ye
- Institute of Intelligent Simulation and Early Warning for Subsurface Environment, Jilin University, Changchun 130026, China
| | - Zhenxue Dai
- Institute of Intelligent Simulation and Early Warning for Subsurface Environment, Jilin University, Changchun 130026, China; College of Construction Engineering, Jilin University, Changchun 130026, China.
| |
Collapse
|
11
|
Shumilina J, Soboleva A, Abakumov E, Shtark OY, Zhukov VA, Frolov A. Signaling in Legume-Rhizobia Symbiosis. Int J Mol Sci 2023; 24:17397. [PMID: 38139226 PMCID: PMC10743482 DOI: 10.3390/ijms242417397] [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: 10/05/2023] [Revised: 11/19/2023] [Accepted: 12/02/2023] [Indexed: 12/24/2023] Open
Abstract
Legumes represent an important source of food protein for human nutrition and animal feed. Therefore, sustainable production of legume crops is an issue of global importance. It is well-known that legume-rhizobia symbiosis allows an increase in the productivity and resilience of legume crops. The efficiency of this mutualistic association strongly depends on precise regulation of the complex interactions between plant and rhizobia. Their molecular dialogue represents a complex multi-staged process, each step of which is critically important for the overall success of the symbiosis. In particular, understanding the details of the molecular mechanisms behind the nodule formation and functioning might give access to new legume cultivars with improved crop productivity. Therefore, here we provide a comprehensive literature overview on the dynamics of the signaling network underlying the development of the legume-rhizobia symbiosis. Thereby, we pay special attention to the new findings in the field, as well as the principal directions of the current and prospective research. For this, here we comprehensively address the principal signaling events involved in the nodule inception, development, functioning, and senescence.
Collapse
Affiliation(s)
- Julia Shumilina
- Laboratory of Analytical Biochemistry and Biotechnology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia; (J.S.); (A.S.)
| | - Alena Soboleva
- Laboratory of Analytical Biochemistry and Biotechnology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia; (J.S.); (A.S.)
- Biological Faculty, Saint Petersburg State University, 199034 St. Petersburg, Russia;
| | - Evgeny Abakumov
- Biological Faculty, Saint Petersburg State University, 199034 St. Petersburg, Russia;
| | - Oksana Y. Shtark
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (O.Y.S.); (V.A.Z.)
| | - Vladimir A. Zhukov
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (O.Y.S.); (V.A.Z.)
| | - Andrej Frolov
- Laboratory of Analytical Biochemistry and Biotechnology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia; (J.S.); (A.S.)
- Biological Faculty, Saint Petersburg State University, 199034 St. Petersburg, Russia;
| |
Collapse
|
12
|
Zartdinova R, Nikitin A. Calcium in the Life Cycle of Legume Root Nodules. Indian J Microbiol 2023; 63:410-420. [PMID: 38031601 PMCID: PMC10682328 DOI: 10.1007/s12088-023-01107-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 10/07/2023] [Indexed: 12/01/2023] Open
Abstract
The present review highlights both the fundamental questions of calcium localization, compartmentation, and its participation in symbiosome signaling cascades during nodule formation and functioning. Apparently, the main link of such signaling is the calmodulin…calcium- and calmodulin-dependent protein kinases…CYCLOPS…NIN…target genes cascade. The minimum threshold level of calcium as a signaling agent in the presence of intracellular reserves determines the possibility of oligotrophy and ultraoligotrophy in relation to this element. During the functioning of root nodules, the Ca2+-ATPases activity maintains homeostasis of low calcium concentrations in the cytosol of nodule parenchyma cells. Disturbation of this homeostasis can trigger the root nodule senescence. The same reasons determine the increase in the effectiveness of symbiosis with the help of seed priming with sources of calcium. Examples of calcium response polymorphism in components of nitrogen fixing simbiosis important in practical terms are shown.
Collapse
Affiliation(s)
- Rozaliya Zartdinova
- Nitrogen Exchange Laboratory, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Nikitin
- Nitrogen Exchange Laboratory, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
13
|
Schnabel E, Thomas J, El-Hawaz R, Gao Y, Poehlman WL, Chavan S, Pasha A, Esteban E, Provart N, Feltus FA, Frugoli J. Laser Capture Microdissection Transcriptome Reveals Spatiotemporal Tissue Gene Expression Patterns of Medicago truncatula Roots Responding to Rhizobia. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:805-820. [PMID: 37717250 DOI: 10.1094/mpmi-03-23-0029-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
We report a public resource for examining the spatiotemporal RNA expression of 54,893 Medicago truncatula genes during the first 72 h of response to rhizobial inoculation. Using a methodology that allows synchronous inoculation and growth of more than 100 plants in a single media container, we harvested the same segment of each root responding to rhizobia in the initial inoculation over a time course, collected individual tissues from these segments with laser capture microdissection, and created and sequenced RNA libraries generated from these tissues. We demonstrate the utility of the resource by examining the expression patterns of a set of genes induced very early in nodule signaling, as well as two gene families (CLE peptides and nodule specific PLAT-domain proteins) and show that despite similar whole-root expression patterns, there are tissue differences in expression between the genes. Using a rhizobial response dataset generated from transcriptomics on intact root segments, we also examined differential temporal expression patterns and determined that, after nodule tissue, the epidermis and cortical cells contained the most temporally patterned genes. We circumscribed gene lists for each time and tissue examined and developed an expression pattern visualization tool. Finally, we explored transcriptomic differences between the inner cortical cells that become nodules and those that do not, confirming that the expression of 1-aminocyclopropane-1-carboxylate synthases distinguishes inner cortical cells that become nodules and provide and describe potential downstream genes involved in early nodule cell division. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Elise Schnabel
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
| | - Jacklyn Thomas
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
| | - Rabia El-Hawaz
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
| | - Yueyao Gao
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
| | - William L Poehlman
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
- Sage Bionetworks, Seattle, WA 98121, U.S.A
| | - Suchitra Chavan
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
- Leidos, Inc., Atlanta, GA 30345, U.S.A
| | - Asher Pasha
- Department of Cell and Systems Biology, University of Toronto, ON M5S 3B2, Canada
| | - Eddi Esteban
- Department of Cell and Systems Biology, University of Toronto, ON M5S 3B2, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology, University of Toronto, ON M5S 3B2, Canada
| | - F Alex Feltus
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
- Biomedical Data Science and Informatics Program, Clemson University, Clemson, SC 29634, U.S.A
- Clemson Center for Human Genetics, Clemson University, Greenwood, SC 29636, U.S.A
| | - Julia Frugoli
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
| |
Collapse
|
14
|
Suresh PS, Kumari S, Sahal D, Sharma U. Innate functions of natural products: A promising path for the identification of novel therapeutics. Eur J Med Chem 2023; 260:115748. [PMID: 37666044 DOI: 10.1016/j.ejmech.2023.115748] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/14/2023] [Accepted: 08/17/2023] [Indexed: 09/06/2023]
Abstract
In the course of evolution, living organisms have become well equipped with diverse natural products that serve important functions, including defence from biotic and abiotic stress, growth regulation, reproduction, metabolism, and epigenetic regulation. It seems to be the organism's ecological niche that influences the natural product's structural and functional diversity. Indeed, natural products constitute the nuts and bolts of molecular co-evolution and ecological relationships among different life forms. Since natural products in the form of specialized secondary metabolites exhibit biological functions via interactions with specific target proteins, they can provide a simultaneous glimpse of both new therapeutics and therapeutic targets in humans as well. In this review, we have discussed the innate role of natural products in the ecosystem and how this intrinsic role provides a futuristic opportunity to identify new drugs and therapeutic targets rapidly.
Collapse
Affiliation(s)
- Patil Shivprasad Suresh
- C-H Activation & Phytochemistry Lab, Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India
| | - Surekha Kumari
- C-H Activation & Phytochemistry Lab, Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India
| | - Dinkar Sahal
- Malaria Drug Discovery Laboratory, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Upendra Sharma
- C-H Activation & Phytochemistry Lab, Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India.
| |
Collapse
|
15
|
Uchimiya M, DeRito CM, Hay AG. Sugarcane mill mud-induced putative host (soybean (Glycine max))-rhizobia symbiosis in sandy loam soil. PLoS One 2023; 18:e0293317. [PMID: 37917645 PMCID: PMC10621829 DOI: 10.1371/journal.pone.0293317] [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: 07/18/2023] [Accepted: 10/09/2023] [Indexed: 11/04/2023] Open
Abstract
Domestic production of controlled-release, compost-based, and microbe-enhanced fertilizers is being expanded in the U.S. as a part of rural development. Sugarcane mill mud is a sterilized (≈90°C) agricultural byproduct in surplus that has received interests as a soil amendment in several Southern states, because of its high phosphorus and organic carbon contents. Addition of mill mud to sandy loam significantly increased the nodule formation compared to fertilized and unfertilized controls. Mill mud addition also resulted in pod yields similar to the fertilized control. Though not found in mill mud itself, mill mud additions correlated with an increase in soil Rhizobia as determined by deep 16S rRNA gene sequencing. We hypothesize that Firmicutes in sterilized mill mud induced Rhizobia that in turn enhanced soybean (Glycine max) growth. Collectively, mill mud enhanced the plant growth promoting bacteria when applied to a silt loam, although the relative influence of mill mud-derived bacteria, organic carbon, and nutrients is yet to be determined.
