Search

Archaea adjust the number of cyclopentane rings in their glycerol dibiphytanyl glycerol tetraether (GDGT) membrane lipids as a homeostatic response to environmental stressors such as temperature, pH, and energy availability shifts. However, archaeal expression patterns that correspond with changes in GDGT composition are less understood. Here we characterize the acid and cold stress responses of the thermoacidophilic crenarchaeon Saccharolobus islandicus REY15A using growth rates, core GDGT lipid profiles, transcriptomics and proteomics. We show that both stressors result in impaired growth, lower average GDGT cyclization, and differences in gene and protein expression. Transcription data revealed differential expression of the GDGT ring synthase grsB in response to both acid stress and cold stress. Although the GDGT ring synthase encoded by grsB forms highly cyclized GDGTs with =5 ring moieties, S. islandicus grsB upregulation under acidic pH conditions did not correspond with increased abundances of highly cyclized GDGTs. Our observations highlight the inability to predict GDGT changes from transcription data alone. Broader analysis of transcriptomic data revealed that S. islandicus differentially expresses many of the same transcripts in response to both acid and cold stress. These included upregulation of several biosynthetic pathways and downregulation of oxidative phosphorylation and motility. Transcript responses specific to either of the two stressors tested here included upregulation of genes related to proton pumping and molecular turnover in acid stress conditions and upregulation of transposases in cold stress conditions. Overall, our study provides a comprehensive understanding of the GDGT modifications and differential expression characteristic of the acid stress and cold stress responses in S. islandicus. [ABSTRACT FROM AUTHOR]

In modern ecosystems, the carbon stable isotope (δ13C) ratios of consumers generally conform to the principle "you are what you eat, +1‰." However, this metric may not apply to microbial mat systems where diverse communities, using a variety of carbon substrates via multiple assimilation pathways, live in close physical association and phagocytosis is minimal or absent. To interpret the δ13C record of the Proterozoic and early Paleozoic, when mat‐based productivity likely was widespread, it is necessary to understand how a microbially driven producer–consumer structure affects the δ13C compositions of biomass and preservable lipids. Protein Stable Isotope Fingerprinting (P‐SIF) is a recently developed method that allows measurement of the δ13C values of whole proteins, separated from environmental samples and identified taxonomically via proteomics. Here, we use P‐SIF to determine the trophic relationships in a microbial mat sample from Chocolate Pots Hot Springs, Yellowstone National Park (YNP), USA. In this mat, proteins from heterotrophic bacteria are indistinguishable from cyanobacterial proteins, indicating that "you are what you eat, +1‰" is not applicable. To explain this finding, we hypothesize that sugar production and consumption dominate the net ecosystem metabolism, yielding a community in which producers and consumers share primary photosynthate as a common resource. This idea was validated by confirming that glucose moieties in exopolysaccharide were equal in δ13C composition to both cyanobacterial and heterotrophic proteins, and by confirming that highly 13C‐depleted fatty acids (FAs) of Cyanobacteria dominate the lipid pool, consistent with flux‐balance expectations for systems that overproduce primary photosynthate. Overall, the results confirm that the δ13C composition of microbial biomass and lipids is tied to specific metabolites, rather than to autotrophy versus heterotrophy or to individual trophic levels. Therefore, we suggest that aerobic microbial heterotrophy is simply a case of "you are what you eat." [ABSTRACT FROM AUTHOR]

Hopanoid lipids, bacteriohopanols and bacteriohopanepolyols, are membrane components exclusive to bacteria. Together with their diagenetic derivatives, they are commonly used as biomarkers for specific bacterial groups or biogeochemical processes in the geologic record. However, the sources of hopanoids to marine and freshwater environments remain inadequately constrained. Recent marker gene studies suggest a widespread potential for hopanoid biosynthesis in marine bacterioplankton, including nitrifying (i.e., ammonia‐ and nitrite‐oxidizing) bacteria. To explore their hopanoid biosynthetic capacities, we studied the distribution of hopanoid biosynthetic genes in the genomes of cultivated and uncultivated ammonia‐oxidizing (AOB), nitrite‐oxidizing (NOB), and complete ammonia‐oxidizing (comammox) bacteria, finding that biosynthesis of diverse hopanoids is common among seven of the nine presently cultivated clades of nitrifying bacteria. Hopanoid biosynthesis genes are also conserved among the diverse lineages of bacterial nitrifiers detected in environmental metagenomes. We selected seven representative NOB isolated from marine, freshwater, and engineered environments for phenotypic characterization. All tested NOB produced diverse types of hopanoids, with some NOB producing primarily diploptene and others producing primarily bacteriohopanepolyols. Relative and absolute abundances of hopanoids were distinct among the cultures and dependent on growth conditions, such as oxygen and nitrite limitation. Several novel nitrogen‐containing bacteriohopanepolyols were tentatively identified, of which the so called BHP‐743.6 was present in all NOB. Distinct carbon isotopic signatures of biomass, hopanoids, and fatty acids in four tested NOB suggest operation of the reverse tricarboxylic acid cycle in Nitrospira spp. and Nitrospina gracilis and of the Calvin–Benson–Bassham cycle for carbon fixation in Nitrobacter vulgaris and Nitrococcus mobilis. We suggest that the contribution of hopanoids by NOB to environmental samples could be estimated by their carbon isotopic compositions. The ubiquity of nitrifying bacteria in the ocean today and the antiquity of this metabolic process suggest the potential for significant contributions to the geologic record of hopanoids. [ABSTRACT FROM AUTHOR]

