User:Cassidy B. Hart/Notebook/Biology 210 at AU

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7/14/2015 Exercise V Invertebrates and Vertebrates


During the study of the AU transect, bacteria, fungi, plants, algae and protists have all been study. This last transect lab will study another class of organisms; invertebrates and vertebrates. Invertebrates are animals without backbones while vertebrates are animals with backbones (Freeman, 2014). This classification however makes the divide seem simple, in reality both invertebrates and vertebrates are vastly complex and diverse groups of animals. Invertebrates are often characterized by their symmetry; if they can be divided into four symmetrical quarters they have radial symmetry. If they can be divided in to two symmetrical halves, then they have bilateral symmetry. Bilateral symmetric animals have a head and tail as well as a right and left side (Bentley, 2015). Another way for invertebrates to be characterized is by the number of germ tissue types. Cnidaria have only two layers, endoderm and ectoderm, while all other animals have these two layers plus mesoderm (Bentley, 2015). Finally invertebrates can be divided into another two groups; protostomes meaning their mouth forms prior to their anus, and deuterostomes meaning their anus forms prior to their mouth (Bentley, 2015). Using these characteristics it is possible to study the invertebrates in the transect and identify them. Invertebrates, however, are not the only animals that live in the transect. Vertebrate animals can also be found in the transect and are equally important in the cycle of life in the transect.


Last week a Berlese funnel was set up under a hot lamp by placing ethanol in a tube below a funnel filled with leaf debri. In this lab, the Berlese funnel was deconstructed and the captured invertebrates were studied underneath a microscope. Using a dichotomous key, the organisms were identified and these results were recorded. The number of invertebrates in the sample and the size of the invertebrates was also recorded. Finally the transect was visited and five vertebrate species that were found there were recorded (Bentley, 2015).


Multiple invertebrates were found. They are listed and described in the table below as well as individual images of each.

Table 1. Description of Invertebrates Found in Transect TABLEINVERT.png

Neantistea Magna BUGARACH.jpg

Millipede BUGMILLI.jpg

Armadillidiidae BUGROLLY.jpg

Aphid BUGAPHID.jpg

Big Brown Mite BUGMITE.jpg

Vertebrates were also seen in the transect. They are listed in and described in the table below.

Table 2. Description of Vertebrates Found in Transect TABLEVERT.png


The invertebrates that were discovered displayed the diversity of invertebrates in that while they were all the same phylum, only two were the same class. They also ranged in size form 1- 10 mm with the largest organism being the Anthropoda Diplopoda, also known as the millipede, and the smallest one being the Anthropoda Insecta, known as the aphid, which was only 1 mm. The millipede gets its size from its length where as the aphid is a small round bug. The Anthropoda Arachnida, or the big brown mite, was the most common invertebrate found in the results of the Berlese funnel. The vertebrates however were not as varied, with four of the five organisms being from the same class, Aves. This could be indicative of the types of vertebrates found in the transect or it could be that larger animals are more easily spooked by observers and habitat a larger area so that they are harder to observe in the transect. This could also just be because of the biotic and abiotic factors of the transect. The biotic factors of the transect such as the insects and worms would greatly benefit the birds since they are the bird's food source. The trees would also benefit the birds since they provide shelter and a place to create a nest. The trees and plants would also aid the squirrels since they eat tree bark, berries, nuts, and seeds, which all are produced by trees and plants. The abiotic factors that benefit both the birds and the squirrels are the stream, the shade, and the dirt. The birds use the stream to bathe and to drink and the squirrels use the stream to bathe. All the animals benefit from the shade during the hot humid summer months and the dirt provides a benefit to the squirrels so that they can bury their nuts in order to eat them during the winter months. The animals, bacteria, fungi, insects, and plants all intersect in the transect to form a community. This community consists of many different trophic levels. A trophic level is group of organisms that all obtain energy from the same source (Freeman, 2014). These trophic levels are evident in the food web below where it can be seen that millipedes and bacteria are on the same trophic level since they both get their food from logs and dead leaves. Organisms that are on the same trophic levels are often limited by the same carrying capacity since they have to compete against each other for food. The carrying capacity for an organism is the maximum population size the environment can support due to habitat space, food availability, water availability, etc (Freeman, 2014). Not just on a trophic level, but throughout the community these animals often compete for habitat and resources and carrying capacity determines how many of them can survive. However, as seen in the below food web, when an animal does die, it provides the nutrients to other organisms and allows the food web to continue. In this way the circle of life goes on and the community found in the transect continues to survive.

Transect Food Web Foodwebcass.png


Bentley, M., Knight, S., Zeller, N., Walters-Conte, K. 2015. Exercise V- Invertebrates and Vertebrates. Biology 210 Laboratory Manual

Freeman, Scott. 2014. Biological Science. Prentice Hall: New Jersey. 1150-1151.

