Metagenomics in action

'Metagenomics', the direct sequencing of all the DNA found in environmental samples.  From one perspective, this is yet another 'omics', a way to keep all those expensive sequencing machines going.  And a way to avoid having to have hypotheses about what's going on in nature before you start your project--a somewhat strange twist in modern biology.  Still, 'omics' is done because we have the tools to do it and because it does promise to find something, on the single underlying assumption, namely, that something is there, even if we don't know what it might be.

In fact an interesting use of this methodology is reported in Nature this week, in a paper about the sequencing of all the microbes in Alaskan permafrost soil samples pre- and post-thaw.  The paper reports rapid changes in the abundance of many phylogenetic and functional genes and pathways, suggesting a rapid response to changing environment.  In this case, there need not have been any kind of a priori hypothesis about what one would specifically find for this to be a valuable kind of work, which this study has proven to be.

Mackelprang et al. collected 3 frozen soil cores from an area in Alaska that they had previously characterized.  They removed samples from these and let them thaw over 7 days.  They monitored the carbon dioxide and methane concentrations in the headspace of the helium filled tubes in which the samples were incubated, and extracted DNA for 16S ribosomal RNA and metagenome sequencing.

The authors were particularly interested in what happened to the methane and carbon dioxide because, of course, these are greenhouse gases.  They document changing levels of these gases as the soil samples thawed, and corresponding increases in genes in their metagenome from microbes that produce these gases as metabolic byproducts.  

Specifically:

The metagenome data revealed core-specific shifts in some community members, including the orders Proteobacteria, Bacteriodetes and Firmicutes. We found that Actinobacteria increased in both cores during thaw. Actinobacteria have previously been found at high abundance in permafrost, which is thought to be caused by their maintenance of metabolic activity and DNA repair mechanisms at low temperatures. Most archaeal sequences identified in the metagenomic data were methanogens in the phylum Euryarchaeota (62–95%), including the Methanomicrobia that was represented in our draft genome. In total, four orders of methanogens (Methanosarcinales, Methanomicrobiales, Methanomicrobia and Methanobacterales) were detected. As the permafrost thawed, the methanogens (including Methanomicrobia) increased in relative abundance. These orders are known to be metabolically versatile and can use a variety of substrates.

They also found that methane was consumed post-thaw.  But, to us what is most interesting about this, not being climatologists or microbiologists, is what they found about the differences between samples post-thaw, as they describe here.

We tracked simultaneous shifts in the total gene complement from the metagenome data to obtain a global view of functional response to thaw. The active layer samples were relatively similar before and after thaw. By contrast, the two frozen permafrost metagenomes differed dramatically before thaw. In addition, functional genes in frozen active layer and permafrost samples were distinct from each other, including differences in several key metabolic pathways such as energy metabolism, nitrogen fixation, amino-acid transport, oxidative phosphorylation and anaerobic respiration. During thaw, the permafrost metagenomes rapidly converged and neared those in the active layer samples. The convergence of function was not matched by a convergence of phylogenetic composition during this short-term incubation, suggesting that disparate community responses to thaw can have similar functional consequences.

As we said yesterday in our post about ostrich penises, however the job can get done, evolution can support it.  Whether or not the job being done here is good or bad for humans vis-à-vis climate change is another story.  But, convergence of function in the communities of microbes analyzed by these researchers happened in communities with very different compositions of microbes.

Organisms have responsive genomes. Indeed, the 'job' of cells is to sequester their special ingredients within, but to monitor the external environment to determine how to behave most successfully.  They are changeable, within their genomic repertoire.  Mutation followed by natural selection can lead to specific genetically committed responses, but that isn't always necessary, because due to whatever earlier processes, even humble microbes have evolved to be able to respond to the conditions they find themselves in.  And, whether or not warming temperatures are beneficial to specific microbes, the community adapts. 

Based on comparative morphology and modern-day science, roughly 4 billion-year-old aggregates of bacteria (fossil biofilms calleld  'stromatolites') look strikingly like their modern descendants.  Today, biofilms are known to be bacterial responses to changes in conditions--even different species can aggregate in the same biofilm.  This means that not that long after the origin of life (and, indeed, of the earth itself), fundamental facultative adaptability had already been built by evolution into the genomes of the earliest cells--and that means it is a basic property of cells.  This is a point we stress in our book, The Mermaid's Tale, and we're always gratified to see it confirmed.