Viruses that infect microbes are the most abundant biological entities on Earth, yet until recently they were almost absent from the story of how microbial mats become rock. Work by White, Visscher and Burns put them into it.
Three lines of evidence from metagenomes and isolate genomes pointed to viruses as active players in microbialite communities.
Freshwater microbialite metagenomes were rich in genes associated with viral infection, including CRISPR-Cas immune systems and phage shock and phage excision genes, suggesting the communities are under viral selection.
Sequencing the viral fraction of Hamelin Pool stromatolites revealed single-stranded DNA viruses and two putative genomes related to the Genomoviridae. The cellular community was enriched in antiviral defences: CRISPR-Cas, BREX and DISARM.
The genome of Agrococcus pavilionensis, isolated from a Pavilion Lake microbialite, carries a prophage-like element. Genomes reconstructed from Shark Bay’s Blue Holes mats encode CRISPR, BREX and DISARM defences.
One caveat the authors note: the amplification step used for the Shark Bay virome can over-represent single-stranded DNA viruses.
How a soft mat becomes a stromatolite is still debated. White, Visscher and Burns proposed that viruses influence the transition, directly or indirectly, by changing the microbial metabolisms that decide whether carbonate precipitates or dissolves.
Viral infection
Viruses burst their hosts, releasing cell contents, enzymes and polymers into the mat.
Temperate viruses integrate into host genomes and can change what their hosts do and make.
Constant attack favours resistant strains and costly defences, reshaping which microbes dominate.
Changes in the mat
The balance of photosynthesis, sulfate reduction, respiration and fermentation shifts, and with it the alkalinity engine.
The amount and chemistry of extracellular polymers change, altering how much calcium is bound and where crystals can nucleate.
Virus particles and cell debris add surfaces on which minerals may form.
Outcome
If carbonate forms faster than it dissolves, the mat lithifies and a new lamina is added. If not, the mat stays soft.
Our simplified summary of the kinds of pathways the hypothesis involves. Arrows show proposed influences, not measured effects.
If viral activity leaves a recognisable mark in carbonate, geologists would gain a new way to read stromatolites, and astrobiologists a new kind of biosignature. The authors argue that tying host–virus interactions to changes in biogeochemistry will help interpret mineral biosignatures through geological time, on Earth and beyond.