Plutonium Oxidation State Distribution under Aerobic and Anaerobic Subsurface Conditions for Metal-Reducing Bacteria

NASA Astrophysics Data System (ADS)

Reed, D. T.; Swanson, J.; Khaing, H.; Deo, R.; Rittmann, B.

2009-12-01

The fate and potential mobility of plutonium in the subsurface is receiving increased attention as the DOE looks to cleanup the many legacy nuclear waste sites and associated subsurface contamination. Plutonium is the near-surface contaminant of concern at several DOE sites and continues to be the contaminant of concern for the permanent disposal of nuclear waste. The mobility of plutonium is highly dependent on its redox distribution at its contamination source and along its potential migration pathways. This redox distribution is often controlled, especially in the near-surface where organic/inorganic contaminants often coexist, by the direct and indirect effects of microbial activity. The redox distribution of plutonium in the presence of facultative metal reducing bacteria (specifically Shewanella and Geobacter species) was established in a concurrent experimental and modeling study under aerobic and anaerobic conditions. Pu(VI), although relatively soluble under oxidizing conditions at near-neutral pH, does not persist under a wide range of the oxic and anoxic conditions investigated in microbiologically active systems. Pu(V) complexes, which exhibit high chemical toxicity towards microorganisms, are relatively stable under oxic conditions but are reduced by metal reducing bacteria under anaerobic conditions. These facultative metal-reducing bacteria led to the rapid reduction of higher valent plutonium to form Pu(III/IV) species depending on nature of the starting plutonium species and chelating agents present in solution. Redox cycling of these lower oxidation states is likely a critical step in the formation of pseudo colloids that may lead to long-range subsurface transport. The CCBATCH biogeochemical model is used to explain the redox mechanisms and final speciation of the plutonium oxidation state distributions observed. These results for microbiologically active systems are interpreted in the context of their importance in defining the overall migration of plutonium in the subsurface.

Strategic planning features of subsurface management in Kemerovo Oblast

NASA Astrophysics Data System (ADS)

Romanyuk, V.; Grinkevich, A.; Akhmadeev, K.; Pozdeeva, G.

2016-09-01

The article discusses the strategic planning features of regional development based on the production and subsurface management in Kemerovo Oblast. The modern approach - SWOT analysis was applied to assess the regional development strategy. The estimation of regional development plan implementation was given for the foreseeable future.

Dynamics of Reactive Microbial Hotspots in Concentration Gradient.

NASA Astrophysics Data System (ADS)

Hubert, A.; Farasin, J.; Tabuteau, H.; Dufresne, A.; Meheust, Y.; Le Borgne, T.

2017-12-01

In subsurface environments, bacteria play a major role in controlling the kinetics of a broad range of biogeochemical reactions. In such environments, nutrients fluxes and solute concentrations needed for bacteria metabolism may be highly variable in space and intermittent in time. This can lead to the formation of reactive hotspots where and when conditions are favorable to particular microorganisms, hence inducing biogeochemical reaction kinetics that differ significantly from those measured in homogeneous model environments. To investigate the impact of chemical gradients on the spatial structure and temporal dynamics of subsurface microorganism populations, we develop microfluidic cells allowing for a precise control of flow and chemical gradient conditions, as well as quantitative monitoring of the bacteria's spatial distribution and biofilm development. Using the non-motile Escherichia coli JW1908-1 strain and Gallionella capsiferriformans ES-2 as model organisms, we investigate the behavior and development of bacteria over a range of single and double concentration gradients in the concentrations of nutrients, electron donors and electron acceptors. We measure bacterial activity and population growth locally in precisely known hydrodynamic and chemical environments. This approach allows time-resolved monitoring of the location and intensity of reactive hotspots in micromodels as a function of the flow and chemical gradient conditions. We compare reactive microbial hotspot dynamics in our micromodels to classic growth laws and well-known growth parameters for the laboratory model bacteria Escherichia coli.We also discuss consequences for the formation and temporal dynamics of biofilms in the subsurface.

STRUCTURE AND FUNCTION OF SUBSURFACE MICROBIAL COMMUNITIES AFFECTING RADIONUCLIDE TRANSPORT AND BIOIMMOBILIZATION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Joel E. Kostka; Lee Kerkhof; Kuk-Jeong Chin

2011-06-15

The objectives of this project were to: (1) isolate and characterize novel anaerobic prokaryotes from subsurface environments exposed to high levels of mixed contaminants (U(VI), nitrate, sulfate), (2) elucidate the diversity and distribution of metabolically active metal- and nitrate-reducing prokaryotes in subsurface sediments, and (3) determine the biotic and abiotic mechanisms linking electron transport processes (nitrate, Fe(III), and sulfate reduction) to radionuclide reduction and immobilization. Mechanisms of electron transport and U(VI) transformation were examined under near in situ conditions in sediment microcosms and in field investigations at the Oak Ridge Field Research Center (ORFRC), in Oak Ridge, Tennessee, where themore » subsurface is exposed to mixed contamination predominated by uranium and nitrate. A total of 20 publications (16 published or 'in press' and 4 in review), 10 invited talks, and 43 contributed seminars/ meeting presentations were completed during the past four years of the project. PI Kostka served on one proposal review panel each year for the U.S. DOE Office of Science during the four year project period. The PI leveraged funds from the state of Florida to purchase new instrumentation that aided the project. Support was also leveraged by the PI from the Joint Genome Institute in the form of two successful proposals for genome sequencing. Draft genomes are now available for two novel species isolated during our studies and 5 more genomes are in the pipeline. We effectively addressed each of the three project objectives and research highlights are provided. Task I - Isolation and characterization of novel anaerobes: (1) A wide range of pure cultures of metal-reducing bacteria, sulfate-reducing bacteria, and denitrifying bacteria (32 strains) were isolated from subsurface sediments of the Oak Ridge Field Research Center (ORFRC), where the subsurface is exposed to mixed contamination of uranium and nitrate. These isolates which are new to science all show high sequence identity to sequences retrieved from ORFRC subsurface. (2) Based on physiological and phylogenetic characterization, two new species of subsurface bacteria were described: the metal-reducer Geobacter daltonii, and the denitrifier Rhodanobacter denitrificans. (3) Strains isolated from the ORFRC show that Rhodanobacter species are well adapted to the contaminated subsurface. Strains 2APBS1 and 116-2 grow at high salt (3% NaCl), low pH (3.5) and tolerate high concentrations of nitrate (400mM) and nitrite (100mM). Strain 2APBS1 was demonstrated to grow at in situ acidic pHs down to 2.5. (4) R. denitrificans strain 2APBS1 is the first described Rhodanobacter species shown to denitrify. Nitrate is almost entirely converted to N2O, which may account for the large accumulation of N2O in the ORFRC subsurface. (5) G. daltonii, isolated from uranium- and hydrocarbon-contaminated subsurface sediments of the ORFRC, is the first organism from the subsurface clade of the genus Geobacter that is capable of growth on aromatic hydrocarbons. (6) High quality draft genome sequences and a complete eco-physiological description are completed for R. denitrificans strain 2APBS1 and G. daltonii strain FRC-32. (7) Given their demonstrated relevance to DOE remediation efforts and the availability of detailed genotypic/phenotypic characterization, Rhodanobacter denitrificans strain 2APBS1 and Geobacter daltonii strain FRC-32 represent ideal model organisms to provide a predictive understanding of subsurface microbial activity through metabolic modeling. Tasks II and III-Diversity and distribution of active anaerobes and Mechanisms linking electron transport and the fate of radionuclides: (1) Our study showed that members of genus Rhodanobacter and Geobacter are abundant and active in the uranium and nitrate contaminated subsurface. In the contaminant source zone of the Oak Ridge site, Rhodanobacter spp. are the predominant, active organisms detected (comprising 50% to 100% of rRNA detected). (2) We demonstrated for the first time that the function of microbial communities can be quantified in subsurface sediments using messenger RNA assays (molecular proxies) under in situ conditions. (3) Active Geobacteraceae were identified and phylogenetically characterized from the cDNA of messenger RNA extracted from ORFRC subsurface sediment cores. Multiple clone sequences were retrieved from G. uraniireducens, G. daltonii, and G. metallireducens. (4) Results show that Geobacter strain FRC-32 is capable of growth on benzoate, toluene and benzene as the electron donor, thereby providing evidence that this strain is physiologically distinct from other described members of the subsurface Geobacter clade. (5) Fe(III)-reducing bacteria transform structural Fe in clay minerals from their layer edges rather than from their basal surfaces.« less

E. coli transport through surface-connected biopores identified from smoke injection tests

USDA-ARS?s Scientific Manuscript database

Macropores are the primary mechanism by which fecal bacteria from surface-applied manure can be transported into subsurface drains or shallow groundwater bypassing the soil matrix. Limited research has been performed investigating fecal bacteria transport through specific macropores identified in th...

The Active Bacterial Community in a Pristine Confined Aquifer

EPA Science Inventory

This study of the active bacteria residing in a pristine confined aquifer provides unexpected insights into the ecology of iron-reducing and sulfate-reducing bacteria in the subsurface. At 18 wells in east-central Illinois, we trapped the microbes that attached to aquifer sedimen...

Effects of legacy nuclear waste on the compositional diversity and distributions of sulfate-reducing bacteria in a terrestrial subsurface aquifer.

PubMed

Bagwell, Christopher E; Liu, Xuaduan; Wu, Liyou; Zhou, Jizhong

2006-03-01

The impact of legacy nuclear waste on the compositional diversity and distribution of sulfate-reducing bacteria in a heavily contaminated subsurface aquifer was examined. dsrAB clone libraries were constructed and restriction fragment length polymorphism (RFLP) analysis used to evaluate genetic variation between sampling wells. Principal component analysis identified nickel, nitrate, technetium, and organic carbon as the primary variables contributing to well-to-well geochemical variability, although comparative sequence analysis showed the sulfate-reducing bacteria community structure to be consistent throughout contaminated and uncontaminated regions of the aquifer. Only 3% of recovered dsrAB gene sequences showed apparent membership to the Deltaproteobacteria. The remainder of recovered sequences may represent novel, deep-branching lineages that, to our knowledge, do not presently contain any cultivated members; although corresponding phylotypes have recently been reported from several different marine ecosystems. These findings imply resiliency and adaptability of sulfate-reducing bacteria to extremes in environmental conditions, although the possibility for horizontal transfer of dsrAB is also discussed.

Effect of flow on bacterial transport and biofilm formation in saturated porous media

NASA Astrophysics Data System (ADS)

Rusconi, R.

2016-12-01

Understanding the transport of bacteria in saturated porous media is crucial for many applications ranging from the management of pumping wells subject to bio-clogging to the design of new bioremediation schemes for subsurface contamination. However, little is known about the spatial distribution of bacteria at the pore scale, particularly when small-scale heterogeneities - always present even in seemingly homogeneous aquifers - lead to preferential pathways for groundwater flow. In particular, the coupling of flow and motility has recently been shown to strongly affect bacterial transport1, and this leads us to predict that subsurface flow may strongly affect the dispersal of bacteria and the formation of biofilms in saturated aquifers. I present here microfluidic experiments combined with numerical simulations to show how the topological features of the flow correlate with bacterial concentration and promote the attachment of bacteria to specific regions of the pore network, which will ultimately influence the formations of biofilms. These results highlight the intimate link between small-scale biological processes and transport in porous media.

The Serpentinite Subsurface Microbiome

NASA Astrophysics Data System (ADS)

Schrenk, M. O.; Nelson, B. Y.; Brazelton, W. J.

2011-12-01

Microbial habitats hosted in ultramafic rocks constitute substantial, globally-distributed portions of the subsurface biosphere, occurring both on the continents and beneath the seafloor. The aqueous alteration of ultramafics, in a process known as serpentinization, creates energy rich, high pH conditions, with low concentrations of inorganic carbon which place fundamental constraints upon microbial metabolism and physiology. Despite their importance, very few studies have attempted to directly access and quantify microbial activities and distributions in the serpentinite subsurface microbiome. We have initiated microbiological studies of subsurface seeps and rocks at three separate continental sites of serpentinization in Newfoundland, Italy, and California and compared these results to previous analyses of the Lost City field, near the Mid-Atlantic Ridge. In all cases, microbial cell densities in seep fluids are extremely low, ranging from approximately 100,000 to less than 1,000 cells per milliliter. Culture-independent analyses of 16S rRNA genes revealed low-diversity microbial communities related to Gram-positive Firmicutes and hydrogen-oxidizing bacteria. Interestingly, unlike Lost City, there has been little evidence for significant archaeal populations in the continental subsurface to date. Culturing studies at the sites yielded numerous alkaliphilic isolates on nutrient-rich agar and putative iron-reducing bacteria in anaerobic incubations, many of which are related to known alkaliphilic and subsurface isolates. Finally, metagenomic data reinforce the culturing results, indicating the presence of genes associated with organotrophy, hydrogen oxidation, and iron reduction in seep fluid samples. Our data provide insight into the lifestyles of serpentinite subsurface microbial populations and targets for future quantitative exploration using both biochemical and geochemical approaches.

Phylogenetic evidence of noteworthy microflora from the subsurface of the former Homestake gold mine, Lead, South Dakota

PubMed Central

Waddell, Evan J.; Elliott, Terran J.; Sani, Rajesh K.; Vahrenkamp, Jefferey M.; Roggenthen, William M.; Anderson, Cynthia M.; Bang, Sookie S.

2013-01-01

Molecular characterization of subsurface microbial communities in the former Homestake gold mine, South Dakota, was carried out by 16S rDNA sequence analysis using a water sample and a weathered soil–like sample. Geochemical analyses indicated that both samples were high in sulfur, rich in nitrogen and salt, but with significantly different metal concentrations. Microbial diversity comparisons unexpectedly revealed three distinct operational taxonomic units (OTUs) belonging to the archaeal phylum Thaumarchaeota typically identified from marine environments, and one OTU to a potentially novel phylum that falls sister to Thaumarchaeota. To our knowledge this is only the second report of Thaumarchaeota in a terrestrial environment. The majority of the clones from Archaea sequence libraries fell into two closely related OTUs and grouped most closely to an ammonia–oxidizing, carbon–fixing and halophilic thaumarchaeote genus, Nitrosopumilus. The two samples showed neither Euryarchaeota nor Crenarchaeota members that were often identified from other subsurface terrestrial ecosystems. Bacteria OTUs containing the highest percentage of sequences were related to sulfur-oxidizing bacteria of the orders Chromatiales and Thiotrichales. Community members of Bacteria from individual Homestake ecosystems were heterogeneous and distinctive to each community with unique phylotypes identified within each sample. PMID:20662386

Chemotaxis and flow disorder shape microbial dispersion in porous media

NASA Astrophysics Data System (ADS)

De Anna, Pietro; Yawata, Yutaka; Stocker, Roman; Juanes, Ruben

2017-04-01

Bacteria drive a plethora of natural processes in the subsurface, consuming organic matter and catalysing chemical reactions that are key to global elemental cycles. These macro-scale consequences result from the collective action of individual bacteria at the micro-scale, which are modulated by the highly heterogeneous subsurface environment, dominated by flow disorder and strong chemical gradients. Yet, despite the generally recognized importance of these microscale processes, microbe-host medium interaction at the pore scale remain poorly characterized and understood. Here, we introduce a microfluidic model system to directly image and quantify the role of cell motility on bacterial dispersion and residence time in confined, porous, media. Using the soil-dwelling bacterium Bacillus subtilis and the common amino acid serine as a resource, we observe that chemotaxis in highly disordered and confined physico-chemical environment affords bacteria an increase in their ability to persistently occupy the host medium. Our findings illustrate that the interplay between bacterial behaviour and pore-scale disorder in fluid velocity and nutrient concentration directly impacts the residence time, transport and bio-geo-chemical transformation rates of biota in the subsurface, and thus likely the processes they mediate.

Active microbial biofilms in deep poor porous continental subsurface rocks.

PubMed

Escudero, Cristina; Vera, Mario; Oggerin, Monike; Amils, Ricardo

2018-01-24

Deep continental subsurface is defined as oligotrophic environments where microorganisms present a very low metabolic rate. To date, due to the energetic cost of production and maintenance of biofilms, their existence has not been considered in poor porous subsurface rocks. We applied fluorescence in situ hybridization techniques and confocal laser scanning microscopy in samples from a continental deep drilling project to analyze the prokaryotic diversity and distribution and the possible existence of biofilms. Our results show the existence of natural microbial biofilms at all checked depths of the Iberian Pyrite Belt (IPB) subsurface and the co-occurrence of bacteria and archaea in this environment. This observation suggests that multi-species biofilms may be a common and widespread lifestyle in subsurface environments.

Dynamics of reactive microbial hotspots in concentration gradients

NASA Astrophysics Data System (ADS)

Hubert, Antoine; Farasin, Julien; Tabuteau, Hervé; Méheust, Yves; Le Borgne, Tanguy

2017-04-01

In subsurface environments, bacteria play a major role in controlling the kinetics of a broad range of biogeochemical reactions. In such environments, nutrients fluxes and solute concentrations needed for bacteria metabolism may be highly variable in space and intermittent in time. This can lead to the formation of reactive hotspots where and when conditions are favorable to particular microorganisms, hence inducing biogeochemical reaction kinetics that differ significantly from those measured in homogeneous model environments. To investigate the impact of chemical gradients on the spatial structure and temporal dynamics of subsurface microorganism populations, we develop microfluidic cells allowing for a precise control of flow and chemical gradient conditions, as well as a quantitative monitoring of the bacteria's spatial distribution and biofilm development. Using the non-motile Escherichia coli JW1908-1 strain and Gallionella as model organisms, we investigate the behavior and development of bacteria over a range of single and double concentration gradients in the concentrations of nutrients, electron donors and electron acceptors. To quantify bacterial activity we use Fluorescein Diacetate (FDA) hydrolysis by bacterial enzymes which transforms FDA into Fluorescein, whose local concentration is measured optically. We thus measure bacterial activity locally from the time derivative of the measured fluorescence. This approach allows time-resolved monitoring of the location and intensity of reactive hotspots in micromodels as a function of the flow and chemical gradient conditions. We discuss consequences for the formation and temporal dynamics of biofilms in the subsurface.

Uranium Biomineralization by Natural Microbial Phosphatase Activities in the Subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sobecky, Patricia A.

2015-04-06

In this project, inter-disciplinary research activities were conducted in collaboration among investigators at The University of Alabama (UA), Georgia Institute of Technology (GT), Lawrence Berkeley National Laboratory (LBNL), Brookhaven National Laboratory (BNL), the DOE Joint Genome Institute (JGI), and the Stanford Synchrotron Radiation Light source (SSRL) to: (i) confirm that phosphatase activities of subsurface bacteria in Area 2 and 3 from the Oak Ridge Field Research Center result in solid U-phosphate precipitation in aerobic and anaerobic conditions; (ii) investigate the eventual competition between uranium biomineralization via U-phosphate precipitation and uranium bioreduction; (iii) determine subsurface microbial community structure changes of Areamore » 2 soils following organophosphate amendments; (iv) obtain the complete genome sequences of the Rahnella sp. Y9-602 and the type-strain Rahnella aquatilis ATCC 33071 isolated from these soils; (v) determine if polyphosphate accumulation and phytate hydrolysis can be used to promote U(VI) biomineralization in subsurface sediments; (vi) characterize the effect of uranium on phytate hydrolysis by a new microorganism isolated from uranium-contaminated sediments; (vii) utilize positron-emission tomography to label and track metabolically-active bacteria in soil columns, and (viii) study the stability of the uranium phosphate mineral product. Microarray analyses and mineral precipitation characterizations were conducted in collaboration with DOE SBR-funded investigators at LBNL. Thus, microbial phosphorus metabolism has been shown to have a contributing role to uranium immobilization in the subsurface.« less

Lactobacillus backii and Pediococcus damnosus isolated from 170-year-old beer recovered from a shipwreck lack the metabolic activities required to grow in modern lager beer.

PubMed

Kajala, Ilkka; Bergsveinson, Jordyn; Friesen, Vanessa; Redekop, Anna; Juvonen, Riikka; Storgårds, Erna; Ziola, Barry

2018-01-01

In 2010, bottles of beer containing viable bacteria of the common beer-spoilage species Lactobacillus backii and Pediococcus damnosus were recovered from a shipwreck near the Åland Islands, Finland. The 170-year quiescent state maintained by the shipwreck bacteria presented a unique opportunity to study lactic acid bacteria (LAB) evolution vis-a-vis growth and survival in the beer environment. Three shipwreck bacteria (one L. backii strain and two P. damnosus strains) and modern-day beer-spoilage isolates of the same two species were genome sequenced, characterized for hop iso-α-acid tolerance, and growth in degassed lager and wheat beer. In addition, plasmid variants of the modern-day P. damnosus strain were analyzed for the effect of plasmid-encoded genes on growth in lager beer. Coding content on two plasmids was identified as essential for LAB growth in modern lager beer. Three chromosomal regions containing genes related to sugar transport and cell wall polysaccharides were shared by pediococci able to grow in beer. Our results show that the three shipwreck bacteria lack the necessary plasmid-located genetic content to grow in modern lager beer, but carry additional genes related to acid tolerance and biofilm formation compared to their modern counterparts. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Genetic analysis of stress responses in soil bacteria for enhanced bioremediation of mixed contaminants. 1997 annual progress report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wong, K.K.

'To provide increased knowledge of stress responses of indigenous microbes at contaminated sites as well as using microbes as molecular probes for monitoring the performance and effectiveness of bioremediation, the authors propose to identify the stress-inducible genes and promoters from two soil bacteria, Deinococcus radiodurans and Sphingomonas F199. These organisms represent two phylogenetically distinct groups of soil bacteria, each of which has specific features of interest for bioremediation. D. radiodurans exhibits high resistance to external stress; F199 is a deep subsurface (Savannah River Site) organism with unique degradative capabilities. Research Statement To realize the full potential of bioremediation, an understandingmore » of microbial community and individual bacterial responses to the stresses encountered at contaminated sites is needed. Knowledge about genetic responses of soil and subsurface bacteria to environmental stresses, which include low nutrients, low oxygen, and mixed pollutants, will allow extrapolation of basic principles to field applications either using indigenous bacteria or genetically engineered microorganisms. Defining bacterial responses to those stresses presents an opportunity for improving bioremediation strategies, and should contribute to environmental management and restoration actions that would reduce the cost and time required to achieve DOE''s cleanup goals.'« less

Searching for an Acidic Aquifer in the Rio Tinto Basin: First Geobiology Results of MARTE Project

NASA Technical Reports Server (NTRS)

Fernandez-Remolar, D. C.; Prieto-Ballesteros, O.; Stoker, C.

2004-01-01

Among the conceivable modern habitats to be explored for searching life on Mars are those potentially developed underground. Subsurface habitats are currently environments that, under certain physicochemical circumstances, have high thermal and hydrochemical stability [1, 2]. In planets like Mars lacking an atmospheric shield, such systems are obviously protected against radiation, which strongly alters the structure of biological macromolecules. Low porosity but fractured aquifers currently emplaced inside ancient volcano/sedimentary and hydrothermal systems act as excellent habitats [3] due to its thermal and geochemical properties. In these aquifers the temperature is controlled by a thermal balance between conduction and advection processes, which are driven by the rock composition, geological structure, water turnover of aquifers and heat generation from geothermal processes or chemical reactions [4]. Moreover, microbial communities based on chemolithotrophy can obtain energy by the oxidation of metallic ores that are currently associated to these environments. Such a community core may sustain a trophic web composed of non-autotrophic forms like heterotrophic bacteria, fungi and protozoa.

Coupling Genetic and Chemical Microbiome Profiling Reveals Heterogeneity of Archaeome and Bacteriome in Subsurface Biofilms That Are Dominated by the Same Archaeal Species

PubMed Central

Holman, Hoi-Ying N.; DeSantis, Todd Z.; Wanner, Gerhard; Andersen, Gary L.; Perras, Alexandra K.; Meck, Sandra; Völkel, Jörg; Bechtel, Hans A.; Wirth, Reinhard; Moissl-Eichinger, Christine

2014-01-01

Earth harbors an enormous portion of subsurface microbial life, whose microbiome flux across geographical locations remains mainly unexplored due to difficult access to samples. Here, we investigated the microbiome relatedness of subsurface biofilms of two sulfidic springs in southeast Germany that have similar physical and chemical parameters and are fed by one deep groundwater current. Due to their unique hydrogeological setting these springs provide accessible windows to subsurface biofilms dominated by the same uncultivated archaeal species, called SM1 Euryarchaeon. Comparative analysis of infrared imaging spectra demonstrated great variations in archaeal membrane composition between biofilms of the two springs, suggesting different SM1 euryarchaeal strains of the same species at both aquifer outlets. This strain variation was supported by ultrastructural and metagenomic analyses of the archaeal biofilms, which included intergenic spacer region sequencing of the rRNA gene operon. At 16S rRNA gene level, PhyloChip G3 DNA microarray detected similar biofilm communities for archaea, but site-specific communities for bacteria. Both biofilms showed an enrichment of different deltaproteobacterial operational taxonomic units, whose families were, however, congruent as were their lipid spectra. Consequently, the function of the major proportion of the bacteriome appeared to be conserved across the geographic locations studied, which was confirmed by dsrB-directed quantitative PCR. Consequently, microbiome differences of these subsurface biofilms exist at subtle nuances for archaea (strain level variation) and at higher taxonomic levels for predominant bacteria without a substantial perturbation in bacteriome function. The results of this communication provide deep insight into the dynamics of subsurface microbial life and warrant its future investigation with regard to metabolic and genomic analyses. PMID:24971452

A hydrogen-based subsurface microbial community dominated by methanogens

USGS Publications Warehouse

Chapelle, F.H.; O'Neil, Kyle; Bradley, P.M.; Methe, B.A.; Ciufo, S.A.; Knobel, L.L.; Lovley, D.R.

2002-01-01

The search for extraterrestrial life may be facilitated if ecosystems can be found on Earth that exist under conditions analogous to those present on other planets or moons. It has been proposed, on the basis of geochemical and thermodynamic considerations, that geologically derived hydrogen might support subsurface microbial communities on Mars and Europa in which methanogens form the base of the ecosystem1-5. Here we describe a unique subsurface microbial community in which hydrogen-consuming, methane-producing Archaea far outnumber the Bacteria. More than 90% of the 16s ribosomal DNA sequences recovered from hydrothermal waters circulating through deeply buried igneous rocks in Idaho are related to hydrogen-using methanogenic microorganisms. Geochemical characterization indicates that geothermal hydrogen, not organic carbon, is the primary energy source for this methanogen-dominated microbial community. These results demonstrate that hydrogen-based methanogenic communities do occur in Earth's subsurface, providing an analogue for possible subsurface microbial ecosystems on other planets.

Depth-Related Changes in Community Structure of Culturable Mineral Weathering Bacteria and in Weathering Patterns Caused by Them along Two Contrasting Soil Profiles

PubMed Central

Huang, Jing; Xi, Jun; Huang, Zhi; Wang, Qi; Zhang, Zhen-Dong

2014-01-01

Bacteria play important roles in mineral weathering and soil formation. However, few reports of mineral weathering bacteria inhabiting subsurfaces of soil profiles have been published, raising the question of whether the subsurface weathering bacteria are fundamentally distinct from those in surface communities. To address this question, we isolated and characterized mineral weathering bacteria from two contrasting soil profiles with respect to their role in the weathering pattern evolution, their place in the community structure, and their depth-related changes in these two soil profiles. The effectiveness and pattern of bacterial mineral weathering were different in the two profiles and among the horizons within the respective profiles. The abundance of highly effective mineral weathering bacteria in the Changshu profile was significantly greater in the deepest horizon than in the upper horizons, whereas in the Yanting profile it was significantly greater in the upper horizons than in the deeper horizons. Most of the mineral weathering bacteria from the upper horizons of the Changshu profile and from the deeper horizons of the Yanting profile significantly acidified the culture media in the mineral weathering process. The proportion of siderophore-producing bacteria in the Changshu profile was similar in all horizons except in the Bg2 horizon, whereas the proportion of siderophore-producing bacteria in the Yanting profile was higher in the upper horizons than in the deeper horizons. Both profiles existed in different highly depth-specific culturable mineral weathering community structures. The depth-related changes in culturable weathering communities were primarily attributable to minor bacterial groups rather than to a change in the major population structure. PMID:24077700

Biological enhancement of hydrocarbon extraction

DOEpatents

Brigmon, Robin L [North Augusta, SC; Berry, Christopher J [Aiken, SC

2009-01-06

A method of microbial enhanced oil recovery for recovering oil from an oil-bearing rock formation is provided. The methodology uses a consortium of bacteria including a mixture of surfactant producing bacteria and non-surfactant enzyme producing bacteria which may release hydrocarbons from bitumen containing sands. The described bioprocess can work with existing petroleum recovery protocols. The consortium microorganisms are also useful for treatment of above oil sands, ground waste tailings, subsurface oil recovery, and similar materials to enhance remediation and/or recovery of additional hydrocarbons from the materials.

Community dynamics of anaerobic bacteria in deep petroleum reservoirs

NASA Astrophysics Data System (ADS)

Hallmann, Christian; Schwark, Lorenz; Grice, Kliti

2008-09-01

The nature, activity and metabolism of microbes that inhabit the deep subsurface environment are a matter of ongoing debate. Primarily limited by temperature, little is known about secondary factors that restrict or enhance microbial activity or about the extent of a habitable environment deep below the surface. In particular, the degraders of chemically inert organic substrates remain elusive. Petroleum reservoirs can be regarded as natural bioreactors and are ideally suited for the study of microbial metabolism in the deep subsurface. Here we analyse series of oil samples that were biodegraded to different degrees. We find fatty acids after hydrolysis of purified crude oil fractions, indicating the presence of intact phospholipids and suggesting that indigenous bacteria inhabit petroleum reservoirs in sediment depths of up to 2,000m. A major change in bacterial community structure occurs after the removal of n-alkanes, indicating that more than one consortium is responsible for petroleum degradation. Our results suggest that further study of petroleum fluids will help understand bacterial metabolism and diversity in this habitat of the deep subsurface.

Subsurface Biodegradation in a Fractured Basement Reservoir, Shropshire, UK

NASA Astrophysics Data System (ADS)

Parnell, John; Baba, Mas'ud; Bowden, Stephen; Muirhead, David

2017-04-01

Subsurface Biodegradation in a Fractured Basement Reservoir, Shropshire, UK. John Parnell, Mas'ud Baba, Stephen Bowden, David Muirhead Subsurface biodegradation in current oil reservoirs is well established, but there are few examples of fossil subsurface degradation. Biomarker compositions of viscous and solid oil residues ('bitumen') in fractured Precambrian and other basement rocks below the Carboniferous cover in Shropshire, UK, show that they are variably biodegraded. High levels of 25-norhopanes imply that degradation occurred in the subsurface. Lower levels of 25-norhopanes occur in active seepages. Liquid oil trapped in fluid inclusions in mineral veins in the fractured basement confirm that the oil was emplaced fresh before subsurface degradation. A Triassic age for the veins implies a 200 million year history of hydrocarbon migration in the basement rocks. The data record microbial colonization of a fractured basement reservoir, and add to evidence in modern basement aquifers for microbial activity in deep fracture systems. Buried basement highs may be especially favourable to colonization, through channelling fluid flow to shallow depths and relatively low temperatures

Reactive transport codes for subsurface environmental simulation

DOE PAGES

Steefel, C. I.; Appelo, C. A. J.; Arora, B.; ...

2014-09-26

A general description of the mathematical and numerical formulations used in modern numerical reactive transport codes relevant for subsurface environmental simulations is presented. The formulations are followed by short descriptions of commonly used and available subsurface simulators that consider continuum representations of flow, transport, and reactions in porous media. These formulations are applicable to most of the subsurface environmental benchmark problems included in this special issue. The list of codes described briefly here includes PHREEQC, HPx, PHT3D, OpenGeoSys (OGS), HYTEC, ORCHESTRA, TOUGHREACT, eSTOMP, HYDROGEOCHEM, CrunchFlow, MIN3P, and PFLOTRAN. The descriptions include a high-level list of capabilities for each of themore » codes, along with a selective list of applications that highlight their capabilities and historical development.« less

Immunological techniques as tools to characterize the subsurface microbial community at a trichloroethylene contaminated site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fliermans, C.B.; Dougherty, J.M.; Franck, M.M.

Effective in situ bioremediation strategies require an understanding of the effects pollutants and remediation techniques have on subsurface microbial communities. Therefore, detailed characterization of a site`s microbial communities is important. Subsurface sediment borings and water samples were collected from a trichloroethylene (TCE) contaminated site, before and after horizontal well in situ air stripping and bioventing, as well as during methane injection for stimulation of methane-utilizing microorganisms. Subsamples were processed for heterotrophic plate counts, acridine orange direct counts (AODC), community diversity, direct fluorescent antibodies (DFA) enumeration for several nitrogen-transforming bacteria, and Biolog {reg_sign} evaluation of enzyme activity in collected water samples.more » Plate counts were higher in near-surface depths than in the vadose zone sediment samples. During the in situ air stripping and bioventing, counts increased at or near the saturated zone, remained elevated throughout the aquifer, but did not change significantly after the air stripping. Sporadic increases in plate counts at different depths as well as increased diversity appeared to be linked to differing lithologies. AODCs were orders of magnitude higher than plate counts and remained relatively constant with depth except for slight increases near the surface depths and the capillary fringe. Nitrogen-transforming bacteria, as measured by serospecific DFA, were greatly affected both by the in situ air stripping and the methane injection. Biolog{reg_sign} activity appeared to increase with subsurface stimulation both by air and methane. The complexity of subsurface systems makes the use of selective monitoring tools imperative.« less

Aromatic-degrading Sphingomonas isolates from the deep subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fredrickson, J.K.; Romine, M.F.; Balkwill, D.L.

An obligately aerobic chemoheterotrophic bacterium (strain F199) previously isolated from Southeast Coastal Plain subsurface sediments and shown to degrade toluene, naphthalene, and other aromatic compounds was characterized by analysis of its 16S rRNA nucleotide base sequence and cellular lipid composition. Strain F199 contained 2-OH14:0 and 18:1{omega}7c as the predominant cellular fatty acids and sphingolipids that are characteristic of the genus Sphingomonas. Phylogenetic analysis of its 16SrRNA sequence indicated that F199 was most closely related to Sphingomonas capsulata among the bacteria currently in the Ribosomal Database. Five additional isolates from deep Southeast Coastal Plain sediments were determined by 16S rRNA sequencemore » analysis to be closely related to F199. These strains also contained characteristic sphingolipids. Four of these five strains could also grow on a broad range of aromatic compounds and could mineralize [{sup 14C}]toluene and [{sup 14C}]naphthalene. S. capsulata (ATCC 14666), Sphingomonas paucimobiolis (ATCC 29837), and one of the subsurface isolates were unable to grow on any of the aromatic compounds or mineralize toluene or naphthalene. These results indicate that bacteria within the genus Sphingomonas are present in Southeast Coastal Plain subsurface sediments and that the capacity for degrading a broad range of substituted aromatic compounds appears to be common among Sphingomonas species from this environment. 41 refs., 2 figs., 5 tabs.« less

The Importance of Subsurface Production for Carbon Export - Evidence from Past Oceans

NASA Astrophysics Data System (ADS)

Kemp, A. E. S.

2016-02-01

The maxim of the geological concept of uniformitarianism is "the present is the key to the past", but in the context of our temporally and spatially minimal observational record of modern ocean biogeochemical processes, ancient ocean sediments may provide critical evidence of the key species involved in carbon flux. Specifically, laminated marine sediments that preserve the seasonal flux cycle represent "palaeo-sediment traps" that vastly expand our knowledge of the operations of the marine biological carbon pump. Several key subsurface-dwelling diatom taxa, hitherto thought to be biogeochemically insignificant, are dominant components of ancient marine sediments. For example, the sapropels and equivalent horizons that have accumulated in the Mediterranean over the past 5 million years, contain abundant rhizosolenid and hemiaulid diatoms. These deposits contain the highest concentrations of organic carbon and there is extensive evidence that this was produced by subsurface production in a deep chlorophyll maximum. The highly stratified conditions that led to this subsurface production and carbon flux are in contrast to prevailing views that have held upwelling systems as those with the highest potential for export in the global ocean. Similarly, studies of ancient "greenhouse" periods such as the Cretaceous, with highly stratified oceans and which are potential analogues for future climate change, show evidence for extensive subsurface production. Together with emerging evidence from stratified regions of the modern ocean, such as the subtropical gyres, insights from these ancient oceans suggest that a reappraisal is required of current views on key phytoplankton producers and their role the operation of the marine biological carbon pump.

Isolation and Metabolic Characteristics of Previously Uncultured Members of the Order Aquificales in a Subsurface Gold Mine

PubMed Central

Takai, Ken; Hirayama, Hisako; Sakihama, Yuri; Inagaki, Fumio; Yamato, Yu; Horikoshi, Koki

2002-01-01

Culture-dependent and -independent techniques were combined to characterize the physiological properties and the ecological impacts of culture-resistant phylotypes of thermophiles within the order Aquificales from a subsurface hot aquifer of a Japanese gold mine. Thermophilic bacteria phylogenetically associated with previously uncultured phylotypes of Aquificales were successfully isolated. 16S ribosomal DNA clone analysis of the entire microbial DNA assemblage and fluorescence in situ whole-cell hybridization analysis indicated that the isolates dominated the microbial population in the subsurface aquifer. The isolates were facultatively anaerobic, hydrogen- or sulfur/thiosulfate-oxidizing, thermophilic chemolithoautotrophs utilizing molecular oxygen, nitrate, ferric iron, arsenate, selenate, and selenite as electron acceptors. Their versatile energy-generating systems may reflect the geochemical conditions of their habitat in the geothermally active subsurface gold mine. PMID:12039766

Bacterial Oxidation of Iron in Olivine: Implications for the Subsurface Biosphere, Global Chemical Cycles, and Life on Mars

NASA Astrophysics Data System (ADS)

Fisk, M. R.; Popa, R.; Smith, A. R.; Popa, R.; Boone, J.

2011-12-01

We isolated 21 species of bacteria from subseafloor and terrestrial basalt environments and which thrive on olivine at neutral pH. Cell numbers increase four to five orders of magnitude over three weeks in media where the only metabolic energy comes from the oxidation of Fe(II) in olivine. The subseafloor bacteria were isolated from a borehole on the flank of Juan de Fuca Ridge in the northeast Pacific basin where the temperature ranged from 4 up to 64 °C over four years. Terrestrial isolates originated from the basalt-ice boundary in a lava tube on the flank of Newberry Caldera in the Cascades of Oregon. The borehole water was either seawater or seawater plus subseafloor formation water and the lava tube ice was frozen meteoric or ground water. Although microorganisms capable of oxidizing iron for growth are known, microbes that oxidize iron from silicate minerals at neutral pH have not previously been cultured. The 21 species in this study are the first neutrophilic, iron-oxidizing bacteria (nFeOB) to be isolated and cultured that grow on olivine. These nFeOB are primary producers and we believe that they are a widespread component of the subsurface biosphere. In addition to their ability use iron from olivine, these microbes assimilate carbon from bicarbonate in solution and can grow when oxygen pressures are low. They also use nitrate as an alternative electron acceptor to oxygen in anaerobiosis. Since basalt is the most common rock in the Earth's crust and iron is the fourth most abundant element in the crust, we believe nFeOB are likely to be a significant portion of the subsurface biosphere. They are likely to affect, and perhaps in some environments control, the weathering rate of olivine and possibly of pyroxene and basalt glass. Olivine is a component of Mars's surface and it is present on other rocky bodies in the solar system. The ability of these bacteria to use Fe(II) from olivine, to assimilate carbon, to grow at low temperature, and to use low levels of oxygen and nitrate as oxidants would allow them to survive below the surface of Mars. These cultured organisms, which are the first known to oxidize iron from olivine at neutral pH, may be a major component of the subsurface biosphere, may affect global chemical cycles of elements in basalt, and could potentially, live in the Martian subsurface.

Chemical and microbiological water quality of subsurface agricultural drains during a field trial of liquid dairy manure effluent application rate and varying tillage practices, Upper Tiffin Watershed, southeastern Michigan

USGS Publications Warehouse

Haack, Sheridan Kidd; Duris, Joseph W.

2008-01-01

A field trial was done in the Upper Tiffin River Watershed, in southeastern Michigan, to determine the influence of liquid dairy manure effluent (LDME) management practices on the quality of agricultural subsurface-drain water. Samples from subsurface drains were analyzed for nutrients, fecal-coliform and Escherichia coli (E. coli) bacteria, antibiotics, chemicals typically detected in wastewater, and the occurrence of genes indicating the presence of shiga-toxin-producing E. coli, or of bovine-specific Bacteroidetes bacteria. Samples were collected from November 2, 2006, to March 20, 2007, from eight subsurface drains under field plots that received no LDME and no tillage (controls) or received 4,000 or 8,000 gallons per acre (gal/acre) of LDME and either no tillage or two different types of tillage. The two types of tillage tested were (1) ground-driven, rotary, subsurface cultivation and (2) rolling-tine aeration. Samples were collected before LDME application and at 4 hours, and 1, 2, 6, 7, and 14 days post-application. Nutrient concentrations were high in subsurface-drain water throughout the field-trial period and could not be attributed to the field-trial LDME application. Of the 59 drain-water samples, including those collected before LDME application and control samples for each date, 56 had concentrations greater than the U.S. Environmental Protection Agency (USEPA), Ecoregion VI recommended surface-water criterion for total phosphorus, and all samples had concentrations greater than the recommended total nitrogen criterion. Nitrate + nitrite nitrogen concentration exceeded 20 milligrams per liter for every sample and contributed most to the total nitrogen concentrations. Substantial increases in drain-water concentrations of organic and ammonia nitrogen and total phosphorus were found for all treatments, including controls, at 14 days post-application after 0.84 inch of rainfall over 2 days. E. coli concentrations exceeded the USEPA recreational-water-quality single-sample criterion of 235 colony forming units per 100 milliliters in only 3 of 56 samples. Of these three samples, two were collected within 1 day post-LDME application from the treatment receiving 8,000 gal/acre LDME with no tillage (NT8000). The third sample was from the rolling-tine aerator treatment with 4,000 gal/acre LDME application rate after the first significant rainfall. Two wastewater chemicals and two bacterial genes (eaeA and stx1) detected in the LDME, but absent in field blank or pre-application samples, were detected in the 4-hour or 1-day postapplication NT8000 samples. No LDME-associated chemicals were detected in later samples from the NT8000 treatment, and none were detected in samples from other treatments after the first significant rainfall. Results of this field trial were somewhat equivocal with respect to the influence of LDME concentration and tillage practices on subsurface-drain water quality, both immediately after LDME application and in the longer term, after significant rainfall. Interpretation of study findings is limited by the fact that treatments were not replicated, and flow rate or discharge from the subsurface drains was not measured. Nevertheless, study results provide useful information about nutrient and bacteria concentrations in subsurface drains during the non-growing season. In addition, study results demonstrate some potential for the use of chemical and microbiological indicators of LDME transport to subsurface drains.

Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy.

PubMed

Brazelton, William J; Thornton, Christopher N; Hyer, Alex; Twing, Katrina I; Longino, August A; Lang, Susan Q; Lilley, Marvin D; Früh-Green, Gretchen L; Schrenk, Matthew O

2017-01-01

The production of hydrogen and methane by geochemical reactions associated with the serpentinization of ultramafic rocks can potentially support subsurface microbial ecosystems independent of the photosynthetic biosphere. Methanogenic and methanotrophic microorganisms are abundant in marine hydrothermal systems heavily influenced by serpentinization, but evidence for methane-cycling archaea and bacteria in continental serpentinite springs has been limited. This report provides metagenomic and experimental evidence for active methanogenesis and methanotrophy by microbial communities in serpentinite springs of the Voltri Massif, Italy. Methanogens belonging to family Methanobacteriaceae and methanotrophic bacteria belonging to family Methylococcaceae were heavily enriched in three ultrabasic springs (pH 12). Metagenomic data also suggest the potential for hydrogen oxidation, hydrogen production, carbon fixation, fermentation, and organic acid metabolism in the ultrabasic springs. The predicted metabolic capabilities are consistent with an active subsurface ecosystem supported by energy and carbon liberated by geochemical reactions within the serpentinite rocks of the Voltri Massif.

Potential for hydrogen-oxidizing chemolithoautotrophic and diazotrophic populations to initiate biofilm formation in oligotrophic, deep terrestrial subsurface waters.

PubMed

Wu, Xiaofen; Pedersen, Karsten; Edlund, Johanna; Eriksson, Lena; Åström, Mats; Andersson, Anders F; Bertilsson, Stefan; Dopson, Mark

2017-03-23

Deep terrestrial biosphere waters are separated from the light-driven surface by the time required to percolate to the subsurface. Despite biofilms being the dominant form of microbial life in many natural environments, they have received little attention in the oligotrophic and anaerobic waters found in deep bedrock fractures. This study is the first to use community DNA sequencing to describe biofilm formation under in situ conditions in the deep terrestrial biosphere. In this study, flow cells were attached to boreholes containing either "modern marine" or "old saline" waters of different origin and degree of isolation from the light-driven surface of the earth. Using 16S rRNA gene sequencing, we showed that planktonic and attached populations were dissimilar while gene frequencies in the metagenomes suggested that hydrogen-fed, carbon dioxide- and nitrogen-fixing populations were responsible for biofilm formation across the two aquifers. Metagenome analyses further suggested that only a subset of the populations were able to attach and produce an extracellular polysaccharide matrix. Initial biofilm formation is thus likely to be mediated by a few bacterial populations which were similar to Epsilonproteobacteria, Deltaproteobacteria, Betaproteobacteria, Verrucomicrobia, and unclassified bacteria. Populations potentially capable of attaching to a surface and to produce extracellular polysaccharide matrix for attachment were identified in the terrestrial deep biosphere. Our results suggest that the biofilm populations were taxonomically distinct from the planktonic community and were enriched in populations with a chemolithoautotrophic and diazotrophic metabolism coupling hydrogen oxidation to energy conservation under oligotrophic conditions.

