Intact Polar Lipids Research Articles

Novel archaeal tetraether lipids with a cyclohexyl ring identified in Fayetteville Green Lake, NY, and other sulfidic lacustrine settings.

The meromictic Fayetteville Green Lake (FGL) is of significant geobiological interest because of microbial cycling of sulfur within and below the permanent chemocline and in the euxinic deep waters. Studies of glycerol dibiphytanyl glycerol tetraethers (GDGTs) may help shed light on understanding the activity of archaeal communities in these habitats. Normal-phase and reversed-phase liquid chromatography/mass spectrometry (LC/MS) analysis on total lipid extracts of environmental samples revealed series of GDGTs with different biphytane structures. Comparison of the mass spectrum of biphytane obtained from separated novel GDGTs with that of a synthetic C40 biphytane confirms our structural assignments. A unique cyclohexyl ring configured in the middle of a C40 biphytane chain was identified in these novel GDGTs. We suggest the trivial name S-GDGTs for these compounds, where 'S' stands for 'sulfidic' and 'six-membered ring'. S-GDGT derivatives composed of biphytanes modified with double bonds and cyclopentane rings were also detected in the samples we analyzed. Intact polar lipid precursors of S-GDGT include compounds with mono- and diglycosyl head groups. The carbon isotopic composition of S-GDGTs and their occurrence in FGL, Messel Shale as well as Salt Pond and salt marshes on Cape Cod suggest that S-GDGTs may be produced by chemoautotrophic archaea that prefer sulfidic conditions. Copyright © 2016 John Wiley & Sons, Ltd.

Impact of trophic state on the distribution of intact polar lipids in surface waters of lakes

AbstractWe characterized the intact polar lipid (IPL) composition in the surface waters of 22 lakes from Minnesota and Iowa, ranging in trophic state between eutrophic and oligo‐mesotrophic, to investigate the impact of trophic state on IPL composition. A high diversity of IPL classes was detected. Most IPL classes were detected in all lakes, but the eutrophic lakes contained a significantly higher relative abundance of lyso‐phosphatidylcholine (PC) than the oligo‐mesotrophic lakes, which in turn were characterized by significantly higher relative abundance of hydroxymethyltrimethyl‐alanine/trimethyl‐homoserine (DGTA/DGTS) betaines, ornithine lipids and the recently discovered trimethyl ornithine (TMO) lipids. The higher relative abundance of ornithines and TMOs may relate to a higher contribution of heterotrophic bacteria relative to phytoplankton while the higher abundance of the DGTA/DGTS betaines may relate to substitution by microorganisms of these non‐P lipids for PC under P‐stress, as has been observed in other environments. We also detected a variety of heterocyst glycolipids (HGs) derived from N2‐fixing heterocystous Cyanobacteria in all lakes, suggesting the presence of these Cyanobacteria in the full range of trophic conditions. Correlation of HG abundance with environmental data showed that high productivity lakes have high HG abundances, while other distributional differences in HGs, which did not correlate with environmental parameters, are likely due to differences in species composition. We conclude that the significant differences in IPL composition between the eutrophic and oligo‐mesotrophic lakes are either due to adaptation of the membrane composition to nutrient conditions or due to general divergences in microbial composition under the different conditions.

Increasing P limitation and viral infection impact lipid remodeling of the picophytoplankter <i>Micromonas pusilla</i>

