Difference between revisions of "Julia Elledge - Bacillus pumilus"

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(Classification)
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==Classification==
 
==Classification==
  
Domain: Bacteria; Kingdom: Eubacteria
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Domain: Bacteria
 +
 
 +
Kingdom: Eubacteria
 +
 
 
Phylum: Firmicutes
 
Phylum: Firmicutes
 +
 
Class: Bacilli
 
Class: Bacilli
 +
 
Order: Bacillales
 
Order: Bacillales
 +
 
Family: Bacillaceae
 
Family: Bacillaceae
 +
 
Genus: Bacillus
 
Genus: Bacillus
 +
 
Species: B. Pumilus
 
Species: B. Pumilus
  
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==Description and Significance==
 
==Description and Significance==
Describe the appearance (colonial and cellular), possible antimicrobial activity etc. of the organism, and why the organism might be significant.
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Colonial morphology: B. pumilus colonies are opaque and off-white. They are roughly circular, but with an irregular margin, and have a slight filamentous appearance.
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Cellular morphology: B. pumilus is a gram positive rod bacterium with endospores and peritrichous flagella.
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 +
It is being evaluated for use in the commercial production of cellulase, which is an enzyme that can convert cellulolytic (plant) materials into soluble sugars or solvents. [1]
  
 
==Genome Structure==
 
==Genome Structure==
Describe the size and content of the genome. How many chromosomes?  Circular or linear?  Other interesting features?  What is known about its sequence? Include S Ribosomal sequence that you obtained from PCR and sequencing here.
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B. pumilus has a single circular chromosome. There are 3,681 protein genes and 93 RNA genes for a total of 3,704,465 nucleotides. 41% of its base pairs are G-C. [2]
  
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Forward sequence: ACGGAGCAACGCCGCGTGAGTGATGAAGGTTTTCGGAT CGTAAAGCTCTGTTGTTAGGGAAGAACAAGTGCGAGAGTAACTGCTCGCACCTTGACGGTACCTAACCAGAAAGCCACGG CTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGCAGGC GGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGAAACTTGAGTGCAGAAGAG GAGAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAACACCAGTGGCGAAGGCGACTCTCTGGTCTG TAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGC TAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGGTCGCAAGACT GAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACC AGGTCTTGACATCCTCTGACAACCCTAGAGATAGGGCTTTCCCTTCGGGGACAGAGTGACAGGTGGTGCATGGTTGTCGT CAGCTCGTGTCGTGAGATGTCATAGNCTGGTTTC
 +
 +
Reverse sequence: ACGGAGCAACGCCGCGTGAGTGATGAAGGTTTTCGGAT CGTAAAGCTCTGTTGTTAGGGAAGAACAAGTGCGAGAGTAACTGCTCGCACCTTGACGGTACCTAACCAGAAAGCCACGG CTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGCAGGC GGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGAAACTTGAGTGCAGAAGAG GAGAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAACACCAGTGGCGAAGGCGACTCTCTGGTCTG TAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGC TAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGGTCGCAAGACT GAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACC AGGTCTTGACATCCTCTGACAACCCTAGAGATAGGGCTTTCCCTTCGGGGACAGAGTGACAGGTGGTGCATGGTTGTCGT CAGCTCGTGTCGTGAGATGTCATAGNCTGGTTTC
  
 
==Cell Structure, Metabolism and Life Cycle==
 
==Cell Structure, Metabolism and Life Cycle==
Interesting features of cell structure; how it gains energy; what important molecules it produces.
+
B. pumilus is a gram positive bacterium that forms endospores. It is motile due to peritrichous flagella, and aerobic, requiring oxygen for respiration. Based on the results of the phenol red broth tests, it can ferment sucrose and glucose, but not lactose. This was confirmed with positive result for mixed acid fermentation in the MR test (with the accompanying negative VP result). There was also evidence of glucose fermentation in the TSI test. B. pumilus also tested positive for cytochrome c oxidase and catalase. It does not hydrolyze esculin in the presence of bile.
  
 +
The life cycle of B. pumilus follows that of most spore-forming Bacillus species. It consists of three phases: vegetative growth, sporulation, and germination. The vegetative growth phase occurs when there are sufficient nutrients available to the organism. It grows by asexual reproduction, with each cell dividing. When the conditions become less favorable (lack of nutrients, wrong temperature, high cell density), some of the cells will enter the sporulation phase. They divert their resources into the production of an endospore. Then, once the environmental conditions are once again favorable, the spore enters the germination phase. The spore matures into a vegetative cell, and the process repeats.
  
