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Rhizosphere and Bacteria

Three Regions of the Rhizosphere Have Been Described

The rhizosphere characterization has been refined in recent years to include three zones that are distinct based on their relative proximity to the root. Plants respond to nutrient deficiency by physically changing their root structure and pairing up with microbes in the soil to change the chemical environment of the rhizosphere they grow in. The rhizosphere is also active: The physical and chemical properties of the soil, the weather, plant-induced changes in soil water content, the composition and density of soil microbial populations, and the metabolic activities of plants and microbes influence the rhizosphere. Microbes in the rhizosphere can support plants with accessing nutrients by lowering the pH in the soil, changing the chemical conditions within the rhizosphere, or directly using chelation with a nutrient; chelation refers to a compound that connects carbon-hydrogen molecules and nitrogen compounds with a central atom using ionic bonding.

Rhizosphere composition and its know role in interactions between plants and microbes.

rhizosphere layers defined: http://www.cell.com/trends/plant-science/fulltext/S1360-1385(17)30139-5

The Endosphere

The endorhizosphere includes portions of the cortex and endodermis in plant roots in which microbes and cations can occupy the "free space" between cells called the apoplastic space.

The Rhizoplane

The rhizoplane is the medial zone directly adjacent to the root including the root epidermis and mucilage.

The Ectorhizosphere

The outermost zone is the ectorhizosphere which extends from the rhizoplane out into the bulk soil pool.

The Rhizosphere and Its Functions

Inoculation experiments frequently fail to improve rates of nitrogen fixation and are difficult to study in the field; researchers are still trying to find a way to control and suppress selected microorganisms and keep selected microorganisms for crop productivity by allowing certain positive mutualistic relationships to thrive.

A rhizosphere is a plant-root soil pool first described by a German agronomist named Lorenz Hiltner; in 1904 he defined the rhizosphere as the soil zone influenced by plant roots and occurs around the root of a plant. The rhizosphere is inhabited by microbe populations in a hypothesized specialized symbiotic relationship with the plant. The rhizosphere of plants is often occupied by deleterious rhizobacteria (DRB), that can inhibit plant growth, and plant growth promoting rhizobacteria (PGPR).  Coevolution exists between rhizobacteria and plants in the rhizosphere; rhizosphere bacteria can be both DRB and PGPR by inhibiting plant growth and controlling plant diseases. PGPR can colonize the rhizosphere of different plant species at one time and can benefit the plant by promoting plant growth and reducing plant host susceptibility to diseases from a variety of pathogens. PGPR can also cause ‘induced systemic resistance’ (ISR). ISR produced by PGPR has the ability to suppress plant diseases with chemical or physical changes in the greenhouse or in the field. PGPR helps plants with tolerance to abiotic stresses, including drought, salinity, and nutrient deficiency.

Production of Growth-Promoting Hormones

Plant roots consistently deepen for and deplete certain bacterial phyla relative to their abundance in the bulk soil pool. This process depends on salicylic acid synthesis and signaling, indicating that plant hormones regulate the root microbiome composition.

Plant Growth Promoting Rhizobacteria (PGPR) were first defined by Kloepper and Schroth (1978) as organisms that, after being inoculated on seeds, could successfully colonize plant roots and positively enhance plant growth. To date, Over two dozen genera of nonpathogenic rhizobacteria have been identified. Plant growth promotion can be shown to work directly on the plant in the absence of root pathogens by the release of plant secondary metabolic compounds called phytohormones that include auxins and cytokinins.

What is Rhizosphere Bacteria?

