Intact Polar Lipids Research Articles

Provenance of tetraether membrane lipids in a large temperate lake (Loch Lomond, UK): implications for glycerol dialkyl glycerol tetraether (GDGT)-based palaeothermometry

Abstract. The application of glycerol dialkyl glycerol tetraether (GDGT)-based palaeoenvironmental proxies, such as the branched vs. isoprenoidal tetratether (BIT) index, TEX86 and the MBT–CBT palaeothermometer, has lately been expanded to lacustrine sediments. Given recent research identifying the production of branched, bacterial GDGTs (brGDGTs) within lakes, it is necessary to ascertain the effect of this lacustrine production on GDGT-based proxies. This study profiles a temperate, monomictic lake (Loch Lomond, UK), analysing labile intact polar GDGT lipids (IPLs) and resilient core GDGT lipids (CLs) in catchment soils, small tributary rivers, lake water and lake sediments. Loch Lomond consists of two basins bisected by the Highland Boundary Fault, resulting in a mesotrophic to oligotrophic gradient from south to north. The north basin is fjord-like, while the south basin is shallow with a lowland catchment. Besides abundant influxes of allochthonous soil- and peat-derived (CL) brGDGTs, brGDGTs are produced in a variety of settings in Loch Lomond. Rather than integrating a scattered soil signal, there is some evidence that small rivers may contribute to the brGDGT pool through addition of brGDGTs produced in situ in these streams. Three hundred days of settling particles and water column profiles of suspended particulate matter (SPM; March and September 2011) reveal brGDGT production throughout the water column, with (IPL and CL) brGDGT distributions varying by basin. In lake sediments, in situ brGDGT production affects the distributions of sedimentary brGDGTs despite high soil- and peat-derived organic matter influxes from the catchment. MBT–CBT-derived mean annual air temperature (MAAT) estimates from soil, river and lake sediments vary widely. A strong bias towards higher MAATs in the south and lower MAATs in the north basin further complicates the application of the proxy. These results emphasise that caution must be exercised when applying the MBT–CBT palaeothermometer to individual lakes in which the use of the proxy has not been validated and therefore the factors affecting its application are not well understood. Despite elevated BIT indices, (partly) due to in situ brGDGT production, reliable TEX86 lake surface temperature (LST) estimates were obtained from SPM with BIT indices up to 0.9. Lower north basin sediments yielded accurate LST estimates but require further evaluation to properly constrain the application of the TEX86 proxy.

Impact of sedimentary degradation and deep water column production on GDGT abundance and distribution in surface sediments in the Arabian Sea: Implications for the TEX86 paleothermometer

The TEX86 is a widely used paleotemperature proxy based on isoprenoid glycerol dibiphytanyl glycerol tetraethers (GDGTs) produced by Thaumarchaeota. Archaeal membranes are composed of GDGTs with polar head groups (IPL-GDGTs), most of which are expected to be degraded completely or transformed into more recalcitrant core lipid (CL)-GDGTs upon cell lysis. Here, we examined the differences in concentration and distribution of core lipid (CL)- and intact polar lipid (IPL)-GDGTs in surface sediments at different deposition depths, and different oxygen bottom water concentrations (<3–83μmolL−1). Surface sediments were sampled from 900 to 3000m depth on a seamount (Murray Ridge), whose summit protrudes into the oxygen minimum zone of the Arabian Sea. Concentrations of organic carbon, IPL- and CL-GDGTs decreased linearly with increasing maximum residence time in the oxic zone of the sediment (tOZ), suggesting increasing sedimentary degradation of organic matter and GDGTs. IPL-GDGT-0 was the only exception and increased with tOZ, indicating that this GDGT was probably produced in situ in the surface sediment. Concentrations of crenarchaeol with glycosidic headgroups decreased with increasing tOZ, while crenarchaeol with a hexose, phosphohexose head (HPH) group, in contrast, showed an increase with increasing tOZ, indicating that the concentration of HPH crenarchaeol was primarily determined by in situ production in surficial sediments. TEX86 values of both IPL-derived GDGTs and CL-GDGTs decreased by ∼0.08units with increasing water depth, in spite of the sea surface temperatures being identical for the restricted area studied. In situ production in sediments could be excluded as the main cause, due to the slow production rates of GDGTs in sediments, and previous observations of the same trends in TEX86 in sediment trap material. Instead, the incorporation of GDGTs produced in the oxygen minimum zone (with high TEX86 values) and their preferential degradation during the sinking through the water column, or differential degradation of IPL-GDGTs per head group could be the causes for the observed change in TEX86 values. The effect of differential degradation might cause differences between oxic and anoxically deposited sediments, and, together with a potential deep water contribution on TEX86 values, could translate into changes in reconstructed temperature of <3°C, which might have to be accounted for in TEX86 calibration and paleotemperature studies of deep water sedimentary records.

