Metagenomics: how to uncover the unseen majority!

Don Cowan

What is metagenomics?

To understand metagenomics you need to understand genomics.

Genomics is, quite simply, any research relating to the genome of any organism, where the genome comprises the entire DNA of an organism and constitutes the molecular fingerprint for what the organism becomes. The genome of a plant dictates that it will be green (probably) and have leaves (usually), while the genome of a mole rat dictates that it will be furry and spend a lot of its time underground eating the bulbs in your flowerbed.

Metagenomics is just genomics, but a lot more of it all at once. The term is applied to research which focuses on many genomes at the same time, such as is typical in some sections of environmental study. The term is most commonly used in the study of environmental microbiology, where an environment, whether it be agricultural soil, marine sediment or sewerage sludge, contains many microorganisms living together in close proximity. For a sense of scale, a teaspoon of agricultural soil is likely to contain 500 to 1000 bacterial and fungal species, and sewerage sludge (which is a very rich environment for microbes) may have 10 fold more.

‘Metagenomics’ (the term was only coined in 1998) rose rapidly to prominence in the late 1980s with the arrival of new phylogenetic technologies, based on the discovery that all organisms contained molecular markers which could be used to established the relatedness of one organism to another. This technology allowed microbiologists to easily assess the true microbial diversity of environmental samples, and rapidly led to the astonishing realisation that most of the microorganisms on the planet had never been cultured in a laboratory and were completely unknown!
In its simplest form, ‘Metagenomics’ allows us to ask, and answer, the most basic environmental question: “what is there”? Put slightly more rigorously, this means “what is the microbial species diversity in a habitat”? The technology is now very well established. It is based on the recovery of total environmental DNA from a sample; that is, where the DNA preparation will reflect all of the organisms what were present in the sample.

Analysis of the species diversity uses another ground-breaking technology, PCR (the polymerase chain reaction, which just amplifies very small amounts of DNA to much larger amounts). Coupled with the use of phylogenetic primers (short sequences of DNA which specifically target the phylogenetic marker sequences), all the difference markers (from, say, a thousand different bacterial species) can be amplified simultaneously in an automated process that takes just a few hours. Extracting the phylogenetic information from these amplified sequences uses a third ground-breaking technology: high throughput ‘deep’ DNA sequencing, where millions of DNA fragments can be sequenced rapidly and accurately (and at a cost that is actually affordable by most research laboratories).

There is much more to metagenomics. It can be used to study different groups of organisms (bacteria, fungi, viruses), or to focus on a particularly taxonomic group, such as the cyanobacteria which are important nutrient cycling organisms in many environments. If the mRNA in an environmental sample is targeted, rather than the DNA, then metagenomics can inform on the members of the microbial community that are actually functional (rather than just present) under any conditions. This is termed ‘functional metagenomics’.
There is another important sub-discipline of metagenomics: metagenomic gene discovery, or the use of metagenomic methods to access specific genes, biosynthetic pathways or gene products in the a metagenome. This is a powerful tool for both functional metagenomics and for bioprospecting, and is a promising new technology for the discovery of new antibiotics, industrial enzymes and more.

Metagenomics in the University of Pretoria Centre for Microbial Ecology and Genomics (CMEG)

Researchers at the new CMEG laboratory are involved in a wide range of genomics and metagenomics projects, many of which focus on the organisms and microbial populations living in extreme environments. The two major programs involve studies of desert microbial ecology at the two ends of the temperature spectrum. With long standing collaborator Prof Craig Cary from Waikato University, NZ, Don Cowan has been leading studies on the structure, function and adaptation of microbial communities in Antarctic cold desert soils (Figure 1a).

More recently, in collaboration with Prof Marla Tuffin (IMBM, UWC), Prof Ed Rybicki (MCB< UCT) and Dr Mary Seely (Gobabeb Training and Research Centre, Namibia) he has developed a new program focussing on a landscape-scale study of the Namib Desert (Figure 1b).  Bringing together a team of local and international researchers, the program aims to understand the microbial ecology of the many different biotopes present in the sand desert and dunes of the Namib, and to probe the role of micro- and macroclimatic and physicochemical factors in controlling microbial community structure and processes.

In parallel, the CMEG team is involved in a range of other projects; identifying novel enzymes and stress response/adaptation genes using metagenomic expression libraries, full genome sequencing of psychrophilic and thermophilic isolates and (in early 2013) the laboratory’s first full metagenome sequence.

 Oligotrophic desert soils in the Miers Valley, Eastern Antarctica.

 


The eastern Namib Desert after the summer rains.

 

 

The future of metagenomics

The field of genomics (and metagenomics) is expanding at an astounding rate, driven by rapid advances in sequencing technologies and associated computational capacity (bioinformatics). To give a sense of scale, the cost of sequencing a human genome in 2007 was around $10M, compared to the current cost of $10k. This thousand-fold reduction in cost has been paralleled by an equivalent reduction in time. A genome can be sequenced over a weekend! We are now at a point where average laboratories can afford to sequence small (bacterial) genomes routinely, and even contemplate the sequencing of full metagenomes. CMEG plans to sequence its first metagenome, probably an Antarctic hypolithic community (photoautotrophic communities living on the undersides of translucent rocks), early in 2013. These are simple communities in comparison to eutrophic temperate habitat communities, but may still comprise over 400 bacterial species and a smaller number of lower eukaryote species.

The challenge will not be the sequencing, but the bioinformatics. Nevertheless, even a partial assembly will provide an enormous resource of psychrophilic microbial genome data for many future projects: for identification of useful biocatalysts, of cold-response and adaptation genes, of metabolic pathways and so much more.

More information:

* Professor Don Cowan was educated in New Zealand at the University of Waikato and completed a period of Post-Doctoral study there before moving to University College London as a Lecturer in 1985. After 16 years in London, he accepted the position at Professor of Microbiology in the Department of Biotechnology at the University of the Western Cape, Cape Town, where he was a Senior Professor and Director of the 60-strong Institute Microbial Biotechnology and Metagenomics. He has recently taken up a new post at the University of Pretoria as Director of the Institutional Research Theme in Genomics and the new Centre for Microbial Ecology and Genomics. 

 

Key references:

Cary, SC, McDonald, I, Barrett, JE and Cowan, DA. (2010) On the rocks: Microbial ecology of Antarctic cold desert soils. Nature Rev. Microbiol. 8:129-138
Cowan, DA, Sohm, JA, Makhalanyane, T, Capone, DG, Green, TGA and Cary, SC. (2011) Hypolithic communities: important nitrogen sources in Antarctic desert soils, Envir. Microbiol. Rep. 3:581-586
Khan, N, Tuffin, IM, Stafford, W, Cary, SC, Lacap, DC, Pointing, SB, Cowan, DA (2011) Hypolithic microbial community colonization of quartz rocks from Miers Valley, McMurdo Dry Valleys, Antarctica. Polar Biol. 34:1657-1668
Makhalanyane, TP, Valverde, A, Lacap, D, Pointing, SB, Tuffin, IM, Cowan, DA. (2012) Evidence of species recruitment and development of hot desert hypolithic communities. Environ. Microb. Rep. Accepted for publication