Rhizosphere bacteria are microbes of different species that thrive in the environment of rhizospheres on plant roots in a competitive manner. In 1888, Hellriegel and Wilfarth found that rhizosphere bacteria called Rhizobium leguminosarum can improve crop yield by converting atmospheric dinitrogen (N_2(g)) into ammonia (NH₃), a form usable by the plant all inside the root nodules. Rhizosphere bacteria (rhizobacteria) are some of the many microbial inhabitants of the rhizosphere. TIn recent studies, rhizobacteria perhaps can sense and respond to plant signals or secondary metabolites, exchange nutrients with plant cells, suffer damage due to plant chemical defense responses, and colonize or even invade root tissues that can create pathologies, symbioses, or mutualisms. The events between roots and rhizobacteria modify the osmolality of the rhizosphere. Osmolality is the concentration of a solution defined by the number of solute particles per kilogram. Osmoadaptive mechanisms in the rhizosphere can likely stimulate both the survival of rhizosphere bacteria and their interactions with plant roots. Rhizobia are distinguished by their existence as both free living soil bacteria and as nitrogen-fixing root endosymbionts. The primary organisms that directly interact with plants are rhizobial bacteria, fungal mycorrhizae, and endophytes (fungal/bacterial symbionts that reside within plant cells). Some of the main benefits that microbes in the rhizosphere provide to the plant are nitrogen fixation, increased phosphorus uptake, and defense against pathogens. In return, plants provide photosynthetic carbon to the organisms that includes providing 15-20% to rhizobial plant nodules, 4-20% to mycorrhizae, and 15% to the rhizoplane. A multitude of interactions are present in the rhizosphere, ranging from beneficial symbiotic relationships to detrimental pathogenic interactions. However, symbiosis can include microbes that contribute less than the plant and gain more benefit from the plant than the plant from the microbes. Known as "cheaters" in current research, it has been examined that plants can choose their partners to ensure a mutual cooperation can persist. Plants signal potential microbes for symbiosis; these signals are not specific because they can also attract rhizobia and mycorrhizae that can potentially become pathogens or "cheaters."

Above and below ground bacterial composition in soils

Communication between Plant and Rhizobacteria

The mutualism between rhizobia and a plant starts with a chemical signal (flavonoid) released when Nitrogen is limited to the plant. The flavonoid signal induces nodulation genes (nod genes) in the rhizobia which encode enzymes necessary to produce a chemical response (lipochitooligosaccharide) to the plant known as a nod factor. The nod factors initiate a cascade of developmental processes in the plant root which allow for the growth of a root nodule in which the bacteria live. The structure of the nod factors are species specific and encourage the host specificity observed between rhizobia and their plant partners. Microorganisms in the rhizosphere contribute chemical and physical changes in the soil that directly affect plants. Microbes can convert organic matter and microbial biomass to mineral compounds that provides plants with accessible nutrients. Rhizobial bacteria can reduce manganese (Mn4+ to Mn2+) and iron (Fe3+ to Fe2+) for plant uptake. Manganese and iron can help plants resist inoculation of pathogens into their roots.

Genetic Manipulations and Gene Splicing to Create Productive Relationships between Rhizobacteria and Plants

Under stressful conditions plants release the hormone ethylene (C₂H₄) regulates plant homeostasis and results in reduced root and shoot growth. The degradation of the ethylene precursor ACC by bacterial ACC deaminase alleviates plant stress and saves normal plant growth; (PGPR) colonize roots very efficiently and promote plant health. Symbiotic relationships with plants lead to benefits for both the plant and the PGPR, such as better nutrient uptake and stimulation of root growth. It works with volatiles emitted by PGPR that downregulate hkt1 (high affinity K+ transporter 1) expression in roots but upregulate it in shoot tissues, arranging lower Na⁺ levels and recirculation of Na⁺ in the whole plant during high salt conditions. Root tips and root surfaces are sites of nutrient uptake; it is likely that one mechanism by which PGPR lead to increased nutrient uptake is by stimulating root development. PGPR may also be able to increase plant uptake of mineral ions by stimulating the proton (H+) pump ATPase. One PGPR strain, Achromobacter piechaudii ARV8 that produces 1-aminocyclopropane-1-carboxylate (ACC) deaminase, can encourage IST to drought stress in pepper (Capsicum annuum) and tomato (Solanum lycopersicum) plants. 

Solubilization of Minerals and Effect on Plant Growth

The variation of pH is one of the major rhizosphere processes able to modify the solubility of different elements such as phosphorus (P). A pH variation can alter P-adsorption and the precipitation/dissolution of P minerals. Nevertheless, the predominance of the pH changes to other rhizospheric functions on P mobility is still a debate. To determine the relative importance of pH to other rhizospheric functions, Edith et al. compared the distributions of P fractions measured “(i) after controlled pH changes and (ii) after contact with two varieties of wheat cultivated with two forms of nitrogen i.e. ammonium or nitrates to further alter the pH.” Without soil-plant contact, the inorganic phosphorus fractions (Pi) of NaOH, bicarbonate, and resin extractions enhanced by alkalinization (p-value 0.05) lead to the conclusion that plants can induce changes in P fractions that cannot be attributed to pH changes only. Zacharoula and Hodson investigated the effect of nitrogen on rhizosphere chemistry and Cu, Zn and Pb uptake by Brassica species. They demonstrated that Brassica two species of Brassica significantly (p < 0.05) reduced rhizosphere pH in both the presence of ammonium- and nitrate-nitrogen Significantly (p < 0.05) more copper and lead was taken up by all Brassica species when nitrate-nitrogen was added to soils. Sequential extraction analyses of rhizosphere and bulk soils showed that exchangeable copper and lead were significantly higher (p < 0.05) in the rhizosphere compared to bulk soil pool and exchangeable zinc was significantly lower (p < 0.05).The plants are able to use the rhizosphere chemistry created by soil microbes and rhizobia to make this metal uptake possible.

