User:William Jessup/Notebook/Biology 210 at AU

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Invertebrates and Vertebrates from the Transect 07.09.15

Introduction: In every ecosystem there is a wide array of organisms. Each organism belongs to a certain trophic level, or position on the food chain. Each organism within a community relies on one another for sources of nutrients and food. If one organism goes extinct within the ecosystem, it could have a dire consequence on the rest of the species in the area and the community will need a find a way to fill the empty niche within the ecosystem.

Animals area huge part of just about every ecosystem. Any organism in the animal kingdom is multicellular, eukaryotic, and heterotrophic. The kingdom can be split into two sub-groups: vertebrates and invertebrates. Invertebrates make up over 90 percent of all animals on the planet. They come in a variety of shapes and sizes. Invertebrates can have both radial, bilateral, or no symmetry. Bilateral symmetry is where an organism can be cut into two identical halved only one way. Organisms like this consist of an anterior, a posterior, and both a right and left side. Radially symmetric organisms can be divided in half in multiple ways, similar to a pizza. Invertebrates can also have anywhere from zero (sponges) to three (Flatworms and Roundworms) germ layers. Germ layers are layers of cells that are initially formed during embryo development. Organisms with radial symmetry are diploblastic meaning they have two germ layers. On the other hand, organisms with bilateral symmetry are triploblastic and have three germ layers.Vetebrates are also a very diverse group of organisms. A vertebrate is any chrodate with a backbone. These consist of fish, birds, mammals, reptiles, and more. All vertebrates are bilaterally symmetric and triploblastic.

Methods: Using the Berlese funnel set up in the previous lab, we started studying some invertebrates found in our transect. The test tube of water/ethanol was removed from the funnel and split between two petri dishes. The organisms were examined under a microscope after being place in a depression slide. Using a key, the organisms were identified. Then, we traveled to our transect to identify five vertebrates living in the area.



Organism Phylum and Class Length (mm) Number in Sample Description
Aphid Arthopoda, Insecta 1 1 Bilateral Symmetry, Triploblastic
Round Millipede Arthopoda, Diploda 10 2 Bilateral Symmetry, Triploblastic
Pill Bug Arthopoda, Mallacostraca 5 3 Bilateral Symmetry. Triploblastic
Neoantistea manga Arthopoda, Arachnida 4 1 Bilateral Symmetry, Triploblastic
Brown Mite Arthopoda, Arachnida 1 4 Bilateral Symmetry, Triploblastic


American Robin: Chordata, Aves, Passeriformes, Turdidae, Turdus , T. migratorius

Eastern Gray Squirrel: Chordata, Mammalia, Rodentia, Sciuridae, Sciurus , S. carolinensis

European Starling: Chordata, Aves, Passeriformes, Sturnidae, Sturnus , S. vulgaris

Gray Catbird: Chordata, Aves, Passeriformes, Mimidae, Dumetella , D. carolinensis

House Sparrow: Chordata, Aves, Passeriformes, Passeridae, Passer , P. domesticus


Figure 1: Transect Food Web: the following image shows how the organisms found within the transect rely on one another for sources of food. Each organism has its own trophic level within the food web in which it consumes or is consumed by others. The arrows show the direction in which the energy (food) flows between species.


In our transect, we found a large variety of both invertebrates and vertebrates. The macro-biodiversity seems to be much stronger than it did on the micro level because we were able to find and identify many more species. All of the organisms found live together in the community and rely on both the biotic and abiotic factors of their ecosystem. All of the organisms found in the transect, both plants and animals, need water to survive. The stream provided a direct source of water for all of the vertebrates found in the transect. The trees and shrubs provided cover, food, and nesting areas for the birds and mammals that live there. Some of the invertebrates relied on the debris from other organisms as a source of nutrients. Rocks could provide cover for both invertebrates as well as some of the smaller vertebrates. Every factor in the ecosystem plays a crucial role in the survival of the species that call our transect home.

