Exploring Wastewater Microbiome Opportunities

John Tillotson, CEO of Microbe Detectives, recently got together with key wastewater experts to get their perspectives on the water microbiome industry and the Summit.

Trevor Ghylin, Ph.D., P.E.
Founder/CTO, Microbe Detectives

Tell me about your background.

I founded Microbe Detectives during my PhD work. I was doing a PhD in environmental engineering at UW-Madison, applying a lot of this next-generation DNA sequencing technology to understanding lakes. My professional history was in wastewater consulting and it just seemed like this new DNA technology had a lot of applications in drinking water and wastewater, to help solve microbial issues that we couldn’t solve with these older more standardized tools.

What problem are you solving in the wastewater industry?

The problem we’re focused on solving is operators of drinking water and wastewater systems are kind of flying blind, regarding microbiology. The tools they’re using are petri dish culturing and microscopes that show them less than 1% of what’s going on in their systems. We’re able to use DNA sequencing to help identify almost 100% of what’s in those samples.

How does DNA sequencing help wastewater operators?

DNA sequencing has been around since about the 70’s but it’s gotten progressively better over the decades, especially since the human genome project, when more than a billion dollars was invested in decoding the first human genome. Since then, the costs have been dropping exponentially to the point where we can, for an economical price, read DNA straight from a sample of water and start assigning microbial names to it.

PCR, another DNA test method, has been around for a couple decades and is a very economical way to do things, though the one limitation with PCR is typically you are looking for one specific thing. You can do PCR for a certain type of e.coli, for example, but you need to know what you’re searching for before you do the test.

Whereas with DNA sequencing you don’t need to have a target in mind, you are just literally reading DNA from the sample, so you don’t have to go in knowing what you’re looking for. DNA sequencing currently is limited only by science, at this point, and scientists are discovering new microbes that we didn’t even know existed almost daily. Currently we know more than 10,000 different bacteria that are in these databases and that’s growing every day as science continues to progress.

This new DNA sequencing technology is really helping us advance science and understand what’s going on with microbiology. When I first founded Microbe Detectives one of my first ideas was to simply be a lab producing DNA data for clients in the water industry. I quickly realized and understood that this DNA data and microbial names is not very helpful to most people in the industry, because most people aren’t PhD microbiologists. They need some help understanding which bacteria do they care about? what does it mean if I have 1% of my sample as Nitrosomonas? We don’t just provide raw bacterial data, we actually provide a report interpreting this data specifically for drinking water and wastewater professionals. In the wastewater side, for example, we’ll do interpretation of ammonia removing bacteria and phosphorus removing bacteria, filaments, foaming, methanogens and things like that that wastewater people care about and understand.

How does DNA sequencing benefit anaerobic digester operations?

Anaerobic digestion is a microbial process that relies on a lot of different symbiotic relationships, including some of these methanogenic archaea that are really ancient microbes. Essentially what the process does is convert organic waste into a renewable fuel, hydrogen and methane. This fuel can be burned to produce renewable heat energy or it also can be burned in vehicles or even engine generators to produce renewable electricity.

Anaerobic digestion as a microbial process can be somewhat finicky sometimes, and there have been very limited tools on understanding what’s going on in these processes so the DNA is kind of exciting because now we can actually see what’s living in these digesters. Previously there was really no way to know, even a microscope doesn’t show you much of anything in a digester. There’s really no way to see what microbes you have in there, what’s going on, so finally we can track these really important populations of methanogens, fermenters and symbionts, things like that, that we know are critical to digester operation.

Anaerobic digester operators can benefit from DNA data by finally being able to see what’s going on in their digester, so they can see problems before they happen. You’ll see problems with things like foaming bacteria like Microthrix, which you can see at very low levels before they cause problems, and you can act before you have a serious problem occurring. You can also track all the other populations that you care about and see declining abundance or increasing abundance, that might lead to operational issues down the road.

How does DNA sequencing benefit BNR programs?

