Title: The emerging microbial ecosystem of the Greenland Ice Sheet.
Abstract: The surface of the Greenland Ice Sheet (GrIS) is inhabited by a rich microbial community
that plays a role in regional carbon cycling, nutrient export and also ice sheet melting via changing the
albedo. Due to the large area of the ice sheet, considerable spatial and temporal gradients are
present, affecting the microbes. We examine the changes in space and time of the microbial
community structure, abundance, activity, and the proportion of the active microbes within the
community on the surface of the GrIS, using co-extraction of DNA and RNA, quantitative PCR and
pyrosequencing of DNA and cDNA along with in situ productivity measurements. We analyse the
relationships between the physical, chemical and biological variables using multivariate statistical
analysis, identify the significant factors controlling the biological processes on the GrIS, and pave the
way to modeling of the microbe-ice interactions.
Dr Marek Stibal
Department of Geochemistry
Geological Survey of Denmark and Greenland
Øster Voldgade 10
1350 Copenhagen K
Denmark
Email: msti@geus.dk
Functional gene responses in a perfect world – can we trust quantification of transcripts in soil in
response to manmade chemicals?
Carsten Suhr Jacobsen & Jacob Bælum
We are all struggling with it: Analyzing environmental relevant microbial processes in situ is extremely
challenging. Nucleic acid based studies are becoming more and more popular, but pitfalls exist and
should be taken into account. In a perfect world we would know the genes involved, we would know
the expression pattern, we would know the mRNA degradation rate, we would know the nucleic acid
extraction biases, we would trust our DNase treatment, reverse transcriptase reaction and the
quantitative PCR. Does the perfect world exist?
In a less perfect world the functional genes might not be known – or at least only some of them are
known. Such a scenario might be when searching for tfdA degradation genes for modern herbicides in
a soil originating from below a burial mound that has been isolated from the surrounding
environment for more than 5000 year.
Another less perfect world would be RNA/DNA extraction from inorganic clay sediments – in this
scenario the problem is that when cells are lysed in the nucleic acid extraction procedure the nucleic
acids sticks to the clay due to the phosphate backbone. However, using an optimized RNA/DNA
extraction protocol including the patented G2 blocking solution, we were able to obtain high-
resolution expression profiles of the functional reductive dehalogenase genes bvcA and vcrA during
two consecutive dechlorination events of trichlorethene (TCE), cis-dichlorethene (cis-DCE) and vinyl
chloride (VC) in a clay subsurface environment. Up-regulation of the bvcA (for the biostimulated
microcosms) and vcrA (for the bioaugmented microcosms) gene expression fitted well with high rates
of dechlorination of VC, while no known transcripts could be measured during TCE and cis-DCE
dechlorination. But is this trustable?
What is needed to further establish quantitative transcript based analysis of functional genes in
environmental samples? – will we be able to adapt rules for gene expression as used in mammalian
cells? Should a housekeeping gene be used for validation? – if so which?