Showing papers in "Geobiology in 2009"

Towards a consistent classification scheme for geochemical environments, or, why we wish the term 'suboxic' would go away.

Abstract: It is our opinion that the nomenclature used to define geochemical environments is inconsistent and confusing, and in particular the use and meaning of the term ‘suboxic’, which is widely applied in the geochemical and ecological literature. Our purpose here is to review the redox zonation of natural systems and the nomenclature used to designate this. Finally, we will outline what we feel is a straightforward and non-contradictory scheme for classifying metabolic zones and geochemical environments.

Oxygen, animals and oceanic ventilation: an alternative view.

Abstract: Of all the components of biogeochemical cycles, few attract more attention than the waste product of oxygenic photosynthesis. Chemically unstable and biosynthetically dangerous, diatomic oxygen is the key ingredient in aerobic metabolism, and a prerequisite for the evolution of large complex organisms that define the modern biosphere. Exactly how much they require is only loosely constrained, but Catling et al . (2005) suggest something in the order of 10 3 –10 4 pascals [Pa] ( ≈ 1–10% atmospheric partial pressure [ p O 2 ]; ≈ 5–50% present atmospheric level [PAL]). Moreover, geochemical modelling indicates that p O 2 has fluctuated substantially over the course of the Phanerozoic: up to c . 35% in the late Palaeozoic, and down to perhaps 10% in the early Mesozoic (Falkowski et al ., 2005; Berner, 2006). Such shifts have been considered instrumental in directing the course of Phanerozoic evolution and extinction (Falkowski et al ., 2005; Huey & Ward, 2005; Ward et al ., 2006; Berner et al ., 2007), including the Ediacaran–Cambrian radiations of macroscopic life (Berkner & Marshall, 1965; Anbar & Knoll, 2002; Catling et al ., 2005; Holland, 2006; Canfield et al ., 2007). This is certainly a worthy hypothesis, and one that has gained an exceptionally wide following over the past decade – but a popular paradigm still needs to be tested and weighed against competing scenarios. In this editorial, I take critical look at the oxygen-evolution connection and discuss an alternative, biological explanation for geochemical signatures through the terminal Proterozoic. In the absence of direct measurements, the oxygen content of ancient atmospheres is inferred from a combination of geochemical proxies and modelling. These values, however, are accompanied by substantial error (see Berner et al ., 2007: fig. 1; Kump, 2008: fig. 2), and differing modelling assumptions yield conspicuously different results. For example, where Bergman et al . (2004) estimate the oxygen content of Mesozoic atmospheres to be continuously at or above PAL, Berner (2006) puts late Triassic/early Jurassic levels close to 50% PAL, followed by an early Cretaceous rise to more or less modern levels. Falkowski et al . (2005) also recognize an early Jurassic minimum, but with PAL not reached until the Eocene. All models are of course limited by the runaway wildfire induced at p O 2 > 35%, and lack of fire at p O 2 < 15% (Belcher & McElwain, 2008), neither of which have obtained for the past 420 million years (with the possible exception of a ‘charcoal gap’ in the late Devonian (Scott & Glasspool, 2006)). Atmospheric oxygen concentrations are more difficult to constrain in the absence of a land plant record, though the appearance of iron-retaining palaeosols at or around the 2.45 Ga ‘great oxygenation event’ marks the onset of p O 2 > 0.2% (1% PAL), and the rise of conspicuously macroscopic fossils from c . 575 Ma sets a Phanerozoic lower limit of c . 1% p O 2 or 5% PAL (Canfield, 2005; Catling et al ., 2005; Holland, 2006; Kump, 2008). Deep-sea geochemical proxies and modelling have been used to estimate an upper limit of c . 8% p O 2 (40% PAL) for most of the Proterozoic.

Biological weathering and the long-term carbon cycle: integrating mycorrhizal evolution and function into the current paradigm.

Abstract: The dramatic decline in atmospheric CO2 evidenced by proxy data during the Devonian (416.0–359.2 Ma) and the gradual decline from the Cretaceous (145.5–65.5 Ma) onwards have been linked to the spread of deeply rooted trees and the rise of angiosperms, respectively. But this paradigm overlooks the coevolution of roots with the major groups of symbiotic fungal partners that have dominated terrestrial ecosystems throughout Earth history. The colonization of land by plants was coincident with the rise of arbuscular mycorrhizal fungi (AMF), while the Cenozoic (c. 65.5–0 Ma) witnessed the rise of ectomycorrhizal fungi (EMF) that associate with both gymnosperm and angiosperm tree roots. Here, we critically review evidence for the influence of AMF and EMF on mineral weathering processes. We show that the key weathering processes underpinning the current paradigm and ascribed to plants are actually driven by the combined activities of roots and mycorrhizal fungi. Fuelled by substantial amounts of recent photosynthate transported from shoots to roots, these fungi form extensive mycelial networks which extend into soil actively foraging for nutrients by altering minerals through the acidification of the immediate root environment. EMF aggressively weather minerals through the additional mechanism of releasing low molecular weight organic chelators. Rates of biotic weathering might therefore be more usefully conceptualized as being fundamentally controlled by the biomass, surface area of contact, and capacity of roots and their mycorrhizal fungal partners to interact physically and chemically with minerals. All of these activities are ultimately controlled by rates of carbon-energy supply from photosynthetic organisms. The weathering functions in leading carbon cycle models require experiments and field studies of evolutionary grades of plants with appropriate mycorrhizal associations. Representation of the coevolution of roots and fungi in geochemical carbon cycle models is required to further our understanding of the role of the biota in Earth's CO2 and climate history.

