This photograph resembles some of the images captured by the rover Perseverance and sent back to Earth from Mars. Instead, it was taken by a human at one the driest and most inhospitable places on Earth, the hyperarid Atacama Desert in northern Chile. For decades the Atacama has attracted a multitude of explorers for, among other reasons, the fact that some of its soils are thought to be like those of Mars. Not least among those explorers are today's microbe hunters, seeking to characterize microbial life in Earth's most extreme environments. In a post last year, Christoph described how some cyanobacteria make a living in the extremely dry Atacama: they can extract water of crystallization that is normally trapped in rocks. Culture-independent surveys (metagenomics) reveal complex microbial communities, even in the driest Atacama sites such as Yungay (shown in the photograph). Those studies show that as dryness increases microbial diversity decreases, as might be expected given that water is essential for life. When people search the Atacama for microbes using culture-dependent methods much of what they obtain are endospore formers, whose dormant spores are well-known for their resistance to desiccation (think Bacillus subtilis). Since the metagenomic studies clearly show the presence of non-spore formers, some key questions remain unanswered. Does the DNA found in some of Earth's driest habitats come from microbes that are dead or alive? If alive, are those microbes metabolically active or are they able to lie dormant for extremely long times under such hyperarid conditions?
Those are the questions that Dirk Schulze‑Makuch et al. ("et al." here is a lot, 42 authors from 30 centers) sought to answer when they set out to sample soils from several Atacama sites. Their sampling ranged from fog-laden coastal soils (CS on the figure) to extremely dry sites such as Yungay (YU) and Maria Elena (ME), both located about 50 km inland and about 1000 meters above sea level. They did their first sampling during April 2015, one month after the biggest rainfall in the Atacama since recording started in 1978. An entire 8 mm of rain fell at Baquedano station! Whether the timing of the sampling after a rare rainfall event was planned or the result of sheer serendipity, the authors do not reveal. But as you'll read, that rain had a significant effect on their results. To determine if the microbes in the soils they sampled were alive, maybe even dividing, the team used a multi-pronged approach. They sampled surface (0–5 cm) and subsurface (20–30 cm) soils, carefully keeping track of the physico-chemical properties with respect to habitability. Using techniques developed before, they separated the microbial cells from any extracellular components present in their samples. This allowed them to quantitate and characterize as separate pools extracellular and intracellular components such as metabolites, ATP and, of course, DNA. They were dealing with extremely low levels of biomass and the work required extreme care; for those interested in experimental details I refer you to their extensive description of the methods. Suffice to say that from those analyses they found evidence that at least some of the cells in those habitats were active. What I found most exciting was that they obtained evidence that at least some populations of bacteria were growing relatively rapidly!
To obtain such evidence they followed an approach that, in its principle, had been developed to map bacterial replication origins nearly sixty years ago. It relies on the fact that non-replicating chromosomes will have a single copy of their origin of replication as well as of all its other genes. In contrast, replicating chromosomes will have a higher dosage of genes near the origin. While those early experiments relied on transformation or transduction to measure gene dosage, in 2015 Korem et al. developed a way to infer in vivo growth rates based on the frequency of sequence reads in a metagenomic sample. Here's how the authors guide us through the graphic depiction of their method: "Sequenced reads (right) are mapped to complete bacterial genomes and the sequencing coverage across the genome is plotted. Each bacteria cell in a growing population (top) will be at a different stage of DNA replication, generating a coverage pattern that peaks near the known replication origin (green vertical line in graph), and thus produce a prototypical sequencing coverage pattern with a single peak and a single trough. Bacteria from a non-dividing population (bottom) have a single copy of the genome, producing a flat sequencing coverage pattern across the genome. The peak-to-trough coverage ratio is a measure of the growth rate." To make this sort of approach easily accessible, Brown et al. developed an algorithm, which they call iRep (for index of Replication). Sequence data from non-growing bacteria will yield iRep values of 1 while iRep values higher than 1 are indicative of a growing population. The iRep algorithm can be applied to any microbiome study so long as nearly completed draft genomes can be obtained. That is exactly what Schulze‑Makuch et al. did.
Based on their sequencing data, they were able to obtain reasonably high-quality draft genomes for four bacteria, one from the Yungay site and three from the Maria Elena site. Importantly, the iRep values for all four – particularly the Actinobacterium from the Maria Elena site at 3.31 – strongly argue that these bacteria had replicating chromosomes at the time of sampling. The question that immediately comes up is just how long can members of these microbial communities grow? Is such replication activity representative of what is going on all the time or is it representative of something that only happens after a rare rainfall?
The authors do not address this question directly, but they did obtain indirect evidence that high microbial activity in the subsurface likely only occurs during relatively short periods after a rainfall. Turns out, the team went out to the same sites and sampled again in 2016 and 2017. Lucky for them, it did not rain much in the interim. Several of their results were consistent with those habitats becoming less and less propitious for life. Most striking to me were a couple of observations at Yungay in subsurface samples (20–30 cm depth). The water content of the soil dropped from 2.7% in 2015 to 0.1% in 2017. Concomitantly, the concentration of intracellular DNA dropped by some five orders of magnitude! No surprise they were not able to assemble genomes from those samples. But I am willing to bet that the iRep values for those remaining cells – if they could be obtained – would be 1.
The picture that emerges for life in these hyperarid environments is one where short bursts of microbial activity and growth are interspersed by much longer periods of inactivity, what the authors refer to as "transitory microbial habitats" in their title. How long can these periods be? Many might want to extrapolate what happens in the Atacama to what might happen in Mars. I am simply in awe at the resilience of our very own Earth-bound microbes.