Collapse
Affiliation(s)
- Minori Uchimiya
- Southern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, New Orleans, Louisiana, United States of America
| | - Christopher M. DeRito
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | - Anthony G. Hay
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| |
Collapse
|
16
|
Negi NP, Prakash G, Narwal P, Panwar R, Kumar D, Chaudhry B, Rustagi A. The calcium connection: exploring the intricacies of calcium signaling in plant-microbe interactions. FRONTIERS IN PLANT SCIENCE 2023; 14:1248648. [PMID: 37849843 PMCID: PMC10578444 DOI: 10.3389/fpls.2023.1248648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/24/2023] [Indexed: 10/19/2023]
Abstract
The process of plant immune response is orchestrated by intracellular signaling molecules. Since plants are devoid of a humoral system, they develop extensive mechanism of pathogen recognition, signal perception, and intricate cell signaling for their protection from biotic and abiotic stresses. The pathogenic attack induces calcium ion accumulation in the plant cells, resulting in calcium signatures that regulate the synthesis of proteins of defense system. These calcium signatures induct different calcium dependent proteins such as calmodulins (CaMs), calcineurin B-like proteins (CBLs), calcium-dependent protein kinases (CDPKs) and other signaling molecules to orchestrate the complex defense signaling. Using advanced biotechnological tools, the role of Ca2+ signaling during plant-microbe interactions and the role of CaM/CMLs and CDPKs in plant defense mechanism has been revealed to some extent. The Emerging perspectives on calcium signaling in plant-microbe interactions suggest that this complex interplay could be harnessed to improve plant resistance against pathogenic microbes. We present here an overview of current understanding in calcium signatures during plant-microbe interaction so as to imbibe a future direction of research.
Collapse
Affiliation(s)
- Neelam Prabha Negi
- University Institute of Biotechnology, Chandigarh University, Mohali, India
| | - Geeta Prakash
- Department of Botany, Gargi College, New Delhi, India
| | - Parul Narwal
- University Institute of Biotechnology, Chandigarh University, Mohali, India
| | - Ruby Panwar
- Department of Botany, Gargi College, New Delhi, India
| | - Deepak Kumar
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | | | | |
Collapse
|
17
|
Agaras BC, Grossi CEM, Ulloa RM. Unveiling the Secrets of Calcium-Dependent Proteins in Plant Growth-Promoting Rhizobacteria: An Abundance of Discoveries Awaits. PLANTS (BASEL, SWITZERLAND) 2023; 12:3398. [PMID: 37836138 PMCID: PMC10574481 DOI: 10.3390/plants12193398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023]
Abstract
The role of Calcium ions (Ca2+) is extensively documented and comprehensively understood in eukaryotic organisms. Nevertheless, emerging insights, primarily derived from studies on human pathogenic bacteria, suggest that this ion also plays a pivotal role in prokaryotes. In this review, our primary focus will be on unraveling the intricate Ca2+ toolkit within prokaryotic organisms, with particular emphasis on its implications for plant growth-promoting rhizobacteria (PGPR). We undertook an in silico exploration to pinpoint and identify some of the proteins described in the existing literature, including prokaryotic Ca2+ channels, pumps, and exchangers that are responsible for regulating intracellular Calcium concentration ([Ca2+]i), along with the Calcium-binding proteins (CaBPs) that play a pivotal role in sensing and transducing this essential cation. These investigations were conducted in four distinct PGPR strains: Pseudomonas chlororaphis subsp. aurantiaca SMMP3, P. donghuensis SVBP6, Pseudomonas sp. BP01, and Methylobacterium sp. 2A, which have been isolated and characterized within our research laboratories. We also present preliminary experimental data to evaluate the influence of exogenous Ca2+ concentrations ([Ca2+]ex) on the growth dynamics of these strains.
Collapse
Affiliation(s)
- Betina Cecilia Agaras
- Laboratory of Physiology and Genetics of Plant Probiotic Bacteria (LFGBBP), Centre of Biochemistry and Microbiology of Soils, National University of Quilmes, Bernal B1876BXD, Argentina
- National Scientific and Technical Research Council (CONICET), Buenos Aires C1425FQB, Argentina;
| | - Cecilia Eugenia María Grossi
- National Scientific and Technical Research Council (CONICET), Buenos Aires C1425FQB, Argentina;
- Laboratory of Plant Signal Transduction, Institute of Genetic Engineering and Molecular Biology (INGEBI), National Scientific and Technical Research Council (CONICET), Buenos Aires C1425FQB, Argentina
| | - Rita María Ulloa
- National Scientific and Technical Research Council (CONICET), Buenos Aires C1425FQB, Argentina;
- Laboratory of Plant Signal Transduction, Institute of Genetic Engineering and Molecular Biology (INGEBI), National Scientific and Technical Research Council (CONICET), Buenos Aires C1425FQB, Argentina
- Biochemistry Department, Faculty of Exact and Natural Sciences, University of Buenos Aires (FCEN-UBA), Buenos Aires C1428EGA, Argentina
| |
Collapse
|
18
|
Nishida H, Shimoda Y, Win KT, Imaizumi-Anraku H. Rhizosphere frame system enables nondestructive live-imaging of legume-rhizobium interactions in the soil. JOURNAL OF PLANT RESEARCH 2023; 136:769-780. [PMID: 37402088 PMCID: PMC10421814 DOI: 10.1007/s10265-023-01476-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/21/2023] [Indexed: 07/05/2023]
Abstract
Most plants interact with various soil microorganisms as they grow through the soil. Root nodule symbiosis by legumes and rhizobia is a well-known phenomenon of plant-microbe interactions in the soil. Although microscopic observations are useful for understanding the infection processes of rhizobia, nondestructive observation methods have not been established for monitoring interactions between rhizobia and soil-grown roots. In this study, we constructed Bradyrhizobium diazoefficiens strains that constitutively express different fluorescent proteins, which allows identification of tagged rhizobia by the type of fluorophores. In addition, we constructed a plant cultivation device, Rhizosphere Frame (RhizoFrame), which is a soil-filled container made of transparent acrylic plates that allows observation of roots growing along the acrylic plates. Combining fluorescent rhizobia with RhizoFrame, we established a live imaging system, RhizoFrame system, that enabled us to track the nodulation processes with fluorescence stereomicroscope while retaining spatial information about roots, rhizobia, and soil. Mixed inoculation with different fluorescent rhizobia using RhizoFrame enabled the visualization of mixed infection of a single nodule with two strains. In addition, observation of transgenic Lotus japonicus expressing auxin-responsive reporter genes indicated that RhizoFrame system could be used for a real-time and nondestructive reporter assay. Thus, the use of RhizoFrame system is expected to enhance the study of the spatiotemporal dynamics of plant-microbe interactions in the soil.
Collapse
Affiliation(s)
- Hanna Nishida
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan
| | - Yoshikazu Shimoda
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan
| | - Khin Thuzar Win
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan
| | - Haruko Imaizumi-Anraku
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan.
| |
Collapse
|
19
|
Hartman K, Schmid MW, Bodenhausen N, Bender SF, Valzano-Held AY, Schlaeppi K, van der Heijden MGA. A symbiotic footprint in the plant root microbiome. ENVIRONMENTAL MICROBIOME 2023; 18:65. [PMID: 37525294 PMCID: PMC10391997 DOI: 10.1186/s40793-023-00521-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 07/14/2023] [Indexed: 08/02/2023]
Abstract
BACKGROUND A major aim in plant microbiome research is determining the drivers of plant-associated microbial communities. While soil characteristics and host plant identity present key drivers of root microbiome composition, it is still unresolved whether the presence or absence of important plant root symbionts also determines overall microbiome composition. Arbuscular mycorrhizal fungi (AMF) and N-fixing rhizobia bacteria are widespread, beneficial root symbionts that significantly enhance plant nutrition, plant health, and root structure. Thus, we hypothesized that symbiont types define the root microbiome structure. RESULTS We grew 17 plant species from five families differing in their symbiotic associations (no symbioses, AMF only, rhizobia only, or AMF and rhizobia) in a greenhouse and used bacterial and fungal amplicon sequencing to characterize their root microbiomes. Although plant phylogeny and species identity were the most important factors determining root microbiome composition, we discovered that the type of symbioses also presented a significant driver of diversity and community composition. We found consistent responses of bacterial phyla, including members of the Acidobacteria, Chlamydiae, Firmicutes, and Verrucomicrobia, to the presence or absence of AMF and rhizobia and identified communities of OTUs specifically enriched in the different symbiotic groups. A total of 80, 75 and 57 bacterial OTUs were specific for plant species without symbiosis, plant species forming associations with AMF or plant species associating with both AMF and rhizobia, respectively. Similarly, 9, 14 and 4 fungal OTUs were specific for these plant symbiont groups. Importantly, these generic symbiosis footprints in microbial community composition were also apparent in absence of the primary symbionts. CONCLUSION Our results reveal that symbiotic associations of the host plant leaves an imprint on the wider root microbiome - which we term the symbiotype. These findings suggest the existence of a fundamental assembly principle of root microbiomes, dependent on the symbiotic associations of the host plant.
Collapse
Affiliation(s)
- Kyle Hartman
- Department of Agroecology and Environment, Plant Soil Interactions, Reckenholzstrasse 191, Agroscope, Zürich, 8046, Switzerland
| | | | - Natacha Bodenhausen
- Department of Agroecology and Environment, Plant Soil Interactions, Reckenholzstrasse 191, Agroscope, Zürich, 8046, Switzerland
- Department of Soil Sciences, Research Institute of Organic Agriculture FiBL, Frick, 5070, Switzerland
| | - S Franz Bender
- Department of Agroecology and Environment, Plant Soil Interactions, Reckenholzstrasse 191, Agroscope, Zürich, 8046, Switzerland
| | - Alain Y Valzano-Held
- Department of Agroecology and Environment, Plant Soil Interactions, Reckenholzstrasse 191, Agroscope, Zürich, 8046, Switzerland
| | - Klaus Schlaeppi
- Department of Agroecology and Environment, Plant Soil Interactions, Reckenholzstrasse 191, Agroscope, Zürich, 8046, Switzerland.
- Plant Microbe Interactions, Department of Environmental Sciences, University of Basel, Basel, 4056, Switzerland.
