Traditionally the distribution of
microbes in the oceans has thought to be driven by depth. With the Bacteria and
Euryarchaeota being found in the upper water column while the Crenarchaeota
are found at depth. However there is evidences to suggest that microbial
assemblages are not structured by depth per se, but instead could be
associated with specific water masses with discrete temperature and salinity
characteristics. Galand et al. (2009)
set out to test this by sampling the communities of Archaea associated with
water masses from the North Water in the high arctic.
Water samples were taken from
three water masses, the Upper Arctic water (UAW), the Arctic Basin Halocline
(ABH) and the Wintertime Convection Water (WCW), below the photic zone during
summer. Sea water was filtered to remove large particles and then using 3 and
0.2µm filters to obtain samples. 16S rRNA genes were amplified using PCR and
cloned to form clone libraries. Phylogenetic analysis was carried out and
diversity and richness calculated from these sequences. Quantitative real-time PCR
was performed using primers which targeted 16S rRNA genes from the Archaea, as
well as the Archaeal amoA gene which is used in nitrification.
Using the clone libraries and
qPCR data it was found that each water mass harbored distinct communities. ABH was dominated by the Crenarchaeota, specifically
Marine Group I.1a. Whereas UAW and WCW were dominated by the Euryarchaeota,
groups IIa1 and IIa2 respectively. Depth was shown to have no bearing on these
results. This is an interesting result, but I would stress that the authors
were looking at a low resolution of taxonomic detail by using 16S rRNA and microvariation
went untested. Therefore different ecotypes within groups could still be
distributed by depth.
In terms of amoA abundance, 70%
of copies were from the BAH, which suggests water masses vary in their
potential to carry out biogeochemical functions. This correlated with the high
abundance of Crenarchaeota, which are thought to oxidise ammonia to
nitrites for energy. Considering water masses do not remain in one spot and
those in the arctic eventually arrive in the Atlantic, this is an interesting
result. Water bodies which contain groups of organisms with differing nutrient
cycling capabilities could contain different combinations of nutrients when they
arrive. Changes in ocean circulation due to climate change will affect the
eventual fate of water masses and their microbial communities. Potentially
changing the balance of nutrients which reaches ecosystems in the Atlantic. But,
the study does not address whether the communities change as the waters move.
Presumably any changes in community, and therefore nutrient cycling, during
transit affects nutrient composition. So to truly predict changes due to
circulation, the assemblage over the entire journey of a water mass would have
to be examined.
In review, the study adds to our
understanding of how microbes are distributed and how this is important for biogeochemical
processes, ecosystems and by extension us. But it also shows that the plenty of
questions remain and that the picture is not fully complete.
Galand, P.E., Lovejoy, C.,
Hamilton, A.K., Ingram R.G., Pedneault, E. & Carmack, E.C. (2009). Archaeal
diversity and a gene for ammonia oxidation are coupled to ocean circulation. Environmental Microbiology, 11(4), 971-980.
Hi Tom,
ReplyDeleteVery interesting read and definitely something I wanted to explore more of, thank you.
I can see this being a very difficult field of research with so many implications to consider, especially multiple speciation models (allopatric vs. sympatric). Another paper by the same author you have reviewed was explaining that existing environmental factors would shape microbial diversity in multiple habits within one water mass (sympatric speciation). However, alongside this, historical isolation with lack of biological dispersal (allopatric speciation) would explain the presence of microbial communities in multiple water masses but within one habitat.
I wonder if there has been any study or speculation since these papers have been published showing whether the communities change as the waters move or if it is even feasible to track.
Thanks again,
Dean
That paper sounds interesting, probably worth reviewing! I had a quick look at the citations for Galand 2009 and could not find anything specific on that question, although I may have missed it. However I have a feeling (my oceanography is not great) that these water masses slip below more warmer southerner waters, so it might be worth looking at papers on deep Archaeal communities in the Atlantic and seeing if any of these clades e.g. Marine Group I.1a. turn up again at depth.
