Bacillus subtilis

A Microbial Biorealm page on the genus Bacillus subtilis

Classification

Higher order taxa

Domain: Bacteria, phylum: Firmicutes, class: Bacilli, order: Bacillales, family: Bacillaceae (Entrez Genome Project)

Genus

Bacillus subtilis

NCBI: Taxonomy

Description and significance

Originally named Vibrio subtilis in 1835, this organism was renamed Bacillus subtilis in 1872. Other names for this bacteria also include Bacillus uniflagellatus, Bacillus globigii, and Bacillus natto. Bacillus subtilis bacteria were one of the first bacteria to be studied. These bacteria are a good model for cellular development and differentiation (Entrez Genome Project).

Bacillus subtilis cells are rod-shaped, Gram-positive bacteria that are naturally found in soil and vegetation. Bacillus subtilis grow in the mesophilic temperature range. The optimal temperature is 25-35 degrees Celsius (Entrez Genome Project). Stress and starvation is common in this environment, therefore, Bacillus subtilis has evolved a set of strategies that allow survival under these harsh conditions. One strategy, for example, is the formation of stress-resistant endospores. Another strategy is the uptake of external DNA, which allow the bacteria to adapt by recombination. However, these strategies are time-consuming. Bacillus subtilis can also gain protection more quickly against many stress situations such as acidic, alkaline, osmotic, or oxidative conditions, and heat or ethanol. The alternative sigma factor ςB is a global regulator of stress response. Heat, acid, or ethanol and glucose or phosphate starvation are all stimuli that activate ςB (Bandow 2002).

Genome structure

A total of 4,100 genes were identified in Bacillus subtilis, all of which are protein-coding genes (Kunst 1997). Only one DNA molecule is present in these cells. Bacillus subtilis has one circular chromosome. The total size of all the DNA is 4,214,814 bp (4.2 Mbp) (TIGR CMR). 53% of the protein-coding genes are only seen once, while 25% of the genome relates to families of genes that have undergone gene duplication (Kunst 1997).

A great portion of the genome corresponds to carbon source applications (Kunst 1997). 192 of the 4,100 genes are considered indispensable, and an additional 79 are thought to be essential. Most of the essential genes are involved in metabolism. Half of the essential genes are responsible for processing information, one-fifth of them are responsible for cell wall synthesis, cell division and shape, and one-tenth of them were responsible for the energetics of the cell. The essential genes that code for functions that are not known are 4% (Kobayashi 2003). Bacillus subtilis bacteria are capable of secreting antibiotics in great numbers to the exterior of the cell (Ara 2007). Five signal peptidase genes were found to be important for this secretion function. Many of Bacillus subtilis cells' genes are responsible for antibiotic synthesis (Kunst 1997).

Cell structure and metabolism

Bacillus subtilis are rod-shaped bacteria that are Gram-positive (Perez 2000). The cell wall is a rigid structure outside the cell. It is composed of peptidoglycan, which is a polymer of sugars and amino acids. The peptidoglycan that is found in bacteria is known as murein. Other constituents that extend from the murein are teichoic acids, lipoteichoic acids, and proteins. The cell wall forms the barrier between the environment and the bacterial cell. It is also responsible for maintaining the shape of the cell and withstanding the cell's high internal turgor pressure (Schaechter 2006).

Bacillus subtilis is a model organism for studying endospore formation in bacteria. Endospores in Bacillus subtilis bacteria are mostly formed in the tips of protuberances extending from liquid surface pellicles (Schaechter 2006). Depletion of carbon, nitrogen, or phosphorous causes the process of sporulation to begin, however, the process needs to start before the entire exhaustion of nutrients (Perez 2000). Otherwise, the spore formation cannot be completed due to the fact that the nutrients are too low for the energy-requiring sporulation process. This allows the cells to avoid being stuck in a vulnerable position.

The formation of the endospore occurs in several stages, denoted 0 through VI. Sporulation occurs in the following fashion. First the nucleoid lengthens, becoming an axial filament. Then, the cell forms a polar septum, one-fourth of the cell length from one end, and begins to divide. The smaller product of this division is called the forespore and the larger product is called the mother cell (Perez 2000). The mother cell is responsible for nourishing the newly formed spore. When the septum forms, 30% of the chromosome is already on the forespore side (Schaechter 2006). The remaining 70% of the chromosome enters the forespore in a fashion similar to DNA transfer during conjugation; it is pumped by a protein called spoIIIE. The mother cell then engulfs the forespore by acting like a phagocyte. This causes the forespore to have two cytoplasmic membranes with a thick murein layer, namely the cortex, between them. A protein spore coat and an exosporium, a membranous layer, form outside of the forespore membranes. At this time, the forespore undergoes internal changes. Lastly, the forespore leaves the mother cell upon lysis of the mother cell (perez 2000). A mature endospore has no metabolic activity; it is inert. It does not have any ATP or reduced pyridine nucleotides. The interior of the endospore, the core, is very dry and resistant to moisture (Schaechter 2006).

Bacillus subtilis bacteria use their flagella for a swarming motility. This motility occurs on surfaces, for example on agar plates, rather than in liquids. Bacillus subtilis are arranged in singles or chains. Cells arranged next to each other can only swarm together, not individually. These arrangements of cells are called 'rafts'. In order for Bacillus subtilis bacteria to swarm, they need to secrete a slime layer which includes surfactin, a surface tension-reducing lipopeptide, as one of its components (Schaechter 2006).

