The importance of microorganisms in tropical mobile deltaic sediments was examined in the present study using an array of cultivation-independent techniques. Sediments from tropical coastal mobile mud environments used in this study differ from typical marine sulfidogenic sediments in that they often exhibit no net sulfide production over extensive depth intervals. Although oxygen penetrates only a few mm below the sediment surface, physical mixing as a result of tidal currents, seasonal winds and local geomorphologic features, periodically reoxidize them to a depth of >1 m. This reoxidized layer passes through oxic and NO3− reducing conditions within a day followed by Mn reduction stages for several weeks before remaining in a suboxic Fe reduction stage for up to a year after which they become sulfidic. The retrieval of 16S rRNA gene sequences hinted at the presence of bacteria potentially involved in chemolithoautotrophic CO2 fixation and sulfur cycles. Direct evidence of sulfate reduction was found by 35 SO4 radiotracer experiments and detection and quantification of genes encoding dissimilatory sulfite reductase (dsr), one of the key enzymes involved in sulfate reduction. Dsr genes in these mobile muds are highly diverse and a large percentage of sequences are distantly related to dsr sequences of sulfate reducing prokaryotes. Approximately 20% of the retrieved dsr sequences belonged with a cluster of widespread environmental sequences with no known cultured representative. Chemolithotrophic potential was examined by characterization of RubisCO sequences, the major pathway for CO2 fixation. Based on the relatedness of cbbL and cbbM sequences from these sediments and cultured chemolithoautotrophic bacteria, we suggest that the following physiological groups of autotrophic microorganisms are present: (a) anaerobic sulfur and sulfide oxidizers, (b) microaerophilic hydrogen- and iron-oxidizing bacteria, (c) water column aerobic organisms entrapped during mixing. Direct evidence of the occurrence of chemolithoautotrophy is provided by gene expression analysis of RubisCO genes and evidence for sulfate reduction is provided by dsr gene expression analysis. The CO2 fixation potential, as shown by the high expression levels of RubisCOs, especially in French Guiana muds, seems to be large. Interestingly, dsr gene copy number and gene expression levels, although not as high as RubisCOs, are comparable to other sulfidic sedimentary environments. Correlations found between rare RubisCO form II versus ∑CO2; and dsr transcripts versus Fe (II) indicate that gene expression may be regulated by geochemical gradients. Overall, the correlations found between mRNA transcripts and geochemical parameters suggest that gene expression may be regulated by a combination of erosion/redeposition events and chemical gradients in these nonsulfidic unsteady systems.
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