Research Highlights: The Micro-World of Compost and How It Could Solve the Energy Crisis

contributed by Anna Alessi

Bruce Lab

The Bruce Lab studies microbial and plant biochemistry and environmental biotechnology. Image source

When people toss plant scraps onto a pile to decompose, they usually think of the resulting compost as a waste product that might produce fertilizer for their garden (at best). I think of it much more optimistically. As a postdoctoral research associate in the Centre for Novel Agricultural Products (CNAP) at the University of York, I study the use of compost as a fuel source. Our research focuses on various aspects of the industrial production of biofuel. Specifically, CNAP groups led by Professor Neil C. Bruce and Professor Simon McQueen-Mason are studying and modifying plant cell walls to increase their saccharification potential—the ease with which the sturdy cell walls can be broken down into fermentable sugars—as well as investigating new enzymes for pre-treatment of biomass.

Biofuels are conventionally produced from sugar-rich biomasses derived from corn (US market) or sugar cane (Brazil). Those two countries produce more biofuel than the rest of the world combined, accounting for 88% of annual bioethanol production1. However, the conventional first-generation feedstocks are important components of the food market, and their usage as fuel could potentially affect their price and availability. A feedstock with no other use would be preferable; hence, the lignocellulosic biomass derived from agricultural residues (straw, bagasse, husks, stover) or dedicated plant materials (willow, miscanthus) is becoming increasingly popular in the production of biofuel. The commercialization of such second-generation lignocellulosic biofuels involves extensive pre-treatment, including the application of harsh chemicals and enzymes. Many question the practicality and sustainability of second-generation biofuels, given the difficult processing and relatively high cost of production, but they are still an emerging technology, with many improvements to be made in the coming years. It is important to bear in mind the amount of lignocellulose that is produced annually—at 60 Gt/yr in terrestrial and 53 Gt/yr in marine ecosystems, it is the largest global sink for carbon2.

Biofuel generations

While first-generation biofuels are derived from sources that are usable as food, second-generation biofuels are produced from waste. Image source

As a trained microbiologist, I am interested in studying complex environmental systems that evolved to efficiently convert the resistant lignocellulose polymer to monomeric units. The resulting simple sugars are used by fermentative microorganisms to produce bioethanol. Various microbial communities have developed a wide range of mechanisms that successfully degrade woody material. Such microbes are abundant in the human gastrointestinal tract, helping us digest the fibrous food that we consume daily (especially important for vegetarians). They are also part of the microbiomes of animals, including ruminants and insects (e.g. termites). Microbial communities in soil, compost, freshwater and marine sediments allow recycling of the carbon locked in lignocellulose.

Plant cell walls can be broken down into sugar molecules to use as fuel. Source:

Plant cell walls can be broken down into sugar molecules to use as fuel.
Image source

My research interest lies mainly in identifying enzymes and accessory proteins which those microorganisms use for efficient lignocellulose degradation. Natural microbial decomposition is so efficient that a heap of organic plant material in a garden compost bin vanishes within months. Compost is a particularly interesting ecosystem, since the synergistic action of bacterial and fungal enzymes is needed to expose the sugars from the cellulose, hemicellulose, and pectins of plant cell wall and maintain the viability of the whole community.

Unfortunately, nature’s secret to lignocellulose degradation is not easy to unlock. Many of the highly potent bacteria and fungi are difficult to culture in laboratory conditions, making them very mysterious. However, development of advanced molecular biology techniques in addition to the rapidly lowering cost of sequencing makes culture-independent approaches a very attractive way of studying these complex communities.

In my project, we apply conventional microbiology techniques combined with cutting-edge sequencing methods to mine novel enzymes and accessory proteins produced by the compost microbiome. For instance, Ph.D. student Nicola Oates used multiple isolation assays to find enzymatically active bacteria and fungi, which she further identified by sequencing 16S and ITS phylogenetic markers. She is currently studying one of the fungal isolates in greater detail, since the enzymes that this fungus produces could potentially be applied in industry.

Nicola Oates

Nicola Oates is a Ph.D. student studying enzymatically active bacteria and fungi.

As I mentioned earlier, we also use advanced culture-independent ‘omics’ approaches in order to identify and then further characterise compost secretome (proteins excreted by compost microorganisms) and transcriptome. This enormous database will hopefully offer information on the proteins and genes expressed by the microbial community during lignocellulose degradation. We know that the microbes from compost attach very tightly to the plant material and form biofilm-like structures. This plant-microbe interaction must be the best way to facilitate the degradation of lignocellulose, which at the end of our experiment became powdered and structurally modified by the microbial activities.

All of this makes lignocellulolytic microorganisms from a wide range of environments a very attractive source of novel biocatalysts. Using next-generation sequencing, we are able to capture a glimpse of their community life. In addition to expanding our knowledge about these complex ecosystems, we will hopefully “adapt” their mechanisms of converting plant biomass to produce sustainable energy from waste.

  1. Renewables 2014 Global Status Report – Full Report
  2. Cox P., Betts R., Jones C., Spall S. and Todderdell I. 2000. Acceleration of global warming due to carbon cycle feedbacks in a coupled climate model. Nature. 408: 184-187.