User:Nadia Khan/Notebook/Biology 210 at AU

Invertebrates and Vertebrates: A Study of the Transect’s Critters, July 14th,2015

Introduction: Invertebrates consist of the large category of animals that lack a backbone, making up nearly 95% of the world’s species (Freeman, et. al., 2014). Through the progression of our lab experiments, we have come to know that our particular transect on American University’s campus houses various bacteria and plants. However, the purpose of our this last lab was to gain a deeper understanding of the important role that invertebrates play in this ecosystem and to learn how such simple eukarya transformed into more complex creatures in this environment. I predicted that there would be minimal variation in the invertebrates, between both the arthropoda and annelida phylums, that we would discover.

Methods: Firstly, planaria, nematoda, and annelida were analyzed with a dissecting scope to familiarize ourselves with their movements and digestive mechanisms. Then, 10-15 mL of liquid and organisms from the surface of the Berlese Funnel was poured into a petri dish. The rest was poured into another. Materials in the petri dishes were probed to identify any organisms. After discovering what appeared to be five different organisms collectively from both petri dishes, we used a pipet to transfer them to five different slides to observe under a microscope. Resources were used to aid in the identification of these organisms.

Results: Table 1: Invertebrates

Organism	Length (mm)	Number in Sample	Description of Organism
Aphid- arthropoda, insecta	1	1	bilateral, tripoblastic
Round millipede- arthropoda, diplopoda	10	2	bilateral, tripoblastic
Roly poly- arthropoda, (crustacea) malocostraca	5	3	bilateral, tripoblastic
Neoantistea magna- arthropoda, arachnida	4	1	bilateral, tripoblastic
Big brown mite- arthropoda, arachnida	1	4	bilateral, tripoblastic

Table 2: Vertebrates

Vertebrate	Phylum	Class	Order	Family	Genus	Species	Biotic	Abiotic
House Sparrow	Chordata	Aves	Passeriformes	Passeridae	Passer	P. domesticus	lady fern, swamp saw grass, flowering dogwood tree	water, mud
European Starling	Chordata	Aves	Passeriformes	Sturnidae	Sturnus	S. vulgaris	neonantistea magna, aphid, english ivy, flowering dogwood	water, mud
Gray Catbird	Chordata	Aves	Passeriformes	Mimidae	Dumetella	D. carolinensis	flowering dogwood tree, neoantistea magna, round millipede, aphid	water, mud
American Robin	Chordata	Aves	Passeriformes	Turdidae	Turdus	T. migratorius	flowering dogwood tree, roly poly, aphid, neoantistea magna, round millipede	water, mud
Eastern Gray Squirrel	Chordata	Mammalia	Rodentia	Scuiridae	Scuirius	S. carolinensis	flowering dogwood tree, swamp saw grass, birds	water, dirt, sidewalk, gravel

Figure 1: Aphid
Figure 2: Round Millipede
Figure 3: Roly Poly
Figure 4: Neoantistea magna
Figure 5: Big Brown mite

Figure 6: Food Web

Discussion: There was no variation in the phylum of organisms that we found in our transect, however, there was variation in the class that these organisms belonged to. All five organisms were part of the arthropoda phylum. This particular phylum was most common likely due to the fact the phylum itself is so broad and diverse, thus collecting in numbers. Features typical to organisms in this phylum include their segmented bodies, exoskeletons, jointed legs, and numerous appendages. Temperate forests tend to sustain arthropods due to the crucial role that they play in the ecosystem. Arthropods can be vital decomposers and significant in flower pollination and water infiltration (Freeman et. al., 2014). The most common class of arthropoda in our sample were the arachnida. The most common organism was the big brown mite and the least common were the aphid and the roly poly. All of the arthropods we identified were bilaterally symmetrical and tripoblastic, meaning that they had three germ layers- the mesoderm, endoderm, and ectoderm. My hypothesis was partially supported, although there was no organism in the annelida phylum identified. The organisms were all fairly tiny, ranging from 1 mm to 10 mm. The average size was 4.2 mm. In regards to the food web, it demonstrates a community as these various species interact with and rely on each other for survival due to nutrients that they can offer. This community is affected by the resources that its ecosystem can provide, as each species’ carrying capacity (or in other words, their individual maximum population sizes) must be sustained by their environment. Lastly, each individual species represented in the web bears its own trophic level, illustrating its position in the food chain and collectively, illustrating the idea that one organism must be consumed by another and thus die to propel the other’s survival.