Bacillus subtilis bacteria have been considered strictly aerobic, meaning that they require oxygen to grow and they cannot undergo fermentation, however, recent studies show that they can indeed grow in anaerobic conditions. The bacteria can make ATP in anaerobic conditions via fermentation as well as nitrate ammonification. Bacillus subtilis can use nitrite or nitrate as a terminal acceptor of electrons. Bacillus subtilis contains two unique nitrate reductases. One is used for nitrate nitrogen assimilation and the other is used for nitrate respiration. However, there is only one nitrite reductase that serves both purposes. Nitrate reductase reduces nitrate to nitrite in nitrate respiration, which is then reduced to ammonia by nitrite reductase. Bacillus subtilis is different from other anaerobes in that it undergoes fermentation without external acceptors of electrons (Nakano 1998). During fermentation, the regeneration of NAD+ is chiefly mediated by lactate dehydrogenase, which is found in the cytoplasm. Lactate dehydrogenase converts pyruvate to lactate (Marino 2001).

Bacillus subtilis contain catalase Kata and MrgA, an enzyme that is responsible in the catalysis of the decomposition of hydrogen peroxide to water and oxygen, and superoxide dismutase, an enzyme that catalyzes the breakdown of superoxide into oxygen and hydrogen peroxide (Bandow 2002).

Ecology

Bacillus subtilis bacteria form rough biofilms, which are dense organism communities, at the air and liquid interface. Bacillus subtilis biofilms are beneficial. They allow for the control of plant pathogen infections.

Bacillus subtilis biofilms found in the rhizosphere of plants promote growth. Bacillus subtilis strains can act as biofungicides and antibacterial agents.

Pathology

Bacillus subtilis bacteria are non-pathogenic. They can contaminate food, however, they seldom result in food poisoning. They are used on plants as a fungicide. There are also used on agricultural seeds, such as vegetable and soybean seeds, as a fungicide. The bacteria, colonized on root systems, compete with disease causing fungal organisms. Bacillus subtilis bacteria's use as a fungicide fortunately does not affect humans (EMBL EBI). Some strains of Bacillus subtilis cause rots in potatoes. It grows in food that is non-acidic, and can cause ropiness in bread that is spoiled (Todar). Some strains related to Bacillus subtilis are capable of producing toxins for insects. Those strains can also be used for protecting crops as well. Bacillus thuringiensis, for example, is another bacterium in the same genus that is used for insect control (EMBL EBI).

Some Bacillus species can cause food poisoning, such as Bacillus cereus and Bacillus licheniformis. Bacillus cereus can result in two different kinds of intoxications. It can either cause nausea, vomiting, and abdominal cramps for 1-6 hours, or diarrhea and abdominal cramps for 8-16 hours. The food poisoning usually occurs from eating rice that is contaminated with Bacillus cereus (EMBL EBI).

Some Bacillus organisms can cause more severe illnesses. Bacillus anthracis, for example, causes Anthrax. It was the first bacterial organism that was known to cause disease in humans. Bacillus anthracis spores can survive for very long periods of time. Anthrax is very rare in humans, however it is more common in animals. The disease often begins with a very high fever and chest pain, and can be fatal if untreated (EMBL EBI).

References

[1] Ara, K., et al. "Bacillus minimum genome factory: effective utilization of microbial genome information." Biotechnol. Appl. Biochem.. 2007 March; 46(Pt 3):169-78.

[2] Bandow, J.E., H. Brötz, M. Hecker. "Bacillus subtilis Tolerance of Moderate Concentrations of Rifampin Involves the ςB-Dependent General and Multiple Stress Response". Journal of Bacteriology. 2002 January; 184(2): 459–467.

[3] Entrez Genome Project, NCBI

[4] European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL EBI).

[5] Kobayashi, K., et al. "Essential Bacillus subtilis genes". Proc Natl Acad Sci U S A. 2003 April 15; 100(8): 4678–4683.

[6] Kunst, F., et al. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis". Nature. 1997 November; 390, 249-256.

[7] Marino, M., et al. "Modulation of Anaerobic Energy Metabolism of Bacillus subtilis by arfM (ywiD)". J Bacteriol. 2001 December; 183(23): 6815–6821.

[8] Morikawa, M. "Beneficial Biofilm Formation by Industrial Bacteria Bacillus subtilis and Related Species". Journal of Bioscience and Bioengineering. 2006; Vol.101, No.1, 1-8.

[9] Nakano, M.M., P. Zuber. "Anaerobic Growth of a 'Strict Aerobe' (Bacillus subtilis)". Annual Review of Microbiology. 1998 October; Vol. 52: 165-190.

[10] Perez, A.R., A. Abanes-De Mello, K. Pogliano. "SpoIIB Localizes to Active Sites of Septal Biogenesis and Spatially Regulates Septal Thinning during Engulfment in Bacillus subtilis". Journal of Bacteriology. 2000 February; 182(4): 1096–1108.

Schaechter, M., J.L. Ingraham, F.C. Neidhardt. Microbe. (ASM Press, Washington, DC, 2006).

[11] The Institute for Genome Research, Comprehensive Microbial Resource (TIGR CMR).

[12] Todar, K. "Todar's Online Textbook of Bacteriology".

Edited by Margo Ucar, student of Rachel Larsen and Kit Pogliano