Our transect seemed to have a very high carrying capacity for macroorganisms. There was plenty of plant life to feed and shelter herbivores and detrivores, which attracted some more carnivores and insectivores. If the carrying capacity, or maximum population size based on necessities, was pushed beyond its limits by any species, we would likely not have seen as wide of a biodiversity as we did in the area.

Plant Life in the Trasect 07.09.15

Introduction: Plants are multicellular eukaryotes that perform photosynthesis to produce oxygen and glucose. There are thousands of species of plants that come in all shapes, sizes, and colors. They span across the entire globe and play a vital part in every ecosystem. As plants evolved, they became vascular, meaning they can conduct water and other liquids through their xylem and phloem. This enables plants to grow much higher.

Methods: First, we visited our transect again. This time we collected and identified five different plant samples from different areas. In order to identify them, we had to use various apps and web pages. In addition to our samples, we collected a bag of leaf litter and set up a Berlese Funnel to detect invertebrate living in the transect. To do this, we poured 25mL of 50:50 ethanol/water solution into a test tube and taped the test tube to the bottom of the funnel. The funnel was place on a ring stand and had screening material taped to the inside to prevent any debris from falling into the test tube. The leaf litter was then place in the funnel which was then placed under a light.


Plant Locations within the transect:

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Transect Plant Sample Location and Count Description Vascularization Specialized Structures Reproductive Mechanisms
English Ivy (1) 3-4 Long and viney, brown stem with multi-green leaves Vascular Leaves are alternate and palmate (~50mm), No flowers Spread by seeds in berries (none found), Dicot seed
Lady Fern (2) 10 Green leaves, red stem, approximately 1-2 feet Vascular
Cespitose, (leaves are in small clumps instead of from stem) Spores grow on underside of leaves (none found), (neither monocot or dicot)
Flowering Dogwood (3) 1 20 feet tall, not flowering yet Vascular Leaves are opposite and ovate (~7in), No flowers Dicot seed, Seeds are spread by small fruit (~10mm)
Royal Standard Hosta (4) 10 2-4 feet, thin stem, large round leaf, veins curve and follow leaf edge Vascular Single broad ovate leaf per stalk, Grow from either stolons or rhizomes Monocot , No flowers have grown yet, Seeds are found in small pods in the flower, Uses rhizomes to reproduce
Swamp Sawgrass (5) 10 3-4 feet, thin grass-like blades, green Vascular Leaves are narrow singular blades, Spread by rhizomes (underground stems) Monocot, Uses rhizomes to reproduce


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Discussion: Although not every plant from the transect was recorded, these five plants are demonstrate the large variety of plants that can be found in such a small area. Each plant looks different and has different structures that allow for survival.

Bacterial Smears from the Hay Infusion 07.07.15

Introduction: Bacteria are a prokaryotic domain of microorganisms. They are some of the most abundant organisms on the planet and can be found everywhere: desktops, toilet seats, even inside of people. Bacteria have a large range of responsibilities, from helping plants absorb nitrogen to helping larger organisms with digestion. Some can even cause diseases like strep throat, pneumonia, and cholera. Tetracycline is an antibiotic that prevents the synthesis of proteins within a bacterial cell (Klajn). When it was first discovered in the fifties, it was very effective against a wide variety of bacteria as well as some viruses (Klajn). However, because the antibiotic was over used, microorganisms began to develop resistance and tetracycline is no longer used for more common bacterial infections such as streptococcal (Klajn). The use of tetracycline can lead to the increase in the population of unaffected organisms like fungi (Klajn).

