Phylogenetic Analysis of Thermophilic Bacteria

Often scientists work with bacteria that do not come in a labeled test tube— for example, bacterial samples taken from infected human tissue or from the soil—and the scientist must then identify the unknown microorganism in order to understand what behavior to expect from the organism, for example, a certain type of infection or antibiotic resistance. However, because of the relatively few forms of bacteria compared to animals and because of the lack of bacterial fossil records due to their asexually reproductive nature, the taxonomy used to classify animals cannot be applied to bacteria (Brown 275). In order to classify unknown bacteria, a variety of physiological and metabolic tests are available to narrow a sample down from the fathomless number of possibilities into a more manageable range. Once these tests have been performed, the researcher can consult Bergey’s Manual of Determinative Bacteriology, a systematically arranged and continually updated collection of all known bacteria based on their structure, metabolism, and other attributes.

The following results helped obtain the haplogroup that in which the sequence of mtDNA would identify. The PCR reaction worked, and this can be determined by looking at the agarose gel in figure 1. If the PCR reaction was successful, than a band should appear around 550bp. Individual AC displays a band around 550bp, this means the PCR reaction was successful. The band for individual AC, depicts a low concentration of product, because the band faint. After the purification process the concentration, A260/280 ratio, and A260/A230 ratio were determined by using the nanodrop. The concentration of mtDNA in the product was 60.9 ng/uL. The ratio for A260/280 was 1.79 and the ratio for A260/230 was 0.77. The A260 and 280 are a spectrometer measurement that measure absorbance at wavelengths of

The purpose of the following study is to determine where the two unknown bacteria acquired in Microbiology lab should be classified in regards to temperature, pH level, and osmoregularity. It is important to classify bacteria in order to identify them. Identification of bacteria is important because they are not only useful but potentially dangerous as well. The identification of bacteria can lead to breakthroughs in healthcare regarding treatment of old and new diseases alike. Identifying bacteria can also be used in many other areas from better crop production through microbial pesticides to biological warfare. Their uses are endless as are their abilities to evolve and adapt to changing environments. That is why it is so important

The ten most abundant bacterial families detected in our study were Koribacteraceae (Acidobacteria), Acidobacteriaceae (Acidobacteria), Sphingobacteriaceae (Bacteroidetes), Geobacteraceae (proteobacteria), Auto67-4W (Pedosphaerae), Acetobacteraceae (proteobacteria),

Prokaryotes are ubiquitous, successfully adapting to diverse environments as well as developing symbiotic relationships with host organisms (Lengeler, Drews, & Schlegel, 1999). Prokaryotes may have both autotrophic and heterotrophic characteristics. A cyanobacteria is photosynthetic, commonly called blue-green algae, and may produce toxins (Crayton, 1993). Bacteria are most commonly associated in the general

coli are picked and the plasmids are purified. The purified plasmids are used as a template for the sequencing reaction. The objective of the lab was to learn how to use the polymerase chain reaction (PCR) to amplify the small subunit ribosomal RNA gene from a bacteria colony, also be able to run an agarose gel to visualize the resulting PCR amplifications and extract the amplified DNA from the agarose gel.

The best and most accurate way of identifying an unknown microorganism is by sequencing its DNA, but this is very expensive and only used in highly qualified labs. So, the identification of unknown bacteria number 63 was be done by putting the bacteria through numerous laboratory tests. Microorganisms are different among each other by their macroscopic morphology, microscopic morphology, and the unique metabolic processes they use to survive and reproduce. Identifying an unknown microorganism in the laboratory is important because knowledge is gained on the appropriate way to cultivate an organism, how to correctly read the result of a test, and learning about the different characteristics of the bacteria. All of the following tests were done using the best sterile technique and the most new turbid bacterial growth subculture.

A highly conserved gene will be used to identify a prokaryotic species isolated from the body. Fundamental lab techniques will be also explored and utilized, such as amplifying using PCR, cloning, and transforming the gene into a host cell. DNA electrophoresis and specific substrate plating will serve as analysis check points. The final product will be sequenced and compared to similar species to observe phylogenetic relationships.

