Bacterial and archaeal lipids trace chemo(auto)trophy along the redoxcline in Vancouver Island fjords.

Marine oxygen minimum zones play a crucial role in the global oceanic carbon, nitrogen, and sulfur cycles as they harbor microbial communities that are adapted to the water column chemistry and redox zonation, and in turn control the water column chemistry and greenhouse gas release. These micro-organisms have metabolisms that rely on terminal electron acceptors other than O2 and often benefit from syntrophic relationships (metabolic coupling). Here, we study chemo(auto)trophy along the redoxcline in two stratified fjords on Vancouver Island (Canada) using bacterial bacteriohopanepolyols and archaeal ether lipids. We analyze the distribution of these lipid classes in suspended particulate matter (SPM) to trace ammonia oxidation, anaerobic ammonium oxidation (anammox), sulfate reduction/sulfur oxidation, methanogenesis, and methane oxidation, and investigate ecological niches to evaluate potential links between their respective bacterial and archaeal sources. Our results show an unparalleled BHP and ether lipid structural diversity that allows tracing the major redox-driven metabolic processes at the time of sampling: Both fjords are dominated by archaeal ammonia oxidation and anammox; sulfate-reducing bacteria may be present in Deer Bay, but absent from Effingham Inlet; methanogenic Euryarchaeota and archaeal and bacterial methanotrophs are detectable at low abundance. Correlation analysis reveals distinct biomarker clusters that provide constraints on the biogeochemical niches of some orphan BHP and ether lipids such as in situ-produced adenosyl-BHPs or unsaturated archaeols.

Type II photosensitized oxidation in senescent microalgal cells at different latitudes: Does low under-ice irradiance in polar regions enhance efficiency?

Comparison of Type II photosensitized oxidation of lipids (the photodynamic effect) and photodegradation of chlorophyll (sensitizer photobleaching) in samples of particulate matter collected previously from locations representing a diverse range of latitudes reveals an enhancement of the photooxidation of lipids at the expense of chlorophyll photodegradation in the polar regions. The efficiency of the photodynamic effect appears to be particularly high in sinking particles collected under sea ice and is attributed to the rapid settling of highly aggregated sympagic algae to depths of low light transmission favouring the photodynamic effect at the expense of photobleaching of the sensitizer. Paradoxically, the low efficiency of Type II photosensitized oxidation of lipids observed in temperate and equatorial regions is associated with high solar irradiances in these regions. Type II photosensitized oxidation of lipids in senescent phytoplankton seems thus to be strongly dependent of the intensity of solar irradiance.

Stratification of archaeal membrane lipids in the ocean and implications for adaptation and chemotaxonomy of planktonic archaea.

Membrane lipids of marine planktonic archaea have provided unique insights into archaeal ecology and paleoceanography. However, past studies of archaeal lipids in suspended particulate matter (SPM) and sediments mainly focused on a small class of fully saturated glycerol dibiphytanyl glycerol tetraether (GDGT) homologues identified decades ago. The apparent low structural diversity of GDGTs is in strong contrast to the high diversity of metabolism and taxonomy among planktonic archaea. Furthermore, adaptation of archaeal lipids in the deep ocean remains poorly constrained. We report the archaeal lipidome in SPM from diverse oceanic regimes. We extend the known inventory of planktonic archaeal lipids to include numerous unsaturated archaeal ether lipids (uns-AELs). We further reveal (i) different thermal regulations and polar headgroup compositions of membrane lipids between the epipelagic (≤ 100 m) and deep (>100 m) populations of archaea, (ii) stratification of unsaturated GDGTs with varying redox conditions, and (iii) enrichment of tetra-unsaturated archaeol and fully saturated GDGTs in epipelagic and deep oxygenated waters, respectively. Such stratified lipid patterns are consistent with the typical distribution of archaeal phylotypes in marine environments. We, thus, provide an ecological context for GDGT-based paleoclimatology and bring about the potential use of uns-AELs as biomarkers for planktonic Euryarchaeota.

Biogenic polycyclic aromatic hydrocarbons in sediments of the San Joaquin River in California (USA), and current paradigms on their formation.