Methods: After several days of growth, we observed the bacterial growth on the Agar plates that we set up in the previous lab. The numbers of colonies were noted as well as key characteristics including size, shape, etc. Next, we chose four plates, (10-5 and 10-9 for both the agar and tetracycline agar) to do a wet mount for one bacterial colony. In order to this, we took a sterile loop and removed a small amount of growth from the agar. The bacteria was placed on a slide and mixed with a drop of water. The slide was then fixed by moving it across the flame of a Bunsen burner until the solution solidified or gelled. This process was repeated for each of the four plates. Each slide was then stained according to the Gram stain procedure by pouring several different solutions and distilled water over them. The slides were then allowed to air dry and observed under a 40x objective lens. Colony and cell descriptions were recorded. Finally, we prepared two colonies from separate plates for a PCR 16S amplification. To do this we mixed primer with the PCR bead and added a bacterial colony. The tube was placed in the PCR machine and left there. The two plates chosen for the PCR reaction were the 10-5 Tetracycline plate (1.1) and the 10-9 agar plate (1.2).


Table 1: Serial Dilution Results: This table shows the total number of colonies found on each plate and how many colonies could be found in each mL of each dilution

Dilution Agar Type No. of Colonies Conversion Factor Colonies per mL
10^-3 Nutrient Lawn X10^3 N/A
10^-5 Nutrient 600 X10^5 12,000,000
10^-7 Nutrient 300 X10^7 6,000,000
10^-9 Nutrient 60 X10^9 12,000,000,000
10^-3 Nutrient and Tetracyline Lawn X10^3 N/A
10^-5 Nutrient and Tetracyline 500 X10^5 10,000,000
10^-7 Nutrient and Tetracyline 650 X10^7 6,500,000,000
10^-9 Nutrient and Tetracyline 1000 X10^9 200,000,000,000

Table 2: Bacterial Characterization: This is the data collected from the four plates from which bacterial slides were made. It has key characteristics of colonies and cells of the bacteria.

Plate Type Colony Description Cell Description Gram Test
10^-5 Agar Flat, creamy yellow/white, punctiform Non-moving, spherical, clustered growth Gram -
10^-9 Agar Undulate, flat, orange, irregular Non-moving, rod shaped, non-clustered growth Gram +
10^-5 Tetracycline Flat, orange, punctiform Non-moving, rod shaped, connected at ends Gram -
10^-9 Tetracycline Flat, orange, punctiform Non-moving, spherical, clustered growth Gram +

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Figure 1: In the same order of the table, these are drawings of the bacteria found on each slide. All bacteria were drawn at under a 40X objective lens.

Discussion: After checking the Hay Infusion one last time, we noticed that it was much less cloudy. It was almost clear with some white filmy substances floating around. There was still some sediment on the bottom of the jar. There was also more green-brown film growing on the top.

The two types of plates yielded very different results for bacterial growth. The plates with tetracycline grew much more bacteria. For the most part, the tetracycline had more colonies than its regular counterpart. However, the colonies were typically much smaller on the tetracycline plates. There was obviously a tetracycline-resistant gene present in the transect because of the large amount of growth on the tetracycline plates. The larger count of colonies could be due in part to the decrease in competition for food and other resources as bacteria without tetracycline resistance died off.


Klajn, R. (n.d.). Tetracycline - antimicrobial properties. Retrieved from

    University of Bristol website: 

Algae and Protists in the Hay Infusion 07.02.15

Introduction: Out of all the Eukaryotes, the two major groups of unicellular organisms are algae and protists. Algae perform photosynthesis, converting light energy into chemical energy. On the other hand, protists consume nutrients to produce energy. Both unicellular eukaryotes have multiple lineages and a wide variety of species that fall under their kingdom. The goal of this experiment was to observe and identify the protists and algaes that are living in our transect. These organisms are very important to biodiversity because they are often the base of the food chain, supporting all of the organisms later in the chain. The photosynthetic protists also help to produce oxygen, which is consistently consumed by many organisms.