Rationale: The hydrogen isotopic composition of lipids (δ2Hlipid) is widely used in food science and as a proxy for past hydrological conditions. Determining the δ2H values of large, well‐preserved triacylglycerides and other microbial lipids, such as glycerol dialkyl glycerol tetraether (GDGT) lipids, is thus of widespread interest but has so far not been possible due to their low volatility which prohibits analysis by traditional gas chromatography/pyrolysis/isotope ratio mass spectrometry (GC/P/IRMS). Methods: We determined the δ2H values of large, polar molecules and applied high‐temperature gas chromatography (HTGC) methods on a modified GC/P/IRMS system. The system used a high‐temperature 7‐m GC column, and a glass Y‐splitter for low thermal mass. Methods were validated using authentic standards of large, functionalised molecules (triacylglycerides, TGs), purified standards of GDGTs. The results were compared with δ2H values determined by high‐temperature elemental analyser/pyrolysis/isotope ratio mass spectrometry (HTEA/P/IRMS), and subsequently applied to the analysis of GDGTs in a sample from a methane seep and a Welsh peat. Results: The δ2H values of TGs agreed within error between HTGC/P/IRMS and HTEA/IRMS, with HTGC/P/IRMS showing larger errors. Archaeal lipid GDGTs with up to three cyclisations could be analysed: the δ2H values were not significantly different between methods with standard deviations of 5 to 6 ‰. When environmental samples were analysed, the δ2H values of isoGDGTs were 50 ‰ more negative than those of terrestrial brGDGTs. Conclusions: Our results indicate that the HTGC/P/IRMS method developed here is appropriate to determine the δ2H values of TGs, GDGTs with up to two cyclisations, and potentially other high molecular weight compounds. The methodology will widen the current analytical window for biomarker and food light stable isotope analyses. Moreover, our initial measurements suggest that bacterial and archaeal GDGT δ2H values can record environmental and ecological conditions. [ABSTRACT FROM AUTHOR]

Summary: Adaptation of lipid membrane composition is an important component of archaeal homeostatic response. Historically, the number of cyclopentyl and cyclohexyl rings in the glycerol dibiphytanyl glycerol tetraether (GDGT) Archaeal lipids has been linked to variation in environmental temperature. However, recent work with GDGT‐making archaea highlight the roles of other factors, such as pH or energy availability, in influencing the degree of GDGT cyclization. To better understand the role of multiple variables in a consistent experimental framework and organism, we cultivated the model Crenarchaeon Sulfolobus acidocaldarius DSM639 at different combinations of temperature, pH, oxygen flux, or agitation speed. We quantified responses in growth rate, biomass yield, and core lipid compositions, specifically the degree of core GDGT cyclization. The degree of GDGT cyclization correlated with growth rate under most conditions. The results suggest the degree of cyclization in archaeal lipids records a universal response to energy availability at the cellular level, both in thermoacidophiles, and in other recent findings in the mesoneutrophilic Thaumarchaea. Although we isolated the effects of key individual parameters, there remains a need for multi‐factor experiments (e.g., pH + temperature + redox) in order to more robustly establish a framework to better understand homeostatic membrane responses. [ABSTRACT FROM AUTHOR]

Summary: Marine microorganisms play a fundamental role in the global carbon cycle by mediating the sequestration of organic matter in ocean waters and sediments. A better understanding of how biological factors, such as microbial community composition, influence the lability and fate of organic matter is needed. Here, we explored the extent to which organic matter remineralization is influenced by species‐specific metabolic capabilities. We carried out aerobic time‐series incubations of Guaymas Basin sediments to quantify the dynamics of carbon utilization by two different heterotrophic marine isolates (Vibrio splendidus 1A01; Pseudoalteromonas sp. 3D05). Continuous measurement of respiratory CO2 production and its carbon isotopic compositions (13C and 14C) shows species‐specific differences in the rate, quantity and type of organic matter remineralized. Each species was incubated with hydrothermally‐influenced versus unimpacted sediments, resulting in a ~2‐fold difference in respiratory CO2 yield across the experiments. Genomic analysis indicated that the observed carbon utilization patterns may be attributed in part to the number of gene copies encoding for extracellular hydrolytic enzymes. Our results demonstrate that the lability and remineralization of organic matter in marine environments is not only a function of chemical composition and/or environmental conditions, but also a function of the microorganisms that are present and active. [ABSTRACT FROM AUTHOR]

Summary: Microorganisms regulate the composition of their membranes in response to environmental cues. Many Archaea maintain the fluidity and permeability of their membranes by adjusting the number of cyclic moieties within the cores of their glycerol dibiphytanyl glycerol tetraether (GDGT) lipids. Cyclized GDGTs increase membrane packing and stability, which has been shown to help cells survive shifts in temperature and pH. However, the extent of this cyclization also varies with growth phase and electron acceptor or donor limitation. These observations indicate a relationship between energy metabolism and membrane composition. Here we show that the average degree of GDGT cyclization increases with doubling time in continuous cultures of the thermoacidophile Sulfolobus acidocaldarius (DSM 639). This is consistent with the behavior of a mesoneutrophile, Nitrosopumilus maritimus SCM1. Together, these results demonstrate that archaeal GDGT distributions can shift in response to electron donor flux and energy availability, independent of pH or temperature. Paleoenvironmental reconstructions based on GDGTs thus capture the energy available to microbes, which encompasses fluctuations in temperature and pH, as well as electron donor and acceptor availability. The ability of Archaea to adjust membrane composition and packing may be an important strategy that enables survival during episodes of energy stress. [ABSTRACT FROM AUTHOR]