- Institute of Plant Sciences, Faculty of Science, University of Bern, Bern, 3013, Switzerland.
| | - Marcel G A van der Heijden
- Department of Agroecology and Environment, Plant Soil Interactions, Reckenholzstrasse 191, Agroscope, Zürich, 8046, Switzerland.
- Department of Plant and Microbial Biology, University of Zürich, Zürich, 8008, Switzerland.
| |
Collapse
|
20
|
Schnabel EL, Chavan SA, Gao Y, Poehlman WL, Feltus FA, Frugoli JA. A Medicago truncatula Autoregulation of Nodulation Mutant Transcriptome Analysis Reveals Disruption of the SUNN Pathway Causes Constitutive Expression Changes in Some Genes, but Overall Response to Rhizobia Resembles Wild-Type, Including Induction of TML1 and TML2. Curr Issues Mol Biol 2023; 45:4612-4631. [PMID: 37367042 DOI: 10.3390/cimb45060293] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023] Open
Abstract
Nodule number regulation in legumes is controlled by a feedback loop that integrates nutrient and rhizobia symbiont status signals to regulate nodule development. Signals from the roots are perceived by shoot receptors, including a CLV1-like receptor-like kinase known as SUNN in Medicago truncatula. In the absence of functional SUNN, the autoregulation feedback loop is disrupted, resulting in hypernodulation. To elucidate early autoregulation mechanisms disrupted in SUNN mutants, we searched for genes with altered expression in the loss-of-function sunn-4 mutant and included the rdn1-2 autoregulation mutant for comparison. We identified constitutively altered expression of small groups of genes in sunn-4 roots and in sunn-4 shoots. All genes with verified roles in nodulation that were induced in wild-type roots during the establishment of nodules were also induced in sunn-4, including autoregulation genes TML2 and TML1. Only an isoflavone-7-O-methyltransferase gene was induced in response to rhizobia in wild-type roots but not induced in sunn-4. In shoot tissues of wild-type, eight rhizobia-responsive genes were identified, including a MYB family transcription factor gene that remained at a baseline level in sunn-4; three genes were induced by rhizobia in shoots of sunn-4 but not wild-type. We cataloged the temporal induction profiles of many small secreted peptide (MtSSP) genes in nodulating root tissues, encompassing members of twenty-four peptide families, including the CLE and IRON MAN families. The discovery that expression of TML2 in roots, a key factor in inhibiting nodulation in response to autoregulation signals, is also triggered in sunn-4 in the section of roots analyzed, suggests that the mechanism of TML regulation of nodulation in M. truncatula may be more complex than published models.
Collapse
Affiliation(s)
- Elise L Schnabel
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | | | - Yueyao Gao
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | | | - Frank Alex Feltus
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
- Biomedical Data Science and Informatics Program, Clemson University, Clemson, SC 29634, USA
- Clemson Center for Human Genetics, Clemson University, Greenwood, SC 29636, USA
| | - Julia A Frugoli
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| |
Collapse
|
21
|
Ballesteros-Gutiérrez M, Albareda M, Barbas C, López-Gonzálvez Á, Dunn MF, Palacios JM. A host-specific diaminobutyrate aminotransferase contributes to symbiotic performance, homoserine metabolism, and competitiveness in the Rhizobium leguminosarum/ Pisum sativum system. Front Microbiol 2023; 14:1182563. [PMID: 37260681 PMCID: PMC10228743 DOI: 10.3389/fmicb.2023.1182563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/25/2023] [Indexed: 06/02/2023] Open
Abstract
Rhizobium leguminosarum bv. viciae (Rlv) UPM791 effectively nodulates pea and lentil, but bacteroids contain a number of proteins differentially expressed depending on the host. One of these host-dependent proteins (C189) is similar to a diaminobutyrate-2-oxoglutarate aminotransferase (DABA-AT). DABA-AT activity was demonstrated with cell extracts and with purified protein, so C189 was renamed as Dat. The dat gene was strongly induced in the central, active area of pea nodules, but not in lentil. Mutants defective in dat were impaired in symbiotic performance with pea plants, exhibiting reduced shoot dry weight, smaller nodules, and a lower competitiveness for nodulation. In contrast, there were no significant differences between mutant and wild-type in symbiosis with lentil plants. A comparative metabolomic approach using cell-free extracts from bacteroids induced in pea and lentil showed significant differences among the strains in pea bacteroids whereas no significant differences were found in lentil. Targeted metabolomic analysis revealed that the dat mutation abolished the presence of 2,4-diaminobutyrate (DABA) in pea nodules, indicating that DABA-AT reaction is oriented toward the production of DABA from L-aspartate semialdehyde. This analysis also showed the presence of L-homoserine, a likely source of aspartate semialdehyde, in pea bacteroids but not in those induced in lentil. The dat mutant showed impaired growth when cells were grown with L-homoserine as nitrogen source. Inclusion of DABA or L-homoserine as N source suppressed pantothenate auxotropy in Rlv UPM791, suggesting DABA as source of the pantothenate precursor β-alanine. These data indicate that Rlv UPM791 Dat enzyme is part of an adaptation mechanism of this bacterium to a homoserine-rich environment such as pea nodule and rhizosphere.
Collapse
Affiliation(s)
- Marta Ballesteros-Gutiérrez
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Consejo Superior de Investigaciones Científicas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Spain
| | - Marta Albareda
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Consejo Superior de Investigaciones Científicas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Coral Barbas
- Facultad de Farmacia, Center for Metabolomics and Bioanalysis (CEMBIO), Universidad San Pablo-CEU, Boadilla del Monte, Spain
| | - Ángeles López-Gonzálvez
- Facultad de Farmacia, Center for Metabolomics and Bioanalysis (CEMBIO), Universidad San Pablo-CEU, Boadilla del Monte, Spain
| | - Michael F. Dunn
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas-Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - José M. Palacios
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Consejo Superior de Investigaciones Científicas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| |
Collapse
|
22
|
Han K, Li Y, Zhang Z, Sun L, Wang ET, Li Y. Comparative genome analysis of Sesbania cannabina-nodulating Rhizobium spp. revealing the symbiotic and transferrable characteristics of symbiosis plasmids. Microb Genom 2023; 9. [PMID: 37133904 DOI: 10.1099/mgen.0.001004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
Symbiotic nitrogen fixation between legumes and rhizobia makes a great contribution to the terrestrial ecosystem. The successful symbiosis between the partners mainly depends on the nod and nif genes in rhizobia, while the specific symbiosis is mainly determined by the structure of Nod factors and the corresponding secretion systems (type III secretion system; T3SS), etc. These symbiosis genes are usually located on symbiotic plasmids or a chromosomal symbiotic island, both could be transferred interspecies. In our previous studies, Sesbania cannabina-nodulating rhizobia across the world were classified into 16 species of four genera and all the strains, especially those of Rhizobium spp., harboured extraordinarily highly conserved symbiosis genes, suggesting that horizontal transfer of symbiosis genes might have happened among them. In order to learn the genomic basis of diversification of rhizobia under the selection of host specificity, we performed this study to compare the complete genome sequences of four Rhizobium strains associated with S. cannabina, YTUBH007, YTUZZ027, YTUHZ044 and YTUHZ045. Their complete genomes were sequenced and assembled at the replicon level. Each strain represents a different species according to the average nucleotide identity (ANI) values calculated using the whole-genome sequences; furthermore, except for YTUBH007, which was classified as Rhizobium binae, the remaining three strains were identified as new candidate species. A single symbiotic plasmid sized 345-402 kb containing complete nod, nif, fix, T3SS and conjugal transfer genes was detected in each strain. The high ANI and amino acid identity (AAI) values, as well as the close phylogenetic relationships among the entire symbiotic plasmid sequences, indicate that they have the same origin and the entire plasmid has been transferred among different Rhizobium species. These results indicate that S. cannabina stringently selects a certain symbiosis gene background of the rhizobia for nodulation, which might have forced the symbiosis genes to transfer from some introduced rhizobia to the related native or local-condition-adapted bacteria. The existence of almost complete conjugal transfer related elements, but not the gene virD, indicated that the self-transfer of the symbiotic plasmid in these rhizobial strains may be realized via a virD-independent pathway or through another unidentified gene. This study provides insight for the better understanding of high-frequency symbiotic plasmid transfer, host-specific nodulation and the host shift for rhizobia.
Collapse
Affiliation(s)
- Kunming Han
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, Shandong 264005, PR China
| | - Yan Li
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, Shandong 264005, PR China
| | - Zhenpeng Zhang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, PR China
| | - Liqin Sun
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, Shandong 264005, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Yan Li
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, Shandong 264005, PR China
| |
Collapse
|
23
|
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
|
24
|
Hlaváčková K, Šamajová O, Hrbáčková M, Šamaj J, Ovečka M. Advanced microscopy resolves dynamic localization patterns of stress-induced mitogen-activated protein kinase SIMK during alfalfa root hair interactions with Ensifer meliloti. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad111. [PMID: 36951479 DOI: 10.1093/jxb/erad111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Indexed: 06/18/2023]
Abstract
Leguminous plants have established a mutualistic endosymbiotic interaction with nitrogen-fixing rhizobia to secure nitrogen sources in new specialised organs called root nodules. Before nodule formation, the development of early symbiotic structures is essential for rhizobia docking, internalization, targeted delivery and intracellular accommodation. We have recently reported that overexpression of stress-induced mitogen-activated protein kinase (SIMK) in alfalfa affects root hair, nodule and shoot formation, which raised the questions how SIMK may modulate these processes. In particular, detailed subcellular spatial distribution, activation and developmental relocation of SIMK during the early stages of alfalfa nodulation remain unclear. Here, we qualitatively and quantitatively characterised SIMK distribution patterns in Ensifer meliloti-infected root hairs using live-cell imaging and immunolocalization, employing alfalfa stable transgenic lines with genetically manipulated SIMK abundance and kinase activity. In the SIMKK-RNAi line, showing downregulation of SIMKK and SIMK, we found considerably decreased accumulation of phosphorylated SIMK around infection pockets and infection threads. However, this was strongly increased in the GFP-SIMK line, constitutively overexpressing GFP-tagged SIMK. Thus, genetically manipulated SIMK modulates root hair capacity to form infection pockets and infection threads. Employment of advanced light-sheet fluorescence microscopy (LSFM) on intact plants allowed gentle and non-invasive imaging of spatiotemporal interactions between root hairs and symbiotic Ensifer meliloti, while immunofluorescence detection confirmed that SIMK was activated in these locations. Our results shed new light on SIMK spatiotemporal participation in early interactions between alfalfa and Ensifer meliloti, and its internalization into root hairs, showing that local accumulation of active SIMK indeed modulates early nodulation in alfalfa.
