J.N "Ding" Darling National Wildlife Refugee

                             J.N "Ding" Darling National Wild Refugee
Replacing blogs 4 & 5.
Visited on 2/11/2017

Incoming Reflection - What are your initial expectations of Colloquium?

1. Incoming Reflection - What are your initial expectations of Colloquium?

As a Floridian, and being raised by my hippie father, exploring natures plunders has always been an integral part of my life. Whether it was sauntering as a beach bum, jeopardizing my innocence on airboat rides in the Everglades or exploring trails around the state, I have always felt as if I have had a good moral standing with nature. Exploring these assorted environments aided in molding my understanding of how precious nature and her resources are and even, if I dare say, have fashioned me into a tree hugger.

  My sister and I eyes were open to the diverse beauty in nature from Florida and North Carolina to Europe and Australia, but my favorite memories and experiences with the cosmos was camping. One summer we camped for a month with two other families, encountering different landscapes and adventures. Tree climbing was our favorite activity and let me tell you, it was invigorating as a young girl.  Camping is one of the closest enterprises to be in tune with a surrounding ecosystem and being surrounded by nature has always felt like home.

Having a friendly relationship with nature makes me excited for this class.  I hope to see different parts of Florida’s treasures that I perhaps haven’t had a chance to encounter and the perspectives that they hold. I am really trusting that this will not be another cookie cutter class with no exploration of the outside world.  What I would love to see is another understanding of the view of nature and see if it can be melted into the rigors of engineering. Nature is whimsical, poetic and free whereas engineering offers direct solutions backed by laws of science. I hope to be a part of bettering nature and its stability in all aspects of my life and con not wait to aid in a big way. 

Week 1 Quiz

Literature Review Blog 2: Production of biofuels

Literature Review Blog 2: Production of biofuels

Towards Sustainable Production of Biofuels from Microalgae

As the world’s population increases, the consumption of energy is sky rocketing. It is predicted that the world energy demand will increase by more than 60% in 2030 (Trans et al, 2008). With this exponential growth of energy demand, the world is looking into more energy sustainable practices. Transportation is the one of the fastest growing markets for primary energy consumption and the use of biofuels is the cornerstone to change this dynamic. The ability of algae to fix CO₂ has been proposed as a method of removing CO₂ from flue gases from power plants, and thus can be used to reduce emission (Trans et al, 2008). Although the use and expansion of biofuels is a developing sustainable practice, there is some debate as to whether the production of biofuels is in conflict with food supply.

First generation biofuels, like biodiesel and bioethanol’s, are derived from popular food crops such as sugarcane, sugar beet, maize and wheat.  The use of these crops has sparked a “food versus fuel” controversy. The better choice for an all-around sustainable fuel is from the second generation biofuels which are extracted from microalgae. The use of algae as energy crops has potential, due to their easy adaptability to growth conditions, the possibility of growing either in fresh-or marine waters and avoiding the use of land (Tran et al, 2008).

In order to make a real difference in the use of this fuel, it needs to be applied for large scale productions. One method to meet this goal is to grow suitable biomass species in an integrated biomass production conversion system (IBPCS). This approach is still under study and is very dependent upon the culturing of microalgae, harvesting and processing of biomass.  In the idealized case, the conversion plants are located in or near the biomass growth areas to minimize the cost of transporting biomass to the plants, of which all the non-fuel effluents are recycled to the growth areas (Trans et al, 2008). This is still an ideal and has not been put into practice. However, it shows the great strides engineers and scientist are making in converting the world from conventional, dirty, limiting fuel to a cleaner readily available fuel. A sustainable and profitable biofuel production from microalgae is very possible with more time and investigation.

This study is just the beginning of something beautiful. The idea of using a biomass that can be cultured relatively quickly and easily replenished with ample about of obtainable growth space can change the energy game. This biofuel will take more time to be fully grasp but can start a movement to gradually switch from dirty fuels. I believe this study is feasible with more time and money but think that they should start more small scale then jumping into large industrial size production. This study seems to being showing only the tip of the energy iceberg, leaving many complications submerged. This article in particular is just trying to spread the word of biofuel sustainability and idealize the concept of an IBPCS.