7/9/2015 Exercise IV Plantae and Fungi


Two organisms that are incredibly important to the life cycle are Plants and Fungi. Both are incredibly diverse and have numerous functions. Land plants evolved from algae, and were similar to moss. These plants then had to adapt to the on land environment and overtime developed the characteristics that make them the plants known today. Because this development took place over such a long time and in numerous places, there is a huge diversity in both Fungi and Plants. Therefore in this lab they will be characterized by presence of vascularization, presence of speocialized structures, and the mechanism of reproduction. Fungi, in particular, can be divided into three divisions: zygomycota, basidiomyceta, and ascoymceta. Zygomycota are parasitic on plants and insects and reproduce using a zygsospore. Basidiomycota are terrestrial fungi who reproduce using basidia, and ascomycota, which includes yeasts, powdery mildews, molds, morels, and truffles and produce using structures called ascocarps. In this lab these different organisms will be taken from the transect and studied (Bentley, 2015).


A gallon bag worth of leaf litter was collected from the transect along with five different leaf samples. The leaf samples will then be studied and the vascularization, specialized features, and method of reproduction will all be recorded (Bentley, 2015).


The five plants found in the transect were lady fern, english ivy, flowering dogwood, swamp saw grass, and royal standard hosta. They are pictured below.

Lady Fern PLANT573.jpg

Flowering Dogwood PLANT571.jpg

Swamp Saw Grass PLANT572.jpg

Royal Standard Hosta PLANT570.jpg

English Ivy PLANT574.jpg

Table 1: Characteristics of Plants Collected from the Transect TABLE37.png


The plants in the transect were in many ways similar. They all had vascularization and all reproduced using seeds. This similarity could be because they are all from the same habitat and so vascularization and seeds have made these plants the most fit to survive and so it is these traits that are common in the transect. It would be interesting to compare the results from this transect with other transects to see if they were similar or not. For fungi, which was not seen in our transect, sporangia are important for their reproduction. Sporangia are structures that produce spores that fungi use to reproduce (Freeman). This is different from the seeds that the plants found in the transect use to reproduce.


Bentley, M., Knight, S., Zeller, N., Walters-Conte, K. 2015. Exercise IV- Plantae and Fungi. Biology 210 Laboratory Manual

Freeman, Scott. 2014. Biological Science. Prentice Hall: New Jersey.

7/7/2015 Exercise III- Microbiology and Identifying Bacteria with DNA Sequences


When thinking about bacteria, there is generally a negative conotation. However, the reality is that there are many different kinds of bacteria. Some are negative and some are positive but as a whole bacteria can not be classified as negativ Bacteria can, however, be classified based on cell morphology. Bacteria are seen in three different shapes; bacillus which is rod-shaped, coccus which is spherical, and spirillum, which is spiral shaped. Bacteria can also be classified as gram negative or gram positive based on Gram staining. Gram positive bacteria have a thick layer of peptidoglycan and so can retain the dye while gram negative bacteria can not retain the dye and so stain a different color. During the last lab, unicellular organisms from the Hay Infusion Culture were observed. In this lab the prokaryotes from the transect culture will be observed (Bentley, 2015).


First, the agar and tetracyline plates were observed to determine the amount of bacteria growth. The number of colonies on the plate were recorded. The growth from the two different types of plates were then compared. Then the bacteria was Gram stained. This was done by choosing four colonies, two from two different agar plates, and two from two different tet plates, and mixing the colonies in a drop of water on four different slides. The area underneath the drops was then circled and passed over a flame multiple times until they were heat fixed. The bacterial smears were then covered with crystal violet for 1 minute before being rinsed off using a water wash bottle. Then the slides were covered with iodine mordant for 1 minute and again rinsed off. Next the decolarization solvent was used to flood the bacterial smears for 10-20 seconds. Finally the smears were covered with safranin for 20-30 seconds before this was rinsed off with water wash bottle. The slides were then allowed to dry before being examined under a microscope. Information about size and gram-positive/negative was recorded (Bentley, 2015).


The Hay Infusion Culture after a week looked similar to how it did five days ago. The differences were that the water was now almost clear and there was more of the mold like substance growing on top of the water. THe Hay Infusion smelled even worse, but in a more traditional swamp way.

