Microbial community composition in fresh water at different stations

Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes was used to investigate the phylogenetic composition of bacterioplankton communities in several freshwater and marine samples. An average of about 50% of the cells were detected by probes for the domains Bacteria and Archaea. Cells were concentrated from water samples (1 to 100 ml) on white polycarbonate filters (diameter, 47 mm; pore size, 0.2 mm; type GTTP 4700 [Millipore, Eschborn, Germany]) by applying a vacuum of <25 kPa. They were subsequently fixed by covering the filter with 3 ml of a freshly prepared, phosphate-buffered saline (pH 7.2)-4% paraformaldehyde (Sigma, Deisenhofen, Germany) solution for 30 min at room temperature. Airdried filters are ready for hybridization and can be stored at 220°C or room temperature for several months without showing apparent changes. Probes BET42a, GAM42a, and PLA886 were used with competitor oligonucleotides as described previously amongst others in Manz et al., (1992; doi:10.1016/S0723-2020(11)80121-9). The filters were transferred to a vial containing 50 ml of prewarmed (48°C) washing solution (70 mM NaCl, 20 mM Tris-HCl [pH 7.4], 5 mM EDTA, 0.01% sodium dodecyl sulfate) and incubated freely floating without shaking at 48°C for 15 min. The filter sections were dried on Whatman 3M paper (Whatman Ltd., Maidstone, United Kingdom) and covered with 50 ml of DAPI solution (1 mg/ml in distilled water filtered through at 0.2-mm filter) for 5 min at room temperature in the dark. For each sample and probe, more than 500 cells were enumerated; for the DAPI examination, more than 1,500 cells were counted per sample. All probe-specific cell counts are presented as the percentage of cells visualized by DAPI. The mean abundances and standard deviations were calculated from the counts of 10 to 20 randomly chosen fields on each filter section. All counts were corrected by subtracting the counts obtained with the negative control NON338. Mean and standard deviation were calculated from the counts of 10 to 20 randomly chosen fields on each filter section.

Oxygen contents, sulfate concentrations, and changes of IPLs under different storage conditions of samples from ODP Leg 204 and IODP Expedition 311

We have studied the effects of slow infiltration of oxygen on microbial communities in refrigerated legacy samples from ocean drilling expeditions. Storage was in heat-sealed, laminated foil bags with a N2 headspace for geomicrobiological studies. Analysis of microbial lipids suggests that Bacteria were barely detectable in situ but increased remarkably during storage. Detailed molecular examination of a methane-rich sediment horizon showed that refrigeration triggered selective growth of ANME-2 archaea and a drastic change in the bacterial community. Subsequent enrichment targeting methanogens yielded exclusively methylotrophs, which were probably selected for by high sulfate levels caused by oxidation of reduced sulfur species. We provide recommendations for sample storage in future ocean drilling expeditions.

Porewater concentrations, pH, single cell number, anaerobic oxidation of methane (AOM) rate, sulfate reduction (SR) rate of samples during METEOR cruise M76/3b at the REGAB cold seep site from the West African margin in 2008

The giant pockmark REGAB (West African margin, 3160 m water depth) is an active methane-emitting cold seep ecosystem, where the energy derived from microbially mediated oxidation of methane supports high biomass and diversity of chemosynthetic communities. Bare sediments interspersed with heterogeneous chemosynthetic assemblages of mytilid mussels, vesicomyid clams and siboglinid tubeworms form a complex seep ecosystem. To better understand if benthic bacterial communities reflect the patchy distribution of chemosynthetic fauna, all major chemosynthetic habitats at REGAB were investigated using an interdisciplinary approach combining porewater geochemistry, in situ quantification of fluxes and consumption of methane, as well bacterial community fingerprinting. This study revealed that sediments populated by different fauna assemblages show distinct biogeochemical activities and are associated with distinct sediment bacterial communities. The methane consumption and methane effluxes ranged over one to two orders of magnitude across habitats, and reached highest values at the mussel habitat, which hosted a different bacterial community compared to the other habitats. Clam assemblages had a profound impact on the sediment geochemistry, but less so on the bacterial community structure. Moreover, all clam assemblages at REGAB were restricted to sediments characterized by complete methane consumption in the seafloor, and intermediate biogeochemical activity. Overall, variations in the sediment geochemistry were reflected in the distribution of both fauna and microbial communities; and were mostly determined by methane flux.

Organic matter composition and sulfate reduction intensity in Oman Margin sediments

Petrographical and geochemical studies of Neogene marine sediments from the Oman Sea (Leg 117, Sites 720, 724, 726 and 730), show a close relationship between the nature and amount of the organic matter, and the degree of degradation of organic matter by sulfate reduction, i.e. pyritization. Petrographically, three major pyritization types were observed: (1) Finely dispersed pyrite framboids in sediments from Oman Margin and Indus Fan, enriched in autochthonous marine organic matter. (2) Infilling of pores by massive pyrite crystals in Oman Margin sediments with a low TOC and a high microfossil content. (3) Pyrite mineralization of lignaceous fragments in organic-depleted sediments from the Indus Fan leading to more massive pyrite. Geochemically, we can define a sulfate reduction index (SRI) as the percentage of initial organic carbon versus that of residual organic carbon. Finely laminated Pliocene-Pleistocene sediments from the Oman Margin exclusively contain organic matter deriving from organic phytoplankton, for which the quantity (TOC) positively correlates with the geochemical quality (Hydrogen Index). We think that the occurrence of this residual organic matter is linked mainly to a high primary paleo-productivity. The intensity of sulfate reduction is constant for sediments with TOC up to 2% and becomes more important when organic input decreases. This degradation process can destroy up to 50% of the initial organic matter, but is not sufficient to explain some of the encountered very low TOC values. It can be seen that sharp increases of certain plankton species (with mineral skeletons) are responsible for a pronounced degradation of organic matter, due to increased sulfate reduction. In that case, the organic matter may be strongly degraded (high SRI), although deposited in an oxygen-depleted environment. Conversely, Miocene-Pliocene sediments contain an autochthonous organic matter that is typical of both low productivity and oxic processes; their very low sulfate reduction index indicates that very little metabolizable organic matter was initially present.