Soil Sample Research Project: Difference between revisions

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Family: Bacillaceae
Family: Bacillaceae
Genus: Bacillus
Genus: Bacillus
Species: B. safensis
Species: B. safensis  
 
[3]




Line 29: Line 31:
==Description and Significance==
==Description and Significance==


Bacillus safensis is a gram-positive, aerobic, mesophilic, and rod bacterium. It is aerobic and highly resistant to UV and gamma rays. It is also a spore forming chemoheterotroph. It was first discovered in California and Florida on spacecraft and so is believed to have been brought to the USA from Mars. There are numerous strains of this bacterium, everyone belonging to the Firmicutes phylum of Bacteria. This organism is significant because it can tell us a bit about other planets and also how the bacteria spreads. It is also resistant to UV rays, gamma rays and is highly salt resistant, therefore it makes for a great plant growth-promoting rhizobacteria.
Bacillus safensis is a gram-positive, aerobic, mesophilic, and rod bacterium. It is aerobic and highly resistant to UV and gamma rays. It is also a spore forming chemoheterotroph. It was first discovered in California and Florida on spacecraft and so is believed to have been brought to the USA from Mars. There are numerous strains of this bacterium, everyone belonging to the Firmicutes phylum of Bacteria. This organism is significant because it can tell us a bit about other planets and also how the bacteria spreads. It is also resistant to UV rays, gamma rays and is highly salt resistant, therefore it makes for a great plant growth-promoting rhizobacteria. [1][2]


Cell shape: rod. Cell size: ranges from 0.5-0.7 μm in diameter and 1.0-1.2 μm in length.
Cell shape: rod. Cell size: ranges from 0.5-0.7 μm in diameter and 1.0-1.2 μm in length.
Cell movement: motile, and use polar flagella for locomotion.  
Cell movement: motile, and use polar flagella for locomotion. [1]


Colony characteristics: dull white, undulate round, non-luminescent with irregular borders.
Colony characteristics: dull white, undulate round, non-luminescent with irregular borders.
Growth: mesophillic, as they can grow in temperatures ranging between 10-50 °C.
Growth: mesophillic, as they can grow in temperatures ranging between 10-50 °C.  
Salt tolerance: prefers 0-10% salt, and a pH of 4-8.
Salt tolerance: prefers 0-10% salt, and a pH of 4-8.
Resistances: produce spores that are resistant to hydrogen peroxide and UV radiation.
Resistances: produce spores that are resistant to hydrogen peroxide and UV radiation. [1][2]


Bacillus safensis is sensitive to the antibiotic Optichen. Optichen is most commonly used to rule out Streptococcus pneumoniae and not commonly used for bacillus safensis.
Bacillus safensis is sensitive to the antibiotic Optichen. Optichen is most commonly used to rule out Streptococcus pneumoniae and not commonly used for bacillus safensis. [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.
Bacillus safensis is a circular chromosome of 3.68 Mb, with approximately 3928 protein coding sequences and 39 contigs/overlapping DNA fragments greater than 200 base pairs in size. The genome also displays 73 tRNA genes. The strain FO-036b shows a guanine-cytosine content of 41.0-41.4 mol%.[1][2]
 
Bacillus safensis is a circular chromosome of 3.68 Mb, with approximately 3928 protein coding sequences and 39 contigs/overlapping DNA fragments greater than 200 base pairs in size. The genome also displays 73 tRNA genes. The strain FO-036b shows a guanine-cytosine content of 41.0-41.4 mol%.


Sequence 1
Sequence 1
Line 50: Line 50:
5' bases trimmed: 18
5' bases trimmed: 18
3' bases trimmed: 4
3' bases trimmed: 4
Max score 1266, 98% query cover, 99% identification
Max score 1266, 98% query cover 100% identification
CACGCCGCGTGAGTGATGAAGGTTTTCG
GATCNTAAAGCTCTGTTGTTAGGGAAGAACAAGTACGAGAGTAACTGCTCGTACCTTGACGGTACCTAACCAGAAAGCCA
CGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGCA
GGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAAGGTCATTGGAAACTGGGGAACTTGAGTGCAGAA
GAGGAGAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAACACCAGTGGCGAAGGCGACTCTCTGGT
CTGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAG
TGCTAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGGTCGCAAG
ACTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTT
ACCAGGTCTTGACATCCTCTGACAACCCTAGAGATAGGGCTTTCCCTTCGGGGACAGAGTGACAGGTGGTGCATGGTTGT
CGTCAGCTCGTGCCGTGAGATGTCATAGC
 


