Bo Barker Jørgensen

Anaerobic ammonium oxidation by anammox bacteria in the Black Sea

The availability of fixed inorganic nitrogen (nitrate, nitrite and ammonium) limits primary productivity in many oceanic regions. The conversion of nitrate to N2 by heterotrophic bacteria (denitrification) is believed to be the only important sink for fixed inorganic nitrogen in the ocean. Here we provide evidence for bacteria that anaerobically oxidize ammonium with nitrite to N2 in the worlds largest anoxic basin, the Black Sea. Phylogenetic analysis of 16S ribosomal RNA gene sequences shows that these bacteria are related to members of the order Planctomycetales performing the anammox (anaerobic ammonium oxidation) process in ammonium-removing bioreactors. Nutrient profiles, fluorescently labelled RNA probes, 15N tracer experiments and the distribution of specific ‘ladderane’ membrane lipids indicate that ammonium diffusing upwards from the anoxic deep water is consumed by anammox bacteria below the oxic zone. This is the first time that anammox bacteria have been identified and directly linked to the removal of fixed inorganic nitrogen in the environment. The widespread occurrence of ammonium consumption in suboxic marine settings indicates that anammox might be important in the oceanic nitrogen cycle.

Microelectrodes: Their Use in Microbial Ecology

Among the fundamental goals of microbial ecology is the development of methods that will enable the identification and counting of the important microorganisms in nature, the determination of their physical and chemical microenvironment, and the analysis of their metabolic processes and interactions. Due to the small size of the organisms, much effort has been devoted to the development of high-resolution techniques for the observation and understanding of the world of bacteria on a microscale. Scanning and transmission electron microscopy and fluorescent staining, immunofluorescence and other techniques for light microscopy have been the most successful in terms of reaching a high spatial resolution. With respect to our understanding of the microbial microenvironments and of the nature of the microorganisms that carry out the measured metabolic activities, there is still a long way to go. Most chemical and radiotracer techniques in use today operate on a centimeter or at best on a millimeter scale and in most cases their results cannot be directly related to the relevant microorganisms. One notable exception to this is the combined use of autoradiography and fluorescence microscopy on microbial communities.

Measurement of bacterial sulfate reduction in sediments: Evaluation of a single-step chromium reduction method

A procedure which includes the Total Reduced Inorganic Sulfur (TRIS) in a single distillation step is described for the radiotracer measurement of sulfate reduction in sediments. The TRIS includes both Acid Volatile Sulfide (AVS: H2S + FeS) and the remaining Chromium Reducible Sulfur (CRS: S0, FeS2). The single-step distillation was simpler and faster than the consecutive distillations of AVS and CRS. It also resulted in higher (4–50%) sulfate reduction rates than those obtained from the sum of35S in AVS and CRS. The difference was largest when the sediment had been dried after AVS but before CRS distillation. Relative to the35S-AVS distillation alone, the35S-TRIS single-step distallation yielded 8–87% higher reduction rates. The separation and recovery of FeS, S0 and FeS2 was studied under three distillation conditions: 1) cold acid, 2) cold acid with Cr2+, and 3) hot acid with Cr2+. The FeS was recovered by cold acid alone while pyrite was recovered by cold acid with Cr2+. A smaller S0 fraction, presumably of the finer crystal sizes, was recovered also in the cold acid with Cr2+ while most of the S0 required hot acid with Cr2+ for reduction to H2S.

Pathways of organic carbon oxidation in three continental margin sediments

We have combined several different methodologies to quantify rates of organic carbon mineralization by the various electron acceptors in sediments from the coast of Denmark and Norway. Rates of NH4+ and Sigma CO2 liberation sediment incubations were used with O2 penetration depths to conclude that O2 respiration accounted for only between 3.6-17.4% of the total organic carbon oxidation. Dentrification was limited to a narrow zone just below the depth of O2 penetration, and was not a major carbon oxidation pathway. The processes of Fe reduction, Mn reduction and sulfate reduction dominated organic carbon mineralization, but their relative significance varied depending on the sediment. Where high concentrations of Mn-oxide were found (3-4 wt% Mn), only Mn reduction occurred. With lower Mn oxide concentrations more typical of coastal sediments, Fe reduction and sulfate reduction were most important and of a similar magnitude. Overall, most of the measured O2 flux into the sediment was used to oxidized reduced inorganic species and not organic carbon. We suspect that the importance of O2 respiration in many coastal sediments has been overestimated, whereas metal oxide reduction (both Fe and Mn reduction) has probably been well underestimated.

Manganese, iron and sulfur cycling in a coastal marine sediment, Aarhus bay, Denmark

The seasonal variation in oxidized and reduced pools of Mn, Fe and S, as well as the rates of SO42− reduction, were studied in a fine-grained sediment. Below the 1–5 mm thick oxic zone, a zone of net Mn reduction extended to 1–2 cm depth, while iron reduction was found to 4–6 cm depth. Although the reactive Mn oxide pool was ten times smaller than the reactive Fe(III) pool, the average ratio between depth gradients of Fe and Mn oxides was only 1.7, which implied that rates of Mn and Fe reduction were similar. Sulfate reduction was maximal near the bottom of the suboxic zone, but fine-scale measurements showed that it extended to the upper 0–2.5 mm during summer, when the zones of Mn and Fe reduction were compressed towards the surface. Most of the H2S produced precipitated as iron sulfides and S0 by reaction with Fe. Both Fe(III) and a nonsulfur-bound authigenic Fe(II) pool reacted efficiently with H2S. The authigenic Fe(II) pool was present at one hundredfold higher concentration than dissolved Fe2+. Only 15% of the precipitated sulfide was buried permanently. Most of the reoxidation of reduced S occurred within 1 cm of the sediment-water interface and was supported by upward bioturbation. All of the estimated Mn reduction could be coupled to the reoxidation of reduced S and Fe. Partial oxidation of H2S, forming S0 and pyrite, accounted for 63% of the estimated Fe reduction. The remaining Fe reduction was coupled to complete oxidation of reduced S or to C mineralization. The settling of a diatom spring bloom caused distinct maxima in SRR and Mn2+ at 0.5–1 cm depth within two weeks. In autumn, the reactive Mn oxides were depleted due to a net release of Mn2+ to the water column. Thus, the Mn cycle extended significantly into the water column, while a constant Fe pool over the year suggests that the Fe cycle was restricted to the sediment.

