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Biosphere
Kinds of Biosphere Terms modified by Biosphere Selected AbstractsCaloric restriction for longevity: I. Paradigm, protocols and physiological findings in animal researchEUROPEAN EATING DISORDERS REVIEW, Issue 5 2004Kelly M. Vitousek Abstract The initial article in this series reviews basic findings in the field of caloric restriction for longevity (CRL). To eating disorder specialists, the data are disconcerting. The chronic dieting and subnormal weight we endeavour to prevent and treat in humans appear highly beneficial when imposed on animals. In the laboratory, organisms from nematodes to monkeys thrive when forced to undereat, as long as they receive sufficient micronutrients. The most remarkable results are obtained through the most extreme measures: mice, for example, do best if limited to a third of expected caloric intake, beginning soon after weaning and continuing throughout adulthood. Deprivation can be achieved through an ,anorexic' protocol of steady underconsumption or a ,bulimic' pattern in which periods of fasting alternate with bouts of binge eating. The benefits of such regimens include delayed senescence, postponement and/or attenuation of age-related disease and dramatic increases in average and maximum lifespan. Although some biological functions are impaired (including growth, reproduction and perhaps resistance to certain stressors), the cost/benefit ratio clearly favours CRL when calculated on the basis of physical outcomes in late age. Advocacy of comparable regimens for people, however, is ill-considered. Enthusiasm for CRL can be sustained only by detaching deprivation from the context of daily life, ignoring psychological effects, and dismissing data on human semi-starvation and eating disorders. The experiences of participants in Biosphere 2 and individuals with anorexia nervosa suggest that the price of CRL is unacceptably high when a wider range of outcome variables is examined. Copyright © 2004 John Wiley & Sons, Ltd and Eating Disorders Association. [source] Increased leaf area dominates carbon flux response to elevated CO2 in stands of Populus deltoides (Bartr.)GLOBAL CHANGE BIOLOGY, Issue 5 2005Ramesh Murthy Abstract We examined the effects of atmospheric vapor pressure deficit (VPD) and soil moisture stress (SMS) on leaf- and stand-level CO2 exchange in model 3-year-old coppiced cottonwood (Populus deltoides Bartr.) plantations using the large-scale, controlled environments of the Biosphere 2 Laboratory. A short-term experiment was imposed on top of continuing, long-term CO2 treatments (43 and 120 Pa), at the end of the growing season. For the experiment, the plantations were exposed for 6,14 days to low and high VPD (0.6 and 2.5 kPa) at low and high volumetric soil moisture contents (25,39%). When system gross CO2 assimilation was corrected for leaf area, system net CO2 exchange (SNCE), integrated daily SNCE, and system respiration increased in response to elevated CO2. The increases were mainly as a result of the larger leaf area developed during growth at high CO2, before the short-term experiment; the observed decline in responses to SMS and high VPD treatments was partly because of leaf area reduction. Elevated CO2 ameliorated the gas exchange consequences of water stress at the stand level, in all treatments. The initial slope of light response curves of stand photosynthesis (efficiency of light use by the stand) increased in response to elevated CO2 under all treatments. Leaf-level net CO2 assimilation rate and apparent quantum efficiency were consistently higher, and stomatal conductance and transpiration were significantly lower, under high CO2 in all soil moisture and VPD combinations (except for conductance and transpiration in high soil moisture, low VPD). Comparisons of leaf- and stand-level gross CO2 exchange indicated that the limitation of assimilation because of canopy light environment (in well-irrigated stands; ratio of leaf : stand=3.2,3.5) switched to a predominantly individual leaf limitation (because of stomatal closure) in response to water stress (leaf : stand=0.8,1.3). These observations enabled a good prediction of whole stand assimilation from leaf-level data under water-stressed conditions; the predictive ability was less under well-watered conditions. The data also demonstrated the need for a better understanding of the relationship between leaf water potential, leaf abscission, and stand LAI. [source] Simulated and observed fluxes of sensible and latent heat and CO2 at the WLEF-TV tower using SiB2.5GLOBAL CHANGE BIOLOGY, Issue 9 2003Ian Baker Abstract Three years of meteorological data collected at the WLEF-TV tower were used to drive a revised version of the Simple Biosphere (SiB 2.5) Model. Physiological properties and vegetation phenology were specified from satellite imagery. Simulated fluxes of heat, moisture, and carbon were compared to eddy covariance measurements taken onsite as a means of evaluating model performance on diurnal, synoptic, seasonal, and interannual time scales. The model was very successful in simulating variations of latent heat flux when compared to observations, slightly less so in the simulation of sensible heat flux. The model overestimated peak values of sensible heat flux on both monthly and diurnal scales. There was evidence that the differences between observed and simulated fluxes might be linked to wetlands near the WLEF tower, which were not present in the SiB simulation. The model overestimated the magnitude of the net ecosystem exchange of CO2 in both summer and winter. Mid-day maximum assimilation was well represented by the model, but late afternoon simulations showed excessive carbon uptake due to misrepresentation of within-canopy shading in the model. Interannual variability was not well simulated because only a single year of satellite imagery was used to parameterize the model. [source] A differential constraint approach to obtain global stability for radiation-induced double-diffusive convection in a porous mediumMATHEMATICAL METHODS IN THE APPLIED