Fatty acids and intact polar lipids of laminated microbial sediments from St. Peter Ording, German Wadden Sea

Hidden for the untrained eye through a thin layer of sand, laminated microbial sediments occur in supratidal beaches along the North Sea coast. The inhabiting microbial communities organize themselves in response to vertical gradients of light, oxygen or sulfur compounds. We performed a fine-scale investigation on the vertical zonation of the microbial communities using a lipid biomarker approach, and assessed the biogeochemical processes using a combination of microsensor measurements and a 13C-labeling experiment. Lipid biomarker fingerprinting showed the overarching importance of cyanobacteria and diatoms in these systems, and heterocyst glycolipids revealed the presence of diazotrophic cyanobacteria even in 9 to 20 mm depth. High abundance of ornithine lipids (OL) throughout the system may derive from sulfate reducing bacteria, while a characteristic OL profile between 5 and 8 mm may indicate presence of purple non-sulfur bacteria. The fate of 13C-labeled bicarbonate was followed by experimentally investigating the uptake into microbial lipids, revealing an overarching importance of cyanobacteria for carbon fixation. However, in deeper layers, uptake into purple sulfur bacteria was evident, and a close microbial coupling could be shown by uptake of label into lipids of sulfate reducing bacteria in the deepest layer. Microsensor measurements in sediment cores collected at a later time point revealed the same general pattern as the biomarker analysis and the labeling experiments. Oxygen and pH-microsensor profiles showed active photosynthesis in the top layer. The sulfide that diffuses from deeper down and decreases just below the layer of active oxygenic photosynthesis indicates the presence of sulfur bacteria, like anoxygenic phototrophs that use sulfide instead of water for photosynthesis.

Studies of the microbial diversity on analyzed samples from from Peru Margin, Equatorial Pacific, Hydrate Ridge, and Juan de Fuca Ridge

Marine sediments harbor an enormous quantity of microorganisms, including a multitude of novel species. The habitable zone of the marine sediment column begins at the sediment-water interface and probably extends to depths of several thousands of meters. Studies of the microbial diversity in this ecosystem have mostly relied on molecular biological techniques. We used a complementary method - analysis of intact polar membrane lipids - to characterize the in-situ microbial community in sediments covering a wide range of environmental conditions from Peru Margin, Equatorial Pacific, Hydrate Ridge, and Juan de Fuca Ridge. Bacterial and eukaryotic phospholipids were only detected in surface sediments from the Peru Margin. In contrast, deeply buried sediments, independent of their geographic location, were dominated by archaeal diether and tetraether lipids with various polar head groups and core lipids. We compared ring distributions of archaeal tetraether lipids derived from polar glycosidic precursors with those that are present as core lipids. The distributions of these related compound pools were distinct, suggestive of different archaeal sources, i.e., the polar compounds derive from sedimentary communities and the core lipids are fossil remnants from planktonic communities with possible admixtures of decayed sedimentary archaea. This in-situ production of distinct archaeal lipid populations potentially affects applications of the TEX86 paleotemperature proxy as demonstrated by offsets in reconstructed temperatures between both pools. We evaluated how varying cell and lipid stabilities will influence the sedimentary pool by using a box-model. The results are consistent with (i) a requirement of continuous inputs of freshly synthesized lipids in subsurface sediments for explaining the observed distribution of intact polar lipids, and (ii) decreasing lipid inputs with increasing burial depth.

Dissolved lithium and silicon through time in microbial dissolution experiments on ODP Leg 209 peridotite

Using peridotite drilled during Ocean Drilling Program Leg 209, a series of enrichment cultures were initiated on board the ship to stimulate microbially enhanced dissolution of olivine. Dissolution was estimated by measured changes in dissolved Li and Si in the media through time (up to 709 days). The results suggest that there was no significant difference between the amounts of dissolved Li and Si in most of the inoculated microbial cultures compared to the control cultures. Alternative explanations for this are that 1. No microbes are living in the culture tubes that can affect the dissolution rates of olivine, 2. The control cultures have microbes effecting the dissolution of olivine as well as the inoculated cultures, 3. Not enough time has passed to build up a large enough microbial population to effect the dissolution of the olivine in the culture tubes, 4. Microbes act to suppress dissolution of olivine instead of enhancing dissolution, and 5. Abiotic dissolution overshadows microbially enhanced dissolution. Further work is required to test these alternatives.

(Table 1) Stable isotope data of chemoherm carbonates at Hydrate Ridge on the Cascadia continental margin

Two active chemoherm build-ups growing freely up into the oceanic water column, the Pinnacle and the South East-Knoll Chemoherms, have been discovered at Hydrate Ridge on the Cascadia continental margin. These microbially-mediated carbonate formations rise above the seafloor by several tens of meters and display a pinnacle-shaped morphology with steep flanks. The recovered rocks are pure carbonates dominated by aragonite. Based on fabric and mineralogic composition different varieties of authigenic aragonite can be distinguished. Detailed visual and petrographic investigations unambiguously reveal the involvement of microbes during the formation of the carbonates. The fabric of the cryptocrystalline and fibrous aragonite can be described as thrombolitic. Fossilized microbial filaments in the microcrystalline aragonite indicate the intimate relationship between microbes and carbonates. The strongly 13C-depleted carbon isotope values of the samples (as low as -48.1 per mill PDB) are characteristic of methane as the major carbon source for the carbonate formation. The methane-rich fluids from which the carbonates are precipitated originate most probably from a gas reservoir below the bottom-simulating reflector (BSR) and rise through fault systems. The d18O values of the aragonitic chemoherm carbonates are substantially higher (as high as 5.0 per mill PDB) than the expected equilibrium value for an aragonite forming from ambient seawater (3.5 per mill PDB). As a first approximation this indicates formation from glacial ocean water but other factors are considered as well. A conceptual model is presented for the precipitation of these chemoherm carbonates based on in situ observations and the detailed petrographic investigation of the carbonates. This model explains the function of the consortium of archaea and sulfate-reducing bacteria that grows on the carbonates performing anaerobic oxidation of methane (AOM) and enabling the precipitation of the chemoherms above the seafloor surrounded by oxic seawater. Beggiatoa mats growing on the surface of the chemoherms oxidize the sulfide provided by sulfate-dependent anaerobic oxidation of methane within an oxic environment. The contact between Beggiatoa and the underlying microbial consortium represents the interface between the overlying oxic water column and an anoxic micro-environment where carbonate formation takes place.