Sequence 2
Sequence 2
Line 56: Line 67:
5' bases trimmed: 15
5' bases trimmed: 15
3' bases trimmed: 11
3' bases trimmed: 11
Max score 1256, 100% query cover, 99% identificiation
Max score 1256, 100% query cover, 99% identification
GAAGGGAAAGCCCTATCTCTAGGGTTGTCAGAGGA
TGTCAAGACCTGGTAAGGTTCTTCGCGTTGCTTCGAATTAAACCACATGCTCCACCGCTTGTGCGGGCCCCCGTCAATTC
CTTTGAGTTTCAGTCTTGCGACCGTACTCCCCAGGCGGAGTGCTTAATGCGTTAGCTGCAGCACTAAGGGGCGGAAACCC
CCTAACACTTAGCACTCATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTCGCTCCCCACGCTTTCGCTCCTC
AGCGTCAGTTACAGACCAGAGAGTCGCCTTCGCCACTGGTGTTCCTCCACATCTCTACGCATTTCACCGCTACACGTGGA
ATTCCACTCTCCTCTTCTGCACTCAAGTTCCCCAGTTTCCAATGACCTTCCCCGGTTGAGCCGGGGGCTTTCACATCAGA
CTTAAGAAACCGCCTGCGAGCCCTTTACGCCCAATAATTCCGGACAACGCTTGCCACCTACGTATTACCGCGGCTGCTGG
CACGTAGTTAGCCGTGGCTTTCTGGTTAGGTACCGTCAAGGTACGAGCAGTTACTCTCGTACTTGTTCTTCCCTAACAAC
AGAGCTTTACGATCCGAAAACCTTCATCACTCACGCGGCGTTGCTCCGTCAGACTTTCGTCCATTGCGGAAGATTCCCTA


==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.


Growth: mesophillic, as they can grow in temperatures ranging between 10-50 °C.
Growth: mesophillic, as they can grow in temperatures ranging between 10-50 °C.
Salt tolerance: prefers 0-10% salt, and a pH of 4-8.
Salt tolerance: prefers 0-10% salt, and a pH of 4-8.
Resistances: produce spores that are resistant to hydrogen peroxide and UV radiation.
Resistances: produce spores that are resistant to hydrogen peroxide and UV radiation. [1][2]


Positive for oxidase and catalase, Vogues-Proskauer  
Positive for oxidase and catalase, Vogues-Proskauer  
Negative for trypsin, mannitol, ed, but H2S, indole, amylase, agarase, lecithinase, DNase, urease, leucine arylamidase, cystine arylamidase, valine arylamidase, trypsin, α-galactosidase, N-acetyl-β-glucosamidase, α-fucosidase, tryptophan deaminase, phenylalanine deaminase, arginine dihydrolase, lysine decarboxylase and ornithine decarboxylase. Cells do not reduce nitrate, but do hydrolyse gelatin, aesculin and RNA. Negative for gas production from D-glucose. Acid is produced from D-glucose, glycerol, L-arabinose, ribose, D-xylose, galactose
Negative for trypsin, mannitol, indole, amylase, DNase, urease, trypsin, tryptophan deaminase, phenylalanine deaminase, arginine dihydrolase, lysine decarboxylase and ornithine decarboxylase. Cells do not reduce nitrate, but do hydrolyse gelatin, aesculin and RNA. Negative for gas production from D-glucose. Acid is produced from D-glucose, glycerol, L-arabinose, ribose, D-xylose, galactose [2]


Strain VK also contains genes that encode for 1-aminocyclopropane-1-carboxylate deaminase enzyme which enables the plant to tolerate salt, heavy metals, and polyaromatic hydrocarbons. Because it is so tolerant, Bacillus safensis VK is a powerful plant hormone producer.
Strain VK also contains genes that encode for 1-aminocyclopropane-1-carboxylate deaminase enzyme which enables the plant to tolerate salt, heavy metals, and polyaromatic hydrocarbons. Because it is so tolerant, Bacillus safensis VK is a powerful plant hormone producer. [2]


==Physiology and Pathogenesis==
Bacillus safensis bacteria are non-pathogenic and are usually more helpful than harmful. The downside they present is that they can contaminate clean rooms (like NASA), where they can confuse test results. Certain strains are used on plants as way to stimulate root growth. Others are used to digest lipase. [2]
Biochemical characteristics, enzymes made, other characteristics that may be used to identify the organism; contributions to environment (if any).<br>
If relevant, how does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.<br><br>