SCIENCES, Issue 8 2009Antony A. Hill Abstract The stability of double-diffusive porous convection with a concentration-based internal heat source is studied. Owing to the significant sensitivity of standard energy method, a highly desirable reduction in the number of required coupling parameters is achieved through the novel energy method of van Duijn et al. (Environmental Mechanics: Water, Mass and Energy Transfer in the Biosphere. American Geophysical Union: Washington, DC, 2002; 155,169). This approach incorporates the Darcy equation as a differential constraint, and has been shown by van Duijn et al. to generally yield sharper nonlinear results. Owing to the widespread use of coupling parameters in analysing porous media stability, this result strongly advocates the differential constraint approach for obtaining optimal nonlinear stability thresholds. Copyright © 2008 John Wiley & Sons, Ltd. [source] Leaf respiratory CO2 is 13C-enriched relative to leaf organic components in five species of C3 plantsNEW PHYTOLOGIST, Issue 3 2004Cheng-yuan Xu Summary ,,Here, we compared the carbon isotope ratios of leaf respiratory CO2 (,13CR) and leaf organic components (soluble sugar, water soluble fraction, starch, protein and bulk organic matter) in five C3 plants grown in a glasshouse and inside Biosphere 2. One species, Populus deltoides, was grown under three different CO2 concentrations. ,,The Keeling plot approach was applied to the leaf scale to measure leaf ,13CR and these results were compared with the ,13C of leaf organic components. ,,In all cases, leaf respiratory CO2 was more 13C-enriched than leaf organic components. The amount of 13C enrichment displayed a significant species-specific pattern, but the effect of CO2 treatment was not significant on P. deltoides. ,,In C3 plant leaves, 13C-enriched respiratory CO2 appears widespread. Among currently hypothesized mechanisms contributing to this phenomenon, non-statistical carbon isotope distribution within the sugar substrates seems most likely. However, caution should be taken when attempting to predict the ,13C of leaf respiratory CO2 at the ecosystem scale by upscaling the relationship between leaf ,13CR and ,13C of leaf organic components. [source] Evaluation of high-resolution precipitation estimate over the Amazon BasinATMOSPHERIC SCIENCE LETTERS, Issue 4 2009Cláudio Moisés Santos e Silva Abstract Using rainfall data from S-band radar measurements, the estimative of the rainfall from the 3B42_V6 algorithm was evaluated for the region of the Tropical Rainfall Measurement Mission and Large Scale Biosphere,Atmosphere Experiment in Amazonia (TRMM,LBA) experiment, which was conducted in the Amazon Basin during the 1999 rainy season. The algorithm correctly represented the diurnal rainfall cycle, but underestimated overall precipitation rates by about 50%. It adequately represented most of the stratiform (convective) rainfall during the break (active) phase of the South American Monsoon System (SAMS). Thus, some uncertainties, as well as the algorithm applicability for the region and period studied, were demonstrated. Copyright © 2009 Royal Meteorological Society [source] Diurnal and semidiurnal rainfall cycles during the rain season in SW Amazonia, observed via rain gauges and estimated using S-band radarATMOSPHERIC SCIENCE LETTERS, Issue 2 2009Cláudio Moisés Santos e Silva Abstract The rainfall field estimated by an S-band radar was evaluated with rain gauges network measurements during the Tropical Rainfall Measuring Mission and Large-Scale Biosphere,Atmosphere Experiment in Amazonia (TRMM-LBA), then the daily variability associated with the presence (absence) of the South Atlantic convergence zone (SACZ) were studied. The results showed the high spatial variability of the rainfall over southwest (SW) Amazonia and suggest that local mechanisms (topography and/or local circulations induced by contrast of vegetation) may be associated with heavy rainfall episodes; moreover, it was possible to observe the squall line influence on the diurnal and semidiurnal cycles. Copyright © 2009 Royal Meteorological Society [source] Tree-Ring Carbon Isotopic Constraints on Carbon-Water Exchanges between Atmosphere and Biosphere in Drought Regions in Northwestern ChinaACTA GEOLOGICA SINICA (ENGLISH EDITION), Issue 2 2000WANG Shilu Abstract The comparison between the carbon isotope and the index of ring width of a pine disc from the Tuomuer Peak region in Xinjiang shows that the effects of climate changes on the tree-ring growth and carbon isotopic fractionation varies with time. The reason is probably relative to the characters of climate changes and adaptability of the tree-ring growth to climate changes. The relationships between the atmospheric CO2 level and the revised ,13Cair by the tree-ring carbon isotope indicate that the carbon cycle is not in a steady state, but under a stage-change condition in this area. It also can be concluded that the ratio of CO2 from the terrestrial eco-system has increased, and the flux of CO2 exchange between the atmosphere and the biosphere was gradually increasing over the past century. In addition, the results also confirm the validity and superiority of the carbon isotope to the research of the water-use efficiency. [source] Ecological implications of plants' ability to tell the timeECOLOGY LETTERS, Issue 6 2009Víctor Resco Abstract The circadian clock (the endogenous mechanism that anticipates diurnal cycles) acts as a central coordinator of plant activity. At the molecular and organism level, it regulates key traits for plant fitness, including seed germination, gas exchange, growth and flowering, among others. In this article, we explore current evidence on the effect of the clock for the scales of interest to ecologists. We begin by synthesizing available knowledge on the effect of the clock on biosphere,atmosphere interactions and observe that, at least in the systems where it has been tested, the clock regulates gas exchange from the leaf to the ecosystem level, and we discuss its implications for estimates of the carbon balance. Then, we analyse