5S rRNA fingerprints of marine bacteria, halophilic archaea and natural prokaryotic assemblages along a salinity gradient

Natural prokaryotic assemblages from two multi-pond solar salterns and pure cultures of both marine bacteria and halophilic archaea were analyzed and compared by electrophoretic analysis of 5S rRNAs. A salinity gradient from seawater (3.7%) to NaCl precipitation (37%) was studied. The culture-indepe ndent, PCR-free, fingerprinting analysis covered two objectives: (i) to com pare natural assemblages among them and with results previously obtained th rough a PCR-dependent approach and (ii) to estimate the in situ relevance o f those prokaryotic groups obtained with classical culture methodologies. N atural assemblages were analyzed through cluster analysis of quantitative S S rRNA band patterns. The resulting groups were in accordance with environm ental parameters (i.e., NaCl concentration) and with the clustering obtaine d after a PCR-dependent approach, showing the formation of three salinity-b ased groups of samples (< 10%, 10-25% and > 25% salinity). Similarities bet ween the laboratory strains tested and dominant community members were stud ied by comparing 5S rRNA band patterns. The lack of match obtained after cl uster analysis indicated that the prokaryotic populations relevant in the p onds below 25% salinity were neither Flavobacteria nor haloarchaeal strains belonging to the genera Halococcus, Haloarcula and Halobacterium. Members of Proteobacteria and Gram-positive bacteria were found to match bands in t hese samples. The 5S rRNA fingerprint from the dominant community members i n the ponds above 30% salinity did not fit any of the cultured halophilic a rchaea studied, in agreement with earlier PCR results. This is consistent w ith a greater bias introduced by culture-dependent methods than by those ba sed on PCR, especially for archaeal populations. (C) 2000 Federation of Eur opean Microbiological Societies. Published by Elsevier Science B.V. All rig hts reserved.