Climate and vegetational regime shifts in the late Paleozoic ice age earth

Abstract: The late Paleozoic earth experienced alternation between glacial and non-glacial climates at multiple temporal scales, accompanied by atmospheric CO2 fluctuations and global warming intervals, often attended by significant vegetational changes in equatorial latitudes of Pangaea. We assess the nature of climate-vegetation interaction during two time intervals: middle-late Pennsylvanian transition and Pennsylvanian-Permian transition, each marked by tropical warming and drying. In case study 1, there is a catastrophic intra-biomic reorganization of dominance and diversity in wetland, evergreen vegetation growing under humid climates. This represents a threshold-type change, possibly a regime shift to an alternative stable state. Case study 2 is an inter-biome dominance change in western and central Pangaea from humid wetland and seasonally dry to semi-arid vegetation. Shifts between these vegetation types had been occurring in Euramerican portions of the equatorial region throughout the late middle and late Pennsylvanian, the drier vegetation reaching persistent dominance by Early Permian. The oscillatory transition between humid and seasonally dry vegetation appears to demonstrate a threshold-like behavior but probably not repeated transitions between alternative stable states. Rather, changes in dominance in lowland equatorial regions were driven by long-term, repetitive climatic oscillations, occurring with increasing intensity, within overall shift to seasonal dryness through time. In neither case study are there clear biotic or abiotic warning signs of looming changes in vegetational composition or geographic distribution, nor is it clear that there are specific, absolute values or rates of environmental change in temperature, rainfall distribution and amount, or atmospheric composition, approach to which might indicate proximity to a terrestrial biotic-change threshold.

Bacterial, archaeal and eukaryotic diversity of smooth and pustular microbial mat communities in the hypersaline lagoon of Shark Bay.

Abstract: The bacterial, archaeal and eukaryotic populations of nonlithifying mats with pustular and smooth morphology from Hamelin Pool, Shark Bay were characterised using small subunit rRNA gene analysis and microbial isolation. A highly diverse bacterial population was detected for each mat, with 16S rDNA clones related to Actinobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Gemmatimonas, Planctomycetes, Alphaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Verrucomicrobia and candidate division TM6 present in each mat. Spirochaetes were detected in the smooth mat only, whereas candidate division OP11 was only detected in the pustular mat. Targeting populations with specific primers revealed additional cyanobacterial diversity. The archaeal population of the pustular mat was comprised purely of Halobacteriales, whereas the smooth mat contained 16S rDNA clones from the Halobacteriales, two groups of Euryarchaea with no close characterised matches, and the Thaumarchaea. Nematodes and fungi were present in each mat type, with diatom 18S rDNA clones only obtained from the smooth mat, and tardigrade and microalgae clones only retrieved from the pustular mat. Cultured isolates belonged to the Firmicutes, Gammaproteobacteria, Alphaproteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, and Halobacteriales. The mat populations were significantly more diverse than those previously reported for Hamelin Pool stromatolites, suggesting specific microbial populations may be associated with the nonlithifying and lithifying microbial communities of Hamelin Pool.

Coevolution of metal availability and nitrogen assimilation in cyanobacteria and algae

Abstract: Marine primary producers adapted over eons to the changing chemistry of the oceans. Because a number of metalloenzymes are necessary for N assimilation, changes in the availability of transition metals posed a particular challenge to the supply of this critical nutrient that regulates marine biomass and productivity. Integrating recently developed geochemical, biochemical, and genetic evidence, we infer that the use of metals in N assimilation - particularly Fe and Mo - can be understood in terms of the history of metal availability through time. Anoxic, Fe-rich Archean oceans were conducive to the evolution of Fe-using enzymes that assimilate abiogenic NH(4)(+) and NO(2)(-). The N demands of an expanding biosphere were satisfied by the evolution of biological N(2) fixation, possibly utilizing only Fe. Trace O(2) in late Archean environments, and the eventual 'Great Oxidation Event' c. 2.3 Ga, mobilized metals such as Mo, enabling the evolution of Mo (or V)-based N(2) fixation and the Mo-dependent enzymes for NO(3)(-) assimilation and denitrification by prokaryotes. However, the subsequent onset of deep-sea euxinia, an increasingly-accepted idea, may have kept ocean Mo inventories low and depressed Fe, limiting the rate of N(2) fixation and the supply of fixed N. Eukaryotic ecosystems may have been particularly disadvantaged by N scarcity and the high Mo requirement of eukaryotic NO(3)(-) assimilation. Thorough ocean oxygenation in the Neoproterozoic led to Mo-rich oceans, possibly contributing to the proliferation of eukaryotes and thus the Cambrian explosion of metazoan life. These ideas can be tested by more intensive study of the metal requirements in N assimilation and the biological strategies for metal uptake, regulation, and storage.

Precipitation of low-temperature dolomite from an anaerobic microbial consortium: the role of methanogenic Archaea.

Abstract: Here we report precipitation of dolomite at low temperature (30 degrees C) mediated by a mixed anaerobic microbial consortium composed of dissimilatory iron-reducing bacteria (DIRB), fermenters, and methanogens. Initial solution geochemistry is controlled by DIRB, but after 90 days shifts to a system dominated by methanogens. In live experiments conditions are initially saturated with respect to dolomite (Omega(dol) = 19.40) and increase by two orders of magnitude (Omega(dol) = 2 330.77) only after the onset of methanogenesis, as judged by the increasing [CH(4)] and the detection of methanogenic micro-organisms. We identify ordered dolomite in live microcosms after 90 days via powder X-ray diffraction, while sterile controls precipitate only calcite. Scanning electron microscopy and transmitted electron microscopy demonstrate that the precipitated dolomite is closely associated with cell walls and putative extra-cellular polysaccharides. Headspace gas measurements and denaturing gradient gel electrophoresis confirm the presence of both autotrophic and acetoclastic methanogens and exclude the presence of DIRB and sulfate-reducing bacteria after dolomite begins forming. Furthermore, the absence of dolomite in the controls and prior to methanogenesis confirm that methanogenic Archaea are necessary for the low-temperature precipitation of dolomite under the experimental conditions tested.

