Fluidized muds: a novel setting for the generation of biosphere diversity through geologic time.

Reworked and fluidized fine-grained deposits in energetic settings are a major modern-day feature of river deltas and estuaries. Similar environments were probably settings for microbial evolution on the early Earth. These sedimentary systems act as efficient biogeochemical reactors with high bacterial phylogenetic diversity and functional redundancy. They are temporally rather than spatially structured, with repeated cycling of redox conditions and successive stages of microbial metabolic processes. Intense reworking of the fluidized bed entrains bacteria from varied habitats providing new, diverse genetic materials to contribute to horizontal gene transfer events and the creation of new bacterial ecotypes. These vast mud environments may act as exporters and promoters of biosphere diversity and novel adaptations, potentially on a globally important scale.

A philosophy of methods development: The assimilation of new methods and information into aquatic microbial ecology.

Emerging methodologies can be used to provide a strong basic understanding of the diversity of microbial behavior and interactions. However, these new methods should be thoroughly and rigorously validated under controlled conditions before being extended to uncontrolled field conditions. Data based on novel approaches are likely to provide insights that are not easily related to existing information based on conventional methodologies. As an example, measurements of the ribosomal RNA (rRNA) content of bacteria show similar spatial patterns as measurements of thymidine incorporation into DNA and leucine incorporation into protein. However, the spatial patterns are not identical, and these parameters are not equally intercorrelated nor equally predictable from basic oceanographic data. Therefore, rRNA content measurements provide a new dimension of information that can be used to explore the relationship of bacteria to their environment, complementing the information obtained from conventional methods.

Estimating the growth rate of slowly growing marine bacteria from RNA content.

In past studies of enteric bacteria such as Escherichia coli, various measures of cellular RNA content have been shown to be strongly correlated with growth rate. We examined this correlation for four marine bacterial isolates. Isolates were grown in chemostats at four or five dilution rates, yielding growth rates that spanned the range typically determined for marine bacterial communities in nature (mu = 0.01 to 0.25 h). All measures of RNA content (RNA cell, RNA:biovolume ratio, RNA:DNA ratio, RNA:DNA:biovolume ratio) were significantly different among isolates. Normalizing RNA content to cell volume substantially reduced, but did not eliminate, these differences. On average, the correlation between mu and the RNA:DNA ratio accounted for 94% of variance when isolates were considered individually. For data pooled across isolates (analogous to an average measurement for a community), the ratio of RNA:DNA mum (cell volume) accounted for nearly half of variance in mu (r = 0.47). The maximum RNA:DNA ratio for each isolate was extrapolated from regressions. The regression of (RNA:DNA)/(RNA:DNA)(max) on mu was highly significant (r = 0.76 for data pooled across four isolates) and virtually identical for three of the four isolates, perhaps reflecting an underlying common relationship between RNA content and growth rate. The dissimilar isolate was the only one derived from sediment. Cellular RNA content is likely to be a useful predictor of growth rate for slowly growing marine bacteria but in practice may be most successful when applied at the level of individual species.