Holocene evolution of the North Atlantic subsurface transport

NASA Astrophysics Data System (ADS)

Repschläger, Janne; Garbe-Schönberg, Dieter; Weinelt, Mara; Schneider, Ralph

2017-04-01

Previous studies suggested that short-term freshening events in the subpolar gyre can be counterbalanced by advection of saline waters from the subtropical gyre and thus stabilize the Atlantic Meridional Overturning Circulation (AMOC). However, little is known about the inter-gyre transport pathways. Here, we infer changes in surface and subsurface transport between the subtropical and polar North Atlantic during the last 11 000 years, by combining new temperature and salinity reconstructions obtained from combined δ18O and Mg / Ca measurements on surface and subsurface dwelling foraminifera with published foraminiferal abundance data from the subtropical North Atlantic, and with salinity and temperature data from the tropical and subpolar North Atlantic. This compilation implies an overall stable subtropical warm surface water transport since 10 ka BP. In contrast, subsurface warm water transport started at about 8 ka but still with subsurface heat storage in the subtropical gyre. The full strength of intergyre exchange was probably reached only after the onset of northward transport of warm saline subsurface waters at about 7 ka BP, associated with the onset of the modern AMOC mode. A critical evaluation of different potential forcing mechanisms leads to the assumption that freshwater supply from the Laurentide Ice Sheet was the main control on subtropical to subpolar ocean transport at surface and subsurface levels.

Anaerobic consortia of fungi and sulfate reducing bacteria in deep granite fractures.

PubMed

Drake, Henrik; Ivarsson, Magnus; Bengtson, Stefan; Heim, Christine; Siljeström, Sandra; Whitehouse, Martin J; Broman, Curt; Belivanova, Veneta; Åström, Mats E

2017-07-04

The deep biosphere is one of the least understood ecosystems on Earth. Although most microbiological studies in this system have focused on prokaryotes and neglected microeukaryotes, recent discoveries have revealed existence of fossil and active fungi in marine sediments and sub-seafloor basalts, with proposed importance for the subsurface energy cycle. However, studies of fungi in deep continental crystalline rocks are surprisingly few. Consequently, the characteristics and processes of fungi and fungus-prokaryote interactions in this vast environment remain enigmatic. Here we report the first findings of partly organically preserved and partly mineralized fungi at great depth in fractured crystalline rock (-740 m). Based on environmental parameters and mineralogy the fungi are interpreted as anaerobic. Synchrotron-based techniques and stable isotope microanalysis confirm a coupling between the fungi and sulfate reducing bacteria. The cryptoendolithic fungi have significantly weathered neighboring zeolite crystals and thus have implications for storage of toxic wastes using zeolite barriers.Deep subsurface microorganisms play an important role in nutrient cycling, yet little is known about deep continental fungal communities. Here, the authors show organically preserved and partly mineralized fungi at 740 m depth, and find evidence of an anaerobic fungi and sulfate reducing bacteria consortium.

Mobile bacteria and transport of polynuclear aromatic hydrocarbons in porous media.

PubMed Central

Jenkins, M B; Lion, L W

1993-01-01

Sorption of hydrophobic pollutants such as polynuclear aromatic hydrocarbons (PAHs) to soil and aquifer materials can severely retard their mobility and the time course of their removal. Because mobile colloids may enhance the mobility of hydrophobic pollutants in porous media and indigenous bacteria are generally colloidal in size, bacterial isolates from soil and subsurface environments were tested for their ability to enhance the transport of phenanthrene, a model PAH, in aquifer sand. Batch isotherm experiments were performed to measure the ability of selected bacteria, including 14 isolates from a manufactured gas plant waste site, to sorb 14C-phenanthrene and to determine whether the presence of the suspended cells would reduce the distribution coefficient (Kd) for phenanthrene with the sand. Column experiments were then used to test the mobility of isolates that reduced the Kd for phenanthrene and to test the most mobile isolate for its ability to enhance the transport of phenanthrene. All of the isolates tested passively sorbed phenanthrene, and most but not all of the isolates reduced the Kd for phenanthrene. Some, but not all, of those isolates were mobile in column experiments. The most mobile isolate significantly enhanced the transport of phenanthrene in aquifer sand, reducing its retardation coefficient by 25% at a cell concentration of approximately 5 x 10(7) ml-1. The experimental results demonstrated that mobile bacteria may enhance the transport of PAHs in the subsurface. PMID:8250555

Nitrogen loss by anaerobic ammonium oxidation in unconfined aquifer soils

NASA Astrophysics Data System (ADS)

Wang, Shanyun; Radny, Dirk; Huang, Shuangbing; Zhuang, Linjie; Zhao, Siyan; Berg, Michael; Jetten, Mike S. M.; Zhu, Guibing

2017-01-01

Anaerobic ammonium oxidation (anammox) is recognized as an important process for nitrogen cycling, yet little is known about its role in the subsurface biosphere. In this study, we investigated the presence, abundance, and role of anammox bacteria in upland soil cores from Tianjin, China (20 m depth) and Basel, Switzerland (10 m depth), using isotope-tracing techniques, (q)PCR assays, and 16 S rRNA & hzsB gene clone libraries, along with nutrient profiles of soil core samples. Anammox in the phreatic (water-saturated) zone contributed to 37.5-67.6% of the N-loss (up to 0.675 gN m-2 d-1), with anammox activities of 0.005-0.74 nmolN g-1 soil h-1, which were even higher than the denitrification rates. By contrast, no significant anammox was measured in the vadose zone. Higher anammox bacterial cell densities were observed (0.75-1.4 × 107 copies g-1 soil) in the phreatic zone, where ammonia-oxidizing bacteria (AOB) maybe the major source of nitrite for anammox bacteria. The anammox bacterial cells in soils of the vadose zone were all <103 copies g-1 soil. We suggest that the subsurface provides a favorable niche for anammox bacteria whose contribution to N cycling and groundwater nitrate removal seems considerably larger than previously known.

Nitrogen loss by anaerobic ammonium oxidation in unconfined aquifer soils

PubMed Central

Wang, Shanyun; Radny, Dirk; Huang, Shuangbing; Zhuang, Linjie; Zhao, Siyan; Berg, Michael; Jetten, Mike S. M.; Zhu, Guibing

2017-01-01

Anaerobic ammonium oxidation (anammox) is recognized as an important process for nitrogen cycling, yet little is known about its role in the subsurface biosphere. In this study, we investigated the presence, abundance, and role of anammox bacteria in upland soil cores from Tianjin, China (20 m depth) and Basel, Switzerland (10 m depth), using isotope-tracing techniques, (q)PCR assays, and 16 S rRNA & hzsB gene clone libraries, along with nutrient profiles of soil core samples. Anammox in the phreatic (water-saturated) zone contributed to 37.5–67.6% of the N-loss (up to 0.675 gN m−2 d−1), with anammox activities of 0.005–0.74 nmolN g−1 soil h−1, which were even higher than the denitrification rates. By contrast, no significant anammox was measured in the vadose zone. Higher anammox bacterial cell densities were observed (0.75–1.4 × 107 copies g−1 soil) in the phreatic zone, where ammonia-oxidizing bacteria (AOB) maybe the major source of nitrite for anammox bacteria. The anammox bacterial cells in soils of the vadose zone were all <103 copies g−1 soil. We suggest that the subsurface provides a favorable niche for anammox bacteria whose contribution to N cycling and groundwater nitrate removal seems considerably larger than previously known. PMID:28071702

Isolation and characterization of metal-reducing thermoanaerobacter strains from deep subsurface environments of the Piceance Basin, Colorado.

PubMed

Roh, Yul; Liu, Shi V; Li, Guangshan; Huang, Heshu; Phelps, Tommy J; Zhou, Jizhong

2002-12-01

Five bacterial strains were isolated from anaerobic enrichment cultures that had originated from inoculations with samples collected from the deep subsurface environments of the millions-of-years-old, geologically and hydrologically isolated Piceance Basin in Colorado. Small-subunit rRNA gene-based analyses indicated that all of these bacteria were closely related to Thermoanaerobacter ethanolicus, with similarities of 99.4 to 99.5%. Three isolates (X513, X514, and X561) from the five bacterial strains were used to examine physiological characteristics. These thermophilic bacteria were able to use acetate, glucose, hydrogen, lactate, pyruvate, succinate, and xylose as electron donors while reducing Fe(III), cobalt(III), chromium(VI), manganese(IV), and uranium(VI) at 60 degrees C. One of the isolates (X514) was also able to utilize hydrogen as an electron donor for Fe(III) reduction. These bacteria exhibited diverse mineral precipitation capabilities, including the formation of magnetite (Fe(3)O(4)), siderite (FeCO(3)), rhodochrosite (MnCO(3)), and uraninite (UO(2)). The gas composition of the incubation headspace and the ionic composition of the incubation medium exerted profound influences on the types of minerals formed. The susceptibility of the thermophilic Fe(III)-reducing cultures to metabolic inhibitors specific for ferric reductase, hydrogenase, and electron transport indicated that iron reduction by these bacteria is an enzymatic process.

Physiological considerations in applying laboratory-determined buoyant densities to predictions of bacterial and protozoan transport in groundwater: Results of in-situ and laboratory tests

USGS Publications Warehouse

Harvey, R.W.; Metge, D.W.; Kinner, N.; Mayberry, N.

1997-01-01

Buoyant densities were determined for groundwater bacteria and microflagellates (protozoa) from a sandy aquifer (Cape Cod, MA) using two methods: (1) density-gradient centrifugation (DGC) and (2) Stoke's law approximations using sedimentation rates observed during natural-gradient injection and recovery tests. The dwarf (average cell size, 0.3 ??m), unattached bacteria inhabiting a pristine zone just beneath the water table and a majority (~80%) of the morphologically diverse community of free- living bacteria inhabiting a 5-km-long plume of organically-contaminated groundwater had DGC-determined buoyant densities <1.019 g/cm3 before culturing. In the aquifer, sinking rates for the uncultured 2-??m size class of contaminant plume bacteria were comparable to that of the bromide tracer (1.9 x 10-3 M), also suggesting a low buoyant density. Culturing groundwater bacteria resulted in larger (0.8-1.3 ??m), less neutrally- buoyant (1.043-1.081 g/cm3) cells with potential sedimentation rates up to 64-fold higher than those predicted for the uncultured populations. Although sedimentation generally could be neglected in predicting subsurface transport for the community of free-living groundwater bacteria, it appeared to be important for the cultured isolates, at least until they readapt to aquifer conditions. Culturing-induced alterations in size of the contaminant-plume microflagellates (2-3 ??m) were ameliorated by using a lower nutrient, acidic (pH 5) porous growth medium. Buoyant densities of the cultured microflagellates were low, i.e., 1.024-1.034 g/cm3 (using the DGC assay) and 1.017-1.039 g/cm3 (estimated from in-situ sedimentation rates), suggesting good potential for subsurface transport under favorable conditions.

Biodiversity of polycyclic aromatic hydrocarbon-degrading bacteria from deep sea sediments of the Middle Atlantic Ridge.

PubMed

Cui, Zhisong; Lai, Qiliang; Dong, Chunming; Shao, Zongze

2008-08-01

The bacteria involved in the biodegradation of polycyclic aromatic hydrocarbons (PAHs) in deep sea subsurface environments are largely unknown. In order to reveal their biodiversity, sediments from 2.2 m under the bottom surface at a water depth of 3542 m were sampled on the Middle Atlantic Ridge with a gravity column sampler. The sediments were promptly enriched with either crude oil or a mixture of PAHs (naphthalene, phenanthrene and pyrene) as the sole carbon source, and further enriched with the PAH mixture mentioned above in the lab. The resulting consortia were named C2CO and C2PPN respectively. Their bacterial composition was analysed with plate cultivation, PCR-DGGE and 16S rDNA library analysis. On plates, isolates belonging to Pseudoalteromonas, Halomonas, Marinobacter, Thalassospira and Tistrella dominated the culturable populations. With PCR-DGGE, five major bands closely related to Cycloclasticus, Alteromonas, Thalassospira, Alcanivorax and Rhodospirillaceae were detected in consortium C2CO, while only one major band of Cycloclasticus was detected in consortium C2PPN. In addition, the dynamics of community structure in response to aromatic substrate alterations were examined. As a result, three ribotypes of Cycloclasticus were detected by 16S rDNA library analysis, one which played a key role in phenanthrene degradation; two Alteromonas bacteria dominated the naphthalene reselected consortium. Although bacteria of the two genera grew as the main members of the communities, none of them were isolated, probably owing to their poor cultivability. These results confirm that bacteria of Cycloclasticus are important obligate PAH degraders in marine environments, and coexist with other degrading bacteria that inhabit the deep subsurface sediment of the Atlantic. This supports the view that PAH accumulation and bioattenuation occur in remote areas consistently and continuously.

Biodiversity of polycyclic aromatic hydrocarbon-degrading bacteria from deep sea sediments of the Middle Atlantic Ridge

PubMed Central

Cui, Zhisong; Lai, Qiliang; Dong, Chunming; Shao, Zongze

2008-01-01

The bacteria involved in the biodegradation of polycyclic aromatic hydrocarbons (PAHs) in deep sea subsurface environments are largely unknown. In order to reveal their biodiversity, sediments from 2.2 m under the bottom surface at a water depth of 3542 m were sampled on the Middle Atlantic Ridge with a gravity column sampler. The sediments were promptly enriched with either crude oil or a mixture of PAHs (naphthalene, phenanthrene and pyrene) as the sole carbon source, and further enriched with the PAH mixture mentioned above in the lab. The resulting consortia were named C2CO and C2PPN respectively. Their bacterial composition was analysed with plate cultivation, PCR-DGGE and 16S rDNA library analysis. On plates, isolates belonging to Pseudoalteromonas, Halomonas, Marinobacter, Thalassospira and Tistrella dominated the culturable populations. With PCR-DGGE, five major bands closely related to Cycloclasticus, Alteromonas, Thalassospira, Alcanivorax and Rhodospirillaceae were detected in consortium C2CO, while only one major band of Cycloclasticus was detected in consortium C2PPN. In addition, the dynamics of community structure in response to aromatic substrate alterations were examined. As a result, three ribotypes of Cycloclasticus were detected by 16S rDNA library analysis, one which played a key role in phenanthrene degradation; two Alteromonas bacteria dominated the naphthalene reselected consortium. Although bacteria of the two genera grew as the main members of the communities, none of them were isolated, probably owing to their poor cultivability. These results confirm that bacteria of Cycloclasticus are important obligate PAH degraders in marine environments, and coexist with other degrading bacteria that inhabit the deep subsurface sediment of the Atlantic. This supports the view that PAH accumulation and bioattenuation occur in remote areas consistently and continuously. PMID:18445026

Effect of bacteria and dissolved organics on mineral dissolution kinetics:

NASA Astrophysics Data System (ADS)

Pokrovsky, Oleg; Shirokova, Liudmila; Benezeth, Pascale; Zabelina, Svetlana

2010-05-01

Quantification of the effect of microorganisms and associated organic ligands on mineral dissolution rate is one among the last remaining challenges in modeling of water-rock interactions under earth surface and subsurface environments. This is especially true for deep underground settings within the context of CO2 capture, sequestration and storage. First, elevated CO2 pressures create numerous experimental difficulties for performing robust flow-through experiments at a given saturation state. Second, reactivity of main rock-forming minerals in abiotic systems at pCO2 >> 1 atm and circumneutral pH is still poorly constrained. And third, most of microbial habitats of the subsurface biosphere are not suitable for routine culturing in the laboratory, many of them are anaerobic and even strictly anaerobic, and many bacteria and archae cultures can live only in the consortium of microorganisms which is very hard to maintain at a controlled and stable biomass concentration. For experimental modeling of bio-mineral interactions in the laboratory, two other main conceptual challenges exist. Typical concentration of dissolved organic carbon that serves as a main nutrient for heterotrophic bacteria in underground waters rarely exceeds 3-5 mg/L. Typical concentration of DOC in nutrient media used for bacteria culturing is between 100 and 10,000 mg/L. Therefore, performing mineral-bacteria interactions in the laboratory under environmentally-sound conditions requires significant dilution of the nutrient media or the use of flow-through reactors. Concerning the effect of organic ligands and bacterial excudates on rock-forming mineral dissolution, at the present time, mostly empirical (phenomenological) approach can be used. Indeed, the pioneering studies of Stumm and co-workers have established a firm basis for modeling the catalyzing and inhibiting effects of ligands on metal oxide dissolution rate. This approach, very efficient for studying the interaction of organic and inorganic ligands with trivalent metal oxides, is based on applying multiple spectroscopic techniques allowing to reveal the chemical structure of adsorbed complexes. However, due to i) low surface area of most rock-forming minerals (carbonates, non-clay silicates), ii) difficulties of applying surface spectroscopic techniques at elevated pressures, and iii) very complex nature of bacterial exometabolites, it is not possible at the present time, to use rigorous surface complexation approach for rationalizing ligand- and bacteria-affected mineral dissolution under sub-surface CO2 storage environment. In this work, we present examples of overcoming these difficulties via concerted study of olivine, wollastonite and calcite interaction with heterotrophic bacteria and methanogenic archaes.

BACTERIAL TRANSPORT THROUGH HOMOGENEOUS SOIL

EPA Science Inventory

The transport of microorganisms in soils is of major importance for bioremediation of subsurface polluted zones and for pollution of groundwater with pathogens. A procedure for evaluating the relative mobility and recovery of bacteria in the soil matrix was developed. In the meth...

EMULSIFICATION OF HYDROCARBONS BY SUBSURFACE BACTERIA. (R825513C020)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

EMULSIFICATION OF HYDROCARBONS BY SUBSURFACE BACTERIA. (R825513C019)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Crop water productivity and irrigation management

USDA-ARS?s Scientific Manuscript database

Modern irrigation systems offer large increases in crop water productivity compared with rainfed or gravity irrigation, but require different management approaches to achieve this. Flood, sprinkler, low-energy precision application, LEPA, and subsurface drip irrigation methods vary widely in water a...

Assessment of nitrification in groundwater filters for drinking water production by qPCR and activity measurement.

PubMed

de Vet, W W J M; Kleerebezem, R; van der Wielen, P W J J; Rietveld, L C; van Loosdrecht, M C M

2011-07-01

In groundwater treatment for drinking water production, the causes of nitrification problems and the effectiveness of process optimization in rapid sand filters are often not clear. To assess both issues, the performance of a full-scale groundwater filter with nitrification problems and another filter with complete nitrification and pretreatment by subsurface aeration was monitored over nine months. Quantitative real-time polymerase chain reaction (qPCR) targeting the amoA gene of bacteria and archaea and activity measurements of ammonia oxidation were used to regularly evaluate water and filter sand samples. Results demonstrated that subsurface aeration stimulated the growth of ammonia-oxidizing prokaryotes (AOP) in the aquifer. Cell balances, using qPCR counts of AOP for each filter, showed that the inoculated AOP numbers from the aquifer were marginal compared with AOP numbers detected in the filter. Excessive washout of AOP was not observed and did not cause the nitrification problems. Ammonia-oxidizing archaea grew in both filters, but only in low numbers compared to bacteria. The cell-specific nitrification rate in the sand and backwash water samples was high for the subsurface aerated filter, but systematically much lower for the filter with nitrification problems. From this, we conclude that incomplete nitrification was caused by nutrient limitation. Copyright © 2011 Elsevier Ltd. All rights reserved.

Electrode Cultivation and Interfacial Electron Transport in Subsurface Microorganisms

NASA Astrophysics Data System (ADS)

Karbelkar, A. A.; Jangir, Y.; Reese, B. K.; Wanger, G.; Anderson, C.; El-Naggar, M.; Amend, J.

2016-12-01

Continental subsurface environments can present significant energetic challenges to the resident microorganisms. While these environments are geologically diverse, potentially allowing energy harvesting by microorganisms that catalyze redox reactions, many of the abundant electron donors and acceptors are insoluble and therefore not directly bioavailable. Microbes can use extracellular electron transfer (EET) as a metabolic strategy to interact with redox active surfaces. This process can be mimicked on electrode surfaces and hence can lead to enrichment and quantification of subsurface microorganisms A primary bioelectrochemical enrichment with different oxidizing and reducing potentials set up in a single bioreactor was applied in situ to subsurface microorganisms residing in iron oxide rich deposits in the Sanford Underground Research Facility. Secondary enrichment revealed a plethora of classified and unclassified subsurface microbiota on both oxidizing and reducing potentials. From this enrichment, we have isolated a Gram-positive Bacillus along with Gram-negative Cupriavidus and Anaerospora strains (as electrode reducers) and Comamonas (as an electrode oxidizer). The Bacillus and Comamonas isolates were subjected to a detailed electrochemical characterization in half-reactors at anodic and cathodic potentials, respectively. An increase in cathodic current upon inoculation and cyclic voltammetry measurements confirm the hypothesis that Comamonas is capable of electron uptake from electrodes. In addition, measurements of Bacillus on anodes hint towards novel mechanisms that allow EET from Gram-positive bacteria. This study suggests that electrochemical approaches are well positioned to dissect such extracellular interactions that may be prevalent in the subsurface, while using physical electrodes to emulate the microhabitats, redox and geochemical gradients, and the spatially dependent interspecies interactions encountered in the subsurface. Electrochemical characterization of isolated strains can help us establish the possible mechanisms of EET, and hence provide an insight on survival strategies of subsurface microbiota in extreme environments. Continental subsurface environments can present significant energetic challenges to the resident microorganisms. While these environments are geologically diverse, potentially allowing energy harvesting by microorganisms that catalyze redox reactions, many of the abundant electron donors and acceptors are insoluble and therefore not directly bioavailable. Microbes can use extracellular electron transfer (EET) as a metabolic strategy to interact with redox active surfaces. This process can be mimicked on electrode surfaces and hence can lead to enrichment and quantification of subsurface microorganisms A primary bioelectrochemical enrichment with different oxidizing and reducing potentials set up in a single bioreactor was applied in situ to subsurface microorganisms residing in iron oxide rich deposits in the Sanford Underground Research Facility. Secondary enrichment revealed a plethora of classified and unclassified subsurface microbiota on both oxidizing and reducing potentials. From this enrichment, we have isolated a Gram-positive Bacillus along with Gram-negative Cupriavidus and Anaerospora strains (as electrode reducers) and Comamonas (as an electrode oxidizer). The Bacillus and Comamonas isolates were subjected to a detailed electrochemical characterization in half-reactors at anodic and cathodic potentials, respectively. An increase in cathodic current upon inoculation and cyclic voltammetry measurements confirm the hypothesis that Comamonas is capable of electron uptake from electrodes. In addition, measurements of Bacillus on anodes hint towards novel mechanisms that allow EET from Gram-positive bacteria. This study suggests that electrochemical approaches are well positioned to dissect such extracellular interactions that may be prevalent in the subsurface, while using physical electrodes to emulate the microhabitats, redox and geochemical gradients, and the spatially dependent interspecies interactions encountered in the subsurface. Electrochemical characterization of isolated strains can help us establish the possible mechanisms of EET, and hence provide an insight on survival strategies of subsurface microbiota in extreme environments.

Effects of nitrate on the stability of uranium in a bioreduced region of the subsurface.

PubMed

Wu, Wei-Min; Carley, Jack; Green, Stefan J; Luo, Jian; Kelly, Shelly D; Van Nostrand, Joy; Lowe, Kenneth; Mehlhorn, Tonia; Carroll, Sue; Boonchayanant, Benjaporn; Löfller, Frank E; Watson, David; Kemner, Kenneth M; Zhou, Jizhong; Kitanidis, Peter K; Kostka, Joel E; Jardine, Philip M; Criddle, Craig S

2010-07-01

The effects of nitrate on the stability of reduced, immobilized uranium were evaluated in field experiments at a U.S. Department of Energy site in Oak Ridge, TN. Nitrate (2.0 mM) was injected into a reduced region of the subsurface containing high levels of previously immobilized U(IV). The nitrate was reduced to nitrite, ammonium, and nitrogen gas; sulfide levels decreased; and Fe(II) levels increased then deceased. Uranium remobilization occurred concomitant with nitrite formation, suggesting nitrate-dependent, iron-accelerated oxidation of U(IV). Bromide tracer results indicated changes in subsurface flowpaths likely due to gas formation and/or precipitate. Desorption-adsorption of uranium by the iron-rich sediment impacted uranium mobilization and sequestration. After rereduction of the subsurface through ethanol additions, background groundwater containing high levels of nitrate was allowed to enter the reduced test zone. Aqueous uranium concentrations increased then decreased. Clone library analyses of sediment samples revealed the presence of denitrifying bacteria that can oxidize elemental sulfur, H(2)S, Fe(II), and U(IV) (e.g., Thiobacillus spp.), and a decrease in relative abundance of bacteria that can reduce Fe(III) and sulfate. XANES analyses of sediment samples confirmed changes in uranium oxidation state. Addition of ethanol restored reduced conditions and triggered a short-term increase in Fe(II) and aqueous uranium, likely due to reductive dissolution of Fe(III) oxides and release of sorbed U(VI). After two months of intermittent ethanol addition, sulfide levels increased, and aqueous uranium concentrations gradually decreased to <0.1 microM.

Tetracycline Resistance in the Subsurface of a Poultry Farm: Influence of Poultry Wastes

NASA Astrophysics Data System (ADS)

You, Y.; Ball, W. P.; Ward, M. J.; Hilpert, M.

2007-12-01

Concentrated animal feeding operations (CAFOs) are considered to be important man-made reservoir of antibiotic resistant bacteria. Using the electromagnetic induction (EMI) method of geophysical characterization, we measured the apparent subsurface electrical conductivity (ECa) at a CAFO site in order to assess the movement of pollutants associated with animal waste. The map of ECa and other available data suggest that (1) soil surrounding a poultry litter storage shed is contaminated by poultry waste, (2) a contamination plume in the subsurface emanates from that shed, and (3) the development of that plume is due to groundwater flow. We focused on understanding the spread of tetracycline resistance (Tc\\tiny R), because tetracycline is one of the most frequently used antibiotics in food animal production and therefore probably used at our field site. Microbiological experiments show the presence of Tc\\tiny R bacteria in the subsurface and indicate higher concentrations in the top soil than in the aquifer. Environmental DNA was extracted to identify CAFO- associated Tc\\tiny R genes and to explore a link between the presence of Tc\\tiny R and CAFO practices. A "shot-gun" cloning approach is under development to target the most prevalent Tc\\tiny R gene. This gene will be monitored in future experiments, in which we will study the transmission of Tc\\tiny R to naive E.~coli under selective pressure of Tc. Experimental results will be used to develop a mathematical/numerical model in order to describe the transmission process and to subsequently make estimates regarding the large-scale spread of antibiotic resistance.

Analysis of a PAH-degrading bacterial population in subsurface sediments on the Mid-Atlantic Ridge

NASA Astrophysics Data System (ADS)

Shao, Zongze; Cui, Zhisong; Dong, Chunming; Lai, Qiliang; Chen, Liang

2010-05-01

Little is known about the types and concentrations of polycyclic aromatic hydrocarbons (PAHs) existing in the deep-sea subsurface environment, which is believed to be cold, oligothrophic and of high static pressure. PAHs in the upper layers of the water column are unavoidably subjected to degradation while they are deposited to the sea floor and become embedded in the deep-sea sediment. In this report, a high concentration of PAHs was discovered in the sediment 2.7 m beneath the bottom surface at a water depth of 3962 m on the Mid-Atlantic Ridge (MAR). The total concentration of PAHs was 445 ng (g dry wt sediment) -1. Among the seven detected PAHs, the concentrations of phenanthrene (222 ng g -1) and fluorene (79 ng g -1) were relatively high. In addition, PAH-degrading bacteria were found within the sediments. As in a previously detected site on the MAR, in the PAH-enriched region of this site, a bacterium of the genus Cycloclasticus was found to be the predominant isolate detected by PCR-DGGE analysis. In addition, bacteria of the Halomonas, Marinobacter, Alcanivorax, Thalassospira and Maricaulis genera, were also included in the PAH-degrading community. In summary, a high concentration of PAHs was detected in the subsurface of the deep-sea sediment, and once again, the Cycloclasticus bacterium was confirmed to be a ubiquitous marine PAH degrader even in the subsurface marine environment. Considering the abundance of PAHs therein, biodegradation is thus thought to be inactive, probably because of the low temperature, limited oxygen and/or limited nutrients.

Bacterial Influences on Animal Origins

PubMed Central

Alegado, Rosanna A.; King, Nicole

2014-01-01

Animals evolved in seas teeming with bacteria, yet the influences of bacteria on animal origins are poorly understood. Comparisons among modern animals and their closest living relatives, the choanoflagellates, suggest that the first animals used flagellated collar cells to capture bacterial prey. The cell biology of prey capture, such as cell adhesion between predator and prey, involves mechanisms that may have been co-opted to mediate intercellular interactions during the evolution of animal multicellularity. Moreover, a history of bacterivory may have influenced the evolution of animal genomes by driving the evolution of genetic pathways for immunity and facilitating lateral gene transfer. Understanding the interactions between bacteria and the progenitors of animals may help to explain the myriad ways in which bacteria shape the biology of modern animals, including ourselves. PMID:25280764

Immobilization of cobalt by sulfate-reducing bacteria in subsurface sediments

USGS Publications Warehouse

Krumholz, Lee R.; Elias, Dwayne A.; Suflita, Joseph M.

2003-01-01

We investigated the impact of sulfate-reduction on immobilization of metals in subsurface aquifers. Co 2+ was used as a model for heavy metals. Factors limiting sulfate-reduction dependent Co 2+ immobilization were tested on pure cultures of sulfate-reducing bacteria, and in sediment columns from a landfill leachate contaminated aquifer. In the presence of 1 mM Co 2+ , the growth of pure cultures of sulfate-reducing bacteria was not impacted. Cultures of Desulfovibrio desulfuricans, Desulfotomaculum gibsoniae , and Desulfomicrobium hypogeia removed greater than 99.99% of the soluble Co 2+ when CoCl 2 was used with no chelators. The above cultures and Desulfoarcula baarsi removed 98-99.94% of the soluble Co(II) when the metal was complexed with the model ligand nitrilotriacetate (Co-NTA). Factors controlling the rate of sulfate-reduction based Co 2+ precipitation were investigated in sediment-cobalt mixtures. Several electron donors were tested and all but toluene accelerated soluble Co 2+ loss. Ethanol and formate showed the greatest stimulation. All complex nitrogen sources tested slowed and decreased the extent of Co 2+ removal from solution relative to formate-amended sediment incubations. A range of pH values were tested (6.35-7.81), with the more alkaline incubations exhibiting the largest precipitation of Co 2+ . The immobilization of Co 2+ in sediments was also investigated with cores to monitor the flow of Co 2+ through undisturbed sediments. An increase in the amount of Co 2+ immobilized as CoS was observed as sulfate reduction activity was stimulated in flow through columns. Both pure culture and sediment incubation data indicate that stimulation of sulfate reduction is a viable strategy in the immobilization of contaminating metals in subsurface systems.

The emission potential of different land use patterns for the occurrence of coliphages in surface water.

PubMed

Franke, Christiane; Rechenburg, Andrea; Baumanns, Susanne; Willkomm, Marlene; Christoffels, Ekkehard; Exner, Martin; Kistemann, Thomas

2009-05-01

Different land use patterns were investigated for their potential as non-point sources of coliphage emissions into surface waters. Water samples were taken regularly at five locations in the upper reaches of the river Swist, Germany. Samples of surface and subsurface run-off were taken within the same catchment area after rainfall events using a newly developed device that made it possible to collect current concentrations of the effluent compounds. The water quality was examined for the occurrence of somatic coliphages and F(+)-specific RNA-bacteriophages as well as for various bacteria over the period of a hydrological year. The potential of various bacteria as indicators for the occurrence of phages was evaluated using statistical correlations. The load of coliphages varied depending on the land use type, but it did not differ as much as the bacterial parameters. River sections in intensively used areas turned out to be more contaminated than in less intensively used regions. The concentrations of phages from surface and subsurface run-off in most samples were quite low for all land use types and did not show conspicuous variations of surface and subsurface run-off within one land use type. Therefore, high concentrations of phages in river water cannot be explained only by non-point effluent from open ground. Following consideration of the statistical results, conventional indicator bacteria seem not to be reliable indicator organisms for coliphages and subsequently for human pathogen viruses. The detected concentrations of coliphages in several water samples of river sections surrounded by intensively used areas underpin an existing health risk in the use of river water for e.g. recreational activities or irrigation.

[Community Characteristics of ANAMMOX Bacteria in Subsurface Flow Constructed Wetland (SSFCW) for Processing of Aquaculture Waster Water].

PubMed

Zeng, Xian-lei; Liu, Xing-guo; Wu, Zong-fan; Shi, Xu; Lu, Shi-min

2016-02-15

Anaerobic ammonium oxidation (ANAMMOX) is one of the important functions in waste water treatment by subsurface flow constructed wetland (SSFCW), however, there are few studies on ANAMMOX in SSFCW environment at present. The community characteristics of ANAMMOX in the SSFCW of processing aquaculture waste water were explored in this study. In order to analyze the structure, diversity and abundance of ANAMMOX bacteria, several 16S rRNA clone libraries were constructed and real-time PCR targeting specific 16S rRNA genes together with diversity analysis was adopted. The obtained results showed that the SSFCW identified a total of three unknown clusters and two known clusters including Candidatus brocadia and Candidatus kuenenia. The dominant cluster was Candidatus brocadia. The highest diversity levels of ANAMMOX bacteria occurred in autumn (H', 1.21), while the lowest in spring (H', 0.64). The abundance of ANAMMOX bacteria in SSFCW environment ranged from 8.0 x 10(4) to 9.4 x 10(6) copies x g(-1) of fresh weight and the copy number of total bacterial 16S rRNA genes ranged from 7.3 x 10(9) to 9.1 x 10(10) copies x g(-1) of fresh weight during culture cycle. There were significant differences in the ANAMMOX bacteria abundances of different stratum and seasons in SSFCW environment, but the differences in total bacterial abundances were not obvious. In addition, the differences in ANAMMOX bacteria abundances in different stratum and seasons in SSFCW environment were irregular in different culture cycle. According to the distribution characteristics of ANAMMOX bacteria in the wetland, the denitrification effect of SSFCW could be improved by changing the supplying manners of aquaculture wastewater and adjusting the structure of wetland. The research results will provide reference for further optimizing the SSFCW and improving the efficiency of purification.

Genome Sequences for Six Rhodanobacter Strains, Isolated from Soils and the Terrestrial Subsurface, with Variable Denitrification Capabilities

PubMed Central

Green, Stefan J.; Rishishwar, Lavanya; Prakash, Om; Katz, Lee S.; Mariño-Ramírez, Leonardo; Jordan, I. King; Munk, Christine; Ivanova, Natalia; Mikhailova, Natalia; Watson, David B.; Brown, Steven D.; Palumbo, Anthony V.; Brooks, Scott C.

2012-01-01

We report the first genome sequences for six strains of Rhodanobacter species isolated from a variety of soil and subsurface environments. Three of these strains are capable of complete denitrification and three others are not. However, all six strains contain most of the genes required for the respiration of nitrate to gaseous nitrogen. The nondenitrifying members of the genus lack only the gene for nitrate reduction, the first step in the full denitrification pathway. The data suggest that the environmental role of bacteria from the genus Rhodanobacter should be reevaluated. PMID:22843592

Estimating growth rates of uncultivated clades of archaea and bacteria in marine sediments

NASA Astrophysics Data System (ADS)

Lloyd, K. G.

2016-12-01

The vast majority of microbes present in marine sediments have never been cultivated in laboratory conditions. It is therefore difficult to estimate the growth rates of these organisms in situ. Quantitative PCR (qPCR) and 16S rRNA gene libraries from sediments below 10 cm show very little change in abundance of these organisms with depth or with redox conditions. Therefore, we hypothesized that uncultivated clades of bacteria and archaea that are ubiquitous in marine sediments, actually grow in the upper 10 cm of marine sediments. We collected sediment cores from the White Oak River estuary, sectioned them in 1 cm intervals, and examined the changes in abundance of uncultivated microbes with depth using 16S rRNA gene libraries and qPCR. We found that some of the key clades associated with the deep subsurface microbiome, such as Bathyarchaeota and MBG-D, increase in abundance with depth, demonstrating extremely slow growth in these shallow subsurface sediments.

Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy

PubMed Central

Thornton, Christopher N.; Hyer, Alex; Twing, Katrina I.; Longino, August A.; Lang, Susan Q.; Lilley, Marvin D.; Früh-Green, Gretchen L.; Schrenk, Matthew O.

2017-01-01

The production of hydrogen and methane by geochemical reactions associated with the serpentinization of ultramafic rocks can potentially support subsurface microbial ecosystems independent of the photosynthetic biosphere. Methanogenic and methanotrophic microorganisms are abundant in marine hydrothermal systems heavily influenced by serpentinization, but evidence for methane-cycling archaea and bacteria in continental serpentinite springs has been limited. This report provides metagenomic and experimental evidence for active methanogenesis and methanotrophy by microbial communities in serpentinite springs of the Voltri Massif, Italy. Methanogens belonging to family Methanobacteriaceae and methanotrophic bacteria belonging to family Methylococcaceae were heavily enriched in three ultrabasic springs (pH 12). Metagenomic data also suggest the potential for hydrogen oxidation, hydrogen production, carbon fixation, fermentation, and organic acid metabolism in the ultrabasic springs. The predicted metabolic capabilities are consistent with an active subsurface ecosystem supported by energy and carbon liberated by geochemical reactions within the serpentinite rocks of the Voltri Massif. PMID:28149702

Microcosm studies of subsurface PAH-degrading bacteria from a former manufactured gas plant

NASA Astrophysics Data System (ADS)

Durant, Neal D.; Wilson, Liza P.; Bouwer, Edward J.

1995-01-01

A study was conducted to evaluate the potential for natural in situ biodegradation of polycyclic aromatic hydrocarbons (PAH's) in the subsurface at the site of a former manufactured gas plant. Fifty-seven samples of unconsolidated subsurface sediments were aseptically obtained from five boreholes across the site. Bacteria capable of aerobically degrading PAH's without an acclimation period were detected throughout shallow (2.7 m) and deep (24.7 m) areas of the subsurface in both relatively clean (<20 μg L -1 naphthalene) and contaminated (4400 μg L -1 naphthalene) zones. Significant ( p < 0.05) quantities of naphthalene (8±3% to 43±7%) and/or phenanthrene (3±1% to 31±3%) were mineralized in sediment-groundwater microcosms during 4 weeks of aerobic incubation at 22°C. Three samples out of 11 were able to aerobically mineralize significant quantities of benzene (6±2% to 24±1%). Of 11 samples tested for anaerobic mineralization, naphthalene biodegradation (7±1% to 13±2%) in the presence of N03 was observed in two samples. Compound removals were first order with respect to substrate concentration during the first 10-15 days of incubation. Compound biodegradation plateaued in the later stages of incubation (15-40 days), most likely from diminishing bioavailability and nutrient and oxygen depletion. Population densities in the sediments were typically low, with viable aerobic counts ranging from 0 to 10 5 CFU gdw -1, viable anaerobic counts ranging from 0 to 104 CFU gdw -1, and total counts (AODC) usually 10-fold greater than viable counts. Total counts exhibited a strong ( p < 0.01) positive correlation with sample grain size. Viable aerobic and anaerobic populations commonly occurred in the same sample, suggesting the presence of facultative anaerobes. Bacteria were metabolically active in samples from groundwaters with low pH (3.7) and high naphthalene concentrations (11,000 μg L -1). Data from these enumeration and microcosm studies suggest that natural in situ biodegradation is occurring at the site.

Microbial community assembly and evolution in subseafloor sediment.

PubMed

Starnawski, Piotr; Bataillon, Thomas; Ettema, Thijs J G; Jochum, Lara M; Schreiber, Lars; Chen, Xihan; Lever, Mark A; Polz, Martin F; Jørgensen, Bo B; Schramm, Andreas; Kjeldsen, Kasper U

2017-03-14

Bacterial and archaeal communities inhabiting the subsurface seabed live under strong energy limitation and have growth rates that are orders of magnitude slower than laboratory-grown cultures. It is not understood how subsurface microbial communities are assembled and whether populations undergo adaptive evolution or accumulate mutations as a result of impaired DNA repair under such energy-limited conditions. Here we use amplicon sequencing to explore changes of microbial communities during burial and isolation from the surface to the >5,000-y-old subsurface of marine sediment and identify a small core set of mostly uncultured bacteria and archaea that is present throughout the sediment column. These persisting populations constitute a small fraction of the entire community at the surface but become predominant in the subsurface. We followed patterns of genome diversity with depth in four dominant lineages of the persisting populations by mapping metagenomic sequence reads onto single-cell genomes. Nucleotide sequence diversity was uniformly low and did not change with age and depth of the sediment. Likewise, there was no detectable change in mutation rates and efficacy of selection. Our results indicate that subsurface microbial communities predominantly assemble by selective survival of taxa able to persist under extreme energy limitation.

Evaluation of positron emission tomography as a method to visualize subsurface microbial processes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kinsella K.; Schlyer D.; Kinsella, K.

2012-01-18

Positron emission tomography (PET) provides spatiotemporal monitoring in a nondestructive manner and has higher sensitivity and resolution relative to other tomographic methods. Therefore, this technology was evaluated for its application to monitor in situ subsurface bacterial activity. To date, however, it has not been used to monitor or image soil microbial processes. In this study, PET imaging was applied as a 'proof-of-principle' method to assess the feasibility of visualizing a radiotracer labeled subsurface bacterial strain (Rahnella sp. Y9602), previously isolated from uranium contaminated soils and shown to promote uranium phosphate precipitation. Soil columns packed with acid-purified simulated mineral soils weremore » seeded with 2-deoxy-2-[{sup 18}F]fluoro-d-glucose ({sup 18}FDG) labeled Rahnella sp. Y9602. The applicability of [{sup 18}F]fluoride ion as a tracer for measuring hydraulic conductivity and {sup 18}FDG as a tracer to identify subsurface metabolically active bacteria was successful in our soil column studies. Our findings indicate that positron-emitting isotopes can be utilized for studies aimed at elucidating subsurface microbiology and geochemical processes important in contaminant remediation.« less

Spatial variation in the bacterial and denitrifying bacterial community in a biofilter treating subsurface agricultural drainage.

PubMed

Andrus, J Malia; Porter, Matthew D; Rodríguez, Luis F; Kuehlhorn, Timothy; Cooke, Richard A C; Zhang, Yuanhui; Kent, Angela D; Zilles, Julie L

2014-02-01

Denitrifying biofilters can remove agricultural nitrates from subsurface drainage, reducing nitrate pollution that contributes to coastal hypoxic zones. The performance and reliability of natural and engineered systems dependent upon microbially mediated processes, such as the denitrifying biofilters, can be affected by the spatial structure of their microbial communities. Furthermore, our understanding of the relationship between microbial community composition and function is influenced by the spatial distribution of samples.In this study we characterized the spatial structure of bacterial communities in a denitrifying biofilter in central Illinois. Bacterial communities were assessed using automated ribosomal intergenic spacer analysis for bacteria and terminal restriction fragment length polymorphism of nosZ for denitrifying bacteria.Non-metric multidimensional scaling and analysis of similarity (ANOSIM) analyses indicated that bacteria showed statistically significant spatial structure by depth and transect,while denitrifying bacteria did not exhibit significant spatial structure. For determination of spatial patterns, we developed a package of automated functions for the R statistical environment that allows directional analysis of microbial community composition data using either ANOSIM or Mantel statistics.Applying this package to the biofilter data, the flow path correlation range for the bacterial community was 6.4 m at the shallower, periodically in undated depth and 10.7 m at the deeper, continually submerged depth. These spatial structures suggest a strong influence of hydrology on the microbial community composition in these denitrifying biofilters. Understanding such spatial structure can also guide optimal sample collection strategies for microbial community analyses.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wear, Jr., John Edmund

The objective of this study was to examine the hypothesis that select functional groups of bacteria from pristine sites have an innate ability to degrade synthetic aromatics that often contaminate groundwater environments,due to exposure to naturally occurring recalcitrant aromatics in their environment. This study demonstrates that subsurface microbial communities are capable of utilizing lignin and humic acid breakdown products. Utilizers of these compounds were found to be present in most all the wells tested. Even the deepest aquifer tested had utilizers present for all six of the aromatics tested. Highest counts for the aromatics tested were observed with the naturallymore » occurring breakdown products of either lignin or humic acid. Carboxylic acids were found to be an important sole carbon source for groundwater bacteria possibly explained by the fact that they are produced by the oxidative cleavage of aromatic ring structures. The carbohydrate sole carbon sources that demonstrated the greatest densities were ones commonly associated with humics. This study indicates that utilization of naturally occurring aromatic compounds in the subsurface is an important nutritional source for groundwater bacteria. In addition, it suggests that adaptation to naturally occurring recalcitrant substrates is the origin of degradative pathways for xenobiotic compounds with analogous structure. This work has important implications for in situ bioremediation as a method of environmental cleanup.« less

Enrichment of specific protozoan populations during in situ bioremediation of uranium-contaminated groundwater.

PubMed

Holmes, Dawn E; Giloteaux, Ludovic; Williams, Kenneth H; Wrighton, Kelly C; Wilkins, Michael J; Thompson, Courtney A; Roper, Thomas J; Long, Philip E; Lovley, Derek R

2013-07-01

The importance of bacteria in the anaerobic bioremediation of groundwater polluted with organic and/or metal contaminants is well recognized and in some instances so well understood that modeling of the in situ metabolic activity of the relevant subsurface microorganisms in response to changes in subsurface geochemistry is feasible. However, a potentially significant factor influencing bacterial growth and activity in the subsurface that has not been adequately addressed is protozoan predation of the microorganisms responsible for bioremediation. In field experiments at a uranium-contaminated aquifer located in Rifle, CO, USA, acetate amendments initially promoted the growth of metal-reducing Geobacter species, followed by the growth of sulfate reducers, as observed previously. Analysis of 18S rRNA gene sequences revealed a broad diversity of sequences closely related to known bacteriovorous protozoa in the groundwater before the addition of acetate. The bloom of Geobacter species was accompanied by a specific enrichment of sequences most closely related to the ameboid flagellate, Breviata anathema, which at their peak accounted for over 80% of the sequences recovered. The abundance of Geobacter species declined following the rapid emergence of B. anathema. The subsequent growth of sulfate-reducing Peptococcaceae was accompanied by another specific enrichment of protozoa, but with sequences most similar to diplomonadid flagellates from the family Hexamitidae, which accounted for up to 100% of the sequences recovered during this phase of the bioremediation. These results suggest a prey-predator response with specific protozoa responding to increased availability of preferred prey bacteria. Thus, quantifying the influence of protozoan predation on the growth, activity and composition of the subsurface bacterial community is essential for predictive modeling of in situ uranium bioremediation strategies.

