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Particulate pyrogenic carbon (PyC) transported by rivers and aerosols, and deposited in marine sediments, is an important part of the carbon cycle. The chemical composition of PyC is temperature dependent and levoglucosan is a source‐specific burning marker used to trace low‐temperature PyC. Levoglucosan associated to particulate material has been shown to be preserved during riverine transport and marine deposition in high‐ and mid‐latitudes, but it is yet unknown if this is also the case for (sub)tropical areas, where 90% of global PyC is produced. Here, we investigate transport and deposition of levoglucosan in suspended and riverbed sediments from the Amazon River system and adjacent marine deposition areas. We show that the Amazon River exports negligible amounts of levoglucosan and that concentrations in sediments from the main Amazon tributaries are not related to long‐term mean catchment‐wide fire activity. Levoglucosan concentrations in marine sediments offshore the Amazon Estuary are positively correlated to total organic content regardless of terrestrial or marine origin, supporting the notion that association of suspended or dissolved PyC to biogenic particles is critical in the preservation of PyC. We estimate that 0.5–10 × 106 g yr−1 of levoglucosan is exported by the Amazon River. This represents only 0.5–10 ppm of the total exported PyC and thereby an insignificant fraction, indicating that riverine derived levoglucosan and low‐temperature PyC in the tropics are almost completely degraded before deposition. Hence, we suggest caution in using levoglucosan as tracer for past fire activity in tropical settings near rivers. Plain Language Summary: During plant organic matter burning, most of the carbon is emitted to the atmosphere as CO2, but a fraction is retained as pyrogenic biomass. The chemical composition of pyrogenic biomass depends on fire temperature and allows to differentiate between high and low‐temperature pyrogenic biomass. Here, we analyzed if low‐temperature pyrogenic biomass is preserved during transport in the Amazon River and deposited in western tropical Atlantic sediments. We found that only negligible amounts of low‐temperature pyrogenic biomass reach the Atlantic through riverine transport. While most pyrogenic carbon (PyC) originates in the tropics, our study suggests that only an insignificant fraction of low‐temperature PyC is permanently stored in marine sediments, where it would be removed from the short‐term carbon cycle. Key Points: Only negligible amounts of the source‐specific low‐temperature biomass burning tracer levoglucosan are exported by the Amazon River systemMarine sediment levoglucosan yields are controlled by organic carbon content regardless of marine or terrestrial source of organic matterDust and river derived levoglucosan escape burial in the tropical Atlantic, despite the dominant tropical source of pyrogenic carbon [ABSTRACT FROM AUTHOR]

Fire causes dramatic energy and matter exchanges between biosphere and atmosphere on a regional to global scale. Predicting fires, however, is hindered by the complex interplay of fire, climate, and vegetation. Paleo‐fire records provide critical information beyond instrumental records that cover only the past few decades and may be used to assess the role of fire in large‐scale and long‐term environmental changes. Here we present a 22,000‐year multiproxy record of fire regime from a sediment core retrieved offshore South Java, Indonesia. We use microcharcoal in combination with two molecular markers of burning, levoglucosan and polycyclic aromatic hydrocarbons, to reconstruct fire occurrence as well as fire intensity in the past. We show that fire occurrence and intensity were high during the Last Glacial Maximum (LGM; around 21,000 years ago) and low during the Heinrich Stadial 1 and the early Holocene. Both fire regime and vegetation in tropical regions with high annual rainfall were primarily controlled by rainfall seasonality. However, fire additionally stabilized the savannah (rainforest)‐dominated ecosystem during the LGM (early Holocene) but caused transitions between the two vegetation types during the deglaciation and the late Holocene. Key Points: Microcharcoal reflects regional fire occurrence, while the ratio between two novel molecular markers reflects past fire intensityRainfall seasonality controlled both fire regime and vegetationFires of different frequencies and intensities were capable of either stabilizing or destabilizing savannah/rainforest vegetation [ABSTRACT FROM AUTHOR]