Effects of growth phase on the membrane lipid composition of the thaumarchaeon Nitrosopumilus maritimus and their implications for archaeal lipid distributions in the marine environment

The characteristic glycerol dibiphytanyl glycerol tetraether membrane lipids (GDGTs) of marine ammonia-oxidizing archaea (AOA) are widely used as biomarkers for studying their occurrence and distribution in marine environments and for reconstructing past sea surface temperatures using the TEX86 index. Despite an increasing use of GDGT biomarkers in microbial ecology and paleoceanography, the physiological and environmental factors influencing lipid composition in AOA, in particular the cyclization of GDGTs, remain unconstrained. We investigated the effect of metabolic state on the composition of intact polar and core lipids and the resulting TEX86 paleothermometer in pure cultures of the marine AOA Nitrosopumilus maritimus as a function of growth phase. The cellular lipid content ranged from 0.9 to 1.9fgcell−1 and increased during growth but was lower in the stationary phases, indicating changes in average cell size in response to metabolic status. The relative abundances of monoglycosidic GDGTs increased from 27% in early growth phase to 60% in late stationary phase, while monohydroxylated GDGTs increased only slightly. The proportions of characteristic hexose-phosphohexose GDGTs were up to 7-fold higher during growth than in stationary phase, suggesting that they are valuable biomarkers for the metabolically active fraction of AOA assemblages in the environment. Methoxy archaeol was identified as novel, genuine archaeal lipid of yet unknown function; it is one of the most abundant single compounds in the lipidome of N. maritimus. TEX86 values of individual intact GDGTs and total GDGTs differed substantially, were generally lower during early and late growth phases than in stationary phase, and did not reflect growth temperature. Consequently, our results strongly suggest that biosynthesis is at least partially responsible for the systematic offsets in TEX86 values between different intact polar GDGT classes observed previously in environmental samples. Nevertheless, differences in degradation rates of intact polar GDGTs may influence the TEX86 index because the intact polar lipid precursors differ for individual core GDGTs and moreover their relative abundances change with growth stage, which may result in distinct release rates of core GDGTs from their polar precursors. Overall, our findings stress the need to accurately describe the factors influencing GDGT cyclization in thaumarchaea and thus paleotemperature reconstructions.

Microbial lipids reveal carbon assimilation patterns on hydrothermal sulfide chimneys.

Sulfide 'chimneys' characteristic of seafloor hydrothermal venting are diverse microbial habitats. ¹³C/¹²C ratios of microbial lipids have rarely been used to assess carbon assimilation pathways on these structures, despite complementing gene- and culture-based approaches. Here, we integrate analyses of the diversity of intact polar lipids (IPL) and their side-chain δ¹³C values (δ¹³ C(lipid)) with 16S rRNA gene-based phylogeny to examine microbial carbon flow on active and inactive sulfide structures from the Manus Basin. Surficial crusts of active structures, dominated by Epsilonproteobacteria, yield bacterial δ¹³C(lipid) values higher than biomass δ¹³C (total organic carbon), implicating autotrophy via the reverse tricarboxylic acid cycle. Our data also suggest δ¹³C(lipid) values vary on individual active structures without accompanying microbial diversity changes. Temperature and/or dissolved substrate effects - likely relating to variable advective-diffusive fluxes to chimney exteriors - may be responsible for differing ¹³C fractionation during assimilation. In an inactive structure, δ¹³C(lipid) values lower than biomass δ¹³C and a distinctive IPL and 16S rRNA gene diversity suggest a shift to a more diverse community and an alternate carbon assimilation pathway after venting ceases. We discuss here the potential of IPL and δ¹³C(lipid) analyses to elucidate carbon flow in hydrothermal structures when combined with other molecular tools.