The present-day marine nitrogen (N) cycle is strongly regulated by biology. Deficiencies in the availability of fixed and readily bioavailable nitrogen relative to phosphate (P) in the surface ocean are largely corrected by the activity of diazotrophs. This feedback system, termed the "nitrostat," is thought to have provided close regulation of fixed-N speciation and inventory relative to P since the Proterozoic. In contrast, during intervals of intense deoxygenation such as Cretaceous ocean anoxic event (OAE) 2, a few regional sedimentary δ15N records hint at the existence of a different mode of marine N cycling in which ammonium plays a major role in regulating export production. However, the global-scale dynamics during this time remain unknown. Here, using an Earth System model and taking the example of OAE 2, we provide insights into the global marine nitrogen cycle under severe ocean deoxygenation. Specifically, we find that the ocean can exhibit fundamental transitions in the species of nitrogen dominating the fixed-N inventory--from nitrate (NO3 -) to ammonium (NH4 +)--and that as this transition occurs, the inventory can partially collapse relative to P due to progressive spatial decoupling between the loci of NH4 + oxidation, NO3 - reduction, and nitrogen fixation. This finding is relatively independent of the specific state of ocean circulation and is consistent with nitrogen isotope and redox proxy data. The substantive reduction in the ocean fixed-N inventory at an intermediate state of deoxygenation may represent a biogeochemical vulnerability with potential implications for past and future (warmer) oceans. [ABSTRACT FROM AUTHOR]

The TEX86 proxy, based on the distribution of isoprenoid glycerol dialkyl glycerol tetraethers (iGDGTs) from planktonic Thaumarchaeota, is widely used to reconstruct sea surface temperature (SST). Recent observations of species‐specific and regionally dependent TEX86‐SST relationships in cultures and the modern ocean raise the question of whether nonthermal factors may have impacted TEX86 paleorecords. Here we evaluate the effects of ecological changes on TEX86 using one Pliocene and two Pleistocene sapropels from the Mediterranean Sea. We find that TEX86‐derived SSTs deviate from U37K'‐derived SSTs before, during, and after each sapropel event. U37K'‐derived SSTs vary by less than 6 °C, while TEX86‐derived SSTs vary by up to 15 °C within a single record. Compound‐specific carbon isotope compositions indicate minimal confounding influence on TEX86 from exogenous sources. Some of the variation can be accounted for by changes in nitrogen cycling intensity affecting thaumarchaeal iGDGT biosynthesis, as demonstrated by an inverse relationship between TEX86 and δ15NTN. TEX86‐derived SSTs also consistently show warm anomalies in the Pleistocene, while the Pliocene samples exhibit both warmer and cooler relative offsets. These anomalies result from systematic differences between Plio‐Pleistocene iGDGT distributions and both modern Mediterranean and modern, globally distributed core top samples. Through characteristic GDGT distributions, we suggest the existence of three distinct endemic populations of Thaumarchaeota in the Pliocene, Pleistocene, and modern Mediterranean Sea, respectively. Importantly, these communities prevailed during both sapropel and oligotrophic conditions. Our results demonstrate that ecological and community‐specific effects must be considered when applying the TEX86 proxy to paleorecords. Key Points: Mediterranean Pliocene‐Pleistocene sapropels were investigated for TEX86, archaeal lipid carbon isotopic compositions, and UK'37Nontemperature effects on TEX86 ocean temperature reconstructions are observed in all sapropels and surrounding marlsDistinct archaeal lipid distributions could be indicative of changing thaumarchaeal communities through time [ABSTRACT FROM AUTHOR]

Aquatic sediments harbour diverse microbial communities that mediate organic matter degradation and influence biogeochemical cycles. The pool of bioavailable carbon continuously changes as a result of abiotic processes and microbial activity. It remains unclear how microbial communities respond to heterogeneous organic matrices and how this ultimately affects heterotrophic respiration. To explore the relationships between the degradation of mixed carbon substrates and microbial activity, we incubated batches of organic-rich sediments in a novel bioreactor (IsoCaRB) that permitted continuous observations of CO2 production rates, as well as sequential sampling of isotopic signatures (δ13C, Δ14C), microbial community structure and diversity, and extracellular enzyme activity. Our results indicated that lower molecular weight (MW), labile, phytoplankton-derived compounds were degraded first, followed by petroleum-derived exogenous pollutants, and finally by higher MW polymeric plant material. This shift in utilization coincided with a community succession and increased extracellular enzyme activities. Thus, sequential utilization of different carbon pools induced changes at both the community and cellular level, shifting community composition, enzyme activity, respiration rates, and residual organic matter reactivity. Our results provide novel insight into the accessibility of sedimentary organic matter and demonstrate how bioavailability of natural organic substrates may affect the function and composition of heterotrophic bacterial populations. [ABSTRACT FROM AUTHOR]