The intact polar lipid (IPL) composition of phytoplankton is plastic and dependent on environmental factors. Previous studies have shown that phytoplankton under phosphorus (P)-stress substitute phosphatidylglycerols (PGs) with sulphoquinovosyldiacylglycerols (SQDGs) and digalactosyldiacylglycerols (DGDGs). However, these studies focused merely on P-depletion, while phytoplankton in the natural environment often experience P-limitation whereby the degree of limitation depends on the supply rate of the limiting nutrient. Here we demonstrate a linear increase in SQDG : PG and DGDG : PG ratios with increasing cellular P-stress in the picophotoeukaryote Micromonas pusilla, obtained by P-replete, P-limited (chemostat) and P-starved (no supply of P) culturing conditions. These ratios were not affected by the degree of the P-limiting conditions itself (i.e. 0.97 and 0.32 µmax chemostats), suggesting there is a minimum requirement of PGs for the maintenance of cell growth. Viral infection reduced the increase in SQDG : PG and DGDG : PG ratios in P-starved cells, but the extent did depend on the growth rate of the cultures before infection. The membrane of M. pusilla virus MpV itself was lacking some IPLs compared to the host as, e.g. no monogalactosyldiacylglycerols could be detected. Growth of the phytoplankton cultures under enhanced CO2 concentration did not affect the lipid remodeling results. The present study provides new insights into how the P-related trophic state of an ecosystem as well as viral infection can affect phytoplankton IPL composition, and therefore influence food web dynamics and biogeochemical cycling. [ABSTRACT FROM AUTHOR]

In the last decade our understanding of the marine nitrogen cycle has improved considerably thanks to the discovery of two novel groups of microorganisms: ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing (anammox) bacteria. Both groups are important in oxygen deficient zones (ODZs), where they substantially affect the marine N-budget. These two groups of microbes are also well known for producing specific membrane lipids, which can be used as biomarkers to trace their presence in the environment. We investigated the occurrence and distribution of AOA and anammox bacteria in the water column of the Eastern Tropical North Pacific (ETNP) ODZ, one of the most prominent ODZs worldwide. Suspended particulate matter (SPM) was collected at different depths of the water column in high resolution, at both a coastal and an open ocean setting. The SPM was analyzed for AOA- and anammox bacteria-specific intact polar lipids (IPLs), i.e. hexose-phosphohexose (HPH)-crenarchaeol and phosphatidylcholine (PC)-monoether ladderane. Comparison with oxygen profiles reveals that both the microbial groups are able to thrive at low (<1 µM) concentrations of oxygen. Our results indicate a clear niche segregation of AOA and anammox bacteria in the coastal waters of the ETNP, but a partial overlap of the two niches of these microbial species in the open water setting. The latter distribution suggests the potential for an interaction between the two microbial groups at the open ocean site, either as competition or cooperation. [ABSTRACT FROM AUTHOR]

Recent studies showed changes in phytoplankton lipid composition during viral infection and have indicated roles for specific lipids in the mechanisms of algal virus-host interaction. To investigate the generality of these findings and obtain a better understanding of the allocation of specific lipids to viruses, we studied the intact polar lipid (IPL) composition of virally infected and non-infected cultures of the prymnesiophyte Phaeocystis globosa G(A) and its lytic virus PgV-07T. The P. globosa IPL composition was relatively stable over a diel cycle and not strongly affected by viral infection. Glycolipids, phospholipids and betaine lipids were present in both the host and virus, although specific groups such as the diacylglyceryl-hydroxymethyltrimethyl-ß-alanines and the sulfoquinovo-syldiacylglycerols, were present in a lower proportion or were not detected in the virus. Viral glycosphingolipids (vGSLs), which have been shown to play a role in the infection strategy of the virus EhV-86, infecting the prymnesiophyte Emiliania huxleyi CCMP374, were not encountered. Our results show that the involvement of lipids in virus-algal host interactions can be very different amongst virus-algal host systems. [ABSTRACT FROM AUTHOR]

