Day 12 of the Microbial Advent Calendar is a story looking into Alaska’s past by looking into its permafrost. The permafrost is soil, rock or sediment that is frozen for more than two consecutive years. It generally occurs in regions where the climate average is zero degrees Celsius for most of the year, hence most permafrost is located in high latitudes (in and around the Arctic and Antarctic regions), but it may also exist at high altitudes in much lower latitudes, at the top of glaciers for example.
A study published in 2017 (here) by Mackelprang et al., looked at a fascinating concept of the microbial communities and their metabolism according to the age of the permafrost. For this, they had the opportunities to sample small cores at the United States Army Cold Regions and Research and Engineering Laboratory permafrost tunnel in Fox, Alaska (their website here). Apparently, the further you go into the tunnel the more ancient the permafrost is. This is a unique opportunity to look at what is living inside.
The science team sampled three different cores, at permafrost roughly estimated to be 19, 22 and 33 k. years old. This ranges from the earliest sign of domestication of the dog to the first permanent settlements, to the early sign of cooking vessels. Basically going back early-mid prehistorical times.
Beyond the human side of the past, the present study looks at the impact of bacterial communities trapped in permafrost layers from those times. It would not be the exact same bacteria from that time of course, but more bacterial communities that have adapted to a harsh changing environments, where nutrients are slowly disappearing and a plethora of stress factors appearing, such as gamma ray from minerals, a high concentration of reactive oxygen species, which damage DNA, RNA, proteins and lipids as well as small pockets of water which exists in permafrost because of too high solute concentrations. So how are bacteria adapting to these environments?
One cool fact about this study is that by looking at metagenomes they could also pick up DNA markers of fauna, indicating what grew in the region in the past and if this would have an impact on the microbial communities way in the future. I do like the term of Paleovegetation Reconstruction. Those seemed to indicate that the vegetation was quite similar between the 19 and 33k. yo core with some distinct difference with the 22k. yo core which correlates with some climatic data supporting a change. A paleoecological study of interior Alaska showed that the periods around 19 and 33 k. yo were climatically similar to each other, but the period between 20 and 33 k. yo was colder and drier, possibly with more herb tundra coverage than today.
However, besides how cool it is to be able to get basic prehistorical environmental data from metagenomic sequencing, unfortunately, the bacterial populations present today did not seem to be affected by the past vegetation. The study showed that the bacterial populations were mainly shaped by long-term survival strategies in extreme cryogenic environments. What does it mean? Well the further you go, older and colder, the more the genetic material of the different bacteria needs to be adapted to the environment. One interesting fact is that one main metabolic difference between the 22 and 33k yo core and the 19 k. yo one is that the later one showed a higher amount of gene coding for sugar metabolism, and the older cores were enriched in amino-acid and peptide import, degradation and salvage genes, pointing to recycling and use of detrital biomass as a C and N source. In addition, the older permafrost communities had more stress-related pathways. These stress-related molecules maintain RNA secondary structure, and are implicated in responses to cold, low pH, oxidative stress, membrane integrity and biofilm formation.
The lesson to take home here would be: the deeper in the cold soil of the past arctic tundra, the more you need to make the most of what little is availble.