Work Cited

Patil,V., Tran, K., Giselrod, H. 2008. “ Towards Sustainable Production of Biofuels from Microalgae”. International Journal of Molecular Sciences, Volume 9, issue 7 pg 1188-1195.

Literature Review Blog 1

Environmental Microbiology: Microbial players involved in the decline of filamentous and colonial cyanobacterial blooms with a focus on fungal parasitism

Literature Review Blog

Over the last century, an increase in nutrients such as nitrogen (N) and phosphorus (P) has been discharged into freshwater ecosystems by anthropogenic means. The continuous surge of nutrients results in eutrophication; “an abundant accumulation of nutrients that supports the dense growth of algae and other organisms, the decay of which depletes the shallow waters of oxygen in summer” (Dictionary.com, 2009).  This intensification of nutrients is linked to cyanobacteria algae blooms that monopolize other phytoplankton aggregations. Therefore, expanding research and concisely understanding the role biotic factors play in conjunction with environmental factors can aid in advancement in complex microbial interactions from eutrophication. 

Phosphorus is a naturally forming element that is limited in most undistributed, natural setting environments. This natural limit, often restricts the growth of primary producers such as algae, other aquatic plants, cyanobacteria and photosynthetic bacteria (Adkins et al). But, due to human activities phosphorus is more readily available, consequently causing an exponentially unstable situation for fresh water ecosystems. The booming escalation of nutrients in addition to the effects of global warming have lead scientist to anticipate an expansion in dominance of adverse cyanobacteria. As a result, the adverse economic impact of cyanobacterial blooms is expected to worsen, “affecting recreational and angling activities, lake property values, and increasing the cost of drinking water treatment. It has been estimated that the annual cost of eutrophication was approximately $2.2 billion (USD) in US freshwater ecosystems” (Dodds et al., 2008). If eutrophication becomes a staple in fresh water environments, and the cyanobacteria dominance is held, there could potentially be a loss of phytoplankton heterogeneity corresponding to limiting the diversity of fish species in the affected systems.

The inner dynamics of the synergy between microbial and nutrient activities are enigmatic and challenging. There are several studies out in the scientific community, but all are encountering the same intricacies. There are four main natural biotic factors that promote the decline of cyanobacteria blooms; grazing, lysis by heterotrophic bacteria, viral lysis and fungal parasitism. To gather more definable data on the methods behind these interactions, each biotic factor was cross examined in a laboratory setting and natural setting.  The results of these experiments showed that the difference in settings accurately define the relationship between the available microbial communities, nutrients and decline of cyanobacteria blooms. The laboratory results were always different from the natural setting results. For each biotic factor, the reactions produced and decomposed different phytoplankton species.

Grazing deals with the morphology and toxicity of cyanobacteria, but the most important factor influencing zooplankton grazing is prey morphology.  The morphological and behavioral adaptations allow grazers to bypass this size constraint obliging for the size of filaments and colonies to shift for efficiency. Grazing also may limit the nitrogen readily available therefore, minimizing cyanobacterial growth.

 “After more than 20 years of research, interactions between cyanobacteria and zooplankton are still not resolved. Overall, there is no general rule regarding the capacity of grazers to control cyanobacterial blooms. It is clear, however, that herbivores can alter the structure of cyanobacterial populations. This top-down control and the inter-relationship with cyanobacterial morphology and toxicity are dependent on the specific species pairing (Wilson et al., 2006; Lemaire et al., 2012)”.

Lysis by heterotrophic bacteria uses cyanobacteria as a food source. “Bacterial lysis appears to function in three main ways: penetration into the host cell (Caiola and Pellegrini, 1984), cell to cell contact (Shunyu et al., 2006; Gumbo and Cloete, 2013) or most often production of extracellular compounds (Choi et al., 2005; Mu et al., 2007) such as peptides, proteins, amino acids or antibiotics which may or may not be host specific (Gumbo et al., 2008)”. Studies involving lysis by heterotrophic bacteria are mainly done in laboratory conditions. The microbial relationship in natural settings is too dynamic and yields inconsistent results.  It was proven that lysis can control cyanobacteria but is dependent on the setting.

