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  • Microaerophilic Fe‐oxidizing micro‐organisms in Middle Jurassic ferruginous stromatolites and the paleoenvironmental context of their formation (Southern Carpathians, Romania)
    Geobiology (IF 4.100) Pub Date : 2020-01-15
    Mihaela Grădinaru; Iuliana Lazăr; Mihai N. Ducea; Lucian Petrescu

    Ferruginous stromatolites occur associated with Middle Jurassic condensed deposits in several Tethyan and peri‐Tethyan areas. The studied ferruginous stromatolites occurring in the Middle Jurassic condensed deposits of Southern Carpathians (Romania) preserve morphological, geochemical, and mineralogical data that suggest microbial iron oxidation. Based on their macrofabrics and accretion patterns, we classified stromatolites: (1) Ferruginous microstromatolites associated with hardground surfaces and forming the cortex of the macro‐oncoids and (2) Domical ferruginous stromatolites developed within the Ammonitico Rosso‐type succession disposed above the ferruginous microstromatolites (type 1). Petrographic and scanning electron microscope (SEM) examinations reveal that different types of filamentous micro‐organisms were the significant framework builders of the ferruginous stromatolitic laminae. The studied stromatolites yield a large range of δ56Fe values, from −0.75‰ to +0.66‰ with predominantly positive values indicating the prevalence of partial ferrous iron oxidation. The lowest negative δ56Fe values (up to −0.75‰) are present only in domical ferruginous stromatolites samples and point to initial iron mobilization where the Fe(II) was produced by dissimilatory Fe(III) reduction of ferric oxides by Fe(III)‐reducing bacteria. Rare‐earth elements and yttrium (REE + Y) are used to decipher the nature of the seawater during the formation of the ferruginous stromatolites. Cerium anomalies display moderate to small negative values for the ferruginous microstromatolites, indicating weakly oxygenated conditions compatible with slowly reducing environments, in contrast to the domical ferruginous stromatolites that show moderate positive Ce anomalies suggesting that they formed in deeper, anoxic–suboxic waters. The positive Eu anomalies from the studied samples suggest a diffuse hydrothermal input on the seawater during the Middle Jurassic on the sites of ferruginous stromatolite accretion. This study presents the first interpretation of REE + Y in the Middle Jurassic ferruginous stromatolites of Southern Carpathians, Romania.

    更新日期:2020-01-16
  • Identifying microbial life in rocks: Insights from population morphometry
    Geobiology (IF 4.100) Pub Date : 2019-12-26
    Joti Rouillard; Juan Manuel García-Ruiz; Linda Kah; Emmanuelle Gérard; Laurie Barrier; Sami Nabhan; Jian Gong; Mark A. van Zuilen

    The identification of cellular life in the rock record is problematic, since microbial life forms, and particularly bacteria, lack sufficient morphologic complexity to be effectively distinguished from certain abiogenic features in rocks. Examples include organic pore‐fillings, hydrocarbon‐containing fluid inclusions, organic coatings on exfoliated crystals and biomimetic mineral aggregates (biomorphs). This has led to the interpretation and re‐interpretation of individual microstructures in the rock record. The morphologic description of entire populations of microstructures, however, may provide support for distinguishing between preserved micro‐organisms and abiogenic objects. Here, we present a statistical approach based on quantitative morphological description of populations of microstructures. Images of modern microbial populations were compared to images of two relevant types of abiogenic microstructures: interstitial spaces and silica–carbonate biomorphs. For the populations of these three systems, the size, circularity, and solidity of individual particles were calculated. Subsequently, the mean/SD, skewness, and kurtosis of the statistical distributions of these parameters were established. This allowed the qualitative and quantitative comparison of distributions in these three systems. In addition, the fractal dimension and lacunarity of the populations were determined. In total, 11 parameters, independent of absolute size or shape, were used to characterize each population of microstructures. Using discriminant analysis with parameter subsets, it was found that size and shape distributions are typically sufficient to discriminate populations of biologic and abiogenic microstructures. Analysis of ancient, yet unambiguously biologic, samples (1.0 Ga Angmaat Formation, Baffin Island, Canada) suggests that taphonomic effects can alter morphometric characteristics and complicate image analysis; therefore, a wider range of microfossil assemblages should be studied in the future before automated analyses can be developed. In general, however, it is clear from our results that there is great potential for morphometric descriptions of populations in the context of life recognition in rocks, either on Earth or on extraterrestrial bodies.

    更新日期:2019-12-27
  • Free and kerogen‐bound biomarkers from late Tonian sedimentary rocks record abundant eukaryotes in mid‐Neoproterozoic marine communities
    Geobiology (IF 4.100) Pub Date : 2019-12-21
    J. Alex Zumberge; Don Rocher; Gordon D. Love

    Lipid biomarker assemblages preserved within the bitumen and kerogen phases of sedimentary rocks from the ca. 780–729 Ma Chuar and Visingsö Groups facilitate paleoenvironmental reconstructions and reveal fundamental aspects of emerging mid‐Neoproterozoic marine communities. The Chuar and Visingsö Groups were deposited offshore of two distinct paleocontinents (Laurentia and Baltica, respectively) during the Tonian Period, and the rock samples used had not undergone excessive metamorphism. The major polycyclic alkane biomarkers detected in the rock bitumens and kerogen hydropyrolysates consist of tricyclic terpanes, hopanes, methylhopanes, and steranes. Major features of the biomarker assemblages include detectable and significant contribution from eukaryotes, encompassing the first robust occurrences of kerogen‐bound regular steranes from Tonian rocks, including 21‐norcholestane, 27‐norcholestane, cholestane, ergostane, and cryostane, along with a novel unidentified C30 sterane series from our least thermally mature Chuar Group samples. Appreciable values for the sterane/hopane (S/H) ratio are found for both the free and kerogen‐bound biomarker pools for both the Chuar Group rocks (S/H between 0.09 and 1.26) and the Visingsö Group samples (S/H between 0.03 and 0.37). The more organic‐rich rock samples generally yield higher S/H ratios than for organic‐lean substrates, which suggests a marine nutrient control on eukaryotic abundance relative to bacteria. A C27 sterane (cholestane) predominance among total C26–C30 steranes is a common feature found for all samples investigated, with lower amounts of C28 steranes (ergostane and crysotane) also present. No traces of known ancient C30 sterane compounds; including 24‐isopropylcholestanes, 24‐n‐propylcholestanes, or 26‐methylstigmastanes, are detectable in any of these pre‐Sturtian rocks. These biomarker characteristics support the view that the Tonian Period was a key interval in the history of life on our planet since it marked the transition from a bacterially dominated marine biosphere to an ocean system which became progressively enriched with eukaryotes. The eukaryotic source organisms likely encompassed photosynthetic primary producers, marking a rise in red algae, and consumers in a revamped trophic structure predating the Sturtian glaciation.

    更新日期:2019-12-22
  • The microbially driven formation of siderite in salt marsh sediments
    Geobiology (IF 4.100) Pub Date : 2019-12-08
    Chin Yik Lin, Alexandra V. Turchyn, Alexey Krylov, Gilad Antler

    We employ complementary field and laboratory‐based incubation techniques to explore the geochemical environment where siderite concretions are actively forming and growing, including solid‐phase analysis of the sediment, concretion, and associated pore fluid chemistry. These recently formed siderite concretions allow us to explore the geochemical processes that lead to the formation of this less common carbonate mineral. We conclude that there are two phases of siderite concretion growth within the sediment, as there are distinct changes in the carbon isotopic composition and mineralogy across the concretions. Incubated sediment samples allow us to explore the stability of siderite over a range of geochemical conditions. Our incubation results suggest that the formation of siderite can be very rapid (about two weeks or within 400 hr) when there is a substantial source of iron, either from microbial iron reduction or from steel material; however, a source of dissolved iron is not enough to induce siderite precipitation. We suggest that sufficient alkalinity is the limiting factor for siderite precipitation during microbial iron reduction while the lack of dissolved iron is the limiting factor for siderite formation if microbial sulfate reduction is the dominant microbial metabolism. We show that siderite can form via heated transformation (at temperature 100°C for 48 hr) of calcite and monohydrocalcite seeds in the presence of dissolved iron. Our transformation experiments suggest that the formation of siderite is promoted when carbonate seeds are present.

    更新日期:2019-12-09
  • Magnesium isotope fractionation during microbially enhanced forsterite dissolution
    Geobiology (IF 4.100) Pub Date : 2019-12-01
    Aaron Brewer, Zoe Harrold, Elliot Chang, Drew Gorman‐Lewis, Fang‐Zhen Teng

    Bacillus subtilis endospore‐mediated forsterite dissolution experiments were performed to assess the effects of cell surface reactivity on Mg isotope fractionation during chemical weathering. Endospores present a unique opportunity to study the isolated impact of cell surface reactivity because they exhibit extremely low metabolic activity. In abiotic control assays, 24Mg was preferentially released into solution during forsterite dissolution, producing an isotopically light liquid phase (δ26Mg = −0.39 ± 0.06 to −0.26 ± 0.09‰) relative to the initial mineral composition (δ26Mg = −0.24 ± 0.03‰). The presence of endospores did not have an apparent effect on Mg isotope fractionation associated with the release of Mg from the solid into the aqueous phase. However, the endospore surfaces preferentially adsorbed 24Mg from the dissolution products, which resulted in relatively heavy aqueous Mg isotope compositions. These aqueous Mg isotope compositions increased proportional to the fraction of dissolved Mg that was adsorbed, with the highest measured δ26Mg (−0.08 ± 0.07‰) corresponding to the highest degree of adsorption (~76%). The Mg isotope composition of the adsorbed fraction was correspondingly light, at an average δ26Mg of −0.49‰. Secondary mineral precipitation and Mg adsorption onto secondary minerals had a minimal effect on Mg isotopes at these experimental conditions. Results demonstrate the isolated effects of cell surface reactivity on Mg isotope fractionation separate from other common biological processes, such as metabolism and organic acid production. With further study, Mg isotopes could be used to elucidate the role of the biosphere on Mg cycling in the environment.

