Mad Max - Beyond Biosphere (too old a reference?): Ecology of the rare microbial biosphere of the Arctic Ocean.

This review originally was going to be a reply to Tom Gibson’s post on 21.10.2014 but the more I was researching to back up what I was going to say, the more apparent it was that a full review of the paper would be more beneficial and perhaps more insightful. Tom and I had a brief discussion before class yesterday (23.10.2014) which contained what I had responded with previously (see reply 22.10.2014; 11:46) and that implications that was stated in the paper was just part of the discussion and they were highlighting considerations that need to be taken into account when going down this route of research.

For practical reasons, it is not surprising that the main focus of marine microbial studies have been focused on the most abundant phylotypes as they are easier to detect. However, in recent years, literature has found that the diversity of marine bacteria gone from a few thousand taxa to 10⁶–10⁹ taxa (the diversity of marine archaea is said to be 5–10 times less). Studies have suggested that the most abundant taxa are also the most active and most important in fluxes of dissolved organic matter, however, abundant species represent only a small portion of microbial diversity. In 2006, Sogin et al., coined the term ‘rare biosphere’ to explain the analyses of abundance distribution in diversity. Rare biosphere is one component of analyses which comprises of a very high number of rare species that contains the most diversity. In contrast to this, the other component includes the few species that are very abundant, which is the most studied of the two.

Galand et al., (2009) used pyrosequencing to describe the structure and composition of the rare biosphere and to test whether it represents cosmopolitan taxa (biological categories which can be found almost anywhere around the world) or whether, similar to abundant phylotypes, the rare community has a biogeography. During the voyages of various Arctic research projects, samples were collected with a rosette system fitted with PVC bottles and equipped with a conductivity, temperature and depth (CTD) profiler. Samples were taken from surface (ACB) and deep water (DAO) masses in five geographical regions of the Arctic Ocean in the Chukchi Sea, Beaufort Sea, Franklin Bay, Baffin Bay and Laptev Sea. Shortly after collection, sea water (5-6 L) was filtered through a 50 µm, 3 µm and 0.2 µm mesh for the DOA samples and a 0.8 µm for the ACB samples.

The bacterial hypervariable (the location within nuclear DNA or the D-loop of mitochondrial DNA in which base pairs of nucleotides repeat (nuclear DNA) or have substitutions (mitochondrial DNA)) V6 region of the 16S rRNA gene was amplified using a pool of universal primers. For each read from the sequencer, the primer bases were trimmed from the beginning and the end, and low-quality sequences were removed. Both bacteria and archaea communities were investigated to assess the different levels of diversity within the rare members of the microbial communities. Two different phylotype definitions to indicate the ecology of the rare biosphere was used. Reference sequence-based phylotypes were defined as containing all sequences sharing the same RefHVR_V6 database sequence (or group of sequences from the VAMPS database; http://vampsarchive.mbl.edu/resources/databases.php) as their nearest neighbour, a frequently used definition for microbial ecology studies by pyrosequencing and corresponding to a 94 % identity clustering threshold. For comparison, a much more stringent definition was used in which sequences with 100 % identity were grouped as belonging to the same phylotype. Abundant phylotypes were defined as the phylotypes with a representation > 1 % within a sample and rare phylotypes were defined as having an abundance < 0.01 % within a sample.

From the examination of 740,353 16S rRNA gene sequences from 32 bacterial and archaeal communities it was shown that the rare biosphere did not have a cosmopolitan composition, but rather, followed patterns similar to those of the most abundant phylotypes.  Distinct grouping was apparent with one group containing all communities from surface waters (ACB) and the other group containing all deep water mass communities (DAO). On further separation, they found that distinct grouping corresponded with where the communities were found in the five geographical regions.

They concluded that the rare biosphere has a biogeography and that the diversity is most likely subjected to ecological processes such as selection, speciation, and extinction. In Galand’s et al., (2009) study, they noted that distance was much less important than water mass for explaining differences in community composition (i.e. communities originating from the same water mass but separated by thousands of kilometres were much more similar to each other than communities only separated by a few hundred metres but originating from different water mass).

This reiterates my comment on Tom’s review that the multidimensional characteristics of the ocean make this field of research very complicated.

Galand, P.E., Casamayor, E.O., Kirchman, D.L., & Lovejoy, C. (2009) 'Ecology of the rare microbial biosphere of the Arctic Ocean' Proceedings of the National Academy of Sciences 106 (52): 22427-22432.

Sogin, M.L., Morrison, H.G., Huber, J.A., Welch, D.M., Huse, S.M., Neal, P.R., Arrieta, J.M., & Herndl, G.J. (2006) 'Microbial diversity in the deep sea and the under explored “rare biosphere”' Proceedings of the National Academy of Sciences 103: 12115-12120.