Ether- and ester-bound iso-diabolic acid and other lipids in members of acidobacteria subdivision 4.

Recently, iso-diabolic acid (13,16-dimethyl octacosanedioic acid) has been identified as a major membrane-spanning lipid of subdivisions 1 and 3 of the Acidobacteria, a highly diverse phylum within the Bacteria. This finding pointed to the Acidobacteria as a potential source for the bacterial glycerol dialkyl glycerol tetraethers that occur ubiquitously in peat, soil, lakes, and hot springs. Here, we examined the lipid composition of seven phylogenetically divergent strains of subdivision 4 of the Acidobacteria, a bacterial group that is commonly encountered in soil. Acid hydrolysis of total cell material released iso-diabolic acid derivatives in substantial quantities (11 to 48% of all fatty acids). In contrast to subdivisions 1 and 3 of the Acidobacteria, 6 out of the 7 species of subdivision 4 (excepting "Candidatus Chloracidobacterium thermophilum") contained iso-diabolic acid ether bound to a glycerol in larger fractional abundance than iso-diabolic acid itself. This is in agreement with the analysis of intact polar lipids (IPLs) by high-performance liquid chromatography-mass spectrometry (HPLC-MS), which showed the dominance of mixed ether-ester glycerides. iso-Diabolic acid-containing IPLs were not identified, because these IPLs are not released with a Bligh-Dyer extraction, as observed before when studying lipid compositions of subdivisions 1 and 3 of the Acidobacteria. The presence of ether bonds in the membrane lipids does not seem to be an adaptation to temperature, because the five mesophilic isolates contained a larger amount of ether lipids than the thermophile "Ca. Chloracidobacterium thermophilum." Furthermore, experiments with Pyrinomonas methylaliphatogenes did not reveal a major influence of growth temperature over the 50 to 69°C range.

A climatic chamber experiment to test the short term effect of increasing temperature on branched GDGT distribution in Sphagnum peat

Branched glycerol dialkyl glycerol tetraethers (br GDGTs) are membrane lipids produced by unknown Bacteria and are being increasingly used as temperature proxies. Nevertheless, the direct effect of temperature on br GDGT distributions has been rarely evaluated. In this study, the impact of increasing temperature on br GDGT distributions and the speed of adaptation of br GDGT source microorganisms to temperature change were investigated by analysing br GDGTs in Sphagnum peat cores incubated under controlled conditions at two different temperatures – 12 and 15°C – for 1yr. Br GDGTs present as intact polar lipids (IPLs, presumably derived from recently active microorganims) and core lipids (CLs, derived from dead biomass) were analysed. There were no significant differences in the relative abundances of the most abundant br GDGTs in the CL and IPL pools after 3months’ incubation. In contrast, the distribution of the br GDGT IPLs was significantly affected by temperature after 1yr, whereas no change was observed in the CL fraction. This suggests that (i) the CL pool of br GDGTs has a turnover of at least 1yr in peat and (ii) br GDGT source microorganisms rapidly adjust their membrane lipid composition (in>3months and<1yr, based on IPL analysis).