    更新日期:2019-12-02
  • Exploring cycad foliage as an archive of the isotopic composition of atmospheric nitrogen
    Geobiology (IF 4.100) Pub Date : 2019-11-26
    Michael A. Kipp, Eva E. Stüeken, Michelle M. Gehringer, Kim Sterelny, John K. Scott, Paul I. Forster, Caroline A. E. Strömberg, Roger Buick

    Molecular nitrogen (N2) constitutes the majority of Earth's modern atmosphere, contributing ~0.79 bar of partial pressure (pN2). However, fluctuations in pN2 may have occurred on 107–109 year timescales in Earth's past, perhaps altering the isotopic composition of atmospheric nitrogen. Here, we explore an archive that may record the isotopic composition of atmospheric N2 in deep time: the foliage of cycads. Cycads are ancient gymnosperms that host symbiotic N2‐fixing cyanobacteria in modified root structures known as coralloid roots. All extant species of cycads are known to host symbionts, suggesting that this N2‐fixing capacity is perhaps ancestral, reaching back to the early history of cycads in the late Paleozoic. Therefore, if the process of microbial N2 fixation records the δ15N value of atmospheric N2 in cycad foliage, the fossil record of cycads may provide an archive of atmospheric δ15N values. To explore this potential proxy, we conducted a survey of wild cycads growing in a range of modern environments to determine whether cycad foliage reliably records the isotopic composition of atmospheric N2. We find that neither biological nor environmental factors significantly influence the δ15N values of cycad foliage, suggesting that they provide a reasonably robust record of the δ15N of atmospheric N2. Application of this proxy to the record of carbonaceous cycad fossils may not only help to constrain changes in atmospheric nitrogen isotope ratios since the late Paleozoic, but also could shed light on the antiquity of the N2‐fixing symbiosis between cycads and cyanobacteria.

    更新日期:2019-11-27
  • No support for the emergence of lichens prior to the evolution of vascular plants
    Geobiology (IF 4.100) Pub Date : 2019-11-14
    Matthew P. Nelsen, Robert Lücking, C. Kevin Boyce, H. Thorsten Lumbsch, Richard H. Ree

    The early‐successional status of lichens in modern terrestrial ecosystems, together with the role lichen‐mediated weathering plays in the carbon cycle, have contributed to the long and widely held assumption that lichens occupied early terrestrial ecosystems prior to the evolution of vascular plants and drove global change during this time. Their poor preservation potential and the classification of ambiguous fossils as lichens or other fungal–algal associations have further reinforced this view. As unambiguous fossil data are lacking to demonstrate the presence of lichens prior to vascular plants, we utilize an alternate approach to assess their historic presence in early terrestrial ecosystems. Here, we analyze new time‐calibrated phylogenies of ascomycete fungi and chlorophytan algae, that intensively sample lineages with lichen symbionts. Age estimates for several interacting clades show broad congruence and demonstrate that fungal origins of lichenization postdate the earliest tracheophytes. Coupled with the absence of unambiguous fossil data, our work finds no support for lichens having mediated global change during the Neoproterozoic‐early Paleozoic prior to vascular plants. We conclude by discussing our findings in the context of Neoproterozoic‐Paleozoic terrestrial ecosystem evolution and the paleoecological context in which vascular plants evolved.

    更新日期:2019-11-15
  • Desert breath—How fog promotes a novel type of soil biocenosis, forming the coastal Atacama Desert’s living skin
    Geobiology (IF 4.100) Pub Date : 2019-11-13
    Patrick Jung, Karen Baumann, Lukas W. Lehnert, Elena Samolov, Sebastian Achilles, Michael Schermer, Luise M. Wraase, Kai‐Uwe Eckhardt, Maaike Y. Bader, Peter Leinweber, Ulf Karsten, Jörg Bendix, Burkhard Büdel

    The Atacama Desert is the driest non‐polar desert on Earth, presenting precarious conditions for biological activity. In the arid coastal belt, life is restricted to areas with fog events that cause almost daily wet–dry cycles. In such an area, we discovered a hitherto unknown and unique ground covering biocenosis dominated by lichens, fungi, and algae attached to grit‐sized (~6 mm) quartz and granitoid stones. Comparable biocenosis forming a kind of a layer on top of soil and rock surfaces in general is summarized as cryptogamic ground covers (CGC) in literature. In contrast to known CGC from arid environments to which frequent cyclic wetting events are lethal, in the Atacama Desert every fog event is answered by photosynthetic activity of the soil community and thus considered as the desert's breath. Photosynthesis of the new CGC type is activated by the lowest amount of water known for such a community worldwide thus enabling the unique biocenosis to fulfill a variety of ecosystem services. In a considerable portion of the coastal Atacama Desert, it protects the soil from sporadically occurring splash erosion and contributes to the accumulation of soil carbon and nitrogen as well as soil formation through bio‐weathering. The structure and function of the new CGC type are discussed, and we suggest the name grit–crust. We conclude that this type of CGC can be expected in all non‐polar fog deserts of the world and may resemble the cryptogam communities that shaped ancient Earth. It may thus represent a relevant player in current and ancient biogeochemical cycling.

    更新日期:2019-11-13
  • Microbially influenced lacustrine carbonates: A comparison of Late Quaternary Lahontan tufa and modern thrombolite from Fayetteville Green Lake, NY
    Geobiology (IF 4.100) Pub Date : 2019-11-04
    Laura M. DeMott, Stephanie A. Napieralski, Christopher K. Junium, Mark Teece, Christopher A. Scholz

    Carbonate microbialites in lakes can serve as valuable indicators of past environments, so long as the biogenicity and depositional setting of the microbialite can be accurately determined. Late Pleistocene to Early Holocene frondose draping tufa deposits from Winnemucca Dry Lake (Nevada, USA), a subbasin of pluvial Lake Lahontan, were examined in outcrop, petrographically, and geochemically to determine whether microbially induced precipitation is a dominant control on deposition. These observations were compared to modern, actively accumulating microbialites from Fayetteville Green Lake (New York, USA) using similar methods. In addition, preserved microbial DNA was extracted from the Lahontan tufa and sequenced to provide a more complete picture of the microbial communities. Tufas are texturally and geochemically similar to modern thrombolitic microbialites from Fayetteville Green Lake, and the stable isotopic composition of organic C, N, inorganic C, and O supports deposition associated with a lacustrine microbial mat environment dominated by photosynthetic processes. DNA extraction and sequencing indicate that photosynthetic microbial builders were present during tufa deposition, primarily Chloroflexi and Proteobacteria with minor abundances of Cyanobacteria and Acidobacteria. Based on the sequencing results, the depositional environment of the tufas can be constrained to the photic zone of the lake, contrasting with some previous interpretations that put tufa formation in deeper waters. Additionally, the presence of a number of mesothermophilic phyla, including Deinococcus–Thermus, indicates that thermal groundwater may have played a role in tufa deposition at sites not previously associated with groundwater influx. The interpretation of frondose tufas as microbially influenced deposits provides new context to interpretations of lake level and past environments in the Lahontan lake basins.

    更新日期:2019-11-04
  • Sedimentation of ballasted cells‐free EPS in meromictic Fayetteville Green Lake
    Geobiology (IF 4.100) Pub Date : 2019-11-04
    Nina A. Kamennaya, Ping Hu, Christer Jansson

    Fayetteville Green Lake (FGL) is a recognized, extensively studied present‐day model of the stratified Proterozoic ocean. Nonetheless, biomass sedimentation in FGL remains hard to explain: while virtually all sediment pigments belong to photosynthetic sulfur bacteria from a chemocline, the isotopic carbon signature of the bulk organic matter suggests its epilimnetic phytoplankton origin. To explain the epilimnetic origin of sedimented carbon, we studied the dominant Synechococci, isolated from FGL. Here, we present experimental evidence that FGL Synechococci produce copious extracellular polysaccharides (EPS) especially when availability of inorganic carbon (Ci) is high relative to availability of other macronutrients, for example phosphorus. The accumulating EPS become impregnated with calcium, magnesium, and sodium cations and are released to the environment as ballasted cell coverings. Sedimentation of these cell‐free EPS can constitute the bulk of pigment‐free organic material in FGL sediment. Because increased availability of Ci specifically stimulates production of EPS and the accumulated EPS adsorb cations and become ballasted, we propose the universal role of cyanobacterial EPS in biomass sedimentation in the high‐Ci Paleoproterozoic ocean as well as in modern aquatic systems like FGL.

    更新日期:2019-11-04
  • Biomineralization: linking the fossil record to the production of high value functional materials.
    Geobiology (IF 4.100) Pub Date : 2008-05-09
    J R Lloyd,C I Pearce,V S Coker,R A D Pattrick,G van der Laan,R Cutting,D J Vaughan,M Paterson-Beedle,I P Mikheenko,P Yong,L E Macaskie

    The microbial cell offers a highly efficient template for the formation of nanoparticles with interesting properties including high catalytic, magnetic and light-emitting activities. Thus biomineralization products are not only important in global biogeochemical cycles, but they also have considerable commercial potential, offering new methods for material synthesis that eliminate toxic organic solvents and minimize expensive high-temperature and pressure processing steps. In this review we describe a range of bacterial processes that can be harnessed to make precious metal catalysts from waste streams, ferrite spinels for biomedicine and catalysis, metal phosphates for environmental remediation and biomedical applications, and biogenic selenides for a range of optical devices. Recent molecular-scale studies have shown that the structure and properties of bionanominerals can be fine-tuned by subtle manipulations to the starting materials and to the genetic makeup of the cell. This review is dedicated to the late Terry Beveridge who contributed much to the field of biomineralization, and provided early models to rationalize the mechanisms of biomineral synthesis, including those of geological and commercial potential.

    更新日期:2019-11-01
  • Statistical inference and reproducibility in geobiology.
    Geobiology (IF 4.100) Pub Date : 2019-02-13
    Erik A Sperling,Sabrina Tecklenburg,Laramie E Duncan

    更新日期:2019-11-01
  • Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree.
    Geobiology (IF 4.100) Pub Date : 2017-07-04
    B Kacar,V Hanson-Smith,Z R Adam,N Boekelheide

    Ribulose 1,5-bisphosphate (RuBP) carboxylase/oxygenase (RuBisCO, or Rubisco) catalyzes a key reaction by which inorganic carbon is converted into organic carbon in the metabolism of many aerobic and anaerobic organisms. Across the broader Rubisco protein family, homologs exhibit diverse biochemical characteristics and metabolic functions, but the evolutionary origins of this diversity are unclear. Evidence of the timing of Rubisco family emergence and diversification of its different forms has been obscured by a meager paleontological record of early Earth biota, their subcellular physiology and metabolic components. Here, we use computational models to reconstruct a Rubisco family phylogenetic tree, ancestral amino acid sequences at branching points on the tree, and protein structures for several key ancestors. Analysis of historic substitutions with respect to their structural locations shows that there were distinct periods of amino acid substitution enrichment above background levels near and within its oxygen-sensitive active site and subunit interfaces over the divergence between Form III (associated with anoxia) and Form I (associated with oxia) groups in its evolutionary history. One possible interpretation is that these periods of substitutional enrichment are coincident with oxidative stress exerted by the rise of oxygenic photosynthesis in the Precambrian era. Our interpretation implies that the periods of Rubisco substitutional enrichment inferred near the transition from anaerobic Form III to aerobic Form I ancestral sequences predate the acquisition of Rubisco by fully derived cyanobacterial (i.e., dual photosystem-bearing, oxygen-evolving) clades. The partitioning of extant lineages at high clade levels within our Rubisco phylogeny indicates that horizontal transfer of Rubisco is a relatively infrequent event. Therefore, it is possible that the mutational enrichment periods between the Form III and Form I common ancestral sequences correspond to the adaptation of key oxygen-sensitive components of Rubisco prior to, or coincident with, the Great Oxidation Event.