Hopanoids are sterol-like membrane lipids widely used as geochemical proxies for bacteria. Currently, the physiological role of hopanoids is not well understood, and this represents one of the major limitations in interpreting the significance of their presence in ancient or contemporary sediments. Previous analyses of mutants lacking hopanoids in a range of bacteria have revealed a range of phenotypes under normal growth conditions, but with most having at least an increased sensitivity to toxins and osmotic stress. We employed hopanoid-free strains of Methylobacterium extorquens DM4, uncovering severe growth defects relative to the wild-type under many tested conditions, including normal growth conditions without additional stressors. Mutants overproduce carotenoids–the other major isoprenoid product of this strain–and show an altered fatty acid profile, pronounced flocculation in liquid media, and lower growth yields than for the wild-type strain. The flocculation phenotype can be mitigated by addition of cellulase to the medium, suggesting a link between the function of hopanoids and the secretion of cellulose in M. extorquens DM4. On solid media, colonies of the hopanoid-free mutant strain were smaller than wild-type, and were more sensitive to osmotic or pH stress, as well as to a variety of toxins. The results for M. extorquens DM4 are consistent with the hypothesis that hopanoids are important for membrane fluidity and lipid packing, but also indicate that the specific physiological processes that require hopanoids vary across bacterial lineages. Our work provides further support to emerging observations that the role of hopanoids in membrane robustness and barrier function may be important across lineages, possibly mediated through an interaction with lipid A in the outer membrane. [ABSTRACT FROM AUTHOR]

Organic matter is the dominant pool of reduced carbon in marine and freshwater systems. Mineralization of organic matter is largely attributed to complex and diverse microbial communities that mediate degradation and ultimately yield the terminal respiratory product, carbon dioxide (CO2). The factors that constrain the lability and degradation of organic matter remain unclear, but they involve a complex interplay between structural and chemical properties of the compounds, physical properties of the matrices, and the functional potential of the microorganisms that are present. To investigate these relationships, we developed a novel bioreactor system-called Isotopic Carbon Respirometer-Bioreactor (IsoCaRB)-that permits real-time monitoring of microbial CO2 production rates and collects sequential samples of this CO2 for off-line isotopic analyses (13C, 14C). Application of this system to organic-rich sediments from Salt Pond, MA reveals that organic matter is oxidized both abiotically and microbially, and that the pattern of microbial respiration by the native sediment community is complex, accessing different carbon substrates over the course of incubation. Isotopic measurements show modern organic matter of progressively older ages (≤ ca. 50 yr) is consumed, and this material has variable origins (salt marsh grasses, terrestrial, and marine organic matter). Collectively, the IsoCaRB system provides coupled insights into the sources, ages, and inherent biological and abiotic reactivity of natural organic matter. [ABSTRACT FROM AUTHOR]

Archaeal membrane lipids known as glycerol dibiphytanyl glycerol tetraethers (GDGTs) are the basis of the TEX86 paleotemperature proxy. Because GDGTs preserved in marine sediments are thought to originate mainly from planktonic, ammonia-oxidizing Thaumarchaeota, the basis of the correlation between TEX86 and sea surface temperature (SST) remains unresolved: How does TEX86 predict surface temperatures, when maximum thaumarchaeal activity occurs below the surface mixed layer and TEX86 does not covary with in situ growth temperatures? Here we used isothermal studies of the model thaumarchaeon Nitrosopumilus maritimus SCM1 to investigate how GDGT composition changes in response to ammonia oxidation rate.We used continuous culture methods to avoid potential confounding variables that can be associated with experiments in batch cultures. The results show that the ring index scales inversely (R2 = 0.82) with ammonia oxidation rate (ϕ), indicating that GDGT cyclization depends on available reducing power. Correspondingly, the TEX86 ratio decreases by an equivalent of 5.4 °C of calculated temperature over a 5.5 fmol.cell-1.d-1 increase in ϕ. This finding reconciles other recent experiments that have identified growth stage and oxygen availability as variables affecting TEX86. Depth profiles from the marine water column show minimum TEX86 values at the depth of maximum nitrification rates, consistent with our chemostat results. Our findings suggest that the TEX86 signal exported from the water column is influenced by the dynamics of ammonia oxidation. Thus, the global TEX86-SST calibration potentially represents a composite of regional correlations based on nutrient dynamics and global correlations based on archaeal community composition and temperature. [ABSTRACT FROM AUTHOR]

Mahoney Lake in British Columbia is an extreme meromictic system with unusually high levels of sulfate and sulfide present in the water column. As is common in strongly stratified lakes, Mahoney Lake hosts a dense, sulfide-oxidizing phototrophic microbial community where light reaches the chemocline. Below this "plate," the euxinic hypolimnion is anoxic, eutrophic, saline, and rich in sulfide, polysulfides, elemental sulfur, and other sulfur intermediates. While much is known regarding microbial communities in sunlit portions of euxinic systems, the composition and genetic potential of organisms living at aphotic depths have rarely been studied. Metagenomic sequencing of samples from the hypolimnion and the underlying sediments of Mahoney Lake indicate that multiple taxa contribute to sulfate reduction below the chemocline and that the hypolimnion and sediments each support distinct populations of sulfate reducing bacteria (SRB) that differ from the SRB populations observed in the chemocline. After assembling and binning the metagenomic datasets, we recovered near-complete genomes of dominant populations including two Deltaproteobacteria. One of the deltaproteobacterial genomes encoded a 16S rRNA sequence that was most closely related to the sulfur-disproportionating genus Dissulfuribacter and the other encoded a 16S rRNA sequence that was most closely related to the fatty acid- and aromatic acid-degrading genus Syntrophus. We also recovered two near-complete genomes of Firmicutes species. Analysis of concatenated ribosomal protein trees suggests these genomes are most closely related to extremely alkaliphilic genera Alkaliphilus and Dethiobacter. Our metagenomic data indicate that these Firmicutes contribute to carbon cycling below the chemocline. Lastly, we recovered a nearly complete genome from the sediment metagenome which represents a new genus within the FCB (Fibrobacteres, Chlorobi, Bacteroidetes) superphylum. Consistent with the geochemical data, we found little or no evidence for organisms capable of sulfide oxidation in the aphotic zone below the chemocline. Instead, comparison of functional genes below the chemocline are consistent with recovery of multiple populations capable of reducing oxidized sulfur. Our data support previous observations that at least some of the sulfide necessary to support the dense population of phototrophs in the chemocline is supplied from sulfate reduction in the hypolimnion and sediments. These studies provide key insights regarding the taxonomic and functional diversity within a euxinic environment and highlight the complexity of biogeochemical carbon and sulfur cycling necessary to maintain euxinia. [ABSTRACT FROM AUTHOR]