Transformation of vivianite by anaerobic nitrate‐reducing iron‐oxidizing bacteria

Abstract: In phosphate-rich environments, vivianite (Fe(II)(3)(PO(4))(2), 8H(2)O) is an important sink for dissolved Fe(II) and is considered as a very stable mineral due to its low solubility at neutral pH. In the present study, we report the mineralogical transformation of vivianite in cultures of the nitrate-reducing iron-oxidizing bacterial strain BoFeN1 in the presence of dissolved Fe(II). Vivianite was first transformed into a greenish phase consisting mostly of an amorphous mixed valence Fe-phosphate. This precipitate became progressively orange and the final product of iron oxidation consisted of an amorphous Fe(III)-phosphate. The sub-micrometer analysis by scanning transmission X-ray microscopy of the iron redox state in samples collected at different stages of the culture indicated that iron was progressively oxidized at the contact of the bacteria and at a distance from the cells in extracellular minerals. Iron oxidation in the extracellular minerals was delayed by a few days compared with cell-associated Fe-minerals. This led to strong differences of Fe redox in between these two types of minerals and finally to local heterogeneities of redox within the sample. In the absence of dissolved Fe(II), vivianite was not significantly transformed by BoFeN1. Whereas Fe(II) oxidation at the cell contact is most probably directly catalyzed by the bacteria, vivianite transformation at a distance from the cells might result from oxidation by nitrite. In addition, processes leading to the export of Fe(III) from bacterial oxidation sites to extracellular minerals are discussed including some involving colloids observed by cryo-transmission electron microscopy in the culture medium.

Ancestral xerophobia: a hypothesis on the whole plant ecophysiology of early angiosperms.

Abstract: Today, angiosperms are fundamental players in the diversity and biogeochemical functioning of the planet. Yet despite the omnipresence of angiosperms in today’s ecosystems, the basic evolutionary understanding of how the earliest angiosperms functioned remains unknown. Here we synthesize ecophysiological, paleobotanical, paleoecological, and phylogenetic lines of evidence about early angiosperms and their environments. In doing so, we arrive at a hypothesis that early angiosperms evolved in evermoist tropical terrestrial habitats, where three of their emblematic innovations – including net-veined leaves, xylem vessels, and flowers – found ecophysiological advantages. However, the adaptation of early angiosperm ecophysiology to wet habitats did not initially promote massive diversification and ecological dominance. Instead, wet habitats were permissive for the ecological roothold of the clade, a critical phase of early diversification that entailed experimentation with a range of functional innovations in the leaves, wood, and flowers. Later, our results suggest that some of these innovations were co-opted gradually for new roles in the evolution of greater productivity and drought tolerance, which are characteristics seen across the vast majority of derived and ecologically dominant angiosperms today.

Bacterial formation of phosphatic laminites off Peru

Abstract: Authigenic phosphatic laminites enclosed in phosphorite crusts from the shelf off Peru (10°01′ S and 10°24′ S) consist of carbonate fluorapatite layers, which contain abundant sulfide minerals including pyrite (FeS2) and sphalerite (ZnS). Low δ34Spyrite values (average −28.8‰) agree with bacterial sulfate reduction and subsequent pyrite formation. Stable sulfur isotopic compositions of sulfate bound in carbonate fluorapatite are lower than that of sulfate from ambient sea water, suggesting bacterial reoxidation of sulfide by sulfide-oxidizing bacteria. The release of phosphorus and subsequent formation of the autochthonous phosphatic laminites are apparently caused by the activity of sulfate-reducing bacteria and associated sulfide-oxidizing bacteria. Following an extraction–phosphorite dissolution–extraction procedure, molecular fossils of sulfate-reducing bacteria (mono-O-alkyl glycerol ethers, di-O-alkyl glycerol ethers, as well as the short-chain branched fatty acids i/ai-C15:0, i/ai-C17:0 and 10MeC16:0) are found to be among the most abundant compounds. The fact that these molecular fossils of sulfate-reducing bacteria are distinctly more abundant after dissolution of the phosphatic laminite reveals that the lipids are tightly bound to the mineral lattice of carbonate fluorapatite. Moreover, compared with the autochthonous laminite, molecular fossils of sulfate-reducing bacteria are: (1) significantly less abundant and (2) not as tightly bound to the mineral lattice in the other, allochthonous facies of the Peruvian crusts consisting of phosphatic coated grains. These observations confirm the importance of sulfate-reducing bacteria in the formation of the phosphatic laminite. Model calculations highlight that organic matter degradation by sulfate-reducing bacteria has the potential to liberate sufficient phosphorus for phosphogenesis.

