Difference between revisions of "JJDZ Soil"
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Revision as of 21:50, 7 December 2017
- Domain: Bacteria
- Phylum: Proteobacteria
- Class: Gammaproteobacteria
- Order: Enterobacterales
- Family: Enterobacteriaceae
- Escherichia coli
- NCBI Link: Escherichia coli Taxonomy: 
- Soil Sample Location: Copperfield Park and Greenbelt - 1425 E Yager Ln, Austin, TX 78753
- Soil Collection Date & time: 9/7/2017 @ 10:00 AM
- Conditions Present at time of soil collection:
- No recent rain within past 48 hours
- Temperature was 71 degrees F
- Soil sample was retrieved at a depth of roughly 3 inches and about 6-8 inches from creek bed.
- Description of Area:
- Pond and creek area
- Moderate erosion
- Wildlife present (actually saw a coyote when collecting sample)
- Area was damp and wet (close to creek bed)
- Area gets roughly 1/2 day of sunlight everyday
Description and Significance
Antibiotic resistance in E. coli is of particular concern because it is the most common Gram-negative pathogen in humans, the most common cause of urinary tract infections, a common cause of both community and hospital-acquired bacteraemia as well as a cause of diarrhea. In addition, resistant E. coli strains have the ability to transfer antibiotic resistance not only to other strains of E.coli, but also to other bacteria within the gastrointestinal tract and to acquire resistance from other organisms. 
- Colonial Appearance:
- Shape: Circular
- Margin: Entire
- Elevation: Raised
- Size: Punctiform, small
- Texture: Smooth
- Appearance: Shiny
- Pigmentation: Non-pigmented / colorless
- Optical Property: Translucent
- E. coli has only one circular chromosome
- GCACCTGTCTCACGGTTCCCGAAGGCACATTCTCATCTCTGAAAACTTCCGTGGATGTCAAGACCAGGTAAGGTTCTTCGCGTTGCATCGAATTAAACCACATGCTCCACCGCTTGTGCGGGCCCCCGTCAATTCATTTGAGTT TTAACCTTGCGGCCGTACTCCCCAGGCGGTCGACTTAACGCGTTAGCTCCGGAAGCCACGCCTCAAGGGCACAACCTCCAAGTCGACATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTCGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACGAGACTCAAGCTTGCCAGTATCAGATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCTGACTTAACAAACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCGATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAGCCGGTGCTTCTTCTGCGGGTAACGTCAATGAGCAAAGGTATTAACTTTACTCCCTTCCTCCCCGCTGAAAGTACTTTACAACCCGAAGGCCTTCTTCATACACGCGGCATGGCTGCATCNNCTTGCGCCCATTGTGCAATATTCCCCACTGCTGCCTCCCG
- Escherichia coli strain S17-13, complete genome
Genes (total) :: 5,359 CDS (total) :: 5,234 Genes (coding) :: 4,987 CDS (coding) :: 4,987 Genes (RNA) :: 125 rRNAs :: 8, 7, 7 (5S, 16S, 23S) complete rRNAs :: 8, 7, 7 (5S, 16S, 23S) tRNAs :: 90 ncRNAs :: 13
NCBI Link: E. coli Strain S17-13: 
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.
Cell Structure, Metabolism and Life Cycle
- Cell Structure: E. Coli is a Gram-negative, facultatively anaerobic, rod-shaped, coliform bacterium. . It also possesses adhesive fimbriae and a cell wall that consists of an outer membrane containing lipopolysaccharides, a periplasmic space with a peptidoglycan layer, and an inner, cytoplasmic membrane. . The integument, the tough outer protective layer, protects the bacterium from other organisms or oppressors.
- Metabolism: E.coli has fairly simple nutritional requirements. It is a heterotrophic organism, therefor it cannot produce its own food and it must obtain nutrition and energy by taking it from other organisms, most often its host. Carbon is very important to e-coli, and it obtains its carbon from glucose.
- Reproduction Cycle: E-coli has a very rapid growth cycle; it reproduces by either cell (binary) division (asexual) or through conjugation (sex pilus), the most common reproductive method is asexual reproduction. The time required for a complete cycle varies depending on several factors, however in optimal nutrient conditions, E. Coli can duplicate in about 20 minutes.
- Life Cycle: In terms of its life cycle, it has a lag phase (growth is slow), log phase (bacteria multiplies exponentially), stationary phase (bacteria growth stabilizes), and death phase.
Physiology and Pathogenesis
Biochemical characteristics of E. coli:
|Tests||E-Coli||In class results of organism|
|Lactose||Acid+, gas+||Acid+, gas+|
|Mannitol Fermentation||positive, usually with gas||Negative|
|Mannitol||Positive||Negative for fermentation - organism growth|
|Urea||No hydrolysis||No hydrolysis|
|Hemolysis (Alfa/Beta/Gamma)||Some Strains show Hemolysis||Beta Hemolysis|
|Mannitol||Positive||Negative Fermentation / Organism grew|
- Organism Significance:
- E-Coli is typically harmless and lives in gut flora within mammal’s intestines. Most types of E. coli are harmless and even help keep your digestive tract healthy. It produces Vitamin K2 and It normally exists symbiotic relationships with pathogenic bacteria. E-coli is expelled into the environment through fecal matter. Some strains can cause serious food poisoning in humans if food or drinks get contaminated. An example is the Shiga toxin-producing E. coli (STEC), it can cause severe food-borne disease. It is transmitted to humans primarily through consumption of contaminated foods, such as raw or under cooked ground meat products, raw milk, and contaminated raw vegetables and sprouts & ground beef. When cattle are slaughtered and processed, E. coli bacteria in their intestines can get on the meat, unpasteurized milk, fresh produce
- E. coli comprises an extremely large population of bacteria that display a very high amount of genetic and phenotypic diversity. There has been extensive genome sequencing of a large number of E. coli strains, it is reasonable to say that it needs a new taxonomic classification.
- Virulent factors:
- They use an adhesin known as intimin to bind host intestinal cells
- Bacterial frimbriae for attachment
- Produce enterotoxins
- Contributing factors to environment:
- The sustainability of land and water resources is under pressure due to growing demands on agricultural systems to deliver food for an increasing world population. One source of pressure can be attributed to livestock agriculture and the production of large volumes of feces and associated manures. If managed effectively, fecal contributions to agricultural land from livestock can serve as a valuable farm resource and organic fertilizer, but if mismanaged and combined with opportunities for hydro-logical transfer, they can threaten water quality draining from catchment systems with a range of pollutants.
[[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]]
Page authored by Jennifer Jordan and Denise Zamarrippa, student of Prof. Kristine Hollingsworth at Austin Community College.