C25 Highly Branched Isoprenoid Research Articles

A novel tri-unsaturated highly branched isoprenoid (HBI) alkene from the marine diatom Navicula salinicola

A novel tri-unsaturated C25 highly branched isoprenoid (HBI) alkene has been identified in a laboratory culture of the diatom Navicula salinicola and its structure determined using a combination of NMR spectroscopy and gas chromatography–mass spectrometry (GC–MS). This represents the first report of a C25 HBI in a marine diatom from the Navicula genus, although a different tri-unsaturated C25 HBI has been reported previously in the freshwater species N. sclesvicensis and unspecified HBIs have been identified in the brackish N. phyllepta. The newly characterised HBI contains a relatively unusual conjugated diene sub-unit, a structural feature only previously reported in some HBIs biosynthesised by a further marine diatom, Haslea ostrearia.

Identification of C25 highly branched isoprenoid (HBI) alkenes in diatoms of the genus Rhizosolenia in polar and sub-polar marine phytoplankton

We report the identification of a range of C25 highly branched isoprenoid (HBI) alkenes and certain sterols in filtered phytoplankton samples obtained from western Svalbard (Arctic) and near South Georgia (South Atlantic, sub-Antarctic) in 2016 and 2014, respectively. The C25 HBIs contained 3–5 double bonds and had structures identified previously from analysis of laboratory diatom cultures. The same HBIs were also identified in individual diatom taxa isolated from the mixed assemblages and with reasonably similar distributions. Thus, C25 HBIs were identified in Rhizosolenia setigera isolated from western Svalbard near-surface waters, while the same HBIs were also found in R. polydactyla f. polydactylaand R. hebetata f. semispina picked from seawater collected from a site in the South Atlantic. The main sterol composition was slightly different between the two locations, with cholesta-5,24-dien-3β-ol (desmosterol) identified as one of the major components in the sample from West Svalbard, consistent with the diatom assemblage being dominated by R. setigera. In contrast, the major sterol in the South Atlantic sample was cholesta-5,22-dien-3β-ol (22-dehydrocholesterol), likely reflecting the relatively high proportion of the genus Pseudo-nitzschia. For both locations, the suite of HBIs included a tri-unsaturated isomer (HBI III; 6Z-2,6,10,14-tetramethyl-9-(3′-methylpent-4-enylidene)-pentadec-6-ene), proposed in previous studies as a potential proxy measure of pelagic sea ice-edge conditions, and thus a counterpart to the mono- and di-unsaturated HBIs IP25 and IPSO25, which have been used as seasonal sea ice proxies in the Arctic and Antarctic, respectively. HBI III has been reported previously in sediments from West Svalbard and we report here its occurrence in a small number of surface sediments from the South Atlantic. For both regions, HBI III was present as one of the major HBIs in sediments, which contrasts with the HBI distributions in the filtered phytoplankton samples, where HBIs with four and five double bonds were the major components. Differences in HBI distributions between phytoplankton and sediment samples may potentially be due to the presence of other (unanalysed) diatoms in the filtered water samples, seasonal/annual variability in the production of HBIs by a range of diatoms, differential degradation of HBIs between sources and sediments, or a combination of these. Interestingly, we did not detect any C30 HBIs in the water samples, picked cells or sediments from either location, despite earlier reports of these lipids in laboratory cultures of R. setigera. This study represents the first source identification of certain C25 HBI lipids under in situ pelagic conditions.

Distributions of highly branched isoprenoid alkenes and other algal lipids in surface waters from East Antarctica: Further insights for biomarker-based paleo sea-ice reconstruction

The occurrence and variable abundance of certain di- and tri-unsaturated C25 highly branched isoprenoid (HBI) biomarkers in Antarctic marine sediments has previously been proposed as a possible proxy measure of paleo sea-ice extent in the Southern Ocean. In the current study, we obtained 47 near-surface (ca. 0–10m) water samples taken from locations in East Antarctica with different sea ice settings and analysed them for their HBI, sterol and fatty acid content. Sampling locations ranged from the permanently open-ocean zone (POOZ), with no seasonal sea-ice cover, the near-shore summer sea ice zone (SIZ), where sea ice remains long into the summer melt season, and the marginal ice zone (MIZ), located between the POOZ and the SIZ, and with a highly variable latitudinal sea-ice edge throughout the season. A di-unsaturated C25 HBI (diene II) was only identified in surface waters from the MIZ and the SIZ, consistent with a sea-ice diatom origin for this biomarker. In contrast, a tri-unsaturated C25 HBI (triene III) was detected in all samples from the POOZ, the MIZ and the SIZ, and with a stable isotopic composition (δ13C=−35±1.5‰) consistent with a phytoplankton source. The highest concentrations of diene II and triene III were in samples from the SIZ and the MIZ, respectively, thus providing further insights into the sea-ice conditions likely favourable for their production and how their relative abundances (the II/III ratio) in underlying sediments might be better interpreted for paleo sea-ice reconstruction. In this respect, relatively high II/III might be a good indicator of extended (into summer) seasonal sea-ice cover, while lower II/III may provide a better indicator of the MIZ. However, the observation of highly variable II/III within the polynya setting of the SIZ may also have significant impacts on sedimentary values. Distributions of diatom sterols and fatty acids were also variable between the three sampling zones, but these were not as distinctive as those observed for the HBIs.

