This week was very busy. I continued working in the lab. The Biodesign building itself is very large. There are quite a few different projects going on at once in each of the six labs. The labs themselves stretch the length of half of the building. The lab that I am working in, Environmental Bioengineering is only several benches, and there are always other doctors and interns working all around me. My mentor, Dr. Steve VanGinkel, works with three other interns from ASU. Dr. VanGinkel is a research scientist at ASU and will be leaving at the end of this semester to go to Georgia Tech.

My responsibilities in the lab vary from day to day. The most interesting thing I have done is learn how to use a Confocal laser scanning microscopy microscope (CLSM). CLSM is a technique that allows 3D images to be created by scanning in-focus images from selected depths. The images are then used by the computer to create a high-resolution 3D image (as well as each individual section).

I have been going to the Biodesign Lab at ASU for several days now, and after learning much about the history and current states of my mentor's many different projects, I had my first assignment. To put it simply, I had to drill holes in a small plastic circle and thread tiny fibers through it. It was not difficult, but it was time consuming.

I am still unsure of what my future responsibilities will be in relation to the project, and I will be sure to update this as soon as I know.

Here is the second part from the website describing more about the project.

Fortunately, an array of pre-genomic, genomic, and post-genomic tools is available to understand microorganisms involved in bioenergy production. Taking full advantage of these tools will greatly speed up scientific and technological advances, which is what society most needs.

Genomics provides the base sequence of the entire DNA in an organism, and the
complete genome reveals all the possible biological reactions that a microorganism can carry out. In the past, complete genomes were only obtained for those microorganisms that could be isolated into pure culture, but it is now possible to sequence the genomes of uncultivated microorganisms using metagenomics.

To date, approximately 75 genomes are available from microorganisms that have a role in bioenergy production. These include 21 genomes from methane producing archaea, 24 genomes from bacteria that can produce hydrogen or electricity, and 30 genomes from cyanobacteria that are potential biodiesel producers. At least half of the completed microbial genomes that are relevant to bioenergy were released in the past 2 years, and more than 80 bioenergy-related genomes are currently being sequenced.

A great example is the Biodesign Institute’s biofuel bacterium, Synechocystis sp. PCC 6803, the first bioenergy-relevant microorganism to be sequenced; its genome was released in 1995. This photosynthetic bacterium features membranes with high lipid (i.e., oil) content, which makes it an excellent biodiesel candidate.

The growing pool of genomic information provides molecular targets that support pre-genomic and post-genomic investigations, both of which provide essential information on what microorganisms are present in the community and what metabolic reactions they are carrying out. With genomics combined with high-throughput DNA sequencing and proteomics, our understanding of bioenergy-producing microorganisms should surge.

Because success with microbial bioenergy demands in-depth knowledge of the complex microbial communities that normally develop, a wide range of pre-genomic, genomic, and post-genomic tools is needed. Our team has unique expertise in using each kind of tool, and its perspective article provides needed information about these tools and how they can be used to unravel the structures and functions of microbial communities involved in renewable bioenergy.

Information from these tools, when properly integrated with advanced engineering tools and material, should accelerate the rate at which microbial bioenergy processes can be converted from the realm of intriguing science to real world practice.

Hydrogen production

Hydrogen is a proposed “fuel of the future.” The reason for this hope for hydrogen is the development of efficient fuel cells that convert the energy in hydrogen to electricity with high efficiency and zero emissions of air pollutants. However, the future for hydrogen is clouded. Although hydrogen itself is very clean and attractive, almost all of the hydrogen produced at the present time comes from non-renewable fossil sources, such as natural gas and coal. This non-renewable cloud over hydrogen can be lifted by biohydrogen production.

Biohydrogen refers to hydrogen produced by algae, bacteria, or biological components of these organisms. These organisms use renewable biomass or sunlight to produce hydrogen. As our society strives for renewable hydrogen, biohydrogen will be a main alternative. Furthermore, it integrates waste treatment with clean-energy production from renewable sources. For example, biohydrogen can be used to produce electricity in a fuel cell, and it also is a special electron donor for bacteria in treatment processes used for reduced contaminants (such as the hydrogen-based membrane biofilm reactor). Although microorganisms can produce biohydrogen by various processes, fermentation is the simplest process and one we are exploring.

Fermentation is the essential first step in any process to recovery energy from biomass. Biomass is made up of complex organic molecules. Fermentation generates a mixture of simpler molecules: organic acids, alcohols and hydrogen. Thus, a great advantage of fermentation is fast degradation of solids and other complex organics found in wastes and agricultural products. On the other hand, fermentation today converts only about 15 percent of the energy to hydrogen. While fermentation is fast, it is not yet efficient for capturing the energy value of biomass to hydrogen.

Our goal is to increase the biohydrogen yield to around 85 percent. To do this, we are investigating a multi-faceted research agenda that involves two complementary strategies. The first strategy involves controlling the microbial ecology in the fermentation process so that electrons and energy flow to hydrogen, instead of being diverted to other end products. The second strategy involves directing the electrons and energy in the other fermentation end products to biohydrogen in a coupled bioprocess. Each strategy relies on understanding the microbial ecology and using modern materials and good engineering to control the ecology so that the maximum biohydrogen is produced.

Wastewater to energy

In wastewater treatment plants, a complex community of microorganisms degrades the organic solids in sludges and converts the energy value to methane gas (CH4). Microbiological generation of methane, or methanogenesis, has been used for over a century, but it is not yet efficient enough to use in terms of destroying the organic solids in the sludge or capturing the energy value as methane. Often, the methane gas is “flared,” or simply burned in an open flame, because the amount of methane is not worth the cost to capture, clean and convert to electricity. Research in our center aims to overcome these limitations by increasing production and capturing renewable energy as methane.

