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==Introduction==
==Introduction==
[[Image:istockphoto-1347307099-612x612 (2).jpg|thumb|300px|right|Figure 1. Nodules of soybean roots. Atmospheric nitrogen-fixing bacteria live inside.]]
Legumes, which include many common foods such as soybeans and peas, are well known as the only plant family with the capability to fix nitrogen. Most environmental nitrogen is in the form of N₂, or atmospheric nitrogen. However, for plants to uptake and use this vital nutrient, it must be in an organic form such as ammonia (NH₃), nitrate (NO₃-), or nitrite (NO₂-). Legumes possess the ability to fix atmospheric nitrogen into organic compounds through their symbiotic relationship with Rhizobia bacteria.  
Legumes, which include many common foods such as soybeans and peas, are well known as the only plant family with the capability to fix nitrogen. Most environmental nitrogen is in the form of N₂, or atmospheric nitrogen. However, for plants to uptake and use this vital nutrient, it must be in an organic form such as ammonia (NH₃), nitrate (NO₃-), or nitrite (NO₂-). Legumes possess the ability to fix atmospheric nitrogen into organic compounds through their symbiotic relationship with Rhizobia bacteria.  
During rhizobial symbiosis, rhizobia infects plant roots to form root nodules. The bacteria facilitate nitrogen uptake for the plants (S, J. 2023). The rhizobia provides the legume with a source of fixed nitrogen, while in turn, the host legume provides the rhizobia with key nutrients for metabolism (U, M. 2013).
The availability of organic nitrogen in the soil is a major limiting factor for plant growth (S, J. 2023). Because of this symbiosis with rhizobia is crucial for productivity in legumes (P, N. A. 2003). Research on this symbiotic interaction has the potential to enhance food production and make sustainable changes in the field of agriculture (P, N. A. 2003). This page will discuss the process for nodulation and key genes of this symbiosis.


==Initiating Legume-Rhizobia Symbiosis==
During rhizobial symbiosis, rhizobia infects plant roots to form root nodules. The bacteria facilitate nitrogen uptake for the plants.<ref name=" Shumilina ">Shumilina, J., Soboleva, A., Abakumov, E., Shtark, O. Y., Zhukov, V. A., & Frolov, A. (2023). Signaling in legume–rhizobia symbiosis. International Journal of Molecular Sciences, 24(24), 17397. https://doi.org/10.3390/ijms242417397</ref> The rhizobia provides the legume with a source of fixed nitrogen, while in turn, the host legume provides the rhizobia with key nutrients for metabolism.<ref name=" Udvardi ">Udvardi, M., & Poole, P. S. (2013). Transport and metabolism in legume-rhizobia symbioses. Annual Review of Plant Biology, 64(1), 781–805. https://doi.org/10.1146/annurev-arplant-050312-120235
The first step in initiating the symbiotic relationship is the release of flavonoids and isoflavonoids from the plant roots (S, J. 2023). Flavanoids are released by the legume plants during periods of nitrogen deficiency and act as chemical signals that attract rhizobia bacteria. Rhizobia is a type of gram-negative proteobacteria found in soil. They belong to a family of nitrogen-fixing bacteria (S, J. 2023).
</ref>  
Upon receiving these chemical signals, rhizobia colonizes the surface of the plant roots and releases reciprocal signaling molecules known as Nod factors (D, J. J. 2015). Nod factors are synthesized by the enzymes NodM, NodC, NodB, and NodA (S, J. 2023). These signaling molecules induce root hair deformation, cortical cell proliferation, and infection thread formation in the host plant. These are precursory steps to the formation of nodules. (S, J. 2023). The deformed root hairs envelop the rhizobia. The rhizobia then degrade the cell wall to penetrate the plant root and the plant cell’s plasma membrane envelopes the bacteria, forming the infection thread (G, N. 2009, S, J. 2023). Infection thread formation requires continuous generation of the plant's cell membrane and wall (S, J. 2023). The infection thread allows the bacteria to move deeper into the plant tissue to colonize root cells (D, J. J. 2015; U, M 2013).
The deformed root hairs envelop the rhizobia. The rhizobia then degrade the cell wall to penetrate the plant root and the plant cell’s plasma membrane envelopes the bacteria, forming the infection thread (G, N. 2009, S, J. 2023). Infection thread formation requires continuous generation of the plant's cell membrane and wall (S, J. 2023). The infection thread allows the bacteria to move deeper into the plant tissue to colonize root cells (D, J. J. 2015; U, M 2013). The rhizobia are transported into the root cell cytoplasm by endocytosis (U, M. 2013).
Inside the root cell, the rhizobia are contained in a plant-derived membrane. This unit is called a symbiosome and serves as the functional unit of nitrogen fixation in the legume root nodules (D, J. J. 2015; U, M. 2013). Symbiosomes may contain any number of bacteria cells (D, J. J. 2015).
Once the root nodule has developed, Rhizobia begins to differentiate to carry out the necessary functions for symbiotic nitrogen fixation (S, J. 2023). These differentiated bacteria are known as bacteroids. Differentiation is initiated by a peptide released by the host legume which causes the rhizobia to differentiate according to the plant’s specific needs (S, J. 2023). Differentiated bacteroids form either determinate or indeterminate nodules which each have varying functions in nitrogen fixation (S, J. 2023; U, M 2013).  
Following these steps, the nitrogen-fixing process can now occur. Rhizobia will produce nitrogenase enzymes which convert inorganic N₂ into organic NH₃ (P, N. A. 2003). Once the nitrogen is fixed, it is transported and incorporated into amino acids and ureides for plant growth (D, J. J. 2015).  
<br>
<ref name=" abc "></ref>
Include some current research, with at least one image.
Call out each figure by number (Fig. 1).<br><br>


