User:Andrea Lopez/Notebook/Biology 210 at AU

1/24/2015 Transect Observations

Biotic - ants - vegetable plants - worms - tree - grass

Abiotic - soil - wood chips - bark - rocks - water

Our transect included various vegetable plants such as carrots, lettuce, onions, and more; however, some of the plant leaves appeared to be dead possibly by the cold and frigid weather. In addition, there was a pipe running through the entire transect to water the growing plants. There was also an enormous pine tree in the back of the transect which left many pine needles on the floor. The soil in our transect was extremely moist possibly due to the fact that the plants were watered and taken good care of.

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1/21/2015 Hay Infusion Culture Observations

Purpose The purpose of this lab was to examine and observe which organisms were present in our transect. By determining and identifying the differentiating organisms, we will be able to further analyze the content and environment our transect holds. In addition, further information about the organisms within the transect gives us a depend knowledge on eukaryotic and prokaryotic organisms and their preferred environment.

Materials and Methods To begin our observations, we took a drop of each niche within our hay infusion and placed it on a microscope slide. After that was done, a cover slip was placed over the sample. We then began our observations by placing the slide on the microscope and closely examining the various organisms that were found. To correctly determine the type of organism, we used a dichotomous key. To prepare for next week's lab, four tubes of 10mLs containing broth were labeled. Next, eight agar plates were attained to begin the plating (one containing antibiotics and one not). 100 microliters of the content within the hay infusion were added to the 10 mLs of broth. 100 microliters of the previous tube were then added to the next tube labeled 10^-4. This process was repeated to complete the next two dilutions. Once the solutions were prepared, a micropipette dispensed 100 microliters of the culture into the agar plate and spread with an inoculating tube. This procedure was then repeated with each tube so all eight agar plates contained a sample of each diluted solution.

Data and Conclusions The two niches identified within the hay infusion varied to a high extent. The bottom niche contained materials that were more dense such as soil, rocks, and some heavy leaves. In the top niche, a film of green mold covered the entire liquid. Perhaps the reason why the top niche did not contain plant material is because it is not dependent on plant features. In addition, mold grows at best capacity under airy conditions which could explain why there was mold closer to the surface of the container. Because the mold was at the top of the container, the smell of the content appeared to be a mixture of dirty sewage water and fertilizer. By observing the culture from both niches, we found that many of the organisms were motile. The organisms found in the top niche were Volvox, Blepharisma seculum, Euplotes patella and , Oscillatoria curviceps. Out of those four, all of them displayed a form of motility. Volvox displayed a rolling motion despite of the non-motile gonidia in the interior of the organism. Blepharisma moved by organisms specializing in motility. In addition, the organism contains cilia to assist in movement. Euplotes patella have a swimming-like feature and were extremely difficult to observe due to their fast movement. Lastly, the Oscillatoria curviceps moved by means of their microfibrils. In the bottom niche, we found Colpidium campylum and Nostoc azollae. Nostoc azollae moved by relatively short motile filaments called harmogonia whereas Colpidium did not display any motile features. By utilizing the Dichotomous Key, we found that Volvox, Oscillatoria curviceps and, Nostoc azollae all perform photosynthesis. More specifically, Nostocs perform photosynthesis by photosynthetic pigments contained in the cytoplasm. Volvox and Oscillatoria are common in the fact that they are both algae. The rest of the organisms seemed to obtain nutrients by means of specialized organelles such as vacuoles. Volvox displayed all five features that identify a living organism. Firstly, volvox use and receive their energy through photosynthesizing mechanisms. Their DNA is replicated during cleavage and is composed of numerous cells. Volvox is unique in that it can reproduce both asexually and sexually. Lastly, Volvox continues to evolve within each differentiating habitat. It can be predicted that in two months, the ecosystem within the Hay Infusion Culture will continue to grow due to the organism's individual mechanisms. For example, a symbiotic relationship between organisms will allow the ecosystem to continue to grow or obtain stability.

Niche Sample Drawing

Organisms Found in Hay Infusion Culture

Serial Dilution Diagram

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1/28/2015 Identifying Bacteria from Prepared Agar Plates

Purpose For this lab, the purpose was to identify the bacteria on the agar plates using gram stain and microscopes. Characteristics we were looking at included cell morphology, motility, and the type of gram stain. These observations allowed further entail in what our transect entailed and which bacteria grow best in that type of environment.

