Permeability-porosity relationships in seafloor vent deposits : dependence on pore evolution processes

Author Posting. © American Geophysical Union, 2007. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 112 (2007): B05208, doi:10.1029/2006JB004716.Systematic laboratory measurements of permeability and porosity were conducted on three large vent structures from the Mothra Hydrothermal vent field on the Endeavor segment of the Juan de Fuca Ridge. Geometric means of permeability values obtained from a probe permeameter are 5.9 × 10−15 m2 for Phang, a tall sulfide-dominated spire that was not actively venting when sampled; 1.4 × 10−14 m2 for Roane, a lower-temperature spire with dense macrofaunal communities growing on its sides that was venting diffuse fluid of <300°C; and 1.6 × 10−14 m2 for Finn, an active black smoker with a well-defined inner conduit that was venting 302°C fluids prior to recovery. Twenty-three cylindrical cores were then taken from these vent structures. Permeability and porosity of the drill cores were determined on the basis of Darcy's law and Boyle's law, respectively. Permeability values range from ∼10−15 to 10−13 m2 for core samples from Phang, from ∼10−15 to 10−12 m2 for cores from Roane, and from ∼10−15 to 3 × 10−13 m2 for cores from Finn, in good agreement with the probe permeability measurements. Permeability and porosity relationships are best described by two different power law relationships with exponents of ∼9 (group I) and ∼3 (group II). Microstructural analyses reveal that the difference in the two permeability-porosity relationships reflects different mineral precipitation processes as pore space evolves within different parts of the vent structures, either with angular sulfide grains depositing as aggregates that block fluid paths very efficiently (group I), or by late stage amorphous silica that coats existing grains and reduces fluid paths more gradually (group II). The results suggest that quantification of permeability and porosity relationships leads to a better understanding of pore evolution processes. Correctly identifying permeability and porosity relationships is an important first step toward accurately estimating fluid distribution, flow rate, and environmental conditions within seafloor vent deposits, which has important consequences for chimney growth and biological communities that reside within and on vent structures.Support from the National Science Foundation under grants NSF OCE-9986456 (W.Z. and M.K.T.) and NSF OCE-0327488 (P.R.C.) is gratefully acknowledged. We also thank the WHOI summer student fellowship for providing support to H.G

Formation of H2 and CH4 by weathering of olivine at temperatures between 30 and 70°C

Hydrocarbons such as CH4 are known to be formed through the Fischer-Tropsch or Sabatier type reactions in hydrothermal systems usually at temperatures above 100°C. Weathering of olivine is sometimes suggested to account for abiotic formation of CH4 through its redox lowering and water splitting properties. Knowledge about the CH4 and H2 formation processes at low temperatures is important for the research about the origin and cause of early Earth and Martian CH4 and for CO2 sequestration. We have conducted a series of low temperature, long-term weathering experiments in which we have tested the CH4 and H2 formation potential of forsteritic olivine

Genome-Scale Analysis of Mycoplasma agalactiae Loci Involved in Interaction with Host Cells

Mycoplasma agalactiae is an important pathogen of small ruminants, in which it causes contagious agalactia. It belongs to a large group of “minimal bacteria” with a small genome and reduced metabolic capacities that are dependent on their host for nutrients. Mycoplasma survival thus relies on intimate contact with host cells, but little is known about the factors involved in these interactions or in the more general infectious process. To address this issue, an assay based on goat epithelial and fibroblastic cells was used to screen a M. agalactiae knockout mutant library. Mutants with reduced growth capacities in cell culture were selected and 62 genomic loci were identified as contributing to this phenotype. As expected for minimal bacteria, “transport and metabolism” was the functional category most commonly implicated in this phenotype, but 50% of the selected mutants were disrupted in coding sequences (CDSs) with unknown functions, with surface lipoproteins being most commonly represented in this category. Since mycoplasmas lack a cell wall, lipoproteins are likely to be important in interactions with the host. A few intergenic regions were also identified that may act as regulatory sequences under co-culture conditions. Interestingly, some mutants mapped to gene clusters that are highly conserved across mycoplasma species but located in different positions. One of these clusters was found in a transcriptionally active region of the M. agalactiae chromosome, downstream of a cryptic promoter. A possible scenario for the evolution of these loci is discussed. Finally, several CDSs identified here are conserved in other important pathogenic mycoplasmas, and some were involved in horizontal gene transfer with phylogenetically distant species. These results provide a basis for further deciphering functions mediating mycoplasma-host interactions

