Analysis of Subfossil Molecular Remains of Purple Sulfur Bacteria in a Lake Sediment

Abstract

ABSTRACTMolecular remains of purple sulfur bacteria (Chromatiaceae) were detected in Holocene sediment layers of a meromictic salt lake (Mahoney Lake, British Columbia, Canada). The carotenoid okenone and bacteriophaeophytinawere present in sediments up to 11,000 years old. Okenone is specific for only a few species ofChromatiaceae, includingAmoebobacter purpureus, which presently predominates in the chemocline bacterial community of the lake. With a primer set specific forChromatiaceaein combination with denaturing gradient gel electrophoresis, 16S rRNA gene sequences of four differentChromatiaceaespecies were retrieved from different depths of the sediment. One of the sequences, which originated from a 9,100-year-old sample, was 99.2% identical to the 16S rRNA gene sequence ofA. purpureusML1 isolated from the chemocline. Employing primers specific forA. purpureusML1 and dot blot hybridization of the PCR products, the detection limit forA. purpureusML1 DNA could be lowered to 0.004% of the total community DNA. With this approach the DNA of the isolate was detected in 7 of 10 sediment layers, indicating thatA. purpureusML1 constituted at least a part of the ancient purple sulfur bacterial community. The concentrations ofA. purpureusDNA and okenone in the sediment were not correlated, and the ratio of DNA to okenone was much lower in the subfossil sediment layers (2.7 · 10−6) than in intact cells (1.4). This indicates that degradation rates are significantly higher for genomic DNA than for hydrocarbon cell constituents, even under anoxic conditions and at the very high sulfide concentrations present in Mahoney Lake.