We have examined the spatial and seasonal distribution of Thaumarchaeota in the water column and sediment of the southern North Sea using the specific intact polar lipid (IPL) hexose-phosphohexose (HPH) crenarchaeol, as well as thaumarchaeotal 16S rRNA gene abundances and expression. In the water column, a higher abundance of Thaumarchaeota was observed in the winter season than in the summer, which is in agreement with previous studies, but this was not the case in the sediment where Thaumarchaeota were most abundant in spring and summer. This observation corresponds well with the idea that ammonia availability is a key factor in thaumarchaeotal niche determination. In the surface waters of the southern North Sea, we observed a spatial variability in HPH crenarchaeol, thaumarchaeotal 16S rRNA gene abundance and transcriptional activity that corresponded well with the different water masses present. In bottom waters, a clear differentiation based on water masses was not observed; instead, we suggest that observed differences in thaumarchaeotal abundance with depth may be related to resuspension from the sediment. This could be due to suspension of benthic Thaumarchaeota to the water column or due to delivery of e.g. resuspended sediment or ammonium to the water column, which could be utilized by pelagic Thaumarchaeota. This study has shown that the seasonality of Thaumarchaeota in water and sediment is different and highlights the importance of water masses, currents and sedimentary processes in determining the spatial abundance of Thaumarchaeota in the southern North Sea. [ABSTRACT FROM AUTHOR]

Recent studies showed changes in phytoplankton lipid composition during viral infection and have indicated roles for specific lipids in the mechanisms of algal virus-host interaction. To investigate the generality of these findings and obtain a better understanding of the allocation of specific lipids to viruses, we studied the intact polar lipid (IPL) composition of virally infected and non-infected cultures of the Prymnesiophyte Phaeocystis globosa G(A) and its lytic virus PgV-07T. The P globosa IPL composition was relatively stable over a diel cycle and not strongly affected by viral infection. Glycolipids, phospholipids and betaine lipids were present in both the host and virus, although specific groups such as the diacylglyceryl-hydroxymethyltrimethyl-β-alanines and the sulfoquinovosyldiacylglycerols, were present in a lower proportion or were not detected in the virus. Viral glycosphingolipids (vGSLs), which have been shown to play a role in the infection strategy of the virus EhV-86, infecting the Prymnesiophyte Emiliania huxleyi CCMP374, were not encountered. Our results show that the involvement of lipids in virus-algal host interactions can be very different amongst virus-algal host systems. [ABSTRACT FROM AUTHOR]

The intact polar lipid ( IPL) composition of twelve hydrothermal vent deposits from the Rainbow ( RHF) and Lucky Strike hydrothermal fields ( LSHF) has been investigated in order to assess its utility as a proxy for microbial community composition associated with deep-sea hydrothermal locations. Gene-based culture-independent surveys of the microbial populations of the same vent deposits have shown that microbial populations are different in the two locations and appear to be controlled by the geochemical and geological processes that drive hydrothermal circulation. Large differences in the IPL composition between these two sites are evident. In the ultramafic-hosted RHF, mainly archaeal- IPLs were identified, including those known to be produced by hyperthermophilic Euryarchaeota. More specifically, polyglycosyl derivatives of archaeol and macrocyclic archaeol indicate the presence of hyperthermophilic methanogenic archaea in the vent deposits, which are related to members of the Methanocaldococcaceae or Methanococcaceae. In contrast, bacterial IPLs dominate IPL distributions from LSHF, suggesting that bacteria are more predominant at LSHF than at RHF. Bacterial Diacyl glycerol ( DAG) IPLs containing phosphocholine, phosphoethanolamine or phosphoglycerol head groups were identified at both vent fields. In some vent deposits from LSHF ornithine lipids and IPLs containing phosphoaminopentanetetrol head groups were also observed. By comparison with previously characterized bacterial communities at the sites, it is likely the DAG- IPLs observed derive from Epsilon- and Gammaproteobacteria. Variation in the relative amounts of archaeal versus bacterial IPLs appears to indicate differences in the microbial community between vent sites. Overall, IPL distributions appear to be consistent with gene-based surveys. [ABSTRACT FROM AUTHOR]