Sample citations: <ref name=" abc ">[http://www2.umat.edu.gh/gjt/index.php/gjt/article/viewFile/291/100 Zigli DD, Brew L, Obeng-Denteh W, Kwofie S. On the Application of Homeomorphism on Amoeba Proteus. Ghana Journal of Technology. 2021 Mar 31;5(2):43-7.]</ref>
The availability of organic nitrogen in the soil is a major limiting factor for plant growth.<ref name=" Shumilina "></ref> Because of this symbiosis with rhizobia is crucial for productivity in legumes.<ref name=" Provorov ">Provorov, N. A., & Tikhonovich, I. A. (2003). Genetic Resources and Crop Evolution, 50(1), 89–99. https://doi.org/10.1023/a:1022957429160</ref> Research on this symbiotic interaction has the potential to enhance food production and make sustainable changes in the field of agriculture.<ref name=" Provorov "></ref> This page will discuss the process for nodulation and key genes of this symbiosis.
<ref>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3847443/ Bartlett et al.: Oncolytic viruses as therapeutic cancer vaccines. Molecular Cancer 2013 12:103.]</ref>
<br><br>A citation code consists of a hyperlinked reference within "ref" begin and end codes.


<ref>Lee G, Low RI, Amsterdam EA, Demaria AN, Huber PW, Mason DT. <i>Hemodynamic effects of morphine and nalbuphine in acute myocardial infarction</i>. Clinical Pharmacology & Therapeutics. 1981 May;29(5):576-81.</ref>
==Initiating Legume-Rhizobia Symbiosis==
The first step in initiating the symbiotic relationship is the release of flavonoids and isoflavonoids from the plant roots.<ref name=" Shumilina "></ref> Flavanoids are released by the legume plants during periods of nitrogen deficiency and act as chemical signals that attract rhizobia bacteria. Rhizobia is a type of gram-negative proteobacteria found in soil. They belong to a family of nitrogen-fixing bacteria.<ref name=" Shumilina "></ref>
Upon receiving these chemical signals, rhizobia colonizes the surface of the plant roots and releases reciprocal signaling molecules known as Nod factors.<ref name=" Drevon ">Drevon, J.-J., Alkama, N., Bargaz, A., Rodiño, A. P., Sungthongwises, K., & Zaman-Allah, M. (2015). The legume–rhizobia symbiosis. Handbook of Plant Breeding, 267–290. https://doi.org/10.1007/978-1-4939-2797-5_9</ref> Nod factors are synthesized by the enzymes NodM, NodC, NodB, and NodA.<ref name=" Shumilina "></ref> These signaling molecules induce root hair deformation, cortical cell proliferation, and infection thread formation in the host plant. These are precursory steps to the formation of nodules.<ref name=" Shumilina "></ref>  


