The Removal of Invasive Species Through Gene Silencing in Microalgae Cultivation for Biodiesel

EPA Grant Number: FP917166
Title: The Removal of Invasive Species Through Gene Silencing in Microalgae Cultivation for Biodiesel
Investigators: Morse, Thomas Oliver
Institution: Duke University
EPA Project Officer: Zambrana, Jose
Project Period: August 1, 2010 through July 31, 2013
Project Amount: $111,000
RFA: STAR Graduate Fellowships (2010) RFA Text |  Recipients Lists
Research Category: Academic Fellowships , Fellowship - Science & Technology for Sustainability: Green Engineering/Building/Chemistry/Materials


Recently, there has been an increased interest in biodiesel production due to the increasing environmental and economic costs of petroleum sourced fuels. Algae remain a promising feedstock for biodiesel production because the lipids in algae are easily converted into biodiesel. While the idea is technically feasible, invasive species such as viruses, bacteria, rotifers, and low-lipid algae outcompete the high-lipid strains causing a species collapse and a significant algal crop reduction. There have been many attempts to control invasive species using biocides. However, biocides are not selective enough to permit the growth of high-lipid algae. Therefore, there is a need for a selective biocide that will remove the invasive species, while permitting the high-lipid algae to grow. One specific tool that has the potential to fill this need is antisense gene silencing. This research project will investigate the feasibility of using antisense gene silencing for microalgal crop protection.

The efficiency of large-scale microalgal cultivation for biodiesel production is inhibited by invasive species. This project will use gene silencing to remove invasive species to permit the more efficient growth of high-lipid algae. The expected outcome of this project is the development of a green biocide compatible with large-scale microalgal cultivation techniques, which will provide a clean and sustainable source of energy, ultimately reducing U.S. dependency on foreign fuels.


This research project will assess the feasibility of using gene silencing for microalgal crop protection. The first phase will be dedicated to elucidating the environmental parameters for optimal silencing. BLAST alignments will be performed to identify genes unique to the invasive species and to eliminate possible off targets. Once the genes have been selected for silencing, a suite of environmental parameters will be tested. In the second phase mixed culture experiments will be performed with a high-lipid algae and either a low-lipid algae or an invasive bacterium. The third phase of the experiment will compare two different delivery methods: direct diffusion and vector delivery. Initial work on vector delivery will focus on lentiviral delivery systems, because of their previous use in gene silencing experiments. The final phase will involve bench-scale experiments in a raceway pond. A plastic raceway pond will be constructed that measures 2 m × 0.5 m and that will be run for 120 days.

Potential to Further Environmental/Human Health Protection
This technology has potential uses for mitigating harmful algal blooms and for the removal of chlorine-resistant pathogens in industrial settings. Additionally, this technology has the potential to be used for inactivating pathogens in point-of-use water filtration systems. There are also many positive externalities in improving the delivery of gene silencing oligonucleotides, as the medical field is evaluating RNAi therapies (e.g., for the treatment of cancer), and a greater understanding of oligonucleotide delivery will have direct applications in the treatment of cancer.

Expected Results:

The successful completion of this project will be a significant advancement in promoting a domestic supply of sustainable biodiesel. Additionally, the “green” biocide proposed in this project is significantly less toxic to the environment compared to current biocides and algaecides.

Supplemental Keywords:

algae, biodiesel, green engineering, gene silencing, RNAi, CRISPR,

Progress and Final Reports:

  • 2011
  • 2012
  • Final