Table 1:100-fold Serial Dilution Results TABLE378.png

Table 2: Bacteria Characterization TABLE576.png

All images below under 10x magnification

10^-9 agar -9ag.jpg

10^-5 tet -5T.jpg

10^-9 tet -9tet.jpg


The differences in the Hay Infusion Culture are most likely because it had more time to sit and develop. The appearance and smell might change from week to week in the Hay Infusion Culture because different bacteria could grow and develop as different food sources become available. For example as the bacteria that are the most fit reproduce more and become the dominant bacteria, their food source could become depleted and another bacteria would become most fit which would cause an increase in that bacteria and a decrease in the previously most fit bacteria. This fluctation is responsible for the changing smell and appearance of the culture.

For the agar and tet plates, the Archaea species grew on the agar plates made from the Hay Infusion because agar is a nutrition that Archaea bacteria can use to grow and reproduce. When the tet plates and the agar plates were observed there were visible differences between the two. The bacteria that grew on the tet plates were an orange color and the colonies were small, and became smaller as the sample became more diluted. The agar plates, however, had orange, cream, and light green colored bacterias. As the dilution became greater, the colonies grew larger and the types of bacteria became visibly more complex. The effect of tetracycline is that it appeared to eliminate all but one species and that it reduced the size of the colonies of that species.

The mechanism of action for tetracycline is that it can traverse the outer membrane of gram-negative enteric bacteria because they do not have a peptidoglycan membrane. Positively charged cations traverse the porin channels and then accumulate in the periplasm. They can then diffuse through the lipid bilayers and the tet is assumed to be species transferred from other bacteria when it is not in fact. In summary, the tet binds to the ribosome of the bacteria, which prevents the attachment of tRNA to RNA and so the bacteria genes cannot be expressed (Chopra, 2001).


Bentley, M., Knight, S., Zeller, N., Walters-Conte, K. 2015. Exercise III- Microbiology and Identifying Bacteria with DNA Sequnces. Biology 210 Laboratory Manual

Chopra, I., & Roberts, M. (2001). Tetracycline Antibiotics: Mode of Action, Applications, Molecular Biology, and Epidemiology of Bacterial Resistance. Microbiology and Molecular Biology Reviews, 65(2), 232–260. doi:10.1128/MMBR.65.2.232-260.2001

7/2/2015 Exercise II - Identifying Algae and Protists


All living organisms can be classified in to three domains; Bacteria, Archaea, and Eukarya. Eukarya are eukaryotes, meaning their cells have organelles and a membrane-bound nuclei. Bacteria and Archaea are both prokaryotes which means they do not have membrane-bound nuclei and organelles. Both prokaryotes and eukaryotes can be unicellular. The two large groups of unicellular eukaryotes are algae and protists. It is important to be able to identify these different organisms because they provide different roles in the environment; algae performs photosynthesis and protists consume nutrients. To identify the organisms in the previously prepared Hay Infusion (See 6/30/2015 entry) a dichotomous key is used. A dichotomous key consists of a series of two morphological questions that leads to the identification of the organism (Bentley, 2015). Using this key allows the unicellular organisms that populate the transect to be identified.


The Hay Infusion culture that was created last class was carefully brought over to the work area. The culture was then observed before two samples were taken from the culture. A sample was taken from the top and a wet mount was created by placing two drops on the slide and covering it with a cover slip. Using the same method, a sample from the bottom was also used to make a wet mount. These samples were then studied under a microscope and when an organism was spotted, a dichotomous key was used to identify it by answering the series of questions surrounding the organism's motion, shape, size, color, etc. Then nutrient agar petri dishes were inoculated with different concentrations of the culture. Four tubes of 5mLs sterile broth was labeled staring with 10^-2 and decreasing by a power of 2 for each tube. Four nutrient agar plates were also labeled starting with 10^-3 and decreasing by a power of 2. Finally four nutrient agar plus tetracycline plates were labeled with "tet" and also with 10^-3 and decreasing by a power of 2 for each plate. The Hay Infusion Culture was then mixed up and 50uL of the culture was added to the first tube, labeled 10^-2. 100uL from this tube was pipetted to the next tube and so forth until all the tubes were appropriately diluted. The serial dilution was then plated by pipetting 100uL from the first tube onto the nutrient agar plate labeled 10^-3 and carefully spreading it on the plate. This was then done for each agar plate and the corresponding tube and then again for the +tet plates. The agar plates were then placed agar side up in a rack to incubate at room temperature for five days (Bentley, 2015).

Serial Dilution Dilution2 2.jpg


The Hay Infusion Culture observations showed that it had a thin layer of a mold like substance growing on top of the water. There was also some leaves floating on top. The water itself was a murky brown/green and at the bottom there was a layer of sediment and some leaves that had sunk. The culture smelled musky and damp. On the top layer Pandorina of 50um were observed. There were lots of these organisms in the samples from the top and they were motile with green cells inside of them. Pandorina is a photosynthesizing green algae. Also on the top Actinosphaerium of 25um were observed. These are slow moving protists who do not photosynthesize. In the bottom sample, only one type of organism was observed. This was the Colpidium of 30um. Many of these motile protists were observed. They do not photosynthesize.

