Ann Pearson

Global cooling during the eocene-oligocene climate transition.

About 34 million years ago, Earths climate shifted from a relatively ice-free world to one with glacial conditions on Antarctica characterized by substantial ice sheets. How Earths temperature changed during this climate transition remains poorly understood, and evidence for Northern Hemisphere polar ice is controversial. Here, we report proxy records of sea surface temperatures from multiple ocean localities and show that the high-latitude temperature decrease was substantial and heterogeneous. High-latitude (45 degrees to 70 degrees in both hemispheres) temperatures before the climate transition were ∼20°C and cooled an average of ∼5°C. Our results, combined with ocean and ice-sheet model simulations and benthic oxygen isotope records, indicate that Northern Hemisphere glaciation was not required to accommodate the magnitude of continental ice growth during this time.

Origins of lipid biomarkers in Santa Monica Basin surface sediment: a case study using compound-specific Δ14C analysis

Abstract Compound-specific Δ 14 C values are reported for 31 different lipid biomarker molecules obtained from Santa Monica Basin and Santa Barbara Basin surface sediments. These organic compounds represent phytoplanktonic, zooplanktonic, bacterial, archaeal, terrestrial higher plant, and fossil carbon sources. The lipid classes include the following: long-chain n -alkanes, fatty acids (as methyl esters; FAMEs), n -alcohols, C 30 midchain ketols and diols, sterols, hopanols, and C 40 isoprenoid side chains from the ether-linked glycerols of Archaea . The data show that the carbon source for the majority of the biomarkers is marine euphotic zone primary production or subsequent heterotrophic consumption of this biomass. A small amount of benthic incorporation of 14 C-depleted dissolved inorganic carbon was identified for the bacterial hopanols and C 15 linear and branched-chain fatty acids. However, there is no apparent uptake of 14 C-depleted dissolved inorganic carbon in Santa Monica Basin by the bacteria, including filamentous Beggiatoa spp., that produce C 18:1ω7 fatty acid. Two of the lipid classes did not reflect carbon originally fixed by marine photoautotrophs. These were the n -alkanes, for which the Δ 14 C data are consistent with mixed fossil carbon and contemporary terrestrial higher plant sources, and the archaeal isoprenoids, for which the Δ 14 C data are consistent with chemoautotrophic growth below the euphotic zone.

Anoxygenic photosynthesis modulated Proterozoic oxygen and sustained Earth's middle age

Molecular oxygen (O2) began to accumulate in the atmosphere and surface ocean ca. 2,400 million years ago (Ma), but the persistent oxygenation of water masses throughout the oceans developed much later, perhaps beginning as recently as 580–550 Ma. For much of the intervening interval, moderately oxic surface waters lay above an oxygen minimum zone (OMZ) that tended toward euxinia (anoxic and sulfidic). Here we illustrate how contributions to primary production by anoxygenic photoautotrophs (including physiologically versatile cyanobacteria) influenced biogeochemical cycling during Earths middle age, helping to perpetuate our planets intermediate redox state by tempering O2 production. Specifically, the ability to generate organic matter (OM) using sulfide as an electron donor enabled a positive biogeochemical feedback that sustained euxinia in the OMZ. On a geologic time scale, pyrite precipitation and burial governed a second feedback that moderated sulfide availability and water column oxygenation. Thus, we argue that the proportional contribution of anoxygenic photosynthesis to overall primary production would have influenced oceanic redox and the Proterozoic O2 budget. Later Neoproterozoic collapse of widespread euxinia and a concomitant return to ferruginous (anoxic and Fe2+ rich) subsurface waters set in motion Earths transition from its prokaryote-dominated middle age, removing a physiological barrier to eukaryotic diversification (sulfide) and establishing, for the first time in Earths history, complete dominance of oxygenic photosynthesis in the oceans. This paved the way for the further oxygenation of the oceans and atmosphere and, ultimately, the evolution of complex multicellular organisms.