Enrichment of specific protozoan populations during in situ bioremediation of uranium-contaminated groundwater

PubMed Central

Holmes, Dawn E; Giloteaux, Ludovic; Williams, Kenneth H; Wrighton, Kelly C; Wilkins, Michael J; Thompson, Courtney A; Roper, Thomas J; Long, Philip E; Lovley, Derek R

2013-01-01

The importance of bacteria in the anaerobic bioremediation of groundwater polluted with organic and/or metal contaminants is well recognized and in some instances so well understood that modeling of the in situ metabolic activity of the relevant subsurface microorganisms in response to changes in subsurface geochemistry is feasible. However, a potentially significant factor influencing bacterial growth and activity in the subsurface that has not been adequately addressed is protozoan predation of the microorganisms responsible for bioremediation. In field experiments at a uranium-contaminated aquifer located in Rifle, CO, USA, acetate amendments initially promoted the growth of metal-reducing Geobacter species, followed by the growth of sulfate reducers, as observed previously. Analysis of 18S rRNA gene sequences revealed a broad diversity of sequences closely related to known bacteriovorous protozoa in the groundwater before the addition of acetate. The bloom of Geobacter species was accompanied by a specific enrichment of sequences most closely related to the ameboid flagellate, Breviata anathema, which at their peak accounted for over 80% of the sequences recovered. The abundance of Geobacter species declined following the rapid emergence of B. anathema. The subsequent growth of sulfate-reducing Peptococcaceae was accompanied by another specific enrichment of protozoa, but with sequences most similar to diplomonadid flagellates from the family Hexamitidae, which accounted for up to 100% of the sequences recovered during this phase of the bioremediation. These results suggest a prey–predator response with specific protozoa responding to increased availability of preferred prey bacteria. Thus, quantifying the influence of protozoan predation on the growth, activity and composition of the subsurface bacterial community is essential for predictive modeling of in situ uranium bioremediation strategies. PMID:23446832

Enrichment of specific protozoan populations during in situ bioremediation of uranium-contaminated groundwater

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holmes, Dawn; Giloteaux, L.; Williams, Kenneth H.

2013-07-28

The importance of bacteria in the anaerobic bioremediation of groundwater polluted with organic and/or metal contaminants is well-recognized and in some instances so well understood that modeling of the in situ metabolic activity of the relevant subsurface microorganisms in response to changes in subsurface geochemistry is feasible. However, a potentially significant factor influencing bacterial growth and activity in the subsurface that has not been adequately addressed is protozoan predation of the microorganisms responsible for bioremediation. In field experiments at a uranium-contaminated aquifer located in Rifle, CO, acetate amendments initially promoted the growth of metal-reducing Geobacter species followed by the growthmore » of sulfate-reducers, as previously observed. Analysis of 18S rRNA gene sequences revealed a broad diversity of sequences closely related to known bacteriovorous protozoa in the groundwater prior to the addition of acetate. The bloom of Geobacter species was accompanied by a specific enrichment of sequences most closely related to the amoeboid flagellate, Breviata anathema, which at their peak accounted for over 80% of the sequences recovered. The abundance of Geobacter species declined following the rapid emergence of B. anathema. The subsequent growth of sulfate-reducing Peptococcaceae was accompanied by another specific enrichment of protozoa, but with sequences most similar to diplomonadid flagellates from the family Hexamitidae, which accounted for up to 100% of the sequences recovered during this phase of the bioremediation. These results suggest a prey-predator response with specific protozoa responding to increased availability of preferred prey bacteria. Thus, quantifying the influence of protozoan predation on the growth, activity, and composition of the subsurface bacterial community is essential for predictive modeling of in situ uranium bioremediation strategies.« less

Intensified nitrate and phosphorus removal in an electrolysis -integrated horizontal subsurface-flow constructed wetland.

PubMed

Gao, Y; Xie, Y W; Zhang, Q; Wang, A L; Yu, Y X; Yang, L Y

2017-01-01

A novel electrolysis-integrated horizontal subsurface-flow constructed wetland system (E-HFCWs) was developed for intensified removal of nitrogen and phosphorus contaminated water. The dynamics of nitrogen and phosphorus removal and that of main water qualities of inflow and outflow were also evaluated. The hydraulic retention time (HRT) greatly enhanced nitrate removal when the electrolysis current intensity was stabilized at 0.07 mA/cm 2 . When the HRT ranged from 2 h to 12 h, the removal rate of nitrate increased from 20% to 84%. Phosphorus (P) removal was also greatly enhanced-exceeding 90% when the HRT was longer than 4 h in the electrolysis-integrated HFCWs. This improved P removal is due to the in-situ formation of ferric ions by anodizing of sacrificial iron anodes, causing chemical precipitation, physical adsorption and flocculation of phosphorus. Thus, electrolysis plays an important role in nitrate and phosphorus removal. The diversity and communities of bacteria in the biofilm of substrate was established by the analysis of 16S rDNA gene sequences, and the biofilm was abundant with Comamonadaceae and Xanthomonadaceae bacteria in E-HFCWs. Test results illustrated that the electrolysis integrated with horizontal subsurface-flow constructed wetland is a feasible and effective technology for intensified nitrogen and phosphorus removal. Copyright © 2016. Published by Elsevier Ltd.

Cultivation of Hard-To-Culture Subsurface Mercury-Resistant Bacteria and Discovery of New merA Gene Sequences▿

PubMed Central

Rasmussen, L. D.; Zawadsky, C.; Binnerup, S. J.; Øregaard, G.; Sørensen, S. J.; Kroer, N.

2008-01-01

Mercury-resistant bacteria may be important players in mercury biogeochemistry. To assess the potential for mercury reduction by two subsurface microbial communities, resistant subpopulations and their merA genes were characterized by a combined molecular and cultivation-dependent approach. The cultivation method simulated natural conditions by using polycarbonate membranes as a growth support and a nonsterile soil slurry as a culture medium. Resistant bacteria were pregrown to microcolony-forming units (mCFU) before being plated on standard medium. Compared to direct plating, culturability was increased up to 2,800 times and numbers of mCFU were similar to the total number of mercury-resistant bacteria in the soils. Denaturing gradient gel electrophoresis analysis of DNA extracted from membranes suggested stimulation of growth of hard-to-culture bacteria during the preincubation. A total of 25 different 16S rRNA gene sequences were observed, including Alpha-, Beta-, and Gammaproteobacteria; Actinobacteria; Firmicutes; and Bacteroidetes. The diversity of isolates obtained by direct plating included eight different 16S rRNA gene sequences (Alpha- and Betaproteobacteria and Actinobacteria). Partial sequencing of merA of selected isolates led to the discovery of new merA sequences. With phylum-specific merA primers, PCR products were obtained for Alpha- and Betaproteobacteria and Actinobacteria but not for Bacteroidetes and Firmicutes. The similarity to known sequences ranged between 89 and 95%. One of the sequences did not result in a match in the BLAST search. The results illustrate the power of integrating advanced cultivation methodology with molecular techniques for the characterization of the diversity of mercury-resistant populations and assessing the potential for mercury reduction in contaminated environments. PMID:18441111

Analytic solutions for colloid transport with time- or depth-dependent retention in porous media

USDA-ARS?s Scientific Manuscript database

Elucidating and quantifying the transport of industrial nanoparticles (e.g. silver, carbon nanotubes, and graphene oxide) and other colloid-size particles such as viruses and bacteria is important to safeguard and manage the quality of the subsurface environment. Analytic solutions were derived for...

An explanation for differences in the process of colloid adsorption in batch and column studies

USDA-ARS?s Scientific Manuscript database

It is essential to understand the mechanisms that control virus and bacteria removal in the subsurface environment to assess the risk of groundwater contamination with fecal microorganisms. This study was conducted to explicitly provide a critical and systematic comparison between batch and column e...

Microbial oxidation and reduction of manganese: consequences in groundwater and applications.

PubMed

Gounot, A M

1994-08-01

In the natural environment, manganese is found as reduced soluble or adsorbed Mn(II) and insoluble Mn(III) and Mn(IV) oxides. Mn oxidation has been reported in various microorganisms. Several possible pathways, indirect or direct, have been proposed. A wider variety of Mn-reducing microorganisms, from highly aerobic to strictly anaerobic, has been described. The mechanisms of Mn reduction can be either an indirect process resulting from interactions with organic or inorganic compounds, or a direct enzymatic (electron-transfer) reaction. The role of microorganisms in Mn cycle is now well demonstrated by various methods in superficial natural environments, and research has been initiated on subsurface sediments. Observations in vivo (Rhône valley) and under in vitro suggested that bacterial activities are the main processes that promote manganese evolution and migration in shallow aquifers. After the building of hydroelectric dams, the stream of the Rhône was modified, giving rise to mud deposition on the bank. In the mud, bacteria are stimulated by the high organic content and consume oxygen. The redox potential drops. The manganese oxides previously formed under aerobic conditions are reduced and soluble manganese (Mn(II)) migrates into the aquifer. If the subsurface sediments are coarse-grained, the aquifer is well aerated, allowing the re-oxidation of Mn(II) by the oligotrophic attached bacteria in aquifer sediments. If the aquifer is confined, aeration is not sufficient for Mn-reoxidation. Mn(II) remains in a reduced state and migrates to the wells. Furthermore, the presence of organic matter in subsurface sediments results in the reduction of previously formed Mn oxides. Pseudo-amorphous manganese oxides, which were probably recently formed by bacteria, are more readily reduced than old crystalline manganese oxides. Although the concentrations of soluble manganese found in groundwaters are not toxic, it still is a problem since its oxidation results in darkening of water and plugging of pipes in drinking or industrial water systems. Soluble manganese can be removed from water by biological processes involving manganese-oxidizing bacteria, either in situ, or in sand filters after pumping. Various procedures are mentioned.

Tracer transport in soils and shallow groundwater: model abstraction with modern tools

USDA-ARS?s Scientific Manuscript database

Vadose zone controls contaminant transport from the surface to groundwater, and modeling transport in vadose zone has become a burgeoning field. Exceedingly complex models of subsurface contaminant transport are often inefficient. Model abstraction is the methodology for reducing the complexity of a...

Nematoda from the terrestrial deep subsurface of South Africa.

PubMed

Borgonie, G; García-Moyano, A; Litthauer, D; Bert, W; Bester, A; van Heerden, E; Möller, C; Erasmus, M; Onstott, T C

2011-06-02

Since its discovery over two decades ago, the deep subsurface biosphere has been considered to be the realm of single-cell organisms, extending over three kilometres into the Earth's crust and comprising a significant fraction of the global biosphere. The constraints of temperature, energy, dioxygen and space seemed to preclude the possibility of more-complex, multicellular organisms from surviving at these depths. Here we report species of the phylum Nematoda that have been detected in or recovered from 0.9-3.6-kilometre-deep fracture water in the deep mines of South Africa but have not been detected in the mining water. These subsurface nematodes, including a new species, Halicephalobus mephisto, tolerate high temperature, reproduce asexually and preferentially feed upon subsurface bacteria. Carbon-14 data indicate that the fracture water in which the nematodes reside is 3,000-12,000-year-old palaeometeoric water. Our data suggest that nematodes should be found in other deep hypoxic settings where temperature permits, and that they may control the microbial population density by grazing on fracture surface biofilm patches. Our results expand the known metazoan biosphere and demonstrate that deep ecosystems are more complex than previously accepted. The discovery of multicellular life in the deep subsurface of the Earth also has important implications for the search for subsurface life on other planets in our Solar System.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yee, Nathan; Barkay, Tamar; Reinfelder, John

Mercury (Hg) associated with mixed waste generated by nuclear weapons manufacturing has contaminated vast areas of the Oak Ridge Reservation (ORR). Neurotoxic methylmercury (MeHg) has been formed from the inorganic Hg wastes discharged into headwaters of East Fork Poplar Creek (EFPC). Thus, understanding the processes and mechanisms that lead to Hg methylation along the flow path of EFPC is critical to predicting the impacts of the contamination and the design of remedial action at the ORR. In part I of our project, we investigated Hg(0) oxidation and methylation by anaerobic bacteria. We discovered that the anaerobic bacterium Desulfovibrio desulfuricans ND132more » can oxidize elemental mercury [Hg(0)]. When provided with dissolved elemental mercury, D. desulfuricans ND132 converts Hg(0) to Hg(II) and neurotoxic methylmercury [MeHg]. We also demonstrated that diverse species of subsurface bacteria oxidizes dissolved elemental mercury under anoxic conditions. The obligate anaerobic bacterium Geothrix fermentans H5, and the facultative anaerobic bacteria Shewanella oneidensis MR-1 and Cupriavidus metallidurans AE104 can oxidize Hg(0) to Hg(II) under anaerobic conditions. In part II of our project, we established anaerobic enrichment cultures and obtained new bacterial strains from the DOE Oak Ridge site. We isolated three new bacterial strains from subsurface sediments collected from Oak Ridge. These isolates are Bradyrhizobium sp. strain FRC01, Clostridium sp. strain FGH, and a novel Negativicutes strain RU4. Strain RU4 is a completely new genus and species of bacteria. We also demonstrated that syntrophic interactions between fermentative bacteria and sulfate-reducing bacteria in Oak Ridge saprolite mediate iron reduction via multiple mechanisms. Finally, we tested the impact of Hg on denitrification in nitrate reducing enrichment cultures derived from subsurface sediments from the Oak Ridge site, where nitrate is a major contaminant. We showed that there is an inverse relationship between Hg concentrations and rates of denitrification in enrichment cultures. In part III of our project, we examined in more detail the effects of microbial interactions on Hg transformations. We discovered that both sulfate reducing and iron reducing bacteria coexist in freshwater sediments and both microbial groups contribute to mercury methylation. We showed that mercury methylation by sulfate reducing and iron reducing bacteria are temporally and spatially separated processes. We also discovered that methanogens can methylate mercury. We showed that Methanospirillum hungatei JF-1 methylated Hg at comparable rates, but with higher yields, than those observed for sulfate-reducing bacteria and iron-reducing bacteria. Finally, we demonstrated that syntrophic interactions between different microbial groups increase mercury methylation rates. We showed that Hg methylation rates are stimulated via inter-species hydrogen and acetate transfer (i) from sulfate-reducing bacteria to methanogens and (ii) from fermenters to the sulfate-reducing bacteria. In part IV of the project, we studied Hg bioavailability and Hg isotope fractionation. We demonstrated that thiol-bound Hg is bioavailable to mercury resistant bacteria. We found that uptake of Hg from Hg-glutathione and Hg-cysteine complexes does not require functioning glutathione and cystine/cysteine transport systems. We demonstrated that a wide range of methylmercury complexes (e.g. MeHgOH, MeHg-cysteine, and MeHg-glutathione) are bioavailable to mercury resistant bacteria. The rate of MeHg demethylation varies more between different species of mercury resistant bacteria than among MeHg complexes. We showed that microbial demethylation of MeHg depends more on the species of microorganism than on the types and relative concentrations of thiols or other MeHg ligands present. Finally, we demonstrated that Hg methylation by Geobacter sulfurreducens PCA and Desulfovibrio desulfuricans ND132 imparts mass-dependent discrimination against 202Hg relative to 198Hg. G. sulfurreducens PCA and D. desulfuricans ND132 have similar kinetic reactant/product Hg fractionation factors. Using the Hg isotope data, we showed that there are multiple intra- and/or extracellular pools provide substrate inorganic Hg for methylation.« less

Audio-magnetotelluric surveys to constrain the origin of a network of narrow synclines in Eocene limestone, Western Desert, Egypt

NASA Astrophysics Data System (ADS)

Tarabees, Elhamy A.; Tewksbury, Barbara J.; Mehrtens, Charlotte J.; Younis, Abdellatif

2017-12-01

Recent work with high resolution satellite imagery has revealed a network of narrow synclines developed during the Oligocene or Miocene over tens of thousands of square kilometers in Eocene limestone of the Thebes Group in the Western Desert of Egypt. The synclines are non-tectonic, and their scale and geometry strongly resemble sag synclines in Qatar that were produced by dissolution of subsurface evaporites and resulting sag of overlying layers. Evaporite dissolution cannot explain the Egypt synclines, because subsurface evaporites of any significance have never been reported in this part of Egypt. In this study, we use audio-magnetotelluric surveys to illuminate the subsurface under the synclines in order to constrain possible models for their formation. We suspected karst dissolution at depth, and, given a modern water table depth of over 400 m, we expected that dry fracture networks and void spaces under the synclines might result in higher electrical resistivities than surrounding coherent limestone. We also anticipated a significant change from high to low resistivity at the contact between the Thebes Group and the underlying Esna Shale at depths of 400 m or more. Instead, we found localized low resistivity zones extending from about 50-100 m below the surface to depths of more than 400 m that are strongly correlated with synclines. We suggest that these localized low resistivity zones are filled with artesian groundwater that has insufficient hydraulic head to rise to the modern topographic surface and that is localized in subsurface voids and collapse breccias produced by dissolution. Sag of overlying limestone layers is a reasonable model for syncline formation but, given the Oligocene/Miocene age of the synclines, dissolution and sag would be unrelated to young groundwater processes.

Horizontal Transfer of Tetracycline Resistance Genes in the Subsurface of a Poultry Farm

NASA Astrophysics Data System (ADS)

You, Y.; Ward, M.; Hilpert, M.

2008-12-01

Concentrated animal feeding operations (CAFOs) are considered to be important man-made reservoirs of antibiotic resistant bacteria and antibiotic resistance genes. At a poultry farm, we, together with Mr.~James Doolittle from USDA, measured the apparent subsurface electrical conductivity (ECa) using a EM38 meter. The resulting ECaR) associated with the poultry farm due to the fact that tetracycline (Tc) is one of the most frequently used antibiotics in food animal production and therefore is probably used at this farm. Soil and aquifer samples were taken from the farm. TcR bacteria were detected, with higher concentrations in the top layer of soil than in the aquifer. TcR bacteria were then enriched from a soil sample, and two classes of TcR genes were detected: tet(M) genes encoding ribosomal protection proteins and tet(L) genes encoding tet efflux pumps. Sequences of the PCR products were compared to known tet(M) and tet(L) genes in GenBank using BLASTN. Phylogenetic trees were also built based on the sequence information. The tet(M) genes found in our soil sample were highly similar to those located on transposons. In a soil microcosm experiment, we used the aforementioned soil sample as incubation medium as well as genetic donor (TcR soil bacteria), and a green fluorescent strain of E. coli as a model genetic recipient to study horizontal transfer of TcR genes from soil bacteria to naïve bacteria. Concentrations of inoculated E. coli were continuously monitored for 15 days, TcR E. coli isolated, and colony PCR performed. The tet(M) genes were found to be transferred to naïve E. coli. The highest horizontal transfer ratio, 0.62 transconjugant per recipient, was observed when Tc was supplemented to a soil microcosm at a concentration of 140 μg/kg soil. Modeling is also ongoing to obtain a better understanding of this complex phenomenon.

Kinetics of conjugative gene transfer on surfaces in granular porous media

NASA Astrophysics Data System (ADS)

Massoudieh, A.; Crain, C.; Lambertini, E.; Nelson, K. E.; Barkouki, T.; L'Amoreaux, P.; Loge, F. J.; Ginn, T. R.

2010-03-01

The transfer of genetic material among bacteria in the environment can occur both in the planktonic and attached state. Given the propensity of organisms to exist in sessile microbial communities in oligotrophic subsurface conditions, and that such conditions typify the subsurface, this study focuses on exploratory modeling of horizontal gene transfer among surface-associated Escherichiacoli in the subsurface. The mathematics so far used to describe the kinetics of conjugation in biofilms are developed largely from experimental observations of planktonic gene transfer, and are absent of lags or plasmid stability that appear experimentally. We develop a model and experimental system to quantify bacterial filtration and gene transfer in the attached state, on granular porous media. We include attachment kinetics described in Nelson et al. (2007) using the filtration theory approach of Nelson and Ginn (2001, 2005) with motility of E. coli described according to Biondi et al. (1998).

Development of Modern Performance Assessment Tools and Capabilities for Underground Disposal of Transuranic Waste at WIPP

NASA Astrophysics Data System (ADS)

Zeitler, T.; Kirchner, T. B.; Hammond, G. E.; Park, H.

2014-12-01

The Waste Isolation Pilot Plant (WIPP) has been developed by the U.S. Department of Energy (DOE) for the geologic (deep underground) disposal of transuranic (TRU) waste. Containment of TRU waste at the WIPP is regulated by the U.S. Environmental Protection Agency (EPA). The DOE demonstrates compliance with the containment requirements by means of performance assessment (PA) calculations. WIPP PA calculations estimate the probability and consequence of potential radionuclide releases from the repository to the accessible environment for a regulatory period of 10,000 years after facility closure. The long-term performance of the repository is assessed using a suite of sophisticated computational codes. In a broad modernization effort, the DOE has overseen the transfer of these codes to modern hardware and software platforms. Additionally, there is a current effort to establish new performance assessment capabilities through the further development of the PFLOTRAN software, a state-of-the-art massively parallel subsurface flow and reactive transport code. Improvements to the current computational environment will result in greater detail in the final models due to the parallelization afforded by the modern code. Parallelization will allow for relatively faster calculations, as well as a move from a two-dimensional calculation grid to a three-dimensional grid. The result of the modernization effort will be a state-of-the-art subsurface flow and transport capability that will serve WIPP PA into the future. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000. This research is funded by WIPP programs administered by the Office of Environmental Management (EM) of the U.S Department of Energy.

Conceptual Model Evaluation using Advanced Parameter Estimation Techniques with Heat as a Tracer

NASA Astrophysics Data System (ADS)

Naranjo, R. C.; Morway, E. D.; Healy, R. W.

2016-12-01

Temperature measurements made at multiple depths beneath the sediment-water interface has proven useful for estimating seepage rates from surface-water channels and corresponding subsurface flow direction. Commonly, parsimonious zonal representations of the subsurface structure are defined a priori by interpretation of temperature envelopes, slug tests or analysis of soil cores. However, combining multiple observations into a single zone may limit the inverse model solution and does not take full advantage of the information content within the measured data. Further, simulating the correct thermal gradient, flow paths, and transient behavior of solutes may be biased by inadequacies in the spatial description of subsurface hydraulic properties. The use of pilot points in PEST offers a more sophisticated approach to estimate the structure of subsurface heterogeneity. This presentation evaluates seepage estimation in a cross-sectional model of a trapezoidal canal with intermittent flow representing four typical sedimentary environments. The recent improvements in heat as a tracer measurement techniques (i.e. multi-depth temperature probe) along with use of modern calibration techniques (i.e., pilot points) provides opportunities for improved calibration of flow models, and, subsequently, improved model predictions.

Contaminated environments in the subsurface and bioremediation: organic contaminants.

PubMed

Holliger, C; Gaspard, S; Glod, G; Heijman, C; Schumacher, W; Schwarzenbach, R P; Vazquez, F

1997-07-01

Due to leakages, spills, improper disposal and accidents during transport, organic compounds have become subsurface contaminants that threaten important drinking water resources. One strategy to remediate such polluted subsurface environments is to make use of the degradative capacity of bacteria. It is often sufficient to supply the subsurface with nutrients such as nitrogen and phosphorus, and aerobic treatments are still dominating. However, anaerobic processes have advantages such as low biomass production and good electron acceptor availability, and they are sometimes the only possible solution. This review will focus on three important groups of environmental organic contaminants: hydrocarbons, chlorinated and nitroaromatic compounds. Whereas hydrocarbons are oxidized and completely mineralized under anaerobic conditions in the presence of electron acceptors such as nitrate, iron, sulfate and carbon dioxide, chlorinated and nitroaromatic compounds are reductively transformed. For the aerobic often persistent polychlorinated compounds, reductive dechlorination leads to harmless products or to compounds that are aerobically degradable. The nitroaromatic compounds are first reductively transformed to the corresponding amines and can subsequently be bound to the humic fraction in an aerobic process. Such new findings and developments give hope that in the near future contaminated aquifers can efficiently be remediated, a prerequisite for a sustainable use of the precious-subsurface drinking water resources.

Biomass measurement of methane forming bacteria in environmental samples

NASA Technical Reports Server (NTRS)

Martz, R. F.; Sebacher, D. I.; White, D. C.

1983-01-01

Methane-forming bacteria contain unusual phytanylglycerol ether phospholipids which can be extracted from the bacteria in sediments and assayed quantitatively by high performance liquid chromatography (HPLC). In this procedure the lipids were extracted, the phospholipids recovered, hydrolyzed, purified by thin layer chromatography, derivatized and assayed by HPLC. Ether lipids were recovered quantitatively from Methanobacterium thermoautotrophicum and sediments at levels as low as 8 x 10(-14) moles. In freshwater and marine sediments the flux of methane to the atmosphere and the methane levels in the pore water reflects the recovery of the phytanyl glycerol ether lipid 'signature'. The proportion of the ether phospholipid to the total recoverable phospholipid was highest in anaerobic digester sewage sludge and deeper subsurface freshwater sediment horizons.

Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids

NASA Astrophysics Data System (ADS)

Jungbluth, Sean P.; Amend, Jan P.; Rappé, Michael S.

2017-03-01

The global deep subsurface biosphere is one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the Juan de Fuca Ridge subseafloor. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs). Of the GFMs, 31 were estimated to be >90% complete, while an additional 17 were >70% complete. Phylogenomic analysis revealed 53 bacterial and 45 archaeal GFMs, of which nearly all were distantly related to known cultivated isolates. In the GFMs, abundant Bacteria included Chloroflexi, Nitrospirae, Acetothermia (OP1), EM3, Aminicenantes (OP8), Gammaproteobacteria, and Deltaproteobacteria, while abundant Archaea included Archaeoglobi, Bathyarchaeota (MCG), and Marine Benthic Group E (MBG-E). These data are the first GFMs reconstructed from the deep basaltic subseafloor biosphere, and provide a dataset available for further interrogation.

Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids.

PubMed

Jungbluth, Sean P; Amend, Jan P; Rappé, Michael S

2017-03-28

The global deep subsurface biosphere is one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the Juan de Fuca Ridge subseafloor. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs). Of the GFMs, 31 were estimated to be >90% complete, while an additional 17 were >70% complete. Phylogenomic analysis revealed 53 bacterial and 45 archaeal GFMs, of which nearly all were distantly related to known cultivated isolates. In the GFMs, abundant Bacteria included Chloroflexi, Nitrospirae, Acetothermia (OP1), EM3, Aminicenantes (OP8), Gammaproteobacteria, and Deltaproteobacteria, while abundant Archaea included Archaeoglobi, Bathyarchaeota (MCG), and Marine Benthic Group E (MBG-E). These data are the first GFMs reconstructed from the deep basaltic subseafloor biosphere, and provide a dataset available for further interrogation.

Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids

PubMed Central

Jungbluth, Sean P.; Amend, Jan P.; Rappé, Michael S.

2017-01-01

The global deep subsurface biosphere is one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the Juan de Fuca Ridge subseafloor. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs). Of the GFMs, 31 were estimated to be >90% complete, while an additional 17 were >70% complete. Phylogenomic analysis revealed 53 bacterial and 45 archaeal GFMs, of which nearly all were distantly related to known cultivated isolates. In the GFMs, abundant Bacteria included Chloroflexi, Nitrospirae, Acetothermia (OP1), EM3, Aminicenantes (OP8), Gammaproteobacteria, and Deltaproteobacteria, while abundant Archaea included Archaeoglobi, Bathyarchaeota (MCG), and Marine Benthic Group E (MBG-E). These data are the first GFMs reconstructed from the deep basaltic subseafloor biosphere, and provide a dataset available for further interrogation. PMID:28350381

Characterization of two subsurface H2-utilizing bacteria, Desulfomicrobium hypogeium sp. nov. and Acetobacterium psammolithicum sp. nov., and their ecological roles.

PubMed

Krumholz, L R; Harris, S H; Tay, S T; Suflita, J M

1999-06-01

We examined the relative roles of acetogenic and sulfate-reducing bacteria in H2 consumption in a previously characterized subsurface sandstone ecosystem. Enrichment cultures originally inoculated with ground sandstone material obtained from a Cretaceous formation in central New Mexico were grown with hydrogen in a mineral medium supplemented with 0.02% yeast extract. Sulfate reduction and acetogenesis occurred in these cultures, and the two most abundant organisms carrying out the reactions were isolated. Based on 16S rRNA analysis data and on substrate utilization patterns, these organisms were named Desulfomicrobium hypogeium sp. nov. and Acetobacterium psammolithicum sp. nov. The steady-state H2 concentrations measured in sandstone-sediment slurries (threshold concentration, 5 nM), in pure cultures of sulfate reducers (threshold concentration, 2 nM), and in pure cultures of acetogens (threshold concentrations 195 to 414 nM) suggest that sulfate reduction is the dominant terminal electron-accepting process in the ecosystem examined. In an experiment in which direct competition for H2 between D. hypogeium and A. psammolithicum was examined, sulfate reduction was the dominant process.

Subsurface Endospore-Forming Bacteria Possess Bio-Sealant Properties.

PubMed

Basha, Sreenivasulu; Lingamgunta, Lakshman Kumar; Kannali, Jayakumar; Gajula, Swarna Kumari; Bandikari, Ramesh; Dasari, Sreenivasulu; Dalavai, Veena; Chinthala, Paramageetham; Gundala, Prasada Babu; Kutagolla, Peera; Balaji, Vinodh Kumar

2018-04-24

Concrete is a strong and fairly inexpensive building substance, but has several disadvantages like cracking that allows corrosion, thus reducing its lifespan. To mitigate these complications, long-lasting microbial self-healing cement is an alternative that is eco-friendly and also actively repairs cracks. The present paper describes the detailed experimental investigation on compressive strength of cement mortars, mixed with six alkaliphilic bacteria, isolated from subsurface mica mines of high alkalinity. The experiments showed that the addition of alkaliphilic isolates at different cell concentrations (10 4 and 10 6 cells/ml) enhanced the compressive strength of cement mortar, because the rapid growth of bacteria at high alkalinity precipitates calcite crystals that lead to filling of pores and densifying the concrete mix. Thus, Bacillus subtilis (SVUNM4) showed the highest compressive strength (28.61%) of cement mortar at 10 4 cells/ml compared to those of other five alkaliphilic isolates (Brevibacillus sp., SVUNM15-22.1%; P. dendritiformis, SVUNM11-19.9%; B. methylotrophicus, SVUNM9-16%; B. licheniformis, SVUNM14-12.7% and S. maltophilia, SVUNM13-9.6%) and controlled cement mortar as well. This method resulted in the filling of cracks in concrete with calcite (CaCO 3 ), which was observed by scanning electron microscopy (SEM). Our results showed that the alkaliphilic bacterial isolates used in the study are effective in self-healing and repair of concrete cracks.

Bacterial contamination of tile drainage water and shallow groundwater under different application methods of liquid swine manure.

PubMed

Samarajeewa, A D; Glasauer, S M; Lauzon, J D; O'Halloran, I P; Parkin, Gary W; Dunfield, K E

2012-05-01

A 2 year field experiment evaluated liquid manure application methods on the movement of manure-borne pathogens (Salmonella sp.) and indicator bacteria (Escherichia coli and Clostridium perfringens) to subsurface water. A combination of application methods including surface application, pre-application tillage, and post-application incorporation were applied in a randomized complete block design on an instrumented field site in spring 2007 and 2008. Tile and shallow groundwater were sampled immediately after manure application and after rainfall events. Bacterial enumeration from water samples showed that the surface-applied manure resulted in the highest concentration of E. coli in tile drainage water. Pre-tillage significantly (p < 0.05) reduced the movement of manure-based E. coli and C. perfringens to tile water and to shallow groundwater within 3 days after manure application (DAM) in 2008 and within 10 DAM in 2007. Pre-tillage also decreased the occurrence of Salmonella sp. in tile water samples. Indicator bacteria and pathogens reached nondetectable levels within 50 DAM. The results suggest that tillage before application of liquid swine manure can minimize the movement of bacteria to tile and groundwater, but is effective only for the drainage events immediately after manure application or initial rainfall-associated drainage flows. Furthermore, the study highlights the strong association between bacterial concentrations in subsurface waters and rainfall timing and volume after manure application.

Aerobic Anoxygenic Phototrophic Bacteria in the Mid-Atlantic Bight and the North Pacific Gyre. Revised

NASA Technical Reports Server (NTRS)

Cottrell, Matthew T.; Mannino, Antonio; Kirchman, David L.

2005-01-01

The abundance of aerobic anoxygenic phototrophic (AM) bacteria, cyanobacteria and heterotrophs was examined in the Mid-Atlantic Bight and the central North Pacific gyre using infrared fluorescence microscopy coupled with image analysis and flow cytometry. AAP bacteria comprised 5% to 16% of total prokaryotes in the Atlantic but only 5% or less in the Pacific. In the Atlantic, AAP bacterial abundance was as much as 2-fold higher than Prochlorococcus and 10-folder higher than Synechococcus. In contrast, Prochlorococcus outnumbered AAP bacteria 5- to 50-fold in the Pacific. In both oceans, subsurface abundance maxima occurred within the photic zone, and AAP bacteria were least abundant below the 1% light depth. Concentrations of bacteriochlorophyll a (BChl a) were low (approx.1%) compared to chlorophyll a. Although the BChl a content of AAP bacteria per cell was typically 20- to 250-fold lower than the divinyl-chlorophyll a content of Prochlorococcus, in shelf break water the pigment content of AAP bacteria approached that of Prochlorococcus. The abundance of AAP bacteria rivaled some groups of strictly heterotrophic bacteria and was often higher than the abundance of known AAP genera (Erythrobacter and Roseobacter spp.). The distribution of AAP bacteria in the water column, which was similar in the Atlantic and the Pacific, was consistent with phototrophy.

Deep Subsurface Life from North Pond: Enrichment, Isolation, Characterization and Genomes of Heterotrophic Bacteria

PubMed Central

Russell, Joseph A.; León-Zayas, Rosa; Wrighton, Kelly; Biddle, Jennifer F.

2016-01-01

Studies of subsurface microorganisms have yielded few environmentally relevant isolates for laboratory studies. In order to address this lack of cultivated microorganisms, we initiated several enrichments on sediment and underlying basalt samples from North Pond, a sediment basin ringed by basalt outcrops underlying an oligotrophic water-column west of the Mid-Atlantic Ridge at 22°N. In contrast to anoxic enrichments, growth was observed in aerobic, heterotrophic enrichments from sediment of IODP Hole U1382B at 4 and 68 m below seafloor (mbsf). These sediment depths, respectively, correspond to the fringes of oxygen penetration from overlying seawater in the top of the sediment column and upward migration of oxygen from oxic seawater from the basalt aquifer below the sediment. Here we report the enrichment, isolation, initial characterization and genomes of three isolated aerobic heterotrophs from North Pond sediments; an Arthrobacter species from 4 mbsf, and Paracoccus and Pseudomonas species from 68 mbsf. These cultivated bacteria are represented in the amplicon 16S rRNA gene libraries created from whole sediments, albeit at low (up to 2%) relative abundance. We provide genomic evidence from our isolates demonstrating that the Arthrobacter and Pseudomonas isolates have the potential to respire nitrate and oxygen, though dissimilatory nitrate reduction could not be confirmed in laboratory cultures. The cultures from this study represent members of abundant phyla, as determined by amplicon sequencing of environmental DNA extracts, and allow for further studies into geochemical factors impacting life in the deep subsurface. PMID:27242705

Subsurface low dissolved oxygen occurred at fresh- and saline-water intersection of the Pearl River estuary during the summer period.

PubMed

Li, Gang; Liu, Jiaxing; Diao, Zenghui; Jiang, Xin; Li, Jiajun; Ke, Zhixin; Shen, Pingping; Ren, Lijuan; Huang, Liangmin; Tan, Yehui

2018-01-01

Estuarine oxygen depletion is one of the worldwide problems, which is caused by the freshwater-input-derived severe stratification and high nutrients loading. In this study we presented the horizontal and vertical distributions of dissolved oxygen (DO) in the Pearl River estuary, together with temperature, salinity, chlorophyll a concentration and heterotrophic bacteria abundance obtained from two cruises during the summer (wet) and winter (dry) periods of 2015. In surface water, the DO level in the summer period was lower and varied greater, as compared to the winter period. The DO remained unsaturated in the summer period if salinity is <12 and saturated if salinity is >12; while in the winter period it remained saturated throughout the estuary. In subsurface (>5m) water, the DO level varied from 0.71 to 6.65mgL -1 and from 6.58 to 8.20mgL -1 in the summer and winter periods, respectively. Particularly, we observed an area of ~1500km 2 low DO zone in the subsurface water with a threshold of 4mgDOL -1 during this summer period, that located at the fresh- and saline-water intersection where is characterized with severe stratification and high heterotrophic bacteria abundance. In addition, our results indicate that spatial DO variability in surface water was contributed differently by biological and physio-chemical variables in the summer and winter periods, respectively. Copyright © 2017 Elsevier Ltd. All rights reserved.

Deep Subsurface Life from North Pond: Enrichment, Isolation, Characterization and Genomes of Heterotrophic Bacteria.

PubMed

Russell, Joseph A; León-Zayas, Rosa; Wrighton, Kelly; Biddle, Jennifer F

2016-01-01

Studies of subsurface microorganisms have yielded few environmentally relevant isolates for laboratory studies. In order to address this lack of cultivated microorganisms, we initiated several enrichments on sediment and underlying basalt samples from North Pond, a sediment basin ringed by basalt outcrops underlying an oligotrophic water-column west of the Mid-Atlantic Ridge at 22°N. In contrast to anoxic enrichments, growth was observed in aerobic, heterotrophic enrichments from sediment of IODP Hole U1382B at 4 and 68 m below seafloor (mbsf). These sediment depths, respectively, correspond to the fringes of oxygen penetration from overlying seawater in the top of the sediment column and upward migration of oxygen from oxic seawater from the basalt aquifer below the sediment. Here we report the enrichment, isolation, initial characterization and genomes of three isolated aerobic heterotrophs from North Pond sediments; an Arthrobacter species from 4 mbsf, and Paracoccus and Pseudomonas species from 68 mbsf. These cultivated bacteria are represented in the amplicon 16S rRNA gene libraries created from whole sediments, albeit at low (up to 2%) relative abundance. We provide genomic evidence from our isolates demonstrating that the Arthrobacter and Pseudomonas isolates have the potential to respire nitrate and oxygen, though dissimilatory nitrate reduction could not be confirmed in laboratory cultures. The cultures from this study represent members of abundant phyla, as determined by amplicon sequencing of environmental DNA extracts, and allow for further studies into geochemical factors impacting life in the deep subsurface.

Bacterial Iron Uptake Pathways: Gates for the Import of Bactericide Compounds.

PubMed

Schalk, Isabelle J; Mislin, Gaëtan L A

2017-06-08

Bacterial resistance to most antibiotics in clinical use has reached alarming proportions. A challenge for modern medicine will be to discover new antibiotics or strategies to combat multidrug resistant bacteria, especially Gram-negative bacteria for which the situation is particularly critical. Vectorization of bactericide compounds by siderophores (iron chelators produced by bacteria) is a promising strategy able to considerably increase the efficacy of drugs. Such a Trojan horse strategy can also extend activity of specific Gram-positive antibiotics to Gram-negative bacteria.

Ecology, physiology, and phylogeny of deep subsurface Sphingomonas sp.

PubMed

Fredrickson, J K; Balkwill, D L; Romine, M F; Shi, T

1999-10-01

Several new species of the genus Sphingomonas including S. aromaticivorans, S. stygia, and S. subterranea that have the capacity for degrading a broad range of aromatic compounds including toluene, naphthalene, xylenes, p-cresol, fluorene, biphenyl, and dibenzothiophene, were isolated from deeply-buried (>200 m) sediments of the US Atlantic coastal plain (ACP). In S. aromaticivorans F199, many of the genes involved in the catabolism of these aromatic compounds are encoded on a 184-kb conjugative plasmid; some of the genes involved in aromatic catabolism are plasmid-encoded in the other strains as well. Members of the genus Sphingomonas were common among aerobic heterotrophic bacteria cultured from ACP sediments and have been detected in deep subsurface environments elsewhere. The major source of organic carbon for heterotrophic metabolism in ACP deep aquifers is lignite that originated from plant material buried with the sediments. We speculate that the ability of the subsurface Sphingomonas strains to degrade a wide array of aromatic compounds represents an adaptation for utilization of sedimentary lignite. These and related subsurface Sphingomonas spp may play an important role in the transformation of sedimentary organic carbon in the aerobic and microaerobic regions of the deep aquifers of the ACP.

Microbial Diversity Associated With Geochemical Changes in a Deep Subsurface Aquifer

NASA Astrophysics Data System (ADS)

Davidson, M. M.; Onstott, T. C.; Pratt, L. M.; Boice, E.; Southam, G.; Wanger, G.; Sherwood-Lollar, B.; Lippmann, J.; Seymoor, W.

2003-12-01

The microbial diversity of a 1.83km deep, thermophilic, fluid-filled subterranean fracture was monitored over a three and a half month period and correlated to observed changes in the geochemistry of the system. Three water samples were analyzed using 16S rDNA molecular techniques for microbial diversity, isotopic and geochemical composition. Gibbs' free energy of microbial redox reactions predicted that at in situ conditions sulfate reduction, methanogenesis and acetogenesis should be dominant metabolic pathways utilized by microbes, whereas Fe(III)-reduction should only have been favorable in the last sample. Noble gas isotopic data yielded a subsurface residence time of ˜10-100 Myr. and the non-meteoric δ D vs. δ 18O values were indicative of water-rock alteration at <100° C. δ 34S of sulfide and sulfate differed by 15‰ , consistent with fractionation by sulfate reducing bacteria. H2 concentrations declined with time, which in conjunction with the δ 34S data, suggested that hydrogenotrophic sulfate reducing bacteria dominate the community. This was compatible with 16S rDNA analysis, which yielded clones similar to Desulfotomaculum and Desulfofustis species appearing in the three 16S libraries. δ 13C and δ D values of CH4 and light hydrocarbons indicated methanogenic CH4 was mixing with abiogenically formed CH4. This is consistent with the presence of Archaeal 16S sequences similar to Methanosaeta and Methanosarcina species. The temporal increase in acetate concentration could be attributed to clone types similar to known acetogenic bacteria such as Moorella glycerini, which were present in the last sample. Clones similar to known Fe(III)-reducing bacteria such as Geovibrio species were observed in the first and last samples.

Significant contribution of Archaea to extant biomass in marine subsurface sediments.

PubMed

Lipp, Julius S; Morono, Yuki; Inagaki, Fumio; Hinrichs, Kai-Uwe

2008-08-21

Deep drilling into the marine sea floor has uncovered a vast sedimentary ecosystem of microbial cells. Extrapolation of direct counts of stained microbial cells to the total volume of habitable marine subsurface sediments suggests that between 56 Pg (ref. 1) and 303 Pg (ref. 3) of cellular carbon could be stored in this largely unexplored habitat. From recent studies using various culture-independent techniques, no clear picture has yet emerged as to whether Archaea or Bacteria are more abundant in this extensive ecosystem. Here we show that in subsurface sediments buried deeper than 1 m in a wide range of oceanographic settings at least 87% of intact polar membrane lipids, biomarkers for the presence of live cells, are attributable to archaeal membranes, suggesting that Archaea constitute a major fraction of the biomass. Results obtained from modified quantitative polymerase chain reaction and slot-blot hybridization protocols support the lipid-based evidence and indicate that these techniques have previously underestimated archaeal biomass. The lipid concentrations are proportional to those of total organic carbon. On the basis of this relationship, we derived an independent estimate of amounts of cellular carbon in the global marine subsurface biosphere. Our estimate of 90 Pg of cellular carbon is consistent, within an order of magnitude, with previous estimates, and underscores the importance of marine subsurface habitats for global biomass budgets.

In-Well Sediment Incubators to Evaluate Microbial Community Stability and Dynamics following Bioimmobilization of Uranium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baldwin, Brett R.; Peacock, Aaron D.; Gan, M.

2009-09-23

An in-situ incubation device (ISI) was developed in order to investigate the stability and dynamics of sediment associated microbial communities to prevailing subsurface oxidizing or reducing conditions. Here we describe the use of these devices at the Old Rifle Uranium Mill Tailings Remedial Action (UMTRA) site. During the 7 month deployment oxidized Rifle aquifer background sediments (RABS) were deployed in previously biostimulated wells under iron reducing conditions, cell densities of known iron reducing bacteria including Geobacteraceae increased significantly showing the microbial community response to local subsurface conditions. PLFA profiles of RABS following in situ deployment were strikingly similar to thosemore » of adjacent sediment cores suggesting ISI results could be extrapolated to the native material of the test plots. Results for ISI deployed reduced sediments showed only slight changes in community composition and pointed toward the ability of the ISIs to monitor microbial community stability and response to subsurface conditions.« less

Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations

PubMed Central

Wu, Xiaofen; Holmfeldt, Karin; Hubalek, Valerie; Lundin, Daniel; Åström, Mats; Bertilsson, Stefan; Dopson, Mark

2016-01-01

Microorganisms in the terrestrial deep biosphere host up to 20% of the earth's biomass and are suggested to be sustained by the gases hydrogen and carbon dioxide. A metagenome analysis of three deep subsurface water types of contrasting age (from <20 to several thousand years) and depth (171 to 448 m) revealed phylogenetically distinct microbial community subsets that either passed or were retained by a 0.22 μm filter. Such cells of <0.22 μm would have been overlooked in previous studies relying on membrane capture. Metagenomes from the three water types were used for reconstruction of 69 distinct microbial genomes, each with >86% coverage. The populations were dominated by Proteobacteria, Candidate divisions, unclassified archaea and unclassified bacteria. The estimated genome sizes of the <0.22 μm populations were generally smaller than their phylogenetically closest relatives, suggesting that small dimensions along with a reduced genome size may be adaptations to oligotrophy. Shallow ‘modern marine' water showed community members with a predominantly heterotrophic lifestyle. In contrast, the deeper, ‘old saline' water adhered more closely to the current paradigm of a hydrogen-driven deep biosphere. The data were finally used to create a combined metabolic model of the deep terrestrial biosphere microbial community. PMID:26484735

Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations.