    更新日期:2019-11-01
  • Quantitative hopanoid analysis enables robust pattern detection and comparison between laboratories.
    Geobiology (IF 4.100) Pub Date : 2015-04-14
    C-H Wu,L Kong,M Bialecka-Fornal,S Park,A L Thompson,G Kulkarni,S J Conway,D K Newman

    Hopanoids are steroid-like lipids from the isoprenoid family that are produced primarily by bacteria. Hopanes, molecular fossils of hopanoids, offer the potential to provide insight into environmental transitions on the early Earth, if their sources and biological functions can be constrained. Semiquantitative methods for mass spectrometric analysis of hopanoids from cultures and environmental samples have been developed in the last two decades. However, the structural diversity of hopanoids, and possible variability in their ionization efficiencies on different instruments, have thus far precluded robust quantification and hindered comparison of results between laboratories. These ionization inconsistencies give rise to the need to calibrate individual instruments with purified hopanoids to reliably quantify hopanoids. Here, we present new approaches to obtain both purified and synthetic quantification standards. We optimized 2-methylhopanoid production in Rhodopseudomonas palustris TIE-1 and purified 2Me-diplopterol, 2Me-bacteriohopanetetrol (2Me-BHT), and their unmethylated species (diplopterol and BHT). We found that 2-methylation decreases the signal intensity of diplopterol between 2 and 34% depending on the instrument used to detect it, but decreases the BHT signal less than 5%. In addition, 2Me-diplopterol produces 10× higher ion counts than equivalent quantities of 2Me-BHT. Similar deviations were also observed using a flame ionization detector for signal quantification in GC. In LC-MS, however, 2Me-BHT produces 11× higher ion counts than 2Me-diplopterol but only 1.2× higher ion counts than the sterol standard pregnane acetate. To further improve quantification, we synthesized tetradeuterated (D4) diplopterol, a precursor for a variety of hopanoids. LC-MS analysis on a mixture of (D4)-diplopterol and phospholipids showed that under the influence of co-eluted phospholipids, the D4-diplopterol internal standard quantifies diplopterol more accurately than external diplopterol standards. These new quantitative approaches permit meaningful comparisons between studies, allowing more accurate hopanoid pattern detection in both laboratory and environmental samples.

    更新日期:2019-11-01
  • Molybdenum isotope fractionation by cyanobacterial assimilation during nitrate utilization and N₂ fixation.
    Geobiology (IF 4.100) Pub Date : 2010-11-26
    A L Zerkle,K Scheiderich,J A Maresca,L J Liermann,S L Brantley

    We measured the δ⁹⁸Mo of cells and media from molybdenum (Mo) assimilation experiments with the freshwater cyanobacterium Anabaena variabilis, grown with nitrate as a nitrogen (N) source or fixing atmospheric N₂. This organism uses a Mo-based nitrate reductase during nitrate utilization and a Mo-based dinitrogenase during N₂ fixation under culture conditions here. We also demonstrate that it has a high-affinity Mo uptake system (ModABC) similar to other cyanobacteria, including marine N₂-fixing strains. Anabaena variabilis preferentially assimilated light isotopes of Mo in all experiments, resulting in fractionations of -0.2‰ to -1.0‰ ± 0.2‰ between cells and media (ε(cells-media)), extending the range of biological Mo fractionations previously reported. The fractionations were internally consistent within experiments, but varied with the N source utilized and for different growth phases sampled. During growth on nitrate, A. variabilis consistently produced fractionations of -0.3 ± 0.1‰ (mean ± standard deviation between experiments). When fixing N₂, A. variabilis produced fractionations of -0.9 ± 0.1‰ during exponential growth, and -0.5 ± 0.1‰ during stationary phase. This pattern is inconsistent with a simple kinetic isotope effect associated with Mo transport, because Mo is likely transported through the ModABC uptake system under all conditions studied. We present a reaction network model for Mo isotope fractionation that demonstrates how Mo transport and storage, coordination changes during enzymatic incorporation, and the distribution of Mo inside the cell could all contribute to the total biological fractionations. Additionally, we discuss the potential importance of biologically incorporated Mo to organic matter-bound Mo in marine sediments.

    更新日期:2019-11-01
  • Stars of the terrestrial deep subsurface: a novel 'star-shaped' bacterial morphotype from a South African platinum mine.
    Geobiology (IF 4.100) Pub Date : 2008-05-24
    G Wanger,T C Onstott,G Southam

    We study structure and function. Credit of course, goes to TJB, for it is from him that I inherited the habit of personifying bacteria and attempting to think like a bacterium, to better understand what they do. This work has taken us to wonderful places such as Yellowstone National Park, The Canadian Arctic, Australia, and the deep subsurface in the Republic of South Africa, the subject of this manuscript. From their perspective, why they do what they do is simple, to live. How they do it, is more challenging for us to understand, so it is something that we continue to work on. The marvel of bacteria is something that I, in turn, try to pass on to my students where I hope it will find fertile ground and provide as much enjoyment as it has given me - G. Southam. A biofilm (mine-slime) collected from the Northam Platinum mine in the Republic of South Africa contained a new bacterial morphotype. Mine-slimes are generally considered to be microbiologically compromised, subsurface samples due to the likelihood of contamination from the mining environment. However, careful examination of this biofilm demonstrated that it possessed a diverse bacterial population that included organisms that are consistent with the deep subsurface, suggesting that mine-slimes represent an underutilized, 'natural' bacterial enrichment. Using scanning and transmission electron microscopy, a novel, branching, filamentous, star-shape bacterium (in cross section) has been found, adding a new bacterial morphotype and strategy that bacteria have demonstrated to increase their surface area to volume ratio.

    更新日期:2019-11-01
  • The co-evolution of phytoplankton and trace element cycles in the oceans.
    Geobiology (IF 4.100) Pub Date : 2008-05-24
    François M M Morel

    The composition of the oceans and of its biota have influenced each other through Earth's history. Of all the biologically essential elements, nitrogen is the only one whose seawater concentration is clearly controlled biologically; this is presumably the main reason why the stoichiometry of nitrogen (defined as its mol ratio to phosphorus), but not that of the trace nutrients manganese, iron, cobalt, nickel, copper, zinc and cadmium, is the same in seawater and in the plankton. Like the major nutrients, the trace nutrients are depleted in surface seawater as a result of quasi-complete utilization by the biota. This is made possible in part by the ability of marine phytoplankton to replace one trace metal by another in various biochemical functions. This replacement also results in an equalization of the availability of most essential trace metals in surface seawater. The difference in the stoichiometric composition of the plankton and of deep seawater, which is the dominant source of new nutrients to the surface, indicates that some nutrients are likely recycled with different efficiencies in the photic zone. The difference in the composition of the ocean and its biota provides insight into the coupling of biochemistry and biogeochemistry in seawater.

    更新日期:2019-11-01
  • Benefits of bacterial biomineralization.
    Geobiology (IF 4.100) Pub Date : 2008-05-24
    V R Phoenix,K O Konhauser

    更新日期:2019-11-01
  • 更新日期:2019-11-01
  • Electron transfer at the microbe-mineral interface: a grand challenge in biogeochemistry.
    Geobiology (IF 4.100) Pub Date : 2008-05-24
    J K Fredrickson,J M Zachara

    The interplay between microorganisms and minerals is a complex and dynamic process that has sculpted the geosphere for nearly the entire history of the Earth. The work of Dr Terry Beveridge and colleagues provided some of the first insights into metal-microbe and mineral-microbe interactions and established a foundation for subsequent detailed investigations of interactions between microorganisms and minerals. Beveridge also envisioned that interdisciplinary approaches and teams would be required to explain how individual microbial cells interact with their immediate environment at nano- or microscopic scales and that through such approaches and using emerging technologies that the details of such interactions would be revealed at the molecular level. With this vision as incentive and inspiration, a multidisciplinary, collaborative team-based investigation was initiated to probe the process of electron transfer (ET) at the microbe-mineral interface. The grand challenge to this team was to address the hypothesis that multiheme c-type cytochromes of dissimilatory metal-reducing bacteria localized to the cell exterior function as the terminal reductases in ET to Fe(III) and Mn(IV) oxides. This question has been the subject of extensive investigation for years, yet the answer has remained elusive. The team involves an integrated group of experimental and computational capabilities at US Department of Energy's Environmental Molecular Sciences Laboratory, a national scientific user facility, as the collaborative focal point. The approach involves a combination of in vitro and in vivo biologic and biogeochemical experiments and computational analyses that, when integrated, provide a conceptual model of the ET process. The resulting conceptual model will be evaluated by integrating and comparing various experimental, i.e. in vitro and in vivo ET kinetics, and theoretical results. Collectively, the grand challenge will provide a detailed view of how organisms engage with mineral surfaces to exchange energy and electron density as required for life function.