Sources of core and intact branched tetraether membrane lipids in the lacustrine environment: Anatomy of Lake Challa and its catchment, equatorial East Africa

The MBT/CBT palaeotemperature proxy uses the distribution of branched glycerol dialkyl glycerol tetraethers (brGDGTs), membrane lipids that are supposed to derive from soil bacteria, to reconstruct mean annual air temperature (MAAT). Applied successfully in coastal marine sediments, its extension to lake-sediment records with potentially high time resolution would greatly expand its utility. Over the last years, however, studies have indicated the presence of additional sources of brGDGTs within lake systems. To constrain the factors influencing the MBT/CBT palaeotemperature proxy in lakes, detailed investigation of brGDGT fluxes in a modern lake system is necessary to identify their potential sources. This study concentrates on Lake Challa, a permanently stratified crater lake in equatorial East Africa with limited catchment area. An almost 3-year time series of approximately monthly samples of settling particles, supplemented with a depth profile of suspended particulate matter (SPM) and sets of profundal surface-sediment and catchment soil samples, were analysed for both the ‘living’ intact polar lipids (IPLs) and ‘fossil’ core lipids (CLs) of GDGTs. We found that brGDGTs are produced in oxic, suboxic and anoxic zones of the water column, and in substantial amounts compared to influxes from catchment soils. Additional in situ production within the lake sediments is most probable, but cannot be definitely confirmed at this time. These lacustrine brGDGTs display a different response to temperature variation than soil-derived brGDGTs, signifying either a different physiological adaptation to changing conditions within the water column and/or a different composition of the respective bacterial communities. Using this specific relationship with temperature, a local calibration based on brGDGT distributions in SPM generates relatively accurate water temperature estimates from settling particles but fails for surface sediments.

Sources and distributions of branched and isoprenoid tetraether lipids on the Amazon shelf and fan: Implications for the use of GDGT-based proxies in marine sediments

Branched glycerol dialkyl glycerol tetraethers (brGDGTs) in river fan sediments have been used successfully to reconstruct mean annual air temperature (MAAT) and soil pH of the Congo River drainage basin. However, in a previous study of Amazon deep-sea fan sediments the reconstructed MAATs were ca. 10°C colder than the actual MAAT of the Amazon basin. In this study we investigated this apparent offset, by comparing the concentrations and distributions of brGDGTs in Amazon River suspended particulate matter (SPM) and sediments to those in marine SPM and surface sediments. The riverine brGDGT input was evident from the elevated brGDGT concentrations in marine SPM and surface sediments close to the river mouth. The distributions of brGDGTs in marine SPM and sediments varied widely, but generally showed a higher relative abundance of methylated and cyclic brGDGTs than those in the river. Since this difference in brGDGT distribution was also found in intact polar lipid (IPL)-derived brGDGTs, which were more recently produced, the change in the marine brGDGT distribution was most likely due to marine in situ production. Consequently, the MAATs calculated based on the methylation of branched tetraethers (MBT) and the cyclisation of branched tetraethers (CBT) were lower and the CBT-derived pH values were higher than those of the Amazon basin. However, SPM and sediments from stations close to the river mouth still showed MBT/CBT values that were similar to those of the river. Therefore, we recommend caution when applying the MBT/CBT proxy, it should only be used in sediment cores that were under high river influence. The influence of riverine derived isoprenoid GDGT (isoGDGT) on the isoGDGT-based TEX86 temperature proxy was also examined in marine SPM and sediments. An input of riverine isoGDGTs from the Amazon River was apparent, but its influence on the marine TEX86 was minor since the TEX86 of SPM in the Amazon River was similar to that in the marine SPM and sediments.

