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Biological Sciences Division

August 2016

For BioTechniques, Janet Jansson Weighs in on Science's Ways of Unlocking Microbial Communities

Janet Jansson

Vastly ubiquitous microbial communities live on, in, and around everything on Earth, from within the human gut to across the biggest ocean. But they are as little known as they are vital to life, health, and the environment. In soil alone, 99 percent of microbial species have yet to be isolated.

PNNL microbiologist Janet K. Jansson was just quoted at length regarding the stubborn mysteries of microbial communities, which can be good or bad for the ecosystems they populate. "There are many unknown unknowns," she said in a feature story released in the August issue of BioTechniques. Among nine scientists quoted or cited, she was the most frequently heard.

Up front, the story outlined the challenges of understanding the structure and function of microbial communities. Then it outlined in detail the techniques researchers are using to make headway. Carrying the narrative thread was one frontier of research in particular: biofilms, the largely bacterial multicellular communities that colonize surfaces everywhere.

Every bacterium plays a role in these layered ecosystems, within a diversity of chemical and physical environments. Up close, the feature said, biofilm structures are city-like, "with water channels and skyscrapers, mushroom shapes, or thick layers peppered with pores."

Cell by cell, even single-species biofilms are complex, so scientists have gone beyond simple chemical analysis to a variety of tools that help investigate the spatial and temporal relationships of these cooperating cells.

Researchers use imaging mass spectrometry to get a two-dimensional picture of biofilm surfaces; vibrational spectroscopy to get at the chemistry of biofilm polymers; fluorescence microscopy to show biofilms down to the resolution of a single cell; and something called spinning disk confocal microscopy to examine biofilm cells up to 35 microns deep, a 10-fold improvement over previous techniques.

But scientists, Jansson among them, want to go beyond visualizations to explore techniques that reveal how genes and proteins work within microbial communities. In part, that means using next-generation sequencing (NGS), "a powerful tool for examining highly heterogeneous natural microbial communities," the article states.

"Now sequencing isn't the bottle neck," Jansson said of NGS and other technologies that have improved so much in her 30 years of research. "It's interpretation of the data."

But assembling all that data from NGS and elsewhere in meaningful ways is the challenge now, she said. Microbial diversity in soil is especially daunting, and getting good gene assemblies is hard too. But once science has a technique to "bin" entire microbial genomes, said Jansson, it will be a "gamechanger."

Her recent paper with colleagues at PNNL, spelled out in the feature, used a long-lead technique called Moleculo to facilitate a very productive round of genetic binning and gene re-assembly in a sampling of soils from the Kansas prairie.

Jansson and her colleagues also got attention for going beyond metagenomics to integrate that approach with other "omics" techniques. Those include metaproteomics and metabolomics, which another scientist speculated would be where in the near future the microbiome field "sees the greatest technical advances."

By the article's end, Jansson was wishing out loud she could unravel all the metabolic pathways in just one soil-bound microbial community. After all, she added, a better understanding of those pathways could improve predictive models of how climate change will affect the planet's ecosystems.

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