We investigated the microbial pathways of nitrogen (N) loss in an April 2005 transect through the Peruvian oxygen minimum zone (OMZ) at 12uS latitude using short anaerobic incubations with 15 N-labeled substrates and molecular-ecological and lipid-biomarker studies. In incubations with 15 NH z 4 , immediate production of 14 N 15 N, but not 15 N 15 N, indicated that N 2 was produced by the pairing of labeled 15 NH z 4 with in situ 14 NO { 2 via anaerobic ammonium oxidation (anammox). Supporting this finding, we also found anammox-related 16S ribosomal ribonucleic acid gene sequences similar to those previously known from other marine water columns in which anammox activity was measured. We identified and enumerated anammox bacteria via fluorescence in situ hybridization and quantitative polymerase chain reaction and found ladderane membrane lipids specific to anammox bacteria wherever anammox activity was measured by our isotope tracer method. However, in incubations with 15 NO { 3 or 15 NO { 2 , in which denitrification would have been expected to produce 15 N 15 N by pairing of oxidized 15 N ions, 15 N 15 N production was not detected before 24 h, showing that denitrification of fixed N to N 2 was not taking place in our samples. At the time and locality of our study, anammox, rather than denitrification, was responsible for N 2 production in the Peruvian OMZ waters.

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The Black Sea is the world's largest anoxic basin and a model system for studying processes across redox gradients. In between the oxic surface and the deeper sulfidic waters there is an unusually broad layer of 10-40 m, where neither oxygen nor sulfide are detectable. In this suboxic zone, dissolved phosphate profiles display a pronounced minimum at the upper and a maximum at the lower boundary, with a peak of particulate phosphorus in between, which was suggested to be caused by the sorption of phosphate on sinking particles of metal oxides. Here we show that bacterial polyphosphate inclusions within large magnetotactic bacteria related to the genus Magnetococcus contribute substantially to the observed phosphorus peak, as they contain 26-34% phosphorus compared to only 1-5% in metal-rich particles. Furthermore, we found increased gene expression for polyphosphate kinases by several groups of bacteria including Magnetococcaceae at the phosphate maximum, indicating active bacterial polyphosphate degradation. We propose that large magnetotactic bacteria shuttle up and down within the suboxic zone, scavenging phosphate at the upper and releasing it at the lower boundary. In contrast to a passive transport via metal oxides, this bacterial transport can quantitatively explain the observed phosphate profiles.

An analysis of the microbial metabolism is fundamental to understanding globally important element transformations. One culture-independent approach to deduce those prokaryotic metabolic functions is to analyze metatranscriptomes. Unfortunately, since mRNA is extremely labile, it is unclear whether the abundance patterns detected in nature are vulnerable to considerable modification in situ simply due to sampling procedures. Exemplified on comparisons of metatranscriptomes retrieved from pelagic suboxic zones of the central Baltic Sea (70-120 m depth), earlier identified as areas of high aerobic ammonium oxidation activity, and quantification of specific transcripts in them, we show that different sampling techniques significantly influence the relative abundance of transcripts presumably diagnostic of the habitat. In situ fixation using our newly developed automatic flow injection sampler resulted in an abundance of thaumarchaeal ammonia monooxygenase transcripts that was up to 30-fold higher than that detected in samples obtained using standard oceanographic sampling systems. By contrast, the abundance of transcripts indicative of cellular stress was significantly greater in non-fixed samples. Thus, the importance of in situ fixation in the reliable evaluation of distinct microbial activities in the ecosystem based on metatranscriptomics is obvious. In consequence, our data indicate that the significance of thaumarchaeota to aerobic ammonium oxidation could yet have been considerably underestimated. Taken these results, this could in general also be the case in attempts aimed at an unbiased gene expression analysis of areas below the epipelagic zone, which cover 90% of the world's oceans. The ISME Journal (2012) 6, 461-470; doi:10.1038/ismej.2011.94; published online 21 July 2011 Subject Category: microbial ecology and functional diversity of natural habitats

It is a great challenge to sample seawater across interfaces, for example the halocline or the redoxcline, to investigate trace metal distribution. With the use of 10l sampling bottles mounted to a wire or a CTD-Rosette it is possible to obtain a maximum vertical resolution of 5m. For the detection of small vertical structures in the vertical distribution of trace metals across the redoxcline, the CTD-Bottle-Rosette is not sufficient. Therefore, a PUMP-CTD-System was developed, which enables water sampling with high resolution (1m maximum) along a vertical profile. To investigate the suitability and possible contamination sources of this device two experiments were carried out in the Gotland Basin. The first experiment consisted of two separate profiles. The first profile was obtained with the CTD-Bottle-Rosette and the second with the PUMP-CTD-System. Both were taken from the bottom to the surface water layer. The second experiment was a combined profile obtained from the surface to the bottom with the PUMP-CTD-System attached to the CTD-Bottle-Rosette. Concentrations of dissolved Pb, Cd, Cu, Zn, Fe, Mn, Co and Ni from the "Niskin Bottles" and from the PUMP were measured and compared for each investigation. We demonstrate that it is useful to perform vertical sampling from lower to higher concentrations, e.g. surface to bottom in this environment, and that a longer flushing is required for sampling seawater in the anoxic bottom water. A comparison of the two systems for oxygen and hydrogen sulphide measurements showed an improvement of the precision and the quality of the sampling when using the PUMP. Thus, metal speciation at the oxic-anoxic gradient zone and on a high vertical resolution will be accessible. As concentrations of dissolved Pb, Cd, Cu, Zn, Co, Ni, Fe and Mn in seawater sampled with both devices were in the same range, we conclude that the PUMP-CTD-System is well suited to sample seawater for trace metal analyses.