A novel proxy for continental mean annual air temperature (MAAT) and soil pH, the MBT/CBTpaleothermometer, is based on the temperature (T) and pHdependent distribution of specific bacterial membrane lipids (branched glycerol dialkyl glycerol tetraethers - GDGTs) in soil organic matter. Here, we tested the applicability of the MBT/CBT-paleothermometer to sediments from Lake Cadagno, a high Alpine lake in southern Switzerland with a small catchment of 2.4 km2. We analysed the distribution of bacterial GDGTs in catchment soils and in a radiocarbondated sediment core from the centre of the lake, covering the past 11 000 yr. The distribution of bacterial GDGTs in the catchment soils is very similar to that in the lake's surface sediments, indicating a common origin of the lipids. Consequently, their transfer from the soils into the sediment record seems undisturbed, probably without any significant alteration of their distribution through in situ production in the lake itself or early diagenesis of branched GDGTs. The MBT/CBT-inferred MAAT estimates from soils and surface sediments are in good agreement with instrumental values for the Lake Cadagno region (∼0.5°C). Moreover, downcore MBT/CBT-derived MAAT estimates match in timing and magnitude other proxy-based T reconstructions from nearby locations for the last two millennia. Major climate anomalies recorded by the MBT/CBT-paleothermometer are, for instance, the Little Ice Age (∼14th to 19th century) and the Medieval Warm Period (MWP, ∼9th to 14th century). Together, our observations indicate the quantitative applicability of the MBT/CBT-paleothermometer to Lake Cadagno sediments. In addition to the MWP, our lacustrine paleo T record indicates Holocene warm phases at about 3, 5, 7 and 11 kyr before present, which agrees in timing with other records from both the Alps and the sub-polar North-East Atlantic Ocean. The good temporal match of the warm periods determined for the central Alpine region with north-west European winter precipitation strength implies a strong and far-reaching influence of the North Atlantic Oscillation on continental European T variations during the Holocene. [ABSTRACT FROM AUTHOR]

Ladderane fatty acids are commonly used as biomarkers for bacteria involved in anaerobic ammonium oxidation (anammox). These lipids have been experimentally shown to undergo aerobic microbial degradation to form short chain ladderane fatty acids. However, nothing is known of the production or the distribution of these oxic biodegradation products in the natural environment. In this study, we analysed marine water column particulate matter and sediment from three different oceanic regimes for the presence of ladderane oxidation products (C14 ladderane fatty acids) and of original ladderane fatty acids (C18 and C20 ladderane fatty acids). We found that ladderane oxidation products, i.e. C14 ladderane fatty acids, are already produced within the water column of the Arabian Sea oxygen minimum zone (OMZ) and thus only low amounts of oxygen (< 3 µM) are needed for the β-oxidation of original ladderane fatty acids to proceed. However, no short chain ladderane fatty acids were detected in the Cariaco Basin water column, where oxygen concentrations were below detection limit, suggesting that the β-oxidation pathway is inhibited by the absence of molecular oxygen, or that the microbes performing the degradation are not proliferating under these conditions. Comparison of distributions of ladderane fatty acids indicates that short chain ladderane fatty acids are mostly produced in the water column and at the sediment surface, before being preserved deeper in the sediments. Short chain ladderane fatty acids were abundant in Arabian Sea and Peru Margin sediments (ODP Leg 201), often in higher concentrations than the original ladderane fatty acids. In a sediment core taken from within the Arabian Sea OMZ, short chain ladderanes made up more than 90% of the total ladderanes at depths greater than 5 cm below sea floor. We also found short chain ladderanes in higher concentrations in hydrolysed sediment residues compared to those freely occurring in lipid extracts, suggesting that they had become bound to the sediment matrix. Furthermore, these matrix-bound short chain ladderanes were found at greater sediment depths than short chain ladderanes in the lipid extract, suggesting that binding to the sediment matrix aids the preservation of these lipids. Though sedimentary degradation of short chain ladderane fatty acids did occur, it appeared to be at a slower rate than that of the original ladderane fatty acids, and short chain ladderane fatty acids were found in sediments from the Late Pleistocene (-100 kyr). Together these results suggest that the oxic degradation products of ladderane fatty acids may be suitable biomarkers for past anammox activity in OMZs. [ABSTRACT FROM AUTHOR]