After inoculating an agar plate with the bacteria taken from a phone screen in Durham during winter, various tests were performed to attempt to identify the organism’s genus. We hypothesized that the bacteria was a member of the Staphylococcus genus. The Gram Stain results indicate that the bacterium is either Gram negative, but the KOH test indicates a Gram-positive isolate. Upon further consideration, we decided that the bacterium is a Gram-positive destainer. Gram-positive bacteria have a thick cell wall composed of peptidoglycan. As expected, the Gas Pak and TSA stab results indicate that the bacterium cannot grow in the absence of oxygen. A motility stab indicated that the bacteria were motile. Motility provides an ability to change direction and move away from repellents and toward attractants. Thus, the microbe can avoid unfavorable conditions, and live longer. The positive lysine decarboxylase test indicates that the microbe can use the amino acid lysine as a source of carbon and energy for growth. First, the bacteria use glucose as its primary carbon source, which causes the pH to drop. The enzyme lysine decarboxylase degrades lysine to produce basic products. This change in pH is what causes the broth to turn purple again, a positive result. An endospore stain indicated that the bacterium does not produce spores under stress to protect the cells from dying. Spores are metabolically inactive and

Eli Gendron carried out the experiment of the microbe’s distribution on the Green Lake. His main focus was on Eukaryal Beta Bacteria and Bacterial Beta Bacteria diversity, distribution within the Green Lake. The Green lake valley is surrounded by Navajo peak of 4088 meter and Apache peak of 4003 meters from sea level and it gets most of the water from these two mountains. Eli’s main focus was on how microbial assemblages are distributed around the lake. Samples were collected from 3 meters depth of inlet, outlet and middle of the lake. He found major colonies of Eukaryal Beta diversity in the middle of the lake and second largest in the Inlet zone. Whereas

Ralstonia solanacearum has been classified in numerous genera since it was first described (E.F. Smith, 1896). Although Thomas J. Burrill was probably the first to isolate the bacterium in 1890, E.F. Smith was the first to publish a scientific description and classify it in the genus Bacillus as B. solanacearum in 1896 (E.F. Smith, 1896, 1907; Kelman, 1953). However, afterward it was moved to the genus Bacterium, and to the genus, Pseudomonas with the name of P. solanacearum (Kelman, 1953), temporarily reclassified in the genera Phytomonas and Xanthomonas and eventually transferred back to the genus Pseudomonas in 1948 (Kelman, 1953). In 1992 it was placed in the genus Burkholderia (Yabuuchi et al., 1992). But, more recent phylogenetic and polyphasic phenotypic analyses pointed out that it would rather be accommodated in the newly

After the incubation, 1.5 mL of each of the three cultures were added to eppendorf tubes and centrifuged at 13,200 rpm for 1 minute. An alkaline lysis procedure like that of Birnboim and Doly was then performed to extract the plasmid DNA with 200 μl of alkaline SDS detergent solution (Birnboim & Doly, 1979). After

The purpose of the two experiments was to determine the fundamental effects that temperature has on the growth and survival of bacteria. During the first experiment five different bacterial broth cultures of Escherichia coli, Pseudomonas fluorescens, Enterococcus faecalis, Bacillus subtilis and Bacillus stearothermophilus were individually incubated at temperatures of 5, 25, 37, 45 and 55°C for one week in an aim to distinguish the effect temperature has on growth and survival of the five different species. After one week they were observed for distinguishable changes by the turbidity showing an indication of bacterial growth, or the clarity an indication of no survival.

The chemical and reagents used for the extraction and quantitation of DNA were: Plant DNAzol (0.3ml/0.1g), 100% ethanol (100%: 0.225 ml/0.1 g, 75%: 0.3 ml/0.1 g), Chloroform (0.3 ml/0.1 g), Plant DNAzol-ethanol solution: Plant DNAzol, 100% ethanol (1:0.75 v/v), TE buffer (10 mM Tris, 1 mM EDTA pH 8.0), 1.2% agarose gel (Agarose, 1X TAE buffer), 6X loading buffer (glycerol, Tris/EDTA pH 8.0, ethidium bromide), .25X TAE buffer, Restriction enzymes and Restriction endonuclease buffers. All the chemicals used were quality grade. The restriction

This essay based on the principle of real time PCR which uses CYBR green dye that combines to any double stand DNA. This process included two maim steps. The first step was designing of HSV-1 primer and /or HSV-2 primer (we have chosen only HSV-1). BioEdit software has been used to edit the nuclide sequences where necessary. After that the primer has been ordered. The second step was in the laboratory which included applying the HSV-1 primers to real time PCR protocol. The final results of this protocols aim to demonstrate the quality of HSV-1 primer that we have designed by interpretation three criteria. These are specificity, efficiency and