Because some strains of Bacillus safensis are resistant to UV rays, gamma rays and is highly salt resistant, it makes for a great plant growth-promoting rhizobacteria. This is very important in agriculture and crop health. Rhizobacteris is found on the root of the cumin plant.
Because some strains of Bacillus safensis are resistant to UV rays, gamma rays and is highly salt resistant, it makes for a great plant growth-promoting rhizobacteria. This is very important in agriculture and crop health. Rhizobacteris is found on the root of the cumin plant. [2]


Thirteen strains of Bacillus were isolated from the Mars Odyssey Orbiter surfaces and assembly-facility surfaces at the Jet Propulsion Laboratory in California and the Kennedy Space Center in Florida. 165 rRNA and gyrB gene sequences were tested phylogenetically and with PCR fingerprinting and DNA hybrization. The 13 isolates represent genus Bacillus, for which Bacillus safensis is suspected. [2]


''Bacillus safensis'' bacteria are non-pathogenic and are usually more helpful than harmful. The downside they present is that they can contaminate clean rooms (like NASA), where they can confuse test results. Certain strains are used on plants as way to stimulate root growth. Others are used to digest lipase.  
Scientist Ram S. Singh and colleagues from the Punjabi University in India discovered one of the strains of Bacillus safensis to have unulase activity which is used for the production of high fructose corn syrup and fructooligosaccharides. This strain is found in the root tubers of asparagus plants. [1]


Scientist Davender Kumar and his colleagues from Kurukshetra University in India found a strain of Bacillus safensis that was found to possess an enzyme for fat digestion called lipase. Lipases are also widely found in plants, microorganisms, and animals which are used in the production of bio deisel fuild, food, paper and detergents [1]


''Bacillus cereus''. Bacillus cereus can cause gastrointestinal illness causing nausea, vomiting, severe cramping and diarrhea. It is often found in contaminated rice.  
Bharathiar University in India was able to isolate a strain of Bacillus safensis from soil samples contaminated with explosive residue. It has been cataloged but no use has been found for it yet. [1]


''Bacillus subtilis'' can be used as a pesticide as it produces chemicals which are toxic to some insects, 
==References==


[1] http://en.wikipedia.org/w/index.php?title=Bacillus_safensis&oldid=660912220]
Bacillus safensis. (2015, May 5). In Wikipedia, The Free Encyclopedia. Retrieved 20:41, May 8, 2015, from http://en.wikipedia.org/w/index.php?title=Bacillus_safensis&oldid=660912220


''[[Bacillus anthracis]]'' 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 are are often used for chemical warfare. Anthrax can be fatal and causes chest pain and high fever


[2] http://ijs.sgmjournals.org/content/56/8/1735.full.pdf+html?sid=fdd91ac2-6473-43bc-8b43-a0e218117f84
NEW TAXA - Other Gram-positive Bacteria:
Masataka Satomi, Myron T. La Duc, and Kasthuri Venkateswaran
Bacillus safensis sp. nov., isolated from spacecraft and assembly-facility surfaces
Int J Syst Evol Microbiol August 2006 56:1735-1740; doi:10.1099/ijs.0.64189-0


Thirteen strains of Bacillus were isolated from the Mars Odyssey Orbiter surfaces and assembly-facility surfaces at the Jet Propulsion Laboratory in California and the Kennedy Space Center in Florida. 165 rRNA and gyrB gene sequences were tested phylogenetically and with PCR fingerprinting and DNA hybrization. The 13 isolates represent genus Bacillus, for which Bacillus safensis is suspected.


Scientist Ram S. Singh and colleagues from the Punjabi University in India discovered one of the strains of Bacillus safensis to have unulase activity which is used for the production of high fructose corn syrup and fructooligosaccharides. This strain is found in the root tubers of asparagus plants.
[3] http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1326975&lvl=3&p=mapview&p=has_linkout&p=blast_url&p=genome_blast&lin=f&keep=1&srchmode=1&unlock


Scientist Davender Kumar and his colleagues from Kurukshetra University in India found a strain of Bacillus safensis that was found to possess an enzyme for fat digestion called lipase. Lipases are also widely found in plants, microorganisms, and animals which are used in the production of bio deisel fuild, food, paper and detergents
Bharathiar University in India was able to isolate a strain of Bacillus safensis from soil samples contaminated with explosive residue. It has been cataloged but no use has been found for it yet.
==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.]