Temporal variations in the abundance and composition of intact polar lipids (IPLs) in North Sea coastal marine water were assessed over a one-year seasonal cycle, and compared with environmental parameters and the microbial community composition. Sulfoquinovosyldiacylglycerol (SQDG) was the most abundant IPL class, followed by phosphatidylcholine (PC), phosphatidylglycerol (PG) and diacylglyceryl-(N,N,N)-trimethylhomoserine (DGTS) in roughly equal concentrations, and smaller amounts of phosphatidylethanolamine (PE). Although the total concentrations of these IPL classes varied substantially throughout the year, the composition of the IPL pool remained remarkably constant. Statistical analysis yielded negative correlations between IPL concentrations and dissolved inorganic nutrient concentrations, but possible phosphorous limitation during the spring bloom did not result in changes in the overall planktonic IPL composition. Significant correlations between SQDG, PC, PG and DGTS concentrations and chlorophyll-a concentrations and algal abundances indicated that eukaryotic primary producers were the predominant source of IPLs at this site. However, whilst IPL concentrations in the water were closely tied to total algal abundances, the rapid succession of different algal groups blooming throughout the year did not result in major shifts in IPL composition. This shows that the most commonly occurring IPLs have limited chemotaxonomic potential, and highlights the need to use targeted assays of more specific biomarker IPLs. [ABSTRACT FROM AUTHOR]

A novel proxy for continental mean annual air temperature (MAAT) and soil-pH, the MBT/CBT-paleothermometer, is based on the temperature (T) and pH-dependent distribution of specific bacterial membrane lipids (branched glycerol dialkyl glycerol tetraethers - GDGTs) in soil organic matter. Here, we tested the applicability of the MBT/CBT-paleothermometer to sediments from Lake Cadagno, a small high-alpine lake in southern Switzerland with a small catchment of 2.4 km⊃2. We analysed the distribution of bacterial GDGTs in catchment soils and in a radiocarbon-dated sediment core from the centre of the lake, covering the entire Holocene. The composition of bacterial GDGTs in soils are almost identical to that in the lake's surface sediments, indicating a common origin of the lipids. Consequently, their transfer from the soils into the sediment record is undisturbed, apparently without any significant alteration of their distribution through in situ production or early diagenesis of branched GDGTs. The MBT/CBT-inferred MAAT-estimates from soils and surface sediments are in good agreement with instrumental values for the Lake Cadagno region (~0.5 °C). Moreover, downcore MBT/CBT-derived MAAT-estimates match in timing and magnitude other proxy-based T -reconstructions from nearby locations for the last two millennia. Major climate anomalies recorded by the MBT/CBT-paleothermometer are, for instance, the Little Ice Age (~14th to 19th century) and the Medieval Warm Period (~10th to 14th century). Together, our observations confirm the applicability of the MBT/CBT-paleothermometer to Lake Cadagno sediments. Consistent with other T-records from both the Alps and from the subpolar NE-Atlantic, our lacustrine paleotemperature record indicates Holocene MAAT-variations with an apparent cyclicity of ~2 kyr. The good temporal match of the warm periods determined for the S-Alpine region with NW-European winter precipitation strength implies a strong and far-reaching influence of the North Atlantic Oscillation on continental European Holocene T-variations. [ABSTRACT FROM AUTHOR]