C25 highly branched isoprenoid alkenes in the Baltic Sea produced by the marine planktonic diatom Pseudosolenia calcar-avis

C25 and C30 highly branched isoprenoid (HBI) alkenes are lipid biomarkers produced exclusively by certain diatoms and found in sediments worldwide. Here, for the first time, it is shown that the marine planktonic diatom Pseudosolenia calcar-avis (Schultze) (Sundström, B.G., 1986. The Marine Diatom Genus Rhizosolenia (A New Approach to the Taxonomy) (Ph.D. thesis). Lund University, Lund), isolated from near surface waters in Mecklenburg Bay (southwestern Baltic Sea) biosynthesizes one C25:2 and two C25:3 HBI alkenes previously reported in some benthic diatoms. The presence of the same C25 HBI alkenes in surface sediments from Mecklenburg Bay and the Arkona Sea, as well as their co-occurrence with remnant frustules of P. calcar-avis in a sediment core from the northern Baltic Sea, indicates that these lipids are very likely specific biomarkers for this diatom in this region at least. Further, since P. calcar-avis has a tolerance for low salinities (8–10), we also suggest that the occurrence of some of the HBIs produced by this diatom might represent a useful proxy for measuring past changes in inflowing water from the North Sea. The same C25 HBIs, previously found in sediments from the Caspian Sea and the Black Sea, may also be produced by P. calcar-avis in such settings.

Cloning and characterization of farnesyl pyrophosphate synthase from the highly branched isoprenoid producing diatom Rhizosolenia setigera.

The diatom Rhizosolenia setigera Brightwell produces highly branched isoprenoid (HBI) hydrocarbons that are ubiquitously present in marine environments. The hydrocarbon composition of R. setigera varies between C25 and C30 HBIs depending on the life cycle stage with regard to auxosporulation. To better understand how these hydrocarbons are biosynthesized, we characterized the farnesyl pyrophosphate (FPP) synthase (FPPS) enzyme of R. setigera. An isolated 1465-bp cDNA clone contained an open reading frame spanning 1299-bp encoding a protein with 432 amino acid residues. Expression of the RsFPPS cDNA coding region in Escherichia coli produced a protein that exhibited FPPS activity in vitro. A reduction in HBI content from diatoms treated with an FPPS inhibitor, risedronate, suggested that RsFPPS supplies precursors for HBI biosynthesis. Product analysis by gas chromatography-mass spectrometry also revealed that RsFPPS produced small amounts of the cis-isomers of geranyl pyrophosphate and FPP, candidate precursors for the cis-isomers of HBIs previously characterized. Furthermore, RsFPPS gene expression at various life stages of R. setigera in relation to auxosporulation were also analyzed. Herein, we present data on the possible role of RsFPPS in HBI biosynthesis, and it is to our knowledge the first instance that an FPPS was cloned and characterized from a diatom.

Identification of a novel di-unsaturated C25 highly branched isoprenoid in the marine tube-dwelling diatom Berkeleya rutilans

Highly branched isoprenoids (HBIs) are known to be biosynthesised by diatoms and are a common component of many marine and freshwater environments. However, the ability to produce these unusual hydrocarbons appears to be restricted to a few diatom species that are represented by just four genera (Haslea, Pleurosigma, Rhizosolenia and Navicula). Despite this, we routinely observe some HBIs in the natural environment that are absent from cultures of known HBI-producing diatoms, indicating the possibility of further sources. Having identified one commonly observed, yet unknown HBI isomer in estuarine sediments, we isolated and cultured diatoms in the laboratory to identify the source of this novel di-unsaturated C25 HBI. Here, we show that analysis of purified extracts obtained from a laboratory culture of the tube-dwelling diatom Berkeleya rutilans enabled determination of the structure of this new compound by combined NMR spectroscopic and mass spectrometric analysis. This represents the first identification of an HBI alkene within the Berkeleya genus and adds to the growing number of reports of genera that produce these unusual hydrocarbons. The newly characterised HBI diene appears to be common in marine sediments and has also been reported in a range of marine biota, thus making it a potential tracer of source organic matter, as has been found for other HBI alkenes.