PubMed

Wu, Xiaofen; Holmfeldt, Karin; Hubalek, Valerie; Lundin, Daniel; Åström, Mats; Bertilsson, Stefan; Dopson, Mark

2016-05-01

Microorganisms in the terrestrial deep biosphere host up to 20% of the earth's biomass and are suggested to be sustained by the gases hydrogen and carbon dioxide. A metagenome analysis of three deep subsurface water types of contrasting age (from <20 to several thousand years) and depth (171 to 448 m) revealed phylogenetically distinct microbial community subsets that either passed or were retained by a 0.22 μm filter. Such cells of <0.22 μm would have been overlooked in previous studies relying on membrane capture. Metagenomes from the three water types were used for reconstruction of 69 distinct microbial genomes, each with >86% coverage. The populations were dominated by Proteobacteria, Candidate divisions, unclassified archaea and unclassified bacteria. The estimated genome sizes of the <0.22 μm populations were generally smaller than their phylogenetically closest relatives, suggesting that small dimensions along with a reduced genome size may be adaptations to oligotrophy. Shallow 'modern marine' water showed community members with a predominantly heterotrophic lifestyle. In contrast, the deeper, 'old saline' water adhered more closely to the current paradigm of a hydrogen-driven deep biosphere. The data were finally used to create a combined metabolic model of the deep terrestrial biosphere microbial community.

Detoxification of sulphidic African shelf waters by blooming chemolithotrophs

NASA Astrophysics Data System (ADS)

Lavik, Gaute; Stührmann, Torben; Brüchert, Volker; van der Plas, Anja; Mohrholz, Volker; Lam, Phyllis; Mußmann, Marc; Fuchs, Bernhard M.; Amann, Rudolf; Lass, Ulrich; Kuypers, Marcel M. M.

2009-01-01

Coastal waters support ~90 per cent of global fisheries and are therefore an important food reserve for our planet. Eutrophication of these waters, due to human activity, leads to severe oxygen depletion and the episodic occurrence of hydrogen sulphide-toxic to multi-cellular life-with disastrous consequences for coastal ecosytems. Here we show that an area of ~7,000km2 of African shelf, covered by sulphidic water, was detoxified by blooming bacteria that oxidized the biologically harmful sulphide to environmentally harmless colloidal sulphur and sulphate. Combined chemical analyses, stoichiometric modelling, isotopic incubations, comparative 16S ribosomal RNA, functional gene sequence analyses and fluorescence in situ hybridization indicate that the detoxification proceeded by chemolithotrophic oxidation of sulphide with nitrate and was mainly catalysed by two discrete populations of γ- and ɛ-proteobacteria. Chemolithotrophic bacteria, accounting for ~20 per cent of the bacterioplankton in sulphidic waters, created a buffer zone between the toxic sulphidic subsurface waters and the oxic surface waters, where fish and other nekton live. This is the first time that large-scale detoxification of sulphidic waters by chemolithotrophs has been observed in an open-ocean system. The data suggest that sulphide can be completely consumed by bacteria in the subsurface waters and, thus, can be overlooked by remote sensing or monitoring of shallow coastal waters. Consequently, sulphidic bottom waters on continental shelves may be more common than previously believed, and could therefore have an important but as yet neglected effect on benthic communities.

Deep subsurface life from North Pond: Enrichment, isolation, characterization and genomes of heterotrophic bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Russell, Joseph A.; Leon-Zayas, Rosa; Wrighton, Kelly

Studies of subsurface microorganisms have yielded few environmentally relevant isolates for laboratory studies. In order to address this lack of cultivated microorganisms, we initiated several enrichments on sediment and underlying basalt samples from North Pond, a sediment basin ringed by basalt outcrops underlying an oligotrophic watercolumn west of the Mid-Atlantic Ridge at 22° N. In contrast to anoxic enrichments, growth was observed in aerobic, heterotrophic enrichments from sediment of IODP Hole U1382B at 4 and 68 m below seafloor (mbsf). These sediment depths, respectively, correspond to the fringes of oxygen penetration from overlying seawater in the top of the sedimentmore » column and upward migration of oxygen from oxic seawater from the basalt aquifer below the sediment. Here we report the enrichment, isolation, initial characterization and genomes of three isolated aerobic heterotrophs from North Pond sediments; an Arthrobacter species from 4 mbsf, and Paracoccus and Pseudomonas species from 68 mbsf. These cultivated bacteria are represented in the amplicon 16S rRNA gene libraries created from whole sediments, albeit at low (up to 2%) relative abundance. We provide genomic evidence from our isolates demonstrating that the Arthrobacter and Pseudomonas isolates have the potential to respire nitrate and oxygen, though dissimilatory nitrate reduction could not be confirmed in laboratory cultures. Furthermore, the cultures from this study represent members of abundant phyla, as determined by amplicon sequencing of environmental DNA extracts, and allow for further studies into geochemical factors impacting life in the deep subsurface.« less

Deep subsurface life from North Pond: Enrichment, isolation, characterization and genomes of heterotrophic bacteria

DOE PAGES

Russell, Joseph A.; Leon-Zayas, Rosa; Wrighton, Kelly; ...

2016-05-10

Studies of subsurface microorganisms have yielded few environmentally relevant isolates for laboratory studies. In order to address this lack of cultivated microorganisms, we initiated several enrichments on sediment and underlying basalt samples from North Pond, a sediment basin ringed by basalt outcrops underlying an oligotrophic watercolumn west of the Mid-Atlantic Ridge at 22° N. In contrast to anoxic enrichments, growth was observed in aerobic, heterotrophic enrichments from sediment of IODP Hole U1382B at 4 and 68 m below seafloor (mbsf). These sediment depths, respectively, correspond to the fringes of oxygen penetration from overlying seawater in the top of the sedimentmore » column and upward migration of oxygen from oxic seawater from the basalt aquifer below the sediment. Here we report the enrichment, isolation, initial characterization and genomes of three isolated aerobic heterotrophs from North Pond sediments; an Arthrobacter species from 4 mbsf, and Paracoccus and Pseudomonas species from 68 mbsf. These cultivated bacteria are represented in the amplicon 16S rRNA gene libraries created from whole sediments, albeit at low (up to 2%) relative abundance. We provide genomic evidence from our isolates demonstrating that the Arthrobacter and Pseudomonas isolates have the potential to respire nitrate and oxygen, though dissimilatory nitrate reduction could not be confirmed in laboratory cultures. Furthermore, the cultures from this study represent members of abundant phyla, as determined by amplicon sequencing of environmental DNA extracts, and allow for further studies into geochemical factors impacting life in the deep subsurface.« less

Detection of Survival and Proliferation of Sulfate Reducers Under Simulated Martian Atmospheric and Soil Conditions

NASA Astrophysics Data System (ADS)

Mora, Sergio Mosquera

Numerous studies have tried to determine the survivability and proliferation of microorganisms under simulated Martian conditions. Furthermore, most of them have been focused on the ability of these microbes to cope with high brines' salt (NaCl) concentrations inherent of the Martian surface. However, there are not studies related to the ability of bacteria to survive on subsurface environments that have increasing concentrations of sulfate compounds. For this research, a group of microorganisms known as sulfate-reducing bacteria or simply sulfate reducers were chosen due to their ability to use sulfate compounds as terminal electron acceptors to produce metabolic energy, their tolerance to low temperatures (psychrophilic microbes) and their anaerobic metabolism. Moreover, the principal purpose of this study was to determine the ability of sulfate reducers to carry active metabolism under conditions similar to those present on Mars subsurface (low temperature, high concentration of sulfate compounds, anoxic atmosphere-95% carbon dioxide, low nutrients availability, among others). Furthermore, we cultivated strains of Desulfotalea psychrophila, Desulfuromusa ferrireducens and Desulfotomaculum arcticum using different concentrations of minerals. The latter (CaSO 4, MgSO4, FeSO4 and Fe2(SO4) 3) are normally found as part of the Martian subsurface components and they can act as terminal electron acceptors in sulfate respiration. Moreover, PCR amplifications of the 16S rDNA gene and the dsrAB genes were performed in order to determine the growth and survivability of the three microorganisms tested. Finally, we were able to determine that they were metabolically active at the different types and mineral concentrations under study.

Roadside IED detection using subsurface imaging radar and rotary UAV

NASA Astrophysics Data System (ADS)

Qin, Yexian; Twumasi, Jones O.; Le, Viet Q.; Ren, Yu-Jiun; Lai, C. P.; Yu, Tzuyang

2016-05-01

Modern improvised explosive device (IED) and mine detection sensors using microwave technology are based on ground penetrating radar operated by a ground vehicle. Vehicle size, road conditions, and obstacles along the troop marching direction limit operation of such sensors. This paper presents a new conceptual design using a rotary unmanned aerial vehicle (UAV) to carry subsurface imaging radar for roadside IED detection. We have built a UAV flight simulator with the subsurface imaging radar running in a laboratory environment and tested it with non-metallic and metallic IED-like targets. From the initial lab results, we can detect the IED-like target 10-cm below road surface while carried by a UAV platform. One of the challenges is to design the radar and antenna system for a very small payload (less than 3 lb). The motion compensation algorithm is also critical to the imaging quality. In this paper, we also demonstrated the algorithm simulation and experimental imaging results with different IED target materials, sizes, and clutters.

Mercury distribution in ancient and modern sediments of northeastern Bering Sea

USGS Publications Warehouse

Nelson, C. Hans; Pierce, D.E.; Leong, K.W.; Wang, F.F.

1972-01-01

A reconnaissance of surface and subsurface sediments to a maximum depth of 244 feet below the sea floor shows that natural mercury anomalies from 0.2 to 1.3 ppm have been present in northeastern Bering Sea since early Pliocene. The anomalies and mean values are highest in modern beach (maximum 1.3 and mean 0.22 ppm Hg) and nearshore subsurface gravels (maximum 0.6 and mean .06 ppm Hg) along the highly mineralized Seward Peninsula and in organic rich silt (maximum 0.16 and mean 0.10 ppm Hg) throughout the region; the mean values are lowest in offshore sands (0.03 ppm Hg) . Although gold mining may be partially responsible for high mercury levels in the beaches near Nome, Alaska, equally high or greater concentrations of mercury occur in ancient glacial sediments immediately offshore (0.6 ppm) and in modern unpolluted beach sediments at Bluff (0.45 - 1.3 ppm); this indicates that the contamination effects of mining may be no greater than natural concentration processes in the Seward Peninsula region. The background content of mercury (0.03) throughout the central area of northeastern Bering Sea is similar to that elsewhere in the world. The low mean values (0.04 ppm) even immediately offshore from mercury-rich beaches, suggests that in the surface sediments of northeastern Bering Sea, the highest concentrations are limited to the beaches near mercury sources; occasionally, however, low mercury anomalies occur offshore in glacial drift derived from mercury source regions of Chukotka and Seward Peninsula and reworked by Pleistocene shoreline processes. The minimal values offshore may be attributable to beach entrapment of heavy minerals containing mercury and/or dilution effects of modern sedimentation.

Biogeochemistry of microbial coal-bed methane

USGS Publications Warehouse

Strc, D.; Mastalerz, Maria; Dawson, K.; MacAlady, J.; Callaghan, A.V.; Wawrik, B.; Turich, C.; Ashby, M.

2011-01-01

Microbial methane accumulations have been discovered in multiple coal-bearing basins over the past two decades. Such discoveries were originally based on unique biogenic signatures in the stable isotopic composition of methane and carbon dioxide. Basins with microbial methane contain either low-maturity coals with predominantly microbial methane gas or uplifted coals containing older, thermogenic gas mixed with more recently produced microbial methane. Recent advances in genomics have allowed further evaluation of the source of microbial methane, through the use of high-throughput phylogenetic sequencing and fluorescent in situ hybridization, to describe the diversity and abundance of bacteria and methanogenic archaea in these subsurface formations. However, the anaerobic metabolism of the bacteria breaking coal down to methanogenic substrates, the likely rate-limiting step in biogenic gas production, is not fully understood. Coal molecules are more recalcitrant to biodegradation with increasing thermal maturity, and progress has been made in identifying some of the enzymes involved in the anaerobic degradation of these recalcitrant organic molecules using metagenomic studies and culture enrichments. In recent years, researchers have attempted lab and subsurface stimulation of the naturally slow process of methanogenic degradation of coal. Copyright ?? 2011 by Annual Reviews. All rights reserved.

Respiratory interactions of soil bacteria with (semi)conductive iron-oxide minerals.

PubMed

Kato, Souichiro; Nakamura, Ryuhei; Kai, Fumiyoshi; Watanabe, Kazuya; Hashimoto, Kazuhito

2010-12-01

Pure-culture studies have shown that dissimilatory metal-reducing bacteria are able to utilize iron-oxide nanoparticles as electron conduits for reducing distant terminal acceptors; however, the ecological relevance of such energy metabolism is poorly understood. Here, soil microbial communities were grown in electrochemical cells with acetate as the electron donor and electrodes (poised at 0.2 V versus Ag/AgCl) as the electron acceptors in the presence and absence of iron-oxide nanoparticles, and respiratory current generation and community structures were analysed. Irrespective of the iron-oxide species (hematite, magnetite or ferrihydrite), the supplementation with iron-oxide minerals resulted in large increases (over 30-fold) in current, while only a moderate increase (∼10-fold) was observed in the presence of soluble ferric/ferrous irons. During the current generation, insulative ferrihydrite was transformed into semiconductive goethite. Clone-library analyses of 16S rRNA gene fragments PCR-amplified from the soil microbial communities revealed that iron-oxide supplementation facilitated the occurrence of Geobacter species affiliated with subsurface clades 1 and 2. We suggest that subsurface-clade Geobacter species preferentially thrive in soil by utilizing (semi)conductive iron oxides for their respiration. © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.

Characterization of Two Subsurface H2-Utilizing Bacteria, Desulfomicrobium hypogeium sp. nov. and Acetobacterium psammolithicum sp. nov., and Their Ecological Roles

PubMed Central

Krumholz, Lee R.; Harris, Steve H.; Tay, Stephen T.; Suflita, Joseph M.

1999-01-01

We examined the relative roles of acetogenic and sulfate-reducing bacteria in H2 consumption in a previously characterized subsurface sandstone ecosystem. Enrichment cultures originally inoculated with ground sandstone material obtained from a Cretaceous formation in central New Mexico were grown with hydrogen in a mineral medium supplemented with 0.02% yeast extract. Sulfate reduction and acetogenesis occurred in these cultures, and the two most abundant organisms carrying out the reactions were isolated. Based on 16S rRNA analysis data and on substrate utilization patterns, these organisms were named Desulfomicrobium hypogeium sp. nov. and Acetobacterium psammolithicum sp. nov. The steady-state H2 concentrations measured in sandstone-sediment slurries (threshold concentration, 5 nM), in pure cultures of sulfate reducers (threshold concentration, 2 nM), and in pure cultures of acetogens (threshold concentrations 195 to 414 nM) suggest that sulfate reduction is the dominant terminal electron-accepting process in the ecosystem examined. In an experiment in which direct competition for H2 between D. hypogeium and A. psammolithicum was examined, sulfate reduction was the dominant process. PMID:10347005

Determining the 3D Subsurface Density Structure of Taurus Littrow Valley Using Apollo 17 Gravity Data

NASA Technical Reports Server (NTRS)

Urbancic, N.; Ghent, R.; Stanley, S,; Johnson, C. L.; Carroll, K. A.; Hatch, D.; Williamson, M. C.; Garry, W. B.; Talwani, M.

2016-01-01

Surface gravity surveys can detect subsurface density variations that can reveal subsurface geologic features. In 1972, the Apollo 17 (A17) mission conducted the Traverse Gravimeter Experiment (TGE) using a gravimeter that measured the local gravity field near Taurus Littrow Valley (TLV), located on the south-eastern rim of the Serenitatis basin. TLV is hypothesized to be a basaltfilled radial graben resulting from the impact that formed Mare Serenitatis. It is bounded by both the North and South Massifs (NM and SM) as well as other smaller mountains to the East that are thought to be mainly composed of brecciated highland material. The TGE is the first and only successful gravity survey on the surface of the Moon. Other more recent satellite surveys, such as NASA's Gravity Recovery and Interior Laboratory (GRAIL) mission (2011- 2012), have produced the best global gravity field to date (approx. 13km resolution). However, these satellite surveys are not sensitive enough to detect fine-scale (<1km) lunar subsurface structures. This underscores the value of the data collected at the surface by A17. In the original analysis of the data a 2D forward-modelling approach was used to derive a thickness of the subsurface basalt layer of 1.0 km by assuming a simple flat-faced rectangular geometry and using densities derived from Apollo lunar samples. We are investigating whether modern 3D modelling techniques in combination with high-resolution topographical and image datasets can reveal additional fine-scale subsurface structure in TLV.

[Modern bacterial taxonomy: techniques review--application to bacteria that nodulate leguminous plants (BNL)].

PubMed

Zakhia, Frédéric; de Lajudie, Philippe

2006-03-01

Taxonomy is the science that studies the relationships between organisms. It comprises classification, nomenclature, and identification. Modern bacterial taxonomy is polyphasic. This means that it is based on several molecular techniques, each one retrieving the information at different cellular levels (proteins, fatty acids, DNA...). The obtained results are combined and analysed to reach a "consensus taxonomy" of a microorganism. Until 1970, a small number of classification techniques were available for microbiologists (mainly phenotypic characterization was performed: a legume species nodulation ability for a Rhizobium, for example). With the development of techniques based on polymerase chain reaction for characterization, the bacterial taxonomy has undergone great changes. In particular, the classification of the legume nodulating bacteria has been repeatedly modified over the last 20 years. We present here a review of the currently used molecular techniques in bacterial characterization, with examples of application of these techniques for the study of the legume nodulating bacteria.

PCR detection of groundwater bacteria associated with colloidal transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cruz-Perez, P.; Stetzenbach, L.D.; Alvarez, A.J.

1996-02-29

Colloidal transport may increase the amount of contaminant material than that which could be transported by water flow alone. The role of colloids in groundwater contaminant transport is complicated and may involve many different processes, including sorption of elements onto colloidal particles, coagulation/dissolution, adsorption onto solid surfaces, filtration, and migration. Bacteria are known to concentrate minerals and influence the transport of compounds in aqueous environments and may also serve as organic colloids, thereby influencing subsurface transport of radionuclides and other contaminants. The initial phase of the project consisted of assembling a list of bacteria capable of sequestering or facilitating mineralmore » transport. The development and optimization of the PCR amplification assay for the detection of the organisms of interest, and the examination of regional groundwaters for those organisms, are presented for subsequent research.« less

A constant flux of diverse thermophilic bacteria into the cold Arctic seabed.

PubMed

Hubert, Casey; Loy, Alexander; Nickel, Maren; Arnosti, Carol; Baranyi, Christian; Brüchert, Volker; Ferdelman, Timothy; Finster, Kai; Christensen, Flemming Mønsted; Rosa de Rezende, Júlia; Vandieken, Verona; Jørgensen, Bo Barker

2009-09-18

Microorganisms have been repeatedly discovered in environments that do not support their metabolic activity. Identifying and quantifying these misplaced organisms can reveal dispersal mechanisms that shape natural microbial diversity. Using endospore germination experiments, we estimated a stable supply of thermophilic bacteria into permanently cold Arctic marine sediment at a rate exceeding 10(8) spores per square meter per year. These metabolically and phylogenetically diverse Firmicutes show no detectable activity at cold in situ temperatures but rapidly mineralize organic matter by hydrolysis, fermentation, and sulfate reduction upon induction at 50 degrees C. The closest relatives to these bacteria come from warm subsurface petroleum reservoir and ocean crust ecosystems, suggesting that seabed fluid flow from these environments is delivering thermophiles to the cold ocean. These transport pathways may broadly influence microbial community composition in the marine environment.

Color images of Kansas subsurface geology from well logs

USGS Publications Warehouse

Collins, D.R.; Doveton, J.H.

1986-01-01

Modern wireline log combinations give highly diagnostic information that goes beyond the basic shale content, pore volume, and fluid saturation of older logs. Pattern recognition of geology from logs is made conventionally through either the examination of log overlays or log crossplots. Both methods can be combined through the use of color as a medium of information by setting the three color primaries of blue, green, and red light as axes of three dimensional color space. Multiple log readings of zones are rendered as composite color mixtures which, when plotted sequentially with depth, show lithological successions in a striking manner. The method is extremely simple to program and display on a color monitor. Illustrative examples are described from the Kansas subsurface. ?? 1986.

Subsurface geomicrobiology in a Mars terrestrial analogue, Río Tinto (SW, Spain)

NASA Astrophysics Data System (ADS)

Amils, R.; Fernández-Remolar, D.; Gómez, F.; González-Toril, E.; Rodríguez, N.; Prieto-Ballesteros, O.; Sanz, J. L.; Díaz, E.; Stoker, C.

2008-09-01

Since its discovery, only few years ago, subsurface geomicrobiology is a matter of growing interest [1]. From a fundamental point of view, it seeks to determine whether life can be sustained in the absence of radiation. From an astrobiological point of view, it is an interesting model for life in other planetary bodies, e.g., Mars, as well as early life on Earth. Río Tinto is an unusual extreme acidic environment due to its size (around 100 km), constant acidic pH (mean pH 2.3), high concentrations of heavy metals and high level of microbial diversity [2]. Río Tinto rises in the core of the Iberian Pyritic Belt, one of the biggest sulfidic ore deposits in the world [3]. Today it is well stablished that the extreme characteristics of Río Tinto are not due to acid mine drainage from mining activity, as has been suggested in the past. To explore the hypothesis that a continuous underground reactor of chemolithotrophic microorganisms thriving in the rich sulfidic minerals of the Iberian Pyritic Belt is responsible for the extreme conditions found in the system, a drilling project has been developed to detect evidence of subsurface microbial activity and potential resources to support these microbial communities in situ (MARTE project) [4]. Here we report a search for subsurface life in volcanically hosted massive sulfidic deposits from the Iberian Pyritic Belt. Aseptic core samples were obtained within and down-gradient from the massive sulfide deposits and formation water was sampled within the resulting bore holes. Microbial activity was detected in un-contaminated samples by culture-dependent and culture-independent methods. Aerobic iron- and sulfide- oxidizing bacteria, and anaerobic denitrifying thiosulfate-oxidizing bacteria, sulfate reducing bacteria and methanogenic archaea have been identified. Potential energy fluxes detected in the system include oxidation of reduced iron and sulfur, or hydrogen gas coupled to nitrite, sulfate, ferric iron, inorganic carbon or transient oxygen. These results suggest that multiple energy sources are available from sulfide-mineral weathering to support microbial metabolism, even in the absence of atmospheric oxygen. [1] Stevens, T.O and McKinley, J.P. (1995) Scienc,, 270, 450-454. [2] Amis, R. et al. (2007) Planet Space Sci, 55, 370- 381. [3] Fernández-Remolar, D. et al. (2005) Earth Planet Sci Lett, 240, 149-167. [4] Amils, R. et al. (2008) Microbiology of Extreme Soils, 205-223.

Geomicrobiology and Metagenomics of Terrestrial Deep Subsurface Microbiomes.

PubMed

Itävaara, M; Salavirta, H; Marjamaa, K; Ruskeeniemi, T

2016-01-01

Fractures in the deep subsurface of Earth's crust are inhabited by diverse microbial communities that participate in biogeochemical cycles of the Earth. Life on Earth, which arose c. 3.5-4.0 billion years ago, reaches down at least 5 km in the crust. Deep mines, caves, and boreholes have provided scientists with opportunities to sample deep subsurface microbiomes and to obtain information on the species diversity and functions. A wide variety of bacteria, archaea, eukaryotes, and viruses are now known to reside in the crust, but their functions are still largely unknown. The crust at different depths has varying geological composition and hosts endemic microbiomes accordingly. The diversity is driven by geological formations and gases evolving from deeper depths. Cooperation among different species is still mostly unexplored, but viruses are known to restrict density of bacterial and archaeal populations. Due to the complex growth requirements of the deep subsurface microbiomes, the new knowledge about their diversity and functions is mostly obtained by molecular methods, eg, meta'omics'. Geomicrobiology is a multidisciplinary research area combining disciplines from geology, mineralogy, geochemistry, and microbiology. Geomicrobiology is concerned with the interaction of microorganisms and geological processes. At the surface of mineralogical or rock surfaces, geomicrobial processes occur mainly under aerobic conditions. In the deep subsurface, however, the environmental conditions are reducing and anaerobic. The present chapter describes the world of microbiomes in deep terrestrial geological environments as well as metagenomic and metatranscriptomic methods suitable for studies of these enigmatic communities. Copyright © 2016 Elsevier Inc. All rights reserved.

Biolog(TM) ID as compared to 16S ribosomal RNA ID for environmental isolates from the deep subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

McKinsey, P.C.

2000-05-05

The U.S. Dept of Energy (DOE) Subsurface Microbial Culture Collection (SMCC) contains nearly 10,000 strains of microorganisms isolated from terrestrial subsurface environments. Many of the aerobic, gram-negative, chemoheterotrophs isolated from the DOE Savannah River Site (SRS) have previously been identified by phylogenetic analysis of 16S ribosomal RNA (rRNA) gene nucleotide sequences. These SMCC isolates are currently being examined using Biolog GN Microplates and the Biolog Microstation System in order to gain knowledge of their metabolic capabilities and to compare Biolog IDs with 16S IDs. To accommodate the particular needs of these subsurface isolates, which are often incapable of growing undermore » high-nutrient conditions, Biolog's recommendations for inoculating isolates into Biolog GN Microplates have been altered. The isolates are grown on low nutrient media, sodium thioglycolate (3mM) is added to the culture media to inhibit capsule formation, and a low density of bacteria is inoculated into the microplate. Using these altered inoculation criteria, 60 percent of these SMCC isolates have a Biolog genus ID that matches the 16S rRNA ID. These results indicate that the Biolog System can be a good means of identifying unusual environmental isolates, even when recommended inoculation procedures are altered to accommodate particular isolate needs.« less

Characterization of microbial communities in subsurface nuclear blast cavities of the Nevada Test Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moser, Duane P; Czerwinski, Ken; Russell, Charles E

2010-07-13

This US Department of Energy (DOE) Environmental Remediation Sciences Project (ERSP) was designed to test fundamental hypotheses concerning the existence and nature of indigenous microbial populations of Nevada Test Site subsurface nuclear test/detonation cavities. Now called Subsurface Biogeochemical Research (SBR), this program's Exploratory Research (ER) element, which funded this research, is designed to support high risk, high potential reward projects. Here, five cavities (GASCON, CHANCELLOR, NASH, ALEMAN, and ALMENDRO) and one tunnel (U12N) were sampled using bailers or pumps. Molecular and cultivation-based techniques revealed bacterial signatures at five sites (CHANCELLOR may be lifeless). SSU rRNA gene libraries contained diverse andmore » divergent microbial sequences affiliated with known metal- and sulfur-cycling microorganisms, organic compound degraders, microorganisms from deep mines, and bacteria involved in selenate reduction and arsenite oxidation. Close relatives of Desulforudis audaxviator, a microorganism thought to subsist in the terrestrial deep subsurface on H2 and SO42- produced by radiochemical reactions, was detected in the tunnel waters. NTS-specific media formulations were used to culture and quantify nitrate-, sulfate-, iron-reducing, fermentative, and methanogenic microorganisms. Given that redox manipulations mediated by microorganisms can impact the mobility of DOE contaminants, our results should have implications for management strategies at this and other DOE sites.« less

Characterization of Microbial Communities in Subsurface Nuclear Blast Cavities of the Nevada Test Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moser, Duane P.; Bruckner, Jim; Fisher, Jen

2010-09-01

This U.S. Department of Energy (DOE) Environmental Remediation Sciences Project (ERSP) was designed to test fundamental hypotheses concerning the existence and nature of indigenous microbial populations of Nevada Test Site subsurface nuclear test/detonation cavities. Now called Subsurface Biogeochemical Research (SBR), this program’s Exploratory Research (ER) element, which funded this research, is designed to support high risk, high potential reward projects. Here, five cavities (GASCON, CHANCELLOR, NASH, ALEMAN, and ALMENDRO) and one tunnel (U12N) were sampled using bailers or pumps. Molecular and cultivation-based techniques revealed bacterial signatures at five sites (CHANCELLOR may be lifeless). SSU rRNA gene libraries contained diverse andmore » divergent microbial sequences affiliated with known metal- and sulfur-cycling microorganisms, organic compound degraders, microorganisms from deep mines, and bacteria involved in selenate reduction and arsenite oxidation. Close relatives of Desulforudis audaxviator, a microorganism thought to subsist in the terrestrial deep subsurface on H2 and SO42- produced by radiochemical reactions, was detected in the tunnel waters. NTS-specific media formulations were used to culture and quantify nitrate-, sulfate-, iron-reducing, fermentative, and methanogenic microorganisms. Given that redox manipulations mediated by microorganisms can impact the mobility of DOE contaminants, our results should have implications for management strategies at this and other DOE sites.« less

Fast-Turnoff Transient Electro-Magnetic (TEM) geophysical survey in the Peña de Hierro ("Berg of Iron") field area of the Mars Analog Research and Technology Experiment (MARTE)

NASA Astrophysics Data System (ADS)

Jernsletten, J. A.

2004-12-01

This report describes the outcome of a Fast-Turnoff Transient Electro-Magnetic (TEM) geophysical survey carried out in the Peña de Hierro ("Berg of Iron") field area of the Mars Analog Research and Technology Experiment (MARTE), during May and June of 2003. The MARTE Peña de Hierro field area is located between the towns of Rio Tinto and Nerva in the Andalucia region of Spain. It is about one hour drive West of the city of Sevilla, and also about one hour drive North of Huelva. The high concentration of dissolved iron (and smaller amounts of other metals) in the very acidic water in the Rio Tinto area gives the water its characteristic wine red color, and also means that the water is highly conductive, and such an acidic and conductive fluid is highly suited for exploration by electromagnetic methods. This naturally acidic environment is maintained by bacteria in the groundwater and it is these bacteria that are the main focus of the MARTE project overall, and of this supporting geophysical work. It is the goal of this study to be able to map the subsurface extent of the high conductivity (low resistivity) levels, and thus by proxy the subsurface extent of the acidic groundwater and the bacteria populations. In so doing, the viability of using electromagnetic methods for mapping these subsurface metal-rich water bodies is also examined and demonstrated, and the geophysical data will serve to support drilling efforts. The purpose of this field survey was an initial effort to map certain conductive features in the field area, in support of the drilling operations that are central to the MARTE project. These conductive features include the primary target of exploration for MARTE, the very conductive acidic groundwater in the area (which is extremely rich in metals). Other conductive features include the pyretic ore bodies in the area, as well as extensive mine tailings piles.

Mineralizing Filamentous Bacteria from the Prony Bay Hydrothermal Field Give New Insights into the Functioning of Serpentinization-Based Subseafloor Ecosystems

PubMed Central

Pisapia, Céline; Gérard, Emmanuelle; Gérard, Martine; Lecourt, Léna; Lang, Susan Q.; Pelletier, Bernard; Payri, Claude E.; Monnin, Christophe; Guentas, Linda; Postec, Anne; Quéméneur, Marianne; Erauso, Gaël; Ménez, Bénédicte

2017-01-01

Despite their potential importance as analogs of primitive microbial metabolisms, the knowledge of the structure and functioning of the deep ecosystems associated with serpentinizing environments is hampered by the lack of accessibility to relevant systems. These hyperalkaline environments are depleted in dissolved inorganic carbon (DIC), making the carbon sources and assimilation pathways in the associated ecosystems highly enigmatic. The Prony Bay Hydrothermal Field (PHF) is an active serpentinization site where, similar to Lost City (Mid-Atlantic Ridge), high-pH fluids rich in H2 and CH4 are discharged from carbonate chimneys at the seafloor, but in a shallower lagoonal environment. This study aimed to characterize the subsurface microbial ecology of this environment by focusing on the earliest stages of chimney construction, dominated by the discharge of hydrothermal fluids of subseafloor origin. By jointly examining the mineralogy and the microbial diversity of the conduits of juvenile edifices at the micrometric scale, we find a central role of uncultivated bacteria belonging to the Firmicutes in the ecology of the PHF. These bacteria, along with members of the phyla Acetothermia and Omnitrophica, are identified as the first chimneys inhabitants before archaeal Methanosarcinales. They are involved in the construction and early consolidation of the carbonate structures via organomineralization processes. Their predominance in the most juvenile and nascent hydrothermal chimneys, and their affiliation with environmental subsurface microorganisms, indicate that they are likely discharged with hydrothermal fluids from the subseafloor. They may thus be representative of endolithic serpentinization-based ecosystems, in an environment where DIC is limited. In contrast, heterotrophic and fermentative microorganisms may consume organic compounds from the abiotic by-products of serpentinization processes and/or from life in the deeper subsurface. We thus propose that the Firmicutes identified at PHF may have a versatile metabolism with the capability to use diverse organic compounds from biological or abiotic origin. From that perspective, this study sheds new light on the structure of deep microbial communities living at the energetic edge in serpentinites and may provide an alternative model of the earliest metabolisms. PMID:28197130

Mineralizing Filamentous Bacteria from the Prony Bay Hydrothermal Field Give New Insights into the Functioning of Serpentinization-Based Subseafloor Ecosystems.

PubMed

Pisapia, Céline; Gérard, Emmanuelle; Gérard, Martine; Lecourt, Léna; Lang, Susan Q; Pelletier, Bernard; Payri, Claude E; Monnin, Christophe; Guentas, Linda; Postec, Anne; Quéméneur, Marianne; Erauso, Gaël; Ménez, Bénédicte

2017-01-01

Despite their potential importance as analogs of primitive microbial metabolisms, the knowledge of the structure and functioning of the deep ecosystems associated with serpentinizing environments is hampered by the lack of accessibility to relevant systems. These hyperalkaline environments are depleted in dissolved inorganic carbon (DIC), making the carbon sources and assimilation pathways in the associated ecosystems highly enigmatic. The Prony Bay Hydrothermal Field (PHF) is an active serpentinization site where, similar to Lost City (Mid-Atlantic Ridge), high-pH fluids rich in H 2 and CH 4 are discharged from carbonate chimneys at the seafloor, but in a shallower lagoonal environment. This study aimed to characterize the subsurface microbial ecology of this environment by focusing on the earliest stages of chimney construction, dominated by the discharge of hydrothermal fluids of subseafloor origin. By jointly examining the mineralogy and the microbial diversity of the conduits of juvenile edifices at the micrometric scale, we find a central role of uncultivated bacteria belonging to the Firmicutes in the ecology of the PHF. These bacteria, along with members of the phyla Acetothermia and Omnitrophica , are identified as the first chimneys inhabitants before archaeal Methanosarcinales . They are involved in the construction and early consolidation of the carbonate structures via organomineralization processes. Their predominance in the most juvenile and nascent hydrothermal chimneys, and their affiliation with environmental subsurface microorganisms, indicate that they are likely discharged with hydrothermal fluids from the subseafloor. They may thus be representative of endolithic serpentinization-based ecosystems, in an environment where DIC is limited. In contrast, heterotrophic and fermentative microorganisms may consume organic compounds from the abiotic by-products of serpentinization processes and/or from life in the deeper subsurface. We thus propose that the Firmicutes identified at PHF may have a versatile metabolism with the capability to use diverse organic compounds from biological or abiotic origin. From that perspective, this study sheds new light on the structure of deep microbial communities living at the energetic edge in serpentinites and may provide an alternative model of the earliest metabolisms.

viral abundance distribution in deep waters of the Northern of South China Sea

NASA Astrophysics Data System (ADS)

He, Lei; Yin, Kedong

2017-04-01

Little is known about the vertical distribution and interaction of viruses and bacteria in the deep ocean water column. The vertical distribution of viral-like particles and bacterial abundance was investigated in the deep water column in the South China Sea during September 2005 along with salinity, temperature and dissolved oxygen. There were double maxima in the ratio of viral to bacterial abundance (VBR) in the water column: the subsurface maximum located at 50-100 m near the pycnocline layer, and the deep maximum at 800-1000 m. At the subsurface maximum of VBR, both viral and bacterial abundance were maximal in the water column, and at the deep maximum of VBR, both viral and bacterial abundance were low, but bacterial abundance was relatively lower than viral abundance. The subsurface VBR maximum coincided with the subsurface chlorophyll maximum while the deep VBR maximum coincided with the minimum in dissolved oxygen (2.91mg L-1). Therefore, we hypothesize that the two maxima were formed by different mechanisms. The subsurface VBR maximum was formed due to an increase in bacterial abundance resulting from the stimulation of abundant organic supply at the subsurface chlorophyll maximum, whereas the deep VBR maximum was formed due to a decrease in bacterial abundance caused by more limitation of organic matter at the oxygen minimum. The evidence suggests that viruses play an important role in controlling bacterial abundance in the deep water column due to the limitation of organic matter supply. In turn, this slows down the formation of the oxygen minimum in which oxygen may be otherwise lower. The mechanism has a great implication that viruses could control bacterial decomposition of organic matter, oxygen consumption and nutrient remineralization in the deep oceans.

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock

DOE PAGES

Bagnoud, Alexandre; Chourey, Karuna; Hettich, Robert L.; ...

2016-10-14

A significant fraction (~ 20%) of microbial life is found in the terrestrial deep subsurface, yet the metabolic processes extant in those environments are poorly understood. Here we show that H 2, injected into the Opalinus Clay formation in a borehole located 300 meters below the surface, fuels a community of microorganisms with interconnected metabolisms. Metagenomic binning and metaproteomic analysis reveal a complete carbon cycle, driven by autotrophic hydrogen oxidizers. Dead biomass from these organisms is a substrate for a fermenting bacterium that produces acetate as a product. In turn, complete oxidizer heterotrophic sulfate- reducing bacteria utilize acetate and oxidizemore » it to CO 2, closing the cycle. This metabolic reconstruction sheds light onto a hydrogen-driven carbon cycle, and a sunlight-independent ecosystem in the deep subsurface.« less

Non-enzymatic U(VI) interactions with biogenic mackinawite

NASA Astrophysics Data System (ADS)

Veeramani, H.; Qafoku, N. P.; Kukkadapu, R. K.; Murayama, M.; Hochella, M. F.

2011-12-01

Reductive immobilization of hexavalent uranium [U(VI)] by stimulation of dissimilatory metal and/or sulfate reducing bacteria (DMRB or DSRB) has been extensively researched as a remediation strategy for subsurface U(VI) contamination. These bacteria derive energy by reducing oxidized metals as terminal electron acceptors, often utilizing organic substrates as electron donors. Thus, when evaluating the potential for in-situ uranium remediation in heterogeneous subsurface media, it is important to understand how the presence of alternative electron acceptors such as Fe(III) and sulfate affect U(VI) remediation and the long term behavior and reactivity of reduced uranium. Iron, an abundant subsurface element, represents a substantial sink for electrons from DMRB, and the reduction of Fe(III) leads to the formation of dissolved Fe(II) or to reactive biogenic Fe(II)- and mixed Fe(II)/Fe(III)- mineral phases. Consequently, abiotic U(VI) reduction by reactive forms of biogenic Fe(II) minerals could be a potentially important process for uranium immobilization. In our study, the DMRB Shewanella putrefaciens CN32 was used to synthesize a biogenic Fe(II)-bearing sulfide mineral: mackinawite, that has been characterized by XRD, SEM, HRTEM and Mössbauer spectroscopy. Batch experiments involving treated biogenic mackinawite and uranium (50:1 molar ratio) were carried out at room temperature under strict anoxic conditions. Following complete removal of uranium from solution, the biogenic mackinawite was analyzed by a suite of analytical techniques including XAS, HRTEM and Mössbauer spectroscopy to determine the speciation of uranium and investigate concomitant Fe(II)-phase transformation. Determining the speciation of uranium is critical to success of a remediation strategy. The present work elucidates non-enzymatic/abiotic molecular scale redox interactions between biogenic mackinawite and uranium.

Subsurface microbial diversity in deep-granitic-fracture water in Colorado

USGS Publications Warehouse

Sahl, J.W.; Schmidt, R.; Swanner, E.D.; Mandernack, K.W.; Templeton, A.S.; Kieft, Thomas L.; Smith, R.L.; Sanford, W.E.; Callaghan, R.L.; Mitton, J.B.; Spear, J.R.

2008-01-01

A microbial community analysis using 16S rRNA gene sequencing was performed on borehole water and a granite rock core from Henderson Mine, a >1,000-meter-deep molybdenum mine near Empire, CO. Chemical analysis of borehole water at two separate depths (1,044 m and 1,004 m below the mine entrance) suggests that a sharp chemical gradient exists, likely from the mixing of two distinct subsurface fluids, one metal rich and one relatively dilute; this has created unique niches for microorganisms. The microbial community analyzed from filtered, oxic borehole water indicated an abundance of sequences from iron-oxidizing bacteria (Gallionella spp.) and was compared to the community from the same borehole after 2 weeks of being plugged with an expandable packer. Statistical analyses with UniFrac revealed a significant shift in community structure following the addition of the packer. Phospholipid fatty acid (PLFA) analysis suggested that Nitrosomonadales dominated the oxic borehole, while PLFAs indicative of anaerobic bacteria were most abundant in the samples from the plugged borehole. Microbial sequences were represented primarily by Firmicutes, Proteobacteria, and a lineage of sequences which did not group with any identified bacterial division; phylogenetic analyses confirmed the presence of a novel candidate division. This "Henderson candidate division" dominated the clone libraries from the dilute anoxic fluids. Sequences obtained from the granitic rock core (1,740 m below the surface) were represented by the divisions Proteobacteria (primarily the family Ralstoniaceae) and Firmicutes. Sequences grouping within Ralstoniaceae were also found in the clone libraries from metal-rich fluids yet were absent in more dilute fluids. Lineage-specific comparisons, combined with phylogenetic statistical analyses, show that geochemical variance has an important effect on microbial community structure in deep, subsurface systems. Copyright ?? 2008, American Society for Microbiology. All Rights Reserved.

Influence of microorganisms on the oxidation state distribution of multivalent actinides under anoxic conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reed, Donald Timothy; Borkowski, Marian; Lucchini, Jean - Francois

2010-12-10

The fate and potential mobility of multivalent actinides in the subsurface is receiving increased attention as the DOE looks to cleanup the many legacy nuclear waste sites and associated subsurface contamination. Plutonium, uranium and neptunium are the near-surface multivalent contaminants of concern and are also key contaminants for the deep geologic disposal of nuclear waste. Their mobility is highly dependent on their redox distribution at their contamination source as well as along their potential migration pathways. This redox distribution is often controlled, especially in the near-surface where organic/inorganic contaminants often coexist, by the direct and indirect effects of microbial activity.more » Under anoxic conditions, indirect and direct bioreduction mechanisms exist that promote the prevalence of lower-valent species for multivalent actinides. Oxidation-state-specific biosorption is also an important consideration for long-term migration and can influence oxidation state distribution. Results of ongoing studies to explore and establish the oxidation-state specific interactions of soil bacteria (metal reducers and sulfate reducers) as well as halo-tolerant bacteria and Archaea for uranium, neptunium and plutonium will be presented. Enzymatic reduction is a key process in the bioreduction of plutonium and uranium, but co-enzymatic processes predominate in neptunium systems. Strong sorptive interactions can occur for most actinide oxidation states but are likely a factor in the stabilization of lower-valent species when more than one oxidation state can persist under anaerobic microbiologically-active conditions. These results for microbiologically active systems are interpreted in the context of their overall importance in defining the potential migration of multivalent actinides in the subsurface.« less

Subsurface Microbial Diversity in Deep-Granitic-Fracture Water in Colorado▿

PubMed Central

Sahl, Jason W.; Schmidt, Raleigh; Swanner, Elizabeth D.; Mandernack, Kevin W.; Templeton, Alexis S.; Kieft, Thomas L.; Smith, Richard L.; Sanford, William E.; Callaghan, Robert L.; Mitton, Jeffry B.; Spear, John R.

