Bacterial activity and genetic richness along an estuarine gradient (Rhone River plume, France)

Abstract

Bacterial diversity and activity were simultaneously investigated by microbial ecological and molecular biological methods along an estuarine gradient from the Rhone River to the Mediterranean Sea. Following a Lagrangian strategy, we sampled plume, frontal and marine layers. The sampled estuarine gradient exhibited large changes both in physico-chemical and in microbiological characteristics. Bacterial abundances and activities showed a more drastic decrease in the low salinity range of the gradient than expected from simple dilution models, indicating that an important fraction of freshwater bacteria disappeared in the mixing area. High specific activities, in particular for leucine, in the marine end-part of the gradient suggested important bacterial protein synthesis, which may be a sign of an active survival strategy for bacterial communities subjected to oligotrophic conditions. Bacterial genetic diversity of the sampled estuarine area, as estimated by the number of DNA-derived denaturing gradient gel electrophoresis (DGGE) bands, was high (13 to 55 bands) compared to that reported in other aquatic ecosystems. This high diversity may be the consequence of the interface position of estuaries. The proportion of active populations was estimated using the ratio of DGGE bands derived from RNA and DNA. This ratio was lower in Rhone water than in marine water, indicating that only a part of the constitutive populations were active, while the activity was distributed within a larger fraction of populations in the marine assemblage. Very few DGGE bands detected in freshwater samples were also detected in the marine end-part of the gradient, suggesting that a very limited number of freshwater bacteria could survive under marine conditions. Detection of these freshwater populations from RNA might indicate that these bacteria were able to synthesize different stress proteins as the result of a survival strategy or that these bacteria were able to maintain metabolic activity under marine conditions. The structure of marine communities was strongly affected by decreasing salinity. However, it seems that the decrease of DNAderived bands may simply have been the consequence of the mixing of marine and freshwater. No obvious relationship between genetic richness and activity changes was observed. This lack of a relationship may be the consequence of a very short residence time of water in the mixing area studied.

Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu

“…Furthermore, higher abundance of AOA was shown in the bulk community in comparison to the potentially active community. Such discrepancy between DNA-and RNA-based studies of surface waters has also been observed in freshwater ecosystems [4,68]. The denitrification genes nirK and nosZ were slightly higher in the oxic zone than in the anoxic zone (Fig.…”

Pyrosequencing reveals contrasting seasonal dynamics of taxa within Baltic Sea bacterioplankton communities

“…Freshwater and marine bacterioplankton communities typically show limited overlap in composition (Troussellier et al, 2002;Selje and Simon, 2003), whereas estuaries appear as mixing zones. However, given the location of the sampling station far from any river mouth, direct influence of advected freshwater bacteria on the indigenous bacterioplankton community is unlikely (Riemann et al, 2008).…”

Activity profiles for marine sponge-associated bacteria obtained by 16S rRNA vs 16S rRNA gene comparisons

“…However, other techniques are more appropriate in situations requiring high sample numbers, for example when examining biological and/or environmental variability. Fortunately, the DNA vs RNA approach is equally applicable to high-throughput community fingerprinting techniques such as denaturing gradient gel electrophoresis Troussellier et al, 2002), terminal restriction fragment length polymorphism (T-RFLP) ) and single-stranded conformational polymorphism (SSCP) (West et al, 2008;Rodriguez-Blanco et al, 2009). It could also be used in conjunction with next-generation sequencing methods such as tag pyrosequencing (Sogin et al, 2006;Huse et al, 2008).…”

“…The analysis of 16S rRNA genes through clone libraries and fingerprinting approaches such as denaturing gradient gel electrophoresis (DGGE) has greatly extended our knowledge about the phylogenetic richness of sponge-associated bacteria and archaea (Webster et al, 2001(Webster et al, , 2004Hentschel et al, 2002;Taylor et al, 2004Taylor et al, , 2007bHolmes and Blanch, 2006;Longford et al, 2007;Schmitt et al, 2007Schmitt et al, , 2008Thiel et al, 2007;Mohamed et al, 2008b;Zhu et al, 2008). Researchers in other systems have taken this approach one step further, yielding insights into both richness and activity by comparing 16S rRNA gene-and 16S rRNA-derived sequences, respectively (Moeseneder et al, , 2005Winter et al, 2001;Troussellier et al, 2002;Mills et al, 2005;Gentile et al, 2006;Martinez et al, 2006;Brinkmann et al, 2008;McIlroy et al, 2008;West et al, 2008;Rodriguez-Blanco et al, 2009). In general, cellular concentrations of rRNA are correlated with growth rate and activity (DeLong et al, 1989;Poulsen et al, 1993), hence-with acknowledgement of certain caveats (e.g., for ammoniaoxidizing bacteria; Morgenroth et al, 2000)-the rRNA itself can yield useful information about which community members are active.…”