Rhizobium etli
A Microbial Biorealm page on the genus Rhizobium etli
Classification
Higher order taxa
Bacteria (Domain); Proteobacteria (Phylum); Alphaproteobacteria (Class); Rhizobiales (Order); Rhizobiaceae (family)
Species
Rhizobium Etli
Description and significance
Rhizobium Etli is one of the many soil-living bacteria able to live in conditions of nitrogen limitation due to its distinctive ability to settle onto root nodules of legumes. Like other rhizobia, it is characterized as aerobic,gram negative and able to form symbiotic relationship with legumes. (1, 2) In specific, rhizobium etli is the predominant bacteria found in legumes such as the common bean, P. Vulgaris. (3)
Rhizobium Etli is found world wide and discovered as early as 16th century. Due to its early existence, attempts to identify origin of the species was performed by identifying its molecular marker. This was performed by searching a diversity within different Rhizobium etli species from P. Vulgaris. Isolation of the rhizobia strain from the nodule of the root of the plant was removed, sterilized with ethanol and hydrogen peroxides, and grown on YEM-Congo red agar medium. Isolation and identification was done by 16S rRNA-encoding DNA-RFLP analysis. The analysis showed most to be from species Rhizobium etli. The nodC gene was identified and isolated to be used as a molecular marker. Results from the experiment showed Rhizobium etli is not only found in the America’s but also identified in parts of Africa, Asia, and Europe. (3)
Rhizobium Etli is important enough to have its genome sequence because of its unique ability to form symbiotic relationship with legumes. The detail in which it performs this are in the following two sections (genome structure, cell structure and metabolism). To give a general idea of its importance, the host benefits by being provided nitrogen in the form of ammonia from the bacteria, while the bacteria is provided carbon and nutrients from the host. (2)
Genome structure
Rhizobium Etli has a complete genome sequence of 6,530,228 base pairs. It contains 4,381,608 circular chromosomes averaging 61.27% GC content. (5)
Six plasmids: p42a, p42b, p42c, p42d, p42e, and p42f, contain the complete metabolic pathways. The p42a and p42d plasmids is abnormal as it contains a lower GC value of 58% as compared to the other four plasmids at 61.5%. Also, the complete genome sequence reveals identical of more then 100 nucleotide repeats which are located in plasmid p42a and p42d. The plasmids appear to have been acquired at some point of divergence which is unknown. (5)
Its plasmids also contain Rep ABC replicator which allows stability with distinct initiators and origins of replication. An advantage to the separation of genomes is faster duplication to replicate its genome. (5)
In addition, rhizobium etli contains the most abundant number of replicons when comparing to other known nitrogen-fixing bacteria. Its protein-coding genes are classified as COGs, and are indicated to be overrepresented. Carbohydrate transport and metabolism, amino acid metabolism and transcription are several of the COGs overrepresented. (5)
As for its transcriptional regulation, 23 sigma factors are found. Though most of the roles are unknown, they are thought to required for gene expression under the different environmental conditions faced. (5) 536 transcriptional factors are found, and 331 which are one-component regulators. The majority (65%) of the one component regulators are near ABC transporters or permease genes which may activate in response to the environmental stress in the soil.(5)
The unique genomic structure, special feature of the plasmids, and overrepresentation of certain COGs and transcription regulation contribute to the genomic plasticity. All of the factors mentioned, contribute and are vital for its symbiotic lifestyle in the soil. (5)
Cell structure and metabolism
3.1 Quorum sensing
An interesting feature of rhizobium etli is its ability to swarm as a mean of motility and colonization onto plant roots. The swarming is produced by flagella movement located in its extracellular slime layer. The organism contains a quorum sensing genes which binds a protein called N-acylhomoserine lactones. Its function is responsible for swarming, promoting surface colonization, and the ability to sense areas of low oxygen. Since the microbe is aerobic, sensing areas of low oxygen is an important component to its survival. (6)
3.2 Metabolic Pathways
Though the exact number of pathways is not known, 263 metabolic pathways composing of 1,340 enzymatic reactions are thought to exit. A unique ability of rhizobia is its capability of switching from an ammonium assimilation metabolism to nitrogen fixation when it undergoes symbiosomes. The end product from its metabolism is used as a precursor by the plant. In exchange, the microbe receives nutrients and energy from the plant. (7) Pathways such as glycerol metabolism, thiamine biosynthesis, cobalamine biosynthesis, and the incomplete denitrification pathway are located in the plasmids. Also, it contains high number of fermentation pathways, catabolism and anabolism pathways of amino acids, and polysaccharides. These pathway are important for the metabolism of the products it receives from the host plant. (6)
