Team 1 Spring 2022


Ensifer is a nitrogen fixing bacteria that often attaches to host plants and causes their destruction. However, a unique trait of this microbe is that it is extremely prevalent in heavy metal contaminated soil, and often helps in bioaccumulation of these metals. This could make Ensifer an extremely crucial organism in helping deal with the electronic waste crisis. E-waste is often not recycled properly or thrown out in areas where it contaminates the environment around it. The heavy metals such as copper, zinc, and nickel found in electronics seep into the ground and soil, contaminating the environment. This also makes it extremely difficult for any vegetation to grow in that area. However, in places where Ensifer is present, plants are able to survive even in heavy metal contaminated soils, showing that the microbe could be used to recycle e-waste more effectively. Since it is able to biosorb and bioaccumulate the heavy metals, it can be used to recover the metals for more electronic production. This project looks into the genetic sequence of Ensifer to identify potential genes that could be beneficial to e-waste management. Several future experiments and next steps are also highlighted to determine the feasibility of Ensifer in proper e-waste recycling and management.


Over the past few years, our technology consumption has increased, and with it, so has electronic waste. Ewaste refers to any electronic product that is disposed of after its useful life. According to the United Nations, almost fifty million tons of ewaste is produced per year, and only approximately twenty percent of it is properly recycled (UN 2022). Ewaste is a global problem, since it is often not discarded properly, leading to many environmental problems. In addition, technology companies use more resources to create new electronic devices. Most ewaste ends up in landfills, where it continues to accumulate, contaminating soil, water, and the air with toxic chemicals and metals. In addition to health and environmental concerns, many valuable materials are lost, such as gold and many other precious materials. Therefore, it is important to find sustainable solutions to ewaste management. 

Microbial Solutions 

One possible solution to the e-waste problem is using microbes. Microbes are described as “tiny living things that are found all around us and are too small to be seen by the naked eye. They live in water, soil, and in the air” (National Library of Medicine, 2019). They most commonly include bacteria, fungi, and viruses. Bacteria have shown positive signs of the breakdown and bioaccumulation of heavy metals found in electronic waste. For example, C.violaceum is a bacteria that is able to bioaccumulate gold according to Yen-Peng Ting, a researcher studying how bacteria can be used to solve the e-waste problem (Kwok). This research is important because it is now being used in industry. Mint Innovations is a recycling company that is able to gold from e-waste using bacteria. However, it is important to find bacteria that can accumulate metals other than gold such as heavy metals found in computer chips and batteries.

Experimental Approach 

Fifteen types of microbes were isolated from pokeweed in acid mine drainage by Dr. Amy Grunden and Dr. Jason Whitham (Experimental Approach). These microbes were chosen from this source because they were shown to grow on and accumulate rare Earth metals. The bacteria were then grown on plates and initial guesses were made on the types of bacteria that were collected. These results were then isolated on Tryptic Soy Broth plates (Experimental Approach). Once the samples were grown cell lysis was performed to isolate the DNA for identification. The samples also had to be tested to see if they were pure enough using Nanodrop and Tapestation. After this the 15 bacteria samples were narrowed down to four potential options that showed promising results of being able to break down e-waste (Experimental Approach). Once the four suspected types of bacteria were narrowed down the bacteria were sequenced using 16S sequencing to further confirm if the microbes were the correct bacteria. Our assigned bacteria Ensifer came back as a match. After this was done, the bacteria’s entire genome was sequenced using Nanopore sequencing. This data was then assembled by Dr.Goller using CLC Genomics Workbench (Experimental Approach).


Link to KBase Narrative


Microbe Species

Ensifer is a nitrogen fixing bacteria that may attach to other bacteria and cause their destruction. However, it also acts as a symbiotic organism and forms nitrogen fixing nodules on the hosts, improving soil quality. Ensifer has a high heavy metal tolerance, meaning it can survive even in soil that has high amounts of metals such as zinc, copper, silver, and nickel. It is able to biosorb these metals and cause bioaccumulation within the microbe. According to a study conducted on heavy metal accumulation with Ensifer, there were several strains that were able to tolerate high amounts of cadmium, zinc, copper, and nickel, showing high levels of resorption (Oves 542). The ability to promote plant growth and biosorption makes Ensifer an extremely significant microbe for gathering heavy metals.

Improper e-waste disposal often results in soil contamination, where heavy metals seep into the soil, making it difficult for plants to grow. Ensifer could serve as a solution to this problem, as it helps clear the soil of heavy metals that are used in electronics, like zinc, copper, and nickel. By isolating the species from a soil sample with heavy metals present, it is possible to gather the metals from the microbe. Since the microbe bioaccumulates the metals, a potential means of research would be to attempt to recover the metals from e-waste in soil. These metals could also be reused in the production of new electronic products. A possible research study would be to measure the amount of heavy metals in a soil sample, and find the percent recovered through the introduction of an Ensifer within the sample.

Future Directions 

The next step in understanding the role of Ensifer in e-waste management would be to find out the amounts of heavy metals the microbe can handle within a soil sample. In order to do this, a potential experiment would be to look at how well plants are able to grow in soils with heavy metals. First, the microbe would have to be isolated in equal amounts for each of the samples. Then, there would be several control groups including a plant in regular soil and a plant in soil with heavy metals. The next step would be to have an experimental group in which a plant is in soil with heavy metals, as well as the sample of the Ensifer microbe. The rate of plant growth would help determine how much of the heavy metals the microbe is able to biosorb. Ensifer can later be isolated from the experimental sample to figure out how much of the heavy metals were recovered through bioaccumulation. The hypothesis is that the sample with Ensifer in the soil would result in better plant growth. This would help determine the effectiveness of Ensifer’s nitrogen fixing and bioaccumulation capabilities in e-waste management. 

There are several strains of Ensifer that could be used for e-waste management, and figuring out the specific strain would narrow down the possibilities. Therefore, another experiment could be designed in which various strains of Ensifer are used to gather heavy metals from a soil sample. Then, the percent of heavy metals recovered from the original sample would determine the effectiveness of each strain in a given environment. This would help determine the specific strain that is most beneficial for e-waste management and tolerance of heavy metals. There could also be future studies on the nitrogen fixation and sulfur metabolism capabilities of Ensifer. From the K base data from our experiment, it was discovered that both of these genes were found in Ensifer. These traits of the microbe could be used to help with plant growth in soils with heavy metal contamination.


  • Biondi, E. G., Tatti, E., Comparini, D., Giuntini, E., Mocali, S., Giovannetti, L., Bazzicalupo, M., Mengoni, A., & Viti, C. (2009). Metabolic capacity of sinorhizobium ( ensifer ) meliloti strains as determined by phenotype microarray analysis. Applied and Environmental Microbiology, 75(16), 5396–5404. 
  • “E-Waste Recycling: Mint Innovation.” E-Waste Recycling | Mint Innovation, 
  • “Experimental Approach”, Carlos Goller , Carly Sjogren , March 29th, 2022 
  • Han, H., Wu, X., Yao, L., & Chen, Z. (2020). Heavy metal-immobilizing bacteria combined with calcium polypeptides reduced the uptake of CD in wheat and shifted the rhizosphere bacterial communities. Environmental Pollution, 267, 115432. 
  • Jr., L. E. Casida. “Ensifer Adhaerens Gen. Nov., Sp. Nov.: A Bacterial Predator of Bacteria in Soil.” International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, 1 July 1982, 
  • 2-3-339. 
  • Kwok, Roberta. “How Bacteria Could Help Recycle Electronic Waste.” PNAS, 15 Jan. 2019, 
  • Le Quéré, A., Tak, N., Gehlot, H. S., Lavire, C., et al. (2017). Genomic characterization of Ensifer Aridi, a proposed new species of nitrogen-fixing Rhizobium recovered from Asian, African and American deserts. BMC Genomics, 18(1). 
  • Liu, H., Cui, Y., Zhou, J., Penttinen, P., Liu, J., Zeng, L., Chen, Q., Gu, Y., Zou, L., Zhao, K., Xiang, Q., & Yu, X. (2022). Nickel mine soil is a potential source for soybean plant growth promoting and heavy metal tolerant Rhizobia. PeerJ, 10. 
  • Ma, L., Chen, S., Yuan, J., Yang, P., Liu, Y., & Stewart, K. (2017). Rapid biodegradation of atrazine by Ensifer sp. strain and its degradation genes. International Biodeterioration & Biodegradation, 116, 133–140. 
  • Oves, Mohammad, et al. “Ensifer Adhaerens for Heavy Metal Bioaccumulation, Biosorption, and Phosphate Solubilization under Metal Stress Condition.” Journal of the Taiwan Institute of Chemical Engineers, Elsevier, 1 Sept. 2017, 
  • R;, Kwok. “Inner Workings: How Bacteria Could Help Recycle Electronic Waste.” Proceedings of the National Academy of Sciences of the United States of America, U.S. National Library of Medicine, 
  • Rogel, M A, et al. “Nitrogen-Fixing Nodules with Ensifer Adhaerens Harboring Rhizobium Tropici Symbiotic Plasmids.” Applied and Environmental Microbiology, American Society for Microbiology, July 2001, 
  • Sun, S., Fan, Z., Zhao, J., Dai, Z., Zhao, Y., & Dai, Y. (2021). Copper stimulates neonicotinoid insecticide thiacloprid degradation by ensifer adhaerens TMX‐23. Journal of Applied Microbiology, 131(6), 2838–2848. 
  • “UN Report: Time to Seize Opportunity, Tackle Challenge of e-Waste.” UN Environment, unity-tackle-challenge-e-waste. 
  • Wei, L., Wang, S., Zuo, Q., Liang, S., Shen, S., & Zhao, C. (2016). Nano-hydroxyapatite alleviates the detrimental effects of heavy metals on plant growth and soil microbes in e-waste-contaminated soil. Environmental Science: Processes & Impacts, 18(6), 760–767. 
  • “What Are Microbes?” [Internet]., U.S. National Library of Medicine, 29 Aug. 2019, 
  • What we do: Mint innovation. What We Do | Mint Innovation. Retrieved from