2008-01-01

A microbial community analysis using 16S rRNA gene sequencing was performed on borehole water and a granite rock core from Henderson Mine, a >1,000-meter-deep molybdenum mine near Empire, CO. Chemical analysis of borehole water at two separate depths (1,044 m and 1,004 m below the mine entrance) suggests that a sharp chemical gradient exists, likely from the mixing of two distinct subsurface fluids, one metal rich and one relatively dilute; this has created unique niches for microorganisms. The microbial community analyzed from filtered, oxic borehole water indicated an abundance of sequences from iron-oxidizing bacteria (Gallionella spp.) and was compared to the community from the same borehole after 2 weeks of being plugged with an expandable packer. Statistical analyses with UniFrac revealed a significant shift in community structure following the addition of the packer. Phospholipid fatty acid (PLFA) analysis suggested that Nitrosomonadales dominated the oxic borehole, while PLFAs indicative of anaerobic bacteria were most abundant in the samples from the plugged borehole. Microbial sequences were represented primarily by Firmicutes, Proteobacteria, and a lineage of sequences which did not group with any identified bacterial division; phylogenetic analyses confirmed the presence of a novel candidate division. This “Henderson candidate division” dominated the clone libraries from the dilute anoxic fluids. Sequences obtained from the granitic rock core (1,740 m below the surface) were represented by the divisions Proteobacteria (primarily the family Ralstoniaceae) and Firmicutes. Sequences grouping within Ralstoniaceae were also found in the clone libraries from metal-rich fluids yet were absent in more dilute fluids. Lineage-specific comparisons, combined with phylogenetic statistical analyses, show that geochemical variance has an important effect on microbial community structure in deep, subsurface systems. PMID:17981950

Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm

PubMed Central

Probst, Alexander J; Holman, Hoi-Ying N; DeSantis, Todd Z; Andersen, Gary L; Birarda, Giovanni; Bechtel, Hans A; Piceno, Yvette M; Sonnleitner, Maria; Venkateswaran, Kasthuri; Moissl-Eichinger, Christine

2013-01-01

Archaea are usually minor components of a microbial community and dominated by a large and diverse bacterial population. In contrast, the SM1 Euryarchaeon dominates a sulfidic aquifer by forming subsurface biofilms that contain a very minor bacterial fraction (5%). These unique biofilms are delivered in high biomass to the spring outflow that provides an outstanding window to the subsurface. Despite previous attempts to understand its natural role, the metabolic capacities of the SM1 Euryarchaeon remain mysterious to date. In this study, we focused on the minor bacterial fraction in order to obtain insights into the ecological function of the biofilm. We link phylogenetic diversity information with the spatial distribution of chemical and metabolic compounds by combining three different state-of-the-art methods: PhyloChip G3 DNA microarray technology, fluorescence in situ hybridization (FISH) and synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy. The results of PhyloChip and FISH technologies provide evidence for selective enrichment of sulfate-reducing bacteria, which was confirmed by the detection of bacterial dissimilatory sulfite reductase subunit B (dsrB) genes via quantitative PCR and sequence-based analyses. We further established a differentiation of archaeal and bacterial cells by SR-FTIR based on typical lipid and carbohydrate signatures, which demonstrated a co-localization of organic sulfate, carbonated mineral and bacterial signatures in the biofilm. All these results strongly indicate an involvement of the SM1 euryarchaeal biofilm in the global cycles of sulfur and carbon and support the hypothesis that sulfidic springs are important habitats for Earth's energy cycles. Moreover, these investigations of a bacterial minority in an Archaea-dominated environment are a remarkable example of the great power of combining highly sensitive microarrays with label-free infrared imaging. PMID:23178669

Characterizing the Catalytic Potential of Deinococcus, Arthrobacter and other Robust Bacteria in Contaminated Subsurface Environments of the Hanford Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daly, Michael J.

2006-05-01

Ionizing Radiation (IR) Resistance in Bacteria. Until recently, there have been no clear physiologic predictors of a cell's ability to recover from ionizing radiation (IR) and other DOE-relevant oxidative stress conditions. In general, the most resistant bacteria have been Gram-positive (e.g., Deinococcus, Arthrobacter, Lactobacillus & Enterococcus spp.) and the most sensitive have been Gram-negative (e.g., Pseudomonas, Shewanella & Neisseria spp.). However, there are several reported exceptions to this paradigm, the Gram-negative cyanobacterium Chroococcidiopsis is extremely resistant to IR, whereas the Gram-positive Micrococcus luteus is sensitive. We have identified biomolecular signatures for radiation sensitivity and resistance which are independent of phylogeny,more » where very high and very low intracellular Mn/Fe concentration ratios correlated with very high and very low resistances, respectively; and restricting Mn(II) in the famously resistant Deinococcus radiodurans sensitized this eubacterium to IR.« less

Quantification of hydrophobic interaction affinity of colloids

NASA Astrophysics Data System (ADS)

Saini, G.; Nasholm, N.; Wood, B. D.

2009-12-01

Colloids play an important role in a wide variety of disciplines, including water and wastewater treatment, subsurface transport of metals and organic contaminants, migration of fines in oil reservoirs, biocolloid (virus and bacteria) transport in subsurface, and are integral to laboratory transport studies. Although the role of hydrophobicity in adhesion and transport of colloids, particularly bacteria, is well known; there is scarcity of literature regarding hydrophobicity measurement of non-bacterial colloids and other micron-sized particles. Here we detail an experimental approach based on differential partitioning of colloids between two liquid phases (hydrocarbon and buffer) as a measure of the hydrophobic interaction affinity of colloids. This assay, known as Microbial adhesion to hydrocarbons or MATH, is frequently used in microbiology and bacteriology for quantifying the hydrophobicity of microbes. Monodispersed colloids and particles, with sizes ranging from 1 micron to 33 micron, were used for the experiments. A range of hydrophobicity values were observed for different particles. The hydrophobicity results are also verified against water contact angle measurements of these particles. This liquid-liquid partitioning assay is quick, easy-to-perform and requires minimal instrumentation. Estimation of the hydrophobic interaction affinity of colloids would lead to a better understanding of their adhesion to different surfaces and subsequent transport in porous media.

Molecular hydrogen: An abundant energy source for bacterial activity in nuclear waste repositories

NASA Astrophysics Data System (ADS)

Libert, M.; Bildstein, O.; Esnault, L.; Jullien, M.; Sellier, R.

A thorough understanding of the energy sources used by microbial systems in the deep terrestrial subsurface is essential since the extreme conditions for life in deep biospheres may serve as a model for possible life in a nuclear waste repository. In this respect, H 2 is known as one of the most energetic substrates for deep terrestrial subsurface environments. This hydrogen is produced from abiotic and biotic processes but its concentration in natural systems is usually maintained at very low levels due to hydrogen-consuming bacteria. A significant amount of H 2 gas will be produced within deep nuclear waste repositories, essentially from the corrosion of metallic components. This will consequently improve the conditions for microbial activity in this specific environment. This paper discusses different study cases with experimental results to illustrate the fact that microorganisms are able to use hydrogen for redox processes (reduction of O 2, NO3-, Fe III) in several waste disposal conditions. Consequences of microbial activity include: alteration of groundwater chemistry and shift in geochemical equilibria, gas production or consumption, biocorrosion, and potential modifications of confinement properties. In order to quantify the impact of hydrogen bacteria, the next step will be to determine the kinetic rate of the reactions in realistic conditions.

Molecular diversity of bacterial communities from subseafloor rock samples in a deep-water production basin in Brazil.

PubMed

von der Weid, Irene; Korenblum, Elisa; Jurelevicius, Diogo; Rosado, Alexandre Soares; Dino, Rodolfo; Sebastian, Gina Vasquez; Seldin, Lucy

2008-01-01

The deep subseafloor rock in oil reservoirs represents a unique environment in which a high oilcontamination and very low biomass can be observed. Sampling this environment has been a challenge owing to the techniques used for drilling and coring. In this study, the facilities developed by the Brazilian oil company PETROBRAS for accessing deep subsurface oil reservoirs were used to obtain rock samples at 2,822-2,828 m below the ocean floor surface from a virgin field located in the Atlantic Ocean, Rio de Janeiro. To address the bacterial diversity of these rock samples, PCR amplicons were obtained using the DNA from four core sections and universal primers for 16S rRNA and for APS reductase (aps) genes. Clone libraries were generated from these PCR fragments and 87 clones were sequenced. The phylogenetic analyses of the 16S rDNA clone libraries showed a wide distribution of types in the domain bacteria in the four core samples, and the majority of the clones were identified as belonging to Betaproteobacteria. The sulfate-reducing bacteria community could only be amplified by PCR in one sample, and all clones were identified as belonging to Gammaproteobacteria. For the first time, the bacterial community was assessed in such deep subsurface environment.

Molecular evidence of Late Archean archaea and the presence of a subsurface hydrothermal biosphere

PubMed Central

Ventura, Gregory T.; Kenig, Fabien; Reddy, Christopher M.; Schieber, Juergen; Frysinger, Glenn S.; Nelson, Robert K.; Dinel, Etienne; Gaines, Richard B.; Schaeffer, Philippe

2007-01-01

Highly cracked and isomerized archaeal lipids and bacterial lipids, structurally changed by thermal stress, are present in solvent extracts of 2,707- to 2,685-million-year-old (Ma) metasedimentary rocks from Timmins, ON, Canada. These lipids appear in conventional gas chromatograms as unresolved complex mixtures and include cyclic and acyclic biphytanes, C36–C39 derivatives of the biphytanes, and C31–C35 extended hopanes. Biphytane and extended hopanes are also found in high-pressure catalytic hydrogenation products released from solvent-extracted sediments, indicating that archaea and bacteria were present in Late Archean sedimentary environments. Postdepositional, hydrothermal gold mineralization and graphite precipitation occurred before metamorphism (≈2,665 Ma). Late Archean metamorphism significantly reduced the kerogen's adsorptive capacity and severely restricted sediment porosity, limiting the potential for post-Archean additions of organic matter to the samples. Argillites exposed to hydrothermal gold mineralization have disproportionately high concentrations of extractable archaeal and bacterial lipids relative to what is releasable from their respective high-pressure catalytic hydrogenation product and what is observed for argillites deposited away from these hydrothermal settings. The addition of these lipids to the sediments likely results from a Late Archean subsurface hydrothermal biosphere of archaea and bacteria. PMID:17726114

Potential Physiologies of Deep Branches on the Tree of Life with Deep Subsurface Samples from IODP Leg 347: Baltic Sea Paleoenvironment

NASA Astrophysics Data System (ADS)

Lloyd, K. G.; Bird, J. T.; Shumaker, A.

2014-12-01

Very little is known about how evolutionary branches that are distantly related to cultured microorganisms make a living in the deep subsurface marine environment. Here, sediments are cut-off from surface inputs of organic substrates for tens of thousands of years; yet somehow support a diverse population of microorganisms. We examined the potential metabolic and ecological roles of uncultured archaea and bacteria in IODP Leg 347: Baltic Sea Paleoenvironment samples, using quantitative PCR holes 60B, 63E, 65C, and 59C and single cell genomic analysis for hole 60B. We quantified changes in total archaea and bacteria, as well as deeply-branching archaeal taxa with depth. These sediment cores alternate between high and low salinities, following a glacial cycle. This allows changes in the quantities of these groups to be placed in the context of potentially vastly different organic matter sources. In addition, single cells were isolated, and their genomes were amplified and sequenced to allow a deeper look into potential physiologies of uncultured deeply-branching organisms found up to 86 meters deep in marine sediments. Together, these data provide deeper insight into the relationship between microorganisms and their organic matter substrates in this extreme environments.

Microbial contamination of vegetable crop and soil profile in arid regions under controlled application of domestic wastewater

PubMed Central

Balkhair, Khaled S.

2015-01-01

Increasing lack of potable water in arid countries leads to the use of treated wastewater for crop production. However, the use of inappropriate irrigation practices could result in a serious contamination risk to plants, soils, and groundwater with sewage water. This research was initiated in view to the increasing danger of vegetable crops and groundwater contamination with pathogenic bacteria due to wastewater land application. The research was designed to study: (1) the effect of treated wastewater irrigation on the yield and microbial contamination of the radish plant under field conditions; (2) contamination of the agricultural soil profile with fecal coliform bacteria. Effluent from a domestic wastewater treatment plant (100%) in Jeddah city, Saudi Arabia, was diluted to 80% and 40% with the groundwater of the experimental site constituting three different water qualities plus groundwater as control. Radish plant was grown in two consecutive seasons under two drip irrigation systems and four irrigation water qualities. Upon harvesting, plant weight per ha, total bacterial, fecal coliform, fecal streptococci were detected per 100 g of dry matter and compared with the control. The soil profile was also sampled at an equal distance of 3 cm from soil surface for fecal coliform detection. The results indicated that the yield increased significantly under the subsurface irrigation system and the control water quality compared to surface irrigation system and other water qualities. There was a considerable drop in the count of all bacteria species under the subsurface irrigation system compared to surface irrigation. The bacterial count/g of the plant shoot system increased as the percentage of wastewater in the irrigation water increased. Most of the fecal coliform bacteria were deposited in the first few centimeters below the column inlet and the profile exponentially decreased with increasing depth. PMID:26858571

Functional Characterization of Bacteria Isolated from Ancient Arctic Soil Exposes Diverse Resistance Mechanisms to Modern Antibiotics

PubMed Central

Perron, Gabriel G.; Whyte, Lyle; Turnbaugh, Peter J.; Goordial, Jacqueline; Hanage, William P.; Dantas, Gautam; Desai, Michael M.

2015-01-01

Using functional metagenomics to study the resistomes of bacterial communities isolated from different layers of the Canadian high Arctic permafrost, we show that microbial communities harbored diverse resistance mechanisms at least 5,000 years ago. Among bacteria sampled from the ancient layers of a permafrost core, we isolated eight genes conferring clinical levels of resistance against aminoglycoside, β-lactam and tetracycline antibiotics that are naturally produced by microorganisms. Among these resistance genes, four also conferred resistance against amikacin, a modern semi-synthetic antibiotic that does not naturally occur in microorganisms. In bacteria sampled from the overlaying active layer, we isolated ten different genes conferring resistance to all six antibiotics tested in this study, including aminoglycoside, β-lactam and tetracycline variants that are naturally produced by microorganisms as well as semi-synthetic variants produced in the laboratory. On average, we found that resistance genes found in permafrost bacteria conferred lower levels of resistance against clinically relevant antibiotics than resistance genes sampled from the active layer. Our results demonstrate that antibiotic resistance genes were functionally diverse prior to the anthropogenic use of antibiotics, contributing to the evolution of natural reservoirs of resistance genes. PMID:25807523

Microbial Diversity in Natural Asphalts of the Rancho La Brea Tar Pits▿

PubMed Central

Kim, Jong-Shik; Crowley, David E.

2007-01-01

Bacteria commonly inhabit subsurface oil reservoirs, but almost nothing is known yet about microorganisms that live in naturally occurring terrestrial oil seeps and natural asphalts that are comprised of highly recalcitrant petroleum hydrocarbons. Here we report the first survey of microbial diversity in ca. 28,000-year-old samples of natural asphalts from the Rancho La Brea Tar Pits in Los Angeles, CA. Microbiological studies included analyses of 16S rRNA gene sequences and DNA encoding aromatic ring-hydroxylating dioxygenases from two tar pits differing in chemical composition. Our results revealed a wide range of phylogenetic groups within the Archaea and Bacteria domains, in which individual taxonomic clusters were comprised of sets of closely related species within novel genera and families. Fluorescent staining of asphalt-soil particles using phylogenetic probes for Archaea, Bacteria, and Pseudomonas showed coexistence of mixed microbial communities at high cell densities. Genes encoding dioxygenases included three novel clusters of enzymes. The discovery of life in the tar pits provides an avenue for further studies of the evolution of enzymes and catabolic pathways for bacteria that have been exposed to complex hydrocarbons for millennia. These bacteria also should have application for industrial microbiology and bioremediation. PMID:17416692

The Experimental Study of Bacterial Evolution and Its Implications for the Modern Synthesis of Evolutionary Biology.

PubMed

O'Malley, Maureen A

2018-06-01

Since the 1940s, microbiologists, biochemists and population geneticists have experimented with the genetic mechanisms of microorganisms in order to investigate evolutionary processes. These evolutionary studies of bacteria and other microorganisms gained some recognition from the standard-bearers of the modern synthesis of evolutionary biology, especially Theodosius Dobzhansky and Ledyard Stebbins. A further period of post-synthesis bacterial evolutionary research occurred between the 1950s and 1980s. These experimental analyses focused on the evolution of population and genetic structure, the adaptive gain of new functions, and the evolutionary consequences of competition dynamics. This large body of research aimed to make evolutionary theory testable and predictive, by giving it mechanistic underpinnings. Although evolutionary microbiologists promoted bacterial experiments as methodologically advantageous and a source of general insight into evolution, they also acknowledged the biological differences of bacteria. My historical overview concludes with reflections on what bacterial evolutionary research achieved in this period, and its implications for the still-developing modern synthesis.

Unique microbial community in drilling fluids from Chinese continental scientific drilling

USGS Publications Warehouse

Zhang, Gengxin; Dong, Hailiang; Jiang, Hongchen; Xu, Zhiqin; Eberl, Dennis D.

2006-01-01

Circulating drilling fluid is often regarded as a contamination source in investigations of subsurface microbiology. However, it also provides an opportunity to sample geological fluids at depth and to study contained microbial communities. During our study of deep subsurface microbiology of the Chinese Continental Scientific Deep drilling project, we collected 6 drilling fluid samples from a borehole from 2290 to 3350 m below the land surface. Microbial communities in these samples were characterized with cultivation-dependent and -independent techniques. Characterization of 16S rRNA genes indicated that the bacterial clone sequences related to Firmicutes became progressively dominant with increasing depth. Most sequences were related to anaerobic, thermophilic, halophilic or alkaliphilic bacteria. These habitats were consistent with the measured geochemical characteristics of the drilling fluids that have incorporated geological fluids and partly reflected the in-situ conditions. Several clone types were closely related to Thermoanaerobacter ethanolicus, Caldicellulosiruptor lactoaceticus, and Anaerobranca gottschalkii, an anaerobic metal-reducer, an extreme thermophile, and an anaerobic chemoorganotroph, respectively, with an optimal growth temperature of 50–68°C. Seven anaerobic, thermophilic Fe(III)-reducing bacterial isolates were obtained and they were capable of reducing iron oxide and clay minerals to produce siderite, vivianite, and illite. The archaeal diversity was low. Most archaeal sequences were not related to any known cultivated species, but rather to environmental clone sequences recovered from subsurface environments. We infer that the detected microbes were derived from geological fluids at depth and their growth habitats reflected the deep subsurface conditions. These findings have important implications for microbial survival and their ecological functions in the deep subsurface.

Contrasting styles of large-scale displacement of unconsolidated sand: examples from the early Jurassic Navajo Sandstone on the Colorado Plateau, USA

NASA Astrophysics Data System (ADS)

Bryant, Gerald

2015-04-01

Large-scale soft-sediment deformation features in the Navajo Sandstone have been a topic of interest for nearly 40 years, ever since they were first explored as a criterion for discriminating between marine and continental processes in the depositional environment. For much of this time, evidence for large-scale sediment displacements was commonly attributed to processes of mass wasting. That is, gravity-driven movements of surficial sand. These slope failures were attributed to the inherent susceptibility of dune sand responding to environmental triggers such as earthquakes, floods, impacts, and the differential loading associated with dune topography. During the last decade, a new wave of research is focusing on the event significance of deformation features in more detail, revealing a broad diversity of large-scale deformation morphologies. This research has led to a better appreciation of subsurface dynamics in the early Jurassic deformation events recorded in the Navajo Sandstone, including the important role of intrastratal sediment flow. This report documents two illustrative examples of large-scale sediment displacements represented in extensive outcrops of the Navajo Sandstone along the Utah/Arizona border. Architectural relationships in these outcrops provide definitive constraints that enable the recognition of a large-scale sediment outflow, at one location, and an equally large-scale subsurface flow at the other. At both sites, evidence for associated processes of liquefaction appear at depths of at least 40 m below the original depositional surface, which is nearly an order of magnitude greater than has commonly been reported from modern settings. The surficial, mass flow feature displays attributes that are consistent with much smaller-scale sediment eruptions (sand volcanoes) that are often documented from modern earthquake zones, including the development of hydraulic pressure from localized, subsurface liquefaction and the subsequent escape of fluidized sand toward the unconfined conditions of the surface. The origin of the forces that produced the lateral, subsurface movement of a large body of sand at the other site is not readily apparent. The various constraints on modeling the generation of the lateral force required to produce the observed displacement are considered here, along with photodocumentation of key outcrop relationships.

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems

DOE PAGES

Jungbluth, Sean P.; Glavina del Rio, Tijana; Tringe, Susannah G.; ...

2017-04-06

It is generally accepted that diverse, poorly characterized microorganisms reside deep within Earth’s crust. One such lineage of deep subsurface-dwelling bacteria is an uncultivated member of the Firmicutes phylum that can dominate molecular surveys from both marine and continental rock fracture fluids, sometimes forming the sole member of a single-species microbiome. Here, we reconstructed a genome from basalt-hosted fluids of the deep subseafloor along the eastern Juan de Fuca Ridge flank and used a phylogenomic analysis to show that, despite vast differences in geographic origin and habitat, it forms a monophyletic clade with the terrestrial deep subsurface genome of “more » Candidatus Desulforudis audaxviator” MP104C. While a limited number of differences were observed between the marine genome of “ Candidatus Desulfopertinax cowenii” modA32 and its terrestrial relative that may be of potential adaptive importance, here it is revealed that the two are remarkably similar thermophiles possessing the genetic capacity for motility, sporulation, hydrogenotrophy, chemoorganotrophy, dissimilatory sulfate reduction, and the ability to fix inorganic carbon via the Wood-Ljungdahl pathway for chemoautotrophic growth. Finally, our results provide insights into the genetic repertoire within marine and terrestrial members of a bacterial lineage that is widespread in the global deep subsurface biosphere, and provides a natural means to investigate adaptations specific to these two environments.« less

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jungbluth, Sean P.; Glavina del Rio, Tijana; Tringe, Susannah G.

It is generally accepted that diverse, poorly characterized microorganisms reside deep within Earth’s crust. One such lineage of deep subsurface-dwelling bacteria is an uncultivated member of the Firmicutes phylum that can dominate molecular surveys from both marine and continental rock fracture fluids, sometimes forming the sole member of a single-species microbiome. Here, we reconstructed a genome from basalt-hosted fluids of the deep subseafloor along the eastern Juan de Fuca Ridge flank and used a phylogenomic analysis to show that, despite vast differences in geographic origin and habitat, it forms a monophyletic clade with the terrestrial deep subsurface genome of “more » Candidatus Desulforudis audaxviator” MP104C. While a limited number of differences were observed between the marine genome of “ Candidatus Desulfopertinax cowenii” modA32 and its terrestrial relative that may be of potential adaptive importance, here it is revealed that the two are remarkably similar thermophiles possessing the genetic capacity for motility, sporulation, hydrogenotrophy, chemoorganotrophy, dissimilatory sulfate reduction, and the ability to fix inorganic carbon via the Wood-Ljungdahl pathway for chemoautotrophic growth. Finally, our results provide insights into the genetic repertoire within marine and terrestrial members of a bacterial lineage that is widespread in the global deep subsurface biosphere, and provides a natural means to investigate adaptations specific to these two environments.« less

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems

PubMed Central

Glavina del Rio, Tijana; Tringe, Susannah G.; Stepanauskas, Ramunas

2017-01-01

It is generally accepted that diverse, poorly characterized microorganisms reside deep within Earth’s crust. One such lineage of deep subsurface-dwelling bacteria is an uncultivated member of the Firmicutes phylum that can dominate molecular surveys from both marine and continental rock fracture fluids, sometimes forming the sole member of a single-species microbiome. Here, we reconstructed a genome from basalt-hosted fluids of the deep subseafloor along the eastern Juan de Fuca Ridge flank and used a phylogenomic analysis to show that, despite vast differences in geographic origin and habitat, it forms a monophyletic clade with the terrestrial deep subsurface genome of “Candidatus Desulforudis audaxviator” MP104C. While a limited number of differences were observed between the marine genome of “Candidatus Desulfopertinax cowenii” modA32 and its terrestrial relative that may be of potential adaptive importance, here it is revealed that the two are remarkably similar thermophiles possessing the genetic capacity for motility, sporulation, hydrogenotrophy, chemoorganotrophy, dissimilatory sulfate reduction, and the ability to fix inorganic carbon via the Wood-Ljungdahl pathway for chemoautotrophic growth. Our results provide insights into the genetic repertoire within marine and terrestrial members of a bacterial lineage that is widespread in the global deep subsurface biosphere, and provides a natural means to investigate adaptations specific to these two environments. PMID:28396823

Metagenomic Evidence for H2 Oxidation and H2 Production by Serpentinite-Hosted Subsurface Microbial Communities

PubMed Central

Brazelton, William J.; Nelson, Bridget; Schrenk, Matthew O.

2012-01-01

Ultramafic rocks in the Earth’s mantle represent a tremendous reservoir of carbon and reducing power. Upon tectonic uplift and exposure to fluid flow, serpentinization of these materials generates copious energy, sustains abiogenic synthesis of organic molecules, and releases hydrogen gas (H2). In order to assess the potential for microbial H2 utilization fueled by serpentinization, we conducted metagenomic surveys of a marine serpentinite-hosted hydrothermal chimney (at the Lost City hydrothermal field) and two continental serpentinite-hosted alkaline seeps (at the Tablelands Ophiolite, Newfoundland). Novel [NiFe]-hydrogenase sequences were identified at both the marine and continental sites, and in both cases, phylogenetic analyses indicated aerobic, potentially autotrophic Betaproteobacteria belonging to order Burkholderiales as the most likely H2-oxidizers. Both sites also yielded metagenomic evidence for microbial H2 production catalyzed by [FeFe]-hydrogenases in anaerobic Gram-positive bacteria belonging to order Clostridiales. In addition, we present metagenomic evidence at both sites for aerobic carbon monoxide utilization and anaerobic carbon fixation via the Wood–Ljungdahl pathway. In general, our results point to H2-oxidizing Betaproteobacteria thriving in shallow, oxic–anoxic transition zones and the anaerobic Clostridia thriving in anoxic, deep subsurface habitats. These data demonstrate the feasibility of metagenomic investigations into novel subsurface habitats via surface-exposed seeps and indicate the potential for H2-powered primary production in serpentinite-hosted subsurface habitats. PMID:22232619

Metagenomic evidence for h(2) oxidation and h(2) production by serpentinite-hosted subsurface microbial communities.

PubMed

Brazelton, William J; Nelson, Bridget; Schrenk, Matthew O

2012-01-01

Ultramafic rocks in the Earth's mantle represent a tremendous reservoir of carbon and reducing power. Upon tectonic uplift and exposure to fluid flow, serpentinization of these materials generates copious energy, sustains abiogenic synthesis of organic molecules, and releases hydrogen gas (H(2)). In order to assess the potential for microbial H(2) utilization fueled by serpentinization, we conducted metagenomic surveys of a marine serpentinite-hosted hydrothermal chimney (at the Lost City hydrothermal field) and two continental serpentinite-hosted alkaline seeps (at the Tablelands Ophiolite, Newfoundland). Novel [NiFe]-hydrogenase sequences were identified at both the marine and continental sites, and in both cases, phylogenetic analyses indicated aerobic, potentially autotrophic Betaproteobacteria belonging to order Burkholderiales as the most likely H(2)-oxidizers. Both sites also yielded metagenomic evidence for microbial H(2) production catalyzed by [FeFe]-hydrogenases in anaerobic Gram-positive bacteria belonging to order Clostridiales. In addition, we present metagenomic evidence at both sites for aerobic carbon monoxide utilization and anaerobic carbon fixation via the Wood-Ljungdahl pathway. In general, our results point to H(2)-oxidizing Betaproteobacteria thriving in shallow, oxic-anoxic transition zones and the anaerobic Clostridia thriving in anoxic, deep subsurface habitats. These data demonstrate the feasibility of metagenomic investigations into novel subsurface habitats via surface-exposed seeps and indicate the potential for H(2)-powered primary production in serpentinite-hosted subsurface habitats.

Sulphur bacteria mediated formation of Palaeoproterozoic phosphorites

NASA Astrophysics Data System (ADS)

Joosu, Lauri; Lepland, Aivo; Kirsimäe, Kalle

2014-05-01

Modern phosphorite formation is typically associated with high productivity in upwelling areas where apatite (Ca-phosphate) precipitation is mediated by sulphur oxidising bacteria [1]. They inhabit the oxic/anoxic interface within the upper few centimetres of sediment column, accumulating phosphate in their cells under oxic conditions and releasing it rapidly when conditions become anoxic. Sulphur bacteria are known to live in close association with a consortium of anaerobic methane oxidising archaea and syntrophic sulphate-reducing bacteria. Paleoproterozoic, c. 2.0 Ga Zaonega Formation in Karelia, Russia contains several P-rich intervals in the upper part of 1500 m thick succession of organic-rich sedimentary rocks interlayered with mafic tuffs and lavas. Apatite in these P-rich intervals forms impure laminae, lenses and round-oval nodules which diameters typically range from 300 to 1000 μm. Individual apatite particles in P-rich laminae and nodules commonly occur as cylinders that are 1-8 μm long and have diameters of 0.5-4 μm. Cross-sections of best preserved cylindrical apatite particles reveal a thin outer rim whereas the internal parts consist of small anhedral elongated crystallites, intergrown with carbonaceous material. During recrystallization the outer rim thickens towards interior and cylinders may attain hexagonal crystal habit, but their size and shape remains largely unchanged [2]. The sizes of Zaonega nodules are similar to giant sulphide-oxidising bacteria known from modern and ancient settings [3, 4]. Individual apatite cylinders and aggregates have shapes and sizes similar to the methanotrophic archaea that inhabit microbial mats in modern seep/vent areas where they operate in close associations with sulphur-oxidising microbial communities [5]. Seep/vent influence during the Zaonega phosphogenesis is indicated by variable, though positive Eu anomaly, expected in magmatically active sedimentary environment experiencing several lava flows. Moreover, P-rich intervals in the Zaonega Formation are found in organic-rich sediments exhibiting strongly negative δ13Corg values (-37 to -34 per mil) which is interpreted to reflect the methanotrophic biomass. We conclude that modern-style phosphogenesis, mediated by sulphide-oxidising bacteria living in consortium with methanotrophs, was established at least 2 Ga ago. [1] Schulz and Schulz (2005) Science 307, 416-418 [2] Lepland, Joosu, Kirsimäe, Prave, Romashkin, Črne, Martin, Fallick, Somelar, Üpraus, Mänd, Roberts, van Zuilen, Wirth, Schreiber (2014) Nature geoscience 7, 20-24 [3] Bailey, Joye, Kalanetra, Flood, and Corsetti (2007) Nature 445, 198-201 [4] Schulz, Brinkhoff, Ferdelman, Marine, Teske and Jorgensen (1999) Science 284, 493-495 [5] Knittel, Losekann, Boetius, Kort and Amann (2005) Applied and Environmental Microbiology 71, 467-479.

Carbonate Biogenic Structures in Storrs Lake, Bahamas

NASA Technical Reports Server (NTRS)

Byrne, Monica; Morris, Penny A.; Wentworth, Susan J.; Brigmon, Robin L.; McKay, David S.

2001-01-01

Storr's Lake, an inland hypersaline lake on San Salvador Island, Bahamas, contains calcium carbonate-rich lithified mats of filamentous microorganisms, diatoms, associated photosynthetic and chemotrophic bacteria, and trapped sediment. In addition, 16S rRNA analysis indicates the presence of five sulfur-reducing genera of bacteria. These microbes are potential modern-day analogs to some ancient stromatolitic structures. The goals of this study are to identify unique compositional and biogenic features, possibly correlating some of these with some of the sulfate-reducing bacteria. Additional information is contained in the original extended abstract.

Effect of flagellates on free-living bacterial abundance in an organically contaminated aquifer

USGS Publications Warehouse

Kinner, N.E.; Harvey, R.W.; Kazmierkiewicz-Tabaka, M.

1997-01-01

Little is known about the role of protists in the saturated subsurface. Porous media microcosms containing bacteria and protists, were used to determine whether flagellates from an organically contaminated aquifer could substantively affect the number of free- living bacteria (FLB). When flagellates were present, the 3-40% maximum breakthrough of fluorescent y labelled FLB injected into the microcosms was much lower than the 60-130% observed for killed controls Grazing and clearance rates (3-27 FLB flag-1 h-1 and 12-23 nI flag-1 h-1, respectively) calculated from the data were in the range reported for flagellates in other aqueous environments. The data provide evidence that flagellate bacterivory is an important control on groundwater FLB populations.

The Role of Chromohalobacter on Transport of Lanthanides and Cesium in the Dolomite Mineral System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zengotita, Frances; Emerson, Hilary Palmer; Dittrich, Timothy M.

2017-12-01

The chemical behavior of actinide series elements and fission products is a concern for the Waste Isolation Pilot Plant repository due to their uncertain mobility in the subsurface salt formation. In this work, we are observing the behavior of the halophilic bacterium, Chromohalobacter, and its effect on the mobility of lanthanides and cesium in the presence of dolomite. Batch and minicolumn experiments were conducted with Cs + and lanthanides (Nd 3+, Eu 3+) to quantify potential transport with bacteria. Preliminary results show that Cs does not interact strongly with dolomite or Chromohalobacter, while the lanthanides can interact strongly with bothmore » minerals and bacteria depending on which the Ln contacts first.« less

Efficiency of phenol biodegradation by planktonic Pseudomonas pseudoalcaligenes (a constructed wetland isolate) vs. root and gravel biofilm.

PubMed

Kurzbaum, Eyal; Kirzhner, Felix; Sela, Shlomo; Zimmels, Yoram; Armon, Robert

2010-09-01

In the last two decades, constructed wetland systems gained increasing interest in wastewater treatment and as such have been intensively studied around the world. While most of the studies showed excellent removal of various pollutants, the exact contribution, in kinetic terms, of its particular components (such as: root, gravel and water) combined with bacteria is almost nonexistent. In the present study, a phenol degrader bacterium identified as Pseudomonas pseudoalcaligenes was isolated from a constructed wetland, and used in an experimental set-up containing: plants and gravel. Phenol removal rate by planktonic and biofilm bacteria (on sterile Zea mays roots and gravel surfaces) was studied. Specific phenol removal rates revealed significant advantage of planktonic cells (1.04 × 10(-9) mg phenol/CFU/h) compared to root and gravel biofilms: 4.59 × 10(-11)-2.04 × 10(-10) and 8.04 × 10(-11)-4.39 × 10(-10) (mg phenol/CFU/h), respectively. In batch cultures, phenol biodegradation kinetic parameters were determined by biomass growth rates and phenol removal as a function of time. Based on Haldane equation, kinetic constants such as μ(max) = 1.15/h, K(s) = 35.4 mg/L and K(i) = 198.6 mg/L fit well phenol removal by P. pseudoalcaligenes. Although P. pseudoalcaligenes planktonic cells showed the highest phenol removal rate, in constructed wetland systems and especially in those with sub-surface flow, it is expected that surface associated microorganisms (biofilms) will provide a much higher contribution in phenol and other organics removal, due to greater bacterial biomass. Factors affecting the performance of planktonic vs. biofilm bacteria in sub-surface flow constructed wetlands are further discussed. Copyright © 2010 Elsevier Ltd. All rights reserved.

High performance constructed wetlands for cold climates.

PubMed

Jenssen, Petter D; Maehlum, Trend; Krogstad, Tore; Vråle, Lasse

2005-01-01

In 1991, the first subsurface flow constructed wetland for treatment of domestic wastewater was built in Norway. Today, this method is rapidly becoming a popular method for wastewater treatment in rural Norway. This is due to excellent performance even during winter and low maintenance. The systems can be constructed regardless of site conditions. The Norwegian concept for small constructed wetlands is based on the use of a septic tank followed by an aerobic vertical down-flow biofilter succeeded by a subsurface horizontal-flow constructed wetland. The aerobic biofilter, prior to the subsurface flow stage, is essential to remove BOD and achieve nitrification in a climate where the plants are dormant during the cold season. When designed according to present guidelines a consistent P-removal of > 90% can be expected for 15 years using natural iron or calcium rich sand or a new manufactured lightweight aggregate with P-sorption capacities, which exceeds most natural media. When the media is saturated with P it can be used as soil conditioner and P-fertilizer. Nitrogen removal in the range of 40-60% is achieved. Removal of indicator bacteria is high and < 1000 thermotolerant coliforms/100 ml is normally achieved.

Sorption of Pseudomonas putida onto differently structured kaolinite minerals

NASA Astrophysics Data System (ADS)

Vasiliadou, I. A.; Papoulis, D.; Chrysikopoulos, C.; Panagiotaras, D.; Karakosta, E.; Fardis, M.; Papavassiliou, G.

2010-12-01

The presence of bio-colloids (e.g. bacteria and viruses) in the subsurface could be attributed to the release of particles from septic tanks, broken sewer lines or from artificial recharge with treated municipal wastewater. Bio-colloid transport in the subsurface is significantly affected by sorption onto the solid matrix. Bio-colloid attachment onto mobile or suspended in the aqueous phase soil particles (e.g. clay or other minerals) also may influence their fate and transport in the subsurface. The present study focuses on the investigation of Pseudomonas (Ps.) putida sorption onto well (KGa-1) and poorly (KGa-2) crystallized kaolinite minerals. Batch experiments were carried out to determine the sorption isotherms of Ps. putida onto both types of kaolinite particles. The sorption process of Ps. putida onto KGa-1 and KGa-2 is adequately described by a Langmuir isotherm. Attenuated Total Reflection Fourier Transform Infrared Spectroscopy as well as Nuclear Magnetic Resonance were employed to study the sorption mechanisms of Ps. putida. Experimental results indicated that KGa-2 presented higher affinity and sorption capacity than KGa-1. It was shown that electrostatic interactions and structural disorders can influence the sorption capacity of clay particles.

Microbial Life of North Pacific Oceanic Crust

NASA Astrophysics Data System (ADS)

Schumann, G.; Koos, R.; Manz, W.; Reitner, J.

2003-12-01

Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed reactions that influence the geophysical properties of these environments. Drilling into 45-Ma oceanic basaltic crust in a deepwater environment during ODP Leg 200 provided a promising opportunity to explore the abundance, diversity and activity of micro-organisms. The combined use of culture-independent molecular phylogenetic analyses and enrichment culture techniques is an advantageous approach in investigating subsurface microbial ecosystems. Enrichment culture methods allow the evaluation of potential activities and functions. Microbiological investigations revealed few aerobic cultivable, in part hitherto unknown, micro-organisms in deep submarine sediments and basaltic lava flows. 16S rDNA sequencing of isolates from sediment revealed the next relatives to be members of the genera Halomonas, Pseudomonas, and Lactobacillus. Within the Pseudomonadaceae the closest relative is Acinetobacter sp., which was isolated from a deep subsurface environment. The next phylogenetical relatives within the Halomonadaceae are bacteria typically isolated from Soda lakes, which are considered as model of early life conditions. Interestingly, not only sediment bacteria could be obtained in pure culture. Aerobic strains could also be successfully isolated from the massive tholeiitic basalt layer at a depth of 76.16 mbsf (46 m below the sediment/basement contact). These particular isolates are gram-positive with low G+C content of DNA, phylogenetically affiliated to the phylum Firmicutes. The closest neighbors are e.g. a marine Bacillus isolated from the Gulf of Mexico and a low G+C gram-positive bacterium, which belongs to the microbial flora in the deepest sea mud of the Mariana Trench, isolated from a depth of 10,897 m. Based on the similarity values, the isolates represent hitherto undescribed species of the deep biosphere. Molecular microbial diversity is currently determined by cloning und comparative 16S rRNA gene analyses. The first results will also be presented. In summary, the low number of isolates, cultivated under aerobic conditions, is in good agreement with the common opinion that most of the bacteria within the deep biosphere are anaerobic. Thus, studies of microbial community structure in solid geological materials are feasible and constitute further evidence that continuing microbiological activity in the challenging exploration of the deep sub-seafloor biosphere environment is absolutely promising.

Anaerobic U(IV) Bio-oxidation and the Resultant Remobilization of Uranium in Contaminated Sediments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coates, John D.

2005-06-01

A proposed strategy for the remediation of uranium (U) contaminated sites is based on immobilizing U by reducing the oxidized soluble U, U(VI), to form a reduced insoluble end product, U(IV). Due to the use of nitric acid in the processing of nuclear fuels, nitrate is often a co-contaminant found in many of the environments contaminated with uranium. Recent studies indicate that nitrate inhibits U(VI) reduction in sediment slurries. However, the mechanism responsible for the apparent inhibition of U(VI) reduction is unknown, i.e. preferential utilization of nitrate as an electron acceptor, direct biological oxidation of U(IV) coupled to nitrate reduction,more » and/or abiotic oxidation by intermediates of nitrate reduction. Recent studies indicates that direct biological oxidation of U(IV) coupled to nitrate reduction may exist in situ, however, to date no organisms have been identified that can grow by this metabolism. In an effort to evaluate the potential for nitrate-dependent bio-oxidation of U(IV) in anaerobic sedimentary environments, we have initiated the enumeration of nitrate-dependent U(IV) oxidizing bacteria. Sediments, soils, and groundwater from uranium (U) contaminated sites, including subsurface sediments from the NABIR Field Research Center (FRC), as well as uncontaminated sites, including subsurface sediments from the NABIR FRC and Longhorn Army Ammunition Plant, Texas, lake sediments, and agricultural field soil, sites served as the inoculum source. Enumeration of the nitrate-dependent U(IV) oxidizing microbial population in sedimentary environments by most probable number technique have revealed sedimentary microbial populations ranging from 9.3 x 101 - 2.4 x 103 cells (g sediment)-1 in both contaminated and uncontaminated sites. Interestingly uncontaminated subsurface sediments (NABIR FRC Background core FB618 and Longhorn Texas Core BH2-18) both harbored the most numerous nitrate-dependent U(IV) oxidizing population 2.4 x 103 cells (g sediment)-1. The nitrate-dependent U(IV) oxidizing microbial population in groundwaters is less numerous ranging from 0 cells mL-1 (Well FW300, Uncontaminated Background NABIR FRC) to 4.3 x 102 cells mL-1 (Well TPB16, Contaminated Area 2 NABIR FRC). The presence of nitrate-dependent U(IV) oxidizing bacteria supports our hypothesis that bacteria capable of anaerobic U(IV) oxidation are ubiquitous and indigenous to sedimentary and groundwater environments.« less

Deep subsurface microbiology of 64-71 million year old inactive seamounts along the Louisville Seamount Chain

NASA Astrophysics Data System (ADS)

Sylvan, J. B.; Morono, Y.; Grim, S.; Inagaki, F.; Edwards, K. J.

2013-12-01

One of the objectives of IODP Expedition 330, Louisville Seamount Trail, was to sample and learn about the subsurface biosphere in the Louisville Seamount Chain (LSC). Seamounts are volcanic constructs that are ubiquitous along the seafloor - models suggest there are >100,000 seamounts of >1 km in height globally (Wessel et al., 2010). Therefore, knowledge about microbiology in the LSC subsurface can broadly be interpreted as representative of much the seafloor. In addition, despite the fact that the vast majority of the sea floor is comprised of crust >10 Ma, the majority of work to date has focused on young sites with active hydrology. Our presentation summarizes work focusing on subsurface microbiology from two different LSC seamounts: holes U1374A (65-71 Ma) and U1376A (64 Ma). We here present data for microbial biomass in the LSC subsurface using a method we developed to quantify microbial biomass in subseafloor ocean crust. We also present results from pyrotag analysis of 15 samples from holes U1374A and holes U1376A, representing several different lithologies from 40-491 meters below seafloor (mbsf) in hole U1374A and from 29-174 mbsf in hole U1376A. Finally, we present preliminary analysis of metagenomic sequencing from three of the samples from Hole U1376A. Biomass was low in the subsurface of both seamounts, ranging from below detection to ~104 cells cm-3. Bacteria comprised >99% of the prokaryotic community in LSC subsurface samples, therefore, bacterial diversity was assessed through 454 pyrosequencing of the V4V6 region of the 16S rRNA gene. Rarefaction analysis indicates that bacterial communities from the LSC subsurface are low diversity, on the order of a few hundred operational taxonomic units per sample. The phyla Actinobacteria, Bacteroidetes, Firmicutes and the classes α-, β- and γ-Proteobacteria are most abundant in the LSC subsurface. Within these, the orders Actinomycetales, Sphingobacteriales, Bacillales and Burkholderiales are the most common. Samples from different lithologies in hole U1374A grouped together, indicating more similarity to each other than to samples from hole U1376A. However, samples from different lithologies in hole U1376A were not similar to other samples from the same site, indicating some differences in the microbial communities between the two seamounts. Preliminary analysis of the metagenomic data will provide further assessment of community structure and reveal likely metabolisms present in the LSC subsurface. Altogether, the biomass data, pyrotag analysis and metagenomic sequencing provide a well-balanced analysis of subsurface microbiology in an old oceanic crustal environment. Wessel, P., Sandwell, D. T. & Kim, S. S. (2010). The Global Seamount Census. Oceanography 23, 24-33.

Toward a Mechanistic Understanding of Anaerobic Nitrate-Dependent Iron Oxidation: Balancing Electron Uptake and Detoxification

PubMed Central

Carlson, Hans K.; Clark, Iain C.; Melnyk, Ryan A.; Coates, John D.

2011-01-01

The anaerobic oxidation of Fe(II) by subsurface microorganisms is an important part of biogeochemical cycling in the environment, but the biochemical mechanisms used to couple iron oxidation to nitrate respiration are not well understood. Based on our own work and the evidence available in the literature, we propose a mechanistic model for anaerobic nitrate-dependent iron oxidation. We suggest that anaerobic iron-oxidizing microorganisms likely exist along a continuum including: (1) bacteria that inadvertently oxidize Fe(II) by abiotic or biotic reactions with enzymes or chemical intermediates in their metabolic pathways (e.g., denitrification) and suffer from toxicity or energetic penalty, (2) Fe(II) tolerant bacteria that gain little or no growth benefit from iron oxidation but can manage the toxic reactions, and (3) bacteria that efficiently accept electrons from Fe(II) to gain a growth advantage while preventing or mitigating the toxic reactions. Predictions of the proposed model are highlighted and experimental approaches are discussed. PMID:22363331

Transport of subsurface bacteria in porous media. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arnold, R.G.; Baygents, J.C.; Ogden, K.L.

The aims of our project have not changed significantly since the original proposal. Our primary goals were to support field experiments by screening strains of bacteria to find favorable transport characteristics among field isolates and to estimate collision efficiencies for those bacteria in typical Oyster site sediments. The data we obtained were disseminated to other members of the subprogram. For example, Tim Ginn of PNL incorporated our results into his field model; Aaron Mills used our work for comparison purposes; and John Wilson used our results to determine if there is a correlation between facies type and cell adhesion. Copiesmore » of all information were also sent to Mary DeFlaun of Envirogen for incorporation into the Sample Tables. In addition to the originally proposed work, we performed longer column studies, examining the effects of aluminum, iron, and water chemistry on bacterial transport, and beginning to understand the role of electrostatic interactions as determinants of biocolloid/collector affinity.« less

Kinetics of conjugative gene transfer on surfaces in granular porous media

NASA Astrophysics Data System (ADS)

Ginn, T.; Massoudieh, A.; Nelson, K.; Mathew, A.; Lambertini, E.