Distribution of intact and core tetraether lipids in water column profiles of suspended particulate matter off Cape Blanc, NW Africa

In the reconstruction of sea surface temperature (SST) from sedimentary archives, secondary sources, lateral transport and selective preservation are considered to be mainly negligible in terms of influencing the primary signal. This is also true for the archaeal glycerol dialkyl glycerol tetraethers (GDGTs) that form the basis for the TEX86 SST proxy. Our samples represent four years variability on a transect off Cape Blanc (NW Africa). We studied the subsurface production, vertical and lateral transport of intact polar lipids and core GDGTs in the water column at high vertical resolution on the basis of suspended particulate matter (SPM) samples from the photic zone, the subsurface oxygen minimum zone (OMZ), nepheloid layers (NL) and the water column between these. Furthermore we compared the water column SPM GDGT composition with that in underlying surface sediments. This is the first study that reports TEX86 values from the precursor intact polar lipids (IPLs) associated with specific head groups (IPL-specific TEX86). We show a clear deviation from the sea surface GDGT composition in the OMZ between 300 and 600m. Since neither lateral transport nor selective degradation provides a satisfactory explanation for the observed TEX-derived temperature profiles, with a bias towards higher temperatures for both core- and IPL-specific TEX86 values, we suggest that subsurface in situ production of archaea with a distinct relationship between lipid biosynthesis and temperature is a responsible mechanism. However, in the NW-African upwelling system the GDGT contribution of the OMZ to the surface sediments did not seem to affect the sedimentary TEX86 as it showed no bias and still reflected the signal of the surface waters between 0 and 60m.

Identification and significance of unsaturated archaeal tetraether lipids in marine sediments

Studies of archaeal glycerol dibiphytanyl glycerol tetraethers (GDGTs) in the environment and cultures have exclusively focused on compounds with fully saturated alkyl moieties. Here we report a number of novel unsaturated GDGTs (uns-GDGTs) whose alkyl chains contain up to six double bonds and zero to two cyclopentyl moieties. The identification of these lipids was achieved via comparison of lipid distribution before and after hydrogenation, characteristic retention time patterns, and diagnostic ions using liquid chromatography/tandem mass spectrometry (LC/MS/MS), and ether cleavage products using gas chromatography/mass spectrometry (GC/MS). Isomerism resulting from different unsaturation patterns in the alkyl moieties was observed and specific positions of double bonds in the biphytene and biphytadiene moieties were tentatively assigned. Uns-GDGTs were detected in sediment and microbial mat samples as both core lipids (CLs) and intact polar lipids (IPLs) associated with mono- or diglycosyl or phosphatidylglycerol headgroups. However, these lipids were overlooked in past investigations because conventional methods for archaeal lipid analysis are unsuitable for uns-GDGTs. Samples from distinct marine environments (Black Sea, Cariaco Basin, Discovery Basin, Eastern Mediterranean Sea, upwelling area off NW Africa, and seep sites off Crimea and Pakistan) were screened for uns-GDGTs using a new LC/MS protocol. The results show that uns-GDGTs contribute significantly to the archaeal lipid pool in anoxic methane-rich environments (Black Sea, Cariaco Basin, and both seep sites) but they were barely detected in the oxic or hypersaline settings. The characteristic distribution of uns-GDGTs implies that they are attractive targets for future studies aiming at the chemotaxonomy of uncultivated archaea and regulation of uns-GDGT biosynthesis.

Fossilization and degradation of archaeal intact polar tetraether lipids in deeply buried marine sediments (Peru Margin)