BNR stands for biological nutrient removal in wastewater treatment plants. It’s becoming more and more important as states are restricting nutrient discharges from wastewater treatment plants. BNR is a way to remove nitrogen and phosphorus biologically rather than using chemicals. It helps them meet these new permit limits on nutrient discharges that cause algae blooms and surface waters.

When plants switch from a kind of a traditional fully aerated mode to a BNR mode they can save a lot of energy. You’re recovering energy from nitrate, that’s kind of the main one, you could also you’re having anoxic zones, where you are not having to put any air in, so there’s a significant energy savings potential.

BNR plants can also see a reduction in solids production, from if you’re trying to remove phosphorus chemically that actually produces a lot of solids, but if you do a biological you’re getting rid of that solids production. DNA sequencing can help operators that are trying to do BNR in their plant finally see the bacteria that are necessary for that process. Without DNA data it’s really hard to know what’s going on in a plant. You can see phosphorus levels going down but you don’t know if that’s just normal biological uptake or are your chemicals doing something? With DNA data you can actually see you have the biological phosphorous bacteria in there, there’s only a couple different types to do that. Either you’ve got them or you don’t and you can see how many are, and you can track those populations over time. The same goes for ammonia removers and denitrifying.

What are your hopes for the Microbiome Water Summit?

My main hope for the Microbiome Water Summit is that we educate water industry professionals on DNA sequencing. Most of the industry is not aware that this tool exists or what they can do for you. I’d like to educate as many people as possible and get them passionate about this technology so they can help us drive the industry forward to using this new tool. The key benefit to attending the summit is that I’m hoping is to make people passionate about what they do and passionate about the water industry. This is a very exciting time to be in the water industry. One reason is because new DNA technology is helping us to finally understand what’s living in our drinking water, wastewater and other waters that we deal with.

Leon Downing, Ph.D. 
Senior Technologist, CH2M

Tell me about your background and responsibilities.

I’m Leon Downing, Senior Technologist with CH2M, and in that role I work with wastewater process optimization, design, troubleshooting, mainly with biological processes for water reclamation. Within the wastewater industry, the majority of the treatment that we do is driven by biological processes. Historically we had to infer what biology was there, based on microscopy or some special sampling and kind of guessing at who (what microbes) are actually in the system. With metagenomics we can quickly get an assessment of all the bacteria that are present, how we are selecting for them. This allows us to make more efficient designs, operate more efficiently to intensify our infrastructure, use less energy, produce cleaner water, and in the end, actually reduce the burden on ratepayers for wastewater infrastructure.

Why is DNA sequencing important to the wastewater industry?

I think it’s really in the understanding of new processes so we can come up with a new idea of how we might be able to treat water more efficiently and recover resources from it more effectively. It’s being able to understand the biology that’s present and getting a better sense of who’s really there. This helps us to better understand the process and not make it a “black box.” This gives us more confidence to apply technologies more rapidly and to to accelerate adoption. That’s a big part of it. The other part is the optimization component, where we have existing processes they aren’t working as well as we need them to, and figuring out how to make them work better.

What do you see as the biggest opportunity for DNA sequencing?

Biological Nutrient Removal [BNR]. What we’re looking at is finding ways to remove phosphorus and nitrogen from the wastewater biologically instead of chemically. That results in a lower net resource consumption. It also allows us to actually recover phosphorus and nitrogen. Instead of treating it, where we are removing it from the water but have another environmental impact (which is the disposal of solid waste), it actually allows us to concentrate those nutrients, pull them out, and get them back into the fertilizer cycle. Biological Nutrient Removal really drives a lot that is protecting the waterways. It’s recovering valuable resources and at the end of day it actually uses less energy to treat water than conventional processes.

What are the energy savings of BNR program?

10 to 15 % of the aeration energy, which is half the total plant energy. So it’s not getting rid of energy, but it’s every little bit that makes a big impact as we try to move towards less and less energy intensive processes.

What are the impacts of BNR on chemicals and solids?

By going to biological processes we don’t have to add a lot of expensive iron salts or aluminium salts into our water. We’re making it more of a natural process with the biology, not having to bring in chemicals and that also reduces the chemical sludge that we make. From a utility perspective, the main driver is an overall cost benefit, but from an environmental standpoint it also reduces our impact of treating and reclaiming water.