Fixation of Nitrogen

Hiltner described bacterial events as the processes of the nitrogen cycle including denitrification, nitrification and nitrogen fixation, which was the major focus Hiltner. He referred to the nitrogen fixing bacteria as symbiotic bacteria in nodules of legumes. “… After learning about the different processes involved in nitrogen metabolism, which are catalyzed by organisms freely living in the soil, the most important question arises, how these organisms, probably coexisting in every agricultural soil and interact with each other.” Hiltner described the conditions of the rhizosphere as different from those used in pure cultures. As we could demonstrate, the known cases of soil sickness (tiredness) are indeed caused mainly by the action of those organisms, which enter the roots of plants grown repeatedly on the same soil pool. The nutrients most limiting to plant growth are nitrogen and phosphorus. Even though 78% of the Earth's atmosphere is composed of nitrogen (N₂ gas), it is in a form that is only utilizable by nitrogen-fixing organisms. As such, inorganic forms of N (NO₃^-,NH₄⁺) that can be used by plants are converted and added to soils by microbes capable of fixing inorganic nitrogen. The availability of nitrogen in most soils is low because of the leaching losses of soluble nitrate (NO₃^-) with infiltrating rainwater, fixation of ammonium (NH₄⁺) in clays and soil organic matter and bacterial denitrification. Plants respond differently to the soil pool depending on the chemical form of nitrogen in the soil. The rhizosphere consists of a gradient in chemical, biological and physical properties that change both radially and longitudinally along plant roots. For example, ammonium (NH₄₊) has a positive charge, allowing the plant to release one proton (H⁺) for every NH₄⁺ taken up leading to a reduction in rhizosphere pH. When supplied with NO₃^-, the opposite can occur where the plant releases bicarbonate (HCO₃^-) and increases the pH in the rhizosphere. These changes in pH can influence the availability of other plant essential micronutrients including Zn, Ca, Mg.

Removal of Pollutants

Competitive Suppression of Pathogens

An example of plants utilizing microbes in a symbiotic relationship is demonstrated in tobacco bacterial wilt, a plant disease caused by Ralstonia solanacearum, a destructive soil-spreading disease that is globally distributed. Continuous cropping and soil acidification over the last century has caused the disease to become increasingly resistant in south of China. Currently, antibiotics such as streptomycin sulfate and chemical antiseptics including copper fungicides are methods used to counteract the disease. Adverse effects of the antibiotics and antiseptics range from chemical residues on tobacco to environment pollution. Zhang et al. demonstrated the disease incidence and the disease index of tobacco significantly differed (P < 0.05) between the biochar and non-biochar treatment in their investigation. Biochar made from rice straw suppresses the incidence and disease index of tobacco bacterial wilt under field conditions. Biochar application caused soil pH to increase to a value more suitable for growing tobacco. Biochar application also caused CEC (Cation Exchange Capacity) values to rise in tobacco rhizosphere soil. Furthermore, alkaline N, available K and P, and organic carbon also sharply increased with biochar application. These changes enhance the growth of both plants and inhibit their pathogens. Biochar application induces an environment that is favorable for tobacco but unfavorable for R. solanacearum. The addition of biochar increased the richness and diversity of bacteria in the tobacco rhizosphere Biochar application improved the abundance of certain genera of microorganisms, especially those belonging to Pseudomonas, Brevibacillus, Bacillus, and Trichoderma, resulting in higher crop yield.

Areas of Active Research

Improved crop responses have emphasized the study of rhizosphere bacteria indigenous to rhizospheres of cereal crops and other grasses. Rudnick et al. verified that part of the rhizosphere bacteria of a grass and sedge has the ability to rapidly form tight associations with hyphae of saprotrophic fungi and are able to grow with no other energy sources than the hyphae. They hypothesized that for those bacteria, fungal hyphae might be an important source of organic nutrients in the rhizosphere. They observed attachment to fungal hyphae within 24 h after inoculating the bacterial communities. The researchers concluded that such quick attachment suggests that mycophagous bacteria and association with the fungal hypha is of importance. Fungi perhps stimulate colonization by mycophagous bacteria using exudates, guiding mycophagous bacteria to the hyphae and secreting exudates or possibly quorum sensing molecules. The research showed that saprotrophic rhizosphere fungi may be a major source of energy for many members of the rhizosphere bacterial community. This could indicate that secondary consumption of saprotrophic fungi by rhizosphere bacteria may represent an important process in the rhizosphere. Identifying the flow of nutrients by saprotrophs can influence the current view on the functioning of rhizosphere bacterial communities and their relationship with the functioning of plants.