The diazotrophic community in microbial mats growing along the shore of the North Sea barrier island Schiermonnikoog (The Netherlands) was studied using microscopy, lipid biomarkers, stable carbon (δC) and nitrogen (δN) isotopes as well as by constructing and analyzing 16S rRNA gene libraries. Depending on their position on the littoral gradient, two types of mats were identified, which showed distinct differences regarding the structure, development and composition of the microbial community. Intertidal microbial mats showed a low species diversity with filamentous non-heterocystous Cyanobacteria providing the main mat structure. In contrast, supratidal microbial mats showed a distinct vertical zonation and a high degree of species diversity. Morphotypes of non-heterocystous Cyanobacteria were recognized as the main structural component in these mats. In addition, unicellular Cyanobacteria were frequently observed, whereas filamentous heterocystous Cyanobacteria occurred only in low numbers. Besides the apparent visual dominance of cyanobacterial morphotpyes, 16S rRNA gene libraries indicated that both microbial mat types also included members of the Proteobacteria and the Cytophaga-Flavobacterium-Bacteroides group as well as diatoms. Bulk δN isotopes of the microbial mats ranged from +6.1‰ in the lower intertidal to −1.2‰ in the supratidal zone, indicating a shift from predominantly nitrate utilization to nitrogen fixation along the littoral gradient. This conclusion was supported by the presence of heterocyst glycolipids, representing lipid biomarkers for nitrogen-fixing heterocystous Cyanobacteria, in supratidal but not in intertidal microbial mats. The availability of combined nitrogen species might thus be a key factor in controlling and regulating the distribution of the diazotrophic microbial community of Schiermonnikoog. [ABSTRACT FROM AUTHOR]

Branched Glycerol Dialkyl Glycerol Tetraethers (GDGTs) are membrane spanning lipids synthesised by as yet unknown bacteria that thrive in soils and peat. In order to obtain more information on their ecological niche, the stable carbon isotopic composition of branched GDGT-derived alkanes, obtained upon ether bond cleavage, has been determined in various soils, i.e. peat, forest, grassland and cropland, covered by various vegetation types, i.e., C3- vs. C4-plant type. These δ13C values are compared with those of bulk organic matter and higher plant derived n-alkanes from the same soils. With average δ13C values of -28%, branched GDGTs in C3 soils are only slightly depleted (ca. 1%) relative to bulk organic carbon and on average 8.5% enriched relative to plant wax-derived long-chain n-alkanes (nC29-nC33). In an Australian soil covered with C4 type vegetation, the branched GDGTs have a δ13C value of -18‰, clearly higher than observed in soils with C3 type vegetation. As with C3 vegetated soils, branched GDGT δ13C values are slightly depleted (1%) relative to bulk organic carbon and enriched (ca. 5%) relative to n-alkanes in this soil. The δ13C values of branched GDGT lipids being similar to bulk organic carbon and their co-variation with those of bulk organic carbon and plant waxes, suggest a heterotrophic life style and assimilation of relatively heavy and likely labile substrates for the as yet unknown soil bacteria that synthesise the branched GDGT lipids. However, a chemoautotrophic lifestyle, i.e. consuming respired CO2, could not be fully excluded based on these data alone. Based on a natural labelling experiment of a C3/C4 crop change introduced on one of the soils 23 years before sampling and based on a free air CO2 enrichment experiment with labelled CO2 on another soil, a turnover time of ca. 17 years has been estimated for branched GDGTs in these arable soils. [ABSTRACT FROM AUTHOR]