Collapse
Affiliation(s)
- Kateřina Hlaváčková
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Olga Šamajová
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Miroslava Hrbáčková
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Jozef Šamaj
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Miroslav Ovečka
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| |
Collapse
|
25
|
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
|
26
|
Lace B, Su C, Invernot Perez D, Rodriguez-Franco M, Vernié T, Batzenschlager M, Egli S, Liu CW, Ott T. RPG acts as a central determinant for infectosome formation and cellular polarization during intracellular rhizobial infections. eLife 2023; 12:80741. [PMID: 36856086 PMCID: PMC9991063 DOI: 10.7554/elife.80741] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 02/21/2023] [Indexed: 03/02/2023] Open
Abstract
Host-controlled intracellular accommodation of nitrogen-fixing bacteria is essential for the establishment of a functional Root Nodule Symbiosis (RNS). In many host plants, this occurs via transcellular tubular structures (infection threads - ITs) that extend across cell layers via polar tip-growth. Comparative phylogenomic studies have identified RPG (RHIZOBIUM-DIRECTED POLAR GROWTH) among the critical genetic determinants for bacterial infection. In Medicago truncatula, RPG is required for effective IT progression within root hairs but the cellular and molecular function of the encoded protein remains elusive. Here, we show that RPG resides in the protein complex formed by the core endosymbiotic components VAPYRIN (VPY) and LUMPY INFECTION (LIN) required for IT polar growth, co-localizes with both VPY and LIN in IT tip- and perinuclear-associated puncta of M. truncatula root hairs undergoing infection and is necessary for VPY recruitment into these structures. Fluorescence Lifetime Imaging Microscopy (FLIM) of phosphoinositide species during bacterial infection revealed that functional RPG is required to sustain strong membrane polarization at the advancing tip of the IT. In addition, loss of RPG functionality alters the cytoskeleton-mediated connectivity between the IT tip and the nucleus and affects the polar secretion of the cell wall modifying enzyme NODULE PECTATE LYASE (NPL). Our results integrate RPG into a core host machinery required to support symbiont accommodation, suggesting that its occurrence in plant host genomes is essential to co-opt a multimeric protein module committed to endosymbiosis to sustain IT-mediated bacterial infection.
Collapse
Affiliation(s)
- Beatrice Lace
- University of Freiburg, Faculty of BiologyFreiburgGermany
| | - Chao Su
- University of Freiburg, Faculty of BiologyFreiburgGermany
| | | | | | - Tatiana Vernié
- LRSV, Université de Toulouse, CNRS, UPS, INP ToulouseCastanet-TolosanFrance
| | | | - Sabrina Egli
- University of Freiburg, Faculty of BiologyFreiburgGermany
| | - Cheng-Wu Liu
- School of Life Sciences, Division of Life Sciences and Medicine, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of ChinaHefeiChina
| | - Thomas Ott
- University of Freiburg, Faculty of BiologyFreiburgGermany
- CIBSS – Centre of Integrative Biological Signalling Studies, University of FreiburgFreiburgGermany
| |
Collapse
|
27
|
Abstract
Developmental processes in animals are influenced by colonization and/or signaling from microbial symbionts. Here, we show that bacteria from the environment are linked to development of a symbiotic organ that houses a bacterial consortium in female Hawaiian bobtail squid, Euprymna scolopes. In addition to the well-characterized light organ association with the bioluminescent bacterium Vibrio fischeri, female E. scolopes house a simple bacterial community in a reproductive organ, the accessory nidamental gland (ANG). In order to understand the influences of bacteria on ANG development, squid were raised in the laboratory under conditions where exposure to environmental microorganisms was experimentally manipulated. Under conditions where hosts were exposed to depleted environmental bacteria, ANGs were completely absent or stunted, a result independent of the presence of the light organ symbiont V. fischeri. When squid were raised in the laboratory with substrate from the host's natural environment containing the native microbiota, normal ANG development was observed, and the bacterial communities were similar to wild-caught animals. Analysis of the bacterial communities from ANGs and substrates of wild-caught and laboratory-raised animals suggests that certain bacterial groups, namely, the Verrucomicrobia, are linked to ANG development. The ANG community composition was also experimentally manipulated. Squid raised with natural substrate supplemented with a specific ANG bacterial strain, Leisingera sp. JC1, had high proportions of this strain in the ANG, suggesting that once ANG development is initiated, specific strains can be introduced and subsequently colonize the organ. Overall, these data suggest that environmental bacteria are required for development of the ANG in E. scolopes. IMPORTANCE Microbiota have profound effects on animal and plant development. Hosts raised axenically or without symbionts often suffer negative outcomes resulting in developmental defects or reduced organ function. Using defined experimental conditions, we demonstrate that environmental bacteria are required for the formation of a female-specific symbiotic organ in the Hawaiian bobtail squid, Euprymna scolopes. Although nascent tissues from this organ that are involved with bacterial recruitment formed initially, the mature organ failed to develop and was absent or severely reduced in sexually mature animals that were not exposed to microbiota from the host's natural environment. This is the first example of complete organ development relying on exposure to symbiotic bacteria in an animal host. This study broadens the use of E. scolopes as a model organism for studying the influence of beneficial bacteria on animal development.
Collapse
|
28
|
A Germin-Like Protein GLP1 of Legumes Mediates Symbiotic Nodulation by Interacting with an Outer Membrane Protein of Rhizobia. Microbiol Spectr 2023; 11:e0335022. [PMID: 36633436 PMCID: PMC9927233 DOI: 10.1128/spectrum.03350-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Rhizobia can infect legumes and induce the coordinated expression of symbiosis and defense genes for the establishment of mutualistic symbiosis. Numerous studies have elucidated the molecular interactions between rhizobia and host plants, which are associated with Nod factor, exopolysaccharide, and T3SS effector proteins. However, there have been relatively few reports about how the host plant recognizes the outer membrane proteins (OMPs) of rhizobia to mediate symbiotic nodulation. In our previous work, a gene (Mhopa22) encoding an OMP was identified in Mesorhizobium huakuii 7653R, whose homologous genes are widely distributed in Rhizobiales. In this study, a germin-like protein GLP1 interacting with Mhopa22 was identified in Astragalus sinicus. RNA interference of AsGLP1 resulted in a decrease in nodule number, whereas overexpression of AsGLP1 increased the number of nodules in the hairy roots of A. sinicus. Consistent symbiotic phenotypes were identified in Medicago truncatula with MtGLPx (refer to medtr7g111240.1, the isogeny of AsGLP1) overexpression or Tnt1 mutant (glpx-1) in symbiosis with Sinorhizobium meliloti 1021. The glpx-1 mutant displayed hyperinfection and the formation of more infection threads but a decrease in root nodules. RNA sequencing analysis showed that many differentially expressed genes were involved in hormone signaling and symbiosis. Taken together, AsGLP1 and its homology play an essential role in mediating the early symbiotic process through interacting with the OMPs of rhizobia. IMPORTANCE This study is the first report to characterize a legume host plant protein to sense and interact with an outer membrane protein (OMP) of rhizobia. It can be speculated that GLP1 plays an essential role to mediate early symbiotic process through interacting with OMPs of rhizobia. The results provide deeper understanding and novel insights into the molecular interactive mechanism of a legume symbiosis signaling pathway in recognition with rhizobial OMPs. Our findings may also provide a new perspective to improve the symbiotic compatibility and nodulation of legume.
Collapse
|
29
|
Singh J, Verma PK. Role of Nod factor receptors and its allies involved in nitrogen fixation. PLANTA 2023; 257:54. [PMID: 36780015 DOI: 10.1007/s00425-023-04090-7] [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: 11/02/2022] [Accepted: 02/04/2023] [Indexed: 06/18/2023]
Abstract
Lysin motif (LysM)-receptor-like kinase (RLK) and leucine-rich repeat (LRR)-RLK mediated signaling play important roles in the development and regulation of root nodule symbiosis in legumes. The availability of water and nutrients in the soil is a major limiting factor affecting crop productivity. Plants of the Leguminosae family form a symbiotic association with nitrogen-fixing Gram-negative soil bacteria, rhizobia for nitrogen fixation. This symbiotic relationship between legumes and rhizobia depends on the signal exchange between them. Plant receptor-like kinases (RLKs) containing lysin motif (LysM) and/or leucine-rich repeat (LRR) play an important role in the perception of chemical signals from rhizobia for initiation and establishment of root nodule symbiosis (RNS) that results in nitrogen fixation. This review highlights the diverse aspects of LysM-RLK and LRR receptors including their specificity, functions, interacting partners, regulation, and associated signaling in RNS. The activation of LysM-RLKs and LRR-RLKs is important for ensuring the successful interaction between legume roots and rhizobia. The intracellular regions of the receptors enable additional layers of signaling that help in the transduction of signals intracellularly. Additionally, symbiosis receptor-like kinase (SYMRK) containing the LRR motif acts as a co-receptor with Nod factors receptors (LysM-RLK). Cleavage of the malectin-like domain from the SYMRK ectodomain is a mechanism for controlling SYMRK stability. Overall, this review has discussed different aspects of legume receptors that are critical to the perception of signals from rhizobia and their subsequent role in creating the mutualistic relationship necessary for nitrogen fixation. Additionally, it has been discussed how crucial it is to extrapolate the knowledge gained from model legumes to crop legumes such as chickpea and common bean to better understand the mechanism underlying nodule formation in crop legumes. Future directions have also been proposed in this regard.