CO2-forced evolution of plant gas exchange capacity and water-use efficiency over the Phanerozoic

Abstract: The capacity of plants to fix carbon is ultimately constrained by two core plant attributes: photosynthetic biochemistry and the conductance to CO2diffusion from the atmosphere to sites of carboxylation in chloroplasts, predominantly stomatal conductance. Analysis of fossilized plant remains shows that stomatal density (number per unit area, D) and size (length by width, S) have fluctuated widely over the Phanerozoic Eon, indicating changes in maximum stomatal conductance. Parallel changes are likely to have taken place in leaf photosynthetic biochemistry, of which maximal rubisco carboxylation rate, Vcmax is a central element. We used measurements of S and D from fossilized plant remains spanning the last 400 Myr (most of the Phanerozoic), together with leaf gas exchange data and modeled Phanerozoic trends in atmospheric CO2 concentration, [CO2]a, to calibrate a [CO2]a-driven model of the long-term environmental influences on S, D and Vcmax. We show that over the Phanerozoic large changes in [CO2]a forced S, D and Vcmax to co-vary so as to reduce the impact of the change in [CO2]a on leaf CO2 assimilation for minimal energetic cost and reduced nitrogen requirements. Underlying this is a general negative correlation between S and D, and a positive correlation between water-use efficiency and [CO2]a. Furthermore, the calculated steady rise in stomatal conductance over the Phanerozoic is consistent with independent evidence for the evolution of plant hydraulic capacity, implying coordinated and sustained increase in gas exchange capacity and hydraulic capacity parallel long-term increases in land plant diversity.

CaCO3 nucleation by cyanobacteria: laboratory evidence for a passive, surface-induced mechanism.

Abstract: Calcite nucleation on the surface of cyanobacteria of the Synechococcus leopoliensis strain PCC 7942 was investigated to assess the influence of photosynthetic uptake of inorganic carbon and active ion exchange processes across the cell membrane on the nucleation and precipitation mechanisms. We performed long-term precipitation experiments at a constant CO(2) level in ambient air by adding suspensions of previously washed cyanobacteria to solutions of NaHCO(3)/CaCl(2) which were supersaturated with respect to calcite. Induction times between 4 and 110 h were measured over a range of saturation states, Omega, between 8 and 4. The kinetics of CaCO(3) nucleation was compared between experiments: (i) with ongoing photosynthesis, (ii) with cells metabolizing but not undergoing photosynthetic uptake of inorganic carbon and (iii) in darkness without photosynthesis. No significant differences were observed between the three treatments. The results reveal that under low nutrient concentrations and permanent CO(2) supply, photosynthetic uptake of inorganic carbon predominantly uses CO(2) and consequently does not directly influence the nucleation process of CaCO(3) at the surface of S. leopoliensis. Furthermore, ion exchange processes did not affect the kinetics, indicating a passive nucleation process wherein the cell surface or extracellular polymers provided preferential sites for mineral nucleation. The catalyzing effect of the cyanobacteria on calcite nucleation was equivalent to a approximately 18% reduction in the specific interfacial free energy of the calcite nuclei. This result and the ubiquitous abundance of cyanobacteria suggest that this process may have an impact on local and global carbon cycling.

Diatom elemental and morphological changes in response to iron limitation: a brief review with potential paleoceanographic applications

Abstract: Diatoms are a major group of phytoplankton that account for approximately 40% of the ocean carbon fixation and the vast majority of biogenic silica production through the construction of their cell walls (termed frustules). These frustules accumulate and are partially preserved in the ocean sediments. Diatom growth and nutrient utilization in high-nitrate, low-chlorophyll regions of the world's oceans are mostly regulated by iron availability. Diatoms acclimate to iron limitation by decreasing cell size. The associated increase in surface area-to-volume ratio and decrease in diffusive boundary layer thickness may improve nutrient uptake kinetics. In parallel, cellular silicon (Si) contents are elevated in iron-limited diatoms relative to nitrogen (N) and carbon (C). Variations in degree of silicification and nutritional requirements of iron-limited diatoms have been hypothesized to account for higher cellular Si and/or lower cellular N and C, respectively. However, in some diatoms, frustule silicification does not significantly change when cells are iron-limited. Instead, changes in the Si-containing valve surface area relative to volume within these diatoms is hypothesized to be responsible for the variations in the cellular Si : N and Si : C ratios. In particular, some examined iron-limited pennate diatoms have reduced widths relative to their lengths (i.e. lower length-normalized widths, LNW) compared to iron-replete cells. In the pennate diatom Fragilariopsis kerguelensis, the mean LNWs of valves preserved in sediments throughout the Southern Ocean (a well-characterized iron-limited region) is positively correlated with satellite-derived, climatological net primary productivity in the overlying waters. Because of the specific morphological changes in pennate diatom frustules in response to iron availability, the valve morphometerics (e.g. LNWs) can potentially be used as a diagnostic tool for iron-limited diatom growth and relative changes in the Si : N (and Si : C) ratios in extant diatom assemblages as well as those preserved in the sediments.

Effect of biological soil crusts on soil elemental concentrations: implications for biogeochemistry and as traceable biosignatures of ancient life on land

Abstract: Biological soil crusts (BSCs) are topsoil biosedimentary structures built by photosynthetic microbes commonly found today on arid soils. They play a role in soil stabilization and the fertility of arid lands, and are considered modern analogues of ancient terrestrial microbial communities. We determined the concentrations of four biogenic and 21 other elements, mostly metals, in surface soils that hosted BSCs, in the soils underneath those crusts, and in proximate but non-crusted surface soils. The samples were from six sites in the Colorado Plateau highlands and the Sonoran Desert lowlands. In spite of the variability in climate and geologic setting, we found statistically significant overall trends of enrichment in biogenic elements and depletion in non-biogenic elements when BSCs were compared with non-crusted soils. The differences between crusted and non-crusted soils were statistically significant at approximately 95% confidence for C, N (enrichments) and for Ca, Cr, Mn, Cu, Zn, As, and Zr (depletions). These trends are best explained by the activity of microbes. As expected, no differences in the concentrations of C, N, P, and S were detected between the soils underneath the crusts and the non-crusted soils, but the former showed depletion of non-biogenic elements, indicating that the leaching effect of crust microbes extends downward in the soil. These patterns speak to the need for a sustained input of allochthonous material, possibly dust, to maintain BSC fertility. These elemental patterns can be considered a biosignature that may be preserved in the rock record and might help identify ancient microbial communities on land.