    更新日期:2019-11-01
  • Redox-reactive membrane vesicles produced by Shewanella.
    Geobiology (IF 4.100) Pub Date : 2008-05-24
    Y Gorby,J McLean,A Korenevsky,K Rosso,M Y El-Naggar,T J Beveridge

    This manuscript is dedicated to our friend, mentor, and coauthor Dr Terry Beveridge, who devoted his scientific career to advancing fundamental aspects of microbial ultrastructure using innovative electron microscopic approaches. During his graduate studies with Professor Robert Murray, Terry provided some of the first glimpses and structural evaluations of the regular surface arrays (S-layers) of Gram-negative bacteria (Beveridge & Murray, 1974, 1975, 1976a). Beginning with his early electron microscopic assessments of metal binding by cell walls from Gram-positive bacteria (Beveridge & Murray, 1976b, 1980) and continuing with more than 30 years of pioneering research on microbe-mineral interactions (Hoyle & Beveridge, 1983, 1984; Ferris et al., 1986; Gorby et al., 1988; Beveridge, 1989; Mullen et al., 1989; Urrutia Mera et al., 1992; Mera & Beveridge, 1993; Brown et al., 1994; Konhauser et al., 1994; Beveridge et al., 1997; Newman et al., 1997; Lower et al., 2001; Glasauer et al., 2002; Baesman et al., 2007), Terry helped to shape the developing field of biogeochemistry. Terry and his associates are also widely regarded for their research defining the structure and function of outer membrane vesicles from Gram-negative bacteria that facilitate processes ranging from the delivery of pathogenic enzymes to the possible exchange of genetic information. The current report represents the confluence of two of Terry's thematic research streams by demonstrating that membrane vesicles produced by dissimilatory metal-reducing bacteria from the genus Shewanella catalyze the enzymatic transformation and precipitation of heavy metals and radionuclides. Under low-shear conditions, membrane vesicles are commonly tethered to intact cells by electrically conductive filaments known as bacterial nanowires. The functional role of membrane vesicles and associated nanowires is not known, but the potential for mineralized vesicles that morphologically resemble nanofossils to serve as palaeontological indicators of early life on Earth and as biosignatures of life on other planets is recognized.

    更新日期:2019-11-01
  • Are gram-positive bacteria capable of electron transfer across their cell wall without an externally available electron shuttle?
    Geobiology (IF 4.100) Pub Date : 2008-05-24
    H L Ehrlich

    The extensive contributions by Terry Beveridge to our understanding of the differences in cell wall organization with respect to structure, chemistry and compartmentalization between gram-positive and gram-negative bacteria are summarized. These contributions greatly aided in conceptualization of recent discoveries concerning electron export and import across cell walls of some gram-negative bacteria. Although electron export and import across the cell wall by any gram-positive has not been documented so far, Beveridge's observations and concepts concerning cell walls of gram-positive bacteria suggest potential mechanisms by which such electron transfer may occur.

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  • Geobiology. Preface.
    Geobiology (IF 4.100) Pub Date : 2008-05-24
    D K Newman,K O Konhauser,A-L Reysenbach

    更新日期:2019-11-01
  • Microtubules in basalt glass from Hawaii Scientific Driling Project #2 phase 1 core and Hilina slope, Hawaii: evidence of the occurrence and behavior of endolithic microorganisms.
    Geobiology (IF 4.100) Pub Date : 2008-05-16
    A W Walton

    Elongate, fine tubes, approximately 1 microm wide and up to 200 microm long, extend from fractured surfaces, vesicle walls, and internal fractures into fragments of basalt glass in samples from the Hawaii Scientific Drilling Project #2 phase 1 (HSDP #2(1)) core and the Hilina slope, Hawaii. Several features indicate that these tubes are microbial endolithic microborings: the tubes resemble many described microborings from oceanic basalt glass, their formation is postdepositional but restricted to certain but different ranges of time in the two sets of samples, and they are not uniformly distributed throughout glass fragments. Microtubules record several characteristic behaviors including boring into glass, mining, seeking olivine, and avoiding plagioclase. They also are highly associated with a particular form of glass-replacing smectite. Evidence of behavior should join morphological and geochemical criteria in indicating microbial alteration of basalt glass. In some samples, steeply conical tubes, approximately 10-20 microm in diameter tapering to 1 microm and commonly filled with smectite, appear to be modifications or elaborations of the microtubules. These also curve toward olivine and are associated with replacement smectite. In HSDP #2(1) samples, microtubules initiated at margins of shards before palagonite replaced those margins and are preserved during palagonitization. In fact, microtubules appear to have provided routes that enhanced the efficiency of water's reaching of unaltered glass. In Hilina Slope samples, the microtubules appear to postdate palagonitization because they initiate at the boundary between palagonite and unaltered sideromelane. Preservation of microtubules during palagonitization in samples together with recognition of other associated characteristics representing behavior suggests that such features may be recognizable in more heavily altered ancient rocks.

    更新日期:2019-11-01
  • Constraints in the colonization of natural and engineered subterranean igneous rock aquifers by aerobic methane-oxidizing bacteria inferred by culture analysis.
    Geobiology (IF 4.100) Pub Date : 2008-05-09
    E Chi Fru

    The aerobic methane-oxidizing bacteria (MOB) are suggested to be important for the removal of oxygen from subterranean aquifers that become oxygenated by natural and engineering processes. This is primarily because MOB are ubiquitous in the environment and in addition reduce oxygen efficiently. The biogeochemical factors that will control the success of the aerobic MOB in these kinds of underground aquifers remain unknown. In this study, viable and cultivable MOB occurring at natural and engineered deep granitic aquifers targeted for the disposal of spent nuclear fuel (SNF) in the Fennoscandian Shield (approximately 3-1000 m) were enumerated. The numbers were correlated with in situ salinity, methane concentrations, conductivity, pH, and depth. A mixed population habiting freshwater aquifers (approximately 3-20 m), a potential source for the inoculation of MOB into the deeper aquifers was tested for tolerance to NaCl, temperature, pH, and an ability to produce cysts and exospores. Extrapolations show that due to changing in situ parameters (salinity, conductivity, and pH), the numbers of MOB in the aquifers dropped quickly with depth. A positive correlation between the most probable numbers of MOB and methane concentrations was observed. Furthermore, the tolerance-based tests of cultured strains indicated that the MOB in the shallow aquifers thrived best in mesophilic and neutrophilic conditions as opposed to the hyperthermophilic and alkaliphilic conditions expected to develop in an engineered subterranean SNF repository. Overall, the survival of the MOB both quantitatively and physiologically in the granitic aquifers was under the strong influence of biogeochemical factors that are strongly depth-dependent.

    更新日期:2019-11-01
  • Gram-negative outer membrane vesicles: beyond the cell surface.
    Geobiology (IF 4.100) Pub Date : 2008-05-08
    L Mashburn-Warren,R J C McLean,M Whiteley

    Considerable interest has recently mounted regarding the biological roles of Gram-negative outer membrane vesicles (MVs). The first discovery of MVs was made over four decades ago, and it is now clear that most Gram-negative bacteria produce MVs, with Pseudomonas aeruginosa and Escherichia coli as the most extensively studied. Much of our knowledge of the biological roles of MVs and mechanism of MV formation is due to T.J. Beveridge and colleagues. Beveridge pioneered the field of MV research not only by enhancing our understanding of MV function, but also through the application of a wide variety of physical, chemical, and genetic techniques to complement his elegant electron microscopy investigations. Here we review the contributions of Beveridge's group to our understanding of MV biology.

    更新日期:2019-11-01
  • Microorganisms, mineral surfaces, and aquatic environments: learning from the past for future progress.
    Geobiology (IF 4.100) Pub Date : 2008-05-08
    M Dittrich,A Luttge

    The interactions between the geosphere and the biosphere are central questions in environmental and geological research. The relationship between bacteria and their environment is an important example of these interactions. By studying microbial communities in modern environments, it is possible to understand the underlying mechanisms that shape these environments and apply this knowledge to the rock record. Recently, new experimental and theoretical methods, ranging from nano- and biotechnology to mathematical and conceptual modelling, have come into play. Thus, new opportunities for interdisciplinary research in the field of geobiology have emerged. In this paper, we review aspects of state-of-the-art imaging and modelling techniques and propose a research concept linking the experimental and the theoretical approaches.

    更新日期:2019-11-01
  • Resolving biogeochemical phenomena at high spatial resolution through electron microscopy.
    Geobiology (IF 4.100) Pub Date : 2008-05-08
    G G Geesey,T Borch,C L Reardon

    更新日期:2019-11-01
  • In search of the microbe/mineral interface: quantitative analysis of bacteria on metal surfaces using vertical scanning interferometry.
    Geobiology (IF 4.100) Pub Date : 2008-05-08
    M S Waters,C A Sturm,M Y El-Naggar,A Luttge,F E Udwadia,D G Cvitkovitch,S D Goodman,K H Nealson

    To understand the development of biofilms on metal surfaces, analysis of initial bacterial attachment to surfaces is crucial. Here we present the results of a study, using Shewanella oneidensis MR-1 as a model organism, in which vertical scanning interferometry (VSI) was used to investigate the initial stages of cell attachment to glass, steel and aluminium surfaces. It was found that while VSI gave unambiguous results with opaque surfaces, when reflective surfaces were used, an artifact sometimes appeared, with the bacteria appearing as rod-shaped pits rather than as cells on the surface. When the bacteria were altered to increase opacity, this artifact disappeared, and upon further investigation, it was found that the observational artifact was the result of a conflict between light reflected from the bacteria and the light reflected from the bacteria-metal interface. These results suggest that not only can bacteria be measured on surfaces using VSI, but with some modifications to the analytical software, there may be a unique window for studying the bacterial/substrate interface that can be used for quantitative observations. Imaging and characterization of the bacteria-substrate interface in vivo (previously invisible) will provide new insights into the interactions that occur at this important juncture.

    更新日期:2019-11-01
  • Intracellular minerals and metal deposits in prokaryotes.
    Geobiology (IF 4.100) Pub Date : 2008-05-03
    K J Edwards,D A Bazylinski

    Thanks to the work of Terrance J. Beveridge and other pioneers in the field of metal-microbe interactions, prokaryotes are well known to sequester metals and other ions intracellularly in various forms. These forms range from poorly ordered deposits of metals to well-ordered mineral crystals. Studies on well-ordered crystalline structures have generally focused on intracellular organelles produced by magnetotactic bacteria that are ubiquitous in terrestrial and marine environments that precipitate Fe(3)O(4) or Fe(3)S(4), Fe-bearing minerals that have magnetic properties and are enclosed in intracellular membranes. In contrast, studies on less-well ordered minerals have focused on Fe-, As-, Mn-, Au-, Se- and Cd-precipitates that occur intracellularly. The biological and environmental function of these particles remains a matter of debate.