For multiple use of the same inline citation or footnote, you can use the named references feature, choosing a name to identify the inline citation, and typing <ref name=" name ">text of the citation</ref>
The deformed root hairs envelop the rhizobia. The rhizobia then degrade the cell wall to penetrate the plant root and the plant cell’s plasma membrane envelopes the bacteria, forming the infection thread.<ref name=" Shumilina "></ref><ref name=" Garg ">Garg, N., & Geetanjali. (2009). Symbiotic nitrogen fixation in legume nodules: Process and signaling: A Review. Sustainable Agriculture, 519–531. https://doi.org/10.1007/978-90-481-2666-8_32
</ref> Infection thread formation requires continuous generation of the plant's cell membrane and wall.<ref name=" Shumilina "></ref> The infection thread allows the bacteria to move deeper into the plant tissue to colonize root cells.<ref name=" Udvardi "></ref><ref name=" Drevon "></ref> The rhizobia are transported into the root cell cytoplasm by endocytosis.<ref name=" Udvardi "></ref> 
Inside the root cell, the rhizobia are contained in a plant-derived membrane. This unit is called a symbiosome and serves as the functional unit of nitrogen fixation in the legume root nodules.<ref name=" Udvardi "></ref><ref name=" Drevon "></ref> Symbiosomes may contain any number of bacteria cells.<ref name=" Drevon "></ref>
Once the root nodule has developed, Rhizobia begins to differentiate to carry out the necessary functions for symbiotic nitrogen fixation.<ref name=" Shumilina "></ref> These differentiated bacteria are known as bacteroids. Differentiation is initiated by a peptide released by the host legume which causes the rhizobia to differentiate according to the plant’s specific needs.<ref name=" Shumilina "></ref> Differentiated bacteroids form either determinate or indeterminate nodules which each have varying functions in nitrogen fixation.<ref name=" Shumilina "></ref><ref name=" Udvardi "></ref>
Following these steps, the nitrogen-fixing process can now occur. Rhizobia will produce nitrogenase enzymes which convert inorganic N₂ into organic NH₃.<ref name=" Provorov "></ref> Once the nitrogen is fixed, it is transported and incorporated into amino acids and ureides for plant growth.<ref name=" Drevon "></ref>  


<ref name=" name "></ref>
==Key Genes in Symbiotic Nitrogen Fixation==
 
[[Image:rhizobia.jpg|thumb|300px|right|Figure 2. Epifluorescence microscopy images showing rhizobia colonization of roots of rice plant. Applied and Environmental Microbiology 71: 7271–7278.]]
Second citation of Ref 1: <ref name=" abc "></ref>
Flavanoids released by legumes trigger the expression of nod genes in rhizobia. They do this by inducing the nodD protein to act as a transcription activator.<ref name=" Shumilina "></ref> NodA, NodB, and NodC genes code for the proteins comprising nod factors.<ref name=" Garg "></ref> Therefore, these genes are key for producing the signals necessary for nodule development to begin in the host legume. Another key class of rhizobial genes involved in symbiotic nitrogen fixation are nif and fix genes. Interestingly, these genes are regulated by environmental oxygen levels.<ref name=" Udvardi "></ref> These genes code for many mechanisms involved in nitrogen fixation but notably also control bacteroid differentiation.<ref name=" Udvardi "></ref>  
In response to receiving nod factor signals, nodulin genes in the host legume are expressed. Rapidly expressed nodulin genes include enod12, enod40, rip1, and dd23b. Nodulin genes control important functions for nodule development and maintenance as the proteins expressed comprise the nodule structure.<ref name=" Provorov "></ref><ref name=" Garg "></ref> Another important component for nodulation is NIN. NIN is a plant transcription factor that regulates root cell proliferation and permeability for nodulation. This makes it an important regulator for legume-rhizobia symbiosis, balancing and optimizing the number of nodes.
<ref name=" Shumilina "></ref>
==Future Prospects==
While much has been studied in Legume-Rhizobia symbiosis and nitrogen fixation, many knowledge gaps still exist. Further research is needed to understand the mechanisms behind flavanoid signalers.<ref name=" Shumilina "></ref> Additionally, the gene expression changes behind bacteroid differentiation are not yet understood.<ref name=" Udvardi "></ref>