Experimental silicification of the extremophilic Archaea Pyrococcus abyssi and Methanocaldococcus jannaschii: applications in the search for evidence of life in early Earth and extraterrestrial rocks.

Abstract: Hydrothermal activity was common on the early Earth and associated micro-organisms would most likely have included thermophilic to hyperthermophilic species. 3.5–3.3 billion-year-old, hydrothermally influenced rocks contain silicified microbial mats and colonies that must have been bathed in warm to hot hydrothermal emanations. Could they represent thermophilic or hyperthermophilic micro-organisms and if so, how were they preserved? We present the results of an experiment to silicify anaerobic, hyperthermophilic micro-organisms from the Archaea Domain Pyrococcus abyssi and Methanocaldococcus jannaschii, that could have lived on the early Earth. The micro-organisms were placed in a silica-saturated medium for periods up to 1 year. Pyrococcus abyssi cells were fossilized but the M. jannaschii cells lysed naturally after the exponential growth phase, apart from a few cells and cell remains, and were not silicified although their extracellular polymeric substances were. In this first simulated fossilization of archaeal strains, our results suggest that differences between species have a strong influence on the potential for different micro-organisms to be preserved by fossilization and that those found in the fossil record represent probably only a part of the original diversity. Our results have important consequences for biosignatures in hydrothermal or hydrothermally influenced deposits on Earth, as well as on early Mars, as environmental conditions were similar on the young terrestrial planets and traces of early Martian life may have been similarly preserved as silicified microfossils.

Formation and diagenesis of modern marine calcified cyanobacteria

Abstract: Calcified cyanobacterial microfossils are common in carbonate environments through most of the Phanerozoic, but are absent from the marine rock record over the past 65 Myr. There has been long-standing debate on the factors controlling the formation and temporal distribution of these fossils, fostered by the lack of a suitable modern analog. We describe calcified cyanobacteria filaments in a modern marine reef setting at Highborne Cay, Bahamas. Our observations and stable isotope data suggest that initial calcification occurs in living cyanobacteria and is photosynthetically induced. A single variety of cyanobacteria, Dichothrix sp., produces calcified filaments. Adjacent cyanobacterial mats form well-laminated stromatolites, rather than calcified filaments, indicating there can be a strong taxonomic control over the mechanism of microbial calcification. Petrographic analyses indicate that the calcified filaments are degraded during early diagenesis and are not present in well-lithified microbialites. The early diagenetic destruction of calcified filaments at Highborne Cay indicates that the absence of calcified cyanobacteria from periods of the Phanerozoic is likely to be caused by low preservation potential as well as inhibited formation.

The Eocene Arctic Azolla bloom: environmental conditions, productivity and carbon drawdown.

Abstract: Enormous quantities of the free-floating freshwater fern Azolla grew and reproduced in situ in the Arctic Ocean during the middle Eocene, as was demonstrated by microscopic analysis of microlaminated sediments recovered from the Lomonosov Ridge during Integrated Ocean Drilling Program (IODP) Expedition 302. The timing of the Azolla phase (~48.5 Ma) coincides with the earliest signs of onset of the transition from a greenhouse towards the modern icehouse Earth. The sustained growth of Azolla , currently ranking among the fastest growing plants on Earth, in a major anoxic oceanic basin may have contributed to decreasing atmospheric p CO 2 levels via burial of Azolla -derived organic matter. The consequences of these enormous Azolla blooms for regional and global nutrient and carbon cycles are still largely unknown. Cultivation experiments have been set up to investigate the influence of elevated p CO 2 on Azolla growth, showing a marked increase in Azolla productivity under elevated (760 and 1910 ppm) p CO 2 conditions. The combined results of organic carbon, sulphur, nitrogen content and 15 N and 13 C measurements of sediments from the Azolla interval illustrate the potential contribution of nitrogen fixation in a euxinic stratified Eocene Arctic. Flux calculations were used to quantitatively reconstruct the potential storage of carbon (0.9‐3.5 10 18 gC) in the Arctic during the Azolla interval. It is estimated that storing 0.9 10 18 to 3.5 10 18 g carbon would result in a 55 to 470 ppm drawdown of p CO 2 under Eocene

Soft X-ray spectromicroscopy of nickel sorption in a natural river biofilm.

Abstract: Scanning transmission X-ray microscopy (STXM) at the C 1s, O 1s, Ni 2p, Ca 2p, Mn 2p, Fe 2p, Mg 1s, Al 1s and Si 1s edges was used to study Ni sorption in a complex natural river biofilm. The 10-week grown river biofilm was exposed to 10 mg L(-1) Ni(2+) (as NiCl(2)) for 24 h. The region of the biofilm examined was dominated by filamentous structures, which were interpreted as the discarded sheaths of filamentous bacteria, as well as a sparse distribution of rod-shaped bacteria. The region also contained discrete particles with spectra similar to those of muscovite, SiO(2) and CaCO(3). The Ni(II) ions were selectively adsorbed by the sheaths of the filamentous bacteria. The sheaths were observed to be metal rich with significant amounts of Ca, Fe and Mn, along with the Ni. In addition, the sheaths had a large silicate content but little organic material. The metal content of the rod-shaped bacterial cells was much lower. The Fe on the sheath was mainly in the Fe(III) oxidation state. Mn was found in II, III and IV oxidation states. The Ni was likely sorbed to Mn-Fe minerals on the sheath. These STXM results have probed nano-scale biogeochemistry associated with bacterial species in a complex, natural biofilm community. They have implications for selective Ni contamination of the food chain and for developing bioremediation strategies.

