It’s not the size that counts: teeny tiny SAR11 bacteria play a big role in our oceans

Microbes account for a huge chunk of the diversity on this planet, are essential in all sorts of biogeochemical processes, and we are still figuring out how everything is related. Teeny tiny bacterial cells are abundant both on land as well in the ocean, which (let’s be real) are less well explored than the surface of Mars. The oceans cover more than 70% of the planet and are not at all a homogeneous habitat. In fact, they encompass regions known as oxygen minimum zones (OMZs), where (as you might guess) oxygen is below the level of detection.

slide1In areas in the ocean where water circulation isn’t very strong and productivity is high, the oxygen is nearly completely used up from about 100 to 1000 meters depth. These oxygen deplete areas are important since they are indicators signaling changes in ocean temperature and pH and they occur naturally. Global climate, however, change can affect the expansion of these OMZs.

It wasn’t until the early 1990’s, that tools to investigate diversity on a microbial level in environmental samples were available. Finally, sequencing DNA from environmental samples, basically using ‘non-cultivation’ based techniques to assess microbial diversity, became possible. Analysis of 16S rRNA genes from an unassuming seawater sample from the Sargasso Sea revealed that one particular group of bacteria (named SAR11) was incredibly abundant, accounting for a whopping 25% of all planktonic cells. Turns out that SAR11 are basically found in all open water marine ecosystems. They are cool model organisms as they have incredibly streamlined genomes (among, if not the smallest of any free-living organism, at only about 1.3 million base pairs!), thought to allow for efficient cell replication. While SAR11 has been found to be an abundant community member in OMZs, their ecological role was unclear. With such no-nonsense genomes, any functional genes present probably play an important part in fitting them into their environmental niche.

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In a recent, eloquent study by Tsementzi and colleagues, they identified the probable ecological role of SAR11 by sequencing genomes from two depths (125 m and 300 m) in an OMZ in the Eastern Tropical North Pacific off of Mexico. Generally, in OMZs, the reduction of nitrate to nitrite is the preferred method for microbes to degrade organic matter since oxygen isn’t available. In order to do this, certain enzymes encoded by specific (nar) genes are required.

Tsementzi et al., (2016) Figure 2.

The authors put together trees from the of genomes of individual cells, revealing previously undiscovered SAR11 diversity in these unique habitats. This analysis also found that SAR11 accounted for somewhere between 10% and 30% of the entire bacterial community at the site. These little SAR11 bacteria (I mean really little, as in about 1/500th the volume of an E. coli cell), appear to have unique metabolic adaptations that allow them to thrive in environments with little to no oxygen. The study found that some SAR11 strains have adapted to survive, and even thrive in the OMZ.

Tsementzi et al., (2016). Figure 1.Tsementzi et al., took things a step further and put SAR11 nar operons into an E. coli mutant that initially lacked the genes to survive in anoxic conditions, but did just fine once it was transformed. The authors then searched for these functional genes in metagenome data sets to determine their overall abundance and found PLENTY of diverse nar genes, and suggested that most of them come from SAR11.

Never before has it been shown that this incredibly abundant bacterial lineage adapted to thrive in an anoxic niche.    This study revealed that SAR11 appears to contribute to the loss of nitrogen from OMZs and sets the stage for a new model system in understanding nitrogen and carbon cycling in these unique and currently expanding environmental niches.

Part of what makes microbial oceanography so nifty is the vast diversity that we have yet to uncover. In the case of SAR11, it’s clearly not the size (of the genome) that counts, it’s how they use it.

References

Tsementzi, D., Wu, J., Deutsch, S., Nath, S., Rodriguez-R, L.M., Burns, A.S., Ranjan, P., Sarode, N., Malmstrom, R.R., Padilla, C.C. and Stone, B.K., 2016. SAR11 bacteria linked to ocean anoxia and nitrogen loss. Nature,536(7615), pp.179-183.

Wright, J.J., Konwar, K.M. and Hallam, S.J., 2012. Microbial ecology of expanding oxygen minimum zones. Nature Reviews Microbiology, 10(6), pp.381-394.

 

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About Kelle Freel

I'm currently a postdoc working at the Hawai'i Institute of Marine Biology with Dr. Mike Rappé. I'm interested in the biogeography and ecology of microbes, especially of the marine variety. After studying a unique genus of marine bacteria at Scripps Oceanography in grad school, I moved to France, where I worked with a group studying yeast population genomics. In my free time, I like to do outdoorsy stuff, travel, and cook.
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