Our ability to read the molecular fossil record has advanced significantly in the past decade. Improvements in biomarker sampling and quantification methods, expansion of molecular sequence databases, and the application of genetic and cellular biological tools to problems in biomarker research have enabled much of this progress. By way of example, we review how attempts to understand the biological function of 2-methylhopanoids in modern bacteria have changed our interpretation of what their molecular fossils tell us about the early history of life. They were once thought to be biomarkers of cyanobacteria and hence the evolution of oxygenic photosynthesis, but we now believe that 2-methylhopanoid biosynthetic capacity originated in the Alphaproteobacteria, that 2-methylhopanoids are regulated in response to stress, and that hopanoid 2-methylation enhances membrane rigidity. We present a new interpretation of 2-methylhopanes that bridges the gap between studies of the functions of 2-methylhopanoids and their patterns of occurrence in the rock record. [ABSTRACT FROM AUTHOR]

Sixty percent of the world ocean by area is contained in oligotrophic gyres [Longhurst A (1995) Prog Oceanog 36:77-16], the biomass of which is dominated by picophytoplankton, including cyanobacteria and picoeukaryotic algae, as well as picoheterotrophs. Despite their recognized importance in carbon cycling in the surface ocean, the role of small cells and their detrital remains in the transfer of particulate organic matter (POM) to the deep ocean remains disputed. Because oligotrophic marine conditions are projected to expand under current climate trends, a better understanding of the role of small particles in the global carbon cycle is a timely goal. Here we use the lipid profiles, radiocarbon, and stable carbon isotopic signatures of lipids from the North Pacific Subtropical Gyre to show that in the surface ocean, lipids from submicron POM (here called extrasmall POM) are distinct from larger classes of suspended POM. Remarkably, this distinct extrasmall POM signature dominates the total lipids collected at mesopelagic depth, suggesting that the lipid component of mesopelagic POM primarily contains the exported remains of small particles. Transfer of submicron material to mesopelagic depths in this location is consistent with model results that claim the biological origin of exported carbon should be proportional to the distribution of cell types in the surface community, irrespective of cell size [Richardson IL, Jackson GA (2007) Science 315:838-8401. Our data suggest that the submicron component of exported POM is an important contributor to the global biological pump, especially in oligotrophic waters. [ABSTRACT FROM AUTHOR]

Archaea are abundant in marine and terrestrial aquatic environments, sediments, and soils. They inhabit at least an 85°C temperature range from the polar ocean to hydrothermal springs. Many Archaea produce membrane lipids called glycerol dialkyl glycerol tetraethers (GDGTs). Experiments on pure and enrichment cultures as well as an empirical correlation for marine sediments (the TEX86 index) together show positive relationships between temperature and the number of cyclopentane or cyclohexane rings in GDGTs. The resulting TEX86 paleotemperature proxy has been applied across a wide range of geologic history and depositional settings. The exact relationship between TEX86 and temperature, however, remains poorly understood. Environmental systems and cultures have different temperature dependencies, and the ecological niche(s) of aquatic Archaea are still a subject of active investigation. Here we review some of the remaining questions about GDGT paleotemperature proxies. Better answers to these challenging problems will help refine future paleoceanographic applications. [ABSTRACT FROM AUTHOR]

This theory-testing study is an examination of the influences of perceived information quality and perceived e-service quality in determining perceived value, and the influence of these three constructs in determining web site loyalty intentions. The results indicate that (1) perceived e-service quality and perceived information quality similarly influence loyalty intentions, (2) perceived e-service quality more strongly influences perceived value than does perceived information quality, and (3) perceived information quality partially mediates the relationship between perceived e-service quality and perceived value. The model was significant in explaining loyalty intentions. [ABSTRACT FROM PUBLISHER]