Glycerol dibiphytanyl glycerol tetraether (GDGT) lipids are part of the cellular membranes of Thaumarchaeota, an archaeal phylum composed of aerobic ammonia oxidizers, and are used in the paleotemperature proxy TEX86 . GDGTs in live cells possess polar head groups and are called intact polar lipids (IPL-GDGTs). Their transformation to core lipids (CL) by cleavage of the head group was assumed to proceed rapidly after cell death, but it has been suggested that some of these IPL-GDGTs can, just like the CL-GDGTs, be preserved over geological timescales. Here, we examined IPL-GDGTs in deeply buried (0.2-186 mbsf, ~2.5 Myr) sediments from the Peru Margin. Direct measurements of the most abundant IPL-GDGT, IPL-crenarchaeol, specific for Thaumarchaeota, revealed depth profiles, which differed per head group. Shallow sediments (<1 mbsf) contained IPL-crenarchaeol with both glycosidic and phosphate head groups, as also observed in thaumarchaeal enrichment cultures, marine suspended particulate matter and marine surface sediments. However, hexose, phosphohexose-crenarchaeol is not detected anymore below 6 mbsf (~7 kyr), suggesting a high lability. In contrast, IPL-crenarchaeol with glycosidic head groups is preserved over timescales of Myr. This agrees with previous analyses of deeply buried (>1 m) marine sediments, which only reported glycosidic and no phosphate-containing IPL-GDGTs. TEX86 values of CL-GDGTs did not markedly change with depth, and the TEX86 of IPL-derived GDGTs decreased only when the proportions of monohexose- to dihexose-GDGTs changed, likely due to the enhanced preservation of the monohexose GDGTs. Our results support the hypothesis that in situ GDGT production and differential IPL degradation in sediments is not substantially affecting TEX86 paleotemperature estimations based on CL-GDGTs and indicates that likely only a small amount of IPL-GDGTs present in deeply buried sediments is part of cell membranes of active archaea. The amount of archaeal biomass in the deep biosphere based on these IPLs may have been substantially overestimated.

Identification of isoprenoid glycosidic glycerol dibiphytanol diethers and indications for their biosynthetic origin

A series of archaeal lipid biomarkers, the isoprenoid glycerol dibiphytanol diethers (GDDs), was recently described and proposed to represent either biosynthetic intermediates or diagenetic products of the relatively more abundant glycerol dibiphytanyl glycerol tetraether (GDGT) lipids (Liu, X.-L., Lipp, J.S., Schröder, J.M., Summons, R.E., Hinrichs, K.-U., 2012. Isoprenoid glycerol dialkanol diethers: a series of novel lipids in marine sediments. Organic Geochemistry 43, 50–55). Here we report a novel series of polar lipids comprising a glycosidic head group and GDD core lipids with varying cycloalkyl distributions (1G-GDDs), which were found in estuarine and hot spring sediments, as well as in a pure culture of the mesophilic thaumarchaeon Nitrosopumilus maritimus. 1G-GDDs represented up to 4% of the corresponding monoglycosidic GDGTs (1G-GDGTs). The distinct cycloalkyl distribution patterns of these intact polar lipids (IPLs) and detection of 1G-GDDs in an archaeal culture suggest a biosynthetic source of 1G-GDDs rather than formation exclusively via diagenetic removal of a glycerol moiety from 1G-GDGTs.

Novel molecular determinants of viral susceptibility and resistance in the lipidome of Emiliania huxleyi

Viruses play a key role in controlling the population dynamics of algae, including Emiliania huxleyi, a globally distributed haptophyte with calcite coccoliths that comprise ca. 50% of the sinking carbonate flux from the surface ocean. Emiliania huxleyi viruses (EhVs) routinely infect and terminate E. huxleyi blooms. EhVs are surrounded by a lipid envelope, which we found to be comprised largely of glycosphingolipids (GSLs) with lesser amounts of polar glycerolipids. Infection appears to involve membrane fusion between the virus and host, and we hypothesized that specific polar lipids may facilitate virus attachment. We identified three novel intact polar lipids in E. huxleyi strain CCMP 374 and EhV86, including a GSL with a monosaccharide sialic acid headgroup (sGSL); for all 11 E. huxleyi strains we tested, there was a direct relationship between sGSL content and sensitivity to infection by EhV1, EhV86 and EhV163. In mesocosms, the E. huxleyi population with greatest initial sGSL content had the highest rate of virus-induced mortality. We propose potential physiological roles for sGSL that would be beneficial for growth but leave cells susceptible to infection, thus furthering the discussion of Red Queen-based co-evolution and the cost(s) of sensitivity and resistance in the dynamic E. huxleyi-EhV system.