References

1. Corbin, B. D., Seeley, E. H., Raab, A., Feldmann, J., Miller, M. R., Torres, V. J., ... & Caprioli, R. M. (2008). Metal chelation and inhibition of bacterial growth in tissue abscesses. Science, 319(5865), 962-965.

2. Hinsinger, P., & Marschner, P. (2006). Rhizosphere—perspectives and challenges—a tribute to Lorenz Hiltner 12–17 September 2004—Munich, Germany. Plant and Soil, 283(1), vii-viii.

3. Miller, K. J., & Wood, J. M. (1996). Osmoadaptation by rhizosphere bacteria. Annual Reviews in Microbiology, 50(1), 101-136.

4. Hartmann, A., Rothballer, M., & Schmid, M. (2008). Lorenz Hiltner, a pioneer in rhizosphere microbial ecology and soil bacteriology research. Plant and Soil, 312(1-2), 7-14.

5. Gaskins, M. H., Albrecht, S. L., & Milam, J. R. (1984). Survival of root-associated bacteria in the rhizosphere. In Advances in Nitrogen Fixation Research (pp. 52–52). Springer Netherlands.

6. Nehl, D. B., Allen, S. J., & Brown, J. F. (1997). Deleterious rhizosphere bacteria: an integrating perspective. Applied Soil Ecology, 5(1), 1-20.

7. Zhang, C., Lin, Y., Tian, X., Xu, Q., Chen, Z., & Lin, W. (2017). Tobacco bacterial wilt suppression with biochar soil addition associates to improved soil physiochemical properties and increased rhizosphere bacteria abundance. Applied Soil Ecology, 112, 90-96.

8. Haney, C. H., & Ausubel, F. M. (2015). Plant microbiome blueprints. Science, 349(6250), 788-789.

9. Barea, J. M., Navarro, E., & Montoya, E. (1976). Production of Plant Growth Regulators by Rhizosphere Phosphate‐solubilizing Bacteria. Journal of Applied Microbiology, 40(2), 129-134.

10. Yang, J., Kloepper, J. W., & Ryu, C. M. (2009). Rhizosphere bacteria help plants tolerate abiotic stress. Trends in plant science, 14(1), 1-4.

11. Rudnick, M. B., Van Veen, J. A., & De Boer, W. (2015). Baiting of rhizosphere bacteria with hyphae of common soil fungi reveals a diverse group of potentially mycophagous secondary consumers. Soil Biology and Biochemistry, 88, 73-82.

Outline

I.      What is rhizosphere bacteria

Rhizosphere bacteria are microbes of different species that thrive in the environment of rhizospheres on plant roots. A rhizosphere is a plant-root interface discovered by a German agronomist named Lorenz Hiltner in 1904; this interface exists around the root of a plant and is inhabited by microbe populations in a specialized symbiotic relationship with the plant.  

II.    Three regions of the rhizosphere have been described; they include

1. The endosphere

2. The rhizoplane

3. The ectorhizosphere

III.  The rhizosphere/functions

1.  chemical gradient that holds the passage of charged particles (ions) through a semipermeable membrane of the plant root or the bacterial cell wall.

IV.    Functions of the Rhizosphere bacteria

1. solubilization of minerals/effect on plant growth of metal uptake by rhizosphere bacteria/removal of pollutants

a. Phosphorous

b. Mobilization of Zn

c. Accumulation of Se and Hg

d. Potassium solubility

e. Carbamazepine

f. Phytoremediation of arsenic

g. Nickel resistance

2. fixation of nitrogen

3. production of growth-promoting hormones

4. competitive suppression of pathogens

5. tobacco plant wilt suppression using rhizosphere bacteria

V.      Area of high research

1. improve crop responses has emphasized the study of nitrogen-fixing bacteria indigenous to rhizospheres of cereal crops and other grasses.

