The concealed big players

The story behind the paper: "Uncovering a hidden diversity: optimized protocols for the extraction of dsDNA bacteriophages from soil."

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Virtually all animal life on Earth is dependent on bacteria – including us humans, where bacteria play an essential role in health and outnumber our body cells by a factor of 10. Moving away from the human microbiome into other ecosystems, we typically find 40 million bacterial cells in a gram of soil – which is the same number as individuals currently living in California - and another 1 million bacteria in a drop of seawater. And while the world has focused its attention on bacteria as the director of Life, we have neglected those organisms that control the controller of Life – Bacteriophages. Bacteriophages (phages) are viruses that naturally prey on bacteria and therefore hold critical roles in many ecosystem cycles. For instance, marine phages remove 20-40% of all bacterial cells in seawater daily, thereby influencing global biochemical carbon cycling and ocean productivity.  Similarly, soil is not just dirt and bacteria. An estimated 100 million phages per gram of soil outnumber bacteria 10-100 fold. And deduced from their relevance in marine ecosystems, one can only speculate on the impact of phages on the worlds’ food supplier – agricultural soil.

We have started to investigate the soil “virome” – a collective term for all phage entities in a given sample, due to their yet largely undiscovered significance. However, who would have thought that capturing this massive number of phages requires a year of work and optimization? Naturally, bacteriophages like to interact and easily attach to particles in any solid matrix. We therefore were not surprised to observe a reduction of spiked phages after the initial elution, but were startled by the complete absence of any infective particle with standard buffers on our detection hosts. It took us from there another two months to find an adequate formula that allowed a sufficient recovery of spiked phages from soil samples, and which simultaneously enabled filtration and concentration methods.

Once optimal extraction routes for soil bacteriophages were identified and four soil viromes sequenced, we were excited to obtain a first glimpse using virome analysis. That it would take us another two months of manual phage-bacteria categorization of > 37,000 contigs prior any evaluation, was not expected. This immense repetitive work however, turned out to be critical, enabling reliable conclusions regarding soil viruses and non-viral contaminations. When focusing on the > 13’000 manually identified viral contigs, and their meager annotation with hardly any structural proteins, it became clear that a plethora of knowledge and biological significance awaits to be discovered.

Pauline Carlotta Göller

PhD Student, ETH Zürich