==Author==
==Author==

Latest revision as of 22:35, 15 May 2015

This student page has not been curated.

Classification

Domain; Phylum; Class; Order; family [Others may be used. Use NCBI link to find]

Domain: Bacteria Division/phylum: Firmicutes Class: Bacilli Order: Bacillales Family: Bacillaceae Genus: Bacillus Species: B. safensis

[3]


Genus

Bacillus safensis

NCBI: Taxonomy

Habitat Information

The soil was collected from a flower bed in an Austin TX residential neighborgood on January 29, 2014 at 1030am. The flower bed is west facing with very little sunlight as it is shaded by a structure. Location: 30degree14'05"N 97degree44'01"W. Humidity 78 percent.Temperature 72 degrees Fahrenheit. Pressure 29.83in. Elevation at 613 feet. Sky is overcast. No precipitation in the last 24 hours.

Description and Significance

Bacillus safensis is a gram-positive, aerobic, mesophilic, and rod bacterium. It is aerobic and highly resistant to UV and gamma rays. It is also a spore forming chemoheterotroph. It was first discovered in California and Florida on spacecraft and so is believed to have been brought to the USA from Mars. There are numerous strains of this bacterium, everyone belonging to the Firmicutes phylum of Bacteria. This organism is significant because it can tell us a bit about other planets and also how the bacteria spreads. It is also resistant to UV rays, gamma rays and is highly salt resistant, therefore it makes for a great plant growth-promoting rhizobacteria. [1][2]

Cell shape: rod. Cell size: ranges from 0.5-0.7 μm in diameter and 1.0-1.2 μm in length. Cell movement: motile, and use polar flagella for locomotion. [1]

Colony characteristics: dull white, undulate round, non-luminescent with irregular borders. Growth: mesophillic, as they can grow in temperatures ranging between 10-50 °C. Salt tolerance: prefers 0-10% salt, and a pH of 4-8. Resistances: produce spores that are resistant to hydrogen peroxide and UV radiation. [1][2]

Bacillus safensis is sensitive to the antibiotic Optichen. Optichen is most commonly used to rule out Streptococcus pneumoniae and not commonly used for bacillus safensis. [1]

Genome Structure

Bacillus safensis is a circular chromosome of 3.68 Mb, with approximately 3928 protein coding sequences and 39 contigs/overlapping DNA fragments greater than 200 base pairs in size. The genome also displays 73 tRNA genes. The strain FO-036b shows a guanine-cytosine content of 41.0-41.4 mol%.[1][2]

Sequence 1 Sample Patch MR#1 5' bases trimmed: 18 3' bases trimmed: 4 Max score 1266, 98% query cover 100% identification CACGCCGCGTGAGTGATGAAGGTTTTCG GATCNTAAAGCTCTGTTGTTAGGGAAGAACAAGTACGAGAGTAACTGCTCGTACCTTGACGGTACCTAACCAGAAAGCCA CGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGCA GGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAAGGTCATTGGAAACTGGGGAACTTGAGTGCAGAA GAGGAGAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAACACCAGTGGCGAAGGCGACTCTCTGGT CTGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAG TGCTAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGGTCGCAAG ACTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTT ACCAGGTCTTGACATCCTCTGACAACCCTAGAGATAGGGCTTTCCCTTCGGGGACAGAGTGACAGGTGGTGCATGGTTGT CGTCAGCTCGTGCCGTGAGATGTCATAGC


Sequence 2 Sample Patch MR#2 5' bases trimmed: 15 3' bases trimmed: 11 Max score 1256, 100% query cover, 99% identification GAAGGGAAAGCCCTATCTCTAGGGTTGTCAGAGGA TGTCAAGACCTGGTAAGGTTCTTCGCGTTGCTTCGAATTAAACCACATGCTCCACCGCTTGTGCGGGCCCCCGTCAATTC CTTTGAGTTTCAGTCTTGCGACCGTACTCCCCAGGCGGAGTGCTTAATGCGTTAGCTGCAGCACTAAGGGGCGGAAACCC CCTAACACTTAGCACTCATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTCGCTCCCCACGCTTTCGCTCCTC AGCGTCAGTTACAGACCAGAGAGTCGCCTTCGCCACTGGTGTTCCTCCACATCTCTACGCATTTCACCGCTACACGTGGA ATTCCACTCTCCTCTTCTGCACTCAAGTTCCCCAGTTTCCAATGACCTTCCCCGGTTGAGCCGGGGGCTTTCACATCAGA CTTAAGAAACCGCCTGCGAGCCCTTTACGCCCAATAATTCCGGACAACGCTTGCCACCTACGTATTACCGCGGCTGCTGG CACGTAGTTAGCCGTGGCTTTCTGGTTAGGTACCGTCAAGGTACGAGCAGTTACTCTCGTACTTGTTCTTCCCTAACAAC AGAGCTTTACGATCCGAAAACCTTCATCACTCACGCGGCGTTGCTCCGTCAGACTTTCGTCCATTGCGGAAGATTCCCTA

