Are you my mother? Exploring the possible microbial ecology of LUCA

Figure modified from Darwin (1837), Haeckel (1866), Woese (1990), Hug et al., (2016), and Weiss et al., (2016)

One persistent question has always been: where did it all begin? What was the origin of the complex life that we have today? What happened billions of years ago that resulted in beautiful giant manta rays, magnificent Sequoias, and even humans that are incredibly adept at posting cat videos on YouTube?

Ever since the phylogenetic tree was sketched by Darwin in 1837, there has been a search for how life on this planet is connected, and relatively recent advances in sequencing (not to mention how affordable it all is now-a-days) has led to revolutionary studies detailing relationships among extant organisms. It seems that we might be one step closer to painting a picture of the habitat of the last universal common ancestor, or LUCA. Originally, it was thought that LUCA represented the ancestor of bacteria, archaea, AND eukaryotes, although more recently it looks like eukaryotes actually arose from the bacteria and archaea.

In an article out this week by Madeline C. Weiss and co-authors, (which is unfortunately not open access) they reveal an analysis of over 6.1 million protein coding genes from currently available prokaryotic genomes to gather clues in order figure out what the habitat / lifestyle / microbial ecology of LUCA might have been.

Figure 1. Weiss et al., (2016)

Figure 2. Weiss et al., (2016)

The study identified 355 protein families from 286,514 protein clusters that they determined were likely in LUCA’s genome. While it’s tricky to account for confounding factors such as horizontal gene transfer, which might have swapped genetic info around over time, the genes included in this theorized version of LUCA indicate that this organism was anaerobic, fixed CO2 and N2, was dependent on H2, and thermophilic, not to mention required cofactors that depended on a variety of molecules including transition metals, coenzyme A, ferredoxin, and selenium.
In order to figure out the common denominator among all these protein families, phylogenies were built, revealing that clostridia and methanogens represent the most basal lineages. From these data, it looks like LUCA lived it up in a geochemically active environment filled with H2, CO2 and Fe. Carefully analyzing the function of the genes encoded by LUCA revealed that this ancestor had a particular set of abilities, suggesting it probably lived in a hydrothermal vent, quite an extreme environment.
Hydrothermal vents are kind of amazing. Just last year, a study by Spang and colleagues reported a microbe that has a bunch of features only before identified in eukaryotes, which scientists suggested could represent the link between microbes and eukaryotes. These Lokiarchaeum were originally found in sediment near a hydrothermal vent after a metagenomic analysis of the sample. Although this proposed genus has not yet been cultured, it does suggest that hydrothermal vents are literally a hotbed for microbial evolution events.

Hydrothermal vents are amazing habitats where geothermally heated water is released and can be colonized by a suite of interesting organisms, including chemosynthetic bacteria and archaea, and are also famous for harboring cool things like giant tube worms that rely on symbiotic bacteria. They’re often associated Somehow, it seems like little wonder that hydrothermal vents might have been LUCA’s old stomping grounds.

Figure 3. Weiss et al., (2016)

However, this story is not without a bit of controversy, which of course makes it more interesting anyway. This study is clearly a big step towards elucidating the kind of organism LUCA might have been, and also enhances the understanding of the origin of life. Part of the controversy related to the paper’s findings stems from Dr. Martin’s suggestion that this LUCA is a close representation of the beginning of life, estimated to have occurred about 3.8 to 4 billion years ago. In fact, Dr. Martin has stated that LUCA appears to lack so many genes that it is not completely self-sufficient and instead only “half alive”. As we all know, there’s a big difference between mostly dead (aka slightly alive) and all dead. While the idea of a Frankenmicrobe lurking in hydrothermal vents is interesting, other researchers are pretty sure that there is a big gap between LUCA and the origin of life.
A commonly held belief is that life actually began in a “warm little pond”, a theory put forth by Darwin. This hypothesis is championed by Dr. Sutherland from the University of Cambridge in England, who is cool with the idea that LUCA might have been found at hydrothermal vents, but also thinks it is unlikely that this recent study describes an organism close to the origin of life. Specifically, proponents of the pond theory, state that one of the essential drivers creating life, include ultraviolet light from the sun, not something readily available at hydrothermal vents, which can be found between about 2,000 and 7,000 meters deep.
Regardless of the controversy, this latest study depicting the possible habitat and genomic profile of LUCA is awesome, and I don’t know about you, but I’m definitely looking forward to understanding what / where / when life on this crazy planet got started.
Weiss, Madeline C. et al. “The physiology and habitat of the last universal common ancestor.” Nature Microbiology 16116 (2016). Published online 25 July 2016.
Spang, Anja, et al. “Complex archaea that bridge the gap between prokaryotes and eukaryotes.” Nature 521.7551 (2015): 173-179.

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