Laverock et al.,
(2014) looked at the effects of a burrowing mud shrimp Upogebia deltaura on the temporal changes of certain bacterial and
archaeal genes that represented the main nitrogen (N)-cycling guilds in the
sediment. To determine whether there was any temporal variation in the
abundance of N—cycling bacterial and archaeal genes, the study utilised
quantitative polymerase chain reaction (q-PCR) to analyse sediment samples
taken from the burrow walls of U.
deltaura and from surface sediments in Plymouth Sound. The q-PCR counted
the bacterial and archaeal 16S rRNA genes (to gauge overall numbers of bacteria
and archaea), as well as genes that represented betaproteobacteria and archaeal
ammonia oxidizers (amoA), bacterial
denitrifiers (nirS) and bacteria that
undertook the anammox process. These specific phyloptypes that other studies
had previously identified in marine sediments were targeted with particular
primers.
Bioturbation did appear to affect the temporal variation of
certain N-cycling genes and these effects differed between the ammonia oxidising
bacteria (AOB) and the ammonia oxidising archaea (AOA). There were seasonal variations
in the guilds of AOB in burrow sediments compared to surface sediments and
these variations were believed to be affected by bioturbation activity. These included
genes represented by bacterial guilds that remove nitrogen (NO3-,
NO2-, and NH4+) from marine
sediments by denitrification (nirS)
and anammox. During the summer, shrimp increase bioturbation and aeration of
their burrows, bringing a greater oxygen influx into these systems. This has an
impact on oxygen-sensitive processes such as denitrification and anammox.
Although the abundances of AOA genes did vary over time,
these changes were not as a result of bioturbation and appeared to be
controlled by independent abiotic factors. These range from the increased
availability of ammonium over the winter months to the dissolved oxygen levels
in the water and salinity gradients. In addition, archaeal amoA genes were four times as abundant as betaproteobacterial amoA genes during the year but it is still
unclear whether it is AOA or AOB that make the greatest contribution to ammonia
oxidation rates in marine sediments.
The authors acknowledged that certain phylotypes were targeted
in this study and this could have introduced an inherent bias. The primer sets
used may have missed gammaproteobacterial amoA
genes and denitrifying nirK genes,
both of which represent important bacterial guilds in marine sediments and
oxygen minimum zones. In addition, no primers yet exist to target archaeal nirS genes.
The effects of burrowing shrimp clearly have an impact on
microbial processes and communities. Any changes in the abundances of
nitrogen-cycling microbes could therefore impact the fluxes of nitrogen across
the sediment interface. Further work should focus on whether the presence of
these genes is in fact associated with the relevant biogeochemical processes or
not.
Reference:
Laverock, B., Tait, K., Gilbert, J.A., Osborn, A.M., and
Widdicombe, S. (2014) Impacts of bioturbation on temporal variation in
bacterial and archaeal nitrogen-cycling gene abundance in coastal sediments, Environmental Microbiology Reports, 6, (1), 113-121.
Hi Anita, thanks for the read! You highlighted that fact there may have been some bias in this study, additionally was there any mention of them testing areas with lesser shrimp burrows or none at all? I had a quick peak at the paper (and forgive me, I did not read all of it) and they mentioned comparing the burrows to surface sediment, but I wonder if this is an adequate control to use considering the varying factors in abiotic processes?
ReplyDeleteHi Dean
ReplyDeleteSorry for such a late reply, too many dissertation distractions! This is a really good point you have raised that I had not considered. Sediment samples were taken from the inside of the burrows and outside, given as “ambient sediment samples”. There was no detail about how the samples were collected which was a bit frustrating. They also mentioned additional abiotic factors that could have an effect such as inorganic nutrient run-off and increased temperatures during spring, which could increase microbial growth, productivity and hence gene abundances.
This paper only looked at one species of shrimp, however previous studies by the same authors looked at two species of shrimp, Upogebia deltaura and Callianassa subterranean in context of how their burrowing activity significantly altered communities of bacteria living in the sediment. The paper that I reviewed was building up on this research, however, the work seemed only to focus on one species of shrimp, rather than the two species in the earlier paper. This paper was earlier than the one that I wrote a review for and the authors merely mentioned at the end of the paper that the burrowing activities of the two shrimp were likely to affect coupled nitrification-denitrification reactions but did not go into any more detail than this. A lot of other work was cited, in particular how U. deltaura has shown to enhance denitrification within it’s burrows but there was no explanation into why only one shrimp species was examined in this case. Also, as they were using specific primers on specific guilds which the authors suspected would be present in connection with this one shrimp species, I wonder if this had a bearing on why they chose this one shrimp species to study. On another note the two shrimp species Upogebia deltaura and Callianassa subterranean have different shaped burrows with a varying number of burrow entrances, which could add another factor affecting the N-cycling microbial guilds in the sediment. Fascinating and lots of room for exploration, thanks for raising a good point!
I have listed the previous paper for below if you’re interested.
Laverock, B., Smith, C.J., Tait, K., Osborn, A.M., Widdicombe, S. and Gilbert, J.A. (2010) Bioturbating shrimp alter the structure and diversity of bacterial communities in coastal marine sediments, The ISME Journal, 4, 1531-1544
Hi Anita, thanks for this informative paper. Well, i kind of agree that this experiment indeed have quite a lot of cofactors that should have been taken into account when designing the experiment. But nevertheless, if i see it from the in situ point of view, it kind of mimics what nature would be like. And these micro-scale activities could inadvertent have an impact on the N- cycling processes.
ReplyDeleteHi Li
ReplyDeleteSo sorry for the late reply, I hadn't realised you had commented on this. Yes, there are a lot of factors to consider but it certainly highlights the complexity and how such activities could impact biogeochemical cycles.