The Secret World of Microbes

emp-green-smallSince the time of Linnaeus, scientists have loved classifying the world around them. But while centuries of biologists have worked to collect and categorize the plants and animals of Earth, all that work likely only covers about a minute fraction of our planet’s life. As much as 99 percent of the biodiversity on Earth is smaller than 2 microns – bacteria, viruses, and tiny eukaryotes – and most of these remain to be discovered by humans. There are more microbial cells on earth (1 nonillion, or 1×10^30) than there are stars in the sky, and all of this new life exists in soil, in seawater, and inside animals, plants, and even us.

“You are mostly microbes,” Jack Gilbert told the Institute for Genomics and Systems Biology in a lecture last month. “The world is mostly microbes, and yet we have less of an understanding of how microbes run the universe than we do of the universe itself.”

Gilbert, an assistant professor of evolution and ecology at the University of Chicago, is part of an international project to remedy that shortage of knowledge about the microbial world. The Earth Microbiome Project, a group bringing together scientists from several different institutions, is dedicated to filling in these gaps in the tree of life and, more importantly, figuring out how they may be secretly pulling the strings of Earth’s ecosystems. In his talk, Gilbert rapidly narrated the group’s aims and his own research projects until he ran out of breath, leading an hour-long tour around globe in search of nature’s smallest and most abundant participants.

Classically, microbiology has taken place in cell culture dishes and incubators, as scientists grew bacteria in the laboratory in order to study its identity and function. But the field has benefited greatly in recent years from genetic advances opening up new paths of discovery. As the price of accurately sequencing DNA and its products has exponentially dropped – driven largely by the demand for human genomics – ecologists interested in microbes have borrowed the technology for their own uses. Now, instead of growing bacterial populations in the laboratory, microbiologists can take a genetic sample of whatever environment they wish and use the genes in that sample to reconstruct its microbial denizens. This process is called “metagenomics,” and it is expanding our knowledge of the bacterial world in leaps and bounds, Gilbert said.

“We can take a sample, sequence it, look at the microbial taxa in there, and identify things we couldn’t culture,” Gilbert said. “There are four trillion base pairs of genetic information in a millileter of seawater, in one teaspoon. In a gram of soil, there are about 4 quadrillion base pairs.”

With so much information out there waiting to be discovered, one of the most important questions is where to start. The Earth Microbiome Project is overseeing dozens of projects, each with their own hypotheses and environmental targets. Gilbert outlined just a few: analyzing samples from near the site of the Gulf of Mexico oil spill; comparing soil samples – some as old as 135 years old – from China, France, Australia, and South America; characterizing the microbial communities from the vaginal canals of fertile and infertile pandas in the San Diego Zoo (seriously). Importantly, the procedures used to analyze such widely different samples are being standardized by the project to ensure that comparisons between different research groups and samples are possible.

“The goal of this project is to systematically approach the problem of characterizing microbial life on Earth,” Gilbert said. “We’re reaching a zenith point in our ability to do things individually, and if we want to start generating synthesis of our understandings, we need to start working as a team, as a group, like the physicists do. We want to do the same thing: Come together as a group and say ‘we have a really good idea, a life-changing idea that will change the way we live on this planet, we just need to do it in a systematic and well organized fashion.’”

As a discrete example, Gilbert offered one of his own research projects, conducted before he relocated to Argonne National Laboratory last summer. As senior scientist at Plymouth Marine Laboratory in England, Gilbert and his team studied a section of the English Channel that has been sampled by scientists every week since 1864 – interrupted only by the two World Wars. Since 2000, the team has taken samples suitable for metagenomic analysis, and has methodically characterized what microbes live in this patch of water and how that population changes.

The dynamics are fascinating. Roughly 23,000 species of bacteria were identified by Gilbert’s group from the samples, but only 12 of them were detected in every single time sample over a six-year period. The rest come and go at different times of year, many of them with cyclical regularity. The researchers discovered that the amount of diversity in the Channel varied with seasonal day length – the richest diversity was always found on December 21st, the lowest on June 21st.

“Because this information is so robust, we can predict, extrapolate, and use this like a weatherman predicts a weather map, to understand how a microbial population might change in an ecosystem,” Gilbert said.

But taking a census of what species are present from month to month only addresses the first portion of the project’s mission. Gilbert and his team were interested in what those bacteria were doing, and so constructed a “metabolome,” a model of the activity of the species present at any one time. As the population changes, the microbial community’s production of oxygen, nitrogen, phosphorous, or other elements will change as well. Because slightly larger forms of life, such as plankton, feed on those elements, and fish in turn feed on those plankton, predictions about microbial populations and their activities can inform fishermen looking for the right time to head out to sea.

“We can give you a weather map of when the abundance of that population will get high enough to start fishing, which has a fundamental impact on the economy,” Gilbert said. “If we can understand how the microbes affect the fish, we can have a happy planet with happy people.”


Gilbert JA, Meyer F, Schriml L, Joint IR, Mühling M, & Field D (2010). Metagenomes and metatranscriptomes from the L4 long-term coastal monitoring station in the Western English Channel. Standards in genomic sciences, 3 (2), 183-93 PMID: 21304748

About Rob Mitchum (511 Articles)
Rob Mitchum is communications manager at the Computation Institute, a joint initiative between The University of Chicago and Argonne National Laboratory.

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