Here we cite April Murphy's paper on microbiomes of the Kokosing river. <ref name="murphy">[https://journals.asm.org/doi/full/10.1128/Spectrum.00941-21 Murphy A, Barich D, Fennessy MS, Slonczewski JL. An Ohio State Scenic River Shows Elevated Antibiotic Resistance Genes, Including Acinetobacter Tetracycline and Macrolide Resistance, Downstream of Wastewater Treatment Plant Effluent. Microbiology Spectrum. 2021 Sep 1;9(2):e00941-21.]</ref>
Research in Legume-Rhizobia Symbiosis has the potential to revolutionize the field of agriculture.  The current use of synthetic fertilizers as a nitrogen source contributes to environmental pollution, climate change, and depletion of fossil fuel stores.<ref name=" Garg "></ref> However, Rhizobium symbiosis offers potential alternatives. Selective breeding of the most productive strains of rhizobia and Legume species could be used to maximize nitrogen fixation for agricultural purposes.<ref name=" Provorov "></ref> Additionally, knowledge of gene functions for rhizobia and legume species could be applied in gene editing technology that makes nitrogen fixation possible in other crop species.<ref name=" Garg "></ref> Optimization of the Rhizobia symbiosis system for nitrogen fixation would bring significant improvements in sustainable agriculture.<ref name=" Provorov "></ref>
 
==Key Genes in Symbiotic Nitrogen Fixation==
Include some current research, with a second image.<br><br>
Here we cite Murphy's microbiome research again.<ref name="murphy"></ref>
<br>


==CFuture Prospects==
You may have a short concluding section.
Overall, cite at least 5 references under <b>References</b> section.<br>


==References==
==References==

Latest revision as of 16:14, 13 December 2024

Introduction

Figure 1. Nodules of soybean roots. Atmospheric nitrogen-fixing bacteria live inside.

Legumes, which include many common foods such as soybeans and peas, are well known as the only plant family with the capability to fix nitrogen. Most environmental nitrogen is in the form of N₂, or atmospheric nitrogen. However, for plants to uptake and use this vital nutrient, it must be in an organic form such as ammonia (NH₃), nitrate (NO₃-), or nitrite (NO₂-). Legumes possess the ability to fix atmospheric nitrogen into organic compounds through their symbiotic relationship with Rhizobia bacteria.

During rhizobial symbiosis, rhizobia infects plant roots to form root nodules. The bacteria facilitate nitrogen uptake for the plants.[1] The rhizobia provides the legume with a source of fixed nitrogen, while in turn, the host legume provides the rhizobia with key nutrients for metabolism.[2]

The availability of organic nitrogen in the soil is a major limiting factor for plant growth.[1] Because of this symbiosis with rhizobia is crucial for productivity in legumes.[3] Research on this symbiotic interaction has the potential to enhance food production and make sustainable changes in the field of agriculture.[3] This page will discuss the process for nodulation and key genes of this symbiosis.

Initiating Legume-Rhizobia Symbiosis

The first step in initiating the symbiotic relationship is the release of flavonoids and isoflavonoids from the plant roots.[1] Flavanoids are released by the legume plants during periods of nitrogen deficiency and act as chemical signals that attract rhizobia bacteria. Rhizobia is a type of gram-negative proteobacteria found in soil. They belong to a family of nitrogen-fixing bacteria.[1]

Upon receiving these chemical signals, rhizobia colonizes the surface of the plant roots and releases reciprocal signaling molecules known as Nod factors.[4] Nod factors are synthesized by the enzymes NodM, NodC, NodB, and NodA.[1] These signaling molecules induce root hair deformation, cortical cell proliferation, and infection thread formation in the host plant. These are precursory steps to the formation of nodules.[1]

The deformed root hairs envelop the rhizobia. The rhizobia then degrade the cell wall to penetrate the plant root and the plant cell’s plasma membrane envelopes the bacteria, forming the infection thread.[1][5] Infection thread formation requires continuous generation of the plant's cell membrane and wall.[1] The infection thread allows the bacteria to move deeper into the plant tissue to colonize root cells.[2][4] The rhizobia are transported into the root cell cytoplasm by endocytosis.[2]

Inside the root cell, the rhizobia are contained in a plant-derived membrane. This unit is called a symbiosome and serves as the functional unit of nitrogen fixation in the legume root nodules.[2][4] Symbiosomes may contain any number of bacteria cells.[4]