Lack of &amp;lt;sup&amp;gt;13&amp;lt;/sup&amp;gt;C-label incorporation suggests low turnover rates of thaumarchaeal intact polar tetraether lipids in sediments from the Iceland shelf

Abstract. Thaumarchaeota are amongst the most abundant microorganisms in aquatic environments, however, their metabolism in marine sediments is still debated. Labeling studies in marine sediments have previously been undertaken, but focused on complex organic carbon substrates which Thaumarchaeota have not yet been shown to take up. In this study, we investigated the activity of Thaumarchaeota in sediments by supplying different 13C-labeled substrates which have previously been shown to be incorporated into archaeal cells in water incubations and/or enrichment cultures. We determined the incorporation of 13C-label from bicarbonate, pyruvate, glucose and amino acids into thaumarchaeal intact polar lipid-glycerol dibiphytanyl glycerol tetraethers (IPL-GDGTs) during 4–6 day incubations of marine sediment cores from three sites on the Iceland shelf. Thaumarchaeal intact polar lipids, in particular crenarchaeol, were detected at all stations and concentrations remained constant or decreased slightly upon incubation. No 13C incorporation in any IPL-GDGT was observed at stations 2 (clay-rich sediment) and 3 (organic-rich sediment). In bacterial/eukaryotic IPL-derived fatty acids at station 3, contrastingly, a large uptake of 13C label (up to + 80‰ ) was found. 13C was also respired during the experiment as shown by a substantial increase in the 13C content of the dissolved inorganic carbon. In IPL-GDGTs recovered from the sandy sediments at station 1, however, some enrichment in δ13C (1–4‰ ) was detected after incubation with bicarbonate and pyruvate. The low incorporation rates suggest a low activity of Thaumarchaeota in marine sediments and/or a low turnover rate of thaumarchaeal IPL-GDGTs due to their low degradation rates. Cell numbers and activity of sedimentary Thaumarchaeota based on IPL-GDGT measurements may thus have previously been overestimated.

Acquisition of intact polar lipids from the prymnesiophyte &amp;lt;i&amp;gt;Phaeocystis globosa&amp;lt;/i&amp;gt; by its lytic virus PgV-07T

Abstract. 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.

Thermococcus kodakarensis modulates its polar membrane lipids and elemental composition according to growth stage and phosphate availability

We observed significant changes in the elemental and intact polar lipid (IPL) composition of the archaeon Thermococcus kodakarensis (KOD1) in response to growth stage and phosphorus supply. Reducing the amount of organic supplements and phosphate in growth media resulted in significant decreases in cell size and cellular quotas of carbon (C), nitrogen (N), and phosphorus (P), which coincided with significant increases in cellular IPL quota and IPLs comprising multiple P atoms and hexose moieties. Relatively more cellular P was stored as IPLs in P-limited cells (2–8%) compared to control cells (<0.8%). We also identified a specific IPL biomarker containing a phosphatidyl-N-acetylhexoseamine headgroup that was relatively enriched during rapid cell division. These observations serve as empirical evidence of IPL adaptations in Archaea that will help to interpret the distribution of these biomarkers in natural systems. The reported cell quotas of C, N, and P represent the first such data for a specific archaeon and suggest that thermophiles are C-rich compared to the cell carbon-to-volume relationship reported for planktonic bacteria.

Seasonality and depth distribution of the abundance and activity of ammonia oxidizing microorganisms in marine coastal sediments (North Sea).

Microbial processes such as nitrification and anaerobic ammonium oxidation (anammox) are important for nitrogen cycling in marine sediments. Seasonal variations of archaeal and bacterial ammonia oxidizers (AOA and AOB) and anammox bacteria, as well as the environmental factors affecting these groups, are not well studied. We have examined the seasonal and depth distribution of the abundance and potential activity of these microbial groups in coastal marine sediments of the southern North Sea. This was achieved by quantifying specific intact polar lipids as well as the abundance and gene expression of their 16S rRNA gene, the ammonia monooxygenase subunit A (amoA) gene of AOA and AOB, and the hydrazine synthase (hzsA) gene of anammox bacteria. AOA, AOB, and anammox bacteria were detected and transcriptionally active down to 12 cm sediment depth. In all seasons, the abundance of AOA was higher compared to the AOB abundance suggesting that AOA play a more dominant role in aerobic ammonia oxidation in these sediments. Anammox bacteria were abundant and active even in oxygenated and bioturbated parts of the sediment. The abundance of AOA and AOB was relatively stable with depth and over the seasonal cycle, while anammox bacteria abundance and transcriptional activity were highest in August. North Sea sediments thus seem to provide a common, stable, ecological niche for AOA, AOB, and anammox bacteria.

