Protists
interact in several ways with bacterial and archaeal populations which has the effect
of substantially shaping the structure of these communities within the marine
environment.
Protists
graze using a mode of nutrition called phagotrophy. This method of grazing can
affect the activity, quantity and physiological state of the prey organisms,
these factors can lead to protists exhibiting prey preferences. An assemblage of
protists feeding in this manner may graze on anything from 25% to >100% of
the daily production of prokaryote plankton.
A study carried
out by Pachiadaki et al (2014) looks at the grazing activities of phagotrophic
protists in the Eastern Mediterranean Sea at depths ranging from 40m down to
3540m at the redoxcline in the Urania basin. The Authors of this paper carried
out the first in situ incubation of samples and due to the fact that the sample
was being suspended at depths of 40 - 3540m for periods of time extending from
4 – 16h they were not able to carry out replicates of the full experiment and
only managed to replicate the counts of the organisms in each treatment. Two
variations of the experiment were carried out. Both experiments used fluorescently
labelled prokaryotes (FLPs) to track the grazing impact of the protistan
communities. The experiments differed in the length of incubation. The shorter
incubation experiments were used to trace the ingested FLPs; the longer
incubation times were used to estimate the rate of disappearance of the FLPs.
The study
found that both prokaryotic and Protistan abundance fell between the euphotic
zone and mesopelagic zone. The difference came when the abundance of prokaryotic
cells stabilised the deeper the sampling went into the mesopelagic layer whereas
the protistan abundance continued to fall with depth. The samples at the
greatest depths of 3000m and 3540m showed an increase in not only prokaryotic
and protistan abundance but also showed elevated rates of daily prokaryotic
turnover. This was especially noticeable at the Urania interface where the
turnover rate was greater than that measured in the photic zone at 40m. The
increased abundance of both prokaryotic and protistan cells was in conflict
with previous counts but this unusual increase in abundance was put down to a resent
eruption of a mud volcano in the vicinity of the test area.
This study
provided a good insight to the microbial assemblages at varying depths and the effects
of protistan grazing on the prokaryotic communities present. It also proved
that in situ incubation and sampling of cultures is possible although the
technology does need some improvement to be able to replicate the whole
experiment to increase the reliability of future experiments.
Hi James,
ReplyDeleteThanks for the post - this paper certainly piqued my interest! While I agree with you that this study was bold in optimising a technical protocol to study in situ microbial interactions at such a depth, I’m not sure what can be learnt from this work on an ecological level. Having since read the paper, I feel the functional groups chosen are far too simplistic to approximate a natural picture of the microbial loop and far too much is assumed. Firstly, the use of the word ‘prokaryote’ ignores the phylogenetic distinction between the Bacteria and the Archaea (see Norman R. Pace’s 2006 ‘Time for a Change’ article in Nature). These domains are more genetically distinct than the Archaea are to the Eukaryota and their molecular differences such as lipid membrane and cell wall composition would have major ramifications in biogeochemical cycling, depending on which group was predominantly grazed. As mentioned in the first lecture, Karner et al, 2001 showed that, at least in the Pacific Ocean, bacterial and archaeal abundance are inversely correlated over depth with major archaeal clades such as the Crenarcheota dominating the mesopelagic zone. Should this be a general trend, this would be a major confounding factor in this study, which used ‘prokaryotes’ from 3,000m as FLP prey for protists in the euphotic zone. They may never encounter such prey species in the wild. There is also an innate assumption that phagotrophy and phototrophy represent a metabolic dichotomy in the eukaryotes, but mixotrophy can be quite prevalent in the euphotic zone which may skew interpretation of the findings. A recent paper in the journal Protist aims to revise the classification scheme of planktonic protists to correct for this:
Mitra, A., Flynn, K. J., Tillmann, U., Raven, J. A., Caron, D., Stoecker, D. K., ... & Wilken, S. (2016). Defining planktonic protist functional groups on mechanisms for energy and nutrient acquisition: incorporation of diverse mixotrophic strategies. Protist, 167(2), 106-120. http://www.sciencedirect.com/science/article/pii/S1434461016000043
As a proof of concept, this paper does however provide a very innovative use of the MS-SID to study in situ protist grazing. I wonder if any recent work by the same authors has been able to refine the biological results using the same technology?
Thanks again,
Davis
Reposted on behalf of James.
DeleteHi Davis, Thank you for your comment on this paper and I totally agree with you in the fact that they are very general in their classification of the microorganisms present in the samples and also agree that the use of FLP’s from 3000m and providing this as a food source for protists in the euphotic zone is not a viable way of accurately measuring grazing for the exact reason you stated, that the 3000m FLP’s are not a natural food source. However, the authors were generalising the food source based on cell size rather than species which would create one less variable when they were trying to record that rate of disappearance of FLP’s.
The paper you referenced in your comment was interesting and makes a very good case for the need to reclassify planktonic protists as their feeding functions are certainly diverse and this in turn would help the scientists in this study some of the lower levels of grazing. However surely at the sampling sites below the euphotic zone any effect of photosynthesis would be null due to the lack of any light sources and therefore would have no effect on the level of grazing recorded.
With regards to the question about the authors publishing a more recent paper refining the biological results from this paper. I have not been able to find one covering the grazing habits of Protists but I have found one comparing the effectivity of Niskin bottle vs .in situ approaches to the analysis of gene expression (Comparison of Niskin vs. in situ approaches for analysis of gene expression in deep Mediterranean Sea water samples). This paper goes into the methods of filtering and then preserving RNA samples from different areas within the water column and goes onto find that in-situ preservation of RNA would be more beneficial as it would reduce and effects from over handling of samples and would have a greater chance of preserving any of the more sensitive molecules that may be damaged if they are recovered to the surface without preservation.
Many Thanks James