Sequencing of Diatom Genome Highlights Genetic Diversity; “Transgenic by Nature”

Jose Michael

Phaetodactylum_2
The diatom Phaeodactylum tricornutum.

Diatoms have profound influence on the climate, producing 20% of atmospheric oxygen by capturing atmospheric carbon and in so doing, countering the greenhouse effect. An international team of researchers led by the US Department of Energy Joint Genome Institute (DOE JGI) and the Ecole Normale Supérieure of Paris have sequenced and analyzed the genome of the diatom Phaeodactylum tricornutum.

The researchers compared Phaeodactylum with the diatom Thalassiosira pseudonana, previously sequenced by DOE JGI, revealing a wealth of information about diatom biology, particularly the rapid diversification among the hundreds of thousands of diatom species that exist today.

The researchers found that the genetic structures of the two diatoms were dramatically different: 40% of their genes were not shared. Interestingly, the researchers found that hundreds of genes from bacteria were present in the genomes of both diatom species. The findings are published in 15 October edition of the journal Nature.

The bacterial genes found in diatoms could contribute to their success, enhancing their ability to perceive environmental signals or to metabolize organic carbon and nitrogen. Some of these bacterial genes might be responsible for certain cell-wall components in diatoms, and others for “unorthodox mechanisms of DNA replication, repair and recombination”. According to the study, “these findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans”.

These organisms represent a veritable melting pot of traits—a hybrid of genetic mechanisms contributed by ancestral lineages of plants, animals, and bacteria, and optimized over the relatively short evolutionary timeframe of 180 million years since they first appeared. Our findings show that gene transfer between diatoms and other organisms has been extremely common, making diatoms ‘transgenic by nature.’

—first author Chris Bowler of the Ecole Normale Supérieure

The study showed that gene transfer between diatoms and other organisms has been extremely common in marine environments. For example, the diatom inherited its photosynthetic capacity from plants, and its ability to process urea from animals (although unlike animals, diatoms use urea to store, not eliminate, nitrogen). The researchers propose that this gene transfer has been a major driving force during diatom evolution.

We believe this is the first time bacterial horizontal gene transfer has been observed in eukaryotes at such scale. This study gets us closer to explaining the dramatic diversity across the genera of diatoms, morphologically, behaviorally, but we still haven’t yet explained all the differences conferred by the genes contributed by the other taxa.

—senior author Igor Grigoriev of DOE JGI

The team documented more than 300 genes sourced from bacteria and found in both types of diatoms, pointing to their ancient origin and suggesting novel mechanisms of managing nutrients—for example utilization of organic carbon and nitrogen—and detecting cues from their environment.

Phaeodactylum was targeted for sequencing due to its value as a diatom model, given the ease with which it can be grown in the lab and the availability of tools to genetically transform it, and the comparisons with the previously sequenced diatom genome of Thalassiosira pseudonana.

Diatoms reside in fresh or salt water and can be divided into two camps, centrics and pennates. Pennates like Phaeodactylum look more like a cross between a boomerang and a narrow three-cornered hat—hence the species name, tricornutum. Not only is their shape and habitat diverse, so too is their behavior; for instance, the centrics get around by floating, the pennates by gliding through the water or on surfaces.

The lifestyle of diatoms can be characterized as “bloom or bust.” When light and nutrient conditions in the upper reaches of the ocean are favorable, particularly at the onset of spring, diatoms gain an edge and tend to dominate their phytoplankton brethren. When food is scarce, they die and sink, carrying their complement of carbon dioxide to the deeper recesses.

Bowler and his colleagues are also trying to understand the role that iron plays in the Phaeodactylum’s development. Iron is even more precious than nitrogen in the ocean and its absence in the southern hemisphere is likely a major cause of oceanic deserts of photosynthesis there. Bowler’s team has demonstrated that when iron deficiency occurs processes such as photosynthesis and nitrogen assimilation are suppressed.

Other studies, which hail diatoms as champions in capturing carbon dioxide, suggest a bold strategy of using iron as a fertilizer to provoke massive diatom blooms.

Once they have feasted, the weight of their silicon shells, which resemble glass, causes the diatoms to sink to the bottom of the ocean when they die, and the carbon that they assimilated is trapped there for millennia. By sequestering carbon in this way we could reverse the damage from the burning of fossil fuels

—Chris Bowler

The US Department of Energy Joint Genome Institute, supported by the DOE Office of Science, unites the expertise of five national laboratories—Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest, along with the HudsonAlpha Institute for Biotechnology—to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup.

The collaboration included partners from 10 countries and was funded in part by the EU-funded DIATOMICS and Marine Genomics projects.

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