Materials and Methods To begin the lab procedure, observations of the Hay Infusion Culture were taken to note any changes that may have occurred. After observations were noted, observations of the agar plates inoculated from the Hay Infusion Culture were taken. We carefully counted the number of colonies on each plate and noted it on the spreadsheet. Four small samples of a chosen colony from the agar plates were taken using a toothpick to place on the microscope slide on top of the drop of water. Using the microscope, one was able to determine cell morphology and motility. Afterwards, another four samples from the same bacterial colonies were placed on a microscope slide using a sterilized inoculating tube to begin the gram staining process. After rinsing the sample with crystal violet, water, iodine, water again, and 95% alcohol, the microscope slide was placed on the stage of a microscope to begin observations on whether the bacteria was gram negative or positive. To prepare for next week's lab, one sample from each of the two plates that had the most characterization were taken. 20 microliters of primer were added to each PCR tube and then mixed. The samples of bacteria were then added to the tubes and mixed with a toothpick. Finally, the complete PCR tube was placed in the PCR machine.

Data and Conclusions The hypothesis which stated that if the samples of bacteria were motile then the gram stain would be positive was supported by the data collected. The two bacteria samples that were taken from the plates without the antibiotic displayed motility. In the plate that was diluted to 10^-4, the bacteria were coccus-shaped, extremely minuscule, and green. Even though the motility was not as apparent compared to the motility in the 10^-6 plate without antibiotic, it could have been described as a slow, rolling motion. The bacteria observed in the other plate displayed obvious movement as it displayed a rapid, swimming-like motion. The other two samples observed did not display any sort of motility and remained stationary. The two samples did not display motility possibly because they were taken from the plate that contained the antibiotic. It could have been that the antibiotic had ceased the bacteria's ability to move. When the gram stain procedure was finished, our data showed that the two bacteria which displayed motility were gram positive. It is unclear if the motility of the cell has an effect on the characteristic of gram positive but, the data collected displayed this particular pattern. The other two bacteria cells that remained stationary were gram negative. This observation supported the hypothesis despite if there is an apparent reasoning behind the pattern noted. Observations of the colonies within the plates showed that the plates without the antibiotic contained a more significant bacteria growth than the plates without. This could be because the antibiotic served as it should and ceased the growth; however, some bacteria did grow in the plates with the antibiotic. The bacteria that grew with the antibiotic can be said that they are antibiotic-resistant. This could be potentially harmful and cautioning as more and more bacteria obtain resistance. Additionally, the plates without the antibiotic displayed darker colors of bacteria colonies such as dark reds and oranges.

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2/4/16 Observing and Determining Plant Characteristics

Purpose The purpose of this lab was to determine certain characteristics of the plants we found within our transect. Through careful observations, we were able to determine plant vascularization, mechanisms of reproduction, and specialized structures. Unveiling plant characteristics allowed us to further understand how the plants within our transect reproduce and grow.

Materials and Methods To begin our observations we obtained two gallon-sized ziploc baggies and filled one bag with live plant matter and the other with what appeared to be dead plant matter. We then took five samples of live plant matter to determine vascularization, specialized structures, and mechanisms of reproduction. To determine these characteristics, we not only looked at the plant matter with the naked eye but, using a razor, we carefully cut off a small segment of the root and placed it inside a depression slide. The sample was then placed under the microscope to begin further observations. To find out the form of vascularization of our plants, we looked at the bottom of the leaf/plant matter to take a closer look at its roots and branching veins. Most of this weeks consisted of observations but, to prepare for next week's lab, a berlese funnel was set up to collect invertebrates. To begin, 25 mL of 50:50 ethanol/water solution was poured into a 50mL conical tube. A small piece of screening material was taped to the bottom of the funnel to keep leaves out of the preservative. Leaf litter was then placed in the top of the funnel. The conical tube was then secured with parafilm to the bottom of the funnel. Once the funnel was set up, it was attached to a ring stand under a 40 watt lamp 1-2 inches from the top of the leaf litter.

Data and Conclusions Based by our observations, we learned that all of our plants are dicots. Dicots can be characterized by having an embryo with two cotyledons whereas monocots only have an embryo with a single cotyledon. Another big difference between monocots and dicots is that the veins are reticulated through the leaf while monocots veins run parallel to one another. In addition, we found the plant mechanisms of reproduction to be a mixture of gymnosperms and amniosperms. Gymnosperms are vascular plants that reproduce by means of a seed or ovule. Unlike angiosperms

Figure 1. Sample Plant Pictures

Table 1. Characteristics of Plants Collected from the Transect

Figure 2. Fungi Observations