Marcel T J van der Meer

Analysis of intact tetraether lipids in archaeal cell material and sediments by high performance liquid chromatography/atmospheric pressure chemical ionization mass spectrometry

A method combining normal phase high performance liquid chromatography (HPLC) with positive ion atmospheric pressure chemical ionization mass spectrometry (APCI-MS) was developed for the analysis of intact glycerol dialkyl glycerol tetraethers (GDGTs) in archaeal cell material and sediments. All GDGTs previously reported to occur in the thermophilic archaeon Sulfolobus solfataricus could be identified based on their mass spectra and retention time. Positive ion mass spectra consisted of abundant protonated molecules and fragment ions corresponding to loss of water and the glycerol moiety. In addition, two novel GDGTs representing alternative combinations of biphytanyl moieties were observed. Using this method, the tetraethers present in the thermophilic archaeon Metallosphaera sedula and two sediment samples were characterized. This rapid method will greatly contribute to the establishment of the sedimentary record of these compounds and increase our understanding of archaea and their occurrence in widely different environments.

Archaeal and bacterial glycerol dialkyl glycerol tetraether lipids in hot springs of yellowstone national park.

ABSTRACT Glycerol dialkyl glycerol tetraethers (GDGTs) are core membrane lipids originally thought to be produced mainly by (hyper)thermophilic archaea. Environmental screening of low-temperature environments showed, however, the abundant presence of structurally diverse GDGTs from both bacterial and archaeal sources. In this study, we examined the occurrences and distribution of GDGTs in hot spring environments in Yellowstone National Park with high temperatures (47 to 83°C) and mostly neutral to alkaline pHs. GDGTs with 0 to 4 cyclopentane moieties were dominant in all samples and are likely derived from both (hyper)thermophilic Crenarchaeota and Euryarchaeota. GDGTs with 4 to 8 cyclopentane moieties, likely derived from the crenarchaeotal order Sulfolobales and the euryarchaeotal order Thermoplasmatales, are usually present in much lower abundance, consistent with the relatively high pH values of the hot springs. The relative abundances of cyclopentane-containing GDGTs did not correlate with in situ temperature and pH, suggesting that other environmental and possibly genetic factors play a role as well. Crenarchaeol, a biomarker thought to be specific for nonthermophilic group I Crenarchaeota, was also found in most hot springs, though in relatively low concentrations, i.e., <5% of total GDGTs. Its abundance did not correlate with temperature, as has been reported previously. Instead, the cooccurrence of relatively abundant nonisoprenoid GDGTs thought to be derived from soil bacteria suggests a predominantly allochthonous source for crenarchaeol in these hot spring environments. Finally, the distribution of bacterial branched GDGTs suggests that they may be derived from the geothermally heated soils surrounding the hot springs.

Diel Variations in Carbon Metabolism by Green Nonsulfur-Like Bacteria in Alkaline Siliceous Hot Spring Microbial Mats from Yellowstone National Park

ABSTRACT Green nonsulfur-like bacteria (GNSLB) in hot spring microbial mats are thought to be mainly photoheterotrophic, using cyanobacterial metabolites as carbon sources. However, the stable carbon isotopic composition of typical Chloroflexus and Roseiflexus lipids suggests photoautotrophic metabolism of GNSLB. One possible explanation for this apparent discrepancy might be that GNSLB fix inorganic carbon only during certain times of the day. In order to study temporal variability in carbon metabolism by GNSLB, labeling experiments with [13C]bicarbonate, [14C]bicarbonate, and [13C]acetate were performed during different times of the day. [14C]bicarbonate labeling indicated that during the morning, incorporation of label was light dependent and that both cyanobacteria and GNSLB were involved in bicarbonate uptake. 13C-labeling experiments indicated that during the morning, GNSLB incorporated labeled bicarbonate at least to the same degree as cyanobacteria. The incorporation of [13C]bicarbonate into specific lipids could be stimulated by the addition of sulfide or hydrogen, which both were present in the morning photic zone. The results suggest that GNSLB have the potential for photoautotrophic metabolism during low-light periods. In high-light periods, inorganic carbon was incorporated primarily into Cyanobacteria-specific lipids. The results of a pulse-labeling experiment were consistent with overnight transfer of label to GNSLB, which could be interrupted by the addition of unlabeled acetate and glycolate. In addition, we observed direct incorporation of [13C]acetate into GNSLB lipids in the morning. This suggests that GNSLB also have a potential for photoheterotrophy in situ.

The effect of the reversed tricarboxylic acid cycle on the 13C contents of bacterial lipids

Abstract Free and esterified lipids of a green sulfur bacterium, Chlorobium limicola, and a purple sulfur bacterium, Thiocapsa roseopersicina, were investigated to examine the effect of the reversed tricarboxylic acid cycle on the 13C contents of their lipids. The lipids of C. limicola are 2 to 16‰ enriched in 13C relative to the total cell material, with the isoprenoid lipids 13 to 14‰ depleted in 13C relative to the straight-chain lipids. Although T. roseopersicina mainly uses the Calvin cycle for CO2 fixation and only partly uses the reversed tricarboxylic acid cycle, the same trends are observed with straight-chain lipids 2 to 4‰ enriched in 13C relative to the cell material and the isoprenoid lipids 7 to 9‰ depleted in 13C relative to the straight-chain lipids. These trends are consistent with the (partial) use of the reversed tricarboxylic acid cycle by C. limicola and T. roseopersicina, resulting in a reversed sequence of fractionation effects on the 13C content of the lipids compared to organisms using ribulose bisphosphate carboxylase to fix CO2.