Biomarker and compound-specific δ13C evidence for changing environmental conditions and carbon limitation at Lake Koucha, eastern Tibetan Plateau

A sediment core from Lake Koucha (eastern Tibetan Plateau) was investigated using organic biomarkers and their stable carbon isotope signatures. The correlation between TOC content, total amount of aquatic macrophyte-derived n-alkanes (e.g. nC23) and δ13C values of TOC and nC23 indicates that Lake Koucha was macrophyte-dominated before 8 cal ka BP. Shortly after the lake turned from a saline to a freshwater system at 7.2 cal ka BP, a variety of algal and bacterial markers such as hopanoids and isoprenoids emerged, of which phytane, pentamethylicosene (PMI), moretene and diploptene are particularly abundant. Phytane and PMI show different isotopic signals (≈−18 and ≈−28‰, respectively), which indicates that they originated from different sources. Phytane may have been derived from cyanobacteria, while methanogenic archaea may be the source of PMI. The isotopic depletion of diploptene and moretene (≈−60‰) indicates the presence of methanotrophs. After 6.1 cal ka BP, the saturated C20 highly branched isoprenoid (HBI) became the dominant constituent of the aliphatic hydrocarbon fraction. Such dominance has rarely been reported in lacustrine environments, and indicates a strong presence of algae (most likely diatoms) or cyanobacteria. At 4.7 cal ka BP, the appearance of an unsaturated C25 HBI, which is a specific biomarker for diatoms, was noted. Furthermore, the level of nC17-alkane was observed to increase in abundance in the uppermost two samples. These results suggest that the lake was phytoplankton-dominated during the last 6.1 ka. Relatively low biomarker concentrations and δ13C values at 6.0, 3.1 and 1.8 cal ka BP indicate the occurrence of cool periods, which is in agreement with inferences from other locations on the Tibetan Plateau. The δ13C values of nC23 range from −23.5 to −12.6‰, with high values at the peak of macrophyte abundance at ca. 11 cal ka BP and at the phytoplankton maximum between ca 6.1 and 2.8 cal ka BP. Thus, aquatic macrophyte-derived mid-chain n-alkanes have been found to be excellent indicators of carbon-limiting conditions, which lead to the assimilation of isotopically-enriched carbon species. The limitation of carbon sources could be a localized phenomenon occurring in dense plant stands (as in the older section of the core), or it may be induced by high primary productivity (as in the younger section). Since the δ13C value of the inorganic carbon source may vary, the offset between the δ13C values of nC23 and TIC could serve as a more precise proxy for carbon-limiting conditions in lacustrine environments, which could in turn be interpreted with respect to lacustrine paleo-productivity.

C25 highly branched isoprenoid alkenes from the marine benthic diatom Pleurosigma strigosum

The hydrocarbon composition of the marine diatom Pleurosigma strigosum isolated from coastal Mediterranean sediments is described. A suite of five C25 highly branched isoprenoid (HBI) alkenes with 2–5 double bonds were detected together with n-C21:4 and n-C21:5 alkenes and squalene. The analysis by 1H and 13C NMR spectroscopy of two isolated HBI alkenes allowed the structural identification of a novel C25 HBI triene (2,6,10,14-tetramethyl-7-(3-methylpent-4-enyl)-pentadeca-5E,13-diene) and the first identification in diatom cells of 2,6,10,14-tetramethyl-7-(3-methylpent-4-enyl)-pentadec-5E-ene, an HBI previously detected in marine sediments and particulate matter. The other minor C25 HBIs detected were a tetraene and a pentaene that have been previously identified in other diatoms from the genera Haslea and Rhizosolenia, and one other C25 tetraene that could not be structurally identified. The structures of the HBI alkenes of P. strigosum were compared with those of C25 homologues previously identified in three other Pleurosigma sp. (Pleurosigma intermedium, Pleurosigma planktonicum and Pleurosigma sp.). Unlike most structures previously reported, none of the HBI alkenes produced by P. strigosum showed an unsaturation at C7–C20, or E/Z isomerism of the trisubstituted double bond at C9–C10 (whenever present).

Alkyl and polynuclear aromatic thiophenes in Neogene sediments of the Shinjo basin, Japan.