Collapse
Affiliation(s)
- Jawahar Singh
- Plant-Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México (UNAM), 54090, Tlalnepantla, State of Mexico, Mexico.
| | - Praveen Kumar Verma
- Plant-Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Plant-Immunity Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 10067, India.
| |
Collapse
|
30
|
Su C, Zhang G, Rodriguez-Franco M, Hinnenberg R, Wietschorke J, Liang P, Yang W, Uhler L, Li X, Ott T. Transcellular progression of infection threads in Medicago truncatula roots is associated with locally confined cell wall modifications. Curr Biol 2023; 33:533-542.e5. [PMID: 36657449 PMCID: PMC9937034 DOI: 10.1016/j.cub.2022.12.051] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 11/18/2022] [Accepted: 12/20/2022] [Indexed: 01/19/2023]
Abstract
The root nodule symbiosis with its global impact on nitrogen fertilization of soils is characterized by an intracellular colonization of legume roots by rhizobia. Although the symbionts are initially taken up by morphologically adapted root hairs, rhizobia persistently progress within a membrane-confined infection thread through several root cortical and later nodular cell layers. Throughout this transcellular passaging, rhizobia have to repeatedly pass host plasma membranes and cell walls. Here, we investigated this essential process and describe the concerted action of one of the symbiosis-specific pectin methyl esterases (SyPME1) and the nodulation pectate lyase (NPL) at the infection thread and transcellular passage sites. Their coordinated function mediates spatially confined pectin alterations in the cell-cell interface that result in the establishment of an apoplastic compartment where bacteria are temporarily released into and taken up from the subjacent cell. This process allows successful intracellular progression of infection threads through the entire root cortical tissue.
Collapse
Affiliation(s)
- Chao Su
- Cell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.
| | - Guofeng Zhang
- Cell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | | | - Rosula Hinnenberg
- Cell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Jenny Wietschorke
- Cell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Pengbo Liang
- Cell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; State Key Laboratory of Plant Physiology and Biochemistry, MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing 100193, P.R. China
| | - Wei Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Hongshan District, Wuhan 430070, Hubei, P.R. China
| | - Leonard Uhler
- Cell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Xia Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Hongshan District, Wuhan 430070, Hubei, P.R. China
| | - Thomas Ott
- Cell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; CIBSS - Centre of Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| |
Collapse
|
31
|
Li X, Liu M, Cai M, Chiasson D, Groth M, Heckmann AB, Wang TL, Parniske M, Downie JA, Xie F. RPG interacts with E3-ligase CERBERUS to mediate rhizobial infection in Lotus japonicus. PLoS Genet 2023; 19:e1010621. [PMID: 36735729 PMCID: PMC9931111 DOI: 10.1371/journal.pgen.1010621] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 02/15/2023] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
Symbiotic interactions between rhizobia and legumes result in the formation of root nodules, which fix nitrogen that can be used for plant growth. Rhizobia usually invade legume roots through a plant-made tunnel-like structure called an infection thread (IT). RPG (Rhizobium-directed polar growth) encodes a coiled-coil protein that has been identified in Medicago truncatula as required for root nodule infection, but the function of RPG remains poorly understood. In this study, we identified and characterized RPG in Lotus japonicus and determined that it is required for IT formation. RPG was induced by Mesorhizobium loti or purified Nodulation factor and displayed an infection-specific expression pattern. Nodule inception (NIN) bound to the RPG promoter and induced its expression. We showed that RPG displayed punctate subcellular localization in L. japonicus root protoplasts and in root hairs infected by M. loti. The N-terminal predicted C2 lipid-binding domain of RPG was not required for this subcellular localization or for function. CERBERUS, a U-box E3 ligase which is also required for rhizobial infection, was found to be localized similarly in puncta. RPG co-localized and directly interacted with CERBERUS in the early endosome (TGN/EE) compartment and near the nuclei in root hairs after rhizobial inoculation. Our study sheds light on an RPG-CERBERUS protein complex that is involved in an exocytotic pathway mediating IT elongation.
Collapse
Affiliation(s)
- Xiaolin Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Miaoxia Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Min Cai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - David Chiasson
- Faculty of Biology, University of Munich, Großhaderner Straße 2–4, Planegg-Martinsried, Germany
| | - Martin Groth
- Faculty of Biology, University of Munich, Großhaderner Straße 2–4, Planegg-Martinsried, Germany
| | - Anne B. Heckmann
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Trevor L. Wang
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Martin Parniske
- Faculty of Biology, University of Munich, Großhaderner Straße 2–4, Planegg-Martinsried, Germany
| | - J. Allan Downie
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Fang Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- * E-mail:
| |
Collapse
|
32
|
Su C, Rodriguez-Franco M, Lace B, Nebel N, Hernandez-Reyes C, Liang P, Schulze E, Mymrikov EV, Gross NM, Knerr J, Wang H, Siukstaite L, Keller J, Libourel C, Fischer AAM, Gabor KE, Mark E, Popp C, Hunte C, Weber W, Wendler P, Stanislas T, Delaux PM, Einsle O, Grosse R, Römer W, Ott T. Stabilization of membrane topologies by proteinaceous remorin scaffolds. Nat Commun 2023; 14:323. [PMID: 36658193 PMCID: PMC9852587 DOI: 10.1038/s41467-023-35976-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 01/10/2023] [Indexed: 01/20/2023] Open
Abstract
In plants, the topological organization of membranes has mainly been attributed to the cell wall and the cytoskeleton. Additionally, few proteins, such as plant-specific remorins have been shown to function as protein and lipid organizers. Root nodule symbiosis requires continuous membrane re-arrangements, with bacteria being finally released from infection threads into membrane-confined symbiosomes. We found that mutations in the symbiosis-specific SYMREM1 gene result in highly disorganized perimicrobial membranes. AlphaFold modelling and biochemical analyses reveal that SYMREM1 oligomerizes into antiparallel dimers and may form a higher-order membrane scaffolding structure. This was experimentally confirmed when expressing this and other remorins in wall-less protoplasts is sufficient where they significantly alter and stabilize de novo membrane topologies ranging from membrane blebs to long membrane tubes with a central actin filament. Reciprocally, mechanically induced membrane indentations were equally stabilized by SYMREM1. Taken together we describe a plant-specific mechanism that allows the stabilization of large-scale membrane conformations independent of the cell wall.
Collapse
Affiliation(s)
- Chao Su
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | | | - Beatrice Lace
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Nils Nebel
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Casandra Hernandez-Reyes
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany.,CIBSS - Centre of Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany
| | - Pengbo Liang
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Eija Schulze
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Evgeny V Mymrikov
- CIBSS - Centre of Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.,Institute for Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - Nikolas M Gross
- CIBSS - Centre of Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.,Institute for Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104, Freiburg, Germany
| | - Julian Knerr
- Institute of Pharmacology, Medical Faculty, University of Freiburg, 79104, Freiburg, Germany
| | - Hong Wang
- CIBSS - Centre of Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.,Institute of Pharmacology, Medical Faculty, University of Freiburg, 79104, Freiburg, Germany
| | - Lina Siukstaite
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany.,BIOSS - Centre for Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany
| | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet Tolosan, France
| | - Cyril Libourel
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet Tolosan, France
| | - Alexandra A M Fischer
- CIBSS - Centre of Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104, Freiburg, Germany.,BIOSS - Centre for Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.,Division of Synthetic Biology, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Katharina E Gabor
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076, Tübingen, Germany
| | - Eric Mark
- Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, 14476, Potsdam-Golm, Germany
| | - Claudia Popp
- Ludwig-Maximilians-University (LMU) Munich, Institute of Genetics, 82152, Martinsried, Germany
| | - Carola Hunte
- CIBSS - Centre of Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.,Institute for Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany.,BIOSS - Centre for Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany
| | - Wilfried Weber
- CIBSS - Centre of Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.,BIOSS - Centre for Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.,Division of Synthetic Biology, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Petra Wendler
- Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, 14476, Potsdam-Golm, Germany
| | - Thomas Stanislas
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076, Tübingen, Germany
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet Tolosan, France
| | - Oliver Einsle
- Institute of Biochemistry, Faculty of Chemistry, University of Freiburg, 79104, Freiburg, Germany
| | - Robert Grosse
- CIBSS - Centre of Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.,Institute of Pharmacology, Medical Faculty, University of Freiburg, 79104, Freiburg, Germany
| | - Winfried Römer
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany.,CIBSS - Centre of Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.,BIOSS - Centre for Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany
| | - Thomas Ott
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany. .,CIBSS - Centre of Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.
| |
Collapse
|
33
|
Kyei-Boahen S, Savala CEN, Muananamuale CP, Malita C, Wiredu AN, Chibeba AM, Elia P, Chikoye D. Symbiotic effectiveness of Bradyrhizobium strains on soybean growth and productivity in Northern Mozambique. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2023. [DOI: 10.3389/fsufs.2022.1084745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Inoculation of soybean [Glycine max (L.) Merr.] with rhizobia strains is a low-cost investment which can increase yields of smallholder farmers in Mozambique. The performance of four Bradyrhizobium strains was evaluated to identify the best strain to inoculate soybean grown in different agro-ecologies. Field experiments were conducted in three ecological zones in 2018 and 2019 using soybean variety Zamboane inoculated with Bradyrhizobium diazoefficiens strain USDA 110, B. japonicum strains USDA 136, USDA 442 and WB74, and a non-inoculated control in a randomized complete block design with four replications. Indigenous rhizobia populations at the sites ranged from 9.0 x 101 to 2.2 x 103 cells g−1 soil. All four strains increased nodulation, but USDA 110 was superior at two sites with low native rhizobia population, whereas USDA 442 and WB74 were the best at the site with relatively high native rhizobia population. On an average, the strains doubled the number of nodules and increased the dry weight up to 5.8-fold. Inoculation increased shoot dry weight and N content at podding, plant biomass, and number of pods plant−1 across sites but the effects of the strains on seeds per pod, and 100-seed weight were inconsistent. Shoot N content did not differ among inoculant strains and ranged from 15.70 g kg−1 in the control to 38.53 g kg−1 across inoculation. All four strains increased soybean grain yield across sites in 2018 but USDA 110 outperformed the other strains and was also the best at one of the two sites in 2019. Grain yield responses associated with USDA 110 ranged from 552 kg ha−1 (56%) to 1,255 kg ha−1 (76%). Positive correlations between nodule dry weight plant−1 and seed yield, and number of pods plant−1 and grain yield were observed. The gross margin ranged from $343.50–$606.80 ha−1 for the control, but it increased to $688.34–$789.36 when inoculants were applied. On an average, inoculation increased gross margin by $182.57-$395.35 ha−1 over that of non-inoculated control in 2018 but drought stress in 2019 reduced the benefit. The results demonstrate that USDA 110 was the best inoculant strain and has the potential of increasing smallholder productivity and net returns.