    更新日期:2019-11-01
  • Electron microscopy encounters with unusual thermophiles helps direct genomic analysis of Aciduliprofundum boonei.
    Geobiology (IF 4.100) Pub Date : 2008-05-01
    A-L Reysenbach,G E Flores

    Terry Beveridge's enthusiasm about the ingenuity of microorganisms has stimulated many new avenues of microbial research. One example where Terry's observations helped direct the scientific process was in the analysis of the draft genome of the thermoacidophilic archaeum, Aciduliprofundum boonei. This deep-sea vent heterotroph ferments peptides as its primary metabolic pathway, using numerous enzymes encoding for proteolytic or peptidolytic activities. An almost complete modified Embden-Meyerhof-Parnas pathway operates in the gluconeogenic direction. Terry was particularly intrigued by the S-layer and flagellum of A. boonei. Although only putative genes for the S-layer protein could be identified, several genes encoding for glycosyl transferases were located in the draft genome that could glycosylate the S-layer proteins and protect the proteins from the acidic environment. Furthermore, A. boonei possesses a unique organization to its flagellum genes and may represent a third organizational type within the Archaea.

    更新日期:2019-11-01
  • Training the next scientific generation--a tribute to Terrance J. Beveridge.
    Geobiology (IF 4.100) Pub Date : 2008-05-01
    L L Graham,R J C McLean

    更新日期:2019-11-01
  • From iron oxides to infections.
    Geobiology (IF 4.100) Pub Date : 2008-05-01
    D K Newman

    更新日期:2019-11-01
  • The pedagogical genealogy of Terrance J. Beveridge--a legacy of bonds.
    Geobiology (IF 4.100) Pub Date : 2008-04-24
    S K Lower

    Terrance J. Beveridge (TJB) was a professor at the University of Guelph for nearly three decades. He died on September 10, 2007. TJB was a pioneer who pushed the frontier of microbiology and bacteriology. His legacy includes 22 postdoctoral scholars and 24 graduate students. His two dozen graduate student progeny have, in turn, mentored at least 52 additional graduate students. This paper presents TJB's pedagogical tree and touches on many of the topics that he studied during his life including: bacteria cell surfaces, biomineralization, biofilms, and geomicrobiology.

    更新日期:2019-11-01
  • Bacterial biomineralization: where to from here?
    Geobiology (IF 4.100) Pub Date : 2008-04-24
    K O Konhauser,S V Lalonde,V R Phoenix

    更新日期:2019-11-01
  • Hard X-ray micro(spectro)scopy: a powerful tool for the geomicrobiologists.
    Geobiology (IF 4.100) Pub Date : 2008-04-09
    K M Kemner

    During the past few decades, the use of electron microscopy approaches - many developed by Terry Beveridge - to probe the physiology of microorganisms has become a mainstay in fields including microbiology, human health, and geomicrobiology. Recent developments of third-generation synchrotron X-ray sources and X-ray-based microscopy approaches for studying microbial systems have proved their utility as complements to the very powerful approaches regularly employed by electron microscopists. In addition, in recent geomicrobiological studies, researchers have begun to take advantage of the strengths of each technique by using the superior spatial resolution of the electron microscope (relative to the X-ray microscope) and the superior elemental sensitivity of the X-ray microscope (relative to the electron microscope), along with the ability of the X-ray microscope to spatially probe the chemical speciation of elements. The benefits of integrating these two nanoprobes for investigating the same microenvironments within a geomicrobial system are far superior to those of independent studies separately employing each probe.

    更新日期:2019-11-01
  • 更新日期:2019-11-01
  • Tube structures of probable microbial origin in the Neoarchean Carawine Dolomite, Hamersley Basin, Western Australia.
    Geobiology (IF 4.100) Pub Date : 2008-04-03
    M A Murphy,D Y Sumner

    The approximately 2.63 Ga Carawine Dolomite, Hamersley Basin, Western Australia, preserves tube structures of probable microbial origin that formed in a low energy environment. The tubes are 0.4-1.8 cm in diameter and at least 10-16 cm long in outcrop. The tubes are defined by dark, 45-microm-thick dolomicritic walls, whereas the tube fill and host rock are composed of 30 microm, cloudy dolomite crystals and rare 170- to 425-microm-wide, dark well-sorted clasts. Closely spaced, rarely discontinuous laminae coat the insides of tubes; less closely spaced, peaked, discontinuous laminae coat the outsides of tubes. The laminae on the outsides of tubes are often intercalated with mammilate structures. The presence of probable microbial coatings on both the insides and the outsides of the tube walls requires that the tubes formed above the sediment-water interface. These tube structures probably formed during gas-charged fluid escape, similar to tubes observed in ancient and modern hydrocarbon seeps and cylindrical water transfer structures in sandstones. The laminae that coat the tubes have very similar geometries to modern biofilms that form in both turbulent and laminar flow, and their geometries probably reflect flow conditions during the fluid escape. The identification of these structures suggests that the preserved interaction between fluid escape and microbial growth in carbonates may be more common than previously thought.

    更新日期:2019-11-01
  • Microalgal mediation of ripple mobility.
    Geobiology (IF 4.100) Pub Date : 2008-04-03
    P L Friend,C H Lucas,P M Holligan,M B Collins

    The interaction between physical and biological factors responsible for the cessation of ripple migration on a sandy intertidal flat was examined during a microalgal bloom period in late winter/early spring, as part of a wider study into the biostabilisation of intertidal sediments. Ripple positions and ripple geometry were monitored, and surface sediment was sampled, at weekly intervals over a 5-week period. Ripples remained in the same position for at least 4 weeks, during which time there was a progressive reduction in bedform height (smoothing) and deposition of some 1.5 cm sediment, mainly in the ripple troughs (surface levelling). The mean chlorophyll a (chl a) sediment content was 6.0 microg gDW(-1) (DW: dry weight) (0-1 mm depth fraction), with a maximum value of 7.4 microg gDW(-1) half way through the bloom. Mean colloidal-S carbohydrate (S: saline extraction) content was 131 microg GE gDW(-1) (GE: glucose equivalent) (0-1 mm), with a maximum of 261 microg GE gDW(-1 )towards the end of the bloom. Important accessory pigments were peridinin (indicative of dinophytes) and fucoxanthin (diatoms). Stepwise multiple regression showed that peridinin was the best predictor of chl a. For the first time, in situ evidence for the mediation of (wave) ripple migration by microalgae is provided. Results indicate that diatoms, and quite possibly dinophytes, can have a significant effect on intertidal flat ripple mobility on a temporal scale of weeks. In addition, microalgal effects appear capable of effecting a reduction in bed roughness on a spatial scale of up to 10(-2 )m, with a subsequent reduction in bottom stress and bed erodability. It is suggested that a unique combination of environmental conditions, in conjunction with the microalgal bloom(s), promoted the initial cessation of ripple movement, and that stationary-phase, diatom-derived extracellular polymeric substances (EPS) (and possibly dinophyte-derived EPS) may have prolonged the condition. It is reasonable to suppose that ripple stabilisation by similar processes may have contributed to ripple mark preservation in the geological record. A conceptual model of sandy intertidal flat processes is presented, illustrating two conditions: (i) a low EPS/microalgae sediment content with low ripple stabilisation and preservation potential; and (ii) a high EPS/microalgae content with higher preservation potential.

    更新日期:2019-11-01
  • Microbial stabilization of riverine sediments by extracellular polymeric substances.
    Geobiology (IF 4.100) Pub Date : 2008-04-03
    Sabine Ulrike Gerbersdorf,Thomas Jancke,Bernhard Westrich,David M Paterson

    Sediment stability is a critical component for the understanding of cohesive sediment dynamics. Traditionally, physico-chemical sediment conditions have been regarded as most important drivers of sediment stability. However, over the last decade, the stabilization of sediment by biological activity, particularly the influence of highly hydrated matrices of extracellular polymeric substances (EPS) has been given increasing attention. However, most studies have focused on the sediment/water interface and, usually, of marine systems. The present study exploits current knowledge of EPS dynamics from marine systems and applies it to freshwater habitats, also considering a wide range of biological and physico-chemical variables. Natural sediments were taken from a freshwater site with high levels of heavy metal pollution (Lauffen reservoir, River Neckar, Germany). Vertical profiles from the flocculent surface layer to depth of 50 cm within the sediment were investigated, monthly, over the course of year. Tubificidae and Chironomidae larvae constituted the majority of the macrofauna. Despite the turbidity of the water column, a highly diverse and abundant microphytobenthic community of diatoms (11-82 microg g(-1) DW) was found at the sediment surface closely associated with high numbers of bacteria (10(9) cells g(-1) DW). The concentrations of all EPS moieties were remarkably high (0.1-0.5, 1.7-3.8, 0.9-5.2 mg g(-1) DW, for colloidal and bound carbohydrates and proteins, respectively) and levels were comparable to those determined in intertidal studies. The microalgal and bacterial biomass both showed strong correlations with the colloidal and bound EPS carbohydrate fractions. The data suggested that the present macrofauna as well as the metabolic activities of microalgae and bacteria interact with sedimentological factors to influence the properties of the sediment by binding fine-grained sediment, changing water content and enhancing the organic content through secretion products. The colloidal and bound EPS moieties showed strong correlation with the critical shear stress for erosion over sediment depth. It is suggested that the cohesive strength of the sediment was controlled by a high number of active adsorption sites and higher charge densities in fine grained sediments. The EPS network may significantly enhance this by embedding particles and permeating the void space but also in offering additional ionic binding sites and cross-linkages.

    更新日期:2019-11-01
  • Calcium carbonate precipitation in cyanobacterial mats from sandy tidal flats of the North Sea.
    Geobiology (IF 4.100) Pub Date : 2008-04-03
    B Kremer,J Kazmierczak,L J Stal

    Precipitated calcium carbonate was found in annual cyanobacterial mats developing on the beaches of the North Sea barrier island Schiermonnikoog (the Netherlands). A variety of different calcium carbonate morphs were found in the cyanobacterial mucous secretions and identified by light- and scanning electron microscopy and X-ray diffraction. Most of the calcium carbonate seemed to be associated with degrading extracellular polymer. It is conceived that supersaturation of calcium carbonate resulted from the periodic evaporation of the mats and from the release of calcium from the cyanobacterial mucous as a result of its degradation. The analysis of the carbon stable isotopic composition of the calcium carbonate showed only a slight depletion of (13)C, indicating that it did not in major part originated from the decomposition of organic matter. The delta(18)O values of the calcium carbonate confirmed the temperature differences between spring and summer but excluded the possibility that excessive evaporative events controlled precipitation. The precipitation of calcium carbonate could represent a potential factor enhancing the stabilization of intertidal siliciclastic sediments through cementing the sand. The discovery of massive calcium carbonate precipitation in these cyanobacterial mats was unexpected and hitherto unknown.