Coral mucus functions as an energy carrier and particle trap in the reef ecosystem

Zooxanthellae, endosymbiotic algae of reef-building corals, substantially contribute to the high gross primary production of coral reefs, but corals exude up to half of the carbon assimilated by their zooxanthellae as mucus. Here we show that released coral mucus efficiently traps organic matter from the water column and rapidly carries energy and nutrients to the reef lagoon sediment, which acts as a biocatalytic mineralizing filter. In the Great Barrier Reef, the dominant genus of hard corals, Acropora, exudes up to 4.8 litres of mucus per square metre of reef area per day. Between 56% and 80% of this mucus dissolves in the reef water, which is filtered through the lagoon sands. Here, coral mucus is degraded at a turnover rate of at least 7% per hour. Detached undissolved mucus traps suspended particles, increasing its initial organic carbon and nitrogen content by three orders of magnitude within 2 h. Tidal currents concentrate these mucus aggregates into the lagoon, where they rapidly settle. Coral mucus provides light energy harvested by the zooxanthellae and trapped particles to the heterotrophic reef community, thereby establishing a recycling loop that supports benthic life, while reducing loss of energy and nutrients from the reef ecosystem.

Feast and famine--microbial life in the deep-sea bed.

The seabed is a diverse environment that ranges from the desert-like deep seafloor to the rich oases that are present at seeps, vents, and food falls such as whales, wood or kelp. As well as the sedimentation of organic material from above, geological processes transport chemical energy — hydrogen, methane, hydrogen sulphide and iron — to the seafloor from the subsurface below, which provides a significant proportion of the deep-sea energy. At the sites on the seafloor where chemical energy is delivered, rich and diverse microbial communities thrive. However, most subsurface microorganisms live in conditions of extreme energy limitation, with mean generation times of up to thousands of years. Even in the most remote subsurface habitats, temperature rather than energy seems to set the ultimate limit for life, and in the deep biosphere, where energy is most depleted, life might even be based on the cleavage of water by natural radioisotopes. Here, we review microbial biodiversity and function in these intriguing environments.

A thiosulfate shunt in the sulfur cycle of marine sediments

The oxidation of sulfide, generated by bacterial sulfate reduction, is a key process in the biogeochemistry of marine sediments, yet the pathways and oxidants are poorly known. By the use of 35S-tracer studies of the S cycle in marine and freshwater sediments, a novel shunt function of thiosulfate (S2O32-) was identified. The S2O32- constituted 68 to 78 percent of the immediate HS--oxidation products and was concurrently (i) reduced back to HS-, (ii) oxidized to SO42-, and (iii) disproportionated to HS- + SO42-. The small thiosulfate pool is thus involved in a dynamic HS- - S2O32- cycle in anoxic sediments. The disproportionation of thiosulfate may help account for the large difference in isotopic composition (34S/32S) of sulfate and sulfides in sediments and sedimentary rocks.

Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria

Chemical analyses of the pore waters from hundreds of deep ocean sediment cores have over decades provided evidence for ongoing processes that require biological catalysis by prokaryotes. This sub-seafloor activity of microorganisms may influence the surface Earth by changing the chemistry of the ocean and by triggering the emission of methane, with consequences for the marine carbon cycle and even the global climate. Despite the fact that only about 1% of the total marine primary production of organic carbon is available for deep-sea microorganisms, sub-seafloor sediments harbour over half of all prokaryotic cells on Earth. This estimation has been calculated from numerous microscopic cell counts in sediment cores of the Ocean Drilling Program. Because these counts cannot differentiate between dead and alive cells, the population size of living microorganisms is unknown. Here, using ribosomal RNA as a target for the technique known as catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH), we provide direct quantification of live cells as defined by the presence of ribosomes. We show that a large fraction of the sub-seafloor prokaryotes is alive, even in very old (16 million yr) and deep (> 400 m) sediments. All detectable living cells belong to the Bacteria and have turnover times of 0.25–22 yr, comparable to surface sediments.

Deep sub-seafloor prokaryotes stimulated at interfaces over geological time

The sub-seafloor biosphere is the largest prokaryotic habitat on Earth but also a habitat with the lowest metabolic rates. Modelled activity rates are very low, indicating that most prokaryotes may be inactive or have extraordinarily slow metabolism. Here we present results from two Pacific Ocean sites, margin and open ocean, both of which have deep, subsurface stimulation of prokaryotic processes associated with geochemical and/or sedimentary interfaces. At 90 m depth in the margin site, stimulation was such that prokaryote numbers were higher (about 13-fold) and activity rates higher than or similar to near-surface values. Analysis of high-molecular-mass DNA confirmed the presence of viable prokaryotes and showed changes in biodiversity with depth that were coupled to geochemistry, including a marked community change at the 90-m interface. At the open ocean site, increases in numbers of prokaryotes at depth were more restricted but also corresponded to increased activity; however, this time they were associated with repeating layers of diatom-rich sediments (about 9 Myr old). These results show that deep sedimentary prokaryotes can have high activity, have changing diversity associated with interfaces and are active over geological timescales.