2. inoculation experiments frequently fail to improve rates of nitrogen fixation and are difficult to study in the field

3. researchers are still trying to find a way to control and suppress selected microorganisms and keep selected microorganisms for crop productivity by allowing certain positive symbiotic relationships to thrive; dominant microbes best suited for the plant productivity would become dominant and suppress other potential symbionts.

a. Baiting rhizosphere bacteria with hyphae

b. Genetic manipulations/gene splicing to create productive relationships

References

1. https://www.nature.com/scitable/knowledge/library/the-rhizosphere-roots-soil-and-67500617

2. Yang, J., Kloepper, J. W., & Ryu, C. M. (2009). Rhizosphere bacteria help plants tolerate abiotic stress. Trends in plant science, 14(1), 1-4.

3. Whiting, S. N., de Souza, M. P., & Terry, N. (2001). Rhizosphere bacteria mobilize Zn for hyperaccumulation by Thlaspi caerulescens. Environmental Science & Technology, 35(15), 3144-3150.

4. Barea, J. M., Navarro, E., & Montoya, E. (1976). Production of Plant Growth Regulators by Rhizosphere Phosphate‐solubilizing Bacteria. Journal of Applied Microbiology, 40(2), 129-134.

5. De Souza, M. P., Huang, C. P. A., Chee, N., & Terry, N. (1999). Rhizosphere bacteria enhance the accumulation of selenium and mercury in wetland plants. Planta, 209(2), 259-263.

6. de Souza, M. P., Chu, D., Zhao, M., Zayed, A. M., Ruzin, S. E., Schichnes, D., & Terry, N. (1999). Rhizosphere bacteria enhance selenium accumulation and volatilization by Indian mustard. Plant Physiology, 119(2), 565-574.

7. Kuffner, M., Puschenreiter, M., Wieshammer, G., Gorfer, M., & Sessitsch, A. (2008). Rhizosphere bacteria affect growth and metal uptake of heavy metal accumulating willows. Plant and Soil, 304(1-2), 35-44.

8. Miller, K. J., & Wood, J. M. (1996). Osmoadaptation by rhizosphere bacteria. Annual Reviews in Microbiology, 50(1), 101-136.

9. Nehl, D. B., Allen, S. J., & Brown, J. F. (1997). Deleterious rhizosphere bacteria: an integrating perspective. Applied Soil Ecology, 5(1), 1-20.

10.        Haney, C. H., & Ausubel, F. M. (2015). Plant microbiome blueprints. Science, 349(6250), 788-789.

11.        Hartmann, A., Rothballer, M., & Schmid, M. (2008). Lorenz Hiltner, a pioneer in rhizosphere microbial ecology and soil bacteriology research. Plant and Soil, 312(1-2), 7-14.

12.        Chanway, C. P., Turkington, R., & Holl, F. B. (1991). Ecological implications of specificity between plants and rhizosphere micro-organisms. Advances in ecological research, 21, 121-169.

13.        Hinsinger, P., & Marschner, P. (2006). Rhizosphere—perspectives and challenges—a tribute to Lorenz Hiltner 12–17 September 2004—Munich, Germany. Plant and Soil, 283(1), vii-viii.

14.        Gaskins, M. H., Albrecht, S. L., & Milam, J. R. (1984). Survival of root-associated bacteria in the rhizosphere. In Advances in Nitrogen Fixation Research (pp. 52–52). Springer Netherlands.

15.        Parmar, P., & Sindhu, S. S. (2013). Potassium solubilization by rhizosphere bacteria: influence of nutritional and environmental conditions. Journal of microbiology research, 3(1), 25-31.

16.        Rudnick, M. B., Van Veen, J. A., & De Boer, W. (2015). Baiting of rhizosphere bacteria with hyphae of common soil fungi reveals a diverse group of potentially mycophagous secondary consumers. Soil Biology and Biochemistry, 88, 73-82.

17.        Francis, I. M., Jochimsen, K. N., De Vos, P., & van Bruggen, A. H. (2014). Reclassification of rhizosphere bacteria including strains causing corky root of lettuce and proposal of Rhizorhapis suberifaciens gen. nov., comb. nov., Sphingobiummellinum sp. nov., Sphingobiumxanthum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov. International Journal of Systematic and Evolutionary Microbiology, 64(4), 1340-1350.

18.        Zhang, C., Lin, Y., Tian, X., Xu, Q., Chen, Z., & Lin, W. (2017). Tobacco bacterial wilt suppression with biochar soil addition associates to improved soil physiochemical properties and increased rhizosphere bacteria abundance. Applied Soil Ecology, 112, 90-96.

19.        Aboudrar, W., Schwartz, C., Morel, J. L., & Boularbah, A. (2013). Effect of nickel-resistant rhizosphere bacteria on the uptake of nickel by the hyperaccumulator Noccaea caerulescens under controlled conditions. Journal of soils and sediments, 13(3), 501-507.