2‐Methylhopanoids are maximally produced in akinetes of Nostoc punctiforme: geobiological implications

Abstract: 2-Methylhopanes, molecular fossils of 2-methylbacteriohopanepolyol (2-MeBHP) lipids, have been proposed as biomarkers for cyanobacteria, and by extension, oxygenic photosynthesis. However, the robustness of this interpretation is unclear, as 2-methylhopanoids occur in organisms besides cyanobacteria and their physiological functions are unknown. As a first step toward understanding the role of 2-MeBHP in cyanobacteria, we examined the expression and intercellular localization of hopanoids in the three cell types of Nostoc punctiforme: vegetative cells, akinetes, and heterocysts. Cultures in which N. punctiforme had differentiated into akinetes contained approximately 10-fold higher concentrations of 2-methylhopanoids than did cultures that contained only vegetative cells. In contrast, 2-methylhopanoids were only present at very low concentrations in heterocysts. Hopanoid production initially increased threefold in cells starved of nitrogen but returned to levels consistent with vegetative cells within 2 weeks. Vegetative and akinete cell types were separated into cytoplasmic, thylakoid, and outer membrane fractions; the increase in hopanoid expression observed in akinetes was due to a 34-fold enrichment of hopanoid content in their outer membrane relative to vegetative cells. Akinetes formed in response either to low light or phosphorus limitation, exhibited the same 2-methylhopanoid localization and concentration, demonstrating that 2-methylhopanoids are associated with the akinete cell type per se. Because akinetes are resting cells that are not photosynthetically active, 2-methylhopanoids cannot be functionally linked to oxygenic photosynthesis in N. punctiforme.

Alteration textures in terrestrial volcanic glass and the associated bacterial community

Abstract: Alteration textures were examined in subglacial (hyaloclastite) deposits at Valafell, Southern Iceland. Pitted and 'elongate' alteration features are observed in the glass similar to granular and tubular features reported previously in deep-ocean basaltic glasses, but elongate features generally did not have a length to width ratio greater than five. Elongate features were found in only 7% of surfaces. Crystalline basalt clasts, which are incorporated into the hyaloclastite, did not display elongate structures. Pitted alteration features were poorly defined in crystalline basalt, comprising only 4% of the surface compared to 47% in the case of basaltic glass. Examination of silica-rich glass (obsidian) and rhyolite similarly showed poorly defined pitted textures that comprised less than 15% of the surface and no elongate features were observed. These data highlight the differences in alteration textures between terrestrial basaltic glass and previously studied deep-ocean and subsurface basaltic glass, and the important role of mineralogy in controlling the type and abundance of alteration features. The hyaloclastite contains a diverse and abundant bacterial population, as determined by 16S rDNA analysis, which could be involved in weathering the glass. Despite the presence of phototrophs, we show that they were not involved in the production of most alteration textures in the basaltic glass materials we examined.

Redox control of N:P ratios in aquatic ecosystems.

Abstract: The ratio of dissolved fixed inorganic nitrogen to soluble inorganic phosphate (N:P) in the ocean interior is relatively constant, averaging ~16 : 1 by atoms. In contrast, the ratio of these two elements spans more than six orders of magnitude in lakes and other aquatic environments. To understand the factors influencing N:P ratios in aquatic environments, we analyzed 111 observational datasets derived from 35 water bodies, ranging from small lakes to ocean basins. Our results reveal that N:P ratios are highly correlated with the concentration of dissolved O 2 below ~100 μ mol L ‐1 . At higher concentrations of O 2 , N:P ratios are highly variable and not correlated with O 2 ; however, the coefficient of variation in N:P ratios is strongly related to the size of the water body. Hence, classical Redfield ratios observed in the ocean are anomalous; this specific elemental stoichiometry emerges not only as a consequence of the elemental ratio of the sinking flux of organic matter, but also as a result of the size of the basins and their ventilation. We propose that the link between N:P ratios, basin size and oxygen levels, along with the previously determined relationship between sedimentary δ 15 N and oxygen, can be used to infer historical N:P ratios for any water body.

Preliminary characterization and biological reduction of putative biogenic iron oxides (BIOS) from the Tonga-Kermadec Arc, southwest Pacific Ocean.

Abstract: Sediment samples were obtained from areas of diffuse hydrothermal venting along the seabed in the Tonga sector of the Tonga-Kermadec Arc, southwest Pacific Ocean. Sediments from Volcano 1 and Volcano 19 were analyzed by X-ray diffraction (XRD) and found to be composed primarily of the iron oxyhydroxide mineral, two-line ferrihydrite. XRD also suggested the possible presence of minor amounts of more ordered iron (hydr)oxides (including six-line ferrihydrite, goethite/lepidocrocite and magnetite) in the biogenic iron oxides (BIOS) from Volcano 1; however, Mossbauer spectroscopy failed to detect any mineral phases more crystalline than two-line ferrihydrite. The minerals were precipitated on the surfaces of abundant filamentous microbial structures. Morphologically, some of these structures were similar in appearance to the known iron-oxidizing genus Mariprofundus spp., suggesting that the sediments are composed of biogenic iron oxides. At Volcano 19, an areally extensive, active vent field, the microbial cells appeared to be responsible for the formation of cohesive chimney-like structures of iron oxyhydroxide, 2-3 m in height, whereas at Volcano 1, an older vent field, no chimney-like structures were apparent. Iron reduction of the sediment material (i.e. BIOS) by Shewanella putrefaciens CN32 was measured, in vitro, as the ratio of [total Fe(II)]:[total Fe]. From this parameter, reduction rates were calculated for Volcano 1 BIOS (0.0521 day(-1)), Volcano 19 BIOS (0.0473 day(-1)), and hydrous ferric oxide, a synthetic two-line ferrihydrite (0.0224 day(-1)). Sediments from both BIOS sites were more easily reduced than synthetic ferrihydrite, which suggests that the decrease in effective surface area of the minerals within the sediments (due to the presence of the organic component) does not inhibit subsequent microbial reduction. These results indicate that natural, marine BIOS are easily reduced in the presence of dissimilatory iron-reducing bacteria, and that the use of common synthetic iron minerals to model their reduction may lead to a significant underestimation of their biological reactivity.