whether incorporating the action of the clock may help in elucidating the effects of climate change on plant distributions. Circadian rhythms are involved in regulating the range of temperatures a species can survive and affects plant interactions. Finally, we review the involvement of the clock in key phenological events, such as flowering time and seed germination. Because the clock may act as a common mechanism affecting many of the diverse branches of ecology, our ultimate goal is to stimulate further research into this pressing, yet unexplored, topic. [source] Managing ecosystem services: what do we need to know about their ecology?ECOLOGY LETTERS, Issue 5 2005Claire Kremen Abstract Human domination of the biosphere has greatly altered ecosystems, often overwhelming their capacity to provide ecosystem services critical to our survival. Yet ecological understanding of ecosystem services is quite limited. Previous work maps the supply and demand for services, assesses threats to them, and estimates economic values, but does not measure the underlying role of biodiversity in providing services. In contrast, experimental studies of biodiversity,function examine communities whose structures often differ markedly from those providing services in real landscapes. A bridge is needed between these two approaches. To develop this research agenda, I discuss critical questions and key approaches in four areas: (1) identifying the important ,ecosystem service providers'; (2) determining the various aspects of community structure that influence function in real landscapes, especially compensatory community responses that stabilize function, or non-random extinction sequences that rapidly erode it; (3) assessing key environmental factors influencing provision of services, and (4) measuring the spatio-temporal scale over which providers and services operate. I show how this research agenda can assist in developing environmental policy and natural resource management plans. [source] "Ultraviolet spring" and the ecological consequences of catastrophic impactsECOLOGY LETTERS, Issue 2 2000Charles S. Cockell Asteroid and comet impacts cause ozone depletion. For the first time, we have quantified the photobiological characteristics of these events and speculate on some of the associated ecological consequences. Following the clearing of stratospheric dust after "impact winter", levels of damaging UVB radiation (280,315 nm) could increase by at least 100%, resulting in an "ultraviolet spring". Many of the taxa stressed by the cold and dark conditions of impact are the same that would be stressed by large increases in UVB radiation. Furthermore, depletion of dissolved organic carbon (DOC) by impact-induced acid rain would increase UVB penetrability into freshwater systems. Although an increase in UVB radiation is an attractive hypothesis for exacerbating the demise of land animals at the Cretaceous-Tertiary (K/T) boundary, e.g. dinosaurs, our calculations suggest the impact into rare sulphate-rich target rock may have prevented an ultraviolet spring in this case. If the K/T impact event had occurred in any other region on Earth, the stress to the biosphere would probably have been considerably greater. [source] Cold adaptation in the marine bacterium, Sphingopyxis alaskensis, assessed using quantitative proteomicsENVIRONMENTAL MICROBIOLOGY, Issue 10 2010Lily Ting Summary The cold marine environment constitutes a large proportion of the Earth's biosphere. Sphingopyxis alaskensis was isolated as a numerically abundant bacterium from several cold marine locations, and has been extensively studied as a model marine bacterium. Recently, a metabolic labelling platform was developed to comprehensively identify and quantify proteins from S. alaskensis. The approach incorporated data normalization and statistical validation for the purpose of generating highly confident quantitative proteomics data. Using this approach, we determined quantitative differences between cells grown at 10°C (low temperature) and 30°C (high temperature). Cold adaptation was linked to specific aspects of gene expression: a dedicated protein-folding system using GroESL, DnaK, DnaJ, GrpE, SecB, ClpB and PPIase; polyhydroxyalkanoate-associated storage materials; a link between enzymes in fatty acid metabolism and energy generation; de novo synthesis of polyunsaturated fatty acids in the membrane and cell wall; inorganic phosphate ion transport by a phosphate import PstB homologue; TonB-dependent receptor and bacterioferritin in iron homeostasis; histidine, tryptophan and proline amino acid metabolism; and a large number of proteins without annotated functions. This study provides a new level of understanding on how important marine bacteria can adapt to compete effectively in cold marine environments. This study is also a benchmark for comparative proteomic analyses with other important marine bacteria and other cold-adapted organisms. [source] Thermophilic anaerobes in Arctic marine sediments induced to mineralize complex organic matter at high temperatureENVIRONMENTAL MICROBIOLOGY, Issue 4 2010Casey Hubert Summary Marine sediments harbour diverse populations of dormant thermophilic bacterial spores that become active in sediment incubation experiments at much higher than in situ temperature. This response was investigated in the presence of natural complex organic matter in sediments of two Arctic fjords, as well as with the addition of freeze-dried Spirulina or individual high-molecular-weight polysaccharides. During 50°C incubation experiments, Arctic thermophiles catalysed extensive mineralization of the organic matter via extracellular enzymatic hydrolysis, fermentation and sulfate reduction. This high temperature-induced food chain mirrors sediment microbial processes occurring at cold in situ temperatures (near 0°C), yet it is catalysed by a completely different set of microorganisms. Using sulfate reduction rates (SRR) as a proxy for organic matter mineralization showed that differences in organic matter reactivity determined the extent of the thermophilic response. Fjord