IMG 2273 7.jpg IMG 2274 2.jpg

Colpidium IMG 2293 6.jpg

Pandorina Pandorina687.jpg

Actinosphaerium Actinosphaerium38.jpg


The observation of only one organism in the bottom sample shows the low variability of the culture. This could be because it only sat out for 48 hours. If the Hay Infusion Culture was allowed to "grow" for another two months, the variability would greatly increase. However selective pressures could cause the bacteria who are best adapted for the environment to survive and reproduce, and so these bacteria would be most prominent. These selective pressures could be the amount of sunlight the culture gets, the temperature of the culture, or the food available to the bacteria in the culture. Certain bacteria could survive better in the different niches of the culture as well. This is because even though the culture is an ecosystem as a whole, the different niches provide different types of environment for the bacteria to grow in. For example, organisms closer to plant matter might be slime or water mold since they feed on decomposing matter such as leaves. In order to be considered an organism, it must have five fundamental characteristics; energy, cells, information, replication, and evolution (Freeman, 2014). An example of how an organism can meet all these characteristics is seen in Pandorina. Pandorina gets energy from photosynthesis, is a colony and so consists of cells, stores information in its nucleus since it is eukaryotic, replicates either asexually through mitosis or sexually, and finally has evolved since it is part of the volvocine line where Chlamydomonas is considered the origin of evolution (Bentley, 2015).


Bentley, M., Knight, S., Zeller, N., Walters-Conte, K. 2015. Exercise I- Examining Biological Life at AU, Exercise II- Identifying Algae and Protists. "Biology 210 Laboratory Manual"

Freeman, Scott. 2014. Biological Science. Prentice Hall: New Jersey. 2.

6/30/2015 Exercise I- Examining Biological Life at AU


Biological sciences wants to understand life, especially the diversity of it (Freeman, 2014) This biodiversity is due to evolution, which occurs through natural selection and other methods. Natural selection is the process where the fittest organisms survive because they are best adapted to the environment and so survive to reproduce more, passing their genes along to the next generation. In this lab, the biodiversity of life is studied by observing a transect, or an ecosystem. The biome of the transect studied in this lab is temperate forest. Transects are important because they provide the opportunity to study the different niches and the organisms that habitat them within an ecosystem and see how all the unique biotic and abiotic factors interact. Biotic factors are the living components of an environment while abiotic factors are the nonliving components. Both play a crucial role in ecosystems and are studied in this lab.


To observe the transect at AU, a 20 x 20 meter area on American University's campus was selected. The area selected is located on the northern side of campus, in between the amphitheater and McDowell Hall. When looking down on the amphitheater, the transect is to the right and to the right of the transect is McDowell Hall. This area was then visited and observations were made about the biotic and abiotic factors. Pictures were taken of the area. A sample was taken of the soil and plants and placed in a large plastic bag. Eleven grams of the sample was then placed in a plastic jar with 500 mLs of deerpark brand water. 0.1 gram dried milk was added to the mixture and the jar was capped. The mixture was then shaken for 10 seconds, labeled, and put on the window sill to sit for 48 hours (Bentley, 2015).


The selected transect consisted of trees, both big and small, with a stream running down the center of the transect. The stream was full of rocks along with sand. There was soil covering all the ground of the transect that was not the stream and there were bushes, ferns, weeds, and other plants. The transect was hilly, with the stream at the bottom and the land rising up on both sides of the stream. The biotic factors were the plants, trees, ferns, weeds, ants, and a few small birds. The plants and trees were spread around the stream, the birds were seen bathing in the stream, and the ants were seen crawling throughout the transect. The abiotic factors were the rocks, found in the stream, the water, dirt, air, and sand. The below images show the transect.

TET2261.JPG IMG 2257.JPG IMG 6287Hart.jpeg IMG 5340.jpg IMG 2255 4.jpg IMG 0906 2.jpg


The transect selected has multiple abiotic and biotic factors. These factors work together to provide habitats and food to the organisms that live in the ecosystem. In the observed ecosystem not many large mammals were seen and there is not much human traffic. However it is possible that deer or other mammals do visit this transect. This would be a good base for future observations. Another interesting question would be whether AU maintains the ecosystem at all since there was evidence of a sprinkler in the transect. If so it could change the natural environment.


Bentley, M., Knight, S., Zeller, N., Walters-Conte, K. 2015. Exercise I- Examining Biological Life at AU. Biology 210 Laboratory Manual

Freeman, Scott. 2014. Biological Science. Prentice Hall: New Jersey. 1.

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