Gaining a better understanding of how tough fibres and complex sugars can be converted into biofuels and industrial products could mean taking an important step towards developing smarter materials and petroleum-free fuels. Making use of the chemical properties stored in plants, however, is no easy feat because whenever we eat vegetables the microbes in our bodies carry out elaborate chemical reactions to convert plant matter into simple sugars the body can use. Finding out what bacteria and fungi form the basis of these processes is one of the main tasks of the science concerned with biofuels.
Now (2021), in the quest for new and more efficient ways to process plant material for industrial purposes, scientists at Berkeley Lab have looked at the gut microbes of ruminant animals. The digestive tract of ruminants hosts numerous microbes, including fungi, which have evolved for millions of years to perform vital chemical processes more effectively than scientists ever could under lab conditions. Understanding the mechanisms of these bacteria and fungi is important for converting plant material into products, such as fuels, that are needed in many industrial applications. For this reason, the team of scientists generated reconstructions of the many thousands of microbial genomes in goat-excrement samples and identified the genes responsible for metabolic enzymes and other digestion-related proteins. The work revealed 700 previously unknown microbial species and also stressed the importance of anaerobic fungi in the goat gut. In earlier research, the team had already discovered the presence of a small minority of fungal species among the bacteria of the gut, but they did not realize how vital these organisms were for digestive processes–fungi produced the main share of the biomass degrading enzymes that the microbial community needed to function.
This research builds on earlier studies concerning the microbial environment in the gut of ruminants. In 2011, for example, scientists characterised biomass-degrading genes and genomes, sequencing and analysing 268 gigabases of metagenomic DNA from microbes belonging to plant fibre in cow rumen. From these data, 27,755 putative carbohydrate-active genes were identified and 90 candidate proteins expressed, of which 57% were enzymatically active against cellulosic substrates. They also analysed 15 uncultured microbial genomes, which received additional validation through complementary methods including single-cell genome sequencing. These data sets gave a substantially expanded catalogue of genes and genomes participating in the deconstruction of cellulosic biomass.
In 2016, scientists designed a systems-level approach that combined transcriptomic sequencing, proteomics, phenotype, and biochemical studies of relatively unexplored basal fungi. They found that gut fungal enzymes did not prefer a particular substrate due to a wealth of xylan-degrading enzymes. These enzymes were universally catabolite-repressed and were further regulated by non-coding regulatory RNAs. Additionally, they identified several promising sequence-divergent enzyme candidates for lignocellulosic bioprocessing.
In 2018, scientists analysed 410 cultured bacteria and archaea, as well as their reference genomes representing every cultivated rumen-associated archaeal and bacterial family. They looked at polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and allocated specific taxa to functions. They found that a total of 336 organisms existed in available rumen metagenomic data sets, and 134 could be found in human gut microbiome data sets. Comparisons with the human microbiome revealed that rumen-specific enrichment occurred for genes encoding the de novo synthesis of vitamin B12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome due to underrepresentation of markers of environmental stress.
Microbial energy has several advantages over fossil-based energy. First and foremost is the fact that the processes involved in microbial energy transformations are more environmentally friendly than. fossil-fuel technologies. For example, microbial energy production does not involve the use or production of hazardous materials. Moreover, biomass conversion is a carbon-neutral process. Microorganisms can also choose their substrate from a complex mixture of chemicals, which reduces the need to purify or refine the raw materials to separate substrates from non-substrates. Finally, microbial energy technologies can be used to produce energy locally, close to where the energy is needed. Such “distributed” energy systems like these can minimize the cost of energy transfer.
The ultimate goal of the study is to facilitate the development an artificial version of an herbivore microbiome that could be used to perform the chemistry needed to break down plant matter on an industrial scale. The scientists are confident that their research is headed in the right direction to achieve more sustainable fuels.