Although most gastric cancers occur in elderly patients, a substantial number of cases of this common disease occur in young patients. Gastric cancer is a heterogeneous disease at the genomic level and different patterns of DNA copy number alterations are associated with different clinical behaviour. The aim of the present study was to explore differences in DNA copy number alterations in relation to age of onset of gastric cancer. DNA isolated from 46 paraffin-embedded gastric cancer tissue samples from 17 patients less than 50 years of age [median 43 (21-49) years] and 29 patients greater than or equal to 70 years of age [median 75 (70-83) years] was analysed by genome-wide microarray comparative genomic hybridization (array CGH) using an array of 5000 BAC clones. Patterns of DNA copy number aberrations were analysed by hierarchical cluster analysis of the mode-normalized and smoothed log2 ratios of tumour to normal reference fluorescence signal intensities using TMEV software, after which cluster membership was correlated with age group. In addition, supervised analysis was performed using CGH Multi-array. Hierarchical cluster analysis of the array CGH data revealed three clusters with different genomic profiles that correlated significantly with age ( p = 0.006). Cluster 1 mainly contained young patients, while elderly patients were divided over clusters 2 and 3. Chromosome regions 11q23.3 and 19p13.3 contributed most to age-related differences in tumour profiles. Gastric cancers of young and old patients belong to groups with different genomic profiles, which likely reflect different pathogenic mechanisms of the disease. Copyright © 2006 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Anaerobic methane-oxidizing microbial communities in sediments at cold methane seeps are important factors in controlling methane emission to the ocean and atmosphere. Here, we investigated the distribution and carbon isotopic signature of specific biomarkers derived from anaerobic methanotrophic archaea (ANME groups) and sulphate-reducing bacteria (SRB) responsible for the anaerobic oxidation of methane (AOM) at different cold seep provinces of Hydrate Ridge, Cascadia margin. The special focus was on their relation to in situ cell abundances and methane turnover. In general, maxima in biomarker abundances and minima in carbon isotope signatures correlated with maxima in AOM and sulphate reduction as well as with consortium biomass. We found ANME-2a/DSS aggregates associated with high abundances of sn-2,3-di- O-isoprenoidal glycerol ethers (archaeol, sn-2-hydroxyarchaeol) and specific bacterial fatty acids (C16:1ω5c, cyC17:0ω5,6) as well as with high methane fluxes ( Beggiatoa site). The low to medium flux site ( Calyptogena field) was dominated by ANME-2c/DSS aggregates and contained less of both compound classes but more of AOM-related glycerol dialkyl glycerol tetraethers (GDGTs). ANME-1 archaea dominated deeper sediment horizons at the Calyptogena field where sn-1,2-di- O-alkyl glycerol ethers (DAGEs), archaeol, methyl-branched fatty acids ( ai-C15:0, i-C16:0, ai-C17:0), and diagnostic GDGTs were prevailing. AOM-specific bacterial and archaeal biomarkers in these sediment strata generally revealed very similar δ13C-values of around −100. In ANME-2-dominated sediment sections, archaeal biomarkers were even more 13C-depleted (down to −120), whereas bacterial biomarkers were found to be likewise 13C-depleted as in ANME-1-dominated sediment layers (δ13C: −100). The zero flux site ( Acharax field), containing only a few numbers of ANME-2/DSS aggregates, however, provided no specific biomarker pattern. Deeper sediment sections (below 20 cm sediment depth) from Beggiatoa covered areas which included solid layers of methane gas hydrates contained ANME-2/DSS typical biomarkers showing subsurface peaks combined with negative shifts in carbon isotopic compositions. The maxima were detected just above the hydrate layers, indicating that methane stored in the hydrates may be available for the microbial community. The observed variations in biomarker abundances and 13C-depletions are indicative of multiple environmental and physiological factors selecting for different AOM consortia (ANME-2a/DSS, ANME-2c/DSS, ANME-1) along horizontal and vertical gradients of cold seep settings. [ABSTRACT FROM AUTHOR]

Epstein-Barr virus (EBV) BamHI-A rightward frame 1 (BARF1) is considered a major viral oncogene in epithelial cells and has immune-modulating properties. However, in B cells and lymphomas, BARF1 expression is restricted to the viral lytic replication cycle. In this report, the transcriptional regulation of BARF1 during lytic replication is unraveled. Bisulfite sequencing of various cell lines indicated a high level of methylation of the BARF1 gene control region. A BARF1 promoter luciferase reporter construct was created using a CpG-free vector, enabling true assessment of promoter methylation. Induction of the EBV lytic cycle is mediated by the immediate-early proteins BZLF1 (Z) and BRLF1 (R). R was found to activate expression of the BARF1 promoter up to 250-fold independently of Z and unaffected by BARF1 promoter methylation. Chromatin immunoprecipitation (ChIP), electrophoretic mobility shift assay (EMSA), and specific mutagenesis of the R-responsive elements (RREs) demonstrated direct binding of R to RREs between nucleotides 554 and ?327 relative to the BARF1 transcriptional ATG start site. The kinetics of BARF1 expression upon transactivation by R showed that BARF1 mRNA was expressed within 6 h in the context of the viral genome. In conclusion, expression of the BARF1 protein during lytic replication is regulated by direct binding of R to multiple RREs in the gene control region and is independent of the promoter methylation status. The early kinetics of BARF1 upon transactivation by R confirm its status as an early gene and emphasize the necessity of early immune modulation during lytic reactivation. [ABSTRACT FROM AUTHOR]