References: Freeman, S., Allison, L., Black, M., Podgroski, G., Quillan, K., Monroe, J., Taylor, E. (2014). Biological Science (5th ed.). Glenview, IL: Pearson Education, Inc.
National Audubon Society. (2015). Guide to North American Birds. Retrieved from http://www.audubon.org/field-guide/bird/gray-catbird

Plantae and Fungi: Transect Biodiversity, July 9th, 2015

Introduction: The purpose of this experiment was to understand the differing traits present in the plethora of plants that exist and to understand the significant role that fungi play in our daily lives. Both plants and fungi are eukaryotes, however plants are autotrophs, giving them the ability to photosynthesize, while fungi are decomposers, allowing them to release enzymes that break down organic materials to absorb. I hypothesized that there would be diversity evident in the vascular systems, specialized structures, and mechanisms of reproduction in the plants and fungi found in our transect.

Methods: A leaf litter sample from our transect was collected and stored in a Ziploc bag. Additionally, five different plants were obtained from the area. To prepare for the Berlese Funnel, 25 mL of 50:50 Ethanol/water solution was poured into a 50 mL tube. Then the test tube was attached to the bottom of a funnel as the funnel was placed on a ring stand. Screening material was inside the funnel that allow filtration of the leaf litter sample after it was placed in the funnel. The ring stand was then placed under a light.

Results: 1)
Lady Fern: This plant was collected on the east side of our transect next to the flowering dogwood tree where there were about 10 of them. The lady fern has green feather-like leaves and ranges from about 2-5 ft. in height. It is vascular and some of its specialized structures include sori and indusia. Its mechanism of reproduction involves the sori growing on the underside of the leaves. 2) ‎
English Ivy: This plant was found on the east side of our transect right next the stream. There were about 3-4 of these plants in the transect. The english ivy has dark green leaves and a vine-like stem. The plant is vascular and some of its specialized structures include aerial roots. Mechanisms of reproduction involved the dispersal of seeds with hard outer-shells (dicot). 3)
Flowering Dogwood: The leaf of this plant was collected from its tree which is located on the east side of the transect. The tree was generally 15-30 ft. tall in height and blooms flowers, however this one did not have any flowers. It is vascular and some of its specialized structures include its roots. Its mechanism of reproduction involves flowers and seeds (dicot). 4) ‎
Royal Standard Hosta: This plant was found on the northern side of our transect across the water and behind the flowering dogwood tree. There were about 10 of them, each with a vascular system. Its leaves are large and round. Specialized structures include its perennial flowers. Its mechanisms of reproduction involve rhizomes and stolons (monocot). 5)
Swamp Saw Grass: This plant was found right next to the stream on the southern side of the transect. There were approximately 15 of them. The leaves are individual blades and their mechanisms of reproduction involve rhizomes (monocot).

Discussion: There was variation in the plants that we discovered confirming the biodiversity evident in our transect. all of the plants that we found had vascular systems and shared blank blank but differed in blank blank However, there were no fungi identified.

Reference: "Plant Finder." Plant Finder. N.p., n.d. Web. 12 July 2015.