Abstract. The intact polar lipid (IPL) composition of phytoplankton is plastic and dependent on environmental factors. Previous studies have shown that phytoplankton under low phosphorus (P) availability substitutes phosphatidylglycerols (PGs) with sulfoquinovosyldiacylglycerols (SQDGs) and digalactosyldiacylglycerols (DGDGs). However, these studies focused merely on P depletion, while phytoplankton in the natural environment often experience P limitation whereby the strength depends on the supply rate of the limiting nutrient. Here we report on the IPL composition of axenic cultures of the picophotoeukaryote Micromonas pusilla under different degrees of P limitation, i.e., P-controlled chemostats at 97 and 32 % of the maximum growth rate, and P starvation (obtained by stopping P supply to these chemostats). P-controlled cultures were also grown at elevated partial carbon dioxide pressure (pCO2) to mimic a future scenario of strengthened vertical stratification in combination with ocean acidification. Additionally, we tested the influence of viral infection for this readily infected phytoplankton host species. Results show that both SQDG : PG and DGDG : PG ratios increased with enhanced P limitation. Lipid composition was, however, not affected by enhanced (750 vs. 370 µatm) pCO2. In the P-starved virally infected cells the increase in SQDG : PG and DGDG : PG ratios was lower, whereby the extent depended on the growth rate of the host cultures before infection. The lipid membrane of the virus MpV-08T itself lacked some IPLs (e.g., monogalactosyldiacylglycerols; MGDGs) in comparison with its host. This study demonstrates that, besides P concentration, also the P supply rate, viral infection and even the history of the P supply rate can affect phytoplankton lipid composition (i.e., the non-phospholipid : phospholipid ratio), with possible consequences for the nutritional quality of phytoplankton.

Elucidation and identification of amino acid containing membrane lipids using liquid chromatography/high-resolution mass spectrometry.

Intact polar lipids (IPLs) are the building blocks of cell membranes, and amino acid containing IPLs have been observed to be involved in response to changing environmental conditions in various species of bacteria. High-performance liquid chromatography/mass spectrometry (HPLC/MS) has become the primary method for analysis of IPLs. Many glycerol-free amino acid containing membrane lipids (AA-IPLs), which are structurally different than abundant aminophospholipids, have not been characterized using HPLC/MS. This results in many lipids remaining unrecognized in IPL analysis of microbial cultures and environmental samples, hampering the study of their occurrence and functionality. We analyzed the amino acid containing IPLs of a number of bacteria (i.e. Gluconobacter cerinus, Cyclobacterium marinus, Rhodobacter sphaeroides, and Pedobacter heparinus) in order to decipher fragmentation pathways, and explore potential novel lipid structures using HPLC/electrospray ionization ion trap MS (HPLC/ESI-IT-MS) and HPLC/high-resolution MS (HPLC/HRMS). We report differentiation between glutamine and lysine lipids with the same nominal masses, novel MS fragmentation pathways of cytolipin, the lipopeptides cerilipin and flavolipin, head group hydroxylated ornithine lipids, and the novel identification of cerilipin with a hydroxylated fatty acid. Non-glycerol AA lipids can be readily recognized as their fragmentation follows a clear pattern with initial dehydration or other loss from the head group, followed by fatty acid losses resulting in a diagnostic fragment ion. Higher level MSn and HRMS are valuable tools in characterizing AA lipid head group structural components.

Tracing the production and fate of individual archaeal intact polar lipids using stable isotope probing

Analysis of cellular membrane lipids has been widely applied to describe the microbial community composition in natural systems. When combined with stable isotope probing (SIP) experiments, deuterium label (D2O) uptake into lipids enables assessment of microbial biomass production. We performed SIP on methane-rich, hydrothermally-heated sediments to examine the de novo production of individual archaeal intact polar lipids (IPLs) by mesophilic anaerobic methane oxidizing group-1 archaea (ANME-1). The greatest extent of label uptake was by phosphatidyl glycerol archaeol (PG-AR), reaching 50% of the medium’s label concentration in only 10days. This indicates PG-AR as an important cell membrane lipid during the active growth phase of mesophilic ANME-1. Much less label uptake was into intact polar glycerol dibiphytanyl glycerol tetraethers (GDGTs), especially for those bound to diglycosidic head groups. The low production of these GDGTs contrasts with their predominance in ANME-1-dominated natural samples. We attribute the differential label uptake among individual IPLs to the ANME-1 tetraether biosynthetic pathway. This mechanism likely involves head-to-head condensation of two molecules of PG-AR and progressive substitution of PG by glycosidic head groups. The observation that ANME-1 invest in the synthesis of diethers during optimum growth suggests intact ARs and/or phosphate-bearing tetraethers as important biomarkers for actively growing populations in natural environments, while the diglycosidic GDGTs appear to signal stationary ANME-1 communities.