Collapse
|
34
|
Liu M, Kameoka H, Oda A, Maeda T, Goto T, Yano K, Soyano T, Kawaguchi M. The effects of ERN1 on gene expression during early rhizobial infection in Lotus japonicus. FRONTIERS IN PLANT SCIENCE 2023; 13:995589. [PMID: 36733592 PMCID: PMC9888413 DOI: 10.3389/fpls.2022.995589] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
Legumes develop root nodules in association with compatible rhizobia to overcome nitrogen deficiency. Rhizobia enter the host legume, mainly through infection threads, and induce nodule primordium formation in the root cortex. Multiple transcription factors have been identified to be involved in the regulation of the establishment of root nodule symbiosis, including ERF Required for Nodulation1 (ERN1). ERN1 is involved in a transcription network with CYCLOPS and NODULE INCEPTION (NIN). Mutation of ERN1 often results in misshapen root hair tips, deficient infection thread formation, and immature root nodules. ERN1 directly activates the expression of ENOD11 in Medicago truncatula to assist cell wall remodeling and Epr3 in Lotus japonicus to distinguish rhizobial exopolysaccharide signals. However, aside from these two genes, it remains unclear which genes are regulated by LjERN1 or what role LjERN1 plays during root nodule symbiosis. Thus, we conducted RNA sequencing to compare the gene expression profiles of wild-type L. japonicus and Ljern1-6 mutants. In total, 234 differentially expressed genes were identified as candidate LjERN1 target genes. These genes were found to be associated with cell wall remodeling, signal transduction, phytohormone metabolism, and transcription regulation, suggesting that LjERN1 is involved in multiple processes during the early stages of the establishment of root nodule symbiosis. Many of these candidate genes including RINRK1 showed decreased expression levels in Ljnin-2 mutants based on a search of a public database, suggesting that LjERN1 and LjNIN coordinately regulate gene expression. Our data extend the current understanding of the pleiotropic role of LjERN1 in root nodule symbiosis.
Collapse
Affiliation(s)
- Meng Liu
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Hiromu Kameoka
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Akiko Oda
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Taro Maeda
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Takashi Goto
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Koji Yano
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Takashi Soyano
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| |
Collapse
|
35
|
Czyż KB, Taylor CM, Kawaliło M, Koczyk G. Gain or Loss? Evidence for Legume Predisposition to Symbiotic Interactions with Rhizobia via Loss of Pathogen-Resistance-Related Gene Families. Int J Mol Sci 2022; 23:ijms232416003. [PMID: 36555644 PMCID: PMC9783688 DOI: 10.3390/ijms232416003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Nodulation is a hallmark yet non-universal characteristic of legumes. It is unknown whether the mechanisms underlying nitrogen-fixing symbioses evolved within legumes and the broader nitrogen-fixing clade (NFC) repeatedly de novo or based on common ancestral pathways. Ten new transcriptomes representing members from the Cercidoideae and Caesalpinioideae subfamilies were supplemented with published omics data from 65 angiosperms, to investigate how gene content correlates with nodulation capacity within Fabaceae and the NFC. Orthogroup analysis categorized annotated genes into 64150 orthogroups, of which 19 were significantly differentially represented between nodulating versus non-nodulating NFC species and were most commonly absent in nodulating taxa. The distribution of six over-represented orthogroups within Viridiplantae representatives suggested that genomic evolution events causing gene family expansions, including whole-genome duplications (WGDs), were unlikely to have facilitated the development of stable symbioses within Fabaceae as a whole. Instead, an absence of representation of 13 orthogroups indicated that losses of genes involved in trichome development, defense and wounding responses were strongly associated with rhizobial symbiosis in legumes. This finding provides novel evidence of a lineage-specific predisposition for the evolution and/or stabilization of nodulation in Fabaceae, in which a loss of pathogen resistance genes may have allowed for stable mutualistic interactions with rhizobia.
Collapse
Affiliation(s)
- Katarzyna B. Czyż
- Biometry and Bioinformatics Team, Institute of Plant Genetics Polish Academy of Science, 60-479 Poznań, Poland
- Correspondence:
| | - Candy M. Taylor
- School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - Michał Kawaliło
- Biometry and Bioinformatics Team, Institute of Plant Genetics Polish Academy of Science, 60-479 Poznań, Poland
| | - Grzegorz Koczyk
- Biometry and Bioinformatics Team, Institute of Plant Genetics Polish Academy of Science, 60-479 Poznań, Poland
| |
Collapse
|
36
|
Vlk D, Trněný O, Řepková J. Genes Associated with Biological Nitrogen Fixation Efficiency Identified Using RNA Sequencing in Red Clover ( Trifolium pratense L.). LIFE (BASEL, SWITZERLAND) 2022; 12:life12121975. [PMID: 36556339 PMCID: PMC9785344 DOI: 10.3390/life12121975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022]
Abstract
Commonly studied in the context of legume-rhizobia symbiosis, biological nitrogen fixation (BNF) is a key component of the nitrogen cycle in nature. Despite its potential in plant breeding and many years of research, information is still lacking as to the regulation of hundreds of genes connected with plant-bacteria interaction, nodulation, and nitrogen fixation. Here, we compared root nodule transcriptomes of red clover (Trifolium pratense L.) genotypes with contrasting nitrogen fixation efficiency, and we found 491 differentially expressed genes (DEGs) between plants with high and low BNF efficiency. The annotation of genes expressed in nodules revealed more than 800 genes not yet experimentally confirmed. Among genes mediating nodule development, four nod-ule-specific cysteine-rich (NCR) peptides were confirmed in the nodule transcriptome. Gene duplication analyses revealed that genes originating from tandem and dispersed duplication are significantly over-represented among DEGs. Weighted correlation network analysis (WGCNA) organized expression profiles of the transcripts into 16 modules linked to the analyzed traits, such as nitrogen fixation efficiency or sample-specific modules. Overall, the results obtained broaden our knowledge about transcriptomic landscapes of red clover's root nodules and shift the phenotypic description of BNF efficiency on the level of gene expression in situ.
Collapse
Affiliation(s)
- David Vlk
- Department of Experimental Biology, Faculty of Sciences, Masaryk University, 611 37 Brno, Czech Republic
| | - Oldřich Trněný
- Agricultural Research, Ltd., Zahradní 1, 664 41 Troubsko, Czech Republic
| | - Jana Řepková
- Department of Experimental Biology, Faculty of Sciences, Masaryk University, 611 37 Brno, Czech Republic
- Correspondence: ; Tel.: +420-549-49-6895
| |
Collapse
|
37
|
Swanson E, Sbissi I, Ktari A, Cherif-Silini H, Ghodhbane-Gtari F, Tisa LS, Gtari M. Decrypting phytomicrobiome of the neurotoxic actinorhizal species, Coriaria myrtifolia, and dispersal boundary of Frankia cluster 2 in soil outward compatible host rhizosphere. Front Microbiol 2022; 13:1027317. [PMID: 36439809 PMCID: PMC9684332 DOI: 10.3389/fmicb.2022.1027317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/21/2022] [Indexed: 11/12/2022] Open
Abstract
The actinorhizal plant, Coriaria myrtifolia, is a neurotoxic plant species endemic to the western Mediterranean area, which forms a nitrogen-fixing symbiosis with members of Frankia cluster 2. Contrarily to other Frankia clusters, the occurrence and mode of dispersal for infective cluster 2 units outside of the host plant rhizosphere remains controversial. The present study was designed to investigate the structure of the microbiomes of C. myrtifolia phytosphere, rhizosphere, and soil samples extending outward linearly up to 1 km. Results showed that the epiphyte and endophyte communities were not significantly different from each other for most of the plant tissues. The communities associated with the below-ground tissues (nodule and root) were significantly different from those found on the above-ground tissues (fruit, leaves, and stems) and had a higher community richness. Coriaria myrtifolia phytomicrobiomes were dominated by Cyanobacteria for leaf, stem, and fruit while Actinobacteria and Proteobacteria were dominant in the root and nodule organelles. The nodule, a special niche for nitrogen fixation, was mainly inhabited by Frankia but contained several non-Frankia bacteria. Beside Frankia cluster 2, the presence of clusters 1, 4, and large numbers of cluster 3 strains have been detected in nodules, roots, and rhizospheres of C. myrtifolia. Despite Frankia being found in all plots using plant trapping bioassays with C. myrtifolia seedlings, Frankia cluster 2 was not detected in soil metagenomes showing the limits of detection by this approach. This result also suggests that in the absence of appropriate host plant species, Frankia cluster 2 has a reduced number of infective units present in the soil outward from the rhizosphere.
