A New Frontier: Biotech in BBE

November 1, 2017

bo hu and researchers in his lab

From left to right, postdoctoral researcher Jingyu Wang, graduate student Tanner Barnharst, and faculty Bo Hu pose with a bioreactor in the bioprocessing lab. Hu and his research team focus on the bioprocess development to convert agricultural residue and waste materials to value-added chemicals and bioproducts.

Originally published in the Fall 2017 issue of BioBrief.

The synergy between molecular biology and biotechnology is an essential one as it has contributed to our quality of life. Molecular biology is fundamental to biotechnology, and biotechnology has provided solutions to meet society’s need for food, health, and energy. Some of the earliest examples of biotechnology include fermentation to make food, using honey as a natural antibiotic for wounds, and selective plant breeding to grow the best crops.

Biotechnology—or biotech, is expanding as new methods and knowledge are emerging in molecular biology. Biotech’s vast potential to improve our quality of life and the environment has garnered enormous attention and significance. It has even become a buzzword.

As the human population is projected to grow to nearly 10 billion in this century, some of the greatest global challenges for humanity are energy, agriculture and food security, and environment and resource security. Thus, it may be that the 21st century will be the century of molecular biology and biotech. Advances in these fields may offer solutions, and faculty in the Department of Bioproducts and Biosystems Engineering are making an impact. Here, we highlight our innovative researchers Jonathan Schilling, Bo Hu, and Brett Barney, who are advancing the forefront of molecular biology and biotechnology.

Jonathan Schilling: Gene Discovery Where Rot Is Hot

Research can be boiled down to a single question: “How do fungi eat wood?”

The answer?

We still don’t know. Imagine that. More than 100 years of research on these fungi as pests of lumber—and we’ve learned a lot—but really, we still don’t know.

brown rot fungi on petri dish in schilling's labFungi, like this brown rot fungus Piptoporus betulinus (a.k.a. the birch polypore fungus), are in focus in the Schilling lab. These “thready” organisms invade wood, with the ability to extract carbohydrates for energy. This is a clever trick of great interest in biotech, and this particular fungus does this trick without first removing extensive amounts of lignin. We don’t know how—Schilling’s group is using molecular biology to get to the bottom of it.

The biggest hurdle has been the lack of research tools to resolve the spatial dynamics of fungal metabolism inside wood cells. These are nano-scale dynamics. Microscopy and molecular tools, however, have made amazing strides in recent years, and our lab is taking advantage.

In 2016, we published our work on isolating a unique oxidative pretreatment pathway that is central to a class of wood decomposers known as brown rot fungi in the Proceedings of the National Academy of Sciences. Brown rot fungi can selectively remove carbohydrates by deploying this oxidative pretreatment, and as they evolved the mechanisms to do this, they lost many other genes we think of as critical in decomposition.

Basically, we went into this knowing which genes are not involved in brown rot. But, we used a clever spatial design, cutting-edge tools, and collaboration to shine the light on those genes that are involved. By narrowing our targets, I think we are getting close to discovering some really important genes and pathways, more than 100 years in the dark.

Finding these genes has been our focus for many years, a continued investment in time that has been matched by long-term investments in dollars, particularly from the U.S. Department of Energy. Plant deconstruction has been an industry goal for decades, but has also been a stumbling block to the commercialization of cellulosic biofuels and other cellulose-based products. Once you have genes relevant to these industrial processes, they can be inserted into the genomes of other organisms, modified, and enhanced to improve the efficiency of the biomanufacturing process.

There is also added value. This is basic science with a clear industrial goal. That means the federally-funded work we do is already worth it to the private sector. On top of that, however, we are learning about a decomposition process that is still of essential relevance to pest management in lumber, an area without much current investment, but that will likely change with regulatory frameworks in the future. We’ll be ready.

Furthermore, these fungi recycle Earth’s largest pool of aboveground carbon in wood and are key players in the global carbon cycle. We are making strategic investments in basic science here that not only yield the intended deliverables, but have collateral benefits in knowledge that offer far more return on investment than I think many people realize.

