Thursday, November 16, 2017

12: Larrea Tridentata Research Paper in the Works!


Larrea Tridentata Research Paper in the Works!

This week I focused primarily on writing my rough draft of the research paper which focuses on the Larrea Tridentata leaf microbiome (see Blog 8). Later in the week, I ran an Endosphore Stain test on nine culture samples from the leaflet that was taken from the White Tank Mountains. I plan to analyze the Endospore Stains tomorrow. Additionally, I ran the Fluid Thioglycollate Media tests and they are currently in the incubator.  Once those results are recorded, I plan to start running the morphological and metabolic tests on the other 14 culture samples. My goal is to finish testing and analyzing data for the remaining culture samples before our final paper is due.

Thursday, November 9, 2017

11: Creosote Bacteria Identification for White Tank Mountain Samples Continued

Gram positive result from Plate 1 Colony 6

Continued:Creosote Bacteria Identification for "White Tank Mountain Samples"

The hunt for the unknown bacteria identification continues! This week I came closer to identifying a portion of the 23 unknown bacteria samples. I am currently focusing on Plate 1 (Colonies 1-7) and am performing a range of tests. I was able to identify the cell morphologies and cell wall types. Of the samples tested, they all are gram positive. I then compared the gram stain results with results from the MacConkey tests I performed on the "Plate 1" samples. The MacConkey tests confirmed that the samples are gram positive. Additionally, I ran Glucose Fermentation tests, Trypone Tests, and Sims Citrate tests on the samples and will document the results when they come out of the room temperature incubator after the weekend. I plan to continue to run the remainder of tests and indicate the results on an excel file that I have created.


Friday, November 3, 2017

10: Larrea Tridentata (Creosote) Project Background

http://www.sci.sdsu.edu/plants/sdpls/plants/Larrea_tridentata.html
Leaf Microbiome of Larrea tridentata Grown in Urban Phoenix Versus Grown in Rural Phoenix

Project Background
Research has shown rising levels of CO2 can alter the chemical composition of leaves in Larrea tridentata. Additionally, the nutrients in the soil can be altered (Wang 2011). Research has also indicated that environmental conditions and changes can influence adaptive traits of plant function over time (Kimball et. al 2012). It is imperative to learn more about the differences in the leaf microbiome of Larrea tridentata in urban and rural areas to gain understanding of how increasing urbanization can impact microbiome development and sustainability over time.
It is imperative to expand on current research of the Larrea tridentata leaves due to continuous changes in environmental conditions and the need to further understand adaptive traits of the leaf microbiome. In the study, "Urbanization alters spatiotemporal patterns of ecosystem primary production: A case study of the Phoenix metropolitan region, USA," research showed that urbanization affects the function of an ecosystem and its surrounding environments. The study also revealed that urbanization affects the net primary production of chemical energy (Buyantuyev and Wu 2009). Additionally, the study "Temporal patterns in near-surface CO2 concentrations over contrasting vegetation types in the Phoenix metropolitan area" addresses the need to study surface levels of CO2 in urban areas and its effect on plant life (Day, et al 2002).
Furthermore, some research suggests that Larrea tridentata possesses antibacterial properties in the aerial parts of the plant which can combat the increase in bacterial infections that are drug-resistant. Currently, Larrea tridentata has antibacterial properties in its leaves and understanding differences in leaf microbiomes in urban and rural areas may provide insight on antibacterial agents and their property types in different environments (urban and rural). In the recent study, "Antibacterial activity of crude methanolic extract and fractions obtained from Larrea tridentata leaves," researchers found that phytochemicals from L. tridentata leaves may aid in the development of natural antibacterial treatment (Martins 2013). The study also indicated the need to further research the hypothesis. By testing the differences in the leaf microbiome of the Larrea tridentata in urban and rural environments, it can aid in a future understanding of how urban and rural environment affects antibacterial properties of the Larrea tridentata aerial parts.

Key Terms
Aerial parts- parts of a plant that are exposed to air (i.e. leafs, stems, roots).
Net primary production- amount of chemical energy created by produces over a period of time.

Research question
Is there a difference in the leaf microbiome of the Larrea tridentata species in the Phoenix urban area and surrounding desert rural area?

