Elemental, biomarker, palynology and maceral data from Seam 1, Schöningen and associated interbeds

Sphagnum moss is the dominant plant type in modern boreal and (sub)arctic ombrotrophic bogs and is of particular interest due to its sensitivity to climate and its important role in wetland biogeochemistry. Here we reconstruct the occurrence of Sphagnum moss - and associated biogeochemical change - within a thermally immature, early Paleogene (~55 Ma) lignite from Schöningen, NW Germany using a high-resolution, multi-proxy approach. Changes in the abundance of Sphagnum-type spores and the C23/C31n-alkane ratio indicate the expansion of Sphagnum moss within the top of the lignite seam. This Sphagnum moss expansion is associated with the development of waterlogged conditions, analogous to what has been observed within modern ombrotrophic bogs. The similarity between biomarkers and palynology also indicates that the C23/C31n-alkane ratio may be a reliable chemotaxonomic indicator for Sphagnum during the early Paleogene. The d13C value of bacterial hopanes and mid-chain n-alkanes indicates that a rise in water table is not associated with a substantial increase in aerobic methanotrophy. The absence of very low d13C values within the top of the seam could reflect either less methanogenesis or less efficient methane oxidation under waterlogged sulphate-rich conditions.

Concentrations and d13C compositions of n-alkanes, n-alcohols, n-alkanoic acids in a 34-month time series of suspended sediments from the outflow of the Congo River

The concentrations, distributions, and stable carbon isotopes (d13C) of plant waxes carried by fluvial suspended sediments contain valuable information about terrestrial ecosystem characteristics. To properly interpret past changes recorded in sedimentary archives it is crucial to understand the sources and variability of exported plant waxes in modern systems on seasonal to inter-annual timescales. To determine such variability, we present concentrations and d13C compositions of three compound classes (n-alkanes, n-alcohols, n-alkanoic acids) in a 34-month time series of suspended sediments from the outflow of the Congo River. We show that exported plant-dominated n-alkanes (C25-C35) represent a mixture of C3 and C4 end members, each with distinct molecular distributions, as evidenced by an 8.1 ± 0.7 per mil (±1Sigma standard deviation) spread in d13C values across chain-lengths, and weak correlations between individual homologue concentrations (r = 0.52-0.94). In contrast, plant-dominated n-alcohols (C26-C36) and n-alkanoic acids (C26-C36) exhibit stronger positive correlations (r = 0.70-0.99) between homologue concentrations and depleted d13C values (individual homologues average <= -31.3 per mil and -30.8 per mil, respectively), with lower d13C variability across chain-lengths (2.6 ± 0.6 per mil and 2.0 ± 1.1 per mil, respectively). All individual plant-wax lipids show little temporal d13C variability throughout the time-series (1 Sigma <= 0.9 per mil), indicating that their stable carbon isotopes are not a sensitive tracer for temporal changes in plant-wax source in the Congo basin on seasonal to inter-annual timescales. Carbon-normalized concentrations and relative abundances of n-alcohols (19-58% of total plant-wax lipids) and n-alkanoic acids (26-76%) respond rapidly to seasonal changes in runoff, indicating that they are mostly derived from a recently entrained local source. In contrast, a lack of correlation with discharge and low, stable relative abundances (5-16%) indicate that n-alkanes better represent a catchment-integrated signal with minimal response to discharge seasonality. Comparison to published data on other large watersheds indicates that this phenomenon is not limited to the Congo River, and that analysis of multiple plant-wax lipid classes and chain lengths can be used to better resolve local vs. distal ecosystem structure in river catchments.

Effect of acidification on an Arctic phytoplankton community from Disko Bay, West Greenland

Long-term measurements (i.e. months) of in situ pH have not previously been reported from the Arctic; this study shows fluctuations between pH 7.5 and 8.3 during the spring bloom 2012 in a coastal area of Disko Bay, West Greenland. The effect of acidification on phytoplankton from this area was studied at both the community and species level in experimental pH treatments within (pH 8.0, 7.7 and 7.4) and outside (pH 7.1) in situ pH. The growth rate of the phytoplankton community decreased during the experimental acidification from 0.50 ± 0.01/day (SD) at pH 8.0 to 0.22 ± 0.01/day at pH 7.1. Nevertheless, the response to acidification was species-specific and divided into 4 categories: I, least affected; II, affected only at pH 7.1; III, gradually affected and IV, highly affected. In addition, the colony size and chain length of selected species were affected by the acidification. Our findings show that coastal phytoplankton from Disko Bay is naturally exposed to pH fluctuations exceeding the experimental pH range used in most ocean acidification studies. We emphasize that studies on ocean acidification should include in situ pH before assumptions on the effect of acidification on marine organisms can be made.