Once the root nodule has developed, Rhizobia begins to differentiate to carry out the necessary functions for symbiotic nitrogen fixation.[1] These differentiated bacteria are known as bacteroids. Differentiation is initiated by a peptide released by the host legume which causes the rhizobia to differentiate according to the plant’s specific needs.[1] Differentiated bacteroids form either determinate or indeterminate nodules which each have varying functions in nitrogen fixation.[1][2]

Following these steps, the nitrogen-fixing process can now occur. Rhizobia will produce nitrogenase enzymes which convert inorganic N₂ into organic NH₃.[3] Once the nitrogen is fixed, it is transported and incorporated into amino acids and ureides for plant growth.[4]

Key Genes in Symbiotic Nitrogen Fixation

Figure 2. Epifluorescence microscopy images showing rhizobia colonization of roots of rice plant. Applied and Environmental Microbiology 71: 7271–7278.

Flavanoids released by legumes trigger the expression of nod genes in rhizobia. They do this by inducing the nodD protein to act as a transcription activator.[1] NodA, NodB, and NodC genes code for the proteins comprising nod factors.[5] Therefore, these genes are key for producing the signals necessary for nodule development to begin in the host legume. Another key class of rhizobial genes involved in symbiotic nitrogen fixation are nif and fix genes. Interestingly, these genes are regulated by environmental oxygen levels.[2] These genes code for many mechanisms involved in nitrogen fixation but notably also control bacteroid differentiation.[2]

In response to receiving nod factor signals, nodulin genes in the host legume are expressed. Rapidly expressed nodulin genes include enod12, enod40, rip1, and dd23b. Nodulin genes control important functions for nodule development and maintenance as the proteins expressed comprise the nodule structure.[3][5] Another important component for nodulation is NIN. NIN is a plant transcription factor that regulates root cell proliferation and permeability for nodulation. This makes it an important regulator for legume-rhizobia symbiosis, balancing and optimizing the number of nodes. [1]

Future Prospects

While much has been studied in Legume-Rhizobia symbiosis and nitrogen fixation, many knowledge gaps still exist. Further research is needed to understand the mechanisms behind flavanoid signalers.[1] Additionally, the gene expression changes behind bacteroid differentiation are not yet understood.[2]

Research in Legume-Rhizobia Symbiosis has the potential to revolutionize the field of agriculture. The current use of synthetic fertilizers as a nitrogen source contributes to environmental pollution, climate change, and depletion of fossil fuel stores.[5] However, Rhizobium symbiosis offers potential alternatives. Selective breeding of the most productive strains of rhizobia and Legume species could be used to maximize nitrogen fixation for agricultural purposes.[3] Additionally, knowledge of gene functions for rhizobia and legume species could be applied in gene editing technology that makes nitrogen fixation possible in other crop species.[5] Optimization of the Rhizobia symbiosis system for nitrogen fixation would bring significant improvements in sustainable agriculture.[3]


References

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 Shumilina, J., Soboleva, A., Abakumov, E., Shtark, O. Y., Zhukov, V. A., & Frolov, A. (2023). Signaling in legume–rhizobia symbiosis. International Journal of Molecular Sciences, 24(24), 17397. https://doi.org/10.3390/ijms242417397
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 Udvardi, M., & Poole, P. S. (2013). Transport and metabolism in legume-rhizobia symbioses. Annual Review of Plant Biology, 64(1), 781–805. https://doi.org/10.1146/annurev-arplant-050312-120235
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 Provorov, N. A., & Tikhonovich, I. A. (2003). Genetic Resources and Crop Evolution, 50(1), 89–99. https://doi.org/10.1023/a:1022957429160
  4. ↑ 4.0 4.1 4.2 4.3 4.4 Drevon, J.-J., Alkama, N., Bargaz, A., Rodiño, A. P., Sungthongwises, K., & Zaman-Allah, M. (2015). The legume–rhizobia symbiosis. Handbook of Plant Breeding, 267–290. https://doi.org/10.1007/978-1-4939-2797-5_9
  5. ↑ 5.0 5.1 5.2 5.3 5.4 Garg, N., & Geetanjali. (2009). Symbiotic nitrogen fixation in legume nodules: Process and signaling: A Review. Sustainable Agriculture, 519–531. https://doi.org/10.1007/978-90-481-2666-8_32


Edited by Rebecca Holland, student of Joan Slonczewski for BIOL 116, 2024, Kenyon College.

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