 
==Physiology and Pathogenesis==
 
==Physiology and Pathogenesis==
Biochemical characteristics, enzymes made, other characteristics that may be used to identify the organism; contributions to environment (if any).<br>
+
Tests for the presence of lipase and casease were negative, but B. pumilus did test positive for DNase. It does not hydrolyze starch or urea. It doesn't hydrolyze tryptophan either, and it cannot reduce sulfur. However, B. pumilus is motile. It cannot utilize citrate as a source of carbon, and it does not reduce nitrate. B. pumilus also does not produce arginine, lysine, or ornithine decarboxylase, nor does it produce phenylalanine deaminase.
If relevant, how does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.<br><br>
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 +
Being gram positive, B. pumilus does not grow on Eosin Methylene Blue agar, Hektoen Enteric agar, or MacConkey agar. It cannot decarboxylate arginine, lysine, or ornithine, and it does not deaminate the amino acid phenylalanine.
 +
 
 +
B. pumilus does not grow on phenylethyl alcohol agar, and it is not salt tolerant, so it will not grow on a Mannitol Salt agar or in a 6.5% NaCl broth. It does not hemolyze red blood cells.
 +
 
 +
Infection of B. pumilus in humans is very rare, but it is possible. Its presence in rice has cause three cases of food poisoning. [3] The symptoms included dizzyness, chills, stomach cramps, and diarrhea. There have also been three reported cases of cutaneous infection. [4] The lesions that developed were similar to those caused by a cutaneous anthrax infection.
 +
 
 +
In testing, B. pumilus showed no susceptibility to a either Bacitracin, Optochin, Nafcillin, or Oxacillin.  However, it was susceptible to novobiocin. Its growth was inhibited by bleach, clove oil, and Lysol, but not lavendar oil.
 +
 
 +
B. pumilus can inhibit nematodes and fungal diseases once it colonizes a plant's root system. In fact, strain GB34 is used as an active ingredient in agricultural fungicides, so it has a significant environmental impact. [1]
  
 
==References==
 
==References==
[Sample reference] [http://ijs.sgmjournals.org/cgi/reprint/50/2/489 Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "''Palaeococcus ferrophilus'' gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". ''International Journal of Systematic and Evolutionary Microbiology''. 2000. Volume 50. p. 489-500.]
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1. United States. National Center for Biotechnology Information. N.p., n.d. Bacillus pumilus: A ubiquitous soil organism. Web. 29 April 2016.  http://www.ncbi.nlm.nih.gov/genome/?term=bacillus%20pumilus
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 +
2. Bacillus pumilus SAFR-032. N.p., n.d. Web. 27 April 2016. http://www.genome.jp/kegg-bin/show_organism?org=bpu
 +
 
 +
3. From, C., Hormazabal, V., and Granum, P. “Food poisoning associated with pumilacidin-producing Bacillus pumilus in rice”. International Journal of Food Microbiology. 2007. Volume 115. p. 319-324.
 +
 
 +
4. Tena, D., Martinez-Torres, J., Perez-Pomata, M., Saez-Nieto, J., Rubio, V., and Bisquert, J. “Cutaneous infection due to Bacillus pumilus: Report of 3 cases”. Clinical Infectious Diseases. 2007. Volume 44. P. e40-2.
  
 
==Author==
 
==Author==
Page authored by _____, student of Prof. Kristine Hollingsworth at Austin Community College.
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Page authored by Julia Elledge, student of Prof. Kristine Hollingsworth at Austin Community College.
  
 
<!-- Do not remove this line-->[[Category:Pages edited by students of Kristine Hollingsworth at Austin Community College]]
 
<!-- Do not remove this line-->[[Category:Pages edited by students of Kristine Hollingsworth at Austin Community College]]

Latest revision as of 17:36, 6 May 2016

This student page has not been curated.

Classification

Domain: Bacteria

Kingdom: Eubacteria

Phylum: Firmicutes

Class: Bacilli

Order: Bacillales

Family: Bacillaceae

Genus: Bacillus

Species: B. Pumilus

Species

NCBI: Taxonomy

Bacillus pumilus

Habitat Information

B. pumilus can be found in a wide variety of soils, plants, and surfaces. My particular sample was found in an area of Lewisville soils and Urban land, with 0 to 2 percent slopes. The temperature and humidity when the sample was taken were 73º F and 22%. Pressure was 30.03 in. and the solar radiation was at 17.55 MJm2. There had been no rainfall in the previous 24 hours. The specific location was a grassy area between my apartment building and the parking lot. The address is 2703 Manor Rd, Austin, TX, 78722.

Description and Significance

Colonial morphology: B. pumilus colonies are opaque and off-white. They are roughly circular, but with an irregular margin, and have a slight filamentous appearance.

Cellular morphology: B. pumilus is a gram positive rod bacterium with endospores and peritrichous flagella.