Diffusible Signal Factor (DSF)-dependent quorum sensing in pathogenic bacteria and its exploitation for disease control

Cell-to-cell signals of the Diffusible Signal Factor (DSF) family are cis-2-unsaturated fatty acids of differing chain length and branching pattern. DSF signalling has been described in diverse bacteria to include plant and human pathogens where it acts to regulate functions such as biofilm formation, antibiotic tolerance and the production of virulence factors. DSF family signals can also participate in interspecies signalling with other bacteria and interkingdom signaling such as with the yeast Candida albicans. Interference with DSF signalling may afford new opportunities for the control of bacterial disease. Such strategies will depend in part on detailed knowledge of the molecular mechanisms underlying the processes of signal synthesis, perception and turnover. Here, I review both recent progress in understanding DSF signalling at the molecular level and prospects for translating this knowledge into approaches for disease control.

Organic-geochemical proxies (UK'37 and TEXH86) records in surface sediments of the tropical Eastern Indian Ocean

In this study we reconstruct sea surface temperatures (SSTs) using two lipid-based biomarker proxies (alkenone unsaturation index UK'37 and TEX86 index based on glycerol dibiphytanyl glycerol tetraethers) in 36 surface sediment samples from the Indonesian continental margin off west Sumatra and south of Java and the Lesser Sunda Islands. Comparison of measured temperatures (World Ocean Atlas 09) to reconstructed temperatures suggests that SST-UK'37 reflects the SE monsoon SST in the upwelling area south of Java and the Lesser Sunda Islands, whereas Temp-TEXH86 estimates are up to 2°C lower than SST-UK'37. This offset is possibly related to either one or a combination of two factors: i) the depth habitats of the source organisms; ii) different seasonal production and/ or seasonality of export associated with phytoplankton blooming triggered by primary productivity. In the non-upwelling area off west Sumatra, the alkenone-based SSTs are cooler than measured temperatures during the entire year, likely due to the reduced sensitivity of the UK'37 proxy beyond 28°C. However, reconstructed temperatures based on TEXH86 are consistent with mean annual SST, implying that the Temp-TEXH86 reflects the mean annual SST in the non-upwelling area of the tropical Eastern Indian Ocean.

Organic geochemistry of sediments from sapropel 94 of ODP Hole 161-974C

Analysis of the molecular composition of the organic matter (OM) from whole sediment samples can avoid analytical bias that might result from isolation of components from the sediment matrix, but has its own analytical challenges. We evaluated the use of GC * GC-ToFMS to analyze the pyrolysis products of six whole sediment samples obtained from above, within and below a 1 million year old OM-rich Mediterranean sapropel layer. We found differences in pyrolysis products chain aliphatic hydrocarbons, pyrroles, furans and alkyl aromatics in the pyrolysates of sapropel samples relative to the marls confirm better preservation of marine OM in the sapropels. In addition, the presence of greater amounts of thiophenes in the sapropels than in the marls is consistent with the existence of euxinic conditions during sapropel deposition. The combination of whole sediment pyrolysis and GC × GC-ToFMS is promising, but the procedure requires careful selection of its multiple analytical variables, particularly the pyrolysis temperature and the operational features of the GC columns.