sediments with higher in situ SRR also supported higher SRR at 50°C. Amendment with Spirulina significantly increased volatile fatty acids production and SRR relative to unamended sediment in 50°C incubations. Spirulina amendment also revealed temporally distinct sulfate reduction phases, consistent with 16S rRNA clone library detection of multiple thermophilic Desulfotomaculum spp. enriched at 50°C. Incubations with four different fluorescently labelled polysaccharides at 4°C and 50°C showed that the thermophilic population in Arctic sediments produce a different suite of polymer-hydrolysing enzymes than those used in situ by the cold-adapted microbial community. Over time, dormant marine microorganisms like these are buried in marine sediments and might eventually encounter warmer conditions that favour their activation. Distinct enzymatic capacities for organic polymer degradation could allow specific heterotrophic populations like these to play a role in sustaining microbial metabolism in the deep, warm, marine biosphere. [source] Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimatesENVIRONMENTAL MICROBIOLOGY, Issue 1 2010Victor Kunin Summary Massively parallel pyrosequencing of the small subunit (16S) ribosomal RNA gene has revealed that the extent of rare microbial populations in several environments, the ,rare biosphere', is orders of magnitude higher than previously thought. One important caveat with this method is that sequencing error could artificially inflate diversity estimates. Although the per-base error of 16S rDNA amplicon pyrosequencing has been shown to be as good as or lower than Sanger sequencing, no direct assessments of pyrosequencing errors on diversity estimates have been reported. Using only Escherichia coli MG1655 as a reference template, we find that 16S rDNA diversity is grossly overestimated unless relatively stringent read quality filtering and low clustering thresholds are applied. In particular, the common practice of removing reads with unresolved bases and anomalous read lengths is insufficient to ensure accurate estimates of microbial diversity. Furthermore, common and reproducible homopolymer length errors can result in relatively abundant spurious phylotypes further confounding data interpretation. We suggest that stringent quality-based trimming of 16S pyrotags and clustering thresholds no greater than 97% identity should be used to avoid overestimates of the rare biosphere. [source] Limits of life in hostile environments: no barriers to biosphere function?ENVIRONMENTAL MICROBIOLOGY, Issue 12 2009Jim P. Williams Summary Environments that are hostile to life are characterized by reduced microbial activity which results in poor soil- and plant-health, low biomass and biodiversity, and feeble ecosystem development. Whereas the functional biosphere may primarily be constrained by water activity (aw) the mechanism(s) by which this occurs have not been fully elucidated. Remarkably we found that, for diverse species of xerophilic fungi at aw values of , 0.72, water activity per se did not limit cellular function. We provide evidence that chaotropic activity determined their biotic window, and obtained mycelial growth at water activities as low as 0.647 (below that recorded for any microbial species) by addition of compounds that reduced the net chaotropicity. Unexpectedly we found that some fungi grew optimally under chaotropic conditions, providing evidence for a previously uncharacterized class of extremophilic microbes. Further studies to elucidate the way in which solute activities interact to determine the limits of life may lead to enhanced biotechnological processes, and increased productivity of agricultural and natural ecosystems in arid and semiarid regions. [source] New ways to break an old bond: the bacterial carbon,phosphorus hydrolases and their role in biogeochemical phosphorus cyclingENVIRONMENTAL MICROBIOLOGY, Issue 10 2007John P. Quinn Summary Phosphonates are organophosphorus molecules that contain the highly stable C,P bond, rather than the more common, and more labile, C,O,P phosphate ester bond. They have ancient origins but their biosynthesis is widespread among more primitive organisms and their importance in the contemporary biosphere is increasingly recognized; for example phosphonate-P is believed to play a particularly significant role in the productivity of the oceans. The microbial degradation of phosphonates was originally thought to occur only under conditions of phosphate limitation, mediated exclusively by the poorly characterized C,P lyase multienzyme system, under Pho regulon control. However, more recent studies have demonstrated the Pho-independent mineralization by environmental bacteria of three of the most widely distributed biogenic phosphonates: 2-aminoethylphosphonic acid (ciliatine), phosphonoacetic acid, and 2-amino-3-phosphonopropionic acid (phosphonoalanine). The three phosphonohydrolases responsible have unique specificities and are members of separate enzyme superfamilies; their expression is regulated by distinct members of the LysR family of bacterial transcriptional regulators, for each of which the phosphonate substrate of the respective degradative operon serves as coinducer. Previously no organophosphorus compound was known to induce the enzymes required for its own degradation. Whole-genome and metagenome sequence analysis indicates that the genes encoding these newly described C,P hydrolases are distributed widely among prokaryotes. As they are able to function under conditions in which C,P lyases are inactive, the three enzymes may play a hitherto-unrecognized role in phosphonate breakdown in the environment and hence make a significant contribution to global biogeochemical P-cycling. [source] Limits of life in MgCl2 -containing environments: chaotropicity defines the windowENVIRONMENTAL MICROBIOLOGY, Issue 3 2007John E. Hallsworth Summary The biosphere of planet Earth is delineated by physico-chemical conditions that are too harsh for, or inconsistent with, life processes and maintenance of the structure and function of