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Team Characterizes Genomic Features Behind Marine Microbe Nutrient Use

NEW YORK (GenomeWeb News) – Scientists have come up with a way to determine whether marine microbes are specialized to grow in nutrient-rich or -poor environments based on their genomic content, according to a feature article scheduled to appear online this week in the Proceedings of the National Academy of Science.

An international research team sequenced and compared the genomes of two marine microbes, Photobacterium angustum S14 and Sphingopyxis alaskensis RB2256. Based on this comparison, they came up with a model for determining a microbe's trophic lifestyle based on its genetic profile. When they applied their approach to nearly 125 more marine microbes, the researchers found evidence suggesting more marine microbes are suited to nutrient-poor than nutrient-rich conditions.

"What we've learned here is that a few genes can tell us much about the nature of the environment that species come from and what influences them to evolve in a specific way," senior author Rick Cavicchioli, a molecular biologist at the University of New South Wales in Sydney, Australia, said in a statement.

Almost three-quarters of the Earth's surface is covered by ocean. And much of the productivity in these marine environments stems from microorganisms such as bacteria and Archea. Some are specialized to survive in low nutrient, "oligotrophic," environments, while others thrive in nutrient-rich, "copiotrophic," sites.

"[T]he study of trophic strategy has been impaired by a lack of understanding of the molecular basis of adaptation," the authors wrote. "Here, we show that trophic strategy is strongly reflected in genomic content and genomic signatures can be used as a proxy for determining the ecological characteristics of uncultured microorganisms, thereby allowing the assessment of trophic life strategies from bacterial genome sequences."

To get to the bottom of the genomic differences related to trophism, the researchers compared the genomes of a P. angustum S14 strain collected from surface and coastal water near New South Wales and a S. alaskensis RB2256 strain collected in surface water near Alaska. P. angustum typically grows in water that is rich in nutrients, while S. alaskensis usually grows in nutrient-poor, oligotrophic environments.

Collaborators at the J. Craig Venter Institute sequenced the P. angustum S14 genome, while team members from the US Department of Energy's Joint Genome Institute sequenced the S. alaskensis RB2256 genome.

The team then compared the two newly sequenced genomes with one another and with sequence information for 32 related microbes or bacteria with well-characterized trophic lifestyles to find 43 genomic markers related to trophism.

For instance, the researchers found that transporter genes — particularly those involved in transporting and regulating sugars — were more common in bugs adapted to nutrient-rich environments. On the other hand, the bacteria specialized for nutrient-poor environments typically had fewer transporters that rely on large amounts of cellular energy.

By creating self-organizing maps that integrated the newly identified genomic markers, the researchers found that they could effectively distinguish microbial lifestyle based on genetics. When they applied their knowledge to another 92 ocean bacteria, for example, the researchers found that more marine bacteria are adapted to low-nutrient environments than to high-nutrient environments.

In a statement issued this week, co-author Nikos Kyrpides, head of JGI's Genome Biology Program, said the study "lends credence to the idea that sequencing cultivated organisms is biased toward sequencing those that thrive in nutrient-rich conditions, even though those that get by in nutrient-poor conditions are more abundant in the environment."

Kyrpides argues that in order to gain a comprehensive view of microbial genomics, researchers need to continue exploring approaches for sequencing microbes that are difficult or impossible to culture in the lab.

"To sequence microbial genomes that are representative of the environments in which they were collected and for a more systematic and comprehensive sampling of the Tree of Life, researchers need to increasingly develop and rely on other techniques such as single-cell sequencing to isolate DNA samples from harder-to-cultivate microbes residing in environments where nutrients are scarce," he said.

Those involved also hope that their findings will prove useful for metagenomic studies of marine microbes aimed at understanding the consequences of climate change on ocean communities.

"By analyzing and comparing the strategies of the dominant organisms we should have an idea of the carbon flux going through the environment which will allow us to monitor the health of the marine ecosystem, including the impact of global warming," Cavicchioli said in a statement.

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