Detection of microbial biomass in subseafloor sediment by pyrolysis⿿GC/MS

The conventional approaches for qualitative and quantitative assessment of microbial biomass in sediments, e.g., via quantitative polymerase chain reaction or intact polar lipids analysis, are rather tedious and time-consuming. Here we present a new, optimized and simple pyrolysis-gas chromatography/mass spectrometry protocol for rapid screening of sediment samples for the presence of microbial signals and quantification of bulk population. Analysis of microbial cultures of different bacterial and archaeal lineages as well as reference substances and model compounds provided molecular fingerprints for tracking microbial biomass. The diagnostic fingerprints consist of benzyl nitrile (derived from DNA and protein), 2-furanmethanol (from DNA and peptidoglycan), indole (from peptidoglycan and protein), phenol (from DNA, peptidoglycan and protein) and pyrrole (from peptidoglycan). Detection of microbial signals through the molecular fingerprints requires a cell density of at least 106cells/g, whereas at least 107cells/g is necessary for quantification. The pyrolysis method was applied to marine sediments from different depths (until ⿼400m below the seafloor at the Canterbury Basin) and with different organic carbon contents (0.11⿿6.99%).

The novel extremely acidophilic, cell-wall-deficient archaeon Cuniculiplasma divulgatum gen. nov., sp. nov. represents a new family, Cuniculiplasmataceae fam. nov., of the order Thermoplasmatales.

Two novel cell-wall-less, acidophilic, mesophilic, organotrophic and facultatively anaerobic archaeal strains were isolated from acidic streamers formed on the surfaces of copper-ore-containing sulfidic deposits in south-west Spain and North Wales, UK. Cells of the strains varied from 0.1 to 2 μm in size and were pleomorphic, with a tendency to form filamentous structures. The optimal pH and temperature for growth for both strains were 1.0-1.2 and 37-40 °C, with the optimal substrates for growth being beef extract (3 g l- 1) for strain S5T and beef extract with tryptone (3 and 1 g l- 1, respectively) for strain PM4. The lipid composition was dominated by intact polar lipids consisting of a glycerol dibiphytanyl glycerol tetraether (GDGT) core attached to predominantly glycosidic polar headgroups. In addition, free GDGT and small relative amounts of intact and core diether lipids were present. Strains S5T and PM4 possessed mainly menaquinones with minor fractions of thermoplasmaquinones. The DNA G+C content was 37.3 mol% in strain S5T and 37.16 mol% for strain PM4. A similarity matrix of 16S rRNA gene sequences (identical for both strains) showed their affiliation to the order Thermoplasmatales, with 73.9-86.3 % identity with sequences from members of the order with validly published names. The average nucleotide identity between genomes of the strains determined in silico was 98.75 %, suggesting, together with the 16S rRNA gene-based phylogenetic analysis, that the strains belong to the same species. A novel family, Cuniculiplasmataceae fam. nov., genus Cuniculiplasma gen. nov. and species Cuniculiplasma divulgatum sp. nov. are proposed based on the phylogenetic, chemotaxonomic analyses and physiological properties of the two isolates, S5T and PM4 ( = JCM 30641 = VKM B-2940). The type strain of Cuniculiplasma divulgatum is S5T ( = JCM 30642T = VKM B-2941T).

Compound-specific stable isotope analysis of nitrogen-containing intact polar lipids.

