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Deep Biosphere Sediment Microbiology
Theme:
Microbiology in marine sediments
Date:
2011 March 6-9
Host: University
of North Carolina (UNC)
Organizers: Andreas
Teske - chair (UNC),
Jen
Biddle (University of Delaware),
Matt Schrenk (East Carolina University)
Scientific Conference: The theme of the
UNC meeting will be the application of novel culture-independent
and culture-dependent microbiological methods to marine sediments
and their pore fluids. By necessity, research in this arena
often focuses on enumerating cells and cataloging phylogenetic
diversity. In the coming years, however, more emphasis will
be placed on the active components of microbial communities
and the expression of functional genes. Accordingly, to diminish
misleading DNA signals from lysed and inactive cells, the
more labile RNA molecules, which occur in proportionally greater
numbers in active cells (Sørensen and Teske 2006),
can be targeted through both molecular and microscopic techniques.
The standardization of molecular (DNA and RNA-dependent) techniques,
and development of consistent protocols in sample handling
and analysis become increasingly important as divergent results
from different groups and teams require cross-checking and
reconciliation (Schippers et al. 2005 vs. Lipp et al.). Although
sequencing capabilities and costs permit ever-growing genetic
databases and an ever-growing dependence on such data, culturing
efforts are also experiencing a scientific renaissance. As
an example, the American
Academy of Microbiology recently reported that "most
environmental microorganisms have yet to be isolated and identified,
let alone rigorously studies", and that research and
technology must help overcome the barriers that prevent the
study of uncultivated microorganisms (Harwood and Buckley
2008). Culturing efforts must target individual species and
microbial communities, as well as the "effects of perturbation"
on these communities.
Education workshop: The training workshop
at this meeting will highlight methods for extracting genetic
material from sediment, porewaters, and hydrothermal fluids;
the development of nucleotide primers for functional gene
analysis; advances in cultivating novel and dominant members
of microbial communities; and ways to control for seawater
contamination in sediments and associated fluids. First, new
methods for analyzing deep subsurface communities based on
16S rRNA, instead of 16S rRNA genes (i.e. DNA), will be made
available to the DEBI community through lectures, tutorials,
and lab exercises; examples include extraction and analysis
of 16S rRNA, instead of 16S rRNA genes (i.e. DNA), and rRNA-tag
or randomly primed high-throughput pyrosequencing techniques
(Sogin et al. 2006; Huber et al. 2007). Second, expertise
in practical aspects of molecular surveys of deep-subsurface
communities will be shared. One obvious example of many is
primer development and functional gene analysis; published
generic primers are frequently insufficient for deep subsurface
studies due to lineage-specific mismatches and inherent bias
(Teske and Sorensen 2008), and due to decreased sensitivity
owing to lineage-specific nucleotide ambiguities; using multiple,
lineage-specific primers allow much more comprehensive analysis
of deep subsurface functional gene cohorts (Lever and Teske,
2007). Third, novel approaches for the enrichment of specific
functional and phylogenetic groups will be discussed and also
demonstrated as much as feasible. The approaches include sediment
microcosms, stable isotope probing, and in situ colonization
experiments. New culturing efforts are relying more heavily
on solid substrates, non-traditional redox pairs, micronutrients,
chemical gradients, and symbiotic relationships. Fourth, contamination
monitoring with chemical tracers will be taught. An approach
pioneered by Smith (Smith et al. 2000) and House (House et
al. 2003), and developed further on IODP leg 301 to the Juan
de Fuca Ridge flanks, can now be applied in microbial community
analyses of deep sediments continuing into basement basalt
(Lever and Teske 2007).
  Support
for this meeting was also provided by the U.S.
Science Support Program associated with the Integrated Ocean
Drilling Program at the Consortium for Ocean Leadership
and the NASA Astrobiology
Institute.
> See the 2011
workshop summary report
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