biomolecules. To define the window of life on Earth (and perhaps gain insights into the limits that life could tolerate elsewhere), and hence understand some of the most unusual biological activities that operate at such extremes, it is necessary to understand the causes and cellular basis of systems failure beyond these windows. Because water plays such a central role in biomolecules and bioprocesses, its availability, properties and behaviour are among the key life-limiting parameters. Saline waters dominate the Earth, with the oceans holding 96.5% of the planet's water. Saline groundwater, inland seas or saltwater lakes hold another 1%, a quantity that exceeds the world's available freshwater. About one quarter of Earth's land mass is underlain by salt, often more than 100 m thick. Evaporite deposits contain hypersaline waters within and between their salt crystals, and even contain large subterranean salt lakes, and therefore represent significant microbial habitats. Salts have a major impact on the nature and extent of the biosphere, because solutes radically influence water's availability (water activity) and exert other activities that also affect biological systems (e.g. ionic, kosmotropic, chaotropic and those that affect cell turgor), and as a consequence can be major stressors of cellular systems. Despite the stressor effects of salts, hypersaline environments can be heavily populated with salt-tolerant or -dependent microbes, the halophiles. The most common salt in hypersaline environments is NaCl, but many evaporite deposits and brines are also rich in other salts, including MgCl2 (several hundred million tonnes of bischofite, MgCl2·6H2O, occur in one formation alone). Magnesium (Mg) is the third most abundant element dissolved in seawater and is ubiquitous in the Earth's crust, and throughout the Solar System, where it exists in association with a variety of anions. Magnesium chloride is exceptionally soluble in water, so can achieve high concentrations (> 5 M) in brines. However, while NaCl-dominated hypersaline environments are habitats for a rich variety of salt-adapted microbes, there are contradictory indications of life in MgCl2 -rich environments. In this work, we have sought to obtain new insights into how MgCl2 affects cellular systems, to assess whether MgCl2 can determine the window of life, and, if so, to derive a value for this window. We have dissected two relevant cellular stress-related activities of MgCl2 solutions, namely water activity reduction and chaotropicity, and analysed signatures of life at different concentrations of MgCl2 in a natural environment, namely the 0.05,5.05 M MgCl2 gradient of the seawater : hypersaline brine interface of Discovery Basin , a large, stable brine lake almost saturated with MgCl2, located on the Mediterranean Sea floor. We document here the exceptional chaotropicity of MgCl2, and show that this property, rather than water activity reduction, inhibits life by denaturing biological macromolecules. In vitro, a test enzyme was totally inhibited by MgCl2 at concentrations below 1 M; and culture medium with MgCl2 concentrations above 1.26 M inhibited the growth of microbes in samples taken from all parts of the Discovery interface. Although DNA and rRNA from key microbial groups (sulfate reducers and methanogens) were detected along the entire MgCl2 gradient of the seawater : Discovery brine interface, mRNA, a highly labile indicator of active microbes, was recovered only from the upper part of the chemocline at MgCl2 concentrations of less than 2.3 M. We also show that the extreme chaotropicity of MgCl2 at high concentrations not only denatures macromolecules, but also preserves the more stable ones: such indicator molecules, hitherto regarded as evidence of life, may thus be misleading signatures in chaotropic environments. Thus, the chaotropicity of MgCl2 would appear to be a window-of-life-determining parameter, and the results obtained here suggest that the upper MgCl2 concentration for life, in the absence of compensating (e.g. kosmotropic) solutes, is about 2.3 M. [source] Quantification of microbial communities in near-surface and deeply buried marine sediments on the Peru continental margin using real-time PCRENVIRONMENTAL MICROBIOLOGY, Issue 7 2006Axel Schippers Summary Deeply buried marine sediments harbour a large fraction of all prokaryotes on Earth but it is still unknown which phylogenetic and physiological microbial groups dominate the deep biosphere. In this study real-time PCR allowed a comparative quantitative microbial community analysis in near-surface and deeply buried marine sediments from the Peru continental margin. The 16S rRNA gene copy numbers of prokaryotes and Bacteria were almost identical with a maximum of 108,1010 copies cm,3 in the near-surface sediments. Archaea exhibited one to three orders of magnitude lower 16S rRNA gene copy numbers. The 18S rRNA gene of Eukarya was always at least three orders of magnitude less abundant than the 16S rRNA gene of prokaryotes. The 16S rRNA gene of the Fe(III)- and Mn(IV)-reducing bacterial family Geobacteraceae and the dissimilatory (bi)sulfite reductase gene (dsrA) of sulfate-reducing prokaryotes were abundant with 106,108 copies cm,3 in near-surface sediments but showed lower numbers and an irregular distribution in the deep sediments. The copy numbers of all genes decreased with sediment depth exponentially. The depth gradients were steeper for the gene copy numbers than for numbers of total prokaryotes (acridine orange direct counts), which reflects the ongoing degradation of the high-molecular-weight DNA with sediment age and depth. The occurrence of eukaryotic DNA also suggests DNA preservation in the deeply buried sediments. [source] Nitrogenase gene diversity and microbial community structure: a cross-system comparisonENVIRONMENTAL MICROBIOLOGY, Issue 7 2003Jonathan P. Zehr Summary Biological nitrogen fixation is an important source of fixed nitrogen for the biosphere. Microorganisms catalyse biological nitrogen fixation with the enzyme nitrogenase, which has been highly conserved through