Lars Holmkvist

Sulfate-reducing bacteria in marine sediment (Aarhus Bay, Denmark): abundance and diversity related to geochemical zonation

In order to better understand the main factors that influence the distribution of sulfate-reducing bacteria (SRB), their population size and their metabolic activity in high- and low-sulfate zones, we studied the SRB diversity in 3- to 5-m-deep sediment cores, which comprised the entire sulfate reduction zone and the upper methanogenic zone. By combining EMA (ethidium monoazide that can only enter damaged/dead cells and may also bind to free DNA) treatment with real-time PCR, we determined the distributions of total intact bacteria (16S rDNA genes) and intact SRB (dsrAB gene), their relative population sizes, and the proportion of dead cells or free DNA with depth. The abundance of SRB corresponded in average to 13% of the total bacterial community in the sulfate zone, 22% in the sulfate-methane transition zone and 8% in the methane zone. Compared with the total bacterial community, there were relatively less dead/damaged cells and free DNA present than among the SRB and this fraction did not change systematically with depth. By DGGE analysis, based on the amplification of the dsrA gene (400 bp), we found that the richness of SRB did not change with depth through the geochemical zones; but the clustering was related to the chemical zonation. A full-length clone library of the dsrAB gene (1900 bp) was constructed from four different depths (20, 110, 280 and 500 cm), and showed that the dsrAB genes in the near-surface sediment (20 cm) was mainly composed of sequences close to the Desulfobacteraceae, including marine complete and incomplete oxidizers such as Desulfosarcina, Desulfobacterium and Desulfococcus. The three other libraries were predominantly composed of Gram-positive SRB.

Physiology and behaviour of marine Thioploca

Among prokaryotes, the large vacuolated marine sulphur bacteria are unique in their ability to store, transport and metabolize significant quantities of sulphur, nitrogen, phosphorus and carbon compounds. In this study, unresolved questions of metabolism, storage management and behaviour were addressed in laboratory experiments with Thioploca species collected on the continental shelf off Chile. The Thioploca cells had an aerobic metabolism with a potential oxygen uptake rate of 1760 μmol O2 per dm3 biovolume per h, equivalent to 4.4 nmol O2 per min per mg protein. When high ambient sulphide concentrations (∼200 μM) were present, a sulphide uptake of 6220±2230 μmol H2S per dm3 per h, (mean±s.e.m., n=4) was measured. This sulphide uptake rate was six times higher than the oxidation rate of elemental sulphur by oxygen or nitrate, thus indicating a rapid sulphur accumulation by Thioploca. Thioploca reduce nitrate to ammonium and we found that dinitrogen was not produced, neither through denitrification nor through anammox activity. Unexpectedly, polyphosphate storage was not detectable by microautoradiography in physiological assays or by staining and microscopy. Carbon dioxide fixation increased when nitrate and nitrite were externally available and when organic carbon was added to incubations. Sulphide addition did not increase carbon dioxide fixation, indicating that Thioploca use excess of sulphide to rapidly accumulate sulphur rather than to accelerate growth. This is interpreted as an adaptation to infrequent high sulphate reduction rates in the seabed. The physiology and behaviour of Thioploca are summarized and the adaptations to an environment, dominated by infrequent oxygen availability and periods of high sulphide abundance, are discussed.

Lipid Biomarker Patterns of Phosphogenic Sediments from Upwelling Regions

Sediments of upwelling regions off Namibia, Peru, and Chile contain dense populations of large nitrate-storing sulfide-oxidizing bacteria, Thiomargarita, Beggiatoa, and Thioploca. Increased contents of monounsaturated C16 and C18 fatty acids have been found at all stations studied, especially when a high density of sulfide oxidizers in the sediments was observed. The distribution of lipid biomarkers attributed to sulfate reducers (10MeC16:0 fatty acid, ai-C15:0 fatty acid, and mono-O-alkyl glycerol ethers) compared to the distribution of sulfide oxidizers indicate a close association between these bacteria. As a consequence, the distributions of sulfate reducers in sediments of Namibia, Peru, and Chile are closely related to differences in the motility of the various sulfide oxidizers at the three study sites. Depth profiles of mono-O-alkyl glycerol ethers have been found to correlate best with the occurrence of large sulfide-oxidizing bacteria. This suggests a particularly close link between mono-O-alkyl glycerol ether-synthesizing sulfate reducers and sulfide oxidizers. The interaction between sulfide-oxidizing bacteria and sulfate-reducing bacteria reveals intense sulfur cycling and degradation of organic matter in different sediment depths.