Ecology
Rhizobium Etli is a soil bacteria which interacts with the root of legumes. The microbe forms a specialized structure called a nodule in the plants root, and differentiates into a bacteroid. The plants cell membrane surrounds the bacteroids in the nodules, to form what is called a peribacteroidal membrane. (6) At this point, the free living microbe has moved from the soil to a low-pH environment which contains certain carbon and nitrogenous, as well as oxidative stress. (2) In the plants cells, it adapts by losing its ability to undergo cell division, and also by switching its metabolism focused on nitrogen fixation. (6) The adaptation is fast and is critical to allowing the organism to have its niche to colonize on the plant of roots. (2) The interaction between the two organisms to form the bacteroid, peribacteroidal membrane, and peribacterial space is a process called symbiosomes. (6)
Pathology
Rhizobium etli is not known to be a pathogen to humans, animals, or plants. Instead, it forms a symbiotic relationship by binding the root of legumous plants. In the plants cells, it forms specialized structures called nodules in the plants root and differentiate into bacteroids which fix nitrogen. The plant is not harmed, but benefits from the presence of the microbe. (7)
Application to Biotechnology
In agriculture, crop rotation and soil fumigation is performed each year to prevent fungal and bacterial diseases. (4) Crop rotation is a tool in which plant species are not allowed to be at the same location year after year. Rotating the crops allows management of soil pathogens which prevents many plants to be infected. (8) While natural selection has allowed many crops to have genetic resistance for pathogens above ground, there is few genetic resistance for soil pathogens. Knowledge of rhizobium etli has allowed research to utilize its niche of binding onto to roots to provide plants with antibiotic resistance. Bioengineering has been successful in producing phenazine-producing bacteria which may one day be used as a biocontrol agent.(8)
Current Research
8.1 Sigma 70 factor
A study has been done to determine the sigma 70 factor of Rhizobium etli. The sigma 70 factor is the main factor which controls genes involved with RNA polymeriase. The sigma 70 factor was determined to be promiscuous as it was able to recognize promoters of E. Coli, but not vice versa. The promiscuous nature of the sigma 70 factor is thought to result from the biological diversity rhizobium etli faces. A more promiscuous factor makes it easier to undergo beneficial lateral gene transfer useful for adapting to different environmental conditions. (9)
8.2 Phenazine producing bacteria
In agriculture, crop rotation and soil fumigation is performed each year to prevent fungal and bacterial diseases. (4) Crop rotation is a tool in which plant species are not allowed to be at the same location year after year. This tool allows management of soil pathogens. (8) While natural selection has allowed many crops to have genetic resistance for pathogens above ground, there is few genetic resistance for soil pathogens. Knowledge of rhizobium etli has allowed research to utilize its niche to provide plants with antibiotic resistance. (8) Bioengineering has been successful in producing phenazine-producing bacteria. Drawbacks exist though, as the antibiotic-producing bacteria cannot fix nitrogen nor inhibit its bacterial growth. These drawbacks causes the wildtype to outcompete the bioengineered bacteria. (8)
8.3 Lipoprotein Polysaccharide
Extracelullar polysaccharides, capsular polysaccharides, and lipopolysaccharides make up the outer surface of Rhizobium Etli. The lipopolysaccharide (LPS) is composed of three regions: lipid A, core, and O-antigen polysaccharide. The article proves that the presence and number of O-antigen in the LPS is necessary for invasion and formation of root nodules on plants such as P. Vulgaris. Follow up research is to be performed to determine the role the plasma membranes plays for survival of the bacteroids. The interaction between the LPS, and bacteroid may give increased knowledge of the molecular basis and inceased sensitify of Rhizobium Etli. (10)
8.4 Outer membrane of Rhizobium Etli
Extracelullar polysaccharides, capsular polysaccharides, and lipopolysaccharides make up the outer surface of Rhizobium Etli. The lipopolysaccharide (LPS) is composed of three regions: lipid A, core, and O-antigen polysaccharide. The article proves that the presence and number of O-antigen in the LPS is necessary for invasion and formation of root nodules on plants such as P. Vulgaris. Since Rhizobium Etli interacts with the cell surface of roots, it is exposed to cationic peptides. The plasma membrane is found to provide protection to the bacteroid during such interaction, allowing survival through structural changes. Follow up research is to be performed to determine the role the plasma membranes plays for survival of the bacteroids. The interaction between the LPS, and bacteroid may give increased knowledge of the molecular basis and increased sensitivity to cationic peptides. (10)
References
Edited by student of Rachel Larsen
