Abstract
Active sulfate-reducing microorganisms (SRM) in freshwater sediments are under-examined, despite the well-documented cryptic sulfur cycle occurring in these low-sulfate habitats. In Lake Constance sediment, sulfate reduction rates of up to 1,800 nmol cm-3 day-1 were previously measured. To characterize its SRM community, we used a tripartite amplicon sequencing approach based on 16S rRNA genes, 16S rRNA, and dsrB transcripts (encoding the beta subunit of dissimilatory sulfite reductase). We followed the respective amplicon dynamics in four anoxic microcosm setups supplemented either with (i) chitin and sulfate, (ii) sulfate only, (iii) chitin only, or (iv) no amendment. Chitin was used as a general substrate for the whole carbon degradation chain. Sulfate turnover in sulfate-supplemented microcosms ranged from 38 to 955 nmol day-1 (g sediment f. wt.)-1 and was paralleled by a decrease of 90–100% in methanogenesis as compared to the respective methanogenic controls. In the initial sediment, relative abundances of recognized SRM lineages accounted for 3.1 and 4.4% of all bacterial 16S rRNA gene and 16S rRNA sequences, respectively. When normalized against the 1.4 × 108 total prokaryotic 16S rRNA gene copies as determined by qPCR and taking multiple rrn operons per genome into account, this resulted in approximately 105–106 SRM cells (g sediment f. wt.)-1. The three amplicon approaches jointly identified Desulfobacteraceae and Syntrophobacteraceae as the numerically dominant and transcriptionally most active SRM in the initial sediment. This was corroborated in the time course analyses of sulfate-consuming sediment microcosms irrespective of chitin amendment. Uncultured dsrAB family-level lineages constituted in sum only 1.9% of all dsrB transcripts, with uncultured lineage 5 and 6 being transcriptionally most active. Our study is the first holistic molecular approach to quantify and characterize active SRM including uncultured dsrAB lineages not only in Lake Constance but for lake sediments in general.
Highlights
Lake Constance is a typical pre-alpine lake that has currently an oligotrophic status and is oxygenated down to the sediment (Güde and Straile, 2016)
The high sulfate reduction rates (SRR) at concomitant low sulfate concentrations in Lake Constance are explained by a fast and effective cycling of sulfur species between their oxidized and reduced states, which is controlled by a cryptic sulfur cycle as is typical for freshwater sediments and wetlands (Pester et al, 2012)
Our results show that sulfate-reducing microorganisms (SRM) constitute about 3% of the total bacterial sediment community with their major representatives being affiliated to the deltaproteobacterial families Desulfobacteraceae and Syntrophobacteraceae
Summary
Lake Constance is a typical pre-alpine lake that has currently an oligotrophic status and is oxygenated down to the sediment (Güde and Straile, 2016). Maximum sulfate reduction rates (SRR) as determined using 35S-SO42− as a radiotracer reached values of 1,800 nmol cm−3 day−1 at 1–2 cm sediment depth (Bak and Pfennig, 1991a). This surpasses typical SRR in sulfate-rich marine surface sediments by one order of magnitude, where sulfate reduction is one of the major anaerobic carbon degradation pathways (Jørgensen, 1982; Bowles et al, 2014). This shows that SRR are not limited by the prevailing sulfate concentrations in Lake Constance (Bak and Pfennig, 1991a; Güde and Straile, 2016), which is true for many other freshwater lakes (Holmer and Storkholm, 2001)
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