The Mesozoic is marked by several widespread occurrences of intense organic matter burial. Sediments from the largest of these events, the Cenomanian-Turonian Oceanic Anoxic Event (OAE 2) are characterized by lower nitrogen isotope ratios than are seen in modern marine settings. It has remained a challenge to describe a nitrogen cycle that could achieve such isotopic depletion. Here we use nitrogen-isotope ratios of porphyrins to show that eukaryotes contributed the quantitative majority of export production throughout OAE 2. whereas cyanobacteria contributed on average approximately 20%. Such data require that any explanation for the OAE nitrogen cycle and its isotopic values be consistent with a eukaryote-dominated ecosystem. Our results agree with models that suggest the OAEs were high-productivity events, supported by vigorous upwelling. Upwelling of anoxic deep waters would have supplied reduced N species (i.e.. NH4+) to primary producers. We propose that new production during OAE 2 primarily was driven by direct NH4+-assimilation supplemented by diazotrophy, whereas chemocline denitrification and anammox quantitatively consumed NO3 -and NO2-. A marine nitrogen reservoir dominated by NH4+, in combination with known kinetic isotope effects, could lead to eukaryotic biomass depleted in 15N. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Cyclization in glycerol dibiphytanyl glycerol tetraethers (GDGTs) results in internal cyclopentane moieties which are believed to confer thermal stability to crenarchaeal membranes. While the average number of rings per GDGT lipid (ring index) is positively correlated with temperature in many temperate environments, poor correlations are often observed in geothermal environments, suggesting that additional parameters may influence GDGT core lipid composition in these systems. However, the physical and chemical parameters likely to influence GDGT cyclization which are often difficult to decouple in geothermal systems, making it challenging to assess their influence on lipid composition. In the present study, the influence of temperature (range 65-81°C), pH (range 3.0-5.0), and ionic strength (range 10.1-55.7 mM) on GDGT core lipid composition was examined in the hyperthermoacidophile Acidilobus sulfurireducens, a crenarchaeon originally isolated from a geothermal spring in Yellowstone National Park, Wyoming. When cultivated under defined laboratory conditions, the composition of individual and total GDGTs varied significantly with temperature and to a lesser extent with the pH of the growth medium. Ionic strength over the range of values tested did not influence GDGT composition. The GDGT core lipid ring index was positively correlated with temperature and negatively correlated with pH, suggesting that A. sulfurireducens responds to increasing temperature and acidity by increasing the number of cyclopentyl rings in GDGT core membrane lipids. [ABSTRACT FROM AUTHOR]

Bacterial hopanoids are ubiquitous in Earth surface environments. They hold promise as environmental and ecological biomarkers, if the phylogeny and physiological drivers of hopanoid biosynthesis can be linked with the distribution of hopanoids observed across a breadth of samples. Here we survey the diversity of hopanoid cyclases from a land-sea gradient across the island of San Salvador, in the easternmost part of the Bahamas. The distribution of lipids was determined for the same sites, for the first time overlaying quantification of bacteriohopanepolyols with sqhC phylogeny. The results are similar to previous reports: environmental sqhCs average < 65% translated amino acid identity to their closest named relatives, and sequences from putative Proteobacteria dominate. Additionally, a new and apparently ubiquitous group of marine hopanoid producers is identified; it has no identifiable close relatives. The greatest diversity of hopanoid lipids occurs in soil, but hopanoids represent a minor fraction of total soil-derived lipids. Marine samples contain fewer identifiable hopanoids, but they are more abundant as a fraction of the total extractable lipids. In soil, the dominant compounds are 35-aminobacteriohopane-32,33,34-triol and adenosylhopane. In an upper estuarine sample, bacteriohopanetetrol and 32,35-anhydrobacteriohopanetetrol dominate; while in lower estuarine and open marine samples, the most abundant are bacteriohopanetetrol and bacteriohopaneribonolactone. Cyclitol ethers are trace components in the soil, absent in the estuary, and of moderate abundance in the open marine setting, suggesting a dominant marine source. Conversely, aminotriol and aminotetrol decrease in abundance or disappear completely from land to ocean, while 2-methyldiplopterol shows the opposite trend. Small quantities of 2-methylbacteriohopanepolyols are detectable in all samples. The overall hopanoid distributions may correlate to the major phylogenetic families of hopanoid producers or to the environments in which they are found. [ABSTRACT FROM AUTHOR]

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 (Δ[sup14]C) 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 aim) 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 ocean's largest reduced carbon reservoir, [sup14]C-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. [ABSTRACT FROM AUTHOR]

The bacterial terpenoid lipids known as hopanoids are fundamental tools for interpreting ancient microbial communities. Their degradation products, the hopanes, are found in sedimentary rocks throughout the geologic record. These compounds are presumed to be analogous to the sterols of eukaryotes, yet although the eukaryotic requirement for sterols is universal, hopanoid biosynthetic capacity is not ubiquitous among marine bacteria. Among the 9.8 million shotgun reads from the Sorcerer II Global Ocean Sampling (GOS) expedition, 148 contain putative coding sequence for bacterial squalene-hopene cyclases (SHCs). SHCs encoded by α-Proteobacteria potentially related to Rhodospirillaceae dominate these hits, especially in the open ocean and in tropical regions. Planctomycetes and β-Proteobacteria contribute more SHC-encoding sequences, and therefore presumably more hopanoid production, to coastal and temperate environments. Although sequences nominally related to α- and β-Proteobacteria outnumber other taxa in marine and coastal environments, there is large phylogenetic distance between GOS sequences and known species. Assuming that the environments sampled here are broadly representative of a wide range of surface ocean climates, depositional settings and temporal periods, the data suggest a fundamental function for Proteobacteria in the development of the geologic record of hopanes.The ISME Journal (2009) 3, 352–363; doi:10.1038/ismej.2008.116; published online 27 November 2008 [ABSTRACT FROM AUTHOR]