Cell Structure, Metabolism and Life Cycle

Growth: mesophillic, as they can grow in temperatures ranging between 10-50 °C. Salt tolerance: prefers 0-10% salt, and a pH of 4-8. Resistances: produce spores that are resistant to hydrogen peroxide and UV radiation. [1][2]

Positive for oxidase and catalase, Vogues-Proskauer Negative for trypsin, mannitol, indole, amylase, DNase, urease, trypsin, tryptophan deaminase, phenylalanine deaminase, arginine dihydrolase, lysine decarboxylase and ornithine decarboxylase. Cells do not reduce nitrate, but do hydrolyse gelatin, aesculin and RNA. Negative for gas production from D-glucose. Acid is produced from D-glucose, glycerol, L-arabinose, ribose, D-xylose, galactose [2]

Strain VK also contains genes that encode for 1-aminocyclopropane-1-carboxylate deaminase enzyme which enables the plant to tolerate salt, heavy metals, and polyaromatic hydrocarbons. Because it is so tolerant, Bacillus safensis VK is a powerful plant hormone producer. [2]

Bacillus safensis bacteria are non-pathogenic and are usually more helpful than harmful. The downside they present is that they can contaminate clean rooms (like NASA), where they can confuse test results. Certain strains are used on plants as way to stimulate root growth. Others are used to digest lipase. [2]

Because some strains of Bacillus safensis are resistant to UV rays, gamma rays and is highly salt resistant, it makes for a great plant growth-promoting rhizobacteria. This is very important in agriculture and crop health. Rhizobacteris is found on the root of the cumin plant. [2]

Thirteen strains of Bacillus were isolated from the Mars Odyssey Orbiter surfaces and assembly-facility surfaces at the Jet Propulsion Laboratory in California and the Kennedy Space Center in Florida. 165 rRNA and gyrB gene sequences were tested phylogenetically and with PCR fingerprinting and DNA hybrization. The 13 isolates represent genus Bacillus, for which Bacillus safensis is suspected. [2]

Scientist Ram S. Singh and colleagues from the Punjabi University in India discovered one of the strains of Bacillus safensis to have unulase activity which is used for the production of high fructose corn syrup and fructooligosaccharides. This strain is found in the root tubers of asparagus plants. [1]

Scientist Davender Kumar and his colleagues from Kurukshetra University in India found a strain of Bacillus safensis that was found to possess an enzyme for fat digestion called lipase. Lipases are also widely found in plants, microorganisms, and animals which are used in the production of bio deisel fuild, food, paper and detergents [1]

Bharathiar University in India was able to isolate a strain of Bacillus safensis from soil samples contaminated with explosive residue. It has been cataloged but no use has been found for it yet. [1]

References

[1] http://en.wikipedia.org/w/index.php?title=Bacillus_safensis&oldid=660912220] Bacillus safensis. (2015, May 5). In Wikipedia, The Free Encyclopedia. Retrieved 20:41, May 8, 2015, from http://en.wikipedia.org/w/index.php?title=Bacillus_safensis&oldid=660912220


[2] http://ijs.sgmjournals.org/content/56/8/1735.full.pdf+html?sid=fdd91ac2-6473-43bc-8b43-a0e218117f84 NEW TAXA - Other Gram-positive Bacteria: Masataka Satomi, Myron T. La Duc, and Kasthuri Venkateswaran Bacillus safensis sp. nov., isolated from spacecraft and assembly-facility surfaces Int J Syst Evol Microbiol August 2006 56:1735-1740; doi:10.1099/ijs.0.64189-0


[3] http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1326975&lvl=3&p=mapview&p=has_linkout&p=blast_url&p=genome_blast&lin=f&keep=1&srchmode=1&unlock


Author

Page authored by Krystal Hess, student of Prof. Kristine Hollingsworth at Austin Community College.

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