Learn more about Schilling's research

Bo Hu: Next Gen Industrial Biotech and Bioprocessing Promoting Sustainable Agriculture

The American agricultural industry has been changing in recent decades, primarily driven by the technology advances for higher efficiency and fluctuating prices of the fossil fuel energy and agricultural products. Farms are moving to intensive practices in order to provide not only more food, feed, and fiber, but also bioproducts to replace fossil fuels.

This signifies careful evaluation of environmental impacts as most of these agricultural residue and waste are generated in large scale at concentrated sites. Improper application of these nutrients are causing significant pollution, for instance, water eutrophication due to nitrogen and phosphorus discharge to the lakes and streams.

On the other side, fertilizer production requires significant amount of energy and drains our natural resources. For instance, the phosphorus in chemical fertilizers is currently produced from mining of rock phosphate, a finite resource that is pending for global depletion; and the cost of extraction and refinement of poor rock phosphate is increasing. Therefore, processes to recycle nutrients and minimize the environmental impacts are needed for the sustainable development of the agricultural industry.

We focus on fundamental and applied approaches to address this research area, emphasizing both agricultural waste treatment and nutrient recycle. We’re developing the next generation of agricultural systems and industrial biotechnologies that are cost-effective, energy- efficient, and environmentally friendly. We’re also working on multiple synthetic ecology platforms—including microbial electro chemical systems and simulated microalgae/fungal lichen cultivation systems— to develop treatment processes for manure, municipal waste water and agricultural run-off.

Because a significant portion of today’s animal feed is the coproductsfrom the biofuel industry, we are also working on the synthetic biology to develop genetically modified yeast and fungal strains that can be applied in the corn ethanol industry. These strains will be able to produce more essential amino acids that will enrich the nutritional value of the corn ethanol coproducts and facilitate their better digestion to farm animals. We are also enabling these strains to better degrade anti-nutrient chemicals in corn and soybeans so that animals can excrete less nutrient pollutants into the environment. With our technology, we are hoping to create a win-win situation to farmers, the corn ethanol industry, and the environment.

Brett Barney: Enhancing Nature to Help Address Sustainability

barney works in his labFaculty researcher Brett Barney works in his lab. His research focuses on bacteria and algae-based biofuels and biofertilizers for aqua/agriculture.

In the simplest sense, our laboratory uses molecular biology and genetic approaches to enhance natural pathways toward sustainable processes. Our two primary targets for this work are associated with the natural process of biological nitrogen fixation and the accumulation of oils in algae and bacteria.

The process of biological nitrogen fixation is responsible for about half of the nitrogen used by all living systems on the planet, including our forests, the oceans, and agriculture. The remainder of the nitrogen is produced by an industrial process that needs between 1-2% of the energy consumed every year to provide the nitrogen that we need to sustain our current level of agricultural output.

Our laboratory works with a model bacterium that is capable of performing the same process, but attains the energy needed to drive this process from simple sugars. We study how this process is regulated at the cellular level, and then, make modifications that result in an organism that produces excess nitrogen well beyond the cell’s own needs. This enables the bacterium to act as a natural biofertilizer and to function in larger communities to make agriculture and aquaculture more sustainable.

Our studies associated with oil production focus on organisms, such as algae or model bacteria, that accumulate high value oils used in cosmetics. We are sequencing a large number of algal strains that produce valuable commodity chemicals such as oils and sugars. These algae can act as drop-in substitutes for other commodity crops, and a better understanding of these processes will allow us to develop approaches that could produce greater levels of these chemicals in a manner that lowers the costs associated with cell harvest and extraction.

We are also focused on a strain of algae that excretes sugars during growth. This strain was of interest to the European Space Agency for potential application in long-term space travel, such as what might be required for missions to Mars. The strain would consume carbon dioxide produced by the human inhabitants of the spacecraft and yield a simple sugar that could be used to make a range of products or as a source of energy for the astronauts.