Compound-specific isotope analysis (CSIA) of nitrogen in amino acids has proven a valuable tool in many fields (e.g. ecology). Several intact polar lipids (IPLs) also contain nitrogen, and their nitrogen isotope ratios have the potential to elucidate food-web interactions or metabolic pathways. Here we have developed novel methodology for the determination of δ(15)N values of nitrogen-containing headgroups of IPLs using gas chromatography coupled with isotope-ratio mass spectrometry. Intact polar lipids with nitrogen-containing headgroups were hydrolyzed and the resulting compounds were derivatized by (1) acetylation with pivaloyl chloride for compounds with amine and hydroxyl groups or (2) esterification using acidified 2-propanol followed by acetylation with pivaloyl chloride for compounds with both carboxyl and amine groups. The δ(15)N values of the derivatives were subsequently determined using gas chromatography/combustion/isotope-ratio mass spectrometry. Intact polar lipids with ethanolamine and amino acid headgroups, such as phosphatidylethanolamine and phosphatidylserine, were successfully released from the IPLs and derivatized. Using commercially available pure compounds it was established that δ(15)N values of ethanolamine and glycine were not statistically different from the offline-determined values. Application of the technique to microbial cultures and a microbial mat showed that the method works well for the release and derivatization of the headgroup of phosphatidylethanolamine, a common IPL in bacteria. A method to enable CSIA of nitrogen of selected IPLs has been developed. The method is suitable for measuring natural stable nitrogen isotope ratios in microbial lipids, in particular phosphatidylethanolamine, and will be especially useful for tracing the fate of nitrogen in deliberate tracer experiments.

Applications of Intact Polar Lipids for Tracing the Marine Microbial Activity and Their Limitations

Applications of Intact Polar Lipids for Tracing the Marine Microbial Activity and Their Limitations

Biological source and provenance of deep-water derived isoprenoid tetraether lipids along the Portuguese continental margin

There is increasing evidence that nitrifying Thaumarchaeota in the deep ocean waters may contribute to the sedimentary composition of isoprenoid glycerol dialkyl glycerol tetraethers (isoGDGTs), impacting TEX86 paleothermometry. We investigated the potential effect of deep-water dwelling Thaumarchaeota in the warm and saline Mediterranean Outflow Water (MOW) on the distribution of isoGDGTs by analysing suspended particulate matter (SPM) and surface sediments collected along five land-ocean transects along the southern Portuguese continental margin. To this end, we directly compared for the first time the composition of intact polar lipid (IPL)-derived isoGDGTs of SPM with the diversity, abundance, and activity of Thaumarchaeota based on the genetic analysis of the genes coding for the archaeal ammonia monooxygenase (amoA) and the geranylgeranylglyceryl phosphate (GGGP) synthase involved in the isoGDGT biosynthetic pathway. Our results revealed a strong positive relationship between water depth and TEX86H values for both SPM and surface sediments. The increasing TEX86H trends for both core lipid (CL) and IPL-derived fractions were accompanied by increasing fractional abundances of GDGT-2 and crenarchaeol regio-isomer and decreasing fractional abundances of GDGT-1 and GDGT-3 with increasing water depth. Phylogenetic analyses based on the archaeal amoA and the GGGP synthase proteins showed that Thaumarchaeota populations detected at 1m and 50m water depth were different from those detected in 200m and 1000m water depth, which had an increased contribution of so-called ‘deep water’ Thaumarchaeota. The differences in the fractional abundances of isoGDGTs with water depth were compatible with the increasing contribution of ‘deep water’ Thaumarchaeota harboring a different GGGP synthase enzyme which has been suggested to relate to changes in the relative proportion of synthesized isoGDGTs. Accordingly, it appears that the sedimentary distribution of CL isoGDGTs used in TEX86H along the Portuguese margin is primarily influenced by water depth due to the increasing contribution of the deep-water population of Thaumarchaeota residing in the MOW. Our study also reveals that the effect of deep water Thaumarchaeotal communities on sedimentary isoGDGT distributions should be considered globally.

Influence of temperature, pH, and salinity on membrane lipid composition and TEX86 of marine planktonic thaumarchaeal isolates

