The bacterial signaling molecule, cyclic diguanosine monophosphate (c-di-GMP), plays a key role in controlling biofilm formation, organelle formation for motility, cell-cycle differentiation, and pathogenic virulence, among many other functions.(Cotter & Stibitz 2007, Hengge 2009, Romling & Amikam 2006, Schirmer & Jenal 2009, Tamayo et al. 2007) It acts by relaying extracellular signals to internal receptors, including PilZ proteins(Ko et al. 2010) as well as two different classes of riboswitches.(Kulshina et al. 2009, Lee et al. 2010, Smith et al. 2009, Smith et al. 2011, Sudarsan et al. 2008) It has widespread consequences for human health, and current research is actively exploring its molecular mechanisms. The convenient one-flask, gram-scale synthesis of c-di-GMP described here will facilitate these efforts.
Stable isotope analyses are increasingly employed to characterise population niche widths. The convex hull area (TA) in a δ13C–δ15N biplot has been used as a measure of isotopic niche width, but concerns exist over its dependence on sample size and associated difficulties in among-population comparisons. Recently a more robust method was proposed for estimating and comparing isotopic niche widths using standard ellipse areas (SEA), but this approach has yet to be tested with empirical stable isotope data. The two methods measure different kind of isotopic niche areas, but both are now widely used to characterise isotopic niche widths of populations. We used simulated data and an extensive empirical dataset from two fish populations to test the influence of sample size on the observed isotopic niche widths (TA and SEA). We resampled the original datasets to generate 5000 new samples for different numbers of observations from 5 to 80 to examine the statistical distributions of niche area estimates for increasing sample size. Our results illustrate how increasing sample size increased the observed TA; even sample sizes much higher than n = 30 did not improve the precision for the TA method. SEA was less sensitive to sample size, but the natural variation in our empirical fish δ13C and δ15N data still resulted in considerable uncertainty around the mean estimates of niche width, reducing the precision particularly with sample sizes n<30. These results confirm that the TA method is less appropriate for estimating population isotopic niche areas using small samples, especially when considerable population level isotope variation is expected. The results also indicate a need for caution when using SEA as a measure of trophic niche widths for consumers, particularly with low sample sizes and when the distribution and range for population isotope values are not known.
Nutrient limitation and resource competition in bacterial and phytoplankton communities may appear different when considering different levels of taxonomic resolution. Nutrient amendment experiments conducted in a boreal lake on three occasions during one open water season revealed complex responses in overall bacterioplankton and phytoplankton abundance and biovolume. In general, bacteria were dominant in spring, while phytoplankton was clearly the predominant group in autumn. Seasonal differences in the community composition of bacteria and phytoplankton were mainly related to changes in observed taxa, while the differences across nutrient treatments within an experiment were due to changes in relative contributions of certain higher- and lower-level phylogenetic groups. Of the main bacterioplankton phyla, only Actinobacteria had a treatment response that was visible even at the phylum level throughout the season. With increasing resolution (from 75 to 99% sequence similarity) major responses to nutrient amendments appeared using 454 pyrosequencing data of 16S rRNA amplicons. This further revealed that OTUs (defined by 97% sequence similarity) annotated to the same highly resolved freshwater groups appeared to occur during different seasons and were showing treatment-dependent differentiation, indicating that OTUs within these groups were not ecologically coherent. Similarly, phytoplankton species from the same genera responded differently to nutrient amendments even though biovolumes of the majority of taxa increased when both nitrogen and phosphorus were added simultaneously. The bacterioplankton and phytoplankton community compositions showed concurrent trajectories that could be seen in synchronous succession patterns over the season. Overall, our data revealed that the response of both communities to nutrient changes was highly dependent on season and that contradictory results may be obtained when using different taxonomic resolutions.