    更新日期:2019-11-01
  • Stromatolite branching in the Neoproterozoic of the Centralian Superbasin, Australia: an investigation into sedimentary and microbial control of stromatolite morphology.
    Geobiology (IF 4.100) Pub Date : 2008-04-03
    Noah Planavsky,Kathleen Grey

    The extensive and well-preserved Neoproterozoic Acaciella australica Stromatolite assemblage of Australia is ideal for examining the relative roles of microbial and environmental influences on stromatolite branching and stromatolite macrostructure across a wide geographical area. Detailed sedimentological analyses indicate that the basal hemispheroidal section of bioherms contains abundant sediment. By contrast, the columnar sections of bioherms are composed almost exclusively of micritic laminae. These micritic laminae display little evidence for environmental, especially sedimentary, control over stromatolite morphology. The change from a hemispheroidal morphology to branching morphology is linked to variations in the relative contributions of sediment and framework growth. The shift to columns appears to be closely linked to a decrease in sediment supply that resulted in a more stable environment in which microbially mediated framework growth began to control stromatolite morphology. Branching in the A. australica assemblage stromatolites appears to be caused by shifting sedimentary and microbial control on stromatolite morphology.

    更新日期:2019-11-01
  • Wave and sediment dynamics along a shallow subtidal sandy beach inhabited by modern stromatolites.
    Geobiology (IF 4.100) Pub Date : 2008-04-03
    J E Eckman,M S Andres,R L Marinelli,E Bowlin,R P Reid,R J Aspden,D M Paterson

    To help define the habitat of modern marine stromatolites, wave-dominated flow and sediment transport were studied in the shallow subtidal region (1-2 m depth) along the slightly concave, windward face of Highborne Cay, Exuma, Bahamas - the only face of the cay that includes a population of stromatolites concentrated near the region of highest curvature of the beach. Wave energy impacting this island's most exposed beach was driven by local wind forcing which increases largely in response to the passage of atmospheric disturbances that typically affect the region for periods of a few days. Although some wave energy is almost always noted (maximum horizontal orbital speeds at the bottom are rarely <10 cm s(-1)), wave conditions remain comparatively calm until local winds increase above speeds of approximately 3-4 m s(-1) at which point maximum wave speeds rapidly increase to 50-80 cm s(-1). Stromatolites, which are largely restricted to the shoreward side of a shallow platform reef, are sheltered by the reef beyond which wave speeds are one to four times higher (depending on tidal stage). Moreover, stromatolite populations are predominantly found along a region of this wave-exposed beach that experiences comparatively reduced wave energy because of the curved morphology of the island's face. Maximum wave speeds are 1.4 to 2 times higher along more northern sections of the beach just beyond the locus of stromatolite populations. A quantitative model of sediment transport was developed that accurately predicted accumulation of suspended sediment in sediment traps deployed in the shallow subtidal zone along this beach. This model, coupled with in situ wave records, indicates that gross rates of suspended sediment deposition should be two to three times higher northward of the main stromatolite populations. Regions of the beach containing stromatolites nevertheless should experience significant rates of gross suspended sediment deposition averaging 7-10 g cm(-2) day(-1) ( approximately 4-6 cm day(-1)). Results suggest that one axis of the habitat of modern marine stromatolites may be defined by a comparatively narrow range of flow energy and sediment transport conditions.

    更新日期:2019-11-01
  • An actualistic perspective into Archean worlds - (cyano-)bacterially induced sedimentary structures in the siliciclastic Nhlazatse Section, 2.9 Ga Pongola Supergroup, South Africa.
    Geobiology (IF 4.100) Pub Date : 2008-04-03
    N Noffke,N Beukes,D Bower,R M Hazen,D J P Swift

    Extensive microbial mats colonize sandy tidal flats that form along the coasts of today's Earth. The microbenthos (mainly cyanobacteria) respond to the prevailing physical sediment dynamics by biostabilization, baffling and trapping, as well as binding. This biotic-physical interaction gives rise to characteristic microbially induced sedimentary structures (MISS) that differ greatly from both purely physical structures and from stromatolites. Actualistic studies of the MISS on modern tidal flats have been shown to be the key for understanding equivalent fossil structures that occur in tidal and shelf sandstones of all Earth ages. However, until now the fossil record of Archean MISS has been poor, and relatively few specimens have been found. This paper describes a study location that displays a unique assemblage with a multitude of exceptionally preserved MISS in the 2.9-Ga-old Pongola Supergroup, South Africa. The 'Nhlazatse Section' includes structures such as 'erosional remnants and pockets', 'multidirected ripple marks', 'polygonal oscillation cracks', and 'gas domes'. Optical and geochemical analyses support the biogenicity of microscopic textures such as filamentous laminae or 'orientated grains'. Textures resembling filaments are lined by iron oxide and hydroxides, as well as clay minerals. They contain organic matter, whose isotope composition is consistent with carbon of biological origin. The ancient tidal flats of the Nhlazatse Section record four microbial mat facies that occur in modern tidal settings as well. We distinguish endobenthic and epibenthic microbial mats, including planar, tufted, and spongy subtypes. Each microbial mat facies is characterized by a distinct set of MISS, and relates to a typical tidal zone. The microbial mat structures are preserved in situ, and are consistent with similar features constructed today by benthic cyanobacteria. However, other mat-constructing microorganisms also could have formed the structures in the Archean tidal flats.

    更新日期:2019-11-01
  • 更新日期:2019-11-01
  • Carbon pools and isotopic trends in a hypersaline cyanobacterial mat.
    Geobiology (IF 4.100) Pub Date : 2008-04-03
    A Wieland,T Pape,J Möbius,J-H Klock,W Michaelis

    The fine-scale depth distribution of major carbon pools and their stable carbon isotopic signatures (delta(13)C) were determined in a cyanobacterial mat (Salin-de-Giraud, Camargue, France) to study early diagenetic alterations and the carbon preservation potential in hypersaline mat ecosystems. Particular emphasis was placed on the geochemical role of extracellular polymeric substances (EPS). Total carbon (C(tot)), organic carbon (C(org)), total nitrogen (N(tot)), total hydrolysable amino acids (THAA), carbohydrates, cyanobacteria-derived hydrocarbons (8-methylhexadecane, n-heptadec-5-ene, n-heptadecane) and EPS showed highest concentrations in the top millimetre of the mat and decreased with depth. The hydrocarbons attributed to cyanobacteria showed the strongest decrease in concentration with depth. This correlated well with the depth profiles of oxygenic photosynthesis and oxygen, which were detected in the top 0.6 and 1.05 mm, respectively, at a high down-welling irradiance (1441 micromol photons m(-2) s(-1)). At depths beneath the surface layer, the C(org) was composed mainly of amino acids and carbohydrates. A resistance towards microbial degradation could have resulted from interactions with diverse functional groups present in biopolymers (EPS) and with minerals deposited in the mat. A (13)C enrichment with depth for the total carbon pool (C(tot)) was observed, with delta(13)C values ranging from -16.3 per thousand at the surface to -11.3 per thousand at 9-10 mm depth. Total lipids depicted a delta(13)C value of -17.2 per thousand in the top millimetre and then became depleted in (13)C with depth (-21.7 to -23.3 per thousand). The delta(13)C value of EPS varied only slightly with depth (-16.1 to -17.3 per thousand) and closely followed the delta(13)C value of C(org) at depths beneath 4 mm. The EPS represents an organic carbon pool of preservation potential during early stages of diagenesis in recent cyanobacterial mats as a result of a variety of possible interactions. Their analyses might improve our understanding of fossilized microbial remains from mat ecosystems.

    更新日期:2019-11-01
  • Fossilized microorganisms associated with zeolite-carbonate interfaces in sub-seafloor hydrothermal environments.
    Geobiology (IF 4.100) Pub Date : 2008-04-03
    M Ivarsson,S Lindblom,C Broman,N G Holm

    In this paper we describe carbon-rich filamentous structures observed in association with the zeolite mineral phillipsite from sub-seafloor samples drilled and collected during the Ocean Drilling Program (ODP) Leg 197 at the Emperor Seamounts. The filamentous structures are approximately 5 microm thick and approximately 100-200 microm in length. They are found attached to phillipsite surfaces in veins and entombed in vein-filling carbonates. The carbon content of the filaments ranges between approximately 10 wt% C and 55 wt% C. They further bind to propidium iodide (PI), which is a dye that binds to damaged cell membranes and remnants of DNA. Carbon-rich globular microstructures, 1-2 microm in diameter, are also found associated with the phillipsite surfaces as well as within wedge-shaped cavities in phillipsite assemblages. The globules have a carbon content that range between approximately 5 wt% C and 55 wt% C and they bind to PI. Ordinary globular iron oxides found throughout the samples differ in that they contain no carbon and do not bind to the dye PI. The carbon-rich globules are mostly concentrated to a film-like structure that is attached to the phillipsite surfaces. This film has a carbon content that ranges between approximately 25 wt% C and 75 wt% C and partially binds to PI. EDS analyses show that the carbon in all structures described are not associated with calcium and therefore not bound in carbonates. The carbon content and the binding to PI may indicate that the filamentous structures could represent fossilized filamentous microorganisms, the globules could represent fossilized microbial cells and the film-like structures could represent a microbially produced biofilm. Our results extend the knowledge of possible habitable niches for a deep biosphere in sub-seafloor environments and suggests, as phillipsite is one of the most common zeolite mineral in volcanic rocks of the oceanic crust, that it could be a common feature in the oceanic crust elsewhere.

    更新日期:2019-11-01
  • Characterization of extracellular minerals produced during dissimilatory Fe(III) and U(VI) reduction at 100 degrees C by Pyrobaculum islandicum.
    Geobiology (IF 4.100) Pub Date : 2008-04-03
    K Kashefi,B M Moskowitz,D R Lovley

    In order to gain insight into the significance of biotic metal reduction and mineral formation in hyperthermophilic environments, metal mineralization as a result of the dissimilatory reduction of poorly crystalline Fe(III) oxide, and U(VI) reduction at 100 degrees C by Pyrobaculum islandicum was investigated. When P. islandicum was grown in a medium with poorly crystalline Fe(III) oxide as an electron acceptor and hydrogen as an electron donor, the Fe(III) oxide was reduced to an extracellular, ultrafine-grained magnetite with characteristics similar to that found in some hot environments and that was previously thought to be of abiotic origin. Furthermore, cell suspensions of P. islandicum rapidly reduced the soluble and oxidized form of uranium, U(VI), to extracellular precipitates of the highly insoluble U(IV) mineral, uraninite (UO(2)). The reduction of U(VI) was dependent on the presence of hydrogen as the electron donor. These findings suggest that microbes may play a key role in metal deposition in hyperthermophilic environments and provide a plausible explanation for such phenomena as magnetite accumulation and formation of uranium deposits at ca. 100 degrees C.