Biogenic perylene and higher plant pentacyclic triterpenoid-derived alkylated and partially aromatized tetra- and pentacyclic derivatives of chrysene (3,4,7-trimethyl- and 3,3,7-trimethyl-1,2,3,4-tetrahydrochrysene, THC) and picene (1,2,9-trimethyl- and 2,2,9-trimethyl-1,2,3,4-tetrahydropicene, THP) were two- to four-fold more abundant than pyrogenic PAH in two sediment cores from the San Joaquin River in Northern California (USA). In a core from Venice Cut (VC), located in the river, PAH concentrations varied little downcore and the whole-core PAH concentration (biogenics + pyrogenics) was 250.6 ± 73.7 ng g(-1) dw; biogenic PAH constituted 67 ± 4 % of total PAH. THC were 26 ± 9 % of total biogenic PAH, THP were 36 ± 7 %, and perylene was 38 ± 7 %. PAH distributions in a core from Franks Tract (FT), a former wetland that was converted to an agricultural tract in the late 1800s and flooded in 1938, were more variable. Surface sediments were dominated by pyrogenic PAH so that biogenic PAH were only ~30 % of total PAH. Deeper in the core, biogenic PAH constituted 60-93 % of total PAH; THC, THP and perylene were 31 ± 28 %, 24 ± 32 %, and 45 ± 36 % of biogenic PAH. At 100-103 cm depth, THP constituted 80 % of biogenic PAH and at 120-123 cm perylene was 95 % of biogenic PAH. Current concepts related to precursors and transformation processes responsible for the diagenetic generation of perylene and triterpenoid-derived PAH are discussed. Distributions of biogenic PAH in VC and FT sediments suggest that they may not form diagenetically within these sediments but rather might be delivered pre-formed from the river's watershed.

Impact of temperature on ladderane lipid distribution in anammox bacteria.

Anaerobic ammonium-oxidizing (anammox) bacteria have the unique ability to synthesize fatty acids containing linearly concatenated cyclobutane rings, termed "ladderane lipids." In this study we investigated the effect of temperature on the ladderane lipid composition and distribution in anammox enrichment cultures, marine particulate organic matter, and surface sediments. Under controlled laboratory conditions we observed an increase in the amount of C(20) [5]-ladderane fatty acids compared with the amount of C(18) [5]-ladderane fatty acids with increasing temperature and also an increase in the amount of C(18) [5]-ladderane fatty acids compared with the amount of C(20) [5]-ladderane fatty acids with decreasing temperature. Combining these data with results from the natural environment showed a significant (R(2) = 0.85, P = <0.0001, n = 121) positive sigmoidal relationship between the amounts of C(18) and C(20) [5]-ladderane fatty acids and the in situ temperature; i.e., there is an increase in the relative abundance of C(18) [5]-ladderane fatty acids at lower temperatures and vice versa, particularly at temperatures between 12 degrees C and 20 degrees C. Novel shorter (C(16)) and longer (C(22) to C(24)) ladderane fatty acids were also identified, but their relative amounts were small and did not change with temperature. The adaptation of ladderane fatty acid chain length to temperature changes is similar to the regulation of common fatty acid composition in other bacteria and may be the result of maintaining constant membrane fluidity under different temperature regimens (homeoviscous adaptation). Our results can potentially be used to discriminate between the origins of ladderane lipids in marine sediments, i.e., to determine if ladderanes are produced in situ in relatively cold surface sediments or if they are fossil remnants originating from the warmer upper water column.

Detection of microbial biomass by intact polar membrane lipid analysis in the water column and surface sediments of the Black Sea.