A hypersaline microbial mat from the Pacific Atoll Kiritimati: insights into composition and carbon fixation using biomarker analyses and a 13C-labeling approach.

Abstract: Modern microbial mats are widely recognized as useful analogs for the study of biogeochemical processes relevant to paleoenvironmental reconstruction in the Precambrian. We combined microscopic observations and investigations of biomarker composition to investigate community structure and function in the upper layers of a thick phototrophic microbial mat system from a hypersaline lake on Kiritimati (Christmas Island) in the Northern Line Islands, Republic of Kiribati. In particular, an exploratory incubation experiment with (13)C-labeled bicarbonate was conducted to pinpoint biomarkers from organisms actively fixing carbon. A high relative abundance of the cyanobacterial taxa Aphanocapsa and Aphanothece was revealed by microscopic observation, and cyanobacterial fatty acids and hydrocarbons showed (13)C-uptake in the labeling experiment. Microscopic observations also revealed purple sulfur bacteria (PSB) in the deeper layers. A cyclic C(19:0) fatty acid and farnesol were attributed to this group that was also actively fixing carbon. Background isotopic values indicate Calvin-Benson cycle-based autotrophy for cycC(19:0) and farnesol-producing PSBs. Biomarkers from sulfate-reducing bacteria (SRB) in the top layer of the mat and their (13)C-uptake patterns indicated a close coupling between SRBs and cyanobacteria. Archaeol, possibly from methanogens, was detected in all layers and was especially abundant near the surface where it contained substantial amounts of (13)C-label. Intact glycosidic tetraether lipids detected in the deepest layer indicated other archaea. Large amounts of ornithine and betaine bearing intact polar lipids could be an indicator of a phosphate-limited ecosystem, where organisms that are able to substitute these for phospholipids may have a competitive advantage.

Geobiological investigations using secondary ion mass spectrometry: microanalysis of extant and paleo-microbial processes.

Abstract: The application of secondary ion mass spectrometry (SIMS) has tremendous value for the field of geobiology, representing a powerful tool for identifying the specific role of micro-organisms in biogeochemical cycles. In this review, we highlight a number of diverse applications for SIMS and nanoSIMS in geobiological research. SIMS performs isotope and elemental analysis at microscale enabling the investigation of the physiology of individual microbes within complex communities. Additionally, through the study of isotopic or chemical characteristics that are common in both living and ancient microbial communities, SIMS allows for direct comparisons of potential biosignatures derived from extant microbial cells and their fossil equivalents.

Biomineralization by photosynthetic organisms: evidence of coevolution of the organisms and their environment?

Abstract: Biomineralization is widespread among photosynthetic organisms in the ocean, in inland waters and on land. The most quantitatively important biogeochemical role of land plants today in biomineralization is silica deposition in vascular plants, especially grasses. Terrestrial plants also increase the rate of weathering, providing the soluble substrates for biomineralization on land and in water bodies, a role that has had global biogeochemical impacts since the Devonian. The dominant photosynthetic biomineralizers in today's ocean are diatoms and radiolarians depositing silica and coccolithophores and foraminifera depositing calcium carbonate. Abiotic precipitation of silica from supersaturated seawater in the Precambrian preceded intracellular silicification dominated by sponges, then radiolarians and finally diatoms, with successive declines in the silicic acid concentration in the surface ocean, resulting in some decreases in the extent of silicification and, probably, increases in the silicic acid affinity of the active influx mechanisms. Calcium and bicarbonate concentrations in the surface ocean have generally been supersaturating with respect to the three common calcium carbonate biominerals through geological time, allowing external calcification as well as calcification in compartments within cells or organisms. The forms of calcium carbonate in biominerals, and presumably the evolution of the organisms that produce them, have been influenced by abiotic variations in calcium and magnesium concentrations in seawater, and calcium carbonate deposition has probably also been influenced by carbon dioxide concentration whose variations are in part biologically determined. Overall, there has been less biological feedback on the availability of substrates for calcification than is the case for silicification.

Haloarchaeal diversity in 23, 121 and 419 MYA salts

Abstract: DNA was extracted from surface-sterilized salt of different geological ages (23, 121, 419 million years of age, MYA) to investigate haloarchaeal diversity. Only Haloarcula and Halorubrum DNA was found in 23 MYA salt. Older crystals contained unclassified groups and Halobacterium. The older crystals yielded a unique 55-bp insert within the 16S rRNA V2 region. The secondary structure of the V2 region completely differed from that in haloarchaea of modern environments. The DNA demonstrates that unknown haloarchaea and the Halobacterium were key components in ancient hypersaline environments. Halorubrum and Haloarcula appear to be a dominant group in relatively modern hypersaline habitats.

