Friday, December 8, 2017

14: Larrea Tridentata Preliminary Results

Me getting my silly faces out before the presentation
Preliminary Results: Leaf Microbiome of Larrea tridentata in Urban Phoenix Versus Rural Phoenix
This week, I focused on preparing to present my preliminary results to the S-STEM Team. During the presentation, I focused on summarizing the project focus and initial results. A summary of the results can be found below:
A total of 25 colony samples were isolated, however only 24 colony samples were analyzed due to a testing error with the colony sample from the Phoenix urban area (See Table 1). Initial results showed that roughly one third of the unknown samples have a Bacillus cell morphology, 29.2% have Cocci cell morphology, and 37.5% of the samples have a Coccobacilli cell morphology. Roughly 90% of the samples tested positive for endospores. Seventy-one percent of the samples tested positive for acid production in glucose, 54.2 % of the samples tested positive for acid production in Triple Sugar Iron Agar media, and over half of the samples tested positive for acid production in Mannitol Salt Agar media.. Approximately 75.0% percent of the samples were able to grow in 42 degrees Celsius. All the samples tested positive for gram stains and negative for Simmons Citrate. Nearly half of the samples tested positive for aerobic growth. 

Sunday, December 3, 2017

13: Larrea Tridentata Metabolic Test Completion

Metabolic Tests
Larrea Tridentata Metabolic Test Completion
I feel like the last two weeks have been a race against time. My goal is to finish testing and analyzing data for the remaining culture samples before our final paper is due. I finally completed all the metabolic and morphological tests on all 25 culture samples. It's definitely been a challenge to try and finish this goal, because for each culture sample, 13 different tests were needed to be completed. In total, that was 325 tests that had to be completed. I used an excel spreadsheet to keep track of all the tests ran and the results. I will focus on presenting the information collected thus far on the 25 culture samples. Next semester, I will focus on identifying the bacteria species of the 25 culture samples. 




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.