Alkyl and polynuclear aromatic thiophenes were detected in sedimentary rocks of a stratigraphic sequence from Miocene to Pliocene in Shinjo basin, Japan. C25 Highly branched isoprenoid (HBI) thiophenes, dibenzothiophene, C1- and C2-alkyldibenzothiophenes, and benzo[b]naphto[1, 2-d]thiophene were rather predominantly present. The C25 HBI thiophenes consist of three isomers including a pair of diastereomers. They were present in sediments from the Nakawatari to the upper part of the Kusanagi Formations and absent at the middle and lower parts of the Formation. The depth profiles of their concentrations do not coincide with those of the C25 HBI alkane concentration and bulk sulfur content in the same sediment samples. It is postulated that the C25 HBI thiophenes and the C25 HBI alkane were produced by the reaction of C25 HBI alkadiene and C25 HBI polyene, respectively, with reduced sulfur during early diagenesis. The variation in composition of the C25 HBI thiophene isomers was observed in the sediments, suggesting that they were derived from different kinds of C25 HBI alkadienes. The concentrations of the polynuclear aromatic thiophenes showed an increasing trend downwards the upper to middle Kusanagi Formation. Among these thiophenes dibenzothiophene and benzo[b]naphto[1, 2-d]thiophene concentrations varied from 10 to 730 and 14 to 210 pmol g-1, respectively. The depth profiles of their concentrations were different from that of the C25 HBI thiophenes. It is likely that the polynuclear aromatic thiophene formation started from different precursors followed by different processes from those of the C25 HBI thiophenes.

Thiophenes in the Cretaceous/Tertiary boundary sediments at Kawaruppu, Hokkaido, Japan.

One C25 highly branched isoprenoid (HBI) thiophene, one C25 HBI alkane, and five polynuclear aromatic thiophenes were detected in the Cretaceous/Tertiary (K/T) boundary sediments at Kawaruppu, Hokkaido, Japan. The C25 HBI thiophene was found only in the sediments below the boundary claystone but not in the claystone and sediments above it. On the other hand, the C25 HBI alkane was present in all the sediments. However, its concentration was low below and over the lower two thirds of the claystone, but increased in the upper one third. This distribution pattern resembles that of the longer chain n-alkanes (Mita and Shimoyama, 1999a). The depth profiles of the thiophene and alkane concentrations possibly reflect the massive extinction of organisms. Among the polynuclear aromatic thiophenes, dibenzothiophene and benzo[b]naphto[1, 2-d]thiophene are relatively abundant. Their concentrations were roughly constant in the sediments below the horizon at the upper one third of the boundary claystone. Their concentrations began to increase at the one third horizon towards the 40 cm horizon (26 cm above the top horizon of the claystone) and then steeply decreased in the sediment above the horizon. A nearly constant ratio of 4- to 1-methyldibenzothiophene found in the sediments above, within, and below the boundary claystone indicates that diagenesis has occurred evenly over the sediments. The depth profile of the dibenzothiophene concentrations resembles that of the reported sulfide contents (Kajiwara and Kaiho, 1992) suggesting that polynuclear aromatic thiophene formation is related in some way to sulfide content at deposition.

Molecular geochemical approach to the Paleoceanographic assessment of Neogene sediments of Yashima area, Akita Basin, Japan.

Specific source marker compounds were analyzed for solvent extracts from the Onnagawa, Funakawa and Tentokuji Formations, Yashima, Akita, NE Japan.Relative abundances of higher plant markers, n-C27 alkane, n-C28 alkanoic acid and ω-hydroxy-C22 alkanoic acid; to algal derived compounds increase upward through the Funakawa Formation, indicating the rapid increase of land plant input associated with the increase of detrital matter during the deposition of the Funakawa Formation. Dinosteranes as specific compounds of dinoflagellates are more abundant in the lower part of the Onnagawa and the Funakawa Formations than in the middle and upper parts of the Onnagawa and the Tentokuji Formations. C25 highly branched isoprenoid (HBI) alkane as a specific compound of diatoms is abundant in the Onnagawa Formation, while less abundant in the Funakawa and Tentokuji Formations. The negative behavior of C25 HBI alkane/n-C21 alkane and dinosterane/4-desmethylsterane ratios through the Onnagawa Formation probably reflects the changes in primary producers likely due to the changes of nutrient silica concentration of surface water. The high dinosterane/4-desmethylsterane ratio in the Tentokuji Formation seems to reflect the increase of coastal dinoflagellates under the influence of riverine water inflow. An increase of hopane/sterane ratio in the Funakawa Formation probably reflects the increase of aerobic bacterial activity during early diagenesis resulted from bottom water oxygenation in this period.