Molecular Fossils of Microbial Interactions

by Einat Segev
 

Microbes have inhabited our planet for many millions of years. While thriving and dying in almost every niche on Earth, microbes leave behind relics, and some of these relics remain preserved in the geological record. Many cell components are rapidly degraded and do not persist but remains that do are like archives of ancient microbial life. As long-time readers of STC will know, hopanoids are microbial lipids that are extremely well preserved in the geological record. Their longevity and consequent abundant accumulation in rocks and petroleum are indeed fascinating, as four prior STC posts along the years attest (2007, 2010, 2014, 2016). I remain in awe of these molecules and wanted to share an exciting new development in the field.
 

Figure 1. Hopanoid lipids increase the stability of the bac­terial membrane. Source. Frontispiece: Geologic re­cord of an Oceanic Anoxic Event. Source

In present-day Earth, diverse bacteria make hopanoids for a variety of biological functions in­clud­ing tuning the rigidity and permeability of the cell membrane. After these bacteria die and are buried under layers of sediments, hopanoids can be degraded to hopanes – these are ex­tremely resilient lipids that can survive millions of years. Petroleum geologists found hopanes in ancient sedimentary rocks from the Precambrian, dating back to 2.7 billion years ago. As such, hopanoids serve as molecular fossils because they indicate the presence of microbes wherever they are found. Geological samples from the Mesozoic (66–252 million years ago) contain special hopanoids that have a methyl group at the 2-C position, the 2-methylhopan­oids. These special hopanoids were found in geological layers that formed during episodes of low oxygen in the ocean, known as oceanic anoxic events (OAE). The source of these 2-methylhopanoids had remained uncertain. For long, in­vestigators assumed that 2-methylhopanoids were produced by cyanobacteria, specifically those that can fix nitrogen. But many uncertainties surrounded this knowledge; there was no conclusive evidence for production of these hopanoids by cyanobacteria and it was clear that some­thing was missing in our understanding of the source of 2-methylhopanoids and their prevalence in the geological record.
 

Recently, a group of researchers decided to study an alternative source of 2-methylhopanoids. Nitrobacter bacteria are extremely abundant in terrestrial and marine environments and have the genetic potential to produce 2-methylhopan­oids. The researchers found that in the lab, under conditions that mimic present-day oceans as well as those of past times, Nitrobacter bacteria produced only small amounts of 2-methylhopan­oids. For production to increase, bacteria were supplemented with vitamin B₁₂, also known as cobalamin, a co-factor for many enzymes. Even though it is essential for several enzymes, not all organisms can produce cobalamin and rely on other microbes to supply it. The bacteria under study could not produce their own cobalamin, they needed a partner to provide it. Indeed, when cultures of Nitrobacter were incubated with B₁₂, abundant production of 2-methylhopanoids was detected. Who supplies B₁₂ to Nitrobacter in the environment? Cobalamin must be supplied by a microbe that shares the same niche. The researchers suggested an intriguing possibility; cobalamin could be provided as part of a mutualistic interaction with a specific archaeon that inhabits the same ecological niche and shares routes of metabolic nitrogen exchange with Nitrobacter.
 

By applying conditions that echo the ecological context, the researchers observed high microbial production of 2-methylhopanoids. In natural settings, similar production of 2-methylhopanoids would require cooperation between Nitrobacter and cobalamin-producing archaea. Based on this study, we now understand that 2-methylhopanoids found in geological samples hold valuable information about past ecology and may pro­vide insight into ancient microbial interactions.

 

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Einat Segev is an Assistant Professor at the Weizmann Institute of Science in Israel. She and her group integrate knowledge and approaches from microbiology and Earth Sciences to un­derstand how marine microbes interact and impact their environment.