Collapse
Affiliation(s)
- Erik Swanson
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Imed Sbissi
- LR Ecologie Pastorale, Institut des Régions Arides, Médenine, Tunisia
| | - Amir Ktari
- USCR Bactériologie Moléculaire and Génomique, Institut National des Sciences Appliquées and de Technologie, Université de Carthage, Tunis Cedex, Tunisia
| | - Hafsa Cherif-Silini
- LR Microbiologie Appliquée, Département de Microbiologie, Faculté des Sciences Naturelles et de la Vie, Université Ferhat Abbas, Sétif, Algeria
| | - Faten Ghodhbane-Gtari
- USCR Bactériologie Moléculaire and Génomique, Institut National des Sciences Appliquées and de Technologie, Université de Carthage, Tunis Cedex, Tunisia
- Institut Supérieur de Biotechnologie de Sidi Thabet, Université de La Manouba, Biotechnopôle, Sidi Thabet, Sidi Thabet, Tunisia
| | - Louis S. Tisa
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
- *Correspondence: Louis S. Tisa,
| | - Maher Gtari
- USCR Bactériologie Moléculaire and Génomique, Institut National des Sciences Appliquées and de Technologie, Université de Carthage, Tunis Cedex, Tunisia
- Maher Gtari,
| |
Collapse
|
38
|
Intracellular infection by symbiotic bacteria requires the mitotic kinase AURORA1. Proc Natl Acad Sci U S A 2022; 119:e2202606119. [PMID: 36252014 PMCID: PMC9618073 DOI: 10.1073/pnas.2202606119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The subcellular events occurring in cells of legume plants as they form transcellular symbiotic-infection structures have been compared with those occurring in premitotic cells. Here, we demonstrate that Aurora kinase 1 (AUR1), a highly conserved mitotic regulator, is required for intracellular infection by rhizobia in Medicago truncatula. AUR1 interacts with microtubule-associated proteins of the TPXL and MAP65 families, which, respectively, activate and are phosphorylated by AUR1, and localizes with them within preinfection structures. MYB3R1, a rhizobia-induced mitotic transcription factor, directly regulates AUR1 through two closely spaced, mitosis-specific activator cis elements. Our data are consistent with a model in which the MYB3R1-AUR1 regulatory module serves to properly orient preinfection structures to direct the transcellular deposition of cell wall material for the growing infection thread, analogous to its role in cell plate formation. Our findings indicate that the eukaryotically conserved MYB3R1-TPXL-AUR1-MAP65 mitotic module was conscripted to support endosymbiotic infection in legumes.
Collapse
|
39
|
Bellés-Sancho P, Liu Y, Heiniger B, von Salis E, Eberl L, Ahrens CH, Zamboni N, Bailly A, Pessi G. A novel function of the key nitrogen-fixation activator NifA in beta-rhizobia: Repression of bacterial auxin synthesis during symbiosis. FRONTIERS IN PLANT SCIENCE 2022; 13:991548. [PMID: 36247538 PMCID: PMC9554594 DOI: 10.3389/fpls.2022.991548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
Rhizobia fix nitrogen within root nodules of host plants where nitrogenase expression is strictly controlled by its key regulator NifA. We recently discovered that in nodules infected by the beta-rhizobial strain Paraburkholderia phymatum STM815, NifA controls expression of two bacterial auxin synthesis genes. Both the iaaM and iaaH transcripts, as well as the metabolites indole-acetamide (IAM) and indole-3-acetic acid (IAA) showed increased abundance in nodules occupied by a nifA mutant compared to wild-type nodules. Here, we document the structural changes that a P. phymatum nifA mutant induces in common bean (Phaseolus vulgaris) nodules, eventually leading to hypernodulation. To investigate the role of the P. phymatum iaaMH genes during symbiosis, we monitored their expression in presence and absence of NifA over different stages of the symbiosis. The iaaMH genes were found to be under negative control of NifA in all symbiotic stages. While a P. phymatum iaaMH mutant produced the same number of nodules and nitrogenase activity as the wild-type strain, the nifA mutant produced more nodules than the wild-type that clustered into regularly-patterned root zones. Mutation of the iaaMH genes in a nifA mutant background reduced the presence of these nodule clusters on the root. We further show that the P. phymatum iaaMH genes are located in a region of the symbiotic plasmid with a significantly lower GC content and exhibit high similarity to two genes of the IAM pathway often used by bacterial phytopathogens to deploy IAA as a virulence factor. Overall, our data suggest that the increased abundance of rhizobial auxin in the non-fixing nifA mutant strain enables greater root infection rates and a role for bacterial auxin production in the control of early stage symbiotic interactions.
Collapse
Affiliation(s)
- Paula Bellés-Sancho
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Yilei Liu
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Benjamin Heiniger
- Agroscope, Molecular Ecology and Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Elia von Salis
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Christian H. Ahrens
- Agroscope, Molecular Ecology and Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Nicola Zamboni
- ETH Zürich, Institute of Molecular Systems Biology, Zurich, Switzerland
| | - Aurélien Bailly
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| |
Collapse
|
40
|
Velandia K, Reid JB, Foo E. Right time, right place: The dynamic role of hormones in rhizobial infection and nodulation of legumes. PLANT COMMUNICATIONS 2022; 3:100327. [PMID: 35605199 PMCID: PMC9482984 DOI: 10.1016/j.xplc.2022.100327] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/24/2022] [Accepted: 04/13/2022] [Indexed: 06/15/2023]
Abstract
Many legume plants form beneficial associations with rhizobial bacteria that are hosted in new plant root organs, nodules, in which atmospheric nitrogen is fixed. This association requires the precise coordination of two separate programs, infection in the epidermis and nodule organogenesis in the cortex. There is extensive literature indicating key roles for plant hormones during nodulation, but a detailed analysis of the spatial and temporal roles of plant hormones during the different stages of nodulation is required. This review analyses the current literature on hormone regulation of infection and organogenesis to reveal the differential roles and interactions of auxin, cytokinin, brassinosteroids, ethylene, and gibberellins during epidermal infection and cortical nodule initiation, development, and function. With the exception of auxin, all of these hormones suppress infection events. By contrast, there is evidence that all of these hormones promote nodule organogenesis, except ethylene, which suppresses nodule initiation. This differential role for many of the hormones between the epidermal and cortical programs is striking. Future work is required to fully examine hormone interactions and create a robust model that integrates this knowledge into our understanding of nodulation pathways.
Collapse
Affiliation(s)
- Karen Velandia
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | - James B Reid
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | - Eloise Foo
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia.
| |
Collapse
|
41
|
Chakraborty S, Harris JM. At the Crossroads of Salinity and Rhizobium-Legume Symbiosis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:540-553. [PMID: 35297650 DOI: 10.1094/mpmi-09-21-0231-fi] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Legume roots interact with soil bacteria rhizobia to develop nodules, de novo symbiotic root organs that host these rhizobia and are mini factories of atmospheric nitrogen fixation. Nodulation is a sophisticated developmental process and is sensitive to several abiotic factors, salinity being one of them. While salinity influences both the free-living partners, symbiosis is more vulnerable than other aspects of plant and microbe physiology, and the symbiotic interaction is strongly impaired even under moderate salinity. In this review, we tease apart the various known components of rhizobium-legume symbiosis and how they interact with salt stress. We focus primarily on the initial stages of symbiosis since we have a greater mechanistic understanding of the interaction at these stages.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Collapse
Affiliation(s)
- Sanhita Chakraborty
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, U.S.A
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, U.S.A
| | - Jeanne M Harris
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, U.S.A
| |
Collapse
|
42
|
Huang R, Snedden WA, diCenzo GC. Reference nodule transcriptomes for Melilotus officinalis and Medicago sativa cv. Algonquin. PLANT DIRECT 2022; 6:e408. [PMID: 35774624 PMCID: PMC9219011 DOI: 10.1002/pld3.408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/14/2022] [Accepted: 05/19/2022] [Indexed: 05/10/2023]
Abstract
Host/symbiont compatibility is a hallmark of the symbiotic nitrogen-fixing interaction between rhizobia and legumes, mediated in part by plant-produced nodule-specific cysteine-rich (NCR) peptides and the bacterial BacA membrane protein that can act as a NCR peptide transporter. In addition, the genetic and metabolic properties supporting symbiotic nitrogen fixation often differ between compatible partners, including those sharing a common partner, highlighting the need for multiple study systems. Here, we report high-quality nodule transcriptome assemblies for Medicago sativa cv. Algonquin and Melilotus officinalis, two legumes able to form compatible symbioses with Sinorhizobium meliloti. The compressed M. sativa and M. officinalis assemblies consisted of 79,978 and 64,593 contigs, respectively, of which 33,341 and 28,278 were assigned putative annotations, respectively. As expected, the two transcriptomes showed broad similarity at a global level. We were particularly interested in the NCR peptide profiles of these plants, as these peptides drive bacterial differentiation during the symbiosis. A total of 412 and 308 NCR peptides were predicted from the M. sativa and M. officinalis transcriptomes, respectively, with approximately 9% of the transcriptome of both species consisting of NCR transcripts. Notably, transcripts encoding highly cationic NCR peptides (isoelectric point > 9.5), which are known to have antimicrobial properties, were ∼2-fold more abundant in M. sativa than in M. officinalis, and ∼27-fold more abundant when considering only NCR peptides in the six-cysteine class. We hypothesize that the difference in abundance of highly cationic NCR peptides explains our previous observation that some rhizobial bacA alleles which can support symbiosis with M. officinalis are unable to support symbiosis with M. sativa.
