2011 Sediment Microbiology Meeting

Next Meeting:           

Microbiology in Marine Sediments

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).



Application and registration information is forthcoming.