evolution. Cloning and sequencing of one of the nitrogenase structural genes, nifH, has provided a large, rapidly expanding database of sequences from diverse terrestrial and aquatic environments. Comparison of nifH phylogenies to ribosomal RNA phylogenies from cultivated microorganisms shows little conclusive evidence of lateral gene transfer. Sequence diversity far outstrips representation by cultivated representatives. The phylogeny of nitrogenase includes branches that represent phylotypic groupings based on ribosomal RNA phylogeny, but also includes paralogous clades including the alternative, non-molybdenum, non-vanadium containing nitrogenases. Only a few alternative or archaeal nitrogenase sequences have as yet been obtained from the environment. Extensive analysis of the distribution of nifH phylotypes among habitats indicates that there are characteristic patterns of nitrogen fixing microorganisms in termite guts, sediment and soil environments, estuaries and salt marshes, and oligotrophic oceans. The distribution of nitrogen-fixing microorganisms, although not entirely dictated by the nitrogen availability in the environment, is non-random and can be predicted on the basis of habitat characteristics. The ability to assay for gene expression and investigate genome arrangements provides the promise of new tools for interrogating natural populations of diazotrophs. The broad analysis of nitrogenase genes provides a basis for developing molecular assays and bioinformatics approaches for the study of nitrogen fixation in the environment. [source] Yeast diversity sampling on the San Juan Islands reveals no evidence for the spread of the Vancouver Island Cryptococcus gattii outbreak to this localeFEMS YEAST RESEARCH, Issue 4 2006James A. Fraser Abstract Biological diversity has been estimated for various phyla of life, such as insects and mammals, but in the microbe world is has been difficult to determine species richness and abundance. Here we describe a study of species diversity of fungi with a yeast-like colony morphology from the San Juan Islands, a group of islands that lies southeast of Vancouver Island, Canada. Our sampling revealed that the San Juan archipelago biosphere contains a diverse range of such fungi predominantly belonging to the Basidiomycota, particularly of the order Tremellales. One member of this group, Cryptococcus gattii, is the etiological agent of a current and ongoing outbreak of cryptococcosis on nearby Vancouver Island. Our sampling did not, however, reveal this species. While the lack of recovery of C. gattii does not preclude its presence on the San Juan Islands, our results suggest that the Strait of Juan de Fuca may be serving as a geographical barrier to restrict the dispersal of this primary human fungal pathogen into the United States. [source] Not so old Archaea , the antiquity of biogeochemical processes in the archaeal domain of lifeGEOBIOLOGY, Issue 5 2009CARRINE E. BLANK 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. [source] Coevolution of metal availability and nitrogen assimilation in cyanobacteria and algaeGEOBIOLOGY, Issue 2 2009J. B. GLASS 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 and The N demands of an expanding biosphere were satisfied by the evolution of biological N2 fixation, possibly utilizing only Fe. Trace O2 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 N2 fixation and the Mo-dependent enzymes for 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 N2 fixation and the supply of fixed N. Eukaryotic ecosystems may have been particularly disadvantaged by N scarcity and the high Mo requirement of eukaryotic 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. [source] The age of Rubisco: the evolution of oxygenic photosynthesisGEOBIOLOGY, Issue 4 2007E. G. NISBET ABSTRACT The evolutionary history of oxygenesis is controversial. Form I of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) in oxygen-tolerant organisms both enables them to carry out oxygenic extraction of carbon from air and enables the competitive process of photorespiration. Carbon isotopic evidence is presented from ~2.9 Ga stromatolites from Steep Rock, Ontario, Canada, ~2.9 Ga stromatolites from Mushandike, Zimbabwe, and ~2.7 Ga stromatolites in the Belingwe belt, Zimbabwe. The data imply that in all three localities the reef-building autotrophs included organisms using Form I Rubisco. This inference, though not conclusive, is supported by other geochemical evidence that these stromatolites formed in oxic conditions. Collectively, the implication is that oxygenic photosynthesizers first appeared ~2.9 Ga ago, and were abundant 2.7,2.65 Ga ago. Rubisco specificity (its preference for CO2 over O2) and compensation constraints (the limits on carbon fixation) may explain the paradox that despite the inferred evolution of oxygenesis 2.9 Ga ago, the Late Archaean air was anoxic. The atmospheric CO2:O2 ratio, and hence greenhouse warming, may reflect Form I Rubisco's specificity for CO2 over O2. The system may be bistable under the warming Sun, with liquid oceans occurring in either anoxic (H2O with abundant CH4 plus CO2) or oxic (H2O with more abundant CO2, but little CH4) greenhouse states. Transition between the two states would involve catastrophic remaking of the biosphere. Build-up of a very high atmospheric inventory of CO2 in the 2.3 Ga glaciation may have allowed the atmosphere to move up the CO2 compensation line to reach stability in an oxygen-rich system. Since then, Form I Rubisco specificity and consequent compensation limits may have maintained the long-term atmospheric disproportion between O2 and CO2, which is now close to both CO2 and O2 compensation barriers. [source] Niches of the pre-photosynthetic biosphere and geologic preservation of Earth's earliest ecologyGEOBIOLOGY, Issue 2 2007NORMAN H. SLEEP ABSTRACT The tree of terrestrial life probably roots in non-photosynthetic microbes. Chemoautotrophs were the first primary producers, and the globally dominant niches in terms of primary productivity were determined by availability of carbon dioxide and