Phylogenetic and biochemical evidence for sterol synthesis in the bacterium Gemmata obscuriglobus

Sterol biosynthesis is viewed primarily as a eukaryotic process, and the frequency of its occurrence in bacteria has long been a subject of controversy. Two enzymes, squalene monooxygenase and oxidosqualene cyclase, are the minimum necessary for initial biosynthesis of sterols from squalene. In this work, 19 protein gene sequences for eukaryotic squalene monooxygenase and 12 protein gene sequences for eukaryotic oxidosqualene cyclase were compared with all available complete and partial prokaryotic genomes. The only unequivocal matches for a sterol biosynthetic pathway were in the proteobacterium, Methylococcus capsulatus, in which sterol biosynthesis is known, and in the planctomycete, Gemmata obscuriglobus. The latter species contains the most abbreviated sterol pathway yet identified in any organism. Analysis shows that the major sterols in Gemmata are lanosterol and its uncommon isomer, parkeol. There are no subsequent modifications of these products. In bacteria, the sterol biosynthesis genes occupy a contiguous coding region and possibly comprise a single operon. Phylogenetic trees constructed for both enzymes show that the sterol pathway in bacteria and eukaryotes has a common ancestry. It is likely that this contiguous reading frame was exchanged between bacteria and early eukaryotes via lateral gene transfer or endosymbiotic events. The primitive sterols produced by Gemmata suggest that this genus could retain the most ancient remnants of the sterol biosynthetic pathway.

A Contemporary Microbially Maintained Subglacial Ferrous “Ocean”

An active microbial assemblage cycles sulfur in a sulfate-rich, ancient marine brine beneath Taylor Glacier, an outlet glacier of the East Antarctic Ice Sheet, with Fe(III) serving as the terminal electron acceptor. Isotopic measurements of sulfate, water, carbonate, and ferrous iron and functional gene analyses of adenosine 5′-phosphosulfate reductase imply that a microbial consortium facilitates a catalytic sulfur cycle. These metabolic pathways result from a limited organic carbon supply because of the absence of contemporary photosynthesis, yielding a subglacial ferrous brine that is anoxic but not sulfidic. Coupled biogeochemical processes below the glacier enable subglacial microbes to grow in extended isolation, demonstrating how analogous organic-starved systems, such as Neoproterozoic oceans, accumulated Fe(II) despite the presence of an active sulfur cycle.

Nonmarine Crenarchaeol in Nevada Hot Springs

ABSTRACT Glycerol dialkyl glycerol tetraethers (GDGTs) are core membrane lipids of the Crenarchaeota. The structurally unusual GDGT crenarchaeol has been proposed as a taxonomically specific biomarker for the marine planktonic group I archaea. It is found ubiquitously in the marine water column and in sediments. In this work, samples of microbial community biomass were obtained from several alkaline and neutral-pH hot springs in Nevada, United States. Lipid extracts of these samples were analyzed by high-performance liquid chromatography-mass spectrometry and by gas chromatography-mass spectrometry. Each sample contained GDGTs, and among these compounds was crenarchaeol. The distribution of archaeal lipids in Nevada hot springs did not appear to correlate with temperature, as has been observed in the marine environment. Instead, a significant correlation with the concentration of bicarbonate was observed. Archaeal DNA was analyzed by denaturing gradient gel electrophoresis. All samples contained 16S rRNA gene sequences which were more strongly related to thermophilic crenarchaeota than to Cenarchaeum symbiosum, a marine nonthermophilic crenarchaeon. The occurrence of crenarchaeol in environments containing sequences affiliated with thermophilic crenarchaeota suggests a wide phenotypic distribution of this compound. The results also indicate that crenarchaeol can no longer be considered an exclusive biomarker for marine species.

The origin of n-alkanes in Santa Monica Basin surface sediment: a model based on compound-specific Δ14C and δ13C data

Δ14C and δ13C values were measured for individual long-chain n-alkanes (C24–33) from Santa Monica Basin sediments. The data were then simulated using a three-component mixing model designed to represent the contributions of different sources. The three selected end members were petroleum, modern plant wax, and shale-derived alkanes. The model was optimized to fit the data and to determine the fractional contribution of each component. The results indicated that petroleum accounted for 12% of the alkanes in 0–2.5 cm sediment and 5% in 2.5–7.5 cm sediment. Modern plant waxes contributed 80% (0–2.5 cm) and 87% (2.5–7.5 cm), and the remaining 8% of each sample was attributed to the shale source. The 14C concentration of the modern terrestrial end member was also determined from the model. Δ14C values of ∼+235‰ for the 0–2.5 cm (post-bomb) horizon and ∼ 0‰ for the 2.5–7.5 cm (pre-bomb) horizon indicate that plant leaf waxes have a continental residence time of decades in the southern California region.