Mineralogical and geochemical features of sulfide chimneys from the 49°39′E hydrothermal field on the Southwest Indian Ridge and their geological inferences

© The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Chinese Science Bulletin 56 (2011): 2828-2838, doi:10.1007/s11434-011-4619-4.During January–May in 2007, the Chinese research cruise DY115-19 discovered an active hydrothermal field at 49°39′E/37°47′S on the ultraslow spreading Southwest Indian Ridge (SWIR). This was also the first active hydrothermal field found along an ultraslow-spreading ridge. We analyzed mineralogical, textural and geochemical compositions of the sulfide chimneys obtained from the 49°39′E field. Chimney samples show a concentric mineral zone around the fluid channel. The mineral assemblages of the interiors consist mainly of chalcopyrite, with pyrite and sphalerite as minor constitunets. In the intermediate portion, pyrite becomes the dominant mineral, with chalcopyrite and sphalerite as minor constitunets. For the outer wall, the majority of minerals are pyrite and sphalerite, with few chalcopyrite. Towards the outer margin of the chimney wall, the mineral grains become small and irregular in shape gradually, while minerals within interstices are abundant. These features are similar to those chimney edifices found on the East Pacific Rise and Mid-Atlantic Ridge. The average contents of Cu, Fe and Zn in our chimney samples were 2.83 wt%, 45.6 wt% and 3.28 wt%, respectively. The average Au and Ag contents were up to 2.0 ppm and 70.2 ppm respectively, higher than the massive sulfides from most hydrothermal fields along mid-ocean ridge. The rare earth elements geochemistry of the sulfide chimneys show a pattern distinctive from the sulfides recovered from typical hydrothermal fields along sediment-starved mid-ocean ridge, with the enrichment of light rare earth elements but the weak, mostly negative, Eu anomaly. This is attributed to the distinct mineralization environment or fluid compositions in this area.This work was supported by the China Ocean Mineral Resources Research and Development Association Program (DY115- 02-1-01) and the State Oceanic Administration Youth Science Fund (2010318)

Characterizing the pathotype of neonatal meningitis causing <i>Escherichia coli</i> (NMEC)

Background Neonatal meningitis-causing Escherichia coli (NMEC) is the predominant Gram-negative bacterial pathogen associated with meningitis in newborn infants. High levels of heterogeneity and diversity have been observed in the repertoire of virulence traits and other characteristics among strains of NMEC making it difficult to define the NMEC pathotype. The objective of the present study was to identify genotypic and phenotypic characteristics of NMEC that can be used to distinguish them from commensal E. coli. Methods A total of 53 isolates of NMEC obtained from neonates with meningitis and 48 isolates of fecal E. coli obtained from healthy individuals (HFEC) were comparatively evaluated using five phenotypic (serotyping, serum bactericidal assay, biofilm assay, antimicorbial susceptibility testing, and in vitro cell invasion assay) and three genotypic (phylogrouping, virulence genotyping, and pulsed-field gel electrophoresis) methods. Results A majority (67.92 %) of NMEC belonged to B2 phylogenetic group whereas 59 % of HFEC belonged to groups A and D. Serotyping revealed that the most common O and H types present in NMEC tested were O1 (15 %), O8 (11.3 %), O18 (13.2 %), and H7 (25.3 %). In contrast, none of the HFEC tested belonged to O1 or O18 serogroups. The most common serogroup identified in HFEC was O8 (6.25 %). The virulence genotyping reflected that more than 70 % of NMEC carried kpsII, K1, neuC, iucC, sitA, and vat genes with only less than 27 % of HFEC possessing these genes. All NMEC and 79 % of HFEC tested were able to invade human cerebral microvascular endothelial cells. No statistically significant difference was observed in the serum resistance phenotype between NMEC and HFEC. The NMEC strains demonstrated a greater ability to form biofilms in Luria Bertani broth medium than did HFEC (79.2 % vs 39.9 %). Conclusion The results of our study demonstrated that virulence genotyping and phylogrouping may assist in defining the potential NMEC pathotype