One excellent example is a research project investigating the use of forced pulse (FP) technology to pre-treat the sludge in order to increase the yield of methanogenesis and decrease the residual solids requiring disposal. We use an FP unit designed by our partner, a private company called OpenCEL, to lyse cells and break apart biosolids, thereby increasing the energy sources (e.g., sugars) available to the microbial community, including the methanogens. We also partner with the Mesa Northwest Water Reclamation Plant, which hopes to increase the yield of methane from their digested sludge enough that they can afford to convert the methane to electricity, perhaps transforming their wastewater treatment facility from an energy consumer to an energy producer.

Two anaerobic digesters containing waste activated sludge from the Mesa Northwest Water Reclamation Plant are producing methane via microbial transformations. The right reactor contains sludge pre-treated with a Pulsed Electric Field (PEF) process that lyses cells and makes organic material more available for the methanogenic bacteria to digest, thereby increasing the destruction of organic solids and the production of methane.

Biological processes are the overwhelming choice for wastewater treatment due to their ease of use, excellent performance, and efficiency. However, when challenged with toxic organic compounds, these processes can be ineffective and in some cases fail, resulting in discharge of harmful pollutants into the environment.

Waste to electricity

A revolutionary new environmental biotechnology—the Microbial Fuel Cell (MFC)— turns the treatment of organic wastes into a source of electricity. Bacteria growing as a biofilm on an electrode in a fuel cell oxidize the organic pollutants and transfer the electrons to the electrode, into an electrical circuit, and eventually to oxygen at a second electrode.

The MFC is revolutionary for three reasons. First, it makes the treatment of organic pollutants a direct producer of electricity, not a consumer. Second, it expands fuel-cell technology to use renewable organic materials as a fuel; conventional fuel cells use hydrogen gas, which is today produced from fossil fuels. Furthermore, the MFC can use organic fuels that are wet, the usual form for wastes and fuel crops. Third, the MFC, by operating at ambient temperature, can double to triple the electricity-capture efficiency over combustion, while eliminating all the air pollution that comes from combustion.

The scientific breakthrough leading to the MFC is the recent discovery that some bacteria can transfer electrons into an electrode and create electricity. This breakthrough is translated into a technology by using modern membrane and electrode materials that are compatible with biofilm growth and operation at ambient temperature. To develop economic opportunity for all people around the world, we are in a race to find a nonpolluting bioenergy source of energy. Bioelectric power, using crop or animal waste, could prove to be the solution.

Project Description: Energy from Waste

As promised, here is a description of the project from the official page at the Biodesign website.

Perhaps there is no greater societal need for scientific know-how than to find new ways to meet future energy demands. Skyrocketing gas prices, an uncertain oil supply, increasing demand from around the world, and the looming threat of climate change have made identifying and developing realistic energy alternatives a national priority.

Microorganisms once reigned supreme on the Earth, thriving by filling every nook and cranny of the environment billions of years before humans first arrived on the scene. Now, this ability of microorganisms to grow from an almost infinite variety of food sources may play a significant role in bailing out society from its current energy crisis, without damaging the environment or competing with our food supply.

What is it about bacteria that make them an attractive tool for bioenergy research? Consider that one species of bacteria, the human gut bacterium E. coli, has become the workhorse of the multi-trillion dollar global biotech industry. Might other unearthed microbial treasures have the same potential in bioenergy applications?

Unlike the E. coli situation, using just one species may not work well for bioenergy, since, in nature, bacteria do not grow in isolation. In other words, no bacterium is an island. The very biodiversity that fills the Earth with bacteria and offers great bioenergy potential also presents a challenge for engineers. Even if one picks the ideal “bug,” growing, maintaining, and optimizing conditions for its use in bioenergy applications remains a daunting challenge in terms of scalability and reliability.

Microbial communities that are used to harvest energy must be resilient to fluctuations in environmental conditions, variations in nutrient and energy inputs and intrusion by microbial invaders that might consume the desired energy product. The key to large-scale success in microbial bioenergy is managing the microbial community so that that the community delivers the desired bioenergy product reliably and at high rate.

Two distinct, but complementary approaches will be needed. The first is to use microbes to convert biomass to useful energy. Different microorganisms can grow without oxygen to take this abundant organic matter and convert it to useful forms of energy such as methane, hydrogen, or even electricity. In addition, different non-photosynthetic microorganisms can grow without oxygen and take abundant organic waste matter, converting the energy value of all kinds of biomass, including wastes, into readily useful energy forms, such as methane, hydrogen, and even electricity.

The second approach uses bacteria or algae that can capture sunlight to produce new biomass that can be turned into liquid fuels like biodiesel, or converted by other microorganisms to useful energy. Photosynthetic bacteria can capture sunlight energy at rates 100 times or greater than plants, and they do not compete for arable land. This high rate of energy capture means that renewable biofuels can be generated in quantities that rival our current use of fossil fuels.

Both approaches currently are intensive areas of biofuel research at the Biodesign Institute.

In the absence of these molecular techniques, our understanding of methanogenic communities progressed through slow, incremental advances over several decades. Today, society cannot wait decades for new bioenergy sources.

Well, this is my first "blog." It seems the most appropriate thing to say is that I just finished my fire and lab safety today. I have been busy over the last few weeks emailing the lab manager and professor, and I am excited to say that I will be officially working (volunteering) in the lab starting the Monday after Spring Break (the professor is leaving town for the week). 

Since I will not have started until next week, and I am sure unsure of my exact job in the lab, I will try and use the next few blog posts to describe the overall goal of the project, starting tomorrow.

Thank you for your patience Mrs. Tumminello.