Unusual is important: how rare Archaea may contribute more to communities than we think.

Recent innovations in molecular metagenomics have improved understanding of the composition and function of the microbial plankton. Archaea are an often overlooked part of the microplankton, and while we appreciate that they significantly contribute to biogeochemical cycles, little is known about their community structure and dynamics. Comprised of three main grroups: Thaumarchaeaota marine group (MGI), and two groups of Euryarchaeota, MGII and MGIII; each group possesses several distinct clusters, potentially indicating ecotypes or evolutionary lineages. 

Whole communities or metabolically active communities can be studied in environmental samples using 16S rDNA and 16s rRNA respectively. This differentiation is important as it gives an indication of growth: often revealing a correlation between abundance and activity. 

 “Rare” OTUs are defined by <1% total reads in the sample; frequently overlooked, the rare community may still have an important role. By utilising metagenomic techniques to characterise the total surface archaeal communities in the Mediterranean sea over 3.5 years, this study from Hugoni et al. (2013) aimed to describe the structure and infer the potential function of the rare archaeal community in different seasons. 

Surface seawater (≈3m) samples were collected every month; from these 16S rDNA/rRNA were co-extracted and rRNA was reverse-transcribed using random primers. Pyrosequencing was carried out on the rDNA and rRNA using universal archaeal primers. Archaeal sequences were used to construct phylogenetic trees. OTUs present were identified and their abundances calculated; they were considered rare if they comprised <1% of sequences and were present in only one sample, otherwise they were abundant. 

Analysis showed that major archaeal groups, MGI, MGIIA and B, were comprised of separate clusters with different levels of activity across the seasons. This could represent adaptation to a variety of niches; different metabolisms are hypothesised to correspond to different ecotypes, as shown in Bacteria (Campbell et al., 2011). Their abundance and activity may differ due to contrasting strategies and competition for resources. 

There were three main factions of OTUs detected in the rare archaeal community. The first OTU group represents the local seed bank of Archaea, which, when rare, had poorly correlated 16S rRNA and rDNA sequences, suggesting that they were inactive. When OTUs became seasonally more abundant, there was a much closer correlation, showing their increase in activity. The variation in activity could represent change rates of metabolic processes over time. 

The second group of OTUs were always rare and inactive. They had a low sequence similarity compared to the existing database of the area, and were considered aliens to the pelagic ecosystem studied. Perhaps they came from deep marine sediment, and other understudied systems, with episodic environmental disturbances initiating dispersal of this non-local seed bank. The different physico-chemical parameters of the surface waters may be a limiting factor of activity, but they may have potential to colonise should amenable conditions arise. 

The third OTU group consisted of Archaea that were always rare but constantly active; their phylogeny and seasonal dynamics resembled those of active and abundant groups. Their higher rate of activity indicates that they are not dormant; they are simply maintained at a low abundance, potentially due to inferior competitive strategy, or a life strategy of rarity to minimise predation. Alternatively, they could be more susceptible to viral attacks than the other groups of Archaea. 

This paper opened the door to discovery of sheer diversity in phylogeny, life histories and activities in the rare Archaeal biosphere. Their potential for impact is immense, and not yet fully understood; and may well be vital to the function of our oceans, especially with regards to biogeochemical cycling through the seasons. Furthermore, it emphasises once more that the use of modern molecular genomics techniques is intrinsic to advancing our understanding of marine microbial community structure and function. Perhaps these powerful techniques should now be used to delve into the more neglected players in marine microbial communities: inherent parts of the puzzle may still remain undiscovered.

Definitions:

Metagemonics - The study of all of the environmental genetic material present, using massively paralleled genetic sequencing.

Active community - The section of a (microbial) community that is contributing to the environmental RNA pool, and therefore is actively transcribing its DNA, producing proteins for growth and metabolism. 

Total community - The total DNA in the environment, some of which may not be actively transcribed and used for growth and metabolism. Used to show which organisms are present, but not necessarily active (ie no differentiation for dormant cells).

OTU - Operational taxanomic unit: a group of closely related organisms, defined as having ≥97% sequence similarity, usually of 16S rRNA sequences. 

Pyrosequencing - A method of massively paralleled sequencing, which uses light released to signify the order of the sequence. 

Seed bank - A dormant community of organisms that can potentially be resurrected under certain environmental conditions.

Reviewed Paper:

Hugoni, M., Taib, N., Debroas, D., Domaizon, I., Dufournel, I. J., Bronner, G., Salter, G., Mary, I., Galand, P. E. (2013). Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters. Proceedings of the National Academy of Sciences, p201216863

References

Campbell, BJ., Yu, L., Heidelberg, JF., Kirchman, D.L. (2011). Activity of abundant and rare bacteria in a coastal ocean. Proceedings of the National Academy of Sciences 108:12776–12781.