Collapse
Affiliation(s)
- Rui Huang
- Department of BiologyQueen's UniversityKingstonOntarioCanada
| | | | | |
Collapse
|
43
|
Visualization of the Crossroads between a Nascent Infection Thread and the First Cell Division Event in Phaseolus vulgaris Nodulation. Int J Mol Sci 2022; 23:ijms23095267. [PMID: 35563659 PMCID: PMC9105610 DOI: 10.3390/ijms23095267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 11/17/2022] Open
Abstract
The development of a symbiotic nitrogen-fixing nodule in legumes involves infection and organogenesis. Infection begins when rhizobia enter a root hair through an inward structure, the infection thread (IT), which guides the bacteria towards the cortical tissue. Concurrently, organogenesis takes place by inducing cortical cell division (CCD) at the infection site. Genetic analysis showed that both events are well-coordinated; however, the dynamics connecting them remain to be elucidated. To visualize the crossroads between IT and CCD, we benefited from the fact that, in Phaseolus vulgaris nodulation, where the first division occurs in subepidermal cortical cells located underneath the infection site, we traced a Rhizobium etli strain expressing DsRed, the plant cytokinesis marker YFP-PvKNOLLE, a nuclear stain and cell wall auto-fluorescence. We found that the IT exits the root hair to penetrate an underlying subepidermal cortical (S-E) cell when it is concluding cytokinesis.
Collapse
|
44
|
Kovács S, Kiss E, Jenei S, Fehér-Juhász E, Kereszt A, Endre G. The Medicago truncatula IEF Gene Is Crucial for the Progression of Bacterial Infection During Symbiosis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:401-415. [PMID: 35171648 DOI: 10.1094/mpmi-11-21-0279-r] [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: 06/14/2023]
Abstract
Legumes are able to meet their nitrogen need by establishing nitrogen-fixing symbiosis with rhizobia. Nitrogen fixation is performed by rhizobia, which has been converted to bacteroids, in newly formed organs, the root nodules. In the model legume Medicago truncatula, nodule cells are invaded by rhizobia through transcellular tubular structures called infection threads (ITs) that are initiated at the root hairs. Here, we describe a novel M. truncatula early symbiotic mutant identified as infection-related epidermal factor (ief), in which the formation of ITs is blocked in the root hair cells and only nodule primordia are formed. We show that the function of MtIEF is crucial for the bacterial infection in the root epidermis but not required for the nodule organogenesis. The IEF gene that appears to have been recruited for a symbiotic function after the duplication of a flower-specific gene is activated by the ERN1-branch of the Nod factor signal transduction pathway and independent of the NIN activity. The expression of MtIEF is induced transiently in the root epidermal cells by the rhizobium partner or Nod factors. Although its expression was not detectable at later stages of symbiosis, complementation experiments indicate that MtIEF is also required for the proper invasion of the nodule cells by rhizobia. The gene encodes an intracellular protein of unknown function possessing a coiled-coil motif and a plant-specific DUF761 domain. The IEF protein interacts with RPG, another symbiotic protein essential for normal IT development, suggesting that combined action of these proteins plays a role in nodule infection.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Szilárd Kovács
- Biological Research Centre, Institute of Plant Biology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Ernő Kiss
- Biological Research Centre, Institute of Genetics, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Sándor Jenei
- Biological Research Centre, Institute of Plant Biology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Erzsébet Fehér-Juhász
- Biological Research Centre, Institute of Genetics, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Attila Kereszt
- Biological Research Centre, Institute of Plant Biology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Gabriella Endre
- Biological Research Centre, Institute of Plant Biology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| |
Collapse
|
45
|
Wang T, Balla B, Kovács S, Kereszt A. Varietas Delectat: Exploring Natural Variations in Nitrogen-Fixing Symbiosis Research. FRONTIERS IN PLANT SCIENCE 2022; 13:856187. [PMID: 35481136 PMCID: PMC9037385 DOI: 10.3389/fpls.2022.856187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
The nitrogen-fixing symbiosis between leguminous plants and soil bacteria collectively called rhizobia plays an important role in the global nitrogen cycle and is an essential component of sustainable agriculture. Genetic determinants directing the development and functioning of the interaction have been identified with the help of a very limited number of model plants and bacterial strains. Most of the information obtained from the study of model systems could be validated on crop plants and their partners. The investigation of soybean cultivars and different rhizobia, however, has revealed the existence of ineffective interactions between otherwise effective partners that resemble gene-for-gene interactions described for pathogenic systems. Since then, incompatible interactions between natural isolates of model plants, called ecotypes, and different bacterial partner strains have been reported. Moreover, diverse phenotypes of both bacterial mutants on different host plants and plant mutants with different bacterial strains have been described. Identification of the genetic factors behind the phenotypic differences did already and will reveal novel functions of known genes/proteins, the role of certain proteins in some interactions, and the fine regulation of the steps during nodule development.
Collapse
Affiliation(s)
- Ting Wang
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
- Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | - Benedikta Balla
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
- Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | - Szilárd Kovács
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
| | - Attila Kereszt
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
| |
Collapse
|
46
|
Burr AA, Woods KD, Cassidy ST, Wood CW. Priority effects alter the colonization success of a host-associated parasite and mutualist. Ecology 2022; 103:e3720. [PMID: 35396706 DOI: 10.1002/ecy.3720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 09/03/2021] [Accepted: 10/25/2021] [Indexed: 11/07/2022]
Abstract
Priority effects shape the assembly of free-living communities and host-associated communities. However, the current literature does not fully incorporate two features of host-symbiont interactions-correlated host responses to multiple symbionts and ontogenetic changes in host responses to symbionts-leading to an incomplete picture of the role of priority effects in host-associated communities. We factorially manipulated the inoculation timing of two plant symbionts (mutualistic rhizobia bacteria and parasitic root-knot nematodes) and tested how host age at arrival, arrival order, and arrival synchrony affected symbiont colonization success in the model legume Medicago truncatula. We found that host age, arrival order, and arrival synchrony significantly affected colonization of one or both symbionts. Host age at arrival only affected nematodes but not rhizobia: younger plants were more heavily infected than older plants. By contrast, arrival order only affected rhizobia but not nematodes: plants formed more rhizobia nodules when rhizobia arrived before nematodes. Finally, synchronous arrival decreased colonization both symbionts, an effect that depended on host age. Our results demonstrate that priority effects compromise the host's ability to control colonization by two major symbionts, and suggest that the role of correlated host responses and host ontogeny in the assembly of host-associated communities deserve further attention.
Collapse
Affiliation(s)
- Audrey A Burr
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kamron D Woods
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Steven T Cassidy
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Corlett W Wood
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| |
Collapse
|
47
|
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
|
48
|
Wang X, Guo X, Hou L, Zhang J, Hu J, Zhang F, Mao J, Wang Z, Zhang C, Han J, Zhu Y, Liu C, Sun J, Shan C. A comparative study of bacterial diversity based on effects of three different shade shed types in the rhizosphere of Panax quiquefolium L. PeerJ 2022; 10:e12807. [PMID: 35186457 PMCID: PMC8840058 DOI: 10.7717/peerj.12807] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 12/27/2021] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Shading is an important factor affecting the cultivation of American ginseng, as it influences crop quality and yield. Rhizosphere microorganisms are also crucial for normal plant growth and development. However, whether different shade types significantly change American ginseng rhizosphere microorganisms is unknown. METHODS This study evaluated the rhizosphere soils of American ginseng under traditional, high flag and high arch shade sheds. High-throughput 16S rRNA gene sequencing determined the change of rhizosphere bacterial communities. RESULTS The microbial diversity in rhizosphere soils of American ginseng significantly changed under different shading conditions. The bacteria diversity was more abundant in the high arch shade than flat and traditional shades. Different bacterial genera, including Bradyrhizobium, Rhizobium, Sphingomonas, Streptomyces and Nitrospira, showed significantly different abundances. Different shading conditions changed the microbial metabolic function in the American ginseng rhizosphere soils. The three types of shade sheds had specific enriched functional groups. The abundance of ATP-binding cassette (ABC) transporters consistently increased in the bacterial microbiota. These results help understand the influence of shading systems on the rhizosphere microecology of American ginseng, and contribute to the American ginseng cultivation.
Collapse
Affiliation(s)
- Xianchang Wang
- Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs/Research Center of Medicinal Plant, Shandong Academy of Agricultural Sciences/Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xu Guo
- Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs/Research Center of Medicinal Plant, Shandong Academy of Agricultural Sciences/Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Lijuan Hou
- Weihai Academy of Agricultural Sciences, Weihai, China
| | - Jiaohong Zhang
- Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs/Research Center of Medicinal Plant, Shandong Academy of Agricultural Sciences/Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jing Hu
- Weihai Academy of Agricultural Sciences, Weihai, China
| | - Feng Zhang
- Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs/Research Center of Medicinal Plant, Shandong Academy of Agricultural Sciences/Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jilei Mao
- Weihai Academy of Agricultural Sciences, Weihai, China
| | - Zhifen Wang
- Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs/Research Center of Medicinal Plant, Shandong Academy of Agricultural Sciences/Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Congjing Zhang
- Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs/Research Center of Medicinal Plant, Shandong Academy of Agricultural Sciences/Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jinlong Han
- Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs/Research Center of Medicinal Plant, Shandong Academy of Agricultural Sciences/Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yanwei Zhu
- Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs/Research Center of Medicinal Plant, Shandong Academy of Agricultural Sciences/Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Chao Liu
- Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs/Research Center of Medicinal Plant, Shandong Academy of Agricultural Sciences/Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jinyue Sun
- Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs/Research Center of Medicinal Plant, Shandong Academy of Agricultural Sciences/Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Chenggang Shan
- Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs/Research Center of Medicinal Plant, Shandong Academy of Agricultural Sciences/Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan, China
| |
Collapse
|
49
|
NoiD, a DedA membrane protein required for homeostasis maintaining of Rhizobium leguminosarum biovar viciae during symbiosis with Pisum sativum. Symbiosis 2022. [DOI: 10.1007/s13199-021-00827-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
50
|
|