Hypothesis
Hypothesis 1: The leaf microbiome of Larrea tridentata found in the urban Phoenix area is detectably different than the leaf microbiome of Larrea tridentata found in the Phoenix rural areas.
Hypothesis 2: As a result of urban area heat islands and a greater concentration of CO2 emitting vehicles, it is hypothesized that elevated CO2 and pollution will result in different microbial communities of Larrea tridentata growing in urban areas.

References:
A. Buyantuyev and J. Wu. "Urbanization alters spatiotemporal patterns of ecosystem primary production: A case study of the Phoenix metropolitan region, USA." Journal of Arid Environments, vol. 73, 2009, p. 512-520. Retrieved from https://ac.els-cdn.com/S0140196308003649/1-s2.0-S0140196308003649-main.pdf?_tid=98c8d5e0-c052-11e7-97a5-00000aab0f01&acdnat=1509684844_197eb558cc325b63cd9a6d7f80089f02

Kimball, Sarah, et al. "Fitness and physiology in a variable environment." Oecologia, vol. 169, no. 2, 2012, p. 319+. Academic OneFile,  go.galegroup.com/ps/i.do?p=AONE&sw=w&u=mcc_main&v=2.1&id=GALE%7CA356445949&it=r&asid=76cf9b7c721d99e2e39e481da1419f8d. Accessed 20 Oct. 2017.  

K.L. Neil et al. / Journal of Arid Environments 74 (2010) 440–444. https://ac.els-cdn.com/S0140196309003231/1-s2.0-S0140196309003231-main.pdf?_tid=ec4d747e-b54d-11e7-80e7-00000aab0f6c&acdnat=1508473374_2658d691676b7ce943e2833f5216b961.

Maki Jitsuno and Yoshihiro Mimaki. "Triterpene glycosides from the aerial parts of Larrea tridentata." Phytochemistry, vol. 71 2010, p. 2157–2167. Retrieved from https://ac.els-cdn.com/S0031942210003687/1-s2.0-S0031942210003687-main.pdf?_tid=82d1fcb8-c060-11e7-96af-00000aacb361&acdnat=1509690820_e82d8b4df86e7520365baba41e5ebc45

Martins,Silvia et al. "Antibacterial activity of crude methanolic extract and fractions obtained from Larrea tridentata leaves." Industrial Crops and Products, vol. 41, 2013, Pages 306-311. Retrieved from https://doi.org/10.1016/j.indcrop.2012.04.037.

Schultz, J. C., & Floyd, T. (1999, February). Desert Survivor. Natural History, 108(1), 24. Retrieved from http://link.galegroup.com.libproxy.maricopa.edu/apps/doc/A53682802/WHIC?u=mcc_main&xid=8b7d7592.

Shen, W., Wu, J., Grimm, N.B. et al. Ecosystems (2008) 11: 138. https://doi.org/10.1007/s10021-007-9085-0.

Thomas A Day, et al. "Temporal patterns in near-surface CO2 concentrations over contrasting vegetation types in the Phoenix metropolitan area." Agricultural and Forest Meteorology, vol 110, Issue 3, 2002, p. 229-245. Retrieved from http://www.sciencedirect.com.libproxy.maricopa.edu/science/article/pii/S016819230100288X#aep-section-id24

Wang, D. (2011). A meta-analysis of plant physiological and growth responses to temperature and elevated CO2. Oecologia, 169(1), 1-13. Retrieved October 19, 2017, from http://hh2wl8hm4u.search.serialssolutions.com/?ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=A meta-analysis of plant physiological and growth responses to temperature and elevated CO2&rft.jtitle=Oecologia&rft.au=Wang%2C Dan&rft.au=Heckathorn%2C Scott A&rft.au=Wang%2C Xianzhong&rft.au=Philpott%2C Stacy M&rft.date=2012-05-01&rft.pub=Springer-Verlag&rft.issn=0029-8549&rft.eissn=1432-1939&rft.volume=169&rft.issue=1&rft.spage=1&rft.epage=13&rft_id=info:doi/10.1007%2Fs00442-011-2172-0&rft.externalDBID=n%2Fa&rft.externalDocID=2012_442_169_1_2172mdict=en-US.

