From Slime to Sublime

FROM the moment we wake up and gaze at our reflection in the mirror, we consume our first precious resource of the day whilst brushing our teeth. Our languid minds might inquire: is it necessary to leave the tap running? Within minutes we go from resource use to waste production; the cereal or milk has run out – where does the empty plastic bag, box and carton go? Hopefully, in the appropriate recycling bins (if you have them).

This story however, is just a microcosm of how as a society, we use lots of precious resources in a linear fashion – “take, make and waste”. This paradigm is occurring on an unprecedented scale. As communities become more affluent, we use more resources and create more waste, from everyday items such as food packaging to high-tech gadgets like smartphones, and let’s not forget the industrial processes involved. But things are beginning to change.

What if we could locally recover the resources from the waste produced by our communities – for example at our landfill sites – by harnessing and directing biological systems to recover the likes of valuable metals?

Engineers have exploited biology for many years, particularly within the waste treatment sector. Microbes have inhabited our planet for millions of years and have evolved an array of metabolic processes to adapt to environments of all sorts of flavours, providing a wonderful repertoire of chemical transformation steps which we can exploit. From providing safe, drinkable water pumped directly to our homes, to producing liquid and gas energy sources, nature-based solutions driven by microbial communities have enabled low cost and sustainable alternatives to polluting or expensive chemical processes. Although I use the word sustainable (which is perhaps one of the most overused words within scientific research these days), the outcome has often been anything but. As an example, each year, we put tremendous emphasis on fixing over 130m t of atmospheric nitrogen into ammonia, a raw material for producing fertilisers to feed crop plants and subsequently support our expanding societies. Although a significant proportion of this fixed nitrogen is lost to the environment, some is collected and treated within wastewater treatment plants, with once again the nitrogen being returned to its gaseous form to the atmosphere. These are energy-intensive processes, considering the scales involved. The term “circular economy” has been banded around for a few years now, and in principle aims to close the loop and move away from the linear model, and help reduce energy-intensive resource mining, providing vast environmental benefits.

Around five years ago, my research team at The University of Sheffield became interested in how we can be inspired by natural microbial communities to create synthetic consortia, either to enable enhanced performance or added functionality. Put simply, we wanted to use the tools we had developed in our lab to better understand the roles of microbes in specific environments. This would enable us to generate a series of design rules to put together specific microbes that interact in a way that can benefit industry as well as the environment. We were mostly excited by the concept of resource recovery. Why bother with using petrochemical-guzzling, environmentally-harmful extraction techniques, together with shipping for thousands of miles all over the globe, when we could look to local waste depots as a source? Our vision entailed recovering everything from the surprising complex variety of precious metals we use in everyday electronic devices through to nutrient sources for crop plants. Could the traditional waste management sector be transformed into profitable bioproduction factories?

Power in a union

Engineering microbial consortia is not a trivial challenge. Naturally-occurring microbial communities are highly structured and complex, with spatial organisation that varies over time, closely governed by environmental conditions. Due to the advent of molecular biology and DNA sequencing, we can estimate the highly diverse microbial assemblages present within soils, water and the atmosphere. The interactions between the microbes also vary, where they can compete for resources if they have very similar metabolic necessities, but they can also cooperate, exchanging nutrients and enhancing each other’s growth rates, yields and resilience. There can also be “cheaters” present – microbes which consume resources within the consortia but offer nothing in return.

At Sheffield, we have been using a variety of techniques to try and untangle the metabolic processes and interaction mechanisms that are occurring within microbial ecosystems. These tools aim to answer three fundamental questions: what type of microorganisms are present? What do these microorganisms do? How can we optimise the activities of these microorganisms for industrial processes (eg energy flow, environmental resilience, resource recovery)? We have applied the engineering paradigm of measure, model, manipulate and manufacture, in an iterative approach, when working with pure cultures of microbes. And whilst pondering the concept of engineering microbial consortia, we decided to create more optimised microbial consortia in the same way.

We use a variety of methods for the measuring, including quantitative multi-omics of communities in changing environments, creating community matrices with isolated microbes, followed by screening for desirable traits, applying adaptive evolution to generate new communities with faster growth rates, and more recently microfluidics, to look for important metabolites involved in interactions. Our favoured omics technique is called proteomics, where the focus is to identify proteins in cells at specific time points. Proteins are the workhorses in cells and the molecular entities that bring cells to life, allowing us to bridge the gap between the upstream genome and the downstream metabolome, and hence giving us a functional understanding of microbial communities. Samples are prepared to extract proteins from the cells, and after being digested and fractionated, are subjected to high mass accuracy mass spectrometry. The resulting spectra are processed by advanced bioinformatics tools and the quantitative information interpreted to construct metabolic pathways that may be involved in pollutant breakdown or interaction mechanisms, and help create design rules for constructing synthetic consortia.

Targeting landfill leachate

For us, targeting landfills was a no brainer. Together with incineration, it is still the most common waste management strategy in the UK. Landfill leachate is formed either through rainwater runoff or from moisture generated within the landfill. With a dark, opaque appearance, domestic landfill leachate is often characterised by high concentrations of ammonia, heavy metals and a wide variety of weird and wonderful organic chemicals. There’s an assortment of treatment methods available – physical, chemical and biological, including aerated lagoons, reverse osmosis or sequential batch reactors. Costs of each can vary, but one thing is certain, the economics are largely driven by detoxification and thereby enabling release of clean water to the environment (or for treatment in wastewater treatment plants).

However, if we instead look at these leachate ponds as a source of useful resources, which require extracting and concentrating, then the economics become profoundly more interesting. Recently, there have also been some headline-grabbing incidents, where unintended leachate release into the environment caused ecological damage and record-breaking costs; in one case last year reaching £0.5m (US$0.65m). Not only this, but there is the growing uncertainty in regional politics, where a report from a leading UK waste and recycling company warned the UK government of an impending crisis due to limited landfill options. A crisis that could be exasperated by global politics – including Brexit and the fact that Chinese recycling firms are no longer importing UK waste. A perfect storm scenario appears to be brewing.