Relative abundances and microbial numbers of organisms from water sample station GeoB15704-2

Due to sampling difficulties, little is known about microbial communities associated with sinking marine snow in the twilight zone. A drifting sediment trap was equipped with a viscous cryogel and deployed to collect intact marine snow from depths of 100 and 400 m off Cape Blanc (Mauritania). Marine snow aggregates were fixed and washed in situ to prevent changes in microbial community composition and to enable subsequent analysis using catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). The attached microbial communities collected at 100 m were similar to the free-living community at the depth of the fluorescence maximum (20 m) but different from those at other depths (150, 400, 550, and 700 m). Therefore, the attached microbial community seemed to be "inherited" from that at the fluorescence maximum. The attached microbial community structure at 400 m differed from that of the attached community at 100 m and from that of any free-living community at the tested depths, except that collected near the sediment at 700 m. The differences between the particle-associated communities at 400 m and 100 m appeared to be due to internal changes in the attached microbial community rather than de novo colonization, detachment, or grazing during the sinking of marine snow. The new sampling method presented here will facilitate future investigations into the mechanisms that shape the bacterial community within sinking marine snow, leading to better understanding of the mechanisms which regulate biogeochemical cycling of settling organic matter.

Sulfur and carbon in mIcrobial processes in waters and sediments of the Kara Sea in September 2007

Results of microbiological, biogeochemical and isotope geochemical studies in the Kara Sea are described. Samples for these studies were obtained during Cruise 54 of R/V Akademik Mstislav Keldysh in September 2007. The studied area covered the northern, central, and southwestern parts of the Kara Sea and the Obskaya Guba (Ob River estuary). Quantitative characteristics of total bacterial population and activity of microbial processes in the water column and bottom sediments were obtained. Total abundance of bacterioplankton (BP) varied from 250000 cells/ml in the northern Kara Sea to 3000000 cells/ml in the Obskaya Guba. BP abundance depended on concentration of suspensded matter. Net BP production was minimal in the central Kara Sea (up to 0.15-0.2 µg C/l/day) and maximal (0.5-0.75 µg C/l/day) in the Obskaya Guba. Organic material at the majority of stations at the Ob transect predominantly contained light carbon isotopes (-28.0 to -30.18 per mil) of terrigenous origin. Methane concentration in the surface water layer varied from 0.18 to 2.0 µl CH4/l, and methane oxidation rate varied from 0.1 to 100 nl CH4/l/day. Methane concentration in the upper sediment layer varied from 30 to 300 µl CH4/dm**3; rate of methane formation was varied from 44 to 500 nl CH4/dm**3/day and rate of methane oxidation - from 30 to 2000 nl CH4/dm**3/day. Rate of sulfate reduction varied from 4 to 184 µg S/dm**3/day.

(Supplemental Table 2) Plant characteristics, GHG fluxes, and soil chemical and microbial properties in experimental treatments in Alexandra Fiord

We evaluated above- and belowground ecosystem changes in a 16 year, combined fertilization and warming experiment in a High Arctic tundra deciduous shrub heath (Alexandra Fiord, Ellesmere Island, NU, Canada). Soil emissions of the three key greenhouse gases (GHGs) (carbon dioxide, methane, and nitrous oxide) were measured in mid-July 2009 using soil respiration chambers attached to a FTIR system. Soil chemical and biochemical properties including Q10 values for CO2, CH4, and N2O, Bacteria and Archaea assemblage composition, and the diversity and prevalence of key nitrogen cycling genes including bacterial amoA, crenarchaeal amoA, and nosZ were measured. Warming and fertilization caused strong increases in plant community cover and height but had limited effects on GHG fluxes and no substantial effect on soil chemistry or biochemistry. Similarly, there was a surprising lack of directional shifts in the soil microbial community as a whole or any change at all in microbial functional groups associated with CH4 consumption or N2O cycling in any treatment. Thus, it appears that while warming and increased nutrient availability have strongly affected the plant community over the last 16 years, the belowground ecosystem has not yet responded. This resistance of the soil ecosystem has resulted in limited changes in GHG fluxes in response to the experimental treatments.

Tab. 3: Substrate pH values of crypthoendolithic microbial communities

Cryploendolithic microbial communities in the Ross Desert (McMurdo Dry Valleys) are characterized on the basis of photosymlictic microorganisms and fungi. Two eukaryotic communities (the lichen-dominated and Hemichloris communities) and three cyanobacterial communities (the red Gloeocapsa, Hormathonema-Gloeocapsa and Chroococcidiopsis communities) are described. Eleven coccoid. ohne pleurocapsoid, and five filamentous cyanobacteria occurring in these communities are characterized and illustrated. The moisture grade of the rock substrate seems to affect pH. Formation of primary iron stain, and the distribution of microbial communities.