2005-12-01

The transfer of genetic material among bacteria in the environment can occur both in the planktonic and attached state. Given the propensity of organisms to exist in sessile microbial communities in oligotrophic conditions, and that such conditions typify the subsurface, this study focuses on exploratory modeling of horizontal gene transfer among surface-associated E. coli in the subsurface. The mathematics so far used to describe the kinetics of conjugation in biofilms are developed largely from experimental observations of planktonic gene transfer, and are absent of lags or plasmid stability that appear experimentally. We develop a model for bacterial filtration and gene transfer in the attached state, for the early stages of biofilm formation using a recently revised filtration theory approach (Nelson and Ginn, 2005) with motility of E. coli described as a continuous time random walk according to data from microflow chamber experiments (Biondi et al., 2002).

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock.

PubMed

Bagnoud, Alexandre; Chourey, Karuna; Hettich, Robert L; de Bruijn, Ino; Andersson, Anders F; Leupin, Olivier X; Schwyn, Bernhard; Bernier-Latmani, Rizlan

2016-10-14

The Opalinus Clay formation will host geological nuclear waste repositories in Switzerland. It is expected that gas pressure will build-up due to hydrogen production from steel corrosion, jeopardizing the integrity of the engineered barriers. In an in situ experiment located in the Mont Terri Underground Rock Laboratory, we demonstrate that hydrogen is consumed by microorganisms, fuelling a microbial community. Metagenomic binning and metaproteomic analysis of this deep subsurface community reveals a carbon cycle driven by autotrophic hydrogen oxidizers belonging to novel genera. Necromass is then processed by fermenters, followed by complete oxidation to carbon dioxide by heterotrophic sulfate-reducing bacteria, which closes the cycle. This microbial metabolic web can be integrated in the design of geological repositories to reduce pressure build-up. This study shows that Opalinus Clay harbours the potential for chemolithoautotrophic-based system, and provides a model of microbial carbon cycle in deep subsurface environments where hydrogen and sulfate are present.

Multiple sulphur and oxygen isotopes reveal microbial sulphur cycling in spring waters in the Lower Engadin, Switzerland.

PubMed

Strauss, Harald; Chmiel, Hannah; Christ, Andreas; Fugmann, Artur; Hanselmann, Kurt; Kappler, Andreas; Königer, Paul; Lutter, Andreas; Siedenberg, Katharina; Teichert, Barbara M A

2016-01-01

Highly mineralized springs in the Scuol-Tarasp area of the Lower Engadin and in the Albula Valley near Alvaneu, Switzerland, display distinct differences with respect to the source and fate of their dissolved sulphur species. High sulphate concentrations and positive sulphur (δ(34)S) and oxygen (δ(18)O) isotopic compositions argue for the subsurface dissolution of Mesozoic evaporitic sulphate. In contrast, low sulphate concentrations and less positive or even negative δ(34)S and δ(18)O values indicate a substantial contribution of sulphate sulphur from the oxidation of sulphides in the crystalline basement rocks or the Jurassic sedimentary cover rocks. Furthermore, multiple sulphur (δ(34)S, Δ(33)S) isotopes support the identification of microbial sulphate reduction and sulphide oxidation in the subsurface, the latter is also evident through the presence of thick aggregates of sulphide-oxidizing Thiothrix bacteria.

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock

PubMed Central

Bagnoud, Alexandre; Chourey, Karuna; Hettich, Robert L.; de Bruijn, Ino; Andersson, Anders F.; Leupin, Olivier X.; Schwyn, Bernhard; Bernier-Latmani, Rizlan

2016-01-01

The Opalinus Clay formation will host geological nuclear waste repositories in Switzerland. It is expected that gas pressure will build-up due to hydrogen production from steel corrosion, jeopardizing the integrity of the engineered barriers. In an in situ experiment located in the Mont Terri Underground Rock Laboratory, we demonstrate that hydrogen is consumed by microorganisms, fuelling a microbial community. Metagenomic binning and metaproteomic analysis of this deep subsurface community reveals a carbon cycle driven by autotrophic hydrogen oxidizers belonging to novel genera. Necromass is then processed by fermenters, followed by complete oxidation to carbon dioxide by heterotrophic sulfate-reducing bacteria, which closes the cycle. This microbial metabolic web can be integrated in the design of geological repositories to reduce pressure build-up. This study shows that Opalinus Clay harbours the potential for chemolithoautotrophic-based system, and provides a model of microbial carbon cycle in deep subsurface environments where hydrogen and sulfate are present. PMID:27739431

Rock weathering by indigenous heterotrophic bacteria of Bacillus spp. at different temperature: a laboratory experiment

NASA Astrophysics Data System (ADS)

Štyriaková, I.; Štyriak, I.; Oberhänsli, H.

2012-07-01

The bio-weathering of basalt, granite and gneiss was experimentally investigated in this study. These rock-forming minerals weathered more rapidly via the ubiquitous psychrotrophic heterotrophic bacteria . With indigenous bacteria of Bacillus spp. from sediments of Lake Baikal, we traced the degradation process of silicate minerals to understand the weathering processes occurring at the change temperature in the subsurface environment with organic input. The bacteria mediated dissolution of minerals was monitored with solution and solid chemistry, X-ray analyses as well as microscopic techniques. We determined the impact of the bacteria on the mineral surface and leaching of K, Ca, Mg, Si, Fe, and Al from silicate minerals. In the samples the release of major structural elements of silicates was used as an overall indicator of silicate mineral degradation at 4°C and 18°C from five medium exchanges over 255 days of rock bioleaching. The increase of temperature importantly affected the efficiency of Fe extraction from granite and basalt as well as Si extraction from granite and gneiss. In comparison with elemental extraction order at 4°C, Ca was substituted first by Fe or Si. It is evident that temperature influences rock microbial weathering and results in a change of elements extraction.

Groundwater mixing at fracture intersections triggers massive iron-rich microbial mats

NASA Astrophysics Data System (ADS)

Bochet, O.; Le Borgne, T.; Bethencourt, L.; Aquilina, L.; Dufresne, A.; Pédrot, M.; Farasin, J.; Abbott, B. W.; Labasque, T.; Chatton, E.; Lavenant, N.; Petton, C.

2017-12-01

While most freshwater on Earth resides and flows in groundwater systems, these deep subsurface environments are often assumed to have little biogeochemical activity compared to surface environments. Here we report a massive microbial mat of iron-oxidizing bacteria, flourishing 60 meters below the surface, far below the mixing zone where most microbial activity is believed to occur. The abundance of microtubular structures in the mat hinted at the prevalence of of Leptothrix ochracea, but metagenomic analysis revealed a diverse consortium of iron-oxidizing bacteria dominated by unknown members of the Gallionellaceae family. This deep biogeochemical hot spot formed at the intersection of bedrock fractures, which maintain redox gradients by mixing water with different residence times and chemical compositions. Using measured fracture properties and hydrological conditions we developed a quantitative model to simulate the reactive zone where such deep hot spots could occur. While seasonal fluctuations are generally thought to decrease with depth, we found that meter-scale changes in water table level moved the depth of the reactive zone hundreds of meters because the microaerophilic threshold for ironoxidizers is highly sensitive to changes in mixing rates at fracture intersections. These results demonstrate that dynamic microbial communities can be sustained deep below the surface in bedrock fractures. Given the ubiquity of fractures at multiple scales in Earth's subsurface, such deep hot spots may strongly influence global biogeochemical cycles.

Annual layers revealed by GPR in the subsurface of a prograding coastal barrier, southwest Washington, U.S.A

USGS Publications Warehouse

Moore, L.J.; Jol, H.M.; Kruse, S.; Vanderburgh, S.; Kaminsky, G.M.

2004-01-01

The southwest Washington coastline has experienced extremely high rates of progradation during the late Holocene. Subsurface stratigraphy, preserved because of progradation and interpreted using ground-penetrating radar (GPR), has previously been used successfully to document coastal response to prehistoric storm and earthquake events. New GPR data collected at Ocean Shores, Washington, suggest that the historic stratigraphy of the coastal barrier in this area represents a higher resolution record of coastal behavior than previously thought. GPR records for this location at 200 MHz reveal a series of gently sloping, seaward-dipping reflections with slopes similar to the modern beach and spacings on the order of 20-45 cm. Field evidence and model results suggest that thin (1-10 cm), possibly magnetite-rich, heavy-mineral lags or low-porosity layers left by winter storms and separated by thick (20-40 cm) summer progradational sequences are responsible for generating the GPR reflections. These results indicate that a record of annual progradation is preserved in the subsurface of the prograding barrier and can be quantified using GPR. Such records of annual coastal behavior, where available, will be invaluable in understanding past coastal response to climatic and tectonic forcing. ?? 2004.

Microbial metabolism of Tholin

NASA Technical Reports Server (NTRS)

Stoker, C. R.; Mancinelli, R. L.; Boston, P. J.; Segal, W.; Khare, B. N.

1990-01-01

Tholin, a class of complex organic heteropolymers hypothesized to possess wide solar system distribution, is shown to furnish the carbon and energy requirements of a wide variety of common soil bacteria which encompasses aerobic, anaerobic, and facultatively anaerobic bacteria. Some of these bacteria are able to derive not merely their carbon but also their nitrogen requirements from tholin. The palatability of tholins to modern microbes is speculated to have implications for the early evolution of microbial life on earth; tholins may have formed the base of the food chain for an early heterotrophic biosphere, prior to the evolution of autotrophy on the early earth.

Impact of human aging and modern lifestyle on gut microbiota.

PubMed

Valle Gottlieb, Maria Gabriela; Closs, Vera Elizabeth; Junges, Vilma Maria; Schwanke, Carla Helena Augustin

2018-06-13

Human evolution and lifestyle changes caused by the agricultural and industrial revolutions have led to great advances in medicine and increased life expectancy, whilst also profoundly altering the ecological relationships and disease patterns of populations. Studies involving populations that still enjoy a rural way of life and with traits similar to the Paleolithic period reveal them to present a more robust, resistant and diverse gut microbiota, in comparison to highly industrialized civilizations. The human diet has expanded and broadened to include the consumption of high-calorie foods, particularly from animal sources such as game meat and eggs. For some time, authors have been alert to the fact that a modern lifestyle leads to reduced intake of beneficial bacteria, suggesting that nonpathogenic bacteria are being eradicated. Furthermore, therapeutic procedures, including the use of probiotics and prebiotics, have been proposed to lead to recovery of this microbiota, which is altered due to both the ageing process and lifestyle related aspects. Accordingly, this article aims to review the impact of human aging and modern lifestyle on gut microbiota, within an evolutionary, ecological, epidemiological and therapeutic context.

Comparison and Correlation of Subsurface Media Properties Reflected in Both Extracted Soil Pore Water From Sectioned Cores and Homogenized Groundwater From Monitoring Wells

NASA Astrophysics Data System (ADS)

Moon, J. W.; Paradis, C. J.; von Netzer, F.; Dixon, E.; Majumder, E.; Joyner, D.; Zane, G.; Fitzgerald, K.; Xiaoxuan, G.; Thorgersen, M. P.; Lui, L.; Adams, B.; Brewer, S. S.; Williams, D.; Lowe, K. A.; Rodriguez, M., Jr.; Mehlhorn, T. L.; Pfiffner, S. M.; Chakraborty, R.; Arkin, A. P.; Terry, A. Y.; Wall, J. D.; Stahl, D. A.; Elias, D. A.; Hazen, T. C.

2017-12-01

Conventional monitoring wells have produced useful long-term data about the contaminants, carbon flux, microbial population and their evolution. The averaged homogenized groundwater matrix from these wells is insufficient to represent all media properties in subsurface. This pilot study investigated the solid, liquid and gas phases from soil core samples from both uncontaminated and contaminated areas of the ENIGMA field research site at Oak Ridge, Tennessee. We focused on a site-specific assessment with depth perspective that included soil structure, soil minerals, major and trace elements and biomass for the solid phase; centrifuged soil pore water including cations, anions, organic acid, pH and conductivity for the liquid phase; and gas (CO2, CH4, N2O) evolution over a 4 week incubation with soil and unfiltered groundwater. Pore water from soil core sections showed a correlation between contamination levels with depth and the potential abundance of sulfate- and nitrate-reducing bacteria based on the 2-order of magnitude decreased concentration. A merged interpretation with mineralogical consideration revealed a more complicated correlation among contaminants, soil texture, clay minerals, groundwater levels, and biomass. This sampling campaign emphasized that subsurface microbial activity and metabolic reactions can be influenced by a variety of factors but can be understood by considering the influence of multiple geochemical factors from all subsurface phases including water, air, and solid along depth rather than homogenized groundwater.

Depositionally controlled recycling of iron and sulfur in marine sediments and its isotopic consequences

NASA Astrophysics Data System (ADS)

Riedinger, N.; Formolo, M.; Arnold, G. L.; Vossmeyer, A.; Henkel, S.; Sawicka, J.; Kasten, S.; Lyons, T. W.

2011-12-01

The continental margin off Uruguay and Argentina is characterized by highly dynamic depositional conditions. This variable depositional regime significantly impacts the biogeochemical cycles of iron and sulfur. Mass deposit related redeposition of reduced minerals can lead to the reoxidation of these phases and thus to an overprint of their geochemical primary signatures. Due to rapid burial these oxidized phases are still present in deeper subsurface sediments. To study the effects of sediment relocation on the sulfur and iron inventory we collected shallow and deep subsurface sediment samples via multicorer and gravity cores, respectively, in the western Argentine Basin during the RV Meteor Expedition M78/3 in May-July 2009. The samples were retrieved from shelf, slope and deep basin sites. The concentration and sulfur isotope composition of acid volatile sulfur (AVS), chromium reducible sulfur (CRS), elemental sulfur and total organic sulfur were determined. Furthermore, sequential iron extraction techniques were applied assess the distribution of iron oxide phases within the sediment. The investigated sediments are dominated by terrigenous inputs, with high amounts of reactive ferric iron minerals and only low concentrations of calcium carbonate. Total organic carbon concentrations show strong variation in the shallow subsurface sediments ranging between approximately 0.7 and 6.4 wt% for different sites. These concentrations do not correlate with water depths. Pore water accumulations of hydrogen sulfide are restricted to an interval at the sulfate-methane transition (SMT) zone a few meters below the sediment surface. In these deeper subsurface sediments pyrite is precipitated in this zone of hydrogen sulfide excess, whereas the accumulation of authigenic AVS and elemental sulfur (up to 2000 ppm) occurs at the upper and lower boundary of the sulfidic zone due the reaction of iron oxides with limited amounts of sulfide. Furthermore, our preliminary results indicate that there is a link between modern deposition in the shallow subsurface sediments and the long-term signals being buried and preserved in the deep subsurface layers. The data show that the burial of elemental sulfur into deep subsurface sediments can fuel the deep biosphere and has consequences for isotopic overprints tied, for example, to oxidation and disproportionation processes in the deeper sediments.

Multi-heme cytochromes provide a pathway for survival in energy-limited environments

PubMed Central

Deng, Xiao; Dohmae, Naoshi; Nealson, Kenneth H.; Hashimoto, Kazuhito; Okamoto, Akihiro

2018-01-01

Bacterial reduction of oxidized sulfur species (OSS) is critical for energy production in anaerobic marine subsurfaces. In organic-poor sediments, H2 has been considered as a major energy source for bacterial respiration. We identified outer-membrane cytochromes (OMCs) that are broadly conserved in sediment OSS-respiring bacteria and enable cells to directly use electrons from insoluble minerals via extracellular electron transport. Biochemical, transcriptomic, and microscopic analyses revealed that the identified OMCs were highly expressed on the surface of cells and nanofilaments in response to electron donor limitation. This electron uptake mechanism provides sufficient but minimum energy to drive the reduction of sulfate and other OSS. These results suggest a widespread mechanism for survival of OSS-respiring bacteria via electron uptake from solid minerals in energy-poor marine sediments. PMID:29464208

Species and Scale Dependence of Bacterial Motion Dynamics

NASA Astrophysics Data System (ADS)

Sund, N. L.; Yang, X.; Parashar, R.; Plymale, A.; Hu, D.; Kelly, R.; Scheibe, T. D.

2017-12-01

Many metal reducing bacteria are motile with their motion characteristics described by run-and-tumble behavior exhibiting series of flights (jumps) and waiting (residence) time spanning a wide range of values. Accurate models of motility allow for improved design and evaluation of in-situ bioremediation in the subsurface. While many bioremediation models neglect the motion of the bacteria, others treat motility using an advection dispersion equation, which assumes that the motion of the bacteria is Brownian.The assumption of Brownian motion to describe motility has enormous implications on predictive capabilities of bioremediation models, yet experimental evidence of this assumption is mixed [1][2][3]. We hypothesize that this is due to the species and scale dependence of the motion dynamics. We test our hypothesis by analyzing videos of motile bacteria of five different species in open domains. Trajectories of individual cells ranging from several seconds to few minutes in duration are extracted in neutral conditions (in the absence of any chemical gradient). The density of the bacteria is kept low so that the interaction between the bacteria is minimal. Preliminary results show a transition from Fickian (Brownian) to non-Fickian behavior for one species of bacteria (Pelosinus) and persistent Fickian behavior of another species (Geobacter).Figure: Video frames of motile bacteria with the last 10 seconds of their trajectories drawn in red. (left) Pelosinus and (right) Geobacter.[1] Ariel, Gil, et al. "Swarming bacteria migrate by Lévy Walk." Nature Communications 6 (2015).[2] Saragosti, Jonathan, Pascal Silberzan, and Axel Buguin. "Modeling E. coli tumbles by rotational diffusion. Implications for chemotaxis." PloS one 7.4 (2012): e35412.[3] Wu, Mingming, et al. "Collective bacterial dynamics revealed using a three-dimensional population-scale defocused particle tracking technique." Applied and Environmental Microbiology 72.7 (2006): 4987-4994.

Role of dissolved organic carbon upon re-entrainment and surface properties of aquifer bacteria and bacteria-sized microspheres during subsurface transport (Invited)

NASA Astrophysics Data System (ADS)

Harvey, R. W.; Metge, D. W.; Mohanram, A.; Gao, X.; Chorover, J.

2010-12-01

Susceptibilities for in-situ re-entrainment of attached 0.2 and 1.0 μm (diameter) microspheres and groundwater bacteria (Pseudomonas stuzeri and uncultured, native bacteria) were assessed during transport studies involving an organically contaminated, sandy aquifer in Cape Cod, MA. Aquifer sediments between pairs of injection and sampling wells were initially loaded with fluorescently labeled, carboxylated microspheres and bacteria that had been stained with the DNA-specific fluorochrome 4',6-diamidino-2-phenylindole. In response to subsequent hydrodynamic perturbations and injections of deionized water (ionic strength reduction), anionic surfactants (77 μM linear alkylbenzene sulfonates, LAS) and non-ionic surfactant (76 μM polyoxyethylene sorbitan monooleate, Tween 80), differing patterns of re-entrainment were evident for the two colloids. Injections of anionic surfactant and deionized water were the most efficient in causing detachment of the highly hydrophilic and negatively charged microspheres, but largely ineffective in causing re-entrainment of bacteria. In contrast, the nonionic surfactant was highly effective in re-entraining bacteria, but not microspheres. The hydrophobicities and zeta potentials of the indigenous bacteria were highly sensitive to modest concentration changes (0.6 to 1.3 mg L-1) in groundwater dissolved organic carbon (DOC), whereas the microspheres were largely unaffected. The most hydrophilic and negatively charged bacterial community was isolated from groundwater having the lowest DOC. FTIR spectra indicated that the community from the lowest DOC groundwater also had the highest average density of surface carboxyl groups. This indicates that DOC may have a biological effect on native bacteria resulting in changes to surface structures or changes in the makeup of the bacterial community.

Neptunium(V) Adsorption to Bacteria at Low and High Ionic Strength

NASA Astrophysics Data System (ADS)

Ams, D.; Swanson, J. S.; Reed, D. T.

2010-12-01

Np(V) is expected to be the predominant oxidation state of neptunium in aerobic natural waters. Np(V), as the NpO2+ aquo and associated complexed species, is readily soluble, interacts weakly with geologic media, and has a high redox stability under a relatively wide range of subsurface conditions. These chemical properties, along with a long half-life make it a primary element of concern regarding long-term nuclear waste storage and subsurface containment. The fate and transport of neptunium in the environment may be influenced by adsorption onto bacterial surfaces. The adsorption of neptunium to bacterial surfaces ties the mobility of the contaminant to the mobility of the bacterium. In this study, the adsorption of the neptunyl (NpO2+) ion was evaluated at low ionic strength on a common soil bacterium and at high ionic strength on a halophilic bacterium isolated from a briny groundwater near the Waste Isolation Pilot Plant (WIPP) in southeast New Mexico. Adsorption experiments were performed in batch reactors as a function of pH, ionic strength, and bacteria/Np mass ratio. Np(V) adsorption was modeled using a surface complexation approach with the mathematical program FITEQL to determine functional group specific binding constants. The data from acid and base titrations of the bacteria used were also modeled to estimate the concentrations and deprotonation constants of discrete bacterial surface functional groups. Bacterial functional group characteristics and Np(V) adsorption behavior between the soil bacterium and the halophilic bacterium were compared. These results highlight key similarities and differences in actinide adsorption behavior in environments of significantly different ionic strength. The observed adsorption behavior may be linked to similarities and differences in the characteristics of the moieties between the cell walls of common gram-negative soil and halophilic bacteria. Moreover, differences in adsorption behavior may also reflect ionic strength effects as the electronic double layer is compressed with increasing ionic strength. These results further highlight the importance of electrostatic interactions in the adsorption process between dissolved metals and bacterial surfaces. This work expands the understanding of actinide-bacteria adsorption phenomena to high ionic strength environmental conditions that are relevant as an aid to predicting Np(V) fate and transport behavior in areas such as the vicinity of salt-based nuclear waste repositories and high ionic-strength groundwaters at DOE sites.

Terrestrial Subsurface Ecosystem

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilkins, Michael J.; Fredrickson, Jim K.

2015-10-15

The Earth’s crust is a solid cool layer that overlays the mantle, with a varying thickness of between 30-50 km on continental plates, and 5-10 km on oceanic plates. Continental crust is composed of a variety of igneous, metamorphic, and sedimentary rocks that weather and re-form over geologic cycles lasting millions to billions of years. At the crust surface, these weathered minerals and organic material combine to produce a variety of soils types that provide suitable habitats and niches for abundant microbial diversity (see Chapter 4). Beneath this soil zone is the subsurface. Once thought to be relatively free ofmore » microorganisms, recent estimates have calculated that between 1016-1017 g C biomass (2-19% of Earth’s total biomass) may be present in this environment (Whitman et al., 1998;McMahon and Parnell, 2014). Microbial life in the subsurface exists across a wide range of habitats: in pores associated with relatively shallow unconsolidated aquifer sediments to fractures in bedrock formations that are more than a kilometer deep, where extreme lithostatic pressures and temperatures are encountered. While these different environments contain varying physical and chemical conditions, the absence of light is a constant. Despite this, diverse physiologies and metabolisms enable microorganisms to harness energy and carbon for growth in water-filled pore spaces and fractures. Carbon and other element cycles are driven by microbial activity, which has implications for both natural processes and human activities in the subsurface, e.g., bacteria play key roles in both hydrocarbon formation and degradation. Hydrocarbons are a major focus for human utilization of the subsurface, via oil and gas extraction and potential geologic CO2 sequestration. The subsurface is also utilized or being considered for sequestered storage of high-level radioactive waste from nuclear power generation and residual waste from past production of weapons grade nuclear materials. While our understanding of the subsurface is continually improving, it is clear that only a small fraction of microbial habitats have been sampled and studied. In this chapter, we will discuss these studies in the context of the distribution of microbial life in the subsurface, the stresses that microorganisms must overcome to survive in these environments, and the metabolic strategies that are employed to harness energy in a region of the planet far-removed from sunlight. Finally, we will consider both beneficial and deleterious effects of microbial activity in the subsurface on human activities in this environment.« less

Modern laboratory diagnosis of tuberculosis.

PubMed

Drobniewski, F A; Caws, M; Gibson, A; Young, D

2003-03-01

One-third of the global population is believed to be infected with bacteria of the Mycobacterium tuberculosis complex, the causative agent of tuberculosis. More than 8 million new cases of tuberculosis occur annually leading to 2 million deaths. Mortality is particularly high in those coinfected with HIV and where the bacteria are multiple-drug-resistant strains--ie, strains resistant to at least isoniazid and rifampicin. Early diagnosis of tuberculosis and drug resistance improves survival and by identifying infectious cases promotes contact tracing, implementation of institutional cross-infection procedures, and other public-health actions. This review addresses significant advances made in the diagnosis of infection, clinical disease, and drug resistance over the past decade. It proposes operational criteria for a modern diagnostic service in the UK (as a model of a low-incidence country) and explores some of the economic issues surrounding the use of these techniques.

Sedimentary silicon isotope indicates the Kuroshio subsurface upwelling in the East China Sea

NASA Astrophysics Data System (ADS)

Zhao, Y.; Yang, S.; Su, N.

2017-12-01

The Kuroshio as the western boundary current of the North Pacific subtropical circulation, originates from east of the Philippine Islands, and flows northeastward along the eastern coast of Taiwan. It's subsurface water intrudes the East China Sea (ECS) and forms a typical upwelling on the inner shelf, which may play an important role in the material and heat transport, biogeochemical process and marine ecosystem of the ECS.To date, most previous studies on the Kuroshio subsurface upwelling focuse on the seasonal and interannual variations, and few researches touch on the upwelling evolution in the geologic past. In this study, eight short sediment cores were taken along the ECS inner shelf (upwelling area), which allow us to reconstruct the upwelling history over the last several hundred years. Although conventional indexes of oceanographic changes, such as salinity, temperature and hydrogen and oxygen isotope, provide valuable constraints on the modern oceanic circulation and water mass movements, how to reconstruct them from geologic records is always a challenging work. In this contribution, we present the data of stable silicon isotope, biogenic opal, diatom assemblages, element geochemistry and stable carbon and nitrogen isotopes of these core sediments, and aim to decipher the Kuroshio subsurface upwelling history on the ECS shelf. We will also illustrate the difference in δ30Si signals between small (<30 um) and large (>150 um) diatom fractions, and test whether it is an effective indicator for paleo-upwelling intensity.

Low Concentration of Salmonella enterica and Generic Escherichia coli in Farm Ponds and Irrigation Distribution Systems Used for Mixed Produce Production in Southern Georgia.

PubMed

Antaki, Elizabeth M; Vellidis, George; Harris, Casey; Aminabadi, Peiman; Levy, Karen; Jay-Russell, Michele T

2016-10-01

Studies have shown that irrigation water can be a vector for pathogenic bacteria. Due to this, the Food Safety Modernization Act's (FSMA) produce safety rule requires that agricultural water directly applied to produce be safe and of adequate sanitary quality for use, which may pose a challenge for some farmers. The purpose of this research was to assess the presence and concentration of Salmonella and generic Escherichia coli in irrigation water from distribution systems in a mixed produce production region of southern Georgia. Water samples were collected during three growing seasons at three farms irrigating crops with surface water (Pond 1, Pond 2) or groundwater (Well) during 2012-2013. Salmonella and generic E. coli populations were monitored by culture and Most Probable Number (MPN). Confirmed isolates were characterized by pulsed-field gel electrophoresis and serotyping. In Pond 1, Salmonella was detected in 2/21 surface, 5/26 subsurface, 10/50 center pivot, and 0/16 solid set sprinkler head water samples. In Pond 2, Salmonella was detected in 2/18 surface, 1/18 subsurface, 6/36 drip line start, and 8/36 drip line end water samples. Twenty-six well pumps and 64 associated drip line water samples were negative. The overall mean Salmonella concentration for positive water samples was 0.03 MPN/100 mL (range <0.0011-1.8 MPN/100 mL). Nine Salmonella serovars comprising 22 pulsotypes were identified. Identical serovars and subtypes were found three times on the same day and location: Pond 1-Pivot-Cantaloupe (serovar Rubislaw), Pond 1-Pivot-Peanut (serovar Saintpaul), and Pond 2-Drip Line Start-Drip Line End-Yellow Squash (serovar III_16z10:e,n,x,z15). Generic E. coli was detected in water from both farm ponds and irrigation distribution systems, but the concentrations met FSMA microbial water quality criteria. The results from this study will allow producers in southern Georgia to better understand how potential pathogens move through irrigation distribution systems.

Organic matter in hydrothermal metal ores and hydrothermal fluids

USGS Publications Warehouse

Orem, W.H.; Spiker, E. C.; Kotra, R.K.

1990-01-01

Massive polymetallic sulfides are currently being deposited around active submarine hydrothermal vents associated with spreading centers. Chemoautolithotrophic bacteria are responsible for the high production of organic matter also associated with modern submarine hydrothermal activity. Thus, there is a significant potential for organic matter/metal interactions in these systems. We have studied modern and ancient hydrothermal metal ores and modern hydrothermal fluids in order to establish the amounts and origin of the organic matter associated with the metal ores. Twenty-six samples from modern and ancient hydrothermal systems were surveyed for their total organic C contents. Organic C values ranged from 0.01% to nearly 4.0% in these samples. Metal ores from modern and ancient sediment-covered hydrothermal systems had higher organic C values than those from modern and ancient hydrothermal systems lacking appreciable sedimentary cover. One massive pyrite sample from the Galapagos spreading center (3% organic C) had stable isotope values of -27.4% (??13C) and 2.1% (??15N), similar to those in benthic siphonophors from active vents and distinct from seep sea sedimentary organic matter. This result coupled with other analyses (e.g. 13C NMR, pyrolysis/GC, SEM) of this and other samples suggests that much of the organic matter may originate from chemoautolithotrophic bacteria at the vents. However, the organic matter in hydrothermal metal ores from sediment covered vents probably arises from complex sedimentary organic matter by hydrothermal pyrolysis. The dissolved organic C concentrations of hydrothermal fluids from one site (Juan de Fuca Ridge) were found to be the same as that of background seawater. This result may indicate that dissolved organic C is effectively scavenged from hydrothermal fluids by biological activity or by co-precipitation with metal ores. ?? 1990.

Bioaccessible Porosity: A new approach to assess residual contamination after bioremediation of hydrophobic organic compounds in sub-surface microporous environments

NASA Astrophysics Data System (ADS)

Akbari, A.; Ghoshal, S.

2016-12-01

We define a new parameter, "bioaccessible porosity", the fraction of aggregate volume accessible to soil bacteria, towards a priori assessment of hydrocarbon bioremediation end points. Microbial uptake of poorly soluble hydrocarbons occurs through direct uptake or micellar solubilzation/emulsification associated with biosurfactant production, and requires close proximity of bacteria and hydrocarbon phase. In subsurface microporous environments, bioremediation rates are attenuated when residual hydrophobic contamination is entrapped in sterically restrictive environments which is not accessible to soil bacteria. This study presents new approaches for characterization of the microstructure of porous media and as well, the ability of indigenous hydrocarbon degraders to access to a range of pore sizes. Bacterial access to poorly soluble hydrocarbons in soil micro pores were simulated with bioreactors with membranes with different pore sizes containing the hydrocarbon degrading bacteria, Dietzia maris. D. maris is Gram-positive, and nonmotile that we isolated as the major hydrocarbon degrader from a fine-grained, weathered, hydrocarbon-contaminated site soil. Under nutritional stress, planktonic D. maris cells were aggregated and accessed 5 µm but not 3 µm and smaller pores. However, when hexadecane was available at the pore mouth, D. maris colonized the pore mouth, and accessed pores as small as 0.4 µm. This suggests bacterial accessibility to different pore sizes is regulated by nutritional conditions. A combination of X-ray micro-CT scanning, gas adsorption and mercury intrusion porosimetry was used to characterize the range of pore sizes of soil aggregates. In case of the studied contaminated soil, the bioaccessible porosity were determined as 25% , 27% and 29% (assuming 4, 1, 0.4 µm respectively as accessibility criteria), and about 2.7% of aggregate volume was attributed to 0.006-0.4 µm pores. The 2% aggregate volume at an assumed saturation of 10% could accommodate 1000 mg/ kg soil of oil. The remediation endpoint after extended biotreatment was at similar order of magnitude of 600 mg/kg. The approach introduced here could be used for qualitative assessment of attainable bioremediation endpoint in soils with different microstructure and hydrocarbon degrading bacterial community.

Is Mars a habitable environment for extremophilic microorganisms from Earth?

NASA Astrophysics Data System (ADS)

Rettberg, Petra; Reitz, Guenther; Flemming, Hans-Curt; Bauermeister, Anja

In the last decades several sucessful space missions to our neighboring planet Mars have deepened our knowledge about its environmental conditions substantially. Orbiters with intruments for remote sensing and landers with sophisticated intruments for in situ investigations resulted in a better understanding of Mars’ radiation climate, atmospheric composition, geology, and mineralogy. Extensive regions of the surface of Mars are covered with sulfate- and ferric oxide-rich layered deposits. These sediments indicate the possible existence of aqueous, acidic environments on early Mars. Similar environments on Earth harbour a specialised community of microorganisms which are adapted to the local stress factors, e.g. low pH, high concentrations of heavy metal ions, oligotrophic conditions. Acidophilic iron-sulfur bacteria isolated from such habitats on Earth could be considered as model organisms for an important part of a potential extinct Martian ecosystem or an ecosystem which might even exist today in protected subsurface niches. Acidithiobacillus ferrooxidans was chosen as a model organism to study the ability of these bacteria to survive or grow under conditions resembling those on Mars. Stress conditions tested included desiccation, radiation, low temperatures, and high salinity. It was found that resistance to desiccation strongly depends on the mode of drying. Biofilms grown on membrane filters can tolerate longer periods of desiccation than planktonic cells dried without any added protectants, and drying under anaerobic conditions is more favourable to survival than drying in the presence of oxygen. Organic compounds such as trehalose and glycine betaine had a positive influence on survival after drying and freezing. A. ferrooxidans was shown to be sensitive to high salt concentrations, ionizing radiation, and UV radiation. However, the bacteria were able to utilize the iron minerals in Mars regolith mixtures as sole energy source. The survival and growth of A. ferrooxidans in a Mars subsurface simulation experiment could be demonstrated. Thus, from a geochemical perspective, these chemolithoautotrophic bacteria are relevant candidates for a hypothetical underground Martian food chain, despite their limited ability to tolerate the harsh physical conditions of the surface of Mars today.

Non-extremophilic 'extremophiles' - Archaeal dominance in the subsurface and their implication for life

NASA Astrophysics Data System (ADS)

Reitschuler, Christoph; Lins, Philipp; Illmer, Paul

2014-05-01

Archaea - besides bacteria and eukaryota constituting the third big domain of life - were so far regarded as typical inhabitants of extreme environments, as indicated by the name (Archaeon, Greek: 'original', 'primal'). Previous research and cultivation successes were basically carried out in habitats characterized by extreme temperature, pH and salinity regimes. Such extreme conditions, as expected at the beginning of the Earth's evolution, are occasionally also prevalent on extraterrestrial planets and moons and make the Archaeal domain a key group to be studied concerning life's evolution and the most likely pioneer organisms to colonize environments that are regarded as hostile. However, in recent years it became obvious that Archaea, in particular non-extremophilic species, can be found almost ubiquitously in marine, freshwater, terrestrial and also subsurface habitats and occasionally outnumber other microbial domains and hold key positions in globally relevant energy and nutrient cycles. Besides extreme environments - the big question remains how to define a parameter as extreme - subsurface and cave environments present a window to the past, where adaptions to early life's conditions can be studied and how microbiomes may be structured in a habitat that represents a refugium on extraterrestrial celestial bodies, were surface conditions might be at first sight too extreme for life. The lower part of the alpine Hundsalm cave in Tyrol (Austria) offered a unique opportunity to study an almost pristine cave habitat, which is separated from the touristic part of the ice cave. The main focus of our research was laid on the microbial communities that were supposed to be in connection with secondary carbonate precipitations ('moonmilk'). For the ascertainment of these so far poorly evaluated structures a multiple approach assessment was chosen to generate a virtually complete picture of these subsurface microbiomes. Thereby, a combination of different cultivation strategies was applied as well as physiological analyses, comprising HPLC and GC analyses, and molecular approaches, covering end-point and quantitative PCRs, DGGE, cloning, and sequencing analyses. Outstanding in the course of this research was that assumed non-extremophilic Archaea clearly outnumbered bacteria within the different moonmilk deposits, while fungi were only of minor importance. Moreover, the Archaeal species formed a constant element within the investigated samples, while bacteria and fungi showed a much more diverse and inhomogeneous community pattern. This indicates that the Archaea might constitute the central element within the microbial communities, holding key positions in nutrient and energy-cycles. Furthermore, it was possible to cultivate the Archaeal community over a certain time period, demonstrating that so far uncultured or as 'not cultivable' regarded organisms are accessible with certain cultivation strategies. On the other hand the vast majority of bacterial and fungal representatives are in close relation to species, which are valuable concerning biotechnological or medical applications. Summing up, further research on cave microbiomes, especially Archaea, might be reasonable with regards to life's evolution, global nutrient cycles, requirements for possible refuges of extraterrestrial life forms and also concerning new technological applications.

Spatial Autocorrelation, Source Water and the Distribution of Total and Viable Microbial Abundances within a Crystalline Formation to a Depth of 800 m

PubMed Central

Beaton, E. D.; Stuart, Marilyne; Stroes-Gascoyne, Sim; King-Sharp, Karen J.; Gurban, Ioana; Festarini, Amy; Chen, Hui Q.

2017-01-01

Proposed radioactive waste repositories require long residence times within deep geological settings for which we have little knowledge of local or regional subsurface dynamics that could affect the transport of hazardous species over the period of radioactive decay. Given the role of microbial processes on element speciation and transport, knowledge and understanding of local microbial ecology within geological formations being considered as host formations can aid predictions for long term safety. In this relatively unexplored environment, sampling opportunities are few and opportunistic. We combined the data collected for geochemistry and microbial abundances from multiple sampling opportunities from within a proposed host formation and performed multivariate mixing and mass balance (M3) modeling, spatial analysis and generalized linear modeling to address whether recharge can explain how subsurface communities assemble within fracture water obtained from multiple saturated fractures accessed by boreholes drilled into the crystalline formation underlying the Chalk River Laboratories site (Deep River, ON, Canada). We found that three possible source waters, each of meteoric origin, explained 97% of the samples, these are: modern recharge, recharge from the period of the Laurentide ice sheet retreat (ca. ∼12000 years before present) and a putative saline source assigned as Champlain Sea (also ca. 12000 years before present). The distributed microbial abundances and geochemistry provide a conceptual model of two distinct regions within the subsurface associated with bicarbonate – used as a proxy for modern recharge – and manganese; these regions occur at depths relevant to a proposed repository within the formation. At the scale of sampling, the associated spatial autocorrelation means that abundances linked with geochemistry were not unambiguously discerned, although fine scale Moran’s eigenvector map (MEM) coefficients were correlated with the abundance data and suggest the action of localized processes possibly associated with the manganese and sulfate content of the fracture water. PMID:28974945

Rescuing the Cahoon Mine drill cores: Opportunities for modern mapping of the ca. 1.7 Ga Freedom Formation in southern Wisconsin

NASA Astrophysics Data System (ADS)

Stanley, V.; Stewart, E.

2016-12-01

Rock cores collected during historic mineral exploration can provide invaluable data for modern analyses, but only if the samples are properly curated. The Cahoon Mine operated in Baraboo, WI during the 1910's and produced iron ore from the ca. 1.7 Ga Freedom Formation. The Freedom Formation is part of the well-known Baraboo-interval stratigraphy and is only present in the subsurface of Wisconsin (Weidman, 1904). Seventeen exploratory drill cores were rescued by Wisconsin Geological and Natural History Survey (WGNHS) from the original drying house at the mine site. The condition of the containers endangered the stratigraphic context of the collection; identifiers and depth markings were often obscured or lost. The individual core pieces were coated in residue and dust. Most of what is known about the Freedom Formation is from core logs and master's theses from the early 1900's (Leith, 1935; Schmidt, 1951). Ongoing subsurface mapping of the Baraboo-interval sediments and underlying basement of southern Wisconsin integrates new and existing subsurface and regional geophysical datasets. Mapping involves calibrating unique signals in regional aeromagnetic data to known lithology from drill core and cuttings. The Freedom Formation is especially important in this process as its iron-rich composition and regional continuity causes it to have a somewhat unique signal in regional aeromagnetic data. The Cahoon Mine cores in the WGNHS repository are the most extensive collection of physical samples from the Freedom Formation still in existence. We are in the process of curating the cores to facilitate their use in ongoing bedrock mapping. Today the cost and logistics of extensive sampling of this unit makes the existing core collection irreplaceable. We transferred the material to new containers, digitally recorded metadata, and created archival labels. As a result of this effort, the Cahoon Mine cores are now stored in a format that is physically and digitally accessible.

Pyrosequencing reveals benthic bacteria changes responsing to heavy deposition of Microcystis scum in lab — searching bacteria for bloom control

NASA Astrophysics Data System (ADS)

Tang, Yali; Cheng, Dongmei; Guan, Baohua; Zhang, Xiufeng; Liu, Zhengwen; Liu, Zejun

2017-05-01

Bacteria capable of degrading cyanobacteria Microcystis are crucial for determining the ecological consequences of Microcystis blooms in freshwater lakes. Scum derived from Microcystis blooms tends to accumulate in bays of large lakes and then sink to the sediments where it is finally consumed by benthic bacteria. Understanding the response of benthic bacterial communities to massive Microcystis deposition events may help identify the bacteria best suited to Microcystis hydrolyzation and even bloom control. For that purpose, an experimental system was set up in which intact sediment cores were incubated in the laboratory with normal and heavy deposits of Microcystis detritus. Pyrosequencing was performed in order to describe a phylogenetic inventory of bacterial communities in samples taken at 0-1, 1-2 and 2-3 cm depths in incubated sediments and in original untreated sediment. A hierarchical cluster tree was constructed expose differences between sediments. Similarity percentage calculations were also performed to identify the bacterial species contributing to variation. The results of this study suggest that: (1) deposition of Microcystis scums exerts a strong effect on the bacterial community composition in the surface (0-1 cm) and sub-surface (1-2 cm) sediment layers; (2) bacterial community responses to Microcystis detritus deposition vary across vertical gradients. A list of bacteria with potential roles in Microcystis degradation was compiled. These findings may inform the development of future measures for Microcystis bloom control in lakes.

Micro-scale experimental study of Microbial-Induced Carbonate Precipitation (MICP) by using microfluidic devices

NASA Astrophysics Data System (ADS)

Wang, Y.; Soga, K.; DeJong, J. T.; Kabla, A.

2017-12-01

Microbial-induced carbonate precipitation (MICP), one of the bio-mineralization processes, is an innovative subsurface improvement technique for enhancing the strength and stiffness of soils, and controlling their hydraulic conductivity. These macro-scale engineering properties of MICP treated soils controlled by micro-scale factors of the precipitated carbonate, such as its content, amount and distribution in the soil matrix. The precipitation process itself is affected by bacteria amount, reaction kinetics, porous medium geometry and flow distribution in the soils. Accordingly, to better understand the MICP process at the pore scale a new experimental technique that can observe the entire process of MICP at the pore-scale was developed. In this study, a 2-D transparent microfluidic chip made of Polydimethylsiloxane (PDMS) representing the soil matrix was designed and fabricated. A staged-injection MICP treatment procedure was simulated inside the microfluidic chip while continuously monitored using microscopic techniques. The staged-injection MICP treatment procedure started with the injection of bacteria suspension, followed with the bacteria setting for attachment, and then ended with the multiple injections of cementation liquid. The main MICP processes visualized during this procedure included the bacteria transport and attachment during the bacteria injection, the bacteria attachment and growth during the bacteria settling, the bacteria detachment during the cementation liquid injection, the cementation development during the cementation liquid injection, and the cementation development after the completion of cementation liquid injection. It is suggested that the visualization of the main MICP processes using the microfluidic technique can improve understating of the fundamental mechanisms of MICP and consequently help improve the treatment technique for in situ implementation of MICP.

Complex community of nitrite-dependent anaerobic methane oxidation bacteria in coastal sediments of the Mai Po wetland by PCR amplification of both 16S rRNA and pmoA genes.

PubMed

Chen, Jing; Zhou, Zhichao; Gu, Ji-Dong

2015-02-01

In the present work, both 16S rRNA and pmoA gene-based PCR primers were employed successfully to study the diversity and distribution of n-damo bacteria in the surface and lower layer sediments at the coastal Mai Po wetland. The occurrence of n-damo bacteria in both the surface and subsurface sediments with high diversity was confirmed in this study. Unlike the two other known n-damo communities from coastal areas, the pmoA gene-amplified sequences in the present work clustered not only with some freshwater subclusters but also within three newly erected marine subclusters mostly, indicating the unique niche specificity of n-damo bacteria in this wetland. Results suggested vegetation affected the distribution and community structures of n-damo bacteria in the sediments and n-damo could coexist with sulfate-reducing methanotrophs in the coastal ecosystem. Community structures of the Mai Po n-damo bacteria based on 16S rRNA gene were different from those of either the freshwater or the marine. In contrast, structures of the Mai Po n-damo communities based on pmoA gene grouped with the marine ones and were clearly distinguished from the freshwater ones. The abundance of n-damo bacteria at this wetland was quantified using 16S rRNA gene PCR primers to be 2.65-6.71 × 10(5) copies/g dry sediment. Ammonium and nitrite strongly affected the community structures and distribution of n-damo bacteria in the coastal Mai Po wetland sediments.

Humic acids contribution to sedimentary organic matter on a shallow continental shelf (northern Adriatic Sea)

NASA Astrophysics Data System (ADS)

Giani, M.; Rampazzo, F.; Berto, D.

2010-12-01

The shallow northern Adriatic Sea receives large river runoff, predominantly from the Po River, which is the main allochthonous source of nutrients and organic matter. The origin and quality of organic matter deposited in the sediments can influence the degradation processes and oxygen consumption in the bottom waters as well as the fate of many pollutants. Therefore the humic acids (HA) were quantified in surface and sub-surface sediments collected in an area of the north-western Adriatic platform south of Po River. HA showed to have a relevant contribution to sedimentary organic matter. HA content in sediments were positively correlated with the organic carbon concentration and negatively with redox potential and pH, particularly in sub-surface reduced sediments, suggesting their important role in the diagenetic processes taking place in anoxic conditions. Elemental composition of HA extracted from surface and sub-surface sediments showed a wide range of variation of the C org/N ratios which could be due to a mixed (terrestrial and marine) origin and/or an elevated bacteria degradation of nitrogen during diagenesis processes in sediments. The spectroscopic ratios A 2/A 4 and A 4/A 6 of HA confirmed a mixed origin with a high degree of condensation of the HA extracted from sediments.