Community genomic analysis of an extremely acidophilic sulfur-oxidizing biofilm

Highly acidic (pH 0–1) biofilms, known as ‘snottites’, form on the walls and ceilings of hydrogen sulfide-rich caves. We investigated the population structure, physiology and biogeochemistry of these biofilms using metagenomics, rRNA methods and lipid geochemistry. Snottites from the Frasassi cave system (Italy) are dominated (>70% of cells) by Acidithiobacillus thiooxidans, with smaller populations including an archaeon in the uncultivated ‘G-plasma’ clade of Thermoplasmatales (>15%) and a bacterium in the Acidimicrobiaceae family (>5%). Based on metagenomic evidence, the Acidithiobacillus population is autotrophic (ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), carboxysomes) and oxidizes sulfur by the sulfide–quinone reductase and sox pathways. No reads matching nitrogen fixation genes were detected in the metagenome, whereas multiple matches to nitrogen assimilation functions are present, consistent with geochemical evidence, that fixed nitrogen is available in the snottite environment to support autotrophic growth. Evidence for adaptations to extreme acidity include Acidithiobacillus sequences for cation transporters and hopanoid synthesis, and direct measurements of hopanoid membrane lipids. Based on combined metagenomic, molecular and geochemical evidence, we suggest that Acidithiobacillus is the snottite architect and main primary producer, and that snottite morphology and distributions in the cave environment are directly related to the supply of C, N and energy substrates from the cave atmosphere.

The radiocarbon signature of microorganisms in the mesopelagic ocean

Several lines of evidence indicate that microorganisms in the meso- and bathypelagic ocean are metabolically active and respiring carbon. In addition, growing evidence suggests that archaea are fixing inorganic carbon in this environment. However, direct quantification of the contribution from deep ocean carbon sources to community production in the dark ocean remains a challenge. In this study, carbon flow through the microbial community at 2 depths in the mesopelagic zone of the North Pacific Subtropical Gyre was examined by exploiting the unique radiocarbon signatures (Δ14C) of the 3 major carbon sources in this environment. The radiocarbon content of nucleic acids, a biomarker for viable cells, isolated from size-fractionated particles (0.2–0.5 μm and >0.5 μm) showed the direct incorporation of carbon delivered by rapidly sinking particles. Most significantly, at the 2 mesopelagic depths examined (670 m and 915 m), carbon derived from in situ autotrophic fixation supported a significant fraction of the free-living microbial community (0.2–0.5 μm size fraction), but the contribution of chemoautotrophy varied markedly between the 2 depths. Results further showed that utilization of the oceans largest reduced carbon reservoir, 14C-depleted, dissolved organic carbon, was negligible in this environment. This isotopic portrait of carbon assimilation by the in situ, free-living microbial community, integrated over >50,000 L of seawater, implies that recent, photosynthetic carbon is not always the major carbon source supporting microbial community production in the mesopelagic realm.

Isolation, Characterization, and Ecology of Sulfur-Respiring Crenarchaea Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Park

ABSTRACT Elemental sulfur (S0) is associated with many geochemically diverse hot springs, yet little is known about the phylogeny, physiology, and ecology of the organisms involved in its cycling. Here we report the isolation, characterization, and ecology of two novel, S0-reducing Crenarchaea from an acid geothermal spring referred to as Dragon Spring. Isolate 18U65 grows optimally at 70 to 72°C and at pH 2.5 to 3.0, while isolate 18D70 grows optimally at 81°C and pH 3.0. Both isolates are chemoorganotrophs, dependent on complex peptide-containing carbon sources, S0, and anaerobic conditions for respiration-dependent growth. Glycerol dialkyl glycerol tetraethers (GDGTs) containing four to six cyclopentyl rings were present in the lipid fraction of isolates 18U65 and 18D70. Physiological characterization suggests that the isolates are adapted to the physicochemical conditions of Dragon Spring and can utilize the natural organic matter in the spring as a carbon and energy source. Quantitative PCR analysis of 16S rRNA genes associated with the S0 flocs recovered from several acid geothermal springs using isolate-specific primers indicates that these two populations together represent 17 to 37% of the floc-associated DNA. The physiological characteristics of isolates 18U65 and 18D70 are consistent with their potential widespread distribution and putative role in the cycling of sulfur in acid geothermal springs throughout the Yellowstone National Park geothermal complex. Based on phenotypic and genetic characterization, the designations Caldisphaera draconis sp. nov. and Acidilobus sulfurireducens sp. nov. are proposed for isolates 18U65 and 18D70, respectively.