Adapted from image by NASA Goddard Space Flight Center

The World is Full of Bacteria

There are over a billion microbes in just one liter of ocean water [1]. The same goes for a liter of soil. As the human population reaches 7 billion individuals worldwide in 2011 [2], it is a fitting time to reflect on the number of microbes that share our home, Planet Earth. Even more astounding than the 10,000,000 bacteria in a gram of soil is their immense diversity; in this same gram there are estimated to be around 100,000 different bacterial species.

Everywhere we have looked on our planet, we find microbes: from Antarctic ice to the bottom of the oceans. Amazingly, we have only begun to explore the tip of the microbial iceberg.

While isolating microorganisms from nature has yielded a brilliant display of biodiversity (Figure 1), current studies suggest that 99% of the world’s microbes remain uncultivated in the lab. It is clear that we have a lot to learn from the vast world of microorganisms. So why are bacteria important in the first place? And how do we know how many and what kinds of microbes are out there?

Figure 1. A sampling of the colorful diversity of fungal microorganisms isolated from tropical plants. (Photo credit: J. Russell, Strobel Lab, Yale University 2009)

The Importance of Knowing your Bacterial Neighbors

Understanding the world of microbes is critically important for understanding many aspects of life on Earth. Microbes are the invisible heroes of our planet, cycling nutrients and generating energy for terrestrial and ocean ecosystems. It is estimated that roughly half of global photosynthesis (the production of sugar and oxygen from sunlight and carbon dioxide) is performed by microbes in the world’s oceans [1]; this means microbes are responsible for nearly half of the oxygen in the Earth’s atmosphere! If that doesn’t impress you enough, microbes have evolved to become a critical part of the human body. We carry more bacterial cells on and in our bodies, than we do human cells! Many microbes play a critical role in protecting our skin from infection and helping our gut with digestion and nutrition.

Just as we begin to appreciate the role of bacteria in our bodies and in our biosphere, it is becoming clear how many microbes we have yet to identify. The biggest obstacle in modern microbiology is that we cannot culture and grow most bacteria in the lab. This makes many bacteria undetectable to microbiologists armed with agar and petri dishes. Some microbiologists say that all we have seen are the weeds of the bacterial world, as we tend to isolate microbes that grow rapidly on agar plates. There is a good chance that, in most of our searches, we have missed the fascinating slow-growers, the roses of the bacterial world.

So how would you go about studying microbes that you cannot culture in the lab? How could you guarantee that you aren’t missing the rarest bacteria that are only present in exceedingly low numbers?

The field of metagenomics is working to answer these kinds of questions. Metagenomics relies on isolating the genetic material from an environmental sample to determine the amount and variety of microbes present without needing to culture anything at all.

Understanding Microbial Diversity by Metagenomics

All forms of life on Earth, including microbes, are defined by their genomes – the sequences of A, T, C and G that make up their DNA. Each organism’s specific DNA sequence frames the story of its life: how it grows and develops, how it uses energy, and how it reproduces. The differences in the DNA sequences between organisms are what account for the vast diversity we see in biology.

Since the origin of life some 3.6 billion years ago, microorganisms have evolved to thrive under dramatically different environments: from the bottom of the ocean to the rinds of cheese. The differences in their genetic sequences reflect this evolution. Thus, we use DNA sequence similarity as a way of telling how similar or different two organisms are from one another. While not everyone agrees, microbiologists tend to consider organisms different species if their genomes differ by at least 2%.

The metagenomics process is a systematic way of isolating and characterizing all of the genetic material present in an environmental sample. Scientists first purify DNA from a sample (such as a scoop of soil or seawater) and determine its sequence. Researchers can then make a list of all of the different genomes that were originally present in the sample using a computer program. The genomes that were sequenced are compared to a library of the DNA sequences from all known microorganisms. In this way, the scientists can determine which bacterial species are present in the sample. As an example, if scientists sequence the DNA contained in a soil sample, and find that it contains 5 different versions of the same gene, they can be confident that they are holding 5 different species. By comparing these samples to all known microbial DNA sequences, ecosystems can be catalogued and new species can be identified.

Exploring the Vast Sea of Microbiology

With tremendous advances in molecular biology and computer science it is possible to compare many different sequences from highly complex environmental samples. This has enabled some of the most cutting-edge science in microbiology, including the recent Global Ocean Sampling Expedition (GOS) spearheaded by Craig Venter, one of the pioneers in sequencing the human genome. The goal of the GOS is to sample the world’s oceans to get a better idea of microbial diversity in our planet’s oceans. This has tremendous potential to not only discover many new species of microorganisms, but also to gain a better understanding of how these microbes impact and are impacted by the global environment. As a part of this study [3], researchers collected ocean samples from dozens of sites in the Atlantic and Pacific oceans (Figure 2).

Figure 2. Voyage routes for the Global Ocean Sampling Expedition. (Image based on original  from J. Craig Venter Institute)

The Future for Microbial Diversity

The exploration of the microbial world by modern metagenomics has helped reveal how much genetic and biochemical diversity exists in the biosphere. Our knowledge of the kinds and numbers of microbes that are responsible for so many critical biological and geological cycles will fundamentally influence our understanding of climate change and ecosystem health. In addition, our increasing access to biodiversity provides a wealth of potential applications in both biomedicine and industry. We still have much to learn from our microbial neighbors.

Jon Russell is a PhD student in the Department of Molecular and Cellular Biology at Harvard University.


[1] Delong, E., D.M. Karl  Genomic perspectives in microbial oceanography. Nature (2005).

[2] World Health Organization, (2011)

[3] Rusch, D.B., J. C. Venter et al, The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biology (2007) .

Link of Interest:

Global Ocean Sampling Expedition, J. Craig Venter Institute:

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