hydrogen for methanogenesis and sulfite reduction. Methanogen niches were most abundant where CO2 -rich ocean water flowed through serpentinite. Black smoker vents from basalt supplied comparable amount of H2. Hydrogen from arc volcanoes supported a significant methanogenic niche at the Earth's surface. SO2 from arc volcanoes reacted with organic matter and hydrogen, providing a significant surface niche. Methane ascended to the upper atmosphere where photolysis produced C-rich haze and CO, and H escaped into space. The CO and C-rich haze supported secondary surface niches. None of these ecologies were bountiful; less than 1% of the CO2 vented by ridge axes, arcs, and metamorphism became organic matter before it was buried in carbonate. In contrast, a photosynthetic biosphere leaves copious amounts of organic carbon, locally concentrated in sediments. Black shales are a classic geologic biosignature for photosynthesis that can survive subduction and high-grade metamorphism. [source] Mass-independent fractionation of sulfur isotopes in sulfides from the pre-3770 Ma Isua Supracrustal Belt, West GreenlandGEOBIOLOGY, Issue 4 2006D. PAPINEAU ABSTRACT Redox chemistry of the coupled atmosphere,hydrosphere system has coevolved with the biosphere, from global anoxia in the Archean to an oxygenated Proterozoic surface environment. However, to trace these changes to the very beginning of the rock record presents special challenges. All known Eoarchean (c. 3850,3600 Ma) volcanosedimentary successions (i.e. supracrustal rocks) are restricted to high-grade gneissic terranes that seldom preserve original sedimentary structures and lack primary organic biomarkers. Although complicated by metamorphic overprinting, sulfur isotopes from Archean supracrustal rocks have the potential to preserve signatures of both atmospheric chemistry and metabolic fractionation from the original sediments. We present a synthesis of multiple sulfur isotope measurements (32S, 33S and 34S) performed on sulfides from amphibolite facies banded iron-formations (BIFs) and ferruginous garnet-biotite (metapelitic) schists from the pre-3770 Ma Isua Supracrustal Belt (ISB) in West Greenland. Because these data come from some of the oldest rocks of interpretable marine sedimentary origin, they provide the opportunity to (i) explore for possible biosignatures of sulfur metabolisms in early life; (ii) assess changes in atmospheric redox chemistry from ,3.8 Ga; and (iii) lay the groundwork to elucidate sulfur biogeochemical cycles on the early Earth. We find that sulfur isotope results from Isua do not unambiguously indicate microbially induced sulfur isotopic fractionation at that time. A significantly expanded data set of ,33S analyses for Isua dictates that the atmosphere was devoid of free oxygen at time of deposition and also shows that the effects of post-depositional metamorphic remobilization and/or dilution can be traced in mass-independently fractionated sulfur isotopes. [source] Biological energy requirements as quantitative boundary conditions for life in the subsurfaceGEOBIOLOGY, Issue 4 2004T. M. HOEHLER ABSTRACT All life requires energy, which must be extracted from the environment. For all known life, free energy must be available at finite minimum levels in order to be usefully harnessed and must be delivered at finite minimum rates in order to support basic biochemical integrity and function. While seldom tested in the high energy light- and oxygen-based metabolisms of the surface biosphere, the magnitude of these requirements , the biological energy quantum (BEQ) and maintenance energy (ME) requirements, respectively , is considerable with respect to the potential metabolisms and energy sources that characterize the deep subsurface realm. As such, they constitute a fundamental constraint on the possible nature, distribution, and activity of microbial life in that environment. Because the energy released in a chemical transformation can be equated to the concentrations of substrates and products, both the BEQ and ME requirements define the minimum substrate concentration and minimum substrate production rate that must be sustained by a given environment for it to be capable of supporting life. The magnitudes of the BEQ and ME requirements are sensitive to a range of environmental parameters that may vary significantly in the subsurface. Temperature exerts a particularly strong control and is among the most important parameters to be considered in evaluating the energetic habitability of subsurface environments. [source] Geobiological analysis using whole genome-based tree building applied to the Bacteria, Archaea, and EukaryaGEOBIOLOGY, Issue 1 2003Christopher H. House ABSTRACT We constructed genomic trees based on the presence and absence of families of protein-encoding genes observed in 55 prokaryotic and five eukaryotic genomes. There are features of the genomic trees that are not congruent with typical rRNA phylogenetic trees. In the bacteria, for example, Deinococcus radiodurans associates with the Gram-positive bacteria, a result that is also seen in some other phylogenetic studies using whole genome data. In the Archaea, the methanogens plus Archaeoglobus form a united clade and the Euryarchaeota are divided with the two Thermoplasma genomes and Halobacterium sp. falling below the Crenarchaeota. While the former appears to be an accurate representation of methanogen-relatedness, the misplacement of Halobacterium may be an artefact of parsimony. These results imply the last common ancestor of the Archaea was not a methanogen, leaving sulphur reduction as the most geochemically plausible metabolism for the base of the archaeal crown group. It also suggests that methanogens were not a component of the Earth's earliest biosphere and that their origin occurred sometime during the Archean. In the Eukarya, the parsimony analysis of five Eukaryotes using the Crenarchaeota as an outgroup seems to counter the Ecdysozoa hypothesis, placing Caenorhabditis elegans (Nematoda) below the common ancestor of Drosophila melanogaster (Arthropoda) and Homo sapiens (Chordata) even