The stratified water column of the Black Sea produces a vertical succession of redox zones, stimulating microbial activity at the interfaces. Our study of intact polar membrane lipids (IPLs) in suspended particulate matter and sediments highlights their potential as biomarkers for assessing the taxonomic composition of live microbial biomass. Intact polar membrane lipids in oxic waters above the chemocline represent contributions of bacterial and eukaryotic photosynthetic algae, while anoxygenic phototrophic bacteria and sulfate-reducing bacteria comprise a substantial amount of microbial biomass in deeper suboxic and anoxic layers. Intact polar membrane lipids such as betaine lipids and glycosidic ceramides suggest unspecified anaerobic bacteria in the anoxic zone. Distributions of polar head groups and core lipids show planktonic archaea below the oxic zone; methanotrophic archaea are only a minor fraction of archaeal biomass in the anoxic zone, contrasting previous observations based on the apolar derivatives of archaeal lipids. Sediments contain algal and bacterial IPLs from the water column, but transport to the sediment is selective; bacterial and archaeal IPLs are also produced within the sediments. Intact polar membrane lipid distributions in the Black Sea are stratified in accordance with geochemical profiles and provide information on vertical successions of major microbial groups contributing to suspended biomass. This study vastly extends our knowledge of the distribution of complex microbial lipids in the ocean.

Effect of depositional regimes on polycyclic aromatic hydrocarbons in Lake Bled (NW Slovenia) sediments.

Polycyclic aromatic hydrocarbons (PAH) were measured in sediment cores from two contrasting depositional regimes in urban Lake Bled (NW Slovenia). The concentration of PAH in surface sediments, mostly derived from combustion, was higher in Zaka Bay where bottom waters are permanently oxic, than in the western basin where bottom waters oscillate between suboxic and anoxic (1930 vs. 1150ngPAHg(-1) dry weight (dw), respectively). This pattern is the reverse of what might be expected if PAH were to preferentially degrade under oxic conditions. Two PAH from non-combustion sources, perylene and retene, are also present in the sediments. Post-depositional diagenetic formation of perylene appeared to occur only in anoxic sediments. Differences in the source of sedimentary organic matter (autochthonous vs. allochthonous) is probably not a major factor in perylene formation, since the two locations have markedly different sources of organic matter but quite similar concentrations of perylene in deeper sediments, ranging from 250 to 350ngg(-1)dw. Thus, redox conditions may play a role in perylene generation. On the other hand, redox conditions in general can not be the only or even the major factor affecting the fate of sedimentary PAH since uniform compositions and depth distributions for pyrolytic PAH were observed in both cores, in spite of the two locations differ in redox, mixing and biota conditions. Thus, degradative loss of PAH is unlikely in Lake Bled sediments.

Changes in sediment and organic carbon accumulation in a highly-disturbed ecosystem: the Sacramento-San Joaquin River Delta (California, USA).

We used the Sacramento-San Joaquin River Delta CA (Delta, hereafter) as a model system for understanding how human activities influence the delivery of sediment and total organic carbon (TOC) over the past 50-60 years. Sediment cores were collected from sites within the Delta representing the Sacramento River (SAC), the San Joaquin River (SJR), and Franks Tract (FT), a flooded agricultural tract. A variety of anthropogenic tracers including (137)Cs, total DDE (Sigma DDE) and brominated diphenyl ether (BDE) congeners were used to quantify sediment accumulation rates. This information was combined with total organic carbon (TOC) profiles to quantify rates of TOC accumulation. Across the three sites, sediment and TOC accumulation rates were four to eight-fold higher prior to 1972. Changes in sediment and TOC accumulation were coincident with completion of several large reservoirs and increased agriculture and urbanization in the Delta watershed. Radiocarbon content of TOC indicated that much of the carbon delivered to the Delta is "pre-aged" reflecting processing in the Delta watershed or during transport to the sites rather than an input of predominantly contemporary carbon (e.g., 900-1400 years BP in surface sediments and 2200 yrs BP and 3610 yrs BP at the base of the SJR and FT cores, respectively). Together, these data suggest that human activities have altered the amount and age of TOC accumulating in the Delta since the 1940s.

Putative ammonia-oxidizing Crenarchaeota in suboxic waters of the Black Sea: a basin-wide ecological study using 16S ribosomal and functional genes and membrane lipids.