Molecular clocks suggest that animals originated well before they first appear as macroscopic fossils, but geologic tests of these hypotheses have been elusive. A rare steroid hydrocarbon, 24- isopropyicholestane, has been hypothesized to be a biomarker for sponges or their immediate ancestors because of its relatively high abundance in pre-Ediacaran to Early Cambrian sedimentary rocks and oils. Biolipid precursors of this sterane have been reported to be prominent in several demosponges. Whether 24-isopropylcholestane can be interpreted as a sponge (and, hence, animal) biomarker, and so provide clues about early metazoan history, depends on an understanding of the distribution of sterol biosynthesis among animals and their protistan relatives. Accordingly, we characterized the sterol profile of the choanoflagellate Monosiga brevicolIis, a representative of the unicellular sister group of animals. M. brevicollis does not produce a candidate sterol precursor for 24-isopropylcholestane under our experimental growth conditions. It does, however, produce a number of other sterols, and comparative genomics confirms its biosynthetic potential to produce the full suite of compounds recovered. Consistent with the phylogenetic position of choanoflagellates, the sterol profile and biosynthetic pathway of M. brevicollis display characteristics of both fungal and poriferan sterol biosynthesis. This is an example in which genomic and biochemical information have been used together to investigate the taxonomic specificity of a fossil biomarker. [ABSTRACT FROM AUTHOR]

Presents literary criticism of the works of W. G. Sebald, focusing on his distinct characteristics of intertextuality and extensive reference within his fiction. The significance of intertextuality as a theme within modern literatures is mentioned and an exploration is given to examples of Sebald's nested references to other works. Additional discussion is offered analyzing whether or not the references are subversive or supportive of traditional conceptions of authorship.

Many colleges of business require a course in computer applications concepts, often consisting of spreadsheet and database applications. Quite often, students resist taking the class because they do not see any worth to it, it duplicates what they already have taken, and they already know much of what is purported to be taught in the class. Instructors too are often frustrated with this class. This article suggests that part of the problem is the method of instruction often used: lecture and demonstration of tools followed by end-of-chapter assignments. We propose that problem-based learning is an alternative instructional method that may produce more positive results for students. To examine this approach, a semester-long study involving 186 business school students enrolled in a computer applications concept course of seven different sections was conducted. Student motivation, computer self-efficacy, knowledge, and satisfaction were studied. Results strongly support a problem-based learning approach as an instructional approach to teaching this class. [ABSTRACT FROM AUTHOR]

Hopanoids are ubiquitous isoprenoid lipids found in modern biota, in recent sediments and in low-maturity sedimentary rocks. Because these lipids primarily are derived from bacteria, they are used as proxies to help decipher geobiological communities. To date, much of the information about sources of hopanoids has come from surveys of culture collections, an approach that does not address the vast fraction of prokaryotic communities that remains uncharacterized. Here we investigated the phylogeny of hopanoid producers using culture-independent methods. We obtained 79 new sequences of squalene-hopene cyclase genes ( sqhC) from marine and lacustrine bacterioplankton and analysed them along with all 31 sqhC fragments available from existing metagenomics libraries. The environmental sqhCs average only 60% translated amino acid identity to their closest relatives in public databases. The data imply that the sources of these important geologic biomarkers remain largely unknown. In particular, genes affiliated with known cyanobacterial sequences were not detected in the contemporary environments analysed here, yet the geologic record contains abundant hopanoids apparently of cyanobacterial origin. The data also suggest that hopanoid biosynthesis is uncommon: < 10% of bacterial species may be capable of producing hopanoids. A better understanding of the contemporary distribution of hopanoid biosynthesis may reveal fundamental insight about the function of these compounds, the organisms in which they are found, and the environmental signals preserved in the sedimentary record. [ABSTRACT FROM AUTHOR]

E-commerce can be an important source of competitive advantage for most business organizations, especially small- and medium-sized (SMEs) businesses. Recently, researchers have focused on e-commerce adoption both in the United States and other countries. This study examines the factors that influence e-commerce adoption in Thailand. The results show that the major reason behind e-commerce non-adoption is that the organization is not ready to make that change because of cultural, technological, financial, and/or logistical reasons. Additionally, organizational readiness strongly influences e-commerce implementation, and managerial support and financial, logistical, and technological factors weigh heavily in determining if an SME in Thailand can pursue e-commerce implementation. We believe that the e-commerce adoption model in this study will have both managerial implication for practitioners in Thailand, as well as those in other developing countries, and academic implications tot researchers who are interested in e-commerce adoption in developing countries. [ABSTRACT FROM AUTHOR]

An ammonia-oxidizing, carbon-fixing archaeon, Candidatus ‘Nitrosopumilus maritimus,’ recently was isolated from a salt-water aquarium, definitively confirming that chemoautotrophy exists among the marine archaea. However, in other incubation studies, pelagic archaea also were capable of using organic carbon. It has remained unknown what fraction of the total marine archaeal community is autotrophic in situ. If archaea live primarily as autotrophs in the natural environment, a large ammonia-oxidizing population would play a significant role in marine nitrification. Here we use the natural distribution of radiocarbon in archaeal membrane lipids to quantify the bulk carbon metabolism of archaea at two depths in the subtropical North Pacific gyre. Our compound-specific radiocarbon data show that the archaea in surface waters incorporate modern carbon into their membrane lipids, and archaea at 670 m incorporate carbon that is slightly more isotopically enriched than inorganic carbon at the same depth. An isotopic mass balance model shows that the dominant metabolism at depth indeed is autotrophy (83%), whereas heterotrophic consumption of modern organic carbon accounts for the remainder of archaeal biomass. These results reflect the in situ production of the total community that produces tetraether lipids and are not subject to biases associated with incubation and/or culture experiments. The data suggest either that the marine archaeal community includes both autotrophs and heterotrophs or is a single population with a uniformly mixotrophic metabolism. The metabolic and phylogenetic diversity of the marine archaea warrants further exploration; these organisms may play a major role in the marine cycles of nitrogen and carbon. [ABSTRACT FROM AUTHOR]