Ketones in hydrothermal petroleums and sediments from Guaymas Basin

The polar compound (NSO) fractions of seabed petroleums and sediment extracts from the Guaymas Basin hydrothermal system have been analyzed by gas chromatography and gas chromatography-mass spectrometry. The oils were collected from the interiors and exteriors of high temperature hydrothermal vents and represent hydrothermal pyrolysates that have migrated to the seafloor by hydrothermal fluid circulation. The downcore samples are representative of both thermally unaltered and thermally altered sediments. The survey has revealed the presence of oxygenated compounds correlated with samples exhibiting a high degree of thermal maturity. Several homologous series of related ketone isomers are enriched in the interiors of the hydrothermal vent samples or in hydrothermally-altered sequences of the downcore sediments (DSDP Holes 477 and 481A). The n-alkanones range in carbon number from C11 to C33 with a Cmax from 14 to 23, distributions that are similar to those of the n-alkanes. The alkan-2-ones are usually in highest concentrations, with lower amounts of 3-, 4-, 5-, 6-, 7- (and higher) alkanones, and they exhibit no carbon number preference (there is an odd carbon number preference of alkanones observed for downcore samples). The alkanones are enriched in the interiors of the hydrothermal vent spires or in downcore hydrothermally-altered sediments, indicating an origin at depth or in the hydrothermal fluids and not from an external biogenic deposition. Minor amounts of C13 and C18 isoprenoid ketones are also present. Simulation of the natural hydrothermal alternation process by laboratory hydrous pyrolysis techniques provided information regarding the mode of alkanone formation. Hydrous pyrolysis of n-C32H66 at 350°C for 72 h with water only or water with inorganic additives has been studied using a stainless steel reaction vessel. In each experiment oxygenated hydrocarbons, including alkanones, were formed from the n-alkane. The product distributions indicate a reaction pathway consisting of n-alkanes and a-olefins as primary cracking products with internal olefins and alkanones as secondary reaction products. Hydrous pyrolyses of Messel shale spiked with molecular probes have been performed under similar time and temperature constraints to produce alkanone distributions like those found in the hydrothermal vent petroleums.

14C specific radiocarbon ages and bulk ages accompanied by geochemical proxys from surface sediment samples in the Black Sea

Transfer of organic carbon (OC) from the terrestrial to the oceanic carbon pool is largely driven by riverine and aeolian transport. Before transport, however, terrigenous organic matter can be retained in intermediate terrestrial reservoirs such as soils. Using compound-specific radiocarbon analysis of terrigenous biomarkers their average terrestrial residence time can be evaluated. Here we show compound-specific radiocarbon (14C) ages of terrigenous biomarkers and bulk 14C ages accompanied by geochemical proxy data from core top samples collected along transects in front of several river mouths in the Black Sea. 14C ages of long chain n-alkanes, long chain n-fatty acids and total organic carbon (TOC) are highest in front of the river mouths, correlating well with BIT (branched and isoprenoid tetraether) indices, which indicates contribution of pre-aged, soil-derived terrigenous organic matter. The radiocarbon ages decrease further offshore towards locations where organic matter is dominated by marine production and aeolian input potentially contributes terrigenous organic matter. Average terrestrial residence times of vascular plant biomarkers deduced from n-C29+31 alkanes and n-C28+30 fatty acids ages from stations directly in front of the river mouths range from 900 ± 70 years to 4400 ± 170 years. These average residence times correlate with size and topography in climatically similar catchments, whereas the climatic regime appears to control continental carbon turnover times in morphologically similar drainage areas of the Black Sea catchment. Along-transect data imply petrogenic contribution of n-C29+31 alkanes and input via different terrigenous biomarker transport modes, i.e., riverine and aeolian, resulting in aged biomarkers at offshore core locations. Because n-C29+31 alkanes show contributions from petrogenic sources, n-C28+30 fatty acids likely provide better estimates of average terrestrial residence times of vascular plant biomarkers. Moreover, sedimentary n-C28 and n-C30 fatty acids appear clearly much less influenced by autochthonous sources than n-C24 and n-C26 fatty acids as indicated by increasing radiocarbon ages with increasing chain-length and are, thus, more representative as vascular plant biomarkers.