First Investigation of the Microbiology of the Deepest Layer of Ocean Crust

We would like to thank Frederick (Rick) Colwell for input on molecular analyses in low biomass environments, Donna Blackman, Benoît Ildefonse, Adélie Delacour, and Gretchen Früh-Green for discussions regarding geological and geochemical aspects of this manuscript, and the Integrated Ocean Drilling Program Expeditions 304/305 Science Party. We would also like to thank Captain Alex Simpson and the entire crew of the JOIDES Resolution.Conceived and designed the experiments: OUM MRF SJG. Performed the experiments: OUM TN MR JDVN AM. Analyzed the data: OUM TN MR JDVN AM. Contributed reagents/materials/analysis tools: TN MR JZ MRF SJG. Wrote the paper: OUM.The gabbroic layer comprises the majority of ocean crust. Opportunities to sample this expansive crustal environment are rare because of the technological demands of deep ocean drilling; thus, gabbroic microbial communities have not yet been studied. During the Integrated Ocean Drilling Program Expeditions 304 and 305, igneous rock samples were collected from 0.45-1391.01 meters below seafloor at Hole 1309D, located on the Atlantis Massif (30 °N, 42 °W). Microbial diversity in the rocks was analyzed by denaturing gradient gel electrophoresis and sequencing (Expedition 304), and terminal restriction fragment length polymorphism, cloning and sequencing, and functional gene microarray analysis (Expedition 305). The gabbroic microbial community was relatively depauperate, consisting of a low diversity of proteobacterial lineages closely related to Bacteria from hydrocarbon-dominated environments and to known hydrocarbon degraders, and there was little evidence of Archaea. Functional gene diversity in the gabbroic samples was analyzed with a microarray for metabolic genes (“GeoChip”), producing further evidence of genomic potential for hydrocarbon degradation - genes for aerobic methane and toluene oxidation. Genes coding for anaerobic respirations, such as nitrate reduction, sulfate reduction, and metal reduction, as well as genes for carbon fixation, nitrogen fixation, and ammonium-oxidation, were also present. Our results suggest that the gabbroic layer hosts a microbial community that can degrade hydrocarbons and fix carbon and nitrogen, and has the potential to employ a diversity of non-oxygen electron acceptors. This rare glimpse of the gabbroic ecosystem provides further support for the recent finding of hydrocarbons in deep ocean gabbro from Hole 1309D. It has been hypothesized that these hydrocarbons might originate abiotically from serpentinization reactions that are occurring deep in the Earth's crust, raising the possibility that the lithic microbial community reported here might utilize carbon sources produced independently of the surface biosphere.Yeshttp://www.plosone.org/static/editorial#pee

Barriers and post-closure monitoring (AL121125)

This project focuses on the rapid implementation of near-surface barriers, biotreatment, and post-closure monitoring technology. It uses water-permeable and biologic barriers that chemically capture and/or degrade contaminants without significantly altering the natural water flow regime. Barrier approaches are being tested for two different applications. The first is the use of barriers for confinement of chemical contaminants for in-trench treatments with leach systems or an in-place bioreactor. The second is an enhancement of the current practice of emplacing grout or clay slurry walls into direct horizontal surface and subsurface water flows around a contaminated area by integrating permeable reactive barriers and petroleum reservoir gel/foam/polymer technology

Physicochemical basis of the Na-K-Ca geothermometer

Regular changes in solution composition were observed experimentally during granite reaction with dilute NaCl (+CaCl/sub 2/) solutions; these changes closely follow the empirical Na-K-Ca geothermometer relationship. Initial minerals forming the granite (quartz, plagioclase, K-feldspar, and biotite) were etched by the reactions. Alteration phases formed include calcium-zeolite at 300/sup 0/C, and minor amounts of clay and calcsilicate at all temperatures. Amphibole overgrowths were also found at 340/sup 0/C. Quartz is near saturation in all experiments, and preliminary calculations of aqueous species distributions and mineral affinities indicate that the solutions achieve super-saturation with feldspars as the temperature increase. A consistent variation attributable to pH differences was observed in the empirical geothermometer relationship for all experimental data. At 340/sup 0/C, the experimental solutions appear to have deviated slightly from the empirical Na-K-Ca relationship. Such deviations may also be found in natural systems that attain such temperatures