Recently, the subject of research relevancy has received a great deal of attention in the IS academic press. Several leading academic journals, such as MIS Quarterly, Information Systems Research, and Information Resources Management Journal have devoted special issues and/or articles to this topic. Typically, these articles have been opinion pieces from leading IS academics (i.e., Benbasat, mud, Robe, Lee, etc.) and have not included significant input from practitioners within the IS area. This chapter fries to capture the IS practitioners' perspective on research relevance through a survey sent to 400 IS practitioners. The results indicate that IS practitioners (1) do not know where academic research is published; (2) find academic research dated; (3) find academic research difficult to read; and/or (4) find the recommendations included in academic research to be of little value. [ABSTRACT FROM AUTHOR]

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 biosyn-thesis 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. [ABSTRACT FROM AUTHOR]

Clinical use of stored electrogram (EGM) configurations currently used in ICDs is limited. The hypothesis that EGMs recorded from electrodes on the ICD surface may improve diagnostic capabilities of the device was tested in the present study. The Buttons on Active Can Emulator (BACE), an ICD-sized device containing four button electrodes, was temporarily placed into a subcutaneous or submuscular left pectoral pocket in 16 patients during ICD implantation. Simultaneous recordings were obtained from the ECC lead II, bipolar EGMs using BACE electrodes, and a bipolar atrial EGM during sinus rhythm (SR), ventricular pacing (VP) at cycle lengths of 500 and 400 ms, and VT. Visible P waves were present in all patients during SR (n = 15), in 5 (33%) of 15 patients during VP, and none of the patients during VT (n = 4) using BACE EGMs and lead II. P and QRS amplitudes and the P:QRS ratio during SR in BACE EGMs were significantly lower than those in lead II. BACE EGMs showed prominent changes in QRS morphology and duration during VP and VT compared to SR, and the magnitude of QRS prolongation during VP was similar to that in lead II. Measurements of PR, QRS, and QT duration during SR showed good agreement between BAGE EGMs and lead II. In conclusion, EGMs recorded from electrodes embedded on the IGD housing may potentially improve visual discrimination between supraventricular and ventricular arrhythmias. They also may be useful as a surrogate of the ECG for analysis and monitoring of different components of P-QRS-T complex. [ABSTRACT FROM AUTHOR]

Evaluates Shirley Ann Grau's vision of nature in her fiction 'The Condor Passes' and 'The Wind Shifting West.' Grau's treatment of the natural surroundings; Consequence of Grau's impartiality; Information on the first novel of Grau.

A negative carbon isotope excursion recorded in terrestrial and marine archives reflects massive carbon emissions into the exogenic carbon reservoir during the Paleocene-Eocene Thermal Maximum. Yet, discrepancies in carbon isotope excursion estimates from different sample types lead to substantial uncertainties in the source, scale, and timing of carbon emissions. Here we show that membrane lipids of marine planktonic archaea reliably record both the carbon isotope excursion and surface ocean warming during the Paleocene-Eocene Thermal Maximum. Novel records of the isotopic composition of crenarchaeol constrain the global carbon isotope excursion magnitude to −4.0 ± 0.4‰, consistent with emission of >3000 Pg C from methane hydrate dissociation or >4400 Pg C for scenarios involving emissions from geothermal heating or oxidation of sedimentary organic matter. A pre-onset excursion in the isotopic composition of crenarchaeol and ocean temperature highlights the susceptibility of the late Paleocene carbon cycle to perturbations and suggests that climate instability preceded the Paleocene-Eocene Thermal Maximum. The Paleocene-Eocene Thermal Maximum (c. 55 million years ago) was a period associated with massive carbon injection into the atmosphere, yet discrepancies in carbon isotope proxy records have led to substantial uncertainties in the source, scale, and timing of carbon emissions. Here, the authors propose that membrane lipids of marine planktonic archaea can reliably record the carbon isotope excursion and surface ocean warming, giving a new constraint for the source and size of the PETM carbon emissions. [ABSTRACT FROM AUTHOR]

The article discusses the microorganisms found in the sea floor such as Archea and Bacteria. It mentions that sediments in deep seas are either controlled by Archea or Bacteria. It refers to different expeditions in search for the microbial biosphere in the sea floor and its theories. The researchers say that study of deep biosphere will face challenges in examining, synthesizing and degrading lipids or DNA. According to the author, biologists and chemists still need to do many studies to find out the inhabitants of sea floor.

Anaerobic oxidation of methane (AOM) by sulfate has been recognized as a critical process to maintain this greenhouse gas stability by limiting methane flux to the atmosphere. We show geochemical evidence for AOM in deep lake sediments and demonstrate that AOM is likely driven by iron (Fe) reduction. Pore-water profiles from Lake Kinneret (Sea of Galilee, Israel) show that this sink for methane is located below the 20-cm depth in the sediment, which is well below the depths at which nitrate and sulfate are completely exhausted, as well as below the zone of methanogenesis. Iron-dependant AOM was verified by Fe(III)-amended mesocosm studies using intact sediment cores, and native iron oxides were detectable throughout the sediments. Because anaerobic Fe(III) respiration is thermodynamically more favorable than both sulfate-dependent methanotrophy and methanogenesis, its occurrence below the zone of methane production supports the idea that reduction of sedimentary iron oxides is kinetically or biologically limited. Similar conditions are likely to prevail in other incompletely pyritized aquatic sediments, indicating that AOM with Fe(III) is an important global sink for methane. [ABSTRACT FROM AUTHOR]