Diversity, activity, and abundance of sulfate-reducing bacteria in saline and hypersaline soda lakes

Abstract

Soda lakes are naturally occurring highly alkaline and saline environments. Although the sulfur cycle is one of the most active element cycles in these lakes, little is known about the sulfate-reducing bacteria (SRB). In this study we investigated the diversity, activity, and abundance of SRB in sediment samples and enrichment cultures from a range of (hyper)saline soda lakes of the Kulunda Steppe in southeastern Siberia in Russia. For this purpose, a polyphasic approach was used, including denaturing gradient gel electrophoresis of dsr gene fragments, sulfate reduction rate measurements, serial dilutions, and quantitative real-time PCR (qPCR). Comparative sequence analysis revealed the presence of several novel clusters of SRB, mostly affiliated with members of the order Desulfovibrionales and family Desulfobacteraceae. We detected sulfate reducers and observed substantial sulfate reducing rates (between 12 and 423 micromol/dm(3) day(-1)) for most lakes, even at a salinity of 475 g/liter. Enrichments were obtained at salt saturating conditions (4 M Na(+)), using H(2) or volatile fatty acids as electron donors, and an extremely halophilic SRB, strain ASO3-1, was isolated. Furthermore, a high dsr gene copy number of 10(8) cells per ml was detected in a hypersaline lake by qPCR. Our results indicate the presence of diverse and active SRB communities in these extreme ecosystems.

FIG. 1.

DGGE analysis of the partial dsrB gene fragments from sediment samples of different soda lakes from the Kulunda Steppe (southwestern Siberia, Russia). Lane 1, 1KL; lane 2, 2KL; lane 3, 3KL; lane 4, 4KL; lane 5, 5KL; lane 6, 6KL; lane 7, 9KL; lane 8, 10KL; lane 9, 11KL; lane 10, 16KL (see Table 1 for more information on the soda lakes). Bands indicated by a white circle and number were excised from the gel and sequenced.

FIG. 2.

Consensus phylogenetic tree based on amino acid sequences of the dsrAB gene. The partial sequences determined in this study are in bold type. They were added to the tree using the QUICK_ADD parsimony tool and individually removed to avoid long branch attraction. Deletions and insertions were not included in the calculation. Branching orders that were not supported by all tree construction methods are shown as multiforcations. The band number (Fig. 1) is preceded by the lake number (Table 1) for sediment samples. For enrichment samples, the following code was used: E_H₂/VFA/EtOH (ethanol [EtOH]) (electron donor)_1/2 (total Na⁺ [in molar concentration])_E/HDE/HDO/LDO (type of enrichment). E stands for enrichment obtained by regular transfers of an incubation that was originally inoculated with the sediment mixture sample. HDE are enrichments that were obtained by regular transfer of the highest positive dilution of the initial sediment incubation at that specific condition, whereas HDO and LDO are the first enrichments with the highest and the lowest positive dilutions, respectively, in which the original sediment sample was used as inoculum.

FIG. 3.

Abundance of the SRB in sediment samples by qPCR. (A) Standard curve for qPCR measurements of the dsr gene. The standard curve was calculated on the basis of a partially dsrB purified PCR product of known copy number. (B) SRB abundance (logarithmic scale) in the different soda lakes. Error bars represent standard deviations.