Microbiology and Identifying Bacteria with DNA Sequences: Bacterial Growth on Plates, July 7th, 2015

Introduction: Bacteria are prokaryotes and are considered one of the three domains of life. There is often a notion that bacteria largely play a negative role in our lives, but there is only a very small amount of bacteria in our bodies that are actually pathogenic- the rest are neutral or serve beneficial purposes. The purpose of the experiment was to witness firsthand the differences in morphology of various bacteria and observe their ability to be antibiotic resistant. Additionally, another goal of this experiment was to identify bacteria using PCR and DNA sequencing techniques. If nutrient agar was on the plate, then I expected that there would be more bacterial growth on the plate because the nutrient agar would provide nourishment for the bacteria. If tetracycline was on the plate, then I expected that there would less bacterial growth on the plate because the tetracycline is an antibiotic. However, it was possible that there would not have been a significant reduction in bacterial growth on the plates with tetracycline if the bacteria happened to be antibiotic resistant.

Methods: Firstly, the bacterial growth on the eight plates was observed and recorded to compare the differences in numbers between the plates with nutrient agar and the plates with tetracycline. Then a wet mount slide was prepared of two distinct colonies from both types of plates and the colonies were described. To prepare the wet mount, a sterilized loop was used to pluck a very miniscule amount of bacteria from the plates. Then the selected bacteria was mixed with a drop of water on the wet mount slide. The shapes of the cells from the bacteria and their motility was observed through 10x and 40x lenses. Then to begin the gram stain, the wet mount slide was fixed by passing it over the flame of a Bunsen burner. The four wet mount slides were placed on a staining tray and drizzled with crystal violet for a minute. Then it was rinsed with a wash bottle. Again, the process was repeated with Gram’s iodine mordant. Then the slides were washed with 95% alcohol for 10-20 seconds for decolorization to occur. Lastly, safranin was drizzled for 20-30 seconds over the slides and rinsed off. Kimwipes were used to remove excess water from the slides before they were observed under the 40x. Lastly, 10^-5 plate with tetracycline and 10^-9 plate with nutrient agar were chosen for the PCR reaction. We extracted a bacterial colony from each and added primer with a PCR bead before leaving the tubes in the PCR machine.

Results:

10^-5 nutrient agar
10^-9 with Tetracycline

Discussion: After checking on the Hay Infusion culture, there appeared to have been some changes in its appearance and smell. The culture was more clear, less foggy, however there was development in the amount of film that was on the surface. There was still dirt settled at the bottom, except now with the addition of white chunks floating in the water. The odor was more powerful and still very swamp-like. The appearance may change from week to week because of the diminishing sources of nutrients in the jar to sustain the life inside of it. The results of the plates were different from what we had anticipated. In regards to the plates, the ones with tetracycline had more bacterial growth than the plates with nutrient agar likely because of the presence of an antibiotic resistant gene in the transect. It was likely that there was no archaeal growth in the colonies because those types of prokaryotes could not flourish in this particular environment.

Serial Dilution of Hay Infusion of Amphitheater Stream, July 2nd, 2015

Introduction: The goal of this lab was to familiarize oneself with identifying unknown unicellular eukaryotes using a dichotomous key as there are several different lineages. Understanding and identifying the algae and protists as well as their structural and functional differences was important in distinguishing them. Algae have the ability to photosynthesize while protists consume nutrients. Surveying the area for these organisms could relay to us information about the way that such environmental factors interact and the causes and effects that such bacteria have on the abiotic and biotic factors that exist in the transect.

Methods: Before beginning the serial dilution, two samples of the hay infusion from the stream was extracted from the top of the jar and two from the bottom and prepared on wet mount slides. They were analyzed under the microscope through 10x and 40x lenses and the eukaryotes on the slides were identified using a dichotomous key. Their sizes were recorded. Then, the hay infusion was shaken in the jar to begin the serial dilution. To begin this, 50μL of the Hay Infusion was added to 5mL of sterile broth. Then, 50μL from this dilution was then added to another tube of 5mL of sterile broth, making the substance more diluted. These steps were done twice more to achieve four tubes of diluted solutions, each at a different level of dilution- 10^-2, 10^-4, 10^-6, and 10^-8. Then, we prepared eight nutrient agar dishes in which four had tetracycline. A dish with and a dish without tetracycline were labeled 10^-3, 10^-5, 10^-7, and 10^-9. 50μL of 10^-2 solution were applied to the both of the 10^-3 plates and 50μL of 10^-4 solution were applied to both of the 10^-5 plates. 50μL of 10^-6 solution were applied to the 10^-7 plates and 50μL of 10^-8 solution to the 10^-9 plates. Lastly, the dishes were set aside to grow.