Marine ammonia-oxidizing archaea of the phylum Thaumarchaeota are a cosmopolitan group of microorganisms representing a major fraction of the picoplankton in the ocean. The cytoplasmic membranes of Thaumarchaeota consist predominantly of intact polar isoprenoid glycerol dibiphytanyl glycerol tetraether (GDGT) lipids, which may be used as biomarkers for living Thaumarchaeota. Fossil thaumarchaeal GDGT core lipids accumulate in marine sediments and serve as the basis for geochemical proxies such as the TEX86 paleothermometer. Here, we demonstrate that the responses of membrane lipid compositions and resulting TEX86 values to growth temperature strongly diverge in three closely related thaumarchaeal pure cultures, i.e., Nitrosopumilus maritimus and two novel strains isolated from South Atlantic surface water, although the inventories of intact polar lipids and core lipids were overall similar in the three strains. N. maritimus and its closely related strain NAOA6 showed linear relationships of TEX86 and growth temperature but no correlation of TEX86 and temperature was observed in the more distantly related strain NAOA2. In contrast, the weighted average number of cycloalkyl moieties (ring index) was linearly correlated with growth temperature in all strains. This disparate relationship of TEX86 to growth temperature among closely related Thaumarchaeota suggests that the ring index but not the TEX86 ratio represents a universal response to growth temperature in marine planktonic Thaumarchaeota. Furthermore, the distinct TEX86-temperature relationships in the cultivated strains indicate that environmental GDGT signals may include an ecological component, which has important implications for ocean temperature reconstructions using the TEX86 proxy. In contrast, different growth medium salinities in the range 27–51‰ tested for N. maritimus showed no systematic effect on intact polar GDGT composition and TEX86. Similarly, N. maritimus showed only small changes in intact polar GDGT composition and TEX86 when grown at different medium pH in the range 7.3–7.9. Overall, our pure culture studies suggest that the TEX86 paleotemperature proxy is not solely dependent on growth temperature, but may amalgamate physiological, environmental, and ecological factors.

Intact polar lipids of Thaumarchaeota and anammox bacteria as indicators of N cycling in the eastern tropical North Pacific oxygen-deficient zone

Abstract. 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, although the nature of this hypothetical interaction (i.e., either competition or cooperation) remains unclear.

Abundant Trimethylornithine Lipids and Specific Gene Sequences Are Indicative of Planctomycete Importance at the Oxic/Anoxic Interface in Sphagnum-Dominated Northern Wetlands.

Northern wetlands make up a substantial terrestrial carbon sink and are often dominated by decay-resistant Sphagnum mosses. Recent studies have shown that planctomycetes appear to be involved in degradation of Sphagnum-derived debris. Novel trimethylornithine (TMO) lipids have recently been characterized as abundant lipids in various Sphagnum wetland planctomycete isolates, but their occurrence in the environment has not yet been confirmed. We applied a combined intact polar lipid (IPL) and molecular analysis of peat cores collected from two northern wetlands (Saxnäs Mosse [Sweden] and Obukhovskoye [Russia]) in order to investigate the preferred niche and abundance of TMO-producing planctomycetes. TMOs were present throughout the profiles of Sphagnum bogs, but their concentration peaked at the oxic/anoxic interface, which coincided with a maximum abundance of planctomycete-specific 16S rRNA gene sequences. The sequences detected at the oxic/anoxic interface were affiliated with the Isosphaera group, while sequences present in the anoxic peat layers were related to an uncultured planctomycete group. Pyrosequencing-based analysis identified Planctomycetes as the major bacterial group at the oxic/anoxic interface at the Obukhovskoye peat (54% of total 16S rRNA gene sequence reads), followed by Acidobacteria (19% reads), while in the Saxnäs Mosse peat, Acidobacteria were dominant (46%), and Planctomycetes contributed to 6% of the total reads. The detection of abundant TMO lipids in planctomycetes isolated from peat bogs and the lack of TMO production by cultures of acidobacteria suggest that planctomycetes are the producers of TMOs in peat bogs. The higher accumulation of TMOs at the oxic/anoxic interface and the change in the planctomycete community with depth suggest that these IPLs could be synthesized as a response to changing redox conditions at the oxic/anoxic interface.

Lysine and novel hydroxylysine lipids in soil bacteria: amino acid membrane lipid response to temperature and pH in Pseudopedobacter saltans.