It is being evaluated for use in the commercial production of cellulase, which is an enzyme that can convert cellulolytic (plant) materials into soluble sugars or solvents. [1]

Genome Structure

B. pumilus has a single circular chromosome. There are 3,681 protein genes and 93 RNA genes for a total of 3,704,465 nucleotides. 41% of its base pairs are G-C. [2]

Forward sequence: ACGGAGCAACGCCGCGTGAGTGATGAAGGTTTTCGGAT CGTAAAGCTCTGTTGTTAGGGAAGAACAAGTGCGAGAGTAACTGCTCGCACCTTGACGGTACCTAACCAGAAAGCCACGG CTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGCAGGC GGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGAAACTTGAGTGCAGAAGAG GAGAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAACACCAGTGGCGAAGGCGACTCTCTGGTCTG TAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGC TAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGGTCGCAAGACT GAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACC AGGTCTTGACATCCTCTGACAACCCTAGAGATAGGGCTTTCCCTTCGGGGACAGAGTGACAGGTGGTGCATGGTTGTCGT CAGCTCGTGTCGTGAGATGTCATAGNCTGGTTTC

Reverse sequence: ACGGAGCAACGCCGCGTGAGTGATGAAGGTTTTCGGAT CGTAAAGCTCTGTTGTTAGGGAAGAACAAGTGCGAGAGTAACTGCTCGCACCTTGACGGTACCTAACCAGAAAGCCACGG CTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGCAGGC GGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGAAACTTGAGTGCAGAAGAG GAGAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAACACCAGTGGCGAAGGCGACTCTCTGGTCTG TAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGC TAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGGTCGCAAGACT GAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACC AGGTCTTGACATCCTCTGACAACCCTAGAGATAGGGCTTTCCCTTCGGGGACAGAGTGACAGGTGGTGCATGGTTGTCGT CAGCTCGTGTCGTGAGATGTCATAGNCTGGTTTC

Cell Structure, Metabolism and Life Cycle

B. pumilus is a gram positive bacterium that forms endospores. It is motile due to peritrichous flagella, and aerobic, requiring oxygen for respiration. Based on the results of the phenol red broth tests, it can ferment sucrose and glucose, but not lactose. This was confirmed with positive result for mixed acid fermentation in the MR test (with the accompanying negative VP result). There was also evidence of glucose fermentation in the TSI test. B. pumilus also tested positive for cytochrome c oxidase and catalase. It does not hydrolyze esculin in the presence of bile.

The life cycle of B. pumilus follows that of most spore-forming Bacillus species. It consists of three phases: vegetative growth, sporulation, and germination. The vegetative growth phase occurs when there are sufficient nutrients available to the organism. It grows by asexual reproduction, with each cell dividing. When the conditions become less favorable (lack of nutrients, wrong temperature, high cell density), some of the cells will enter the sporulation phase. They divert their resources into the production of an endospore. Then, once the environmental conditions are once again favorable, the spore enters the germination phase. The spore matures into a vegetative cell, and the process repeats.

Physiology and Pathogenesis

Tests for the presence of lipase and casease were negative, but B. pumilus did test positive for DNase. It does not hydrolyze starch or urea. It doesn't hydrolyze tryptophan either, and it cannot reduce sulfur. However, B. pumilus is motile. It cannot utilize citrate as a source of carbon, and it does not reduce nitrate. B. pumilus also does not produce arginine, lysine, or ornithine decarboxylase, nor does it produce phenylalanine deaminase.

Being gram positive, B. pumilus does not grow on Eosin Methylene Blue agar, Hektoen Enteric agar, or MacConkey agar. It cannot decarboxylate arginine, lysine, or ornithine, and it does not deaminate the amino acid phenylalanine.

B. pumilus does not grow on phenylethyl alcohol agar, and it is not salt tolerant, so it will not grow on a Mannitol Salt agar or in a 6.5% NaCl broth. It does not hemolyze red blood cells.

Infection of B. pumilus in humans is very rare, but it is possible. Its presence in rice has cause three cases of food poisoning. [3] The symptoms included dizzyness, chills, stomach cramps, and diarrhea. There have also been three reported cases of cutaneous infection. [4] The lesions that developed were similar to those caused by a cutaneous anthrax infection.

In testing, B. pumilus showed no susceptibility to a either Bacitracin, Optochin, Nafcillin, or Oxacillin. However, it was susceptible to novobiocin. Its growth was inhibited by bleach, clove oil, and Lysol, but not lavendar oil.

B. pumilus can inhibit nematodes and fungal diseases once it colonizes a plant's root system. In fact, strain GB34 is used as an active ingredient in agricultural fungicides, so it has a significant environmental impact. [1]

References

1. United States. National Center for Biotechnology Information. N.p., n.d. Bacillus pumilus: A ubiquitous soil organism. Web. 29 April 2016. http://www.ncbi.nlm.nih.gov/genome/?term=bacillus%20pumilus

2. Bacillus pumilus SAFR-032. N.p., n.d. Web. 27 April 2016. http://www.genome.jp/kegg-bin/show_organism?org=bpu

3. From, C., Hormazabal, V., and Granum, P. “Food poisoning associated with pumilacidin-producing Bacillus pumilus in rice”. International Journal of Food Microbiology. 2007. Volume 115. p. 319-324.

4. Tena, D., Martinez-Torres, J., Perez-Pomata, M., Saez-Nieto, J., Rubio, V., and Bisquert, J. “Cutaneous infection due to Bacillus pumilus: Report of 3 cases”. Clinical Infectious Diseases. 2007. Volume 44. P. e40-2.

Author

Page authored by Julia Elledge, student of Prof. Kristine Hollingsworth at Austin Community College.