when efforts are made to counter the possible effects of a faster rate of sequence evolution for the C. elegans genome. Further analysis, however, suggests that the gene loss of ,animal' genes is highest in C. elegans and is obscuring the relationships of these organisms. [source] Faster returns on ,leaf economics' and different biogeochemical niche in invasive compared with native plant speciesGLOBAL CHANGE BIOLOGY, Issue 8 2010JOSEP PENUELAS Abstract Plant-invasive success is one of the most important current global changes in the biosphere. To understand which factors explain such success, we compared the foliar traits of 41 native and 47 alien-invasive plant species in Oahu Island (Hawaii), a location with a highly endemic flora that has evolved in isolation and is currently vulnerable to invasions by exotic plant species. Foliar traits, which in most cases presented significant phylogenetic signal, i.e. closely related species tended to resemble each other due to shared ancestry, separated invasive from native species. Invasive species had lower leaf mass per area and enhanced capacities in terms of productivity (photosynthetic capacity) and nutrient capture both of macro- (N, P, K) and microelements (Fe, Ni, Cu and Zn). All these differences remain highly significant after removing the effects of phylogenetic history. Alien-invasive species did not show higher efficiency at using limiting nutrient resources, but they got faster leaf economics returns and occupied a different biogeochemical niche, which helps to explain the success of invasive plants and suggests that potential increases in soil nutrient availability might favor further invasive plant success. [source] Decadal change in wetland,woodland boundaries during the late 20th century reflects climatic trendsGLOBAL CHANGE BIOLOGY, Issue 8 2010DAVID A. KEITH Abstract Wetlands are important and restricted habitats for dependent biota and play vital roles in landscape function, hydrology and carbon sequestration. They are also likely to be one of the most sensitive components of the terrestrial biosphere to global climate change. An understanding of relationships between wetland persistence and climate is imperative for predicting, mitigating and adapting to the impacts of future climate change on wetland extent and function. We investigated whether mire wetlands had contracted, expanded or remained stable during 1960,2000. We chose a study area encompassing a regional climatic gradient in southeastern Australia, specifically to avoid confounding effects of water extraction on wetland hydrology and extent. We first characterized trends in climate by examining data from local weather stations, which showed a slight increase in precipitation and marked decline in pan evaporation over the relevant period. Remote sensing of vegetation boundaries showed a marked lateral expansion of mires during 1961,1998, and a corresponding contraction of woodland. The spatial patterns in vegetation change were consistent with the regional climatic gradient and showed a weaker co-relationship to fire history. Resource exploitation, wildland fires and autogenic mire development failed to explain the observed expansion of mire vegetation in the absence of climate change. We therefore conclude that the extent of mire wetlands is likely to be sensitive to variation in climatic moisture over decadal time scales. Late 20th-century trends in climatic moisture may be related primarily to reduced irradiance and/or reduced wind speeds. In the 21st century, however, net climatic moisture in this region is projected to decline. As mires are apparently sensitive to hydrological change, we anticipate lateral contraction of mire boundaries in coming decades as projected climatic drying eventuates. This raises concerns about the future hydrological functions, carbon storage capacity and unique biodiversity of these important ecosystems. [source] Assessing the effect of elevated carbon dioxide on soil carbon: a comparison of four meta-analysesGLOBAL CHANGE BIOLOGY, Issue 8 2009BRUCE A. HUNGATE Abstract Soil is the largest reservoir of organic carbon (C) in the terrestrial biosphere and soil C has a relatively long mean residence time. Rising atmospheric carbon dioxide (CO2) concentrations generally increase plant growth and C input to soil, suggesting that soil might help mitigate atmospheric CO2 rise and global warming. But to what extent mitigation will occur is unclear. The large size of the soil C pool not only makes it a potential buffer against rising atmospheric CO2, but also makes it difficult to measure changes amid the existing background. Meta-analysis is one tool that can overcome the limited power of single studies. Four recent meta-analyses addressed this issue but reached somewhat different conclusions about the effect of elevated CO2 on soil C accumulation, especially regarding the role of nitrogen (N) inputs. Here, we assess the extent of differences between these conclusions and propose a new analysis of the data. The four meta-analyses included different studies, derived different effect size estimates from common studies, used different weighting functions and metrics of effect size, and used different approaches to address nonindependence of effect sizes. Although all factors influenced the mean effect size estimates and subsequent inferences, the approach to independence had the largest influence. We recommend that meta-analysts critically assess and report choices about effect size metrics and weighting functions, and criteria for study selection and independence. Such decisions need to be justified carefully because they affect the basis for inference. Our new analysis, with a combined data set, confirms that the effect of elevated CO2 on net soil C accumulation increases with the addition of N fertilizers. Although the effect at low N inputs was not significant, statistical power to detect biogeochemically important effect sizes at low N is limited, even with meta-analysis, suggesting the continued need for long-term experiments. [source] | |||||||||||||||||||||||||||||||