Microbial DNA in deep sediments and the Greatship Manisha's 'genome'

The promise of genomics
Each and every living organism, from humans to trees to animals to microbes, has its structure and function described in its genome. This genome is a collection of molecules called chromosomes, with each chromosome comprising a single continuous pair of DNA strands. These strands are strings of four different kinds of small molecules. The order of the molecules in the strand determine whether a particular organism will become a bacterium adapted to living 50 metres below the seafloor, a palm tree adapted to a tropical beach, or a human being. Passing along as much of its genome as possible to the next generation is the basic goal of every life form.

A genome is often referred to as an organism's 'blueprint' in an analogy to technical drawings, but in reality the genome is much more than a blueprint: take the example of the ship I'm on, the Greatship Manisha. The ship's 'genome' would not only include the blueprints showing the shape of the hull and which cabin gets a porthole (a minor source of friction between lucky and unlucky members of the science party...), but also every technical manual for operating the various propulsion, navigation, water treatment systems etc., the galley's menu and cookbook, as well as the knowledge gained through the crew's experience and training. An organism's genome includes all of the information necessary for building and operating the organism.

Caption: A genome is often called a 'blueprint' for life, but in reality it's a lot more than that. Copyright Ian Marshall/ECORD/IODP.

The limits of genomics
Reading genomes has become a significant part of biology since the first full genomes were sequenced in the 1990s: while the human genome project was what made the public aware of the word 'genome', thousands of microbial genomes have been read (or 'sequenced') from laboratory pure cultures. These have all served to better our understanding of microbes that make us sick or healthy, microbes used in industry, and microbes in the environment. Still, while reading genomes has rapidly become cheaper, faster, and easier, understanding genomes has been struggling to keep up.

Right now scientists cannot understand a genome as easily as they could understand a ship's blueprints and technical manuals. We could understand a lot from a genome - maybe the location of the engine room and what kind of fuel the ship uses, but we could only make educated guesses about the ship's top speed or whether the galley serves pizza on Sundays. We still have a lot to learn when it comes to understanding genomes. This makes genomics an especially exciting field - the genomes that we sequence today provide data for future discoveries.

Caption: Scientists still don't understand a microbe from its genome the way an engineer understands an engine room from its blueprints and technical manuals. Copyright Aarno Kotilainen/ECORD/IODP.

DNA in the Baltic deep subsurface
The DNA that we are collecting from the deep subsurface during IODP Expedition 347 is mostly genomic DNA from the enormous variety of different microorganisms that make the sediment their home. I say 'mostly' because there will be an occasional chunk of dead tree genome or woolly mammoth genome (perhaps?) that Andrea will investigate.

The DNA will be analyzed by groups of scientists in China, Denmark, Germany, Japan, and the United States. Each group has a different set of questions about deep subsurface microbes that the DNA will help to answer. Some groups will be using 'targeted' methods, to answer questions of the variety 'how many of microbe X are present at different locations and depths?', others will be slightly less targeted, of the sort 'what are the different kinds of microbial group Y present in these samples?' Others (including me) will simply be trying to indiscriminately sequence as much DNA from these samples as we can and read as much of all the microbial genomes down there as possible. This is called 'metagenomics', or the study of genomes sequenced from combined mixtures of many genomes. While I have some of my own questions that I would like to address with this broad-ranging data set, the true value of this work may not be seen until many years into the future. A clever and well-informed future scientist might be able understand the metagenomes I generate in a way undreamt of today.

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