Compound specific isotopic fractionation patterns suggest different carbon metabolisms among Chloroflexus-like bacteria in hot spring microbial mats

ABSTRACT Stable carbon isotope fractionations between dissolved inorganic carbon and lipid biomarkers suggest photoautotrophy by Chloroflexus-like organisms in sulfidic and nonsulfidic Yellowstone hot springs. Where co-occurring, cyanobacteria appear to cross-feed Chloroflexus-like organisms supporting photoheterotrophy as well, although the relatively small 13C fractionation associated with cyanobacterial sugar biosynthesis may sometimes obscure this process.

Cultivation and Genomic, Nutritional, and Lipid Biomarker Characterization of Roseiflexus Strains Closely Related to Predominant In Situ Populations Inhabiting Yellowstone Hot Spring Microbial Mats

Roseiflexus sp. strains were cultivated from a microbial mat of an alkaline siliceous hot spring in Yellowstone National Park. These strains are closely related to predominant filamentous anoxygenic phototrophs found in the mat, as judged by the similarity of small-subunit rRNA, lipid distributions, and genomic and metagenomic sequences. Like a Japanese isolate, R. castenholzii, the Yellowstone isolates contain bacteriochlorophyll a, but not bacteriochlorophyll c or chlorosomes, and grow photoheterotrophically or chemoheterotrophically under dark aerobic conditions. The genome of one isolate, Roseiflexus sp. strain RS1, contains genes necessary to support these metabolisms. This genome also contains genes encoding the 3-hydroxypropionate pathway for CO(2) fixation and a hydrogenase, which might enable photoautotrophic metabolism, even though neither isolate could be grown photoautotrophically with H(2) or H(2)S as a possible electron donor. The isolates exhibit temperature, pH, and sulfide preferences typical of their habitat. Lipids produced by these isolates matched much better with mat lipids than do lipids produced by R. castenholzii or Chloroflexus isolates.

Alkane-1,2-diol-based glycosides and fatty glycosides and wax esters in Roseiflexus castenholzii and hot spring microbial mats

Abstract. The lipid composition of Roseiflexus castenholzii, a thermophilic filamentous phototrophic bacterium related to uncultivated filamentous phototrophic bacteria that predominate in hot spring microbial mats, is reported. R. castenholzii lipid extracts were dominated by components characterized by alkane-1-ol-2-alkanoate moieties glycosidically bonded to a C6 sugar. Similar fatty glycosides, with an additional fatty acid esterified, were detected by HPLC-MS. R. castenholzii also produces a suite of wax esters ranging from 37 to 40 carbon atoms in length. In lipid extracts from two nonsulfidic hot spring microbial mats, similar alkane-1,2-diol-based lipids were detected in minor amounts. R. castenholzii lipids are compared to lipids of mats and other thermophilic mat isolates.

Are Marine Group II Euryarchaeota significant contributors to tetraether lipids in the ocean

Lincoln et al. (1) claim that Marine Group II Euryarchaeota (MG-II) are significant contributors to glycerol dibiphytanyl glycerol tetraether (GDGT) lipids in the ocean and biosynthesize crenarchaeol, a membrane lipid generally attributed to Thaumarchaeota (MG-I). The authors present two lines of convergent evidence for their far-reaching claim.

Millennial‐scale variability in Red Sea circulation in response to Holocene insolation forcing

In order to assess how insolation-driven climate change superimposed on sea level rise and millennial events influenced the Red Sea during the Holocene, we present new paleoceanographic records from two sediment cores to develop a comprehensive reconstruction of Holocene circulation dynamics in the basin. We show that the recovery of the planktonic foraminiferal fauna after the Younger Dryas was completed earlier in the northern than in the central Red Sea, implying significant changes in the hydrological balance of the northern Red Sea region during the deglaciation. In the early part of the Holocene, the environment of the Red Sea closely followed the development of the Indian summer monsoon and was dominated by a circulation mode similar to the current summer circulation, with low productivity throughout the central and northern Red Sea. The climatic signal during the late Holocene is dominated by a faunal transient event centered around 2.4 ka BP. Its timing corresponds to that of North Atlantic Bond event 2 and to a widespread regionally recorded dry period. This faunal transient is characterized by a more productive foraminiferal fauna and can be explained by an intensification of the winter circulation mode and high evaporation. The modern distribution pattern of planktonic foraminifera, reflecting the prevailing circulation system, was established after 1.7 ka BP.

Critical assessment of glyco- and phospholipid separation by using silica chromatography.

ABSTRACT Phospholipid-derived fatty acids (PLFAs) are commonly used to characterize microbial communities in situ and the phylogenetic positions of newly isolated microorganisms. PLFAs are obtained through separation of phospholipids from glycolipids and neutral lipids using silica column chromatography. We evaluated the performance of this separation method for the first time using direct detection of intact polar lipids (IPLs) with high-performance liquid chromatography–mass spectrometry (HPLC-MS). We show that under either standard or modified conditions, the phospholipid fraction contains not only phospholipids but also other lipid classes such as glycolipids, betaine lipids, and sulfoquinovosyldiacylglycerols. Thus, commonly reported PLFA compositions likely are not derived purely from phospholipids and perhaps may not be representative of fatty acids present in living microbes.