Viral lysis is  always abundant in freshwater ecosystems due to viruses having an average concentration of 10⁷ and 10⁸ virus particles per mL in freshwater and marine ecosystems (Suttle, 2005; Wilhelm and Matteson, 2008; Gachon et al, 2015).  With the help of cyanophages, viruses-attacking cyanobacteria, the reduction of cyanobacteria is effortless and well maintained in any ecosystem. This natural technique is very affective but is host specific.

Fungal parasitism is still understudied in term of eutrophication. It is widely believe that this form of cyanobacteria control can become formidable with additional resources. Fungus is found in all freshwater sources and can replicate rapidly. Many hypothesize for this control method are still untested, making this practice more of a theoretical insight.  

All of these studies are highly acclaimed in scientific communities and have been performed multiple times, with diverse scenarios, by different scientist. But eventually, there is a breaking point where the research is not able to grasp what or why something is occurring. In natural environments there are too many factors that can contribute to any and all reactions in the system.  In laboratory conditions, it is a controlled environment in every aspect; temperature, air intake, microbial diversity, pH etc.).  The biotic factors are just too numerous and dynamic for scientist to completely perceive.

Studying the effects caused by eutrophication in a microbial aspect are paramount for future generations. There is a plethora of nutrients surging through our waterways. There are no real constrictions when it comes to anthropogenic uses; agriculture and livestock. This article brings to light the past discoveries and advancements for cyanobacteria bloom controls but also shows the many limitations. Scientist as a whole, still do not clearly understand the dynamics of the interactions between the food web involved and microbial behaviors with different conditions. The dynamics of these interactions are implausible for our understanding at the moment. If we can continue to build on the basics and dive deeper in to the subject some real breakthroughs can occur.     

               

Work Cited

Adkins, A., Leduc, D., et al. “ MICROORGANISMS: Role of Microorganisms in Phosphorous Cycling.” Department of Biology, University of Winnipeg.

Caiola, M.G., and Pellegrini, S. (1984). “Lysis of Microcystis aeruginosa (kütz.) by bdellovibrio-like bacteria.” J Phycol 20: 471–475

Choi, H., Kim, B., Kim, J., and Han, M. (2005). “Streptomyces neyagawaensis as a control for the hazardous biomass of Microcystis aeruginosa (Cyanobacteria) in eutrophic freshwaters.” Biol Control 33: 335–343

Dodds, W.K., Bouska, W.W., Eitzmann, J.L., Pilger, T.J., Pitts, K.L., Riley, A.J., et al. (2008) “Eutrophication of U.S. freshwaters: analysis of potential economic damages.” Environ Sci Technol 43: 12–19

Gachon, C., Gerphagonon, M., Gleason, F., Latour, D., Macarthur, D., Ogtrop, F., Sime-Ngando, T., et al. (2015). “ Microbial players involved in the decline of filamentous and colonial cyanobacterial blooms with a focus on fungal parasitism.” Environmental Mircobiology 17(8), 2573-2587.

Gumbo, R.J., Ross, G., and Cloete, E.T. (2008). “Biological control of Microcystis dominated harmful algal blooms.” Afr J Biotechnol 7: 4765–4773

Gumbo, J.R., and Cloete, T.E. (2013). “Light and electron microscope assessment of the lytic activity of Bacillus on Microcystis aeruginosa.” Afr J Biotechnol 10: 8054– 8063.

Lemaire, V., Brusciotti, S., van Gremberghe, I., Vyverman, W., Vanoverbeke, J., and De Meester, L., et al. (2012). “Genotype × genotype interactions between the toxic cyanobacterium Microcystis and its grazer, the waterflea Daphnia.” Evol Appl 5: 168–182.