Within the upper 400 m at western, central and eastern stations in the world's largest stratified basin, the Black Sea, we studied the qualitative and quantitative distribution of putative nitrifying Archaea based on their genetic markers (16S rDNA, amoA encoding for the alpha-subunit of archaeal ammonia monooxygenase), and crenarchaeol, the specific glycerol diphytanyl glycerol tetraether of pelagic Crenarchaeota within the Group I.1a. Marine Crenarchaeota were the most abundant Archaea (up to 98% of the total archaeal 16S rDNA copies) in the suboxic layers with oxygen levels as low as 1 microM including layers where previously anammox bacteria were described. Different marine crenarchaeotal phylotypes (both 16S rDNA and amoA) were found at the upper part of the suboxic zone as compared with the base of the suboxic zone and the upper 15-30 m of the anoxic waters with prevailing sulfide concentrations of up to 30 microM. Crenarchaeol concentrations were higher in the sulfidic chemocline as compared with the suboxic zone. These results indicate an abundance of putative nitrifying Archaea at very low oxygen levels within the Black Sea and might form an important source of nitrite for the anammox reaction.

Comparison of vertical distributions of prokaryotic assemblages in the anoxic Cariaco Basin and Black Sea by use of fluorescence in situ hybridization.

Individual prokaryotic cells from two major anoxic basins, the Cariaco Basin and the Black Sea, were enumerated throughout their water columns using fluorescence in situ hybridization (FISH) with the fluorochrome Cy3 or horseradish peroxidase-modified oligonucleotide probes. For both basins, significant differences in total prokaryotic abundance and phylogenetic composition were observed among oxic, anoxic, and transitional (redoxcline) waters. Epsilon-proteobacteria, Crenarchaeota, and Euryarchaeota were more prevalent in the redoxclines, where previous studies reported high rates of chemoautotrophic production relative to those in waters above and below the redoxclines. Relative abundances of Archaea in both systems varied between 1% and 28% of total prokaryotes, depending on depth. The prokaryotic community composition varied between the two anoxic basins, consistent with distinct geochemical and physical conditions. In the Black Sea, the relative contributions of group I Crenarchaeota (median, 5.5%) to prokaryotic communities were significantly higher (P < 0.001; n = 20) than those of group II Euryarchaeota (median, 2.9%). In contrast, their proportions were nearly equivalent in the Cariaco Basin. Beta-proteobacteria were unexpectedly common throughout the Cariaco Basin's water column, accounting for an average of 47% of 4',6'-diamidino-2-phenylindole (DAPI)-stained cells. This group was below the detection limit (<1%) in the Black Sea samples. Compositional differences between basins may reflect temporal variability in microbial populations and/or systematic differences in environmental conditions and the populations for which they select.

Records of atmospheric delivery of pyrolysis-derived pollutants in recent mountain lake sediments of the Julian Alps (NW Slovenia).

The historical record of the input of pyrolysis-derived pollutants via the atmosphere, i.e. black carbon (BC), polycyclic aromatic hydrocarbons (PAH) and spheroidal carbonaceous particles (SCP) was measured in the sediments of three remote alpine lakes situated in the Julian Alps, northwest Slovenia. Parallel sedimentary trends for BC, PAH and SCP were observed across the Julian Alps and relationships among these contaminants are discussed. Inputs of these pyrolytic-contaminants to sediments of remote lakes started to rise at the end of the 19th century, while their peak inputs were observed in the mid-20th century, amounting up to 6.0 gm(-2) yr(-1) for BC, 5200 x 10(4) m(-2) yr(-1) for SCP and 2900 microg m(-2) yr(-1) for PAH. In the last two to three decades, inputs decreased substantially, by a factor of up to 3 for BC, 7 for SCP and at least 3 for PAH.

Hydrocarbons in Lake Washington sediments. A 25-year retrospective in an urban lake.