(Table 1) Lipid biomarkers in surface sediments from the Gulf of Genoa

A series of molecular organic markers were determined in surface sediments from the Gulf of Genoa (Ligurian Sea) in order to evaluate their potential for palaeo-environmental reconstructions. Allochthonous input can be characterized by the distributions of n-C29 and n-C31 alkanes, n-C26 and n-C28 alkanols and branched glycerol dialkyl glycerol tetraethers (GDGTs), whose concentrations are generally highest near the river mouths. In the open basin however, terrestrial n-alkanes and n-alkanols may have an additional, aeolian source. Autochthonous input is represented by crenarchaeol and isoprenoid GDGTs. Their concentrations are highest in the open basin showing the preference of Thaumarchaeota for oligotrophic waters. Indications of a significant degradation of sterols and C37 alkenones exclude these lipids as reliable productivity proxies. Using terrestrial and aquatic lipids as end-members allows estimating the percentage of terrestrial organic matter between 20% and 58% in the coastal area decreasing to 1 to 30% in the deep basin. The spatial distribution of sea surface temperature (SST) estimates using the alkenone-based UK'37 index is very similar to the autumnal (November) mean satellite-based SST distribution. Conversely, TEXH86-derived SST estimates are close to winter SSTs in the coastal area and summer SSTs in the open basin. This pattern reflects presumably a shift in the main production of Thaumarchaeota from the coastal area in winter to the open basin in summer. This study represents a major prerequisite for the future application of lipid biomarkers on sediment cores from the Gulf of Genoa.

n-Alkane content and compound-specific d13C values of soil samples, river samples, and marine surface samples

Southwestern Africa's coastal marine mudbelt, a prominent Holocene sediment package, provides a valuable archive for reconstructing terrestrial palaeoclimates on the adjacent continent. While the origin of terrestrial inorganic material has been intensively studied, the sources of terrigenous organic material deposited in the mudbelt are yet unclear. In this study, plant wax derived n-alkanes and their compound-specific d13C in soils, flood deposits and suspension loads from regional fluvial systems and marine sediments are analysed to characterize the origin of terrestrial organic material in the southwest African mudbelt. Soils from different biomes in the catchments of the Orange River and small west coast rivers show on average distinct n-alkane distributions and compound-specific d13C values reflecting biome-specific vegetation types, most notably the winter rainfall associated Fynbos Biome of the southwestern Cape. In the fluvial sediment samples from the Orange River, changes in the n-alkane distributions and compound-specific d13C compositions reveal an overprint by local vegetation along the river's course. The smaller west coast rivers show distinct signals, reflecting their small catchment areas and particular vegetation communities. Marine surface sediments spanning a transect from the northern mudbelt (29°S) to St. Helena Bay (33°S) reveal subtle, but spatially coherent, changes in n-alkane distributions and compound-specific d13C, indicating the influence of Orange River sediments in the northern mudbelt, the increasing importance of terrigenous input from the adjacent western coastal biomes in the central mudbelt, and contributions from the Fynbos Biome to the southern mudbelt. These findings indicate the different sources of terrestrial organic material deposited in the mudbelt, and highlight the potential the mudbelt has to preserve evidence of environmental change from the adjacent continent.

Stable carbon isotopic analyses of n-alkanes and the calculated C4 plant-derived fractions in the dust samples

Atmospheric dust samples collected along a transect off the West African coast have been investigated for their lipid content and compound-specific stable carbon isotope compositions. The saturated hydrocarbon fractions of the organic solvent extracts consist mainly of long-chain n-alkanes derived from epicuticular wax coatings of terrestrial plants. Backward trajectories for each sampling day and location were calculated using a global atmospheric circulation model. The main atmospheric transport took place in the low-level trade-wind layer, except in the southern region, where long-range transport in the mid-troposphere occurred. Changes in the chain length distributions of the n-alkane homologous series are probably related to aridity, rather than temperature or vegetation type. The carbon preference of the leaf-wax n-alkanes shows significant variation, attributed to a variable contribution of fossil fuel- or marine-derived lipids. The effect of this nonwax contribution on the d13C values of the two dominant n-alkanes in the aerosols, n-C29 and n-C31 alkane, is, however, insignificant. Their d13C values were translated into a percentage of C4 vs. C3 plant type contribution, using a two-component mixing equation with isotopic end-member values from the literature. The data indicate that only regions with a predominant C4 type vegetation, i.e. the Sahara, the Sahel, and Gabon, supply C4 plant-derived lipids to dust organic matter. The stable carbon isotopic compositions of leaf-wax lipids in aerosols mainly reflect the modern vegetation type along their transport pathway. Wind abrasion of wax particles from leaf surfaces, enhanced by a sandblasting effect, is most probably the dominant process of terrigenous lipid contribution to aerosols.