    更新日期:2019-11-01
  • Early colonization of thermal niches in a silica-depositing hot spring in central Tibet.
    Geobiology (IF 4.100) Pub Date : 2008-04-03
    C Y Lau,J C Aitchison,S B Pointing

    Thermophilic microbial mats dominated by the anoxygenic phototroph Roseiflexus castenholzii commonly develop around sinter-depositing geysers in the Daggyai Tso geothermal field of central Tibet. In this study we used morphological and molecular genetic techniques to reveal a diverse pioneer biofilm community including both archaea and bacteria involved in early colonization of such thermal niches at temperatures ranging from 46 to 77 degrees C. Sinter precipitation and biomineralization were evident at all locations, but the latter was selective between taxa and most evident on filamentous cells. Evidence for possible indirect biosignatures from biofilms overwhelmed by sinter deposition was found. Succession to a mature community appeared to relate to the growth rate for key taxa outpacing that of silicification within an optimum temperature range of 54-61 degrees C. The thin surface layer of silicification-resistant cyanobacteria that developed on the surface of mature mats may play a role in preventing biomineralization of the susceptible R. castenholzii beneath within these communities.

    更新日期:2019-11-01
  • Putative cryptoendolithic life in Devonian pillow basalt, Rheinisches Schiefergebirge, Germany.
    Geobiology (IF 4.100) Pub Date : 2008-04-03
    J Peckmann,W Bach,K Behrens,J Reitner

    Middle Devonian (Givetian) pillow basalt and inter-pillow breccia from the Rheinisches Schiefergebirge in Germany were found to contain putative biogenic filaments that indicate that life once proliferated within these volcanic rocks. Mineralized filaments are found in carbonate amygdules (vesicles filled by carbonate cement) in the volcanic rock, where they started to form on the internal surface of the once water-filled vesicles. Biogenicity of the filaments is indicated by (1) their size and shape resembling modern microorganisms including a constant diameter along the length of curved filaments, (2) their independence of crystal faces or cleavage planes, (3) branching patterns reminiscent of modern microorganisms, and (4) their spatial clustering and preferential occurrence close to the margin of pillows and in the inter-pillow breccias. A time lag between the deposition of pillow basalt and the activity of endoliths is revealed by the sequence of carbonate cements filling the amygdules. The putative filamentous microorganisms thrived after the formation of early fibrous rim cement, but before later equant calcite spar filled most of the remaining porosity. Microbial clay authigenesis analogous to the encrustation of prokaryotes in modern iron-rich environments led to the preservation of filaments. The filaments predominantly consist of the clay minerals chamosite and illite. Having dwelled in water-filled vesicles, the Devonian basalt-hosted filaments apparently represent cryptoendoliths. This finding suggests that a previously unrecognized niche for life exists within volcanic rock.

    更新日期:2019-11-01
  • Earliest fossil record of bacterial-cyanobacterial mat consortia: the early Silurian Passage Creek biota (440 Ma, Virginia, USA).
    Geobiology (IF 4.100) Pub Date : 2008-04-03
    A M F Tomescu,R Honegger,G W Rothwell

    Cyanobacteria in terrestrial and aquatic habitats are frequently associated with heterotrophic bacteria, and such associations are most often metabolically interactive. Functionally, the members of such bacterial-cyanobacterial consortia benefit from diverse metabolic capabilities of their associates, thus exceeding the sum of their parts. Such associations may have been just as ubiquitous in the past, but the fossil record has not produced any direct evidence for such associations to date. In this paper, we document fossil bacteria associated with a macrophytic cyanobacterial mat in the early Silurian (Llandovery) Massanutten Sandstone of Virginia, USA. Both the bacterial and the cyanobacterial cells are preserved by mineral replacement (pyrite subsequently replaced by iron oxyhydroxides) within an amorphous carbonaceous matrix which represents the common exopolysaccharide investment of the cyanobacterial colony. The bacteria are rod-shaped, over 370 nm long and 100 nm in diameter, and occur both as isolated cells and as short filaments. This occurrence represents the oldest fossil evidence for bacterial-cyanobacterial associations, documenting that such consortia were present 440 Ma ago, and revealing the potential for them to be recognized deeper in the fossil record.

    更新日期:2019-11-01
  • Seawater Mg/Ca controls polymorph mineralogy of microbial CaCO3: a potential proxy for calcite-aragonite seas in Precambrian time.
    Geobiology (IF 4.100) Pub Date : 2008-04-03
    J B Ries,M A Anderson,R T Hill

    A previously published hydrothermal brine-river water mixing model driven by ocean crust production suggests that the molar Mg/Ca ratio of seawater (mMg/Ca(sw)) has varied significantly (approximately 1.0-5.2) over Precambrian time, resulting in six intervals of aragonite-favouring seas (mMg/Ca(sw) > 2) and five intervals of calcite-favouring seas (mMg/Ca(sw) < 2) since the Late Archaean. To evaluate the viability of microbial carbonates as mineralogical proxy for Precambrian calcite-aragonite seas, calcifying microbial marine biofilms were cultured in experimental seawaters formulated over the range of Mg/Ca ratios believed to have characterized Precambrian seawater. Biofilms cultured in experimental aragonite seawater (mMg/Ca(sw) = 5.2) precipitated primarily aragonite with lesser amounts of high-Mg calcite (mMg/Ca(calcite) = 0.16), while biofilms cultured in experimental calcite seawater (mMg/Ca(sw) = 1.5) precipitated exclusively lower magnesian calcite (mMg/Ca(calcite) = 0.06). Furthermore, Mg/Ca(calcite )varied proportionally with Mg/Ca(sw). This nearly abiotic mineralogical response of the biofilm CaCO3 to altered Mg/Ca(sw) is consistent with the assertion that biofilm calcification proceeds more through the elevation of , via metabolic removal of CO2 and/or H+, than through the elevation of Ca2+, which would alter the Mg/Ca ratio of the biofilm's calcifying fluid causing its pattern of CaCO3 polymorph precipitation (aragonite vs. calcite; Mg-incorporation in calcite) to deviate from that of abiotic calcification. If previous assertions are correct that the physicochemical properties of Precambrian seawater were such that Mg/Ca(sw) was the primary variable influencing CaCO3 polymorph mineralogy, then the observed response of the biofilms' CaCO3 polymorph mineralogy to variations in Mg/Ca(sw), combined with the ubiquity of such microbial carbonates in Precambrian strata, suggests that the original polymorph mineralogy and Mg/Ca(calcite )of well-preserved microbial carbonates may be an archive of calcite-aragonite seas throughout Precambrian time. These results invite a systematic evaluation of microbial carbonate primary mineralogy to empirically constrain Precambrian seawater Mg/Ca.

    更新日期:2019-11-01
  • Growth of synthetic stromatolites and wrinkle structures in the absence of microbes - implications for the early fossil record.
    Geobiology (IF 4.100) Pub Date : 2008-04-03
    N McLoughlin,L A Wilson,M D Brasier

    Stromatolites and wrinkle structures are often taken to be an important indicator for early life. While both may be shaped by microbial mat growth, this can be open to doubt, so that the contribution of abiotic processes in their construction always needs to be established (Grotzinger & Knoll, 1999). We here report laboratory spray deposition experiments that can generate stromatolites and wrinkle structures in the absence of microbes. These minicolumnar and sometimes branched stromatolites are produced artificially by the aggregation of a synthetic colloid in a turbulent flow regime. They self-organize at the relatively low particle concentrations found in the outer parts of a spray beam. This contrasts with adjacent stratiform deposits that are produced by high rates of colloid deposition and relatively low sediment viscosities found in the centre of a spray beam. These stratiform laminae become subsequently wrinkled during hardening of the colloid. These results support numerical models that together suggest that physicochemical processes are capable of generating laminated sedimentary structures without the direct participation of biology. Geological environments where comparable abiogenic stromatolites and wrinkle structures may be found include: splash-zone silica sinters, desert varnish crusts and early Archean cherts formed from silica gel precursors.

    更新日期:2019-11-01
  • Carotenoid biomarkers as an imperfect reflection of the anoxygenic phototrophic community in meromictic Fayetteville Green Lake.
    Geobiology (IF 4.100) Pub Date : 2011-06-21
    K M Meyer,J L Macalady,J M Fulton,L R Kump,I Schaperdoth,K H Freeman

    Organic biomarkers in marine sedimentary rocks hold important clues about the early history of Earth's surface environment. The chemical relicts of carotenoids from anoxygenic sulfur bacteria are of particular interest to geoscientists because of their potential to signal episodes of marine photic-zone euxinia such as those proposed for extended periods in the Proterozoic as well as brief intervals during the Phanerozoic. It is therefore critical to constrain the environmental and physiological factors that influence carotenoid production and preservation in modern environments. Here, we present the results of coupled pigment and nucleic acid clone library analyses from planktonic and benthic samples collected from a microbially dominated meromictic lake, Fayetteville Green Lake (New York). Purple sulfur bacteria (PSB) are abundant and diverse both in the water column at the chemocline and in benthic mats below oxygenated shallow waters, with different PSB species inhabiting the two environments. Okenone (from PSB) is an abundant carotenoid in both the chemocline waters and in benthic mats. Green sulfur bacteria and their primary pigment Bchl e are also represented in and below the chemocline. However, the water column and sediments are devoid of the green sulfur bacteria carotenoid isorenieratene. The unexpected absence of isorenieratene and apparent benthic production of okenone provide strong rationale for continued exploration of the microbial ecology of biomarker production in modern euxinic environments.

    更新日期:2019-11-01
  • Greenhouse warming by nitrous oxide and methane in the Proterozoic Eon.
    Geobiology (IF 4.100) Pub Date : 2011-06-21
    A L Roberson,J Roadt,I Halevy,J F Kasting

    An anoxic, sulfidic ocean that may have existed during the Proterozoic Eon (0.54-2.4 Ga) would have had limited trace metal abundances because of the low solubility of metal sulfides. The lack of copper, in particular, could have had a significant impact on marine denitrification. Copper is needed for the enzyme that controls the final step of denitrification, from N(2) O to N(2) . Today, only about 5-6% of denitrification results in release of N(2) O. If all denitrification stopped at N(2) O during the Proterozoic, the N(2) O flux could have been 15-20 times higher than today, producing N(2) O concentrations of several ppmv, but only if O(2) levels were relatively high (>0.1 PAL). At lower O(2) levels, N(2) O is rapidly photodissociated. Methane concentrations may also have been elevated during this time, as has been previously suggested. A lack of dissolved O(2) and sulfate in the deep ocean could have produced a high methane flux from marine sediments, as much as 10-20 times today's methane flux from land. The photochemical lifetime of CH(4) increases as more CH(4) is added to the atmosphere, so CH(4) concentrations of up to 100 ppmv are possible during this time. The combined greenhouse effect of CH(4) and N(2) O could have provided up to 10° of warming, thereby keeping the surface warm during the Proterozoic without necessitating high CO(2) levels. A second oxygenation event near the end of the Proterozoic would have resulted in a reduction in both atmospheric N(2) O and CH(4) , perhaps triggering the Neoproterozoic "Snowball Earth" glaciations.