Why is DNA sequencing (metagenomics) needed with a BNR program?

It really comes down to understanding the biology that’s there. We’ve learned a lot over the past decades on how these processes work from an overall perspective, and how to operate them, but we’ve always been trying to just kind of infer what bacteria are present. As we try to be more innovative, using smaller tanks, using less energy, we’re selecting for a different ecology than we have in the past. Without being able to understand those changes and understand who’s there, it’s very difficult to find better ways to do things. With metagenomics, and with the ease of being able to get these samples, it helps us to really understand what is going on, for instance, when we’re shifting from an old population to a new population because the old population couldn’t make things work under our new conditions. At the end of the day, metagenomics gives the utility the confidence they need to invest tens of millions of dollars in a new technology, that in the end will save them money. They need that confidence to invest rate-payer’s money.

What is the public benefit of metagenomics?

The public benefit for metagenomics really comes down to the bottom line. That’s one part of it, right, just the fact that understanding the biology in a biological system helps you to operate it more efficiently and potentially design smaller tanks, so it cost less. The check you write out for your bill at the end of the month can be reduced. The environmental impacts are also a huge component of this. By understanding the biology that’s there, we can try to concentrate our nutrients and recover them. Instead of just fixing more and more nitrogen from the atmosphere and mining more and more phosphorus, we can actually fix those nutrients from a wastewater treatment process and return them back to the cycle. In addition to the environmental aspect of this, there is also a social benefit. When you think about clean waterways, I think a lot of people forget that the Cuyahoga River used to start on fire, right, or that Lake Erie was dead, and now even the Chicago River has people kayaking on it. So again, using metagenomics, to understand the biology and clean water to a higher level, benefits everyone and the use of our natural resources.

Can you provide an example metagenomics success story?

A really great success story of using metagenomics in wastewater treatment and resource recovery involves a facility outside of Dallas, Texas. They’ve been doing metagenomic sequencing for about three years now and over that period of time they’ve used that to understand their ecology and give them confidence in operating their facility in a different way. With that they’ve been able to change operational strategies that reduced annual costs by three-hundred and sixty-thousand dollars a year. By investing in metagenomics they’re saving over a quarter of a million dollars a year in operating costs. To have a service where you can easily collect a sample get it into a filter and just ship it off and in a couple of weeks later know every organism that’s in your system makes it very usable. 

What do you hope we accomplish at the Microbiome Water Summit?

What I think is really interesting about the Microbiome Water Summit is that it’s bringing together a lot of people from different parts of the water sector. It’s not just wastewater. It’s not just purely microbiology. It’s not just animal health. It’s everyone. One of the challenges is just the amount of data that we generate with metagenomics. Just seeing how everyone uses that data, and how to make effective use of it, and then to communicate that to people, I think, will be a huge benefit of the Summit.

For those that are considering attending the Microbiome Water Summit, what do you think the key benefits will be for them to attend?

Some of the key benefits for those that attend the summit are really kind of on the same route. If you’re trying to decide whether to use metagenomics, or how to use metagenomics, or what to do with all of this data, the Summit will provide lots of examples. You will be able to talk to the people that have both developed the techniques but also developed ways of using the data. This can really give you a jump start, so you’re not just, you know, sending in a sample and getting a bunch of data back and not knowing exactly how to manage this information. I think that’s the biggest thing. If you’re thinking about using metagenomics for your application, getting a jump start on managing the information and making effective use of the information will be a huge part of the Summit.

Microbiome Water Summit 2017

  • Learn from leaders in this ground-breaking field
  • Network with a new community of innovators
  • View live streaming on the Internet

Presentations and panel discussions

  • Invisible Influence: The Microbiome in Health
  • Metagenomic Applications in Wastewater
  • Key Findings & Insights:
    • Biological Nutrient Removal (BNR) Study
    • Biogas Anaerobic Digester Study
  • Source Water Characterization
  • The Shedd Aquarium Microbiome Project
microbiome water summit shedd