Weijun Shen, et al. "Effects of Urbanization-Induced Environmental Changes on Ecosystem Functioning in the Phoenix Metropolitan Region, USA." Ecosystems (2008) vol. 11, 2008, p. 138–155. Retrieved from http://leml.la.asu.edu/jingle/Wu-Publications-PDFs/2008/Shen_etal-2008-Ecosystems.pdf

Thursday, October 26, 2017

9: Creosote Bacteria Identification Continued

Continued:Creosote Bacteria Identification for "PC Sample" and "White Tank Mountain Samples"

This week I continued to perform two more tests on the creosote sample that was taken on the Phoenix College campus. The first test I performed was  Mannitol Salt Agar (MSA) which is used to identify if a bacteria can tolerate a high saline concentration. The second test performed this week was called  MacConkey Agar (MAC) which is selective for gram-negative bacteria. The inoculated plates were placed in the incubator at 37 degrees Celsius and results will be recorded by the end of the school week.
Additionally, the creosote plate samples from the White Tank Mountain area were continued to be further isolated with the goal of obtaining pure culture samples.

Friday, October 20, 2017

8: Larrea Tridentata (Creosote) Research Proposal


Retrieved from: Sonora-desert-detective
Leaf Microbiome of Larrea tridentata Grown in Urban Phoenix Versus 
Grown in Rural Phoenix
Background Information

Larrea tridentata is a species of plant common to the Mojave, Sonoran, and Chihuahan deserts. Larrea Tridentata’s unique properties allow for its shrubs not only to grow deep roots but spread out across more surface area in the which allows the shrub to dominate absorption of nutrients in the soil. Due to the chemical durability of the Larrea Tridentata species, many other organisms have adopted the Larrea Tridentata as their host environment (Schultz 1999). However, research has shown rising levels of CO2 can alter the chemical composition of leaves in Larrea tridentata. Additionally,the nutrients in the soil can be altered. (Wang 2011). Research has also indicated that environmental conditions and changes can influence adaptive traits of plant function over time (Kimball et. al 2012). It is imperative to learn more about the differences in the leaf microbiome of Larrea tridentata in urban and rural areas to gain understanding of how increasing urbanization can impact microbiome development and sustainability over time.

Research question
Is there a difference in the leaf microbiome of the Larrea tridentata species in the Phoenix urban area and surrounding desert rural area?

Hypotheses
Hypothesis 1:
The leaf microbiome of Larrea tridentata found in the urban Phoenix area is detectably different than the leaf microbiome of Larrea tridentata found in the Phoenix rural areas.
Hypothesis 2:
As a result of urban area heat islands and a greater concentration of CO2 emitting vehicles, it is hypothesized that elevated CO2 and pollution will result in different microbial communities of Larrea tridentata growing in urban areas.

Wednesday, October 18, 2017

7: Creosote Bacteria Identification from White Tank Mountain Area

Creosote Bacteria Identification from White Tank Mountain Area
This week was focused on completing more bacteria-identification tests on the leaf sample collected from a creosote bush here on Phoenix College's campus. The second focus of this week was to isolate bacteria samples taken from two creosote bushes located in the White Tank Mountain Area (Sample Extraction Coordinates:33⁰ 34’ 31’’ N, 112⁰ 34’ 44’’ W.
The samples obtained included taking swabs from a creosote bush's leaves and streaking them onto three TSA plates (Sample ID Label = Plate 1 C1-C7; Plate 2 C1-C6; and Plate 3 C1-C8). From an additional creosote bush, three vials of leaf samples were collected and are in the process of being streaked on TSA plates. 
Plates 1-3 were taken and observed for different colony types. Next isolation streaks on TSA were performed for each colony type observed. A total of 21 colonies were observed and streaked on TSA. After being incubated at 37 degrees Celsius, the TSA plate samples were observed for colony growth, and it was determined that the TSA plate samples for the 21 colonies should be further isolated with the goal of obtaining pure cultures. Currently, the second round of isolating the colonies is in process. Below are pictures of the three plate samples collected from the one of the creosote bushes in the White Tank Mountain area. 
     


6: Cold Case of the Flu

Cold Case of the Flu
This past week, the identification of the unknown bacteria found on the Creosote sample 1 "PC Sample" was put on hold because I came down with the Flu. Three reasons why I would have rather contracted some other virus or sprained a body part in lieu of getting the Flu:
1. Vomit makes me cry (there was a lot of vomit associated with my Flu).
2. I had the worst headache of my life, I thought I was going to die.
3. It took me like nine days to start to feel better.
It's been nine days since I came down with the flu, I still feel nauseous and have an upset stomach. Nonetheless, I am glad to be back at school and working on my S-Stem project.