DeleteHi Tom
ReplyDeleteThis is a really good subject area to explore, especially given the impact that changes in ocean circulation and water mass movement could have with regards to climate change. Microbes are intimately linked with biogeochemical cycles so this would definitely be a crucial area for follow up study.
In response to your and Dean's question about tracking how the communities change over the journey of the water mass, I was wondering if doing some sort of transect would work. You could sample water at appropriate depths along a transect along the length of the water mass, as well as taking chemical and temperature readings to determine that sampling is taking place at the right point within the water mass. This would also help identify the concentrations of nutrients, DOM and POM present within the sample. You could then look at the communities present and compare them along the points of the transect, which may give you an idea about how they change with distance and depth.
Anita
In the paper they did take a number of samples running along each water mass (at various depths). They had a look at nutrient concentrations, but not DOM/POM, as well but then did not talk about them in the results so I did not mention that! A transect would work, but I was thinking you would have to take each measurement sequentially in time as well as space, so sample on one month, track the water mass then sample again at its new location etc.
ReplyDeleteYes definitely, that was what I was thinking too. I can't think how else you would do it. What an amazing research project that would make!
DeleteHey Tom,
ReplyDeleteThank you for the read, I found it really interesting so I went on to look at how another effect of Climate Change- Ocean Acidification could affect the nitrifying abilities/ dispersal in Archaea and also Bacteria (both ammonia oxidising). The study I looked at, actually found out the rates of ammonia oxidising in the organisms, maybe it would be useful to look at rates in this study as well? This will then allow us to see if the different species of Achaea can actually adapt and oxidise as quickly in their new locations to see if the implications are true. Like you said, this will be hard to investigate as the ocean circulation movement, new locations of water masses and what conditions they hold must be predicted! Thanks, Elyssa
Sounds interesting Elyssa, was that study conducted in the lab or out in the open ocean? I am interested as to how it would be possible to tell which species is oxidising what in the real world i.e. which species are more important etc. Presumably you could look at the bulk oxidation rates of ammonia then work it out based on data on each organism from the lab? On a side note I was reading a paper which suggested that the presence of an amoA gene doesn't necessarily mean (although its strongly suggestive) a microbe can oxidise ammonia. Which is something I think is worth bearing in mind when reading these environmental metagenomic studies.
ReplyDeleteThe study was conducted in the lab- however this wasn't made clear in the paper. About the amoA gene I was actually going to bring that up with you, that in the study by Beman et al. 2011 ( the one I reviewed) I thought they used a much more quantitative and reliable technique to investigate oxidisation. They used stable isotope tracers and very long and complex set of equations! With regards to seeing which species are more important, that would be useful as with the change in climate species specific responses will occur leading to a different array of species, this will be quite easy to study as there is only a few species of bacteria and archaea that can actually oxidise. To do this though, would be such a hard experiment, as to isolate the different species would take a lot of skill! Any ideas- you did the module last year on lab techniques!?
ReplyDeleteHi Elyssa, I have been thinking about my previous comment and it's probably not tractable. I think the best way in terms of finding out which bugs are most important is to look at the relative abundances of amoA genes. Then you don’t have to isolate each individual species which would be extremely difficult. Althought you can use methods such as serial dilutions and filtered seawater (with a small number of nutrients added) as a growth medium, they used that to culture SAR11 (see Munn 2011).
ReplyDeleteWith regards to climate change, AOA communities apparently show little change in response to ocean acidification. I would recommend reading Bowen et al. 2013, Marine Ecology Progress Series, 492, 1-8. It kind of follows on from your blog post.
Hi Tom, sorry for late response I have just seen this. I am a little confused when you say AOA communities show little change in response to ocean acidification? As in both papers it says there is a change- in nitrification (mine) and abundance( the paper you just gave me)!? Am I understanding you correctly- thanks for the paper by the way and the explanation on how to analyse it I agree!!
ReplyDelete