Soil Project- English/Ramos: Difference between revisions

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Domain; Phylum; Class; Order; family [Others may be used.  Use [http://www.ncbi.nlm.nih.gov/Taxonomy/ NCBI] link to find]
Domain; Phylum; Class; Order; family [Others may be used.  Use [http://www.ncbi.nlm.nih.gov/Taxonomy/ NCBI] link to find]
Phylum: Firmicutes Genus: Bacillus Order: Bacillales Species: B. arsenicus


===Species===
===Species===

Revision as of 19:19, 8 December 2017

This student page has not been curated.

Classification

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

Phylum: Firmicutes Genus: Bacillus Order: Bacillales Species: B. arsenicus


Species

Fictibacillus sp

NCBI: Taxonomy

Genus species Classification Bacillus Arsenicus also known as Fictibacillus arsenicus Phylum: Firmicutes Genus: Bacillus Order: Bacillales Species: B. arsenicus

Habitat Information

Describe the location and conditions under which the organism was isolated. Collection Date: September 7, 2017 Air Temp: 76% Humidity: 36% 24Hr Rainfall: 0.00 Pressure: 30.03” Solar Radiation: 22.53 Depth of collection: surface to 1 inch deep Grid Coordinates: Lat 29.9425576 Long -98.4037259 Sample Location: In front of house right next to brick of house. Soil is noted to have large amounts of rocks.

Description and Significance

Describe the appearance (colonial and cellular), possible antimicrobial activity etc. of the organism, and why the organism might be significant.

Colony Morphology

Margin: Smooth Elevation: convex Surface: smooth Color: very light green Soluble Pigment: opaque

Cellular morphology:

Gram positive rods in long chains.

Possible microbial activity: The soil microorganism had antibiotic activity when we performed the mixed culture on an LB culture with a lawn of E. coli; there was clearing around the soil microorganism demonstrating antibiotic activity against E. coli.

Significance

Has nematicidal capability against root-knot nematodes and free-living nematodes. Essentially is it is toxic to nematodes. Arsenic resistant bacterium


Soil microorganism.png

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?

The soil microorganism was sent to a lab for sequencing and this was the result: AGACCTGGTAAGGTTCTTCGCGTTGCTTCNAATTAAACCACATGCTCCACTGCTTGTGCGGGCCCCCGTCAATTCC TTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGCGGAGTGCTTAATGTGTTAACTTCAGCACTGAGGGTGGAACCCCCC AACACCTAGNACTCATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCACCCCACGCTTTCGCGCCTCAGC GTCAGTTACAGGCCAAAAAGCCGCCTTCGCCACTGGTGTTCCTCCACATCTCTACGCATTTCACCGCTACACGTGGAATT CCACTTTTCTCTCCTGCACTCAAGTCTCCCAGTTTCCAATGACCCTCCACGGTTGAGCCGTGGGCTTTCACATCAGACTT AGGAGACCGCCTGCGCGCGCTTTACGCCCAATAATTCCNGATAACGCTTGCCACCTACGTATTACCGCGGCTGCTGGCAC GTAGTTAACCGTGGCTTTCTGGTTANGTACCGTCAAGGTACNAGCANTTACTCTCGTACTTGTTTCTTCTCTAACAA

Include S Ribosomal sequence that you obtained from PCR and sequencing here.

Unable to obtain from the lab; instead entered the sequence in the web site DNA BLAST and obtained this result:

Select seq KM598247.1 Fictibacillus sp. THG-SQK1 16S ribosomal RNA gene, partial sequence


RID 2NMY0NWT015 (Expires on 12-10 01:02 am) Query ID lcl|Query_140973 Description None Molecule type nucleic acid Query Length 553 Database Name nr Description Nucleotide collection (nt) Program BLASTN 2.7.1+

Cell Structure, Metabolism and Life Cycle

Interesting features of cell structure; how it gains energy; what important molecules it produces.

Scanning electron micrographs of the surface of a spheroidal concretion, a comparison of the lipid composition of B. arsenicus sp. nov. and B. barbaricus, and a neighbour-joining tree showing the phylogenetic relationships between B. arsenicus sp. nov. and other species of the genus Bacillus.

The soil microorganism did not show motility on the tests we performed, although in our research the microorganism is described as motile. After one week of being cultured on an LB plate, we did not see endospore formation; this occurred probably because it was too soon to see endospore formation. On our research there is evidence of endospore formation.

Physiology and Pathogenesis

Biochemical characteristics, enzymes made, other characteristics that may be used to identify the organism; contributions to environment (if any).
If relevant, how does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.

Enzyme produced: casein

Biochemical characteristics based on Chemical testing on the soil microorganism:

October 6th tests: Phenol Red Broth: Negative for fermentation. Starch Hydrolysis test: Negative.

Casein Hydrolysis Test: Positive.

Casein Hydrolisis.png

Gelatin Hydrolysis test: negative. DNA hydrolysis: Negative. Lipid hydrolysis: Negative. October 20th: Methyl Red and Voges-Proskauer: Negative. Citrate test: Negative. SIM medium test: Negative. Nitrate reduction: Negative (first step and second step also negative). Urea Hydrolysis test: Negative. Triple Iron Sugar test: Negative for fermentation. Oct. 27th tests: Oxidase test: Negative. MacConkey Agar test: Negative. Eosin Methylene Blue agar test: Negative. Hektoen Enteric Agar test: Negative. Decarboxylation test: Negative. Phenylalanine Deaminase Test: negative. Nov 3rd: Blood agar: soil microorganism had a weak alpha positive result; this means it causes partial hemolysis. Manitol salt agar: Negative. Phenylethyl Alcohol Agar (PEA): Positive, the soil microorganism had growth. This means it is not gram negative because this media inhibits growth of gram negative microorganisms. This media is selective for gram positive microorganisms; it actually promotes the growth of gram positive. This confirms it is a gram positive organism. Catalase test: Positive. When drops of hydrogen peroxide were placed on a colony that had been spread on a slide, it produced bubbles. Salt tolerance test: Negative. Bile Esculin test: Negative. Bacitracin/Optochin Susceptibility test: Soil microorganism was resistant to both. Nov 10th Antimicrobial susceptibility test (Kirby-Bauer method):

soil microorganism was sensitive to Ticarcinin/Clavulanic acid, Vancomycin and Ampicilli/Sulbactam;  

Resistant to: Cefoxitin and Ceftazidime. Disinfectants: highly sensitive to 100% Bleach. Somewhat sensitive to Lavender, 5% Bleach and Rosemary. Not sensitive to orange.Disinfectant susceptibility.png

Antimicrobial susceptibility.png

References

Genome sequence obtained from DNA BLAST web site https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch https://blast.ncbi.nlm.nih.gov/Blast.cgi


Pictures taken in class. References Bacillus arsenicus. (2017, August 13). Retrieved December 07, 2017, from https://en.wikipedia.org/wiki/Bacillus_arsenicus Shivaji, S., Suresh, K., Chaturvedi, P., Dube, S., & Sengupta, S. (2005, May 01). Bacillus arsenicus sp. nov., an arsenic-resistant bacterium isolated from a siderite concretion in West Bengal, India. Retrieved December 07, 2017, from http://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.63476-0

Author

Page authored by Tara English and Teresa Ramos, students of Prof. Kristine Hollingsworth at Austin Community College.