Results: The hay infusion was cloudy and had a white and green tint to the water. There was sediment at the bottom- it appeared as though there was a layer of sandy material. There were green, leafy particles at the top with a grimy film over part of it. There was a strong earthy odor to the substance. We were only able to identify three eukaryotes in the hay infusion. One of them was pandorina, one was colpidium, and the third was acetinosphaerium. There was numerous pandorina (50μm), a green algae, that was found at the top of the substance. They were very motile. There were several colpidium(30μm), a protozoa, found at both the top and bottom of the substance. Like pandorina, they were also motile. The last organism discovered was acitinosphaerium (25μm), another protozoa, found at the top of the hay infusion. The organism was very slow moving. Because the pandorina was an algae, it was able to photosynthesize, while the two other eukaryotes, being protozoa, were not able to.

Discussion: Unfortunately, only three different organisms were distinguished in the hay infusion. This lack of diversity in the sample could suggest that the sample taken was an inaccurate reflection of the transect or that the transect does not suit algae and protists well which is why there was a minimal number of different eukaryotes present. The organisms may have differed due to their distance from the plant matter because of the nutrients that the plants could provide to them. If they hay infusion grew for another two months, I would predict that the numbers of algae and protists in the sample would become less and less. Selective pressures such as lack of energy resources from food and the sun would play a role in their inability to survive.

Examining Biological Life at AU: Hay Infusion of Amphitheater Stream, June 30th, 2015

Introduction: The goal of this experiment was to understand how different organisms in an ecosystem are categorized and to familiarize oneself with observing niches in great detail, seeing natural selection play out as evidenced by the evolution of said organisms. The study of a transect, which is a land sample used to assess the vegetation patterns and animal population of a specific area, is effective in analyzing biodiversity and phylogeny. This in turn helped reach the goal of the experiment. The transect chosen was the stream next to the amphitheater on American University’s campus because of its important role on AU’s campus as a certified wildlife habitat. If there are several different biotic elements present in the transect, then all of these organisms bear traits that were selected for and prove the organisms’ fitness for this particular environment.

Methods: Upon arrival to the stream, we used a meter stick to chalk out a 20 m by 20 m space as the transect for our observations and sample collection. We observed the stream and its surrounding wooded area, taking note of the evident biotic and abiotic elements and photographing the ecosystem. Then we collected a sample of soil next to the stream that was reflective of the majority of soil in our transect and sealed it in a plastic bag. After returning to the classroom, 500 mL of Deerpark water was obtained and kept in a jar. Using a balance, 10 to 12 grams of the soil sample was measured and added to the jar. Again, using the balance, 0.1 gram of dried milk was measured and added to the water and soil mixture that was then shaken up in a now closed jar for 10 seconds. The jar was opened and after having been labeled, kept aside in the lab.

Results: Abiotic factors included water, sand, gravel, pebbles, stones and dirt in the stream. Surrounding the stream there was a sidewalk. Biotic factors included plants, grass, trees, and roots that bordered the stream. There was also a robin, house sparrows, and a gray catbird that flew over the transect. There was low traffic in the area with rarely anyone in the transect itself as it was a fairly isolated space among due to the heavy vegetation.

Discussion: The lack of human invasiveness likely proves beneficial to the ecosystem. After observing the site, there was evidence of a variety of organisms. This transect was an environment that could provide nutrients for several different organisms as they could flourish. They proved to coexist well. This could change due to availability of resources and thus competition due to overpopulation.