Microbial-sized, carboxylate-modified microspheres as surrogate tracers in a variety of subsurface environments: An overview

USGS Publications Warehouse

Harvey, Ronald W.; Metge, David W.; LeBlanc, Denis R.

2017-01-01

Since 1986, fluorescent carboxylate-modified polystyrene/latex microspheres (FCM) have been co-injected into aquifers along with conservative tracers and viruses, bacteria, and (or) protozoa. Use of FCM has resulted in new information about subsurface transport behaviors of microorganisms in fractured crystalline rock, karst limestone, soils, and granular aquifers. FCM have been used as surrogates for oocysts of the pathogenic protist Cryptosporidium parvum in karst limestone and granular drinking-water aquifers. The advantages of FCM in subsurface transport studies are that they are safe in tracer applications, negatively charged, easy to detect, chemically inert, and available in wide range of sizes. The limitations of FCM are that the quantities needed for some field transport studies can be prohibitively expensive and that their surface characteristics may not match the microorganisms of interest. These limitations may be ameliorated, in part by using chemically modified FCM so that their surface characteristics are a better match to that of the organisms. Also, more sensitive methods of detection may allow using smaller quantities of FCM. To assess how the transport behaviors of FCM and pathogens might compare at the field scale, it is helpful to conduct side-by-side comparisons of their transport behaviors using the geologic media and site-specific conditions that characterize the field site.

Processes affecting transport of uranium in a suboxic aquifer

USGS Publications Warehouse

Davis, J.A.; Curtis, G.P.; Wilkins, M.J.; Kohler, M.; Fox, P.; Naftz, D.L.; Lloyd, J.R.

2006-01-01

At the Naturita site in Colorado, USA, groundwaters were sampled and analyzed for chemical composition and by culture and culture-independent microbiological techniques. In addition, sediments were extracted with a dilute sodium carbonate solution to determine quantities of labile uranium within the sediments. Samples from the upgradient portion of the contaminated aquifer, where very little dissolved Fe(II) is found in the groundwater, have uranium content that is controlled by U(VI) adsorption and few metal-reducing bacteria are observed. In the extreme downgradient portion of the aquifer, where dissolved Fe(II) is observed, uranium content of the sediments includes significant quantities of reduced U(IV) and diverse populations of Fe(III)-reducing bacteria were present in the subsurface with the potential of reducing U(VI) to U(IV). ?? 2006 Elsevier Ltd. All rights reserved.

Mercury distribution in ancient and modern sediment of northeastern Bering Sea

USGS Publications Warehouse

Nelson, C.H.; Pierce, D.E.; Leong, K.W.; Wang, F.F.H.

1975-01-01

Reconnaissance sampling of surface and subsurface sediment to a maximum depth of 80 m below the sea floor shows that typical values of 0.03 p.p.m. and anomalies of 0.2-1.3 p.p.m. mercury have been present in northeastern Bering Sea since Early Pliocene time. Values are highest in modern beach (maximum 1.3 and mean 0.22 p.p.m. Hg) and nearshore subsurface gravels (maximum 0.6 and mean 0.06 p.p.m. Hg) along the highly mineralized Seward Peninsula and in clayey silt rich in organic matter (maximum 0.16 and mean 0.10 p.p.m. Hg) throughout the region. Although gold mining may be partly responsible for high mercury levels in the modern beach near Nome, Alaska (maximum 0.45 p.p.m.), equally high or greater concentrations of mercury occur in buried Pleistocene sediments immediately offshore (maximum 0.6 p.p.m.) and in modern unpolluted beach sediments at Bluff (maximum 1.3 p.p.m.); this suggests that the contamination effects of mining may be no greater than natural concentration processes in the Seward Peninsula region. The mercury content of offshore surface sediment, even adjacent to mercury-rich beaches, corresponds to that of unpolluted marine and fresh-water sediment elsewhere. The normal values that prevail offshore may be attributable to entrapment of mercury-bearing heavy minerals on beaches near sources and/or dilution effects of offshore sedimentation. The few minor anomalies offshore occur in glacial drift derived from mercury source regions of Chukotka (Siberia) and Seward Peninsula; Pleistocene shoreline processes have reworked the drift to concentrate the heavy metals. The distribution pattern of mercury indicates that particulate mercury-bearing minerals have not been widely dispersed from onland deposits in quantities sufficient to increase mercury levels above normal in offshore sediments of Bering Sea; however, it shows that natural sedimentary processes can concentrate this mercury in beaches of the coastal zone where there already is concern because of potential pollution from man's activities.

Methane-Oxidizing Bacteria Shunt Carbon to Microbial Mats at a Marine Hydrocarbon Seep

DOE Office of Scientific and Technical Information (OSTI.GOV)

Paul, Blair G.; Ding, Haibing; Bagby, Sarah C.

The marine subsurface is a reservoir of the greenhouse gas methane. While microorganisms living in water column and seafloor ecosystems are known to be a major sink limiting net methane transport from the marine subsurface to the atmosphere, few studies have assessed the flow of methane-derived carbon through the benthic mat communities that line the seafloor on the continental shelf where methane is emitted. We analyzed the abundance and isotope composition of fatty acids in microbial mats grown in the shallow Coal Oil Point seep field off Santa Barbara, CA, USA, where seep gas is a mixture of methane andmore » CO 2. We further used stable isotope probing (SIP) to track methane incorporation into mat biomass. We found evidence that multiple allochthonous substrates supported the rich growth of these mats, with notable contributions from bacterial methanotrophs and sulfur-oxidizers as well as eukaryotic phototrophs. Fatty acids characteristic of methanotrophs were shown to be abundant and 13C-enriched in SIP samples, and DNA-SIP identified members of the methanotrophic family Methylococcaceae as major 13CH 4 consumers. Members of Sulfuricurvaceae, Sulfurospirillaceae, and Sulfurovumaceae are implicated in fixation of seep CO 2. The mats’ autotrophs support a diverse assemblage of co-occurring bacteria and protozoa, with Methylophaga as key consumers of methane-derived organic matter. This study identifies the taxa contributing to the flow of seep-derived carbon through microbial mat biomass, revealing the bacterial and eukaryotic diversity of these remarkable ecosystems.« less

Methane-Oxidizing Bacteria Shunt Carbon to Microbial Mats at a Marine Hydrocarbon Seep

DOE PAGES

Paul, Blair G.; Ding, Haibing; Bagby, Sarah C.; ...

2017-02-27

The marine subsurface is a reservoir of the greenhouse gas methane. While microorganisms living in water column and seafloor ecosystems are known to be a major sink limiting net methane transport from the marine subsurface to the atmosphere, few studies have assessed the flow of methane-derived carbon through the benthic mat communities that line the seafloor on the continental shelf where methane is emitted. We analyzed the abundance and isotope composition of fatty acids in microbial mats grown in the shallow Coal Oil Point seep field off Santa Barbara, CA, USA, where seep gas is a mixture of methane andmore » CO 2. We further used stable isotope probing (SIP) to track methane incorporation into mat biomass. We found evidence that multiple allochthonous substrates supported the rich growth of these mats, with notable contributions from bacterial methanotrophs and sulfur-oxidizers as well as eukaryotic phototrophs. Fatty acids characteristic of methanotrophs were shown to be abundant and 13C-enriched in SIP samples, and DNA-SIP identified members of the methanotrophic family Methylococcaceae as major 13CH 4 consumers. Members of Sulfuricurvaceae, Sulfurospirillaceae, and Sulfurovumaceae are implicated in fixation of seep CO 2. The mats’ autotrophs support a diverse assemblage of co-occurring bacteria and protozoa, with Methylophaga as key consumers of methane-derived organic matter. This study identifies the taxa contributing to the flow of seep-derived carbon through microbial mat biomass, revealing the bacterial and eukaryotic diversity of these remarkable ecosystems.« less

Methane-Oxidizing Bacteria Shunt Carbon to Microbial Mats at a Marine Hydrocarbon Seep

PubMed Central

Paul, Blair G.; Ding, Haibing; Bagby, Sarah C.; Kellermann, Matthias Y.; Redmond, Molly C.; Andersen, Gary L.; Valentine, David L.

2017-01-01

The marine subsurface is a reservoir of the greenhouse gas methane. While microorganisms living in water column and seafloor ecosystems are known to be a major sink limiting net methane transport from the marine subsurface to the atmosphere, few studies have assessed the flow of methane-derived carbon through the benthic mat communities that line the seafloor on the continental shelf where methane is emitted. We analyzed the abundance and isotope composition of fatty acids in microbial mats grown in the shallow Coal Oil Point seep field off Santa Barbara, CA, USA, where seep gas is a mixture of methane and CO2. We further used stable isotope probing (SIP) to track methane incorporation into mat biomass. We found evidence that multiple allochthonous substrates supported the rich growth of these mats, with notable contributions from bacterial methanotrophs and sulfur-oxidizers as well as eukaryotic phototrophs. Fatty acids characteristic of methanotrophs were shown to be abundant and 13C-enriched in SIP samples, and DNA-SIP identified members of the methanotrophic family Methylococcaceae as major 13CH4 consumers. Members of Sulfuricurvaceae, Sulfurospirillaceae, and Sulfurovumaceae are implicated in fixation of seep CO2. The mats’ autotrophs support a diverse assemblage of co-occurring bacteria and protozoa, with Methylophaga as key consumers of methane-derived organic matter. This study identifies the taxa contributing to the flow of seep-derived carbon through microbial mat biomass, revealing the bacterial and eukaryotic diversity of these remarkable ecosystems. PMID:28289403

Profiling bacterial diversity in a limestone cave of the western Loess Plateau of China

PubMed Central

Wu, Yucheng; Tan, Liangcheng; Liu, Wuxing; Wang, Baozhan; Wang, Jianjun; Cai, Yanjun; Lin, Xiangui

2015-01-01

Bacteria and archaea sustain subsurface cave ecosystems by dominating primary production and fueling biogeochemical cyclings, despite the permanent darkness and shortage of nutrients. However, the heterogeneity and underlying mechanism of microbial diversity in caves, in particular those well connect to surface environment are largely unexplored. In this study, we examined the bacterial abundance and composition in Jinjia Cave, a small and shallow limestone cave located on the western Loess Plateau of China, by enumerating and pyrosequencing small subunit rRNA genes. The results clearly reveal the contrasting bacterial community compositions in relation to cave habitat types, i.e., rock wall deposit, aquatic sediment, and sinkhole soil, which are differentially connected to the surface environment. The deposits on the cave walls were dominated by putative cave-specific bacterial lineages within the γ-Proteobacteria or Actinobacteria that are routinely found on cave rocks around the world. In addition, sequence identity with known functional groups suggests enrichments of chemolithotrophic bacteria potentially involved in autotrophic C fixation and inorganic N transformation on rock surfaces. By contrast, bacterial communities in aquatic sediments were more closely related to those in the overlying soils. This is consistent with the similarity in elemental composition between the cave sediment and the overlying soil, implicating the influence of mineral chemistry on cave microhabitat and bacterial composition. These findings provide compelling molecular evidence of the bacterial community heterogeneity in an East Asian cave, which might be controlled by both subsurface and surface environments. PMID:25870592

Profiling bacterial diversity in a limestone cave of the western Loess Plateau of China.

PubMed

Wu, Yucheng; Tan, Liangcheng; Liu, Wuxing; Wang, Baozhan; Wang, Jianjun; Cai, Yanjun; Lin, Xiangui

2015-01-01

Bacteria and archaea sustain subsurface cave ecosystems by dominating primary production and fueling biogeochemical cyclings, despite the permanent darkness and shortage of nutrients. However, the heterogeneity and underlying mechanism of microbial diversity in caves, in particular those well connect to surface environment are largely unexplored. In this study, we examined the bacterial abundance and composition in Jinjia Cave, a small and shallow limestone cave located on the western Loess Plateau of China, by enumerating and pyrosequencing small subunit rRNA genes. The results clearly reveal the contrasting bacterial community compositions in relation to cave habitat types, i.e., rock wall deposit, aquatic sediment, and sinkhole soil, which are differentially connected to the surface environment. The deposits on the cave walls were dominated by putative cave-specific bacterial lineages within the γ-Proteobacteria or Actinobacteria that are routinely found on cave rocks around the world. In addition, sequence identity with known functional groups suggests enrichments of chemolithotrophic bacteria potentially involved in autotrophic C fixation and inorganic N transformation on rock surfaces. By contrast, bacterial communities in aquatic sediments were more closely related to those in the overlying soils. This is consistent with the similarity in elemental composition between the cave sediment and the overlying soil, implicating the influence of mineral chemistry on cave microhabitat and bacterial composition. These findings provide compelling molecular evidence of the bacterial community heterogeneity in an East Asian cave, which might be controlled by both subsurface and surface environments.

Field Evidence for Magnetite Formation by a Methanogenic Microbial Community

NASA Astrophysics Data System (ADS)

Rossbach, S.; Beaver, C. L.; Williams, A.; Atekwana, E. A.; Slater, L. D.; Ntarlagiannis, D.; Lund, A.

2015-12-01

The aged, subsurface petroleum spill in Bemidji, Minnesota, has been surveyed with magnetic susceptibility (MS) measurements. High MS values were found in the free-product phase around the fluctuating water table. Although we had hypothesized that high MS values are related to the occurrence of the mineral magnetite resulting from the activity of iron-reducing bacteria, our microbial analysis pointed to the presence of a methanogenic microbial community at the locations and depths of the highest MS values. Here, we report on a more detailed microbial analysis based on high-throughput sequencing of the 16S rRNA gene of sediment samples from four consecutive years. In addition, we provide geochemical data (FeII/FeIII concentrations) to refine our conceptual model of methanogenic hydrocarbon degradation at aged petroleum spills and demonstrate that the microbial induced changes of sediment properties can be monitored with MS. The methanogenic microbial community at the Bemidji site consisted mainly of the syntrophic, hydrocarbon-degrading Smithella and the hydrogenotrophic, methane-generating Methanoregula. There is growing evidence in the literature that not only Bacteria, but also some methanogenic Archaea are able to reduce iron. In fact, a recent study reported that the methanogen Methanosarcina thermophila produced magnetite during the reduction of ferrihydrite in a laboratory experiment when hydrogen was present. Therefore, our finding of high MS values and the presence of magnetite in the methanogenic zone of an aged, subsurface petroleum spill could very well be the first field evidence for magnetite formation during methanogenic hydrocarbon degradation.

Elemental sulfur in Eddy County, New Mexico

USGS Publications Warehouse

Hinds, Jim S.; Cunningham, Richard R.

1970-01-01

Sulfur has been reported in Eddy County, N. Mex., in rocks ranging from Silurian to Holocene in age at depths of 0-15,020 feet. Targets of present exploration are Permian formations in the Delaware Basin and northwest shelf areas at depths of less than 4,000 feet. Most of the reported sulfur occurrences in the shelf area are in the 'Abo' (as used by some subsurface geologists), Yeso, and San Andres Formations and the Artesia Group. Sulfur deposition in the dense dolomites of the 'Abo,' Yeso, and San Andres Formations is attributed to the reduction of ionic sulfate by hydrogen sulfide in formation waters in zones of preexisting porosity and permeability. A similar origin accounts for most of the sulfur deposits in the formations of the Artesia Group, but some of the sulfur in these formations may have originated in place through the alteration of anhydrite to carbonate and sulfur by the metabolic processes of bacteria in the presence of hydrocarbons. Exploration in the Delaware Basin area is directed primarily toward the Castile Formation. Sulfur deposits in the Castile Formation are found in irregular masses of cavernous brecciated secondary carbonate rock enveloped by impermeable anhydrite. The carbonate masses, or 'castiles,' probably originated as collapse features resulting from subsurface solution and upward stopping. Formation of carbonate rock and sulfur in the castiles is attributed to the reduction of brecciated anhydrite by bacteria and hydrocarbons in the same process ascribed to the formation of carbonate and sulfur in the caprocks of salt domes.

Imaging and locating paleo-channels using geophysical data from meandering system of the Mun River, Khorat Plateau, Northeastern Thailand

NASA Astrophysics Data System (ADS)

Nimnate, P.; Thitimakorn, T.; Choowong, M.; Hisada, K.

2017-12-01

The Khorat Plateau from northeast Thailand, the upstream part of the Mun River flows through clastic sedimentary rocks. A massive amount of sand was transported. We aimed to understand the evolution of fluvial system and to discuss the advantages of two shallow geophysical methods for describing subsurface morphology of modern and paleo-channels. We applied Electrical Resistivity Tomography (ERT) and Ground Penetrating Radar (GPR) to characterize the lateral, vertical morphological and sedimentary structures of paleo-channels, floodplain and recent point bars. Both methods were interpreted together with on-sites boreholes to describe the physical properties of subsurface sediments. As a result, we concluded that four radar reflection patterns including reflection free, shingled, inclined and hummocky reflections were appropriated to apply as criteria to characterize lateral accretion, the meandering rivers with channel-filled sequence and floodplain were detected from ERT profiles. The changes in resistivity correspond well with differences in particle size and show relationship with ERT lithological classes. Clay, silt, sand, loam and bedrock were classified by the resistivity data. Geometry of paleo-channel embayment and lithological differences can be detected by ERT, whereas GPR provides detail subsurface facies for describing point bar sand deposit better than ERT.

Deglacial development of (sub) sea surface temperature and salinity in the subarctic northwest Pacific: Implications for upper-ocean stratification

NASA Astrophysics Data System (ADS)

Riethdorf, Jan-Rainer; Max, Lars; Nürnberg, Dirk; Lembke-Jene, Lester; Tiedemann, Ralf

2013-01-01

Based on models and proxy data, it has been proposed that salinity-driven stratification weakened in the subarctic North Pacific during the last deglaciation, which potentially contributed to the deglacial rise in atmospheric carbon dioxide. We present high-resolution subsurface temperature (TMg/Ca) and subsurface salinity-approximating (δ18Oivc-sw) records across the last 20,000 years from the subarctic North Pacific and its marginal seas, derived from combined stable oxygen isotopes and Mg/Ca ratios of the planktonic foraminiferal species Neogloboquadrina pachyderma (sin.). Our results indicate regionally differing changes of subsurface conditions. During the Heinrich Stadial 1 and the Younger Dryas cold phases, our sites were subject to reduced thermal stratification, brine rejection due to sea-ice formation, and increased advection of low-salinity water from the Alaskan Stream. In contrast, the Bølling-Allerød warm phase was characterized by strengthened thermal stratification, stronger sea-ice melting, and influence of surface waters that were less diluted by the Alaskan Stream. From direct comparison with alkenone-based sea surface temperature estimates (SSTUk'37), we suggest deglacial thermocline changes that were closely related to changes in seasonal contrasts and stratification of the mixed layer. The modern upper-ocean conditions seem to have developed only since the early Holocene.

Microbiology of Drycleaning

PubMed Central

Banville, Robert R.; McNeil, Ethel

1966-01-01

An appreciable number of bacteria on contaminated fabric survived modern drycleaning procedures. Various stages in the process, especially steam pressing, reduced the total number of bacteria, but viable organisms were found on certain areas of garments even after pressing. A significant number of bacteria were redeposited on clean fabric during the washing of ordinary soiled garments in drycleaning units. These bacteria included gram-positive cocci, diphtheroid bacilli, and gram-positive sporeformers. Gram-negative bacilli were seldom found, although some gram-negative bacilli survived drycleaning. The redeposited organisms apparently came mainly from other garments in the same loads, as few bacteria were isolated from the filtered solvent used for washing. The number of bacteria in the drycleaning washwheel was highest shortly after the beginning of the wash, and decreased, with the exchange of solvent in the wheel, to a low level at the end. Although it appears that in most cases several factors combine to reduce to a low level the numbers of bacteria on articles cleaned in a well-operated drycleaning plant, it would seem that under certain conditions pathogenic microorganisms could be disseminated by drycleaning. Images Fig. 2 PMID:4958148

Arsenic Detoxification by Geobacter Species.

PubMed

Dang, Yan; Walker, David J F; Vautour, Kaitlin E; Dixon, Steven; Holmes, Dawn E

2017-02-15

Insight into the mechanisms for arsenic detoxification by Geobacter species is expected to improve the understanding of global cycling of arsenic in iron-rich subsurface sedimentary environments. Analysis of 14 different Geobacter genomes showed that all of these species have genes coding for an arsenic detoxification system (ars operon), and several have genes required for arsenic respiration (arr operon) and methylation (arsM). Genes encoding four arsenic repressor-like proteins were detected in the genome of G. sulfurreducens; however, only one (ArsR1) regulated transcription of the ars operon. Elimination of arsR1 from the G. sulfurreducens chromosome resulted in enhanced transcription of genes coding for the arsenic efflux pump (Acr3) and arsenate reductase (ArsC). When the gene coding for Acr3 was deleted, cells were not able to grow in the presence of either the oxidized or reduced form of arsenic, while arsC deletion mutants could grow in the presence of arsenite but not arsenate. These studies shed light on how Geobacter influences arsenic mobility in anoxic sediments and may help us develop methods to remediate arsenic contamination in the subsurface. This study examines arsenic transformation mechanisms utilized by Geobacter, a genus of iron-reducing bacteria that are predominant in many anoxic iron-rich subsurface environments. Geobacter species play a major role in microbially mediated arsenic release from metal hydroxides in the subsurface. This release raises arsenic concentrations in drinking water to levels that are high enough to cause major health problems. Therefore, information obtained from studies of Geobacter should shed light on arsenic cycling in iron-rich subsurface sedimentary environments, which may help reduce arsenic-associated illnesses. These studies should also help in the development of biosensors that can be used to detect arsenic contaminants in anoxic subsurface environments. We examined 14 different Geobacter genomes and found that all of these species possess genes coding for an arsenic detoxification system (ars operon), and some also have genes required for arsenic respiration (arr operon) and arsenic methylation (arsM). Copyright © 2017 American Society for Microbiology.

Arsenic Detoxification by Geobacter Species

PubMed Central

Walker, David J. F.; Vautour, Kaitlin E.; Dixon, Steven

2016-01-01

ABSTRACT Insight into the mechanisms for arsenic detoxification by Geobacter species is expected to improve the understanding of global cycling of arsenic in iron-rich subsurface sedimentary environments. Analysis of 14 different Geobacter genomes showed that all of these species have genes coding for an arsenic detoxification system (ars operon), and several have genes required for arsenic respiration (arr operon) and methylation (arsM). Genes encoding four arsenic repressor-like proteins were detected in the genome of G. sulfurreducens; however, only one (ArsR1) regulated transcription of the ars operon. Elimination of arsR1 from the G. sulfurreducens chromosome resulted in enhanced transcription of genes coding for the arsenic efflux pump (Acr3) and arsenate reductase (ArsC). When the gene coding for Acr3 was deleted, cells were not able to grow in the presence of either the oxidized or reduced form of arsenic, while arsC deletion mutants could grow in the presence of arsenite but not arsenate. These studies shed light on how Geobacter influences arsenic mobility in anoxic sediments and may help us develop methods to remediate arsenic contamination in the subsurface. IMPORTANCE This study examines arsenic transformation mechanisms utilized by Geobacter, a genus of iron-reducing bacteria that are predominant in many anoxic iron-rich subsurface environments. Geobacter species play a major role in microbially mediated arsenic release from metal hydroxides in the subsurface. This release raises arsenic concentrations in drinking water to levels that are high enough to cause major health problems. Therefore, information obtained from studies of Geobacter should shed light on arsenic cycling in iron-rich subsurface sedimentary environments, which may help reduce arsenic-associated illnesses. These studies should also help in the development of biosensors that can be used to detect arsenic contaminants in anoxic subsurface environments. We examined 14 different Geobacter genomes and found that all of these species possess genes coding for an arsenic detoxification system (ars operon), and some also have genes required for arsenic respiration (arr operon) and arsenic methylation (arsM). PMID:27940542

Microbial diversity in ultra-high-pressure rocks and fluids from the Chinese Continental Scientific Drilling Project in China.

PubMed

Zhang, Gengxin; Dong, Hailiang; Xu, Zhiqin; Zhao, Donggao; Zhang, Chuanlun

2005-06-01

Microbial communities in ultra-high-pressure (UHP) rocks and drilling fluids from the Chinese Continental Scientific Drilling Project were characterized. The rocks had a porosity of 1 to 3.5% and a permeability of approximately 0.5 mDarcy. Abundant fluid and gas inclusions were present in the minerals. The rocks contained significant amounts of Fe2O3, FeO, P2O5, and nitrate (3 to 16 ppm). Acridine orange direct counting and phospholipid fatty acid analysis indicated that the total counts in the rocks and the fluids were 5.2 x 10(3) to 2.4 x 10(4) cells/g and 3.5 x 10(8) to 4.2 x 10(9) cells/g, respectively. Enrichment assays resulted in successful growth of thermophilic and alkaliphilic bacteria from the fluids, and some of these bacteria reduced Fe(III) to magnetite. 16S rRNA gene analyses indicated that the rocks were dominated by sequences similar to sequences of Proteobacteria and that most organisms were related to nitrate reducers from a saline, alkaline, cold habitat; however, some phylotypes were either members of a novel lineage or closely related to uncultured clones. The bacterial communities in the fluids were more diverse and included Proteobacteria, Bacteroidetes, gram-positive bacteria, Planctomycetes, and Candidatus taxa. The archaeal diversity was lower, and most sequences were not related to any known cultivated species. Some archaeal sequences were 90 to 95% similar to sequences recovered from ocean sediments or other subsurface environments. Some archaeal sequences from the drilling fluids were >93% similar to sequences of Sulfolobus solfataricus, and the thermophilic nature was consistent with the in situ temperature. We inferred that the microbes in the UHP rocks reside in fluid and gas inclusions, whereas those in the drilling fluids may be derived from subsurface fluids.

Evaluating Contaminants of Emerging Concern as tracers of wastewater from septic systems.

PubMed

James, C Andrew; Miller-Schulze, Justin P; Ultican, Shawn; Gipe, Alex D; Baker, Joel E

2016-09-15

Bacterial and nutrient contamination from anthropogenic sources impacts fresh and marine waters, reducing water quality and restricting recreational and commercial activities. In many cases the source of this contamination is ambiguous, and a tracer or set of tracers linking contamination to source would be valuable. In this work, the effectiveness of utilizing a suite of Contaminants of Emerging Concern (CECs) as tracers of bacteria from human septic system effluent is investigated. Field sampling was performed at more than 20 locations over approximately 18 months and analyzed for a suite of CECs and fecal coliform bacteria. The sampling locations included seeps and small freshwater discharges to the shoreline. Sites were selected and grouped according to level of impact by septic systems as determined by previous field sampling programs. A subset of selected locations had been positively identified as being impacted by effluent from failing septic systems through dye testing. The CECs were selected based on their predominant use, their frequency of use, and putative fate and transport properties. In addition, two rounds of focused sampling were performed at selected sites to characterize short-term variations in CEC and fecal coliform concentrations, and to evaluate environmental persistence following source correction activities. The results indicate that a suite of common use compounds are suitable as generalized tracers of bacterial contamination from septic systems and that fate and transport properties are important in tracer selection. Highly recalcitrant or highly labile compounds likely follow different loss profiles in the subsurface compared to fecal bacteria and are not suitable tracers. The use of more than one tracer compound is recommended due to source variability of septic systems and to account for variations in the subsurface condition. In addition, concentrations of some CECs were measured in receiving waters at levels which suggested the potential for environmental harm, indicating that the possible risk presented from these sources warrants further investigation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mercury mobilization and speciation linked to bacterial iron oxide and sulfate reduction: A column study to mimic reactive transfer in an anoxic aquifer.

PubMed

Hellal, Jennifer; Guédron, Stéphane; Huguet, Lucie; Schäfer, Jörg; Laperche, Valérie; Joulian, Catherine; Lanceleur, Laurent; Burnol, André; Ghestem, Jean-Philippe; Garrido, Francis; Battaglia-Brunet, Fabienne

2015-09-01

Mercury (Hg) mobility and speciation in subsurface aquifers is directly linked to its surrounding geochemical and microbial environment. The role of bacteria on Hg speciation (i.e., methylation, demethylation and reduction) is well documented, however little data is available on their impact on Hg mobility. The aim of this study was to test if (i) Hg mobility is due to either direct iron oxide reduction by iron reducing bacteria (IRB) or indirect iron reduction by sulfide produced by sulfate reducing bacteria (SRB), and (ii) to investigate its subsequent fate and speciation. Experiments were carried out in an original column setup combining geochemical and microbiological approaches that mimic an aquifer including an interface of iron-rich and iron depleted zones. Two identical glass columns containing iron oxides spiked with Hg(II) were submitted to (i) direct iron reduction by IRB and (ii) to indirect iron reduction by sulfides produced by SRB. Results show that in both columns Hg was leached and methylated during the height of bacterial activity. In the column where IRB are dominant, Hg methylation and leaching from the column was directly correlated to bacterial iron reduction (i.e., Fe(II) release). In opposition, when SRB are dominant, produced sulfide induced indirect iron oxide reduction and rapid adsorption of leached Hg (or produced methylmercury) on neoformed iron sulfides (e.g., Mackinawite) or its precipitation as HgS. At the end of the SRB column experiment, when iron-oxide reduction was complete, filtered Hg and Fe concentrations increased at the outlet suggesting a leaching of Hg bound to FeS colloids that may be a dominant mechanism of Hg transport in aquifer environments. These experimental results highlight different biogeochemical mechanisms that can occur in stratified sub-surface aquifers where bacterial activities play a major role on Hg mobility and changes in speciation. Copyright © 2015 Elsevier B.V. All rights reserved.

Microbial Diversity in Ultra-High-Pressure Rocks and Fluids from the Chinese Continental Scientific Drilling Project in China

PubMed Central

Zhang, Gengxin; Dong, Hailiang; Xu, Zhiqin; Zhao, Donggao; Zhang, Chuanlun

2005-01-01

Microbial communities in ultra-high-pressure (UHP) rocks and drilling fluids from the Chinese Continental Scientific Drilling Project were characterized. The rocks had a porosity of 1 to 3.5% and a permeability of ∼0.5 mDarcy. Abundant fluid and gas inclusions were present in the minerals. The rocks contained significant amounts of Fe2O3, FeO, P2O5, and nitrate (3 to 16 ppm). Acridine orange direct counting and phospholipid fatty acid analysis indicated that the total counts in the rocks and the fluids were 5.2 × 103 to 2.4 × 104 cells/g and 3.5 × 108 to 4.2 × 109 cells/g, respectively. Enrichment assays resulted in successful growth of thermophilic and alkaliphilic bacteria from the fluids, and some of these bacteria reduced Fe(III) to magnetite. 16S rRNA gene analyses indicated that the rocks were dominated by sequences similar to sequences of Proteobacteria and that most organisms were related to nitrate reducers from a saline, alkaline, cold habitat; however, some phylotypes were either members of a novel lineage or closely related to uncultured clones. The bacterial communities in the fluids were more diverse and included Proteobacteria, Bacteroidetes, gram-positive bacteria, Planctomycetes, and Candidatus taxa. The archaeal diversity was lower, and most sequences were not related to any known cultivated species. Some archaeal sequences were 90 to 95% similar to sequences recovered from ocean sediments or other subsurface environments. Some archaeal sequences from the drilling fluids were >93% similar to sequences of Sulfolobus solfataricus, and the thermophilic nature was consistent with the in situ temperature. We inferred that the microbes in the UHP rocks reside in fluid and gas inclusions, whereas those in the drilling fluids may be derived from subsurface fluids. PMID:15933024

Drilling effect on subsurface microbial community structure in groundwater from the -250 m gallery at the Horonobe Underground Research Laboratory, Japan

NASA Astrophysics Data System (ADS)

Ise, K.; Amano, Y.; Sasaki, Y.; Yoshikawa, H.

2014-12-01

The deep geological disposal system is regarded as the most secure and practical disposal method of high-level radioactive waste in the world. In this disposal system, preservation of reducing condition is one of the key requirements, because most of radionuclides have low solubilities in such condition. However, the host rocks near the shafts and galleries would be affected by oxidization during the construction and operation period of a repository (for about 50 years). Therefore, the recovery of reducing condition after closing the repository should be verified. During the recovery processes, it is considered that microbial activities play important roles, but the mechanisms are poorly understood. In this study, we monitored the changes in microbial communities by molecular method to evaluate microbial response toward the oxygen stress. The groundwater samples were collected from a borehole of 250 m depth at the Horonobe Underground Research Laboratory, for two years immediately after drilling of a borehole without any contamination as much as possible. Immediately after drilling of the borehole, the phylotype related to Arcobacter spp. was dominated about 65 % of the total clone library. Arcobacter spp. is known as sulfide oxidizer and which can growth chemoautotrophically. Half a year later, the phylotype related to Azoarcus spp. and Pseudomonas spp. known as nitrate reducing bacteria increased, instead of the phylotype related to Arcobacter spp. One year later, in addition to nitrate reducing bacteria, phylotype related to Dethiobacterspp. known as thiosulfate reducing bacteria was dominantly detected. Two years later, most of detected clones were related to uncultured species such as candidate division WS6 and JS1 which are detected frequently in deep-sea sediments. Our results indicate that these redox sequential reactions could contribute to the recovery and maintenance of reducing conditions and provide a conceptual model for evaluating the capacity to recover reducing conditions in subsurface environments after final geological disposal and the post-closure.

Lower Carboniferous Siderites: A Product of Bottom Seeps and Bacterial Metanogenesis (Subpolar Urals)

NASA Astrophysics Data System (ADS)

Antoshkina, A. I.; Ryabinkina, N. N.

2018-02-01

Complex modern micro- and spectroscopic methods for study of siderite concretions in the Lower Carboniferous terrigenous strata on the Kozhym River (Subpolar Urals) have shown that its formation was caused by destruction of clay minerals due to the activity of bacterial communities. The abundance of these bacteria was caused by gas-fluid seeps and bacterial methanogenesis processes in bottom deposits. In basins with normal marine fauna, this led to local desalination, hydrogen sulfide contamination, mass collapse of primary organisms, and the development of element-specific bacteria. The occurrence of these bacteria caused the formation of specific authigenic mineralization in the concretion of sideritic bacteriolites: the framboidal pyrite, sphalerite, galenite, barite, sulfoselenides, and tellurides.

Microbiological, Geochemical and Hydrologic Processes Controlling Uranium Mobility: An Integrated Field-Scale Subsurface Research Challenge Site at Rifle, Colorado, Quality Assurance Project Plan

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fix, N. J.

The U.S. Department of Energy (DOE) is cleaning up and/or monitoring large, dilute plumes contaminated by metals, such as uranium and chromium, whose mobility and solubility change with redox status. Field-scale experiments with acetate as the electron donor have stimulated metal-reducing bacteria to effectively remove uranium [U(VI)] from groundwater at the Uranium Mill Tailings Site in Rifle, Colorado. The Pacific Northwest National Laboratory and a multidisciplinary team of national laboratory and academic collaborators has embarked on a research proposed for the Rifle site, the object of which is to gain a comprehensive and mechanistic understanding of the microbial factors andmore » associated geochemistry controlling uranium mobility so that DOE can confidently remediate uranium plumes as well as support stewardship of uranium-contaminated sites. This Quality Assurance Project Plan provides the quality assurance requirements and processes that will be followed by the Rifle Integrated Field-Scale Subsurface Research Challenge Project.« less

The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

PubMed Central

Di Rienzi, Sara C; Sharon, Itai; Wrighton, Kelly C; Koren, Omry; Hug, Laura A; Thomas, Brian C; Goodrich, Julia K; Bell, Jordana T; Spector, Timothy D; Banfield, Jillian F; Ley, Ruth E

2013-01-01

Cyanobacteria were responsible for the oxygenation of the ancient atmosphere; however, the evolution of this phylum is enigmatic, as relatives have not been characterized. Here we use whole genome reconstruction of human fecal and subsurface aquifer metagenomic samples to obtain complete genomes for members of a new candidate phylum sibling to Cyanobacteria, for which we propose the designation ‘Melainabacteria’. Metabolic analysis suggests that the ancestors to both lineages were non-photosynthetic, anaerobic, motile, and obligately fermentative. Cyanobacterial light sensing may have been facilitated by regulators present in the ancestor of these lineages. The subsurface organism has the capacity for nitrogen fixation using a nitrogenase distinct from that in Cyanobacteria, suggesting nitrogen fixation evolved separately in the two lineages. We hypothesize that Cyanobacteria split from Melainabacteria prior or due to the acquisition of oxygenic photosynthesis. Melainabacteria remained in anoxic zones and differentiated by niche adaptation, including for symbiosis in the mammalian gut. DOI: http://dx.doi.org/10.7554/eLife.01102.001 PMID:24137540

Subsurface metabolic potential on the Costa Rican Margin

NASA Astrophysics Data System (ADS)

Biddle, J.; Leon, Z. R.; Martino, A. J.; Bousses, K.; House, C. H.

2017-12-01

The distribution of archaea and bacteria and their associated metabolic abilities in the deep subseafloor are poorly understood. In order to explore this, we focused on samples from the Costa Rica margin IODP Expedition 334. The microbial community was analyzed via metagenomics in two different sites at multiple depths. At Site 1378, samples are from 2 meters below the sea floor (mbsf), 33 mbsf and 93 mbsf, and at Site 1379 from 22 mbsf to 45 mbsf. Whole community analysis of conserved gene markers in the metagenome show that the microbial community varies with depth, and drastically differs between the two geographically close sites. Thirty-two genomes were recovered from the metagenomic data with more than 30% completion. Archaea make 49% of all genomes recovered and over 90% of these recovered genomes belong to recently discovered and poorly characterized groups of Archaea. This study explored the relative dynamics of microbial communities in the deep biosphere and presents the metabolic potential of distinct subsurface biosphere archaeal groups.

The deep-subsurface sulfate reducer Desulfotomaculum kuznetsovii employs two methanol-degrading pathways.

PubMed

Sousa, Diana Z; Visser, Michael; van Gelder, Antonie H; Boeren, Sjef; Pieterse, Mervin M; Pinkse, Martijn W H; Verhaert, Peter D E M; Vogt, Carsten; Franke, Steffi; Kümmel, Steffen; Stams, Alfons J M

2018-01-16

Methanol is generally metabolized through a pathway initiated by a cobalamine-containing methanol methyltransferase by anaerobic methylotrophs (such as methanogens and acetogens), or through oxidation to formaldehyde using a methanol dehydrogenase by aerobes. Methanol is an important substrate in deep-subsurface environments, where thermophilic sulfate-reducing bacteria of the genus Desulfotomaculum have key roles. Here, we study the methanol metabolism of Desulfotomaculum kuznetsovii strain 17 T , isolated from a 3000-m deep geothermal water reservoir. We use proteomics to analyze cells grown with methanol and sulfate in the presence and absence of cobalt and vitamin B12. The results indicate the presence of two methanol-degrading pathways in D. kuznetsovii, a cobalt-dependent methanol methyltransferase and a cobalt-independent methanol dehydrogenase, which is further confirmed by stable isotope fractionation. This is the first report of a microorganism utilizing two distinct methanol conversion pathways. We hypothesize that this gives D. kuznetsovii a competitive advantage in its natural environment.

Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment

DOE PAGES

Castelle, Cindy J.; Hug, Laura A.; Wrighton, Kelly C.; ...

2013-08-27

Microorganisms in the subsurface represent a substantial but poorly understood component of the Earth’s biosphere. Subsurface environments are complex and difficult to characterize; thus, their microbiota have remained as a ‘dark matter’ of the carbon and other biogeochemical cycles. Here we deeply sequence two sediment-hosted microbial communities from an aquifer adjacent to the Colorado River, CO, USA. No single organism represents more than ~1% of either community. Remarkably, many bacteria and archaea in these communities are novel at the phylum level or belong to phyla lacking a sequenced representative. The dominant organism in deeper sediment, RBG-1, is a member ofmore » a new phylum. On the basis of its reconstructed complete genome, RBG-1 is metabolically versatile. Its wide respiration-based repertoire may enable it to respond to the fluctuating redox environment close to the water table. We document extraordinary microbial novelty and the importance of previously unknown lineages in sediment biogeochemical transformations.« less

Discovering buried channels of the Yamuna in alluvial plains of NW India using geophysical investigations: implications for major drainage reorganization during Late Quaternary

NASA Astrophysics Data System (ADS)

Paul, D.; Khan, I.; Sinha, R.

2016-12-01

Climatic changes and active tectonic movements in the northwestern plains of India during the Late Quaternary have led to the migration and abandonment of drainage systems and formation of a large number of palaeochannels. It has been postulated by previous workers that the Yamuna was flowing along the present-day dry palaeochannels of Ghaggar-Hakra riverbed >120 Ka ago and was relocated to its current position only during the Late Quaternary. However, till date, no conclusive evidence has been provided as to when and why the Yamuna avulsion occurred. This study aims to establish sub-surface existence of buried channels of paleo-Yamuna as possible courses of the paleo-Ghaggar river. Geo-electric studies using vertical electrical resistivity soundings (1D-VES), multi electrode electrical resistivity tomography (2D-ERT) and multi probe well log surveys have been carried out in one of the paleochannels of the Yamuna to map the large-scale geometry and architecture of the palaeochannel system in the subsurface. The main objective is to reconstruct the shallow subsurface stratigraphy and alluvial architecture of the interfluve between the modern Yamuna and Sutlej Rivers, in particular the linkage of the paleocourses of the Yamuna River to the drainage network of the northwestern alluvial plains. The geophysical signatures recorded as VES on two transects trending NW-SE in Karnal and Kaithal districts of Haryana at 9 and 13 locations respectively along with continuous ERT reveals the presence of subsurface fine to coarse sand bodies (20 to 30m thick) interbedded with silty clay layers that are laterally stacked. The occurrence of thick and wide subsurface sand bodies in the subsurface implies that these are the deposits of a large river system and suggests that the Yamuna was connected to the paleo-Ghaggar River as hypothesized by earlier workers based on remote sensing techniques. However, detailed sedimentological and chronological constraints are required to establish such links to unravel the stratigraphic manifestation of the buried channels, their sediment provenance and paleoclimatic conditions during the period when these river systems were active.

Microbial Community Responses to Organophosphate Substrate Additions in Contaminated Subsurface Sediments

PubMed Central

Martinez, Robert J.; Wu, Cindy H.; Beazley, Melanie J.; Andersen, Gary L.; Conrad, Mark E.; Hazen, Terry C.; Taillefert, Martial; Sobecky, Patricia A.

2014-01-01

Background Radionuclide- and heavy metal-contaminated subsurface sediments remain a legacy of Cold War nuclear weapons research and recent nuclear power plant failures. Within such contaminated sediments, remediation activities are necessary to mitigate groundwater contamination. A promising approach makes use of extant microbial communities capable of hydrolyzing organophosphate substrates to promote mineralization of soluble contaminants within deep subsurface environments. Methodology/Principal Findings Uranium-contaminated sediments from the U.S. Department of Energy Oak Ridge Field Research Center (ORFRC) Area 2 site were used in slurry experiments to identify microbial communities involved in hydrolysis of 10 mM organophosphate amendments [i.e., glycerol-2-phosphate (G2P) or glycerol-3-phosphate (G3P)] in synthetic groundwater at pH 5.5 and pH 6.8. Following 36 day (G2P) and 20 day (G3P) amended treatments, maximum phosphate (PO4 3−) concentrations of 4.8 mM and 8.9 mM were measured, respectively. Use of the PhyloChip 16S rRNA microarray identified 2,120 archaeal and bacterial taxa representing 46 phyla, 66 classes, 110 orders, and 186 families among all treatments. Measures of archaeal and bacterial richness were lowest under G2P (pH 5.5) treatments and greatest with G3P (pH 6.8) treatments. Members of the phyla Crenarchaeota, Euryarchaeota, Bacteroidetes, and Proteobacteria demonstrated the greatest enrichment in response to organophosphate amendments and the OTUs that increased in relative abundance by 2-fold or greater accounted for 9%–50% and 3%–17% of total detected Archaea and Bacteria, respectively. Conclusions/Significance This work provided a characterization of the distinct ORFRC subsurface microbial communities that contributed to increased concentrations of extracellular phosphate via hydrolysis of organophosphate substrate amendments. Within subsurface environments that are not ideal for reductive precipitation of uranium, strategies that harness microbial phosphate metabolism to promote uranium phosphate precipitation could offer an alternative approach for in situ sequestration. PMID:24950228

Chemotaxis Increases the Residence Time Distribution of Bacteria in Granular Media Containing Distributed Contaminant Sources

NASA Astrophysics Data System (ADS)

Adadevoh, J.; Triolo, S.; Ramsburg, C. A.; Ford, R.

2015-12-01

The use of chemotactic bacteria in bioremediation has the potential to increase access to, and biotransformation of, contaminant mass within the subsurface environment. This laboratory-scale study aimed to understand and quantify the influence of chemotaxis on residence times of pollutant-degrading bacteria within homogeneous treatment zones. Focus was placed on a continuous flow sand-packed column system in which a uniform distribution of naphthalene crystals created distributed sources of dissolved phase contaminant. A 10 mL pulse of Pseudomonas putida G7, which is chemotactic to naphthalene, and Pseudomonas putida G7 Y1, a non-chemotactic mutant strain, were simultaneously introduced into the sand-packed column at equal concentrations. Breakthrough curves obtained for the bacteria from column experiments conducted with and without naphthalene were used to quantify the effect of chemotaxis on transport parameters. In the presence of the chemoattractant, longitudinal dispersivity of PpG7 increased by a factor of 3 and percent recovery decreased from 21% to 12%. The results imply that pore-scale chemotaxis responses are evident at an interstitial fluid velocity of 1.7 m/d, which is within the range of typical groundwater flow. Within the context of bioremediation, chemotaxis may work to enhance bacterial residence times in zones of contamination thereby improving treatment.

Prevention of combat-related infections: antimicrobial therapy in battlefield and barrier measures in French military medical treatment facilities.