Identification of unusual butanetriol dialkyl glycerol tetraether and pentanetriol dialkyl glycerol tetraether lipids in marine sediments

Glycerol serves as the principal backbone moiety bound to various acyl/alkyl chains for membrane lipids of Eukarya, Bacteria, and Archaea. In this study, we report a suite of unusual tetraether lipids in which one of the two conventional glycerol backbones is substituted by butanetriol or pentanetriol. Identification of these lipids was achieved via diagnostic fragments and their expected acetylation products using liquid chromatography/mass spectrometry (LC/MS), and their diagnostic ether cleavage products using gas chromatography/mass spectrometry (GC/MS). We observed structural variations in the polyol backbones and alkyl chains and term these core lipid derivatives: isoprenoidal butanetriol dialkyl glycerol tetraethers (iso-BDGTs), isoprenoidal pentanetriol dialkyl glycerol tetraethers (iso-PDGTs), and hybrid isoprenoidal/branched BDGTs and PDGTs (ib-BDGTs, ib-PDGTs). Of these, iso-BDGTs were the most abundant with a methylation at either the sn-1 or sn-3 position of glycerol and were also found as part of intact polar lipids, adjoined to mono- or diglycosidic headgroups. Iso-BDGTs and iso-PDGTs are likely produced by Archaea, as indicated by the presence of the characteristic biphytanyl moieties. Butanetriol- and pentanetriol-based tetraether lipids occur in modern estuarine and deeply buried subseafloor sediments, suggesting the presence of alternative backbones in archaeal lipids.

Different seasonality of pelagic and benthic Thaumarchaeota in the North Sea

Abstract. 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.

Pelolinea submarina gen. nov., sp. nov., an anaerobic, filamentous bacterium of the phylum Chloroflexi isolated from subseafloor sediment

A novel, anaerobic filamentous bacterium, strain MO-CFX1(T), was isolated from a methanogenic community, which was originally established from subseafloor sediments collected from off the Shimokita Peninsula, Japan. Cells were non-spore-forming, non-motile, Gram-stain-negative and filamentous. The filaments were longer than 10 µm and 130-150 nm in width. Growth of the strain was observed at 10-37 °C (optimum 25-30 °C), at pH 5.5-8.5 (optimum pH 7.0) and in 0-50 g NaCl l(-1) (optimum 15 g NaCl l(-1)). The strain was able to grow with a number of carbohydrates in the presence of yeast extract. The major cellular fatty acids were monounsaturated C18 : 1ω9, C16 : 1ω7 and saturated C18 : 0 and C16 : 0. The intact polar lipids of the strain were dominated by diacylglyceride and sphingolipid core lipid structures with monoglycosidic, mixed phosphomonoglycosidic and fatty-acid-modified monoglycosidic polar head groups. The G+C content of the genomic DNA was 52.4 mol%. Based on the comparative 16S rRNA gene sequence analysis, strain MO-CFX1(T) was affiliated with the class Anaerolineae within the phylum Chloroflexi and was most closely related to Leptolinea tardivitalis YMTK-2(T) (sequence identity of 91.0 %). Based on phenotypic and genetic properties of the novel isolate, we propose a novel species representing a new genus Pelolinea submarina gen. nov., sp. nov., for strain MO-CFX1(T) ( = JCM 17238(T), = KCTC 5975(T)). This is the first formal description, to our knowledge, of an isolate of the phylum Chloroflexi from the deep-sea sedimentary environment.