Microbial decomposition of organic matter is an essential process in the global carbon cycle. The soil bacteria Pseudopedobacter saltans and Flavobacterium johnsoniae are both able to degrade complex organic molecules, but it is not fully known how their membrane structures are adapted to their environmental niche. The membrane lipids of these species were extracted and analyzed using high performance liquid chromatography-electrospray ionization/ion trap/mass spectrometry (HPLC-ESI/IT/MS) and high resolution accurate mass/mass spectrometry (HRAM/MS). Abundant unknown intact polar lipids (IPLs) from P. saltans were isolated and further characterized using amino acid analysis and two dimensional nuclear magnetic resonance (NMR) spectroscopy. Ornithine IPLs (OLs) with variable (hydroxy) fatty acid composition were observed in both bacterial species. Lysine-containing IPLs (LLs) were also detected in both species and were characterized here for the first time using HPLC-MS. Novel LLs containing hydroxy fatty acids and novel hydroxylysine lipids with variable (hydroxy) fatty acid composition were identified in P. saltans. The confirmation of OL and LL formation in F. johnsoniae and P. saltans and the presence of OlsF putative homologs in P. saltans suggest the OlsF gene coding protein is possibly involved in OL and LL biosynthesis in both species, however, potential pathways of OL and LL hydroxylation in P. saltans are still undetermined. Triplicate cultures of P. saltans were grown at three temperature/pH combinations: 30°C/pH 7, 15°C/pH 7, and 15°C/pH 9. The fractional abundance of total amino acid containing IPLs containing hydroxylated fatty acids was significantly higher at higher temperature, and the fractional abundance of lysine-containing IPLs was significantly higher at lower temperature and higher pH. These results suggest that these amino acid-containing IPLs, including the novel hydroxylysine lipids, could be involved in temperature and pH stress response of soil bacteria.

Possible roles of uncultured archaea in carbon cycling in methane-seep sediments

Studies on microbial carbon cycling uniformly confirm that anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria represent the dominant and most active fraction of the sedimentary microbial community in methane-seep sediments. However, little is known about other frequently observed and abundant microbial taxa, their role in carbon cycling and association with the anaerobic oxidation of methane (AOM). Here, we provide a comprehensive characterization of stable carbon isotopes (δ13C) from several intact polar lipid (IPL) classes and metabolite pools in a downcore profile at a cold seep within the oxygen minimum zone off Pakistan. We aimed to evaluate microbial carbon metabolism using IPLs in relation to redox conditions, metabolites and 16S rRNA gene libraries. The 13C-depleted signature of carbon pools and microbial metabolites in pore waters (e.g., dissolved inorganic carbon, lactate and acetate) demonstrated high accumulation of AOM-associated biomass and subsequent turnover thereof. ANMEs accounted for a small fraction of the archaeal 16S rRNA gene survey, whereas sequences of other uncultured benthic archaea dominated the clone libraries, particularly the Marine Benthic Group D. On the basis of lipid diversity and carbon isotope information, we suggest that structurally diverse phospho- and glycolipids, including the recently identified unsaturated tetraethers that are particularly abundant in this setting, are likely derived from archaea other than ANMEs. Through the evaluation of δ13C values of individual IPL, our results indicate heterotrophy as a possible metabolic pathway of archaea in these AOM-dominated sediments.

Occurrence and distribution of glycerol dialkanol diethers and glycerol dialkyl glycerol tetraethers in a peat core from SW Tanzania

Isoprenoid and branched glycerol dialkanol diethers (iso GDDs and br GDDs) have recently been detected in various environments, including sediment, soil and peat deposits. Their structures strongly resemble those of glycerol dialkyl glycerol tetraethers (GDGTs). Nevertheless, the origin of GDDs and their link to GDGTs remain unclear. Here we examined the concentration and distribution of iso GDDs and br GDDs, together with those of iso GDGTs and br GDGTs along a 4m peat core from Tanzania. Whereas br GDDs have only been detected to date in their core lipid (CL) form, we report here, for the first time, br GDDs in both CL and intact polar lipid (IPL) forms, suggesting a biosynthetic origin for br GDDs. Concentrations of br GDGTs and br GDDs on one hand and of iso GDGTs and iso GDDs on the other hand, were observed to significantly co-vary (R2 0.49–0.58; p<0.05), both for the CL and IPL fractions. Moreover, the fractional abundance of each GDD correlated significantly with that of its GDGT analogue (R2 0.33–0.97; p<0.05). Taken together, the data show that GDDs and GDGTs are closely related and likely take part in common metabolic pathways, although the hypothesis of GDDs being degradation products of GDGTs cannot be excluded.