PubMed

Mérens, Audrey; Rapp, Christophe; Delaune, Deborah; Danis, Julien; Berger, Franck; Michel, Remy

2014-01-01

Infection is a major complication associated with combat-related injuries. Beside immobilization, wound irrigation, surgical debridement and delayed coverage, post-injury antimicrobials contribute to reduce combat-related infections, particularly those caused by bacteria of the early contamination flora. In modern warfare, bacteria involved in combat-related infections are mainly Gram-negative bacteria belonging to the late contamination flora. These bacteria are frequently resistant or multiresistant to antibiotics and spread through the deployed chain of care. This article exposes the principles of war wounds antimicrobial prophylaxis recommended in the French Armed Forces and highlights the need for high compliance to hygiene standard precautions, adapted contact precautions and judicious use of antibiotics in French deployed military medical treatment facilities (MTF). Copyright © 2014 Elsevier Ltd. All rights reserved.

Preservation of protein globules and peptidoglycan in the mineralized cell wall of nitrate-reducing, iron(II)-oxidizing bacteria: a cryo-electron microscopy study.

PubMed

Miot, J; Maclellan, K; Benzerara, K; Boisset, N

2011-11-01

Iron-oxidizing bacteria are important actors of the geochemical cycle of iron in modern environments and may have played a key role all over Earth's history. However, in order to better assess that role on the modern and the past Earth, there is a need for better understanding the mechanisms of bacterial iron oxidation and for defining potential biosignatures to be looked for in the geologic record. In this study, we investigated experimentally and at the nanometre scale the mineralization of iron-oxidizing bacteria with a combination of synchrotron-based scanning transmission X-ray microscopy (STXM), scanning transmission electron microscopy (STEM) and cryo-transmission electron microscopy (cryo-TEM). We show that the use of cryo-TEM instead of conventional microscopy provides detailed information of the successive iron biomineralization stages in anaerobic nitrate-reducing iron-oxidizing bacteria. These results suggest the existence of preferential Fe-binding and Fe-oxidizing sites on the outer face of the plasma membrane leading to the nucleation and growth of Fe minerals within the periplasm of these cells that eventually become completely encrusted. In contrast, the septa of dividing cells remain nonmineralized. In addition, the use of cryo-TEM offers a detailed view of the exceptional preservation of protein globules and the peptidoglycan within the Fe-mineralized cell walls of these bacteria. These organic molecules and ultrastructural details might be protected from further degradation by entrapment in the mineral matrix down to the nanometre scale. This is discussed in the light of previous studies on the properties of Fe-organic interactions and more generally on the fossilization of mineral-organic assemblies. © 2011 Blackwell Publishing Ltd.

Transition of microbiological and sedimentological features associated with the geochemical gradient in a travertine mound in northern Sumatra, Indonesia

NASA Astrophysics Data System (ADS)

Sugihara, Chiya; Yanagawa, Katsunori; Okumura, Tomoyo; Takashima, Chizuru; Harijoko, Agung; Kano, Akihiro

2016-08-01

Modern travertines, carbonate deposits in Ca-rich hydrothermal water with high pCO2, often display a changing environment along the water path, with corresponding variability in the microbial communities. We investigated a travertine-bearing hot spring at the Blue Pool in northern Sumatra, Indonesia. The thermal water of 62 °C with high H2S (200 μM) and pCO2 ( 1 atm) developed a travertine mound 70 m wide. The concentrations of the gas components H2S and CO2, decrease immediately after the water is discharged, while the dissolved oxygen, pH, and aragonite saturation increase in the downstream direction. Responding to the geochemical gradient in the water, the surface biofilms change color from white to pink, light-green, dark-green, and brown as the water flows from the vent; this corresponds to microbial communities characterized by chemolithoautotrophs (Halothiobacillaceae), purple sulfur bacteria (Chromatiaceae), Anaerolineaceae, and co-occurrence of green non-sulfur bacteria (Chloroflexales)-Cyanobacteria, and green sulfur bacteria (Chlorobiales), respectively. In an environment with a certain level of H2S (> 1 μM), sulfur digestion and anoxygenic photosynthesis can be more profitable than oxygenic photosynthesis by Cyanobacteria. The precipitated carbonate mineral consists of aragonite and calcite, with the proportion of aragonite increasing downstream due to the larger Mg2 +/Ca2 + ratio in the water or the development of thicker biofilm. Where the biofilm is well developed, the aragonite travertines often exhibit laminated structures that were likely associated with the daily metabolism of these bacteria. The microbiological and sedimentological features at the Blue Pool may be the modern analogs of geomicrobiological products in the early Earth. Biofilm of anoxygenic photosynthetic bacteria had the potential to form ancient stromatolites that existed before the appearance of cyanobacteria.

[Microbes on the edge of global biosphere].

PubMed

Naganuma, T

2000-12-01

The search for life on the edge of global biosphere is a frontier to bridge conventional bio/ecology and exo/astrobiology. This communication reviews the foci of microbiological studies on the inhabitants of the selected "edges", i.e., deep-sea, deep subsurface and Antarctic habitats. The deep-sea is characterized as the no-light (non-photosynthetic) habitat, and the primary production is mostly due to the chemosynthetic autotrophy at the hydrothermal vents and methane-rich seeps. Formation of the chemosynthesis-dependent animal communities in the deep leads to the idea that such communities may be found in "ocean" of the Jovian satellite, Europa. The oxygen minimal layer (OML) in mid-water provides another field of deep-sea research. Modern OML is a relatively thin layer, found between the water depth of 200 and 1000 m, but was much thicker during the periods of oceanic anoxia events (OAEs) in the past. The history of oceanic biosphere is regarded as the cycle of OAE and non-OAE periods, and the remnants of the past OAEs may be seen in the modem OML. Anoxic (no-O2) condition is also characteristic of deep subsurface biosphere. Microorganisms in deep subsurface biosphere exploit every available oxidant, or terminal electron acceptor (TEA), for anaerobic respiration. Sulfate, nitrate, iron (III) and CO2 are the representative TEAs in the deep subsurface. Subsurface of hydrothermal vents, or sub-vent biosphere, may house brine (high salt) habitats and halophilic microorganisms. Some sub-vent halophiles were phylogenetically closely similar to the ones found in the Antarctic habitats which are extremely dry by the liophilizing climate. Below the 3000-4000 m-thick glacier on Antarctica, there have been >70 lakes with liquid water located. One of such sub-glacial lakes, Lake Vostok, has been a target of "life in extreme environments" and is about to be drill-penetrated for microbiological studies. These 'microbiological platforms' will provide new knowledge about the diversity and potential of the Earth's life and facilitate the capability of astrobiologial exploration.

Adhesion of Biodegradative Anaerobic Bacteria to Solid Surfaces

PubMed Central

van Schie, Paula M.; Fletcher, Madilyn

1999-01-01

In order to exploit the ability of anaerobic bacteria to degrade certain contaminants for bioremediation of polluted subsurface environments, we need to understand the mechanisms by which such bacteria partition between aqueous and solid phases, as well as the environmental conditions that influence partitioning. We studied four strictly anaerobic bacteria, Desulfomonile tiedjei, Syntrophomonas wolfei, Syntrophobacter wolinii, and Desulfovibrio sp. strain G11, which theoretically together can constitute a tetrachloroethylene- and trichloroethylene-dechlorinating consortium. Adhesion of these organisms was evaluated by microscopic determination of the numbers of cells that attached to glass coverslips exposed to cell suspensions under anaerobic conditions. We studied the effects of the growth phase of the organisms on adhesion, as well as the influence of electrostatic and hydrophobic properties of the substratum. Results indicate that S. wolfei adheres in considerably higher numbers to glass surfaces than the other three organisms. Starvation greatly decreases adhesion of S. wolfei and Desulfovibrio sp. strain G11 but seems to have less of an effect on the adhesion of the other bacteria. The presence of Fe3+ on the substratum, which would be electropositive, significantly increased the adhesion of S. wolfei, whereas the presence of silicon hydrophobic groups decreased the numbers of attached cells of all species. Measurements of transport of cells through hydrophobic-interaction and electrostatic-interaction columns indicated that all four species had negatively charged cell surfaces and that D. tiedjei and Desulfovibrio sp. strain G11 possessed some hydrophobic cell surface properties. These findings are an early step toward understanding the dynamic attachment of anaerobic bacteria in anoxic environments. PMID:10543826

Computational sciences in the upstream oil and gas industry

PubMed Central

Halsey, Thomas C.

2016-01-01

The predominant technical challenge of the upstream oil and gas industry has always been the fundamental uncertainty of the subsurface from which it produces hydrocarbon fluids. The subsurface can be detected remotely by, for example, seismic waves, or it can be penetrated and studied in the extremely limited vicinity of wells. Inevitably, a great deal of uncertainty remains. Computational sciences have been a key avenue to reduce and manage this uncertainty. In this review, we discuss at a relatively non-technical level the current state of three applications of computational sciences in the industry. The first of these is seismic imaging, which is currently being revolutionized by the emergence of full wavefield inversion, enabled by algorithmic advances and petascale computing. The second is reservoir simulation, also being advanced through the use of modern highly parallel computing architectures. Finally, we comment on the role of data analytics in the upstream industry. This article is part of the themed issue ‘Energy and the subsurface’. PMID:27597785

Microbial and Nutrient Concentration and Load Data During Stormwater Runoff at a Swine Concentrated Animal Feeding Operation in the North Carolina Coastal Plain, 2006-2007

USGS Publications Warehouse

Harden, Stephen L.

2008-01-01

This report summarizes water-quality and hydrologic data collected during 2006-2007 to characterize bacteria and nutrient loads associated with overland runoff and subsurface tile drainage in spray fields at a swine concentrated animal feeding operation. Four monitoring locations were established at the Lizzie Research Site in the North Carolina Coastal Plain Physiographic Province for collecting discharge and water-quality data during stormwater-runoff events. Water stage was measured continuously at each monitoring location. A stage-discharge relation was developed for each site and was used to compute instantaneous discharge values for collected samples. Water-quality samples were collected for five storm events during 2006-2007 for analysis of nutrients and fecal indicator bacteria. Instantaneous loads of nitrite plus nitrate, total coliform, Escherichia coli (E. coli), and enterococci were computed for selected times during the five storm events.

Characterizing the Catalytic Potential of Deinococcus, Arthrobacter and other Robust Bacteria in Contaminated Subsurface Environments of the Hanford Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fredrickson, Jim K.; Daly, Michael J.

2006-06-01

Until recently, there have been no clear physiologic predictors of a cell's ability to recover from ionizing radiation (IR), desiccation, and other DOE-relevant oxidative stress conditions. In general, the most resistant bacteria have been Gram-positive (e.g., Deinococcus, Arthrobacter, Lactobacillus & Enterococcus spp.) and the most sensitive have been Gram-negative (e.g., Pseudomonas, Shewanella & Neisseria spp.). However, there are several reported exceptions to this paradigm, the Gram-negative cyanobacterium Chroococcidiopsis is extremely resistant to IR, whereas the Gram-positive Micrococcus luteus is sensitive. We have identified biomolecular signatures for radiation sensitivity and resistance which are independent of phylogeny, where very high and verymore » low intracellular Mn/Fe concentration ratios correlated with very high and very low resistances, respectively; and restricting Mn(II) in the famously resistant Deinococcus radiodurans sensitized this eubacterium to IR (http://cfyn.ifas.ufl.edu/radiation.pdf).« less

The effect of uranium on bacterial viability and cell surface morphology using atomic force microscopy in the presence of bicarbonate ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sepulveda-Medina, Paola; Katsenovich, Yelena; Musaramthota, Vishal

Nuclear production facilities during the Cold War have caused liquid waste to leak and soak into the ground creating multiple radionuclide plumes. The Arthrobacter bacteria are one of the most common groups in soils and are found in large numbers in subsurface environments contaminated with radionuclides. This study experimentally analyzed changes on the bacteria surface after uranium exposure and evaluated the effect of bicarbonate ions on U(VI) toxicity of a less uranium tolerant Arthrobacter strain, G968, by investigating changes in adhesion forces and cells dimensions via atomic force microscopy (AFM). AFM and viability studies showed that samples containing bicarbonate aremore » able to acclimate and withstand uranium toxicity. Samples containing no bicarbonate exhibited deformed surfaces and a low height profile, which might be an indication that the cells are not alive.« less

Fossilization of Iron-Oxidizing Bacteria at Hydrothermal Vents: a Useful Biosignature on Mars?

NASA Astrophysics Data System (ADS)

Leveille, R. J.; Lui, S.

2009-05-01

Iron oxidizing bacteria are ubiquitous in marine and terrestrial environments on Earth, where they often display distinctive cell morphologies and are commonly encrusted by minerals, especially bacteriogenic iron oxides and silica. Putative microfossils of iron oxidizing bacteria have been found in jaspers as old as 490Ma and microbial iron oxidation may be an ancient metabolic pathway. In order to investigate the usefulness of mineralized iron oxidizing bacteria as a biosignature, we have examined mineral samples collected from relict hydrothermal systems along Explorer Ridge, NE Pacific Ocean. In addition, microaerophilic, neutrophilic iron oxidizing bacteria, isolated from Pacific hydrothermal vents, were grown in a Fe-enriched seawater medium at constant pH (6.5) and oxygen concentration (5 percent) in a controlled bioreactor system. Both natural samples and experimental products were examined with a combination of variable pressure scanning electron microscopy (SEM), field emission gun SEM, and in some cases by preparing samples with a focused ion beam (FIB) milling system. Natural seafloor samples display abundant filamentous forms often resembling, in both size and shape, the twisted stalks of Gallionella and the elongated filaments of Leptothrix. Generally, these filamentous features are 1-5 microns in diameter and up to several microns in length. Some samples consist entirely of low- density, porous masses of silica encrusted filamentous forms. Presumably, these masses were formed by a rapid precipitation by the influx of silica-rich fluids into a microbial mat dominated by bacteria with filamentous morphologies. The presence of rare, amorphous (unmineralized) filamentous matter rich in C and Fe suggests that these bacteria were iron oxidizers. There is no evidence that sulfur oxidizers were present. Filamentous features sectioned by FIB milling show internal material within semi-hollow tubular-like features. Silica encrustations also show pseudo-concentric growth bands. In the bioreactor cultures, constant conditions led to abundant microbial growth and formation of an iron oxyhydroxide precipitate, either in direct association with the cells or within the growth medium. This suggests that not all of the iron precipitation is biogenic in origin. Cells typically show a filamentous morphology reminiscent of the mineral-encrusted forms observed in the natural samples. Continuing work includes high-resolution TEM observations of cultured organisms, examination of 2-year long in situ seafloor incubation experiments, and bioreactor silicification experiments in order to better understand the roles of iron and silica in the fossilization process. Microaerophilic iron oxidation could have existed on the early Earth in environments containing small amounts of oxygen produced either by locally concentrated photosynthetic microorganisms (e.g., cyanobacteria) or abiotically, as proposed for the subsurface of the Fe-dominated Rio Tinto (Spain) basin system. By analogy, similar subsurface or near-surface microaerophilic environments could have existed on Mars in the past. The distinctive morphologies and mineralization patterns of iron oxidizing bacteria could be a useful biosignature to search for on Mars. Deposits and biogenic features similar to those described here could theoretically be identified on Mars with existing imaging and analytical technologies. Therefore, future missions to Mars should target ancient hydrothermal systems, some of which have been putatively identified already.

Groundwater mixing dynamics at a Canadian Shield mine

NASA Astrophysics Data System (ADS)

Douglas, M.; Clark, I. D.; Raven, K.; Bottomley, D.

2000-08-01

Temporal and spatial variations in geochemistry and isotopes in mine inflows at the Con Mine, Yellowknife, are studied to access the impact of underground openings on deep groundwater flow in the Canadian Shield. Periodic sampling of inflow at 20 sites from 700 to 1615 m depth showed that salinities range from 1.4 to 290 g/l, with tritium detected at all depths. Three mixing end-members are identified: (1) Ca(Na)-Cl Shield brine; (2) glacial meltwater recharged at the margin of the retreating Laurentide ice sheet at ˜10 ka; and (3) modern meteoric water. Mixing fractions, calculated for inflows on five mine levels, illustrate the infiltration of modern water along specific fault planes. Tritium data for the modern component are corrected for mixing with brine and glacial waters and interpreted with an exponential-piston flow model. Results indicate that the mean transit time from surface to 1300 m depth is about 23 years in the early period after drift construction in 1979, but decreases to about 17 years in the past decade. The persistence of glacial meltwater in the subsurface to the present time, and the rapid circulation of modern meteoric water since the start of mining activities underline the importance of gradient, in addition to permeability, as a control on deep groundwater flow in the Canadian Shield.

Resource conservation program in terms of Vostokgazprom environmental policy

NASA Astrophysics Data System (ADS)

Tsibulnikova, M. R.; Nadyumov, S. V.; Adam, A. M.; Korotchenko, T. V.

2016-09-01

The article examines a number of key areas of environmental policy of Vostokgazprom. The Associated Petroleum Gas program is an important step within the resource conservation and environmental protection framework. In addition, the company undertakes the extensive work on emergency response programs, and carries out continuous protection of the subsurface and control over environmental safety in all production sites. Vostokgazprom continuously modernizes the basic industrial facilities and invests money in new projects. The study analyzes the steps being taken by the company within the energy saving policy that leads to significant costs cut.

Metatranscriptomic Evidence of Chemolithoautotrophy in the Rifle (CO) Subsurface Relevant to C, S, N, and Fe Cycling

NASA Astrophysics Data System (ADS)

Beller, H. R.; Jewell, T. N. M.; Karaoz, U.; Thomas, B. C.; Banfield, J. F.; Brodie, E.; Williams, K. H.

2014-12-01

Although there is a limited understanding of the chemolithoautotrophic activity of aquifer microorganisms, such subsurface microbial activity could greatly influence the cycling of elements such as C, S, N, and Fe. Here, we present transcriptional (RNA-Seq) evidence of the emergence of such chemolithoautotrophic activities in groundwater filter samples from a 2-month experiment in which up to 1.5 mM nitrate (a native electron acceptor) was injected into a perennially suboxic/anoxic aquifer (Rifle, CO) containing a large reservoir of reduced Fe- and S-containing compounds. Illumina sequence data from rRNA-subtracted cDNA libraries was assembled and mapped to phylogenetically binned Rifle metagenome data. Indicative of the activity of Fe(II)-oxidizing bacteria, many high-abundance transcripts mapped to the Gallionellaceae family, whose known members are chemolithoautotrophic bacteria that catalyze Fe(II) oxidation. For example, included among the most abundant transcripts were a cold-shock protein and an acyl carrier protein with 96-98% protein sequence identity to Gallionella capsiferriformans and a nitrite reductase (nirS) gene likely belonging to a Sideroxydans relative. The apparent activity of Gallionellaceae members is consistent with 16S rRNA iTag analyses of these samples, which indicated that Gallionella-related taxa accounted for up to ~50% of these communities. Evidence of sulfide oxidation also was apparent in these samples. For example, highly expressed subunits of APS reductase were very similar to those of the obligately chemolithoautotrophic S- and Fe(II)-oxidizing Thiobacillus denitrificans in terms of sequence identity (98-99%) and synteny of the mapped scaffold. Also highly expressed were a ß-Proteobacterial Form II RubisCO gene and a hydrazine oxidoreductase gene (93% identity to the planctomycete KSU-1), the latter strongly indicative of anaerobic ammonia oxidation (anammox) activity, which has seldom been reported in aquifer environments. Such gene-level data on CO2 fixation and Fe(II), sulfide, and ammonium oxidation in the Rifle subsurface will contribute to genome-enabled modeling efforts aimed at developing a predictive understanding of biogeochemical processes at the site as part of LBNL's Sustainable Systems Scientific Focus Area (SFA) 2.0.

A shifting rift—Geophysical insights into the evolution of Rio Grande rift margins and the Embudo transfer zone near Taos, New Mexico

USGS Publications Warehouse

Grauch, V.J.S.; Bauer, Paul W.; Drenth, Benjamin J.; Kelson, Keith I.

2017-01-01

We present a detailed example of how a subbasin develops adjacent to a transfer zone in the Rio Grande rift. The Embudo transfer zone in the Rio Grande rift is considered one of the classic examples and has been used as the inspiration for several theoretical models. Despite this attention, the history of its development into a major rift structure is poorly known along its northern extent near Taos, New Mexico. Geologic evidence for all but its young rift history is concealed under Quaternary cover. We focus on understanding the pre-Quaternary evidence that is in the subsurface by integrating diverse pieces of geologic and geophysical information. As a result, we present a substantively new understanding of the tectonic configuration and evolution of the northern extent of the Embudo fault and its adjacent subbasin.We integrate geophysical, borehole, and geologic information to interpret the subsurface configuration of the rift margins formed by the Embudo and Sangre de Cristo faults and the geometry of the subbasin within the Taos embayment. Key features interpreted include (1) an imperfect D-shaped subbasin that slopes to the east and southeast, with the deepest point ∼2 km below the valley floor located northwest of Taos at ∼36° 26′N latitude and 105° 37′W longitude; (2) a concealed Embudo fault system that extends as much as 7 km wider than is mapped at the surface, wherein fault strands disrupt or truncate flows of Pliocene Servilleta Basalt and step down into the subbasin with a minimum of 1.8 km of vertical displacement; and (3) a similar, wider than expected (5–7 km) zone of stepped, west-down normal faults associated with the Sangre de Cristo range front fault.From the geophysical interpretations and subsurface models, we infer relations between faulting and flows of Pliocene Servilleta Basalt and older, buried basaltic rocks that, combined with geologic mapping, suggest a revised rift history involving shifts in the locus of fault activity as the Taos subbasin developed. We speculate that faults related to north-striking grabens at the end of Laramide time formed the first west-down master faults. The Embudo fault may have initiated in early Miocene southwest of the Taos region. Normal-oblique slip on these early fault strands likely transitioned in space and time to dominantly left-lateral slip as the Embudo fault propagated to the northeast. During and shortly after eruption of Servilleta Basalt, proto-Embudo fault strands were active along and parallel to the modern, NE-aligned Rio Pueblo de Taos, ∼4–7 km basinward of the modern, mapped Embudo fault zone. Faults along the northeastern subbasin margin had northwest strikes for most of the period of subbasin formation and were located ∼5–7 km basinward of the modern Sangre de Cristo fault. The locus of fault activity shifted to more northerly striking faults within 2 km of the modern range front sometime after Servilleta volcanism had ceased. The northerly faults may have linked with the northeasterly proto-Embudo faults at this time, concurrent with the development of N-striking Los Cordovas normal faults within the interior of the subbasin. By middle Pleistocene(?) time, the Los Cordovas faults had become inactive, and the linked Embudo–Sangre de Cristo fault system migrated to the south, to the modern range front.

The scourge of antibiotic resistance: the important role of the environment.

PubMed

Finley, Rita L; Collignon, Peter; Larsson, D G Joakim; McEwen, Scott A; Li, Xian-Zhi; Gaze, William H; Reid-Smith, Richard; Timinouni, Mohammed; Graham, David W; Topp, Edward

2013-09-01

Antibiotic resistance and associated genes are ubiquitous and ancient, with most genes that encode resistance in human pathogens having originated in bacteria from the natural environment (eg, β-lactamases and fluoroquinolones resistance genes, such as qnr). The rapid evolution and spread of "new" antibiotic resistance genes has been enhanced by modern human activity and its influence on the environmental resistome. This highlights the importance of including the role of the environmental vectors, such as bacterial genetic diversity within soil and water, in resistance risk management. We need to take more steps to decrease the spread of resistance genes in environmental bacteria into human pathogens, to decrease the spread of resistant bacteria to people and animals via foodstuffs, wastes and water, and to minimize the levels of antibiotics and antibiotic-resistant bacteria introduced into the environment. Reducing this risk must include improved management of waste containing antibiotic residues and antibiotic-resistant microorganisms.

Can Analysis of Acetylene and Its Biodegradation Products in Enceladus Plumes be Used to Detect the Presence of Sub-Surface Life?

NASA Astrophysics Data System (ADS)

Miller, L. G.; Baesman, S. M.; Oremland, R. S.

2014-12-01

The search for biosignatures of life on Earth includes measurement of the stable isotope fractionation of reactants and products attributed to enzymatic processes and comparison with the often smaller chemical (abiotic) fractionation. We propose that this approach might be applied to study the origin and fate of organic compounds contained in water vapor plumes emanating from Enceladus or other icy bodies, perhaps revealing information about the potential for biology occurring within a sub-surface "habitable" zone. Methanol and C2-hydrocarbons including ethylene, ethane and acetylene (C2H2) have been identified in the plumes of Enceladus. Biological degradation of acetylene proceeds by anaerobic fermentation via acetylene hydratase through acetaldehyde, with a second enzyme (acetaldehyde dismutase) forming acetate and ethanol. We found that incubation of cultures of acetylene-fermenting bacteria exhibit a kinetic isotope effect (KIE) associated with the net removal of C2H2. Consumption of acetylene by both growing and washed-cell cultures of bacteria closely related to Pelobacter acetylenicus (e.g, strain SFB93) was accompanied by a carbon isotopic fractionation of about 2 per mil (KIE = 1.8-2.7 ‰), a result we are examining with other cultures of acetylene fermenters. In addition, we are measuring the carbon isotopic composition of acetaldehyde, ethanol and acetate during fermentation to learn whether these products are fractionated sufficiently, relative to their substrate, to warrant measurement of their isotopic composition in Enceladus (or Europa) plumes to indicate enzymatic activity in liquid environments below the crust of these moons.

Implications of subzero metabolic activity on long-term microbial survival in terrestrial and extraterrestrial permafrost.

PubMed

Amato, Pierre; Doyle, Shawn M; Battista, John R; Christner, Brent C

2010-10-01

The survival of microorganisms over extended time frames in frozen subsurface environments may be limited by chemical (i.e., via hydrolysis and oxidation) and ionizing radiation-induced damage to chromosomal DNA. In an effort to improve estimates for the survival of bacteria in icy terrestrial and extraterrestrial environments, we determined rates of macromolecular synthesis at temperatures down to -15°C in bacteria isolated from Siberian permafrost (Psychrobacter cryohalolentis K5 and P. arcticus 273-4) and the sensitivity of P. cryohalolentis to ionizing radiation. Based on experiments conducted over ≈400 days at -15°C, the rates of protein and DNA synthesis in P. cryohalolentis were <1 to 16 proteins cell(-1) d(-1) and 83 to 150 base pairs (bp) cell(-1) d(-1), respectively; P. arcticus synthesized DNA at rates of 20 to 1625 bp cell(-1) d(-1) at -15°C under the conditions tested. The dose of ionizing radiation at which 37% of the cells survive (D(37)) of frozen suspensions of P. cryohalolentis was 136 Gy, which was ∼2-fold higher (71 Gy) than identical samples exposed as liquid suspensions. Laboratory measurements of [(3)H]thymidine incorporation demonstrate the physiological potential for DNA metabolism at -15°C and suggest a sufficient activity is possible to offset chromosomal damage incurred in near-subsurface terrestrial and martian permafrost. Thus, our data imply that the longevity of microorganisms actively metabolizing within permafrost environments is not constrained by chromosomal DNA damage resulting from ionizing radiation or entropic degradation over geological time.

Asymmetric Signature of Glacial Antarctic Intermediate Water in the Central South Pacific

NASA Astrophysics Data System (ADS)

Tapia, R.; Nuernberg, D.; Ho, S. L.; Lamy, F.; Ullermann, J.; Gersonde, R.; Tiedemann, R.

2017-12-01

Southern Ocean Intermediate Waters (SOIWs) play a key role in modulating the global climate on glacial-interglacial time scales as they connect the Southern Ocean and the tropics. Despite their importance, the past evolution of the SOIWs in the central South Pacific is largely unknown due to a dearth of sedimentary archives. Here we compare Mg/Ca-temperature, stable carbon and oxygen isotope records from surface-dwelling (G. bulloides) and deep-dwelling (G. inflata) planktic foraminifera at site PS75/059-2 (54°12.9' S, 125°25.53' W; recovery 13.98 m; 3.613 m water depth), located north of the modern Subantarctic Front. Our study focuses on the temperature and salinity variability controlled by SOIWs, which were subducted at the Subantarctic Front during the Last Glacial Maximum (LGM; 29-17ka BP) and the Penultimate Glacial Maximum (PGM; 180-150ka BP). During both glacial periods conditions at the subsurface ocean were colder and fresher relative to the Holocene (<10ka) suggesting an enhanced presence of SOIWs. In spite of the comparable subsurface cooling during both glacial, the subsurface ocean during the PGM was saltier and 0.35‰ more depleted in δ13C in comparison to the LGM. Interestingly, the mean δ13C value of the PGM is comparable to the Carbon Isotope Minimum Events, which might suggests a larger contribution of "old" low δ13C deep waters to the study site during the PGM. A Latitudinal comparison of subsurface proxies suggests glacial asymmetries in the advection of SOIWs into the central Pacific, plausibly related to glacial changes in the convection depth of SOIWs at the South Antarctic Front area rather than changes in production of the SOIWs.

The stratigraphic record of Khawr Al Maqta, Abu Dhabi, United Arab Emirates

NASA Astrophysics Data System (ADS)

Lokier, S. W.; Herrmann, S.

2012-04-01

Well-constrained modern depositional analogues are vital to the development of accurate geological reservoir models. The development of realistic hydrocarbon reservoir models requires the application of high-precision, well-constrained outcrop and sub-surface data sets with accurately-documented facies geometries and depositional sequence architectures. The Abu Dhabi coastline provides the best modern analogue for the study of ramp-style carbonate depositional facies akin to those observed in the sub-surface reservoirs of the United Arab Emirates (UAE). However, all previous studies have relied on temporally limited surface datasets. This study employed thirty five shallow subsurface cores spanning the width of the Khawr Al Maqta - the narrow shallow tidal channel that separates Abu Dhabi Island from the mainland. The cores were taken over a transect measuring 1.2 km in length by 50 m wide thus providing a high-resolution record of sub-surface facies geometries in a stratigraphically complex setting. Geometries in these Pleistocene to Holocene facies are complex with interdigitating, laterally heterogeneous carbonate, siliciclastic and evaporite units represented throughout the area of the study. Carbonate facies range from molluscan rudstones to marls and are all indicative of deposition in a shallow, relatively low energy marine setting akin to that seen in the environs of Abu Dhabi Island today. Texturally mature quartz sands occur as thin lenses and as thin cross bedded or laminated horizons up to twenty five centimetres thick. Glauconitic mudstones are common and locally exhibit evidence of rootlets and desiccation cracks. Evaporites are present in the form of gypsum occurring as isolated crystals and nodules or as massive chicken-wire units in excess of three metres thick. All of these textures are consistent with evaporite development in the shallow subsurface. Early, shallow-burial diagenesis has been important. Bioclasts are pervasively leached throughout the stratigraphic sequence thereby resulting in a significant enhancement in porosity in the carbonate lithologies. This pervasive mouldic porosity is locally occluded by the precipitation of gypsum cements. The displacive precipitation of significant quantities of gypsum has resulted in the deformation of primary sedimentary structures. This complex sequence of mixed carbonate-siliciclastic-evaporite lithofacies is interpreted to record repeated episodes of flooding and sub-aerial exposure associated with the waxing and waning of the Pleistocene ice-sheets. During periods of relative sea-level fall carbonate sequences entered the meteoric realm with the consequent dissolution of unstable bioclasts. Transgression and reflooding once again isolated Abu Dhabi Island from the mainland, thus permitting the precipitation of shallow-water carbonate lithofacies. During sea-level highstands the north-westerly Shamal wind transported carbonate sediments into the lee-of the island resulting in the south-easterly shore-wards development of a tombolo. However, the strong tidal currents of the Khawr Al Maqta prevented final connection to the mainland, thus ensuring the isolation of Abu Dhabi until the subsequent regression.

Quaternary tephrochronology and deposition in the subsurface Sacramento-San Joaquin Delta, California, U.S.A.

USGS Publications Warehouse

Maier, Katherine L.; Gatti, Emma; Wan, Elmira; Ponti, Daniel J.; Pagenkopp, Mark; Starratt, Scott W.; Olson, Holly A.; Tinsley, John

2015-01-01

We document characteristics of tephra, including facies and geochemistry, from 27 subsurface sites in the Sacramento-San Joaquin Delta, California, to obtain stratigraphic constraints in a complex setting. Analyzed discrete tephra deposits are correlative with: 1) an unnamed tephra from the Carlotta Formation near Ferndale, California, herein informally named the ash of Wildcat Grade (<~1.450 - >~0.780 Ma), 2) the Rockland ash bed (~0.575 Ma), 3) the Loleta ash bed (~0.390 Ma), and 4) a middle Pleistocene tephra resembling volcanic ash deposits at Tulelake, California, and Pringle Falls, Bend, and Summer Lake, Oregon, herein informally named the dacitic ash of Hood (<~0.211 to >~0.180 Ma, correlated age). All four tephra are derived from Cascades volcanic sources. The Rockland ash bed erupted from the southern Cascades near Lassen Peak, California, and occurs in deposits up to >7 m thick as observed in core samples taken from ~40 m depth below land surface. Tephra facies and tephra age constraints suggest rapid tephra deposition within fluvial channel and overbank settings, likely related to flood events shortly following the volcanic eruption. Such rapidly deposited tephra are important chronostratigraphic markers that suggest varying sediment accumulation rates (~0.07-0.29 m/1000 yr) in Quaternary deposits below the modern Sacramento-San Joaquin Delta. This study provides the first steps in developing a subsurface Quaternary stratigraphic framework necessary for future hazard assessment.

Geomorphological Evidence for Excess Ice in the Southern Hemisphere of Mars

NASA Astrophysics Data System (ADS)

Viola, D.; McEwen, A. S.

2016-12-01

Abundant water ice is present in the polar caps and in the subsurface at mid to high latitudes on Mars. Subsurface ice can either be confined to regolith pore spaces (pore-filling) or "excess ice" that exceeds the available pore space. The latitudinal bounds of modern excess ice in the northern hemisphere of Mars have been constrained by observations of recent ice-exposing impacts (Dundas et al., 2014, JGR: Planets): >25 have been found as of July 2016 at latitudes above 38°N. However, new impact craters are less commonly found in the southern hemisphere since impacts into relatively dust-free surfaces are difficult to discover; only 5 ice-exposing impacts have been found, all at >55°S. Therefore, we propose the use of other surface morphological features to define the present mid-latitude excess ice boundary in the southern hemisphere. We primarily focus on "expanded craters" that show evidence for thermokarstic diameter enlargement. These craters likely form when an impact exposes a subsurface excess ice layer that subsequently sublimates, leading to an apparent widening of the crater. It is important to note that expanded craters suggest that ice was present both at the time of impact and today, since the widespread loss of an excess ice layer would lead to the collapse of these features. Expanded craters have been mapped across a broad region of the northern plains, and their distribution is consistent with the latitudinal limits of new ice-exposing craters. We also observe expanded craters in and around Hellas Planitia, and will use images from the Context Camera (CTX) on the Mars Reconnaissance Orbiter (MRO) to conduct preliminary mapping of their broader distribution across the southern hemisphere. We will also identify additional features that suggest present or past ice: scallops, polygonal patterned ground, and pedestal craters. This data will be used to infer the latitudinal limit and longitudinal variations of modern excess ice in the southern hemisphere of Mars. This has implications on the history and preservation of water ice on Mars, and may be of interest for future human exploration.

Synthesis of eukaryotic lipid biomarkers in the bacterial domain

NASA Astrophysics Data System (ADS)

Welander, P. V.; Banta, A. B.; Lee, A. K.; Wei, J. H.

2017-12-01

Lipid biomarkers are organic molecules preserved in sediments and sedimentary rocks that can function as geological proxies for certain microbial taxa or for specific environmental conditions. These molecular fossils provide a link between organisms and their environments in both modern and ancient settings and have afforded significant insight into ancient climatic events, mass extinctions, and various evolutionary transitions throughout Earth's history. However, the proper interpretation of lipid biomarkers is dependent on a broad understanding of their diagenetic precursors in modern systems. This includes understanding the taphonomic transformations that these molecules undergo, their biosynthetic pathways, and the ecological conditions that affect their cellular production. In this study, we focus on one group of lipid biomarkers - the sterols. These are polycyclic isoprenoidal lipids that have a high preservation potential and play a critical role in the physiology of most eukaryotes. However, the synthesis and function of these lipids in the bacterial domain has not been fully explored. Here we utilize a combination of bioinformatics, microbial genetics, and biochemistry to demonstrate that bacterial sterol producers are more prevalent in environmental metagenomic samples than in the genomic databases of cultured organisms and to identify novel proteins required to synthesize and modify sterols in bacteria. These proteins represent a distinct pathway for sterol synthesis exclusive to bacteria and indicate that sterol synthesis in bacteria may have evolved independently of eukaryotic sterol biosynthesis. Taken together, these results demonstrate how studies in extant bacteria can provide insight into the biological sources and the biosynthetic pathways of specific lipid biomarkers and in turn may allow for more robust interpretation of biomarker signatures.

Characterization of arsenite-oxidizing bacteria to decipher their role in arsenic bioremediation.

PubMed

Biswas, Rimi; Sarkar, Angana

2018-06-11

High arsenic groundwater contamination causes serious health risks in many developing countries, particularly in India and Bangladesh. The arsenic fluxes in aquifers are primarily controlled by bacterial populations through biogeochemical cycle. In this present study, two gram-positive rod-shaped bacteria were isolated from shallow aquifers of Bhojpur district in Bihar during the early winter season, able to withstand arsenite (As 3+ ) concentration upto 70 mM and 1000 mM of arsenate (As 5+ ) concentration. They showed high resistance to heavy metals up to 30 mM and utilized some complex sugars along with different carbon sources. Growth at wide range of temperature, pH and salinity were observed. Both these isolates showed high efficiency in converting As 3+ into less toxic concentrations of As 5+ respectively from arsenic enriched culture media. Along with superior arsenic transformation and arsenic resistance abilities, the isolates showed a wide variety of metabolic capacity in terms of utilizing a variety of carbon sources under aerobic conditions, respectively. This study reports the potential As 3+ -oxidizing bacteria that can play an important role in subsurface arsenic transformation that will aid in designing future bioremediation strategy for the arsenic affected areas.

Post-Viking microbiology: new approaches, new data, new insights

NASA Technical Reports Server (NTRS)

Nealson, K. H.

1999-01-01

In the 20 years since the Viking experiments, major advances have been made in the areas of microbial systematics, microbial metabolism, microbial survival capacity, and the definition of environments on earth, suggesting that life is more versatile and tenacious than was previously appreciated. Almost all niches on earth which have available energy, and which are compatible with the chemistry of carbon-carbon bonds, are known to be inhabited by bacteria. The oldest known bacteria on earth apparently evolved soon after the formation of the planet, and are heat loving, hydrogen and/or sulfur metabolizing forms. Among the two microbial domains (kingdoms) is a great deal of metabolic diversity, with members of these forms being able to grow on almost any known energy source, organic or inorganic, and to utilize an impressive array of electron acceptors for anaerobic respiration. Both hydrothermal environments and the deep subsurface environments have been shown to support large populations of bacteria, growing on energy supplied by geothermal energy, thus isolating these ecosystems from the rest of the global biogeochemical cycles. This knowledge, coupled with new insights into the history of the solar system, allow one to speculate on possible evolution and survival of life forms on Mars.

Post-Viking microbiology: new approaches, new data, new insights.

PubMed

Nealson, K H

1999-01-01

In the 20 years since the Viking experiments, major advances have been made in the areas of microbial systematics, microbial metabolism, microbial survival capacity, and the definition of environments on earth, suggesting that life is more versatile and tenacious than was previously appreciated. Almost all niches on earth which have available energy, and which are compatible with the chemistry of carbon-carbon bonds, are known to be inhabited by bacteria. The oldest known bacteria on earth apparently evolved soon after the formation of the planet, and are heat loving, hydrogen and/or sulfur metabolizing forms. Among the two microbial domains (kingdoms) is a great deal of metabolic diversity, with members of these forms being able to grow on almost any known energy source, organic or inorganic, and to utilize an impressive array of electron acceptors for anaerobic respiration. Both hydrothermal environments and the deep subsurface environments have been shown to support large populations of bacteria, growing on energy supplied by geothermal energy, thus isolating these ecosystems from the rest of the global biogeochemical cycles. This knowledge, coupled with new insights into the history of the solar system, allow one to speculate on possible evolution and survival of life forms on Mars.

Retention in Treated Wastewater Affects Survival and Deposition of Staphylococcus aureus and Escherichia coli in Sand Columns

PubMed Central

Li, Jiuyi; Zhao, Xiaokang; Tian, Xiujun; Li, Jin; Sjollema, Jelmer

2015-01-01

The fate and transport of pathogenic bacteria from wastewater treatment facilities in the Earth's subsurface have attracted extensive concern over recent decades, while the impact of treated-wastewater chemistry on bacterial viability and transport behavior remains unclear. The influence of retention time in effluent from a full-scale municipal wastewater treatment plant on the survival and deposition of Staphylococcus aureus and Escherichia coli strains in sand columns was investigated in this paper. In comparison to the bacteria cultivated in nutrient-rich growth media, retention in treated wastewater significantly reduced the viability of all strains. Bacterial surface properties, e.g., zeta potential, hydrophobicity, and surface charges, varied dramatically in treated wastewater, though no universal trend was found for different strains. Retention in treated wastewater effluent resulted in changes in bacterial deposition in sand columns. Longer retention periods in treated wastewater decreased bacterial deposition rates for the strains evaluated and elevated the transport potential in sand columns. We suggest that the wastewater quality should be taken into account in estimating the fate of pathogenic bacteria discharged from wastewater treatment facilities and the risks they pose in the aquatic environment. PMID:25595758

Triple-acting lytic enzyme treatment of drug-resistant and intracellular Staphylococcus aureus

USDA-ARS?s Scientific Manuscript database

Multi-drug resistant bacteria are a persistent problem in modern health care, food safety and animal health. There is a need for new antimicrobials to replace over-used conventional antibiotics. Here we describe engineered triple-acting staphylolytic peptidoglycan hydrolases wherein three unique a...

DNA-SIP Reveals the Diversity of Chemolithoautotrophic Bacteria Inhabiting Three Different Soil Types in Typical Karst Rocky Desertification Ecosystems in Southwest China.

PubMed

Li, Baoqin; Li, Zhe; Sun, Xiaoxu; Wang, Qi; Xiao, Enzong; Sun, Weimin

2018-05-04

Autotrophs that inhabit soils receive less attention than their counterparts in other ecosystems, such as deep-sea and subsurface sediments, due to the low abundance of autotrophs in soils with high organic contents. However, the karst rocky desertification region is a unique ecosystem that may have a low level of organic compounds. Therefore, we propose that karst rocky desertification ecosystems may harbor diverse autotrophic microbial communities. In this study, DNA-SIP was employed to identify the chemolithoautotrophic bacteria inhabiting three soil types (i.e., grass, forest, and agriculture) of the karst rocky desertification ecosystems. The results indicated that potential chemolithoautotrophic population was observed in each soil type, even at different time points after amending 13 C-NaHCO 3 , confirming our hypothesis that diverse autotrophs contribute to the carbon cycle in karst soils. Bacteria, such as Ralstonia, Ochrobactrum, Brevibacterium, Acinetobacter, and Corynebacterium, demonstrated their potential to assimilate inorganic carbon and reduce nitrate or thiosulfate as electron acceptors. Putative mixotrophs were identified by DNA-SIP as well, suggesting the metabolic versatility of soil microbiota. A co-occurrence network further indicated that autotrophs and heterotrophs may form associated communities to sustain the ecosystem function. Our current study revealed the metabolic diversity of autotrophic bacteria in soil habitats and demonstrated the potentially important role of chemoautotrophs in karst rocky desertification ecosystems.

Meta-Analysis of Quantification Methods Shows that Archaea and Bacteria Have Similar Abundances in the Subseafloor

PubMed Central

May, Megan K.; Kevorkian, Richard T.; Steen, Andrew D.

2013-01-01

There is no universally accepted method to quantify bacteria and archaea in seawater and marine sediments, and different methods have produced conflicting results with the same samples. To identify best practices, we compiled data from 65 studies, plus our own measurements, in which bacteria and archaea were quantified with fluorescent in situ hybridization (FISH), catalyzed reporter deposition FISH (CARD-FISH), polyribonucleotide FISH, or quantitative PCR (qPCR). To estimate efficiency, we defined “yield” to be the sum of bacteria and archaea counted by these techniques divided by the total number of cells. In seawater, the yield was high (median, 71%) and was similar for FISH, CARD-FISH, and polyribonucleotide FISH. In sediments, only measurements by CARD-FISH in which archaeal cells were permeabilized with proteinase K showed high yields (median, 84%). Therefore, the majority of cells in both environments appear to be alive, since they contain intact ribosomes. In sediments, the sum of bacterial and archaeal 16S rRNA gene qPCR counts was not closely related to cell counts, even after accounting for variations in copy numbers per genome. However, qPCR measurements were precise relative to other qPCR measurements made on the same samples. qPCR is therefore a reliable relative quantification method. Inconsistent results for the relative abundance of bacteria versus archaea in deep subsurface sediments were resolved by the removal of CARD-FISH measurements in which lysozyme was used to permeabilize archaeal cells and qPCR measurements which used ARCH516 as an archaeal primer or TaqMan probe. Data from best-practice methods showed that archaea and bacteria decreased as the depth in seawater and marine sediments increased, although archaea decreased more slowly. PMID:24096423

Pyrosequencing-based assessment of the bacteria diversity in surface and subsurface peat layers of a northern wetland, with focus on poorly studied phyla and candidate divisions.

PubMed

Serkebaeva, Yulia M; Kim, Yongkyu; Liesack, Werner; Dedysh, Svetlana N

2013-01-01

Northern peatlands play a key role in the global carbon and water budget, but the bacterial diversity in these ecosystems remains poorly described. Here, we compared the bacterial community composition in the surface (0-5 cm depth) and subsurface (45-50 cm) peat layers of an acidic (pH 4.0) Sphagnum-dominated wetland, using pyrosequencing of 16S rRNA genes. The denoised sequences (37,229 reads, average length ∼430 bp) were affiliated with 27 bacterial phyla and corresponded to 1,269 operational taxonomic units (OTUