Hacking Bacteria To Do Our Bidding: Photos

Scientists regularly tap into biological systems to find solutions for human problems. Although they work with plants and viruses in the lab, bacteria have many advantages as a starting point. When programmed in certain ways, bacteria can store data, clean dangerous waste, produce film-like images and even make renewable fuel.

David Benjamin is the founder and design principal of the New York architecture firm The Living and directs the Living Architecture Lab at the Columbia University Graduate School of Architecture, Planning and Preservation. His lab does research on the future of architecture, which includes collaborating with computational biologists. One of his projects explores how bacteria could build new custom construction materials for us.

"It's now more than ever possible to engineer biological systems to perform useful tasks for humans," he said. "I like to quote one of my friends, a biology researcher, who says the cheapest way to make anything is to grow it." Here, Benjamin explores ways that bacteria can be engineered to our benefit.

When found in the wrong places, Escherichia coli or E. coli can wreak havoc on our health. But in the lab, biotech researchers like the bacterium's versatility and ease as a host organism. Over the summer, bioengineers led by Chris Voigt at MIT reprogrammed a harmless strain of E. coli to turn black or remain transparent in certain light. This allows for a film-like effect, almost turning petri dishes into Daguerreotypes.

Voigt's colleague Natalie Kuldell has shown synthetic biology teachers how to produce interesting images. The MIT group also grew a detailed portrait for Popular Science depicting the magazine's founder, Edward L. Youmans. For Benjamin, one of the amazing things about this technology is how incredibly high the resolution is compared to non-living technology for making images. "Because bacteria are so small, there are so many 'pixels,'" he said.

Although scientists can hack bacteria in the engineering sense, bacteria can't be hacked or "cracked" in the computer science sense, according to researchers from Hong Kong's Chinese University who developed methods to compress data and store it in bacterial cells. Bacteria have the advantage of being immune from cyber attacks, the group told the Agence France-Presse when it first presented the research in 2011.

"The DNA strands hold so much information that it's really exciting to think of using it as storage," Benjamin said. Although there's still a long way to go in developing bacteria-based data storage, growing new computer hard drives could mean using fewer mined materials. For Benjamin, that's a more appealing way to put physical products into the world.

Transforming bacteria into a mini-factory that can manufacture new building materials for us sounds far-fetched at first. But David Benjamin's collaborative research is inching closer to this reality. He pointed out that bacteria can already do amazing things like manufacture rigid materials through calcium precipitation, make flexible material through cellulose deposition and also produce a paper-like material. His hope is that cutting and pasting genes might allow bacteria to create new materials that never existed before in that same way.

"They can do really interesting things, from being parts of flexible electronics to being membranes in buildings or airplanes, to having certain structural properties, but also certain properties of transparency or malleability," Benjamin said.

Former U.S. Secretary of Energy Steven Chu introduced us to the concept of a glucose economy. His idea: plant fast-growing crops in warm regions and their glucose could be used for making biofuels and bioplastics. The glucose economy concept resonates with David Benjamin. "It's not like you can pull fuel out of thin air," he said. "You feed in sugars and that's what the glucose comes from." Add some extra nutrients and the bacteria or yeast grows in big tanks, then secretes the molecules that we want.

The renewable products company Amyris Biotechnology is known for making fuel this way with yeast. But scientists are making inroads using similar technology with bacteria. Earlier this year at team at the University of Exeter genetically modified E. coli DNA with four other types of bacteria to produce carbon compounds from sugar. When mixed, those compounds become diesel fuel. This petroleum replica fuel still has a long way to go before it's scaled up for commercialization, but it could alleviate the need for biofuel-specific crops and the water they require. Maybe we're headed for a bacteria-based economy.

Given enough time, microorganisms can break down the some of the toughest plastics. In 2009, high school students at two separate schools isolated the ones that were the most successful at chomping plastic waste. Bacteria-based systems for decomposing styrene have since been developed in Japan and Ireland. "We know that bacteria degrade everything, sometimes at different rates," Benjamin said. "Just conceptually we'd kind of amp up the parts of bacteria that eat some of the hardest-to-break down chemicals and then kind of turn off the parts of bacteria that do other things."

Beyond plastics, bacteria can be used for cleaning up heavy metals and even nuclear waste. In 2011, Michigan State University biologists studying the Geobacter sulfurreducens bacteria figured out exactly how it manages to extract uranium from nuclear waste. Unlike brute force approaches to environmental remediation that kill everything in sight, biological systems allow for fine-tuning. They can be programmed to do a job, released into the soil, isolate the problematic molecules, and surround it to make the waste easier to clean, Benjamin explained.

When dirty clothing doesn't pass the smell test, bacteria are usually the culprits. But there are bacteria that do just the opposite, scrubbing the worst possible smells out of the air. Biofilter machines placed near fish processors and pig farms in Denmark have helped the neighbors breathe easier. Early last year scientists at Aalborg University in Denmark studied ways to improve odor-eating filters for industrial uses, determining which bacteria processed sulfur compounds the best. They hoped their research could lead to more affordable industrial biofilters.

Benjamin said that it seems like more and more people are discovering what naturally existing bacteria can do. "They can make rigid materials, they can make flexible materials, they can pull certain things out of the air," he said. Then, with engineering, those abilities can be combined or amplified. "That will result in a greater explosion of possibility."

In discussing synthetic biology, David Benjamin regularly refers to the International Genetically Engineered Machine student competitions. For the past several years, many teams have focused on bacteria. "Although iGEM is supposed to involve any type of genetic engineering, bacterial systems seem to be the easiest ones to work with," Benjamin said. "They have the most known about them, it's most easy to cut and paste their genes together."

Students from Bielefeld University in Germany participating in this year's iGEM competition at MIT have been hard at work on a new bio-battery, also called a microbial fuel cell. They want to make a version using bacteria instead of harmful materials that can end up in the environment. The team is working with E. coli in the lab, optimizing it for use in an anode, where it will break down glucose and produce electrons, according to the university. Currently the bio-battery is still in development. Under results the team put, "Coffee? YEEEESSS!!!!!"

In the age of antibacterial soap, smearing bacteria all over your skin probably sounds unwise. However, that's exactly what scientists are working on. Researchers at the Norwegian institute SINTEF found that the bacteria Micrococcus luteus found in a local fjord contains a special pigment called sarcinaxanthin that has the unique ability to absorb harmful long UV light. Scientists were able to artificially engineer the bacteria so it produced enough of the pigment for commercial production. The Norwegian company Promar patented the technology and is working on a new sunscreen it plans to market called UVA-blue.

Benjamin emphasized how important bacteria are by pointing out how many people are cured of deadly colon infections through fecal transplants. These procedures restore good bacteria that are normally killed off when a patient takes antibiotics. "Thinking about how helpful bacteria are," Benjamin said, "you would die without these certain ones."

Bacteria can be engineered to glow in the dark, which is not only trippy but useful, too. David Benjamin pointed to the University of Cambridge's iGEM team's work on glowing bacteria in 2010. The electronics company Phillips has also been experimenting with this. Two years ago they announced a Bio-light system made from bioluminescent bacteria that feeds on methane generated from household waste.

More recently the Glowing Plant project used an agrobacterium to get plants in the lab to glow brightly. The project, which drew from the same systems that allow fireflies to grow, spurred a firestorm online that prompted the crowd-funding site Kickstarter to ban the practice of rewarding backers with genetically modified organisms. Despite the ban, the project was successfully funded over the summer with nearly half a million dollars.

"I love that natural systems can glow like that, and you can harness that and amp it up or tune it," Benjamin said. "It is really amazing."