Planctomicrobium piriforme gen. nov., sp. nov., a stalked planctomycete from a littoral wetland of a boreal lake

An aerobic, budding, non-pigmented and rosette-forming bacterium was isolated from a littoral wetland of a boreal lake located in Valaam Island, northern Russia, and designated strain P3(T). Ellipsoidal to pear-shaped cells of this bacterium were covered with crateriform pits and possessed stalks suggesting a planctomycete morphotype. 16S rRNA gene sequence analysis confirmed that strain P3(T) was a member of the order Planctomycetales and belonged to a phylogenetic lineage defined by the genus Planctomyces , with 89 and 86% sequence similarity to Planctomyces brasiliensis and Planctomyces maris , respectively. Strain P3(T) was a mildly acidophilic, mesophilic organism capable of growth at pH values between pH 4.2 and 7.1 (with an optimum at pH 6.0-6.5) and at temperatures between 10 and 30 °C (optimum at 20-28 °C). Most sugars, a number of polysaccharides and several organic acids were the preferred growth substrates. Compared with Planctomyces brasiliensis and Planctomyces maris , which require NaCl for growth, strain P3(T) was salt-sensitive and did not develop at NaCl concentrations above 0.5% (w/v). The major fatty acids were C16 : 0 and C16 : 1ω7c; the cells also contained significant amounts of C18 : 1ω7c and C18 : 0. The major intact polar lipids were diacylglycerol-O-(N,N,N-trimethyl)homoserine (DGTS) lipids; the major neutral lipids were long-chain 1,(ω-1)-diols and C31 : 9 hydrocarbon. The quinone was MK-6, and the G+C content of the DNA was 59.0 mol%. Strain P3(T) differed from Planctomyces brasiliensis and Planctomyces maris by cell morphology, substrate utilization pattern and a number of physiological characteristics. Based on these data, the novel isolate should be considered as representing a novel genus and species of planctomycetes, for which the name Planctomicrobium piriforme gen. nov., sp. nov., is proposed. The type strain is P3(T) ( =DSM 26348(T) =VKM B-2887(T)).

A laboratory experiment on the behaviour of soil-derived core and intact polar GDGTs in aquatic environments

Abstract. We have performed incubation experiments in order to examine the behaviour of soil-derived branched glycerol dialkyl glycerol tetraether (brGDGT) membrane lipids upon entering an aquatic environment and to evaluate the processes that potentially take place during their fluvial transport from land to sea. We incubated a soil from the Rakaia River catchment on the South Island of New Zealand using Rakaia River water and ocean water collected near the river mouth as inocula for a period of up to 152 days. The concentrations, as well as the relative distribution of brGDGTs derived from intact polar ("living"; IPL) lipids and core ("fossil"; CL) lipids remained unaltered over the course of the experiment. Although the stability of the brGDGTs may be a consequence of the higher than natural soil : water ratio used in the laboratory experiment, the substantial increase (27–72%) in the total pool of isoprenoid GDGTs (isoGDGTs) in all incubation setups, including the control using distilled water, indicates that entering an aquatic environment does influence the behaviour of soil-derived GDGTs. However, the availability of water appears to be more important than its properties. As a consequence of increasing isoGDGT concentrations, a decrease in Branched and Isoprenoid Tetraether (BIT) index values – a proxy for the relative input of fluvially discharged soil material into a marine system – became evident after an incubation period of 30 days, with a maximum final decrease of 0.88 to 0.74 in the experiment with river water. The relative distribution within the isoGDGT pool shows changes with time, suggesting that isoGDGT producers may either have different rates of membrane adaptation or production/degradation, or that preferential release from the soil matrix or a shift in source organism(s) may take place. While the apparent stability of soil brGDGTs during this incubation experiment reinforces their potential as tracers for land–sea transport of soil organic carbon and their use in paleoclimate reconstructions, the distributional differences between GDGTs in river water and nearby soil, as well as in river and ocean water, indicate that further research is needed to pinpoint the sources of GDGTs that are ultimately discharged to the oceans and are subsequently archived in continental margin sediments.