Aliphatic and polycyclic aromatic hydrocarbon and stable and radiocarbon isotope distributions are compared for dated cores from the 1970s and 2000 for a 25-year retrospective in Lake Washington, Seattle, WA (USA). Contamination of Lake Washington sediments by petrogenic aliphatic hydrocarbons and pyrolytic polycyclic aromatic hydrocarbons via atmospheric deposition and stormwater runoff peaked between the 1950s and 1970s and has since decreased as stormwater inputs have been reduced. Radiocarbon signatures (delta14C, per 1000) of total organic carbon decrease (increased "age") in the depth interval of highest hydrocarbon concentration. Graphitic black carbon in the year 2000 core showed a historical profile similar to that of the PAH; however high background sediments deposited before the founding of Seattle indicates a considerable nonindustrial component derived from weathering in the watershed. Unlike hydrocarbon contamination, input of terrestrial organic matter (tracked by long-chain fatty alcohols) has increased throughout the late 20th century, documenting a shift in pollutant sources away from hydrocarbons and toward anthropogenic erosion of the region's soils.

Polycyclic aromatic hydrocarbons and black carbon in sediments of a remote alpine lake (Lake Planina, northwest Slovenia).

Polycyclic aromatic hydrocarbons (PAH) and black carbon (BC) were measured in alpine Lake Planina (Slovenia) sediment. Lake Planina is a remote mountain lake with almost no direct anthropogenic influence. Long-distance atmospheric deposition is a major pathway for the loading of contaminants to the sediment. The PAH were analyzed by gas chromatography coupled to mass spectrometry, whereas the BC was determined by thermal oxidation method. A flux of PAH to surface sediments of approximately 1,100 microg m(-2) year(-1) was obtained and was higher than that in other alpine lakes of the central European Alps. However, surface sediment PAH concentration, normalized to organic carbon content (OC), amounted to 5 microg PAH(pyr)/g OC and showed that Lake Planina is relatively equally exposed to atmospheric pollution compared with other lakes in the region. The BC:OC ratios ranged from 3 to 8% (w/w). In addition, a huge forest fire occurred in 1948 in the lake's surrounding area, which is recorded in the sediment. Both PAH and BC distributions were affected by the fire in 1948 in the lake's watershed, because their concentration increased remarkably. The concentration of retene, a molecular marker of coniferous wood combustion, increased to 1,000 ng/g dry weight sediment at the sediment interval corresponding to approximately the year 1950.

Biogeochemical evidence that thermophilic archaea mediate the anaerobic oxidation of methane.

Distributions and isotopic analyses of lipids from sediment cores at a hydrothermally active site in the Guaymas Basin with a steep sedimentary temperature gradient revealed the presence of archaea that oxidize methane anaerobically. The presence of strongly (13)C-depleted lipids at greater depths in the sediments suggests that microbes involved in anaerobic oxidation of methane are present and presumably active at environmental temperatures of >30 degrees C, indicating that this process can occur not only at cold seeps but also at hydrothermal sites. The distribution of the membrane tetraether lipids of the methanotrophic archaea shows that these organisms have adapted their membrane composition to these high environmental temperatures.

Distribution of membrane lipids of planktonic Crenarchaeota in the Arabian Sea.

Intact core tetraether membrane lipids of marine planktonic Crenarchaeota were quantified in water column-suspended particulate matter obtained from four depth intervals ( approximately 70, 500, 1,000 and 1,500 m) at seven stations in the northwestern Arabian Sea to investigate the distribution of the organisms at various depths. Maximum concentrations generally occurred at 500 m, near the top of the oxygen minimum zone, and the concentrations at this depth were, in most cases, slightly higher than those in surface waters. In contrast, lipids derived from eukaryotes (cholesterol) and from eukaryotes and bacteria (fatty acids) were at their highest concentrations in surface waters. This indicates that these crenarchaeotes are not restricted to the photic zone of the ocean, which is consistent with the results of recent molecular biological studies. Since the Arabian Sea has a strong oxygen minimum zone between 100 and 1,000 m, with minimum oxygen levels of <1 microM, the abundance of crenarchaeotal membrane lipids at 500 m suggests that planktonic Crenarchaeota are probably facultative anaerobes. The cell numbers we calculated from the concentrations of membrane lipids are similar to those reported for the Central Pacific Ocean, supporting the recent estimation of M. B. Karner, E. F. DeLong, and D. M. Karl ( Nature 409:507-510, 2001) that the world's oceans contain ca. 10(28) cells of planktonic Crenarchaeota.