Production of Polyhydroxyalkanoates by Pseudomonas mendocina using vegetable oils and their characterisation

Synthesis of Polyhydroxyalkanoates (PHAs) by Pseudomonas mendocina, using different vegetable oils such as, coconut oil, groundnut oil, corn oil and olive oil, as the sole carbon source was investigated for the first time. The PHA yield obtained was compared with that obtained during the production of PHAs using sodium octanoate as the sole carbon source. The fermentation profiles at shaken flask and bioreactor levels revealed that vegetable oils supported the growth of Pseudomonas mendocina and PHA accumulation in this organism. Moreover, when vegetable oil (coconut oil) was used as the sole carbon source, fermentation profiles showed better growth and polymer production as compared to conditions when sodium octanoate was used as the carbon source. In addition, comparison of PHA accumulation at shaken flask and fermenter level confirmed the higher PHA yield at shaken flask level production. The highest cell mass found using sodium octanoate was 1.8 g/L, whereas cell mass as high as 5.1 g/L was observed when coconut oil was used as the feedstock at flask level production. Moreover, the maximum PHA yield of 60.5% dry cell weight (dcw) was achieved at shaken flask level using coconut oil as compared to the PHA yield of 35.1% dcw obtained using sodium octanoate as the sole carbon source. Characterisations of the chemical, physical, mechanical, surface and biocompatibility properties of the polymers produced have been carried out by performing different analyses as described in the second chapter of this study. Chemical analysis using GC and FTIR investigations showed medium chain length (MCL) PHA production in all conditions. GC-MS analysis revealed a unique terpolymer production, containing 3-hydroxyoctanoic acid, 3-hydroxydecanoic acid and 3-hydroxydodecanoic acid when coconut oil, groundnut oil, olive oil, and corn oil were used as the carbon source. Whereas production of the homopolymer containing 3-hydroxyoctanoic acid was observed when sodium octanoate was used as the carbon source. MCL-PHAs produced in this study using sodium octanoate, coconut oil, and olive oil exhibited melting transitions, indicating that each of the PHA was crystalline or semi-crystalline polymer. In contrast, the thermal properties of PHAs produced from groundnut and corn oils showed no melting transition, indicating that they were completely amorphous or semi-crystalline, which was also confirmed by the X-Ray Diffraction (XRD) results obtained in this study. Mechanical analysis of the polymers produced showed higher stiffness of the polymer produced from coconut oil than the polymer from sodium octanoate. Surface characterisation of the polymers using Scanning Electron Microscopy (SEM) revealed a rough surface topography and surface contact angle measurement revealed their hydrophobic nature. Moreover, to investigate the potential applicability of the produced polymers as the scaffold materials for dental pulp regeneration, multipotent human Mesenchymal stem cells (hMSCs) were cultured onto the polymer films. Results indicated that these polymers are not cytotoxic towards the hMSCs and could support their attachment and proliferation. Highest cell growth was observed on the polymer samples produced from corn oil, followed by the polymer produced using coconut oil. In conclusion, this work established, for the first time, that vegetable oils are a good economical source of carbon for production of MCL-PHA copolymers effectively by Pseudomonas mendocina. Moreover, biocompatibility studies suggest that the produced polymers may have potential for dental tissue engineering application.

Poly(3-hydroxyoctanoate), a promising new material for cardiac tissue engineering

Cardiac tissue engineering (CTE) is currently a prime focus of research due to an enormous clinical need. In this work, a novel functional material, Poly(3-hydroxyoctanoate), P(3HO), a medium chain length polyhydroxyalkanoate (PHA), produced using bacterial fermentation, was studied as a new potential material for CTE. Engineered constructs with improved mechanical properties, crucial for supporting the organ during new tissue regeneration, and enhanced surface topography, to allow efficient cell adhesion and proliferation, were fabricated. Our results showed that the mechanical properties of the final patches were close to that of cardiac muscle. Biocompatibility of the P(3HO) neat patches, assessed using Neonatal ventricular rat myocytes (NVRM), showed that the polymer was as good as collagen in terms of cell viability, proliferation and adhesion. Enhanced cell adhesion and proliferation properties were observed when porous and fibrous structures were incorporated to the patches. Also, no deleterious effect was observed on the adults cardiomyocytes’ contraction when cardiomyocytes were seeded on the P(3HO) patches. Hence, P(3HO) based multifunctional cardiac patches are promising constructs for efficient CTE. This work will provide a positive impact on the development of P(3HO) and other PHAs as a novel new family of biodegradable functional materials with huge potential in a range of different biomedical applications, particularly CTE, leading to further interest and exploitation of these materials.