The archaeal lipidome in estuarine sediment dominated by members of the Miscellaneous Crenarchaeotal Group.

The anoxic sediments of the White Oak River estuary comprise a distinctive sulfate-methane transition zone (SMTZ) and natural enrichment of the archaea affiliated with the Miscellaneous Crenarchaeotal Group (MCG). Archaeal biphytanes were generally depleted in (13) C, with δ(13) C values being less than -35‰, indicative of production by active sedimentary archaeal populations. Multivariate analysis of the downcore distributions of 63 lipid biomarkers identified three major groups of lipids that were enriched in the surface, SMTZ or subsurface depths. Intact polar lipids with phosphatidylglycerol headgroups and glycerol dibiphytanyl glycerol tetraethers containing one, two or three cyclopentane rings were enriched at the base of the SMTZ and likely represent the accumulated product of a small but active ANME-1 community. The recently identified butanetriol dibiphytanyl glycerol tetraethers (BDGT), which increased relatively to other lipids with depth, were correlated with the relative abundance of MCG in archaeal 16S rRNA clone libraries, and were (13) C depleted throughout the depth profile, suggesting BDGT lipids as putative biomarkers of an MCG community that may either be autotrophic or feeding on (13) C-depleted organic substrates transported by porewater.

Fatty acid dynamics during viral infection of Phaeocystis globosa

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 74:85-94 (2015) - DOI: https://doi.org/10.3354/ame01730 Fatty acid dynamics during viral infection of Phaeocystis globosa N. J. Bale*,**, D. S. Maat**, E. C. Hopmans, A. Mets, J. S. Sinninghe Damsté, C. P. D. Brussaard, S. Schouten Department of Marine Organic Biogeochemistry, and Department of Biological Oceanography, Royal Netherland Institute for Sea Research, PO Box 59, 1790 AB Den Burg, The Netherlands *Corresponding author: nicole.bale@nioz.nl**Joint first authorship (these authors contributed equally to the manuscript) ABSTRACT: Previous studies have shown that viral infection can affect the lipid distribution of phytoplankton, specifically the fatty acid (FA) distribution, and has been hypothesized to affect the nutritional value of phytoplankton for higher trophic levels. Here, we report the bulk FA distribution as well as the FA distribution of individual intact polar lipid (IPL) classes of the alga Phaeocystis globosa infected with the lytic virus PgV-07T. Analysis of the virus PgV-07T itself showed that it contained shorter, more saturated bulk and IPL-bound FAs than the host. Viral infection did not affect the bulk or IPL-bound FA distribution after 24 h post-infection when cell lysis was initiated, but after 48 h the bulk FAs remaining in the particulate phase of the infected cultures contained 22% less polyunsaturated FAs (PUFAs) compared to the control cultures. This change in the bulk FAs was mainly due to the generation of PUFAs that occurred in the control cultures, suggesting that infection prevented P. globosa PUFA accumulation. Two of the 7 IPL classes, the monogalactosyldiacylglycerols and the sulfoquinovosyldiacylglycerols, showed about a 10% reduction in the percentage of PUFAs upon viral infection. In contrast, the digalactosyldiacylglycerols exhibited a 15% increase in PUFAs. This difference between the IPL-PUFAs and the bulk FAs is possibly due to a contribution to the bulk FA pool of e.g. triacylglycerols. Overall, these results suggest that grazing on infected cells and filter feeder uptake of post-lysis cell debris could lead to a transfer of relatively lower amounts of PUFAs to higher trophic levels. KEY WORDS: Phaeocystis globosa · Virus · Fatty acids · Intact polar lipids Full text in pdf format Supplementary material PreviousCite this article as: Bale NJ, Maat DS, Hopmans EC, Mets A, Sinninghe Damsté JS, Brussaard CPD, Schouten S (2015) Fatty acid dynamics during viral infection of Phaeocystis globosa. Aquat Microb Ecol 74:85-94. https://doi.org/10.3354/ame01730 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 74, No. 1. Online publication date: January 12, 2015 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2015 Inter-Research.