Constraining carbon sources and growth rates of freshwater microbialites in Pavilion Lake using 14C analysis

Abstract: This study determined the natural abundance isotopic compositions ((13)C, (14)C) of the primary carbon pools and microbial communities associated with modern freshwater microbialites located in Pavilion Lake, British Columbia, Canada. The Delta(14)C of dissolved inorganic carbon (DIC) was constant throughout the water column and consistent with a primarily atmospheric source. Observed depletions in DIC (14)C values compared with atmospheric CO(2) indicated effects due either to DIC residence time and/or inputs of (14)C-depleted groundwater. Mass balance comparisons of local and regional groundwater indicate that groundwater DIC could contribute a maximum of 9-13% of the DIC. (14)C analysis of microbial phospholipid fatty acids from microbialite communities had Delta(14)C values comparable with lake water DIC, demonstrating that lake water DIC was their primary carbon source. Microbialite carbonate was also primarily derived from DIC. However, some depletion in microbialite carbonate (14)C relative to lake water DIC occurred, due either to residence time or mixing with a (14)C-depleted carbon source. A detrital branch covered with microbialite growth was used to estimate a microbialite growth rate of 0.05 mm year(-1) for the past 1000 years, faster than previous estimates for this system. These results demonstrate that the microbialites are actively growing and that the primary carbon source for both microbial communities and recent carbonate is DIC originating from the atmosphere. While these data cannot conclusively differentiate between abiotic and biotic formation mechanisms, the evidence for minor inputs of groundwater-derived DIC is consistent with the previously hypothesized biological origin of the Pavilion Lake microbialites.

Not so old Archaea - the antiquity of biogeochemical processes in the archaeal domain of life.

Abstract: Since the archaeal domain of life was first recognized, it has often been assumed that Archaea are ancient, and harbor primitive traits. In fact, the names of the major archaeal lineages reflect our assumptions regarding the antiquity of their traits. Ancestral state reconstruction and relaxed molecular clock analyses using newly articulated oxygen age constraints show that although the archaeal domain itself is old, tracing back to the Archean eon, many clades and traits within the domain are not ancient or primitive. Indeed many clades and traits, particularly in the Euryarchaeota, were inferred to be Neoproterozoic or Phanerozoic in age. Both Eury- and Crenarchaeota show increasing metabolic and physiological diversity through time. Early archaeal microbial communities were likely limited to sulfur reduction and hydrogenotrophic methanogenesis, and were confined to high-temperature geothermal environments. However, after the appearance of atmospheric oxygen, nodes containing a wide variety of traits (sulfate and thiosulfate reduction, sulfur oxidation, sulfide oxidation, aerobic respiration, nitrate reduction, mesophilic methanogenesis in sedimentary environments) appear, first in environments containing terrestrial Crenarchaeota in the Meso/Neoproterozoic followed by environments containing marine Euryarchaeota in the Neoproterozoic and Phanerozoic. This provides phylogenetic evidence for increasing complexity in the biogeochemical cycling of C, N, and S through geologic time, likely as a consequence of microbial evolution and the gradual oxygenation of various compartments within the biosphere. This work has implications not only for the large-scale evolution of microbial communities and biogeochemical processes, but also for the interpretation of microbial biosignatures in the ancient rock record.

Soft X‐ray spectro‐tomography study of cyanobacterial biomineral nucleation

Abstract: Quantitative three-dimensional (3D) chemical mapping using angle-scan spectro-tomography in a scanning transmission (soft) X-ray microscope (STXM) has been used for the first time to characterize the early stages of CaCO3 biomineral nucleation on the surface of planktonic freshwater cyanobacterial cells of the strain Synechococcus leopoliensis PCC 7942. The apparatus for STXM angle-scan tomography is described. Aspects of sample preparation, sample mounting and data acquisition and quantitative analysis and interpretation are discussed in detail. Angle-scan tomography and chemically selective 3D imaging at multiple photon energies has been combined with a complete 2D spectromicroscopic characterization of the biochemical and mineralogical composition. This has provided detailed insights into the mechanisms of mineral nucleation, leading to development of a detailed model of CaCO3 nucleation by the cyanobacterial strain S. leopoliensis PCC 7942. It shows that Ca is absorbed by the extracellular polymeric substances (EPS) of the cyanobacteria and that CaCO3 with aragonite-like short-range order is precipitated rather homogeneously within the EPS. The precipitation of the thermodynamically more stable calcite polymorph then starts at Ca-rich hot spots within the EPS and close to the cyanobacteria.

Garnet-filled trails associated with carbonaceous matter mimicking microbial filaments in Archean basalt.

Abstract: The study of the earliest traces of life on Earth can be complicated by abiotically formed biomorphs. We report here the finding of clustered micrometer-sized filaments of iron- and calcium-rich garnets associated with carbonaceous matter in an agate amygdale from a 2.7-billion-year-old basalt of the Maddina Formation, Western Australia. The distribution of carbonaceous matter and the mineral phases composing the filaments were analyzed using a combination of confocal laser scanning microscopy, laser-Raman micro-spectroscopy, focused ion beam sectioning and transmission electron microscopy. The results allow consideration of possible biogenic and abiotic processes that produced the filamentous structures. The filaments have a range of sizes, morphologies and distributions similar to those of certain modern iron-mineralized filamentous bacteria and some ancient filamentous structures interpreted as microfossils. They also share a high morphological similarity with tubular structures produced by microbial boring activity. However, the microstructures and the distribution of carbonaceous matter are more suggestive of an abiotic origin for the filaments. They are characteristic features of trails produced by the displacement of inclusions associated with local dissolution of their silica matrix. Organic compounds found in kerogen or bitumen inclusions may have contributed significantly to the dissolution of the quartz (or silica gel) matrix driving filamentous growth. Discriminating the products of such abiotic organic-mediated processes from filamentous microfossils or microbial borings is important to the interpretation of the scarce Precambrian fossil record and requires investigation down to the nanoscale.