Methods: First, two wet slides were prepared from samples from two different niches (Top and Bottom) in the Hay Infusion. The slides were observed on 10X and 40X objective lenses and any algae or protists were identified using a dichotomous key. After identifying several protists, we shook up the hay infusion and prepared a serial dilution. In order to this, we took 50μL of the Hay Infusion mixture and added it to 5mL of sterile broth creating a 1:100 dilution (10^-2). 50μL of the 1:100 dilution was then added to another tube of 5mL of sterile broth, making a 1:10,000 dilution (10^-4). This process was repeated two more times to produce a 10^-6 and a 10^-8 solution. Additionally, a total of eight nutrient agar plates were set up, four of which had tetracycline added. One of each type of plate was labeled the following: 10^-3, 10^-5, 10^-7, and 10^-9. For each plate, 50μL of a specific solution was added. 50μL of 10^-2 solution were smeared on the both of the 10^-3 plates. 50μL of 10^-4 solution were smeared on the both of the 10^-5 plates. 50μL of 10^-6 solution were smeared on the both of the 10^-7 plates. Finally, 50μL of 10^-8 solution were smeared on the both of the 10^-9 plates. All of the agar nutrients plates were then placed off to the side for the incubation. See image below for more details.

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Results: After sitting out for two days, the Hay Infusion turned a milky white color, with some sediment laying on the bottom of the jar. A greenish brown film was also starting to grow on the top of the mixture. The solution smelled like dirt or mud and very swampy.

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Only three organisms were found and identified. At the bottom of the Hay Infusion, only one organism, Colpidium, was found while at the top two other organisms were found, in addition to more Colpidium. The following table examines key characteristics of of each organism:

Organism Type Size (μm) Location with Hay Infusion Count Motility
Colpidium Protizoa 30 Top and bottom A lot everywhere motile
Pandorina Green Algae 50 Top only A lot everywhere Very motile
Actinosphaerium Protizoa 25 Top only 2 total Very slow moving

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Of the organisms discovered, only the Pandorina was a photosynthesizing eukaryote. The other two consume nutrients produced elsewhere.

Discussion: For some reason, only three separate organisms were identified in the Hay Infusion. This could be in part to the soil sample that was take. Perhaps it was just a bad sample. However, it could also mean that there is a poor biodiversity for protists and algae in our transect. If the Hay Infusion were to continue growing for two or more months, I would expect for the food supplies to slowly decline resulting in a decline in protist population. Eventually I would expect all life within the jar to die. Selective pressures that could affect the life in the jar is the amount of food and sunlight reaching the jar.

Establishing a Transect 06.30.15

Introduction: A transect is an established section of a habitat or ecosystem that is typically monitored for biodiversity. Biodiversity, the number and type of species found in a region, is so important because it increases the opportunity of medical advances, economic development, and biological resource discovery. By studying a specific transect, we can estimate the biodiversity and health of other ecosystems with similar environments. The purpose of this experiment is to analyze the biodiversity of a transect on the campus of American University.

Methods: To establish a transect, we walked to the Woods-Brown Amphitheatre and found a lush area (20x20 m2) with a small stream flowing through it. We walked around the area and looked for any abiotic and biotic factors we could find without disturbing the environment. We collected soil samples from a couple different locations in the transect for the hay infusion. To make the hay infusions, we added ~10g of the soil sample to 500mL of distilled water and 0.1g of dried milk. The solution was mixed and placed by a window without the lid on.

Results: The transect we found was on a hill with a small stream flowing through it. On one side there was a sidewalk and on the other was the McDowell residence hall. The area had several trees and smaller shrubs, as well as tall grasses and ferns. We also observed several species of birds, including American Robins and a Common/European Starling that were drinking from the stream.

Abiotic Factors:  Rocks  Sidewalk  Water (manmade stream)  Dirt  Sprinkler head  McDowell Hall

Biotic Factors:  Plants (Ivy, ferns, tall grass, trees, etc.)  Birds (American Robin, European Starling, House Sparrow, Gray Catbird, unidentified)  Insects (ants, gnats)  Crustacean (Armadillidiidae/ Pill Bug)

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Discussion: There was a large variety of both Biotic and Abiotic factors that were observed in the transect. Although some of the plant and animal species were unable to be identified properly at the time, we got a good idea of the variety of living organisms in the area. It will be interesting to see the actual species count because not only is American University is a certified National Arboretum, but our transect falls directly on a designated wildlife habitat, so it should potentially have numerous plant and animal species.