Shunyu, S., Yongding, L., Yinwu, S., Genbao, L., and Dunhai, L. (2006). “Lysis of Aphanizomenon flos-aquae (Cyanobacterium) by a bacterium Bacillus cereus.” Biol Control 39: 345–351

Suttle, C.A. (2005). “Viruses in the sea.” Nature 437: 356–361

Thesaurus.com "atypical," in Roget's 21st Century Thesaurus, Third Edition. Source location: Philip Lief Group 2009.http://www.thesaurus.com/browse/atypical.

Wilhelm, S.W., and Matteson, A.R. (2008). “Freshwater and marine virioplankton: a brief overview of commonalities and differences.” Freshwater Biol 53: 1076–1089

Wilson, A.E., Sarnelle, O., and Tillmanns, A.R., et al. (2006). “Effects of cyanobacterial toxicity and morphology on the population growth of freshwater zooplankton: meta-analyses of laboratory experiments.” Limnol Oceanogr 51: 1915–1924

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                                                      Lab 1: Working With A Pipette

Introduction

             When conducting an experiment, it is imperative to have fundamental knowledge of laboratory equipment.  Without this rudimentary understanding of the mechanics behind each apparatus one could not conclude an ideal, uniform synthesis. One of the most extensively used fundamental tools in labs are, automatic adjustable pipettes. Automatic adjustable pipettes are highly sought after due to them yielding very consistent results with spot on accuracy, simplex understanding and assortment of volumes.   

The purpose of our first lab was to grasp a better understanding and handling of the automatic adjustable pipette via the Eppendorf line of pipettes.  Students were to familiarize themselves with different volumes and learn how to transition measurements from one capacity to the next with proper use.  Our ideal objective was to feel comfortable with accurately measuring small volumes of liquids.

Methods and Materials

            In order to get the most truthful result from the micropipettes, one needs to know the correct technique. Ensuring optimal performance requires precision, accuracy and clarity of use. For this to occur, one needs to hold the pipette vertical, not slightly at an angle, at all times that there is liquid in the pipette. This allows for an accurate reading. Also, by only immersing the tip of the disposable plastic tip in the liquid solution warrants precision.  As for clarity of use, there are three positions on the delivery button for automatic adjustable pipette; rest position, first stop and second stop or purge. The two stop points are distinguishable through gentle degrees of resistance. The first draws up liquid and the second dispenses liquid. With this knowledge we were able to perform our first experiment!

There were three parts to this lab. The first part was for student to get a chance to feel out the pipettes, through use of the red dye. The second part was to challenge our understanding of which pipette to use based on the amount of volume needed and correctly calibration. Students were to gather different volumes of red, yellow, blue and green food coloring and place a drop of each on top of one another. This allowed students to understand the use of precision and accuracy through proper procedure.  We assess the color that this blob procured, which in our case was black. After examining the color, we were to measure the volume of our black drop through the use of the pipette to see if it was the same volume.

4 microliters of red dye

Red,yellow,blue and green mixed together

                                                              

 The third and final fragment of our first lab was to test our skill. Students were given two micro centrifuge tubes and asked to place certain volumes of the four colors in each. The first had red and blue while the second had green and yellow. Students then see there pipette to the total volume in each centrifuge tube and see if the volume matched the actual volume in the tubes.

200 microliters red, 300 microliters blue

250 microliters green, 200 microliters yellow

Results

           The results from the third part of our first lab are displayed in table 1 and show that all of the liquid originally placed in the centrifuge tubes was able to be recollected.

                Table 1. Volumes of Colors              

Tube	Red	Blue	Green	Yellow	Total	Color
#1	200 µl	300 µl	0	0	500 µl	Purple
#2	0	0	250 µl	200 µl	450 µl	Blue

Discussion

           Through the use of this first lab, students are able to feel confident when using automatic adjustable pipettes in the future. Each section of this lab allowed students to conceptually understand and physically see what proper knowledge of equipment can produce. This lab was fundamental in growing our repertoire in the scientific fields. With a solid foundation of basics procedure with pipettes, we can only build our curiosity and gain in our understandings.