    更新日期:2019-11-01
  • Did sulfate availability facilitate the evolutionary expansion of chlorophyll a+c phytoplankton in the oceans?
    Geobiology (IF 4.100) Pub Date : 2011-06-02
    S Ratti,A H Knoll,M Giordano

    During the Mesozoic Era, dinoflagellates, coccolithophorids and diatoms became prominent primary producers in the oceans, succeeding an earlier biota in which green algae and cyanobacteria had been proportionally more abundant. This transition occurred during an interval marked by increased sulfate concentration in seawater. To test whether increasing sulfate availability facilitated the evolutionary transition in marine phytoplankton, the cyanobacterium Synechococcus sp., the green alga Tetraselmis suecica and three algae containing chlorophyll a+c (the diatom Thalassiosira weissflogii, the dinoflagellate Protoceratium reticulatum and the coccolithophorid Emiliania huxleyi) were grown in media containing 1, 5, 10, 20, or 30 mm SO(4) (2-) . The cyanobacterium and the green alga showed no growth response to varying [SO(4) (2-) ]. By contrast, the three chlorophyll a+c algae showed improved growth with higher [SO(4) (2-) ], but only up to 10 mm. The chlorophyll a+c algae, but not the green alga or cyanobacterium, also showed lower C:S with higher [SO(4) (2-) ]. When the same experiment was repeated in the presence of a ciliate predator (Euplotes sp.), T. suecica and T. weissflogii increased their specific growth rate in most treatments, whereas the growth rate of Synechococcus sp. was not affected or decreased in the presence of grazers. In a third experiment, T. suecica, T. weissflogii, P. reticulatum and Synechococcus sp. were grown in conditions approximating modern, earlier Paleozoic and Proterozoic seawater. In these treatments, sulfate availability, nitrogen source, metal availability and Pco(2) varied. Monospecific cultures exhibited their highest growth rates in the Proterozoic treatment. In mixed culture, T. weissflogii outgrew other species in modern seawater and T.suecica outgrew the others in Paleozoic water. Synechococcus sp. grew best in Proterozoic seawater, but did not outgrow eukaryotic species in any treatment. Collectively, our results suggest that secular increase in seawater [SO(4) (2-) ] may have facilitated the evolutionary expansion of chlorophyll a+c phytoplankton, but probably not to the exclusion of other biological and environmental factors.

    更新日期:2019-11-01
  • Low temperature S(0) biomineralization at a supraglacial spring system in the Canadian High Arctic.
    Geobiology (IF 4.100) Pub Date : 2011-05-20
    D F Gleeson,C Williamson,S E Grasby,R T Pappalardo,J R Spear,A S Templeton

    Elemental sulfur (S(0) ) is deposited each summer onto surface ice at Borup Fiord pass on Ellesmere Island, Canada, when high concentrations of aqueous H(2) S are discharged from a supraglacial spring system. 16S rRNA gene clone libraries generated from sulfur deposits were dominated by β-Proteobacteria, particularly Ralstonia sp. Sulfur-cycling micro-organisms such as Thiomicrospira sp., and ε-Proteobacteria such as Sulfuricurvales and Sulfurovumales spp. were also abundant. Concurrent cultivation experiments isolated psychrophilic, sulfide-oxidizing consortia, which produce S(0) in opposing gradients of Na(2) S and oxygen. 16S rRNA gene analyses of sulfur precipitated in gradient tubes show stable sulfur-biomineralizing consortia dominated by Marinobacter sp. in association with Shewanella, Loktanella, Rubrobacter, Flavobacterium, and Sphingomonas spp. Organisms closely related to cultivars appear in environmental 16S rRNA clone libraries; none currently known to oxidize sulfide. Once consortia were simplified to Marinobacter and Flavobacteria spp. through dilution-to-extinction and agar removal, sulfur biomineralization continued. Shewanella, Loktanella, Sphingomonas, and Devosia spp. were also isolated on heterotrophic media, but none produced S(0) alone when reintroduced to Na(2) S gradient tubes. Tubes inoculated with a Marinobacter and Shewanella spp. co-culture did show sulfur biomineralization, suggesting that Marinobacter may be the key sulfide oxidizer in laboratory experiments. Light, florescence and scanning electron microscopy of mineral aggregates produced in Marinobacter experiments revealed abundant cells, with filaments and sheaths variably mineralized with extracellular submicron sulfur grains; similar biomineralization was not observed in abiotic controls. Detailed characterization of mineral products associated with low temperature microbial sulfur-cycling may provide biosignatures relevant to future exploration of Europa and Mars.

    更新日期:2019-11-01
  • Niche differentiation among mat-forming, sulfide-oxidizing bacteria at cold seeps of the Nile Deep Sea Fan (Eastern Mediterranean Sea).
    Geobiology (IF 4.100) Pub Date : 2011-05-04
    S Grünke,J Felden,A Lichtschlag,A-C Girnth,D De Beer,F Wenzhöfer,A Boetius

    Sulfidic muds of cold seeps on the Nile Deep Sea Fan (NDSF) are populated by different types of mat-forming sulfide-oxidizing bacteria. The predominant sulfide oxidizers of three different mats were identified by microscopic and phylogenetic analyses as (i) Arcobacter species producing cotton-ball-like sulfur precipitates, (ii) large filamentous sulfur bacteria including Beggiatoa species, and (iii) single, spherical Thiomargarita species. High resolution in situ microprofiles revealed different geochemical settings selecting for the different mat types. Arcobacter mats occurred where oxygen and sulfide overlapped above the seafloor in the bottom water interface. Filamentous sulfide oxidizers were associated with steep gradients of oxygen and sulfide in the sediment. A dense population of Thiomargarita was favored by temporarily changing supplies of oxygen and sulfide in the bottom water. These results indicate that the decisive factors in selecting for different mat-forming bacteria within one deep-sea province are spatial or temporal variations in energy supply. Furthermore, the occurrence of Arcobacter spp.-related 16S rRNA genes in the sediments below all three types of mats, as well as on top of brine lakes of the NDSF, indicates that this group of sulfide oxidizers can switch between different life modes depending on the geobiochemical habitat setting.

    更新日期:2019-11-01
  • Diazotrophic microbial community of coastal microbial mats of the southern North Sea.
    Geobiology (IF 4.100) Pub Date : 2011-05-04
    T Bauersachs,J Compaoré,I Severin,E C Hopmans,S Schouten,L J Stal,J S Sinninghe Damsté

    The diazotrophic community in microbial mats growing along the shore of the North Sea barrier island Schiermonnikoog (The Netherlands) was studied using microscopy, lipid biomarkers, stable carbon (δ(13) C(TOC) ) and nitrogen (δ(15) N) isotopes as well as by constructing and analyzing 16S rRNA gene libraries. Depending on their position on the littoral gradient, two types of mats were identified, which showed distinct differences regarding the structure, development and composition of the microbial community. Intertidal microbial mats showed a low species diversity with filamentous non-heterocystous Cyanobacteria providing the main mat structure. In contrast, supratidal microbial mats showed a distinct vertical zonation and a high degree of species diversity. Morphotypes of non-heterocystous Cyanobacteria were recognized as the main structural component in these mats. In addition, unicellular Cyanobacteria were frequently observed, whereas filamentous heterocystous Cyanobacteria occurred only in low numbers. Besides the apparent visual dominance of cyanobacterial morphotpyes, 16S rRNA gene libraries indicated that both microbial mat types also included members of the Proteobacteria and the Cytophaga-Flavobacterium-Bacteroides group as well as diatoms. Bulk δ(15) N isotopes of the microbial mats ranged from +6.1‰ in the lower intertidal to -1.2‰ in the supratidal zone, indicating a shift from predominantly nitrate utilization to nitrogen fixation along the littoral gradient. This conclusion was supported by the presence of heterocyst glycolipids, representing lipid biomarkers for nitrogen-fixing heterocystous Cyanobacteria, in supratidal but not in intertidal microbial mats. The availability of combined nitrogen species might thus be a key factor in controlling and regulating the distribution of the diazotrophic microbial community of Schiermonnikoog.

    更新日期:2019-11-01
  • Decreased N2O reduction by low soil pH causes high N2O emissions in a riparian ecosystem.
    Geobiology (IF 4.100) Pub Date : 2011-04-21
    R N Van den Heuvel,S E Bakker,M S M Jetten,M M Hefting

    Quantification of harmful nitrous oxide (N(2)O) emissions from soils is essential for mitigation measures. An important N(2)O producing and reducing process in soils is denitrification, which shows deceased rates at low pH. No clear relationship between N(2)O emissions and soil pH has yet been established because also the relative contribution of N(2)O as the denitrification end product decreases with pH. Our aim was to show the net effect of soil pH on N(2)O production and emission. Therefore, experiments were designed to investigate the effects of pH on NO(3)(-) reduction, N(2)O production and reduction and N(2) production in incubations with pH values set between 4 and 7. Furthermore, field measurements of soil pH and N(2)O emissions were carried out. In incubations, NO(3)(-) reduction and N(2) production rates increased with pH and net N(2)O production rate was highest at pH 5. N(2)O reduction to N(2) was halted until NO(3)(-) was depleted at low pH values, resulting in a built up of N(2)O. As a consequence, N(2)O:N(2) production ratio decreased exponentially with pH. N(2)O reduction appeared therefore more important than N(2)O production in explaining net N(2)O production rates. In the field, a negative exponential relationship for soil pH against N(2)O emissions was observed. Soil pH could therefore be used as a predictive tool for average N(2)O emissions in the studied ecosystem. The occurrence of low pH spots may explain N(2)O emission hotspot occurrence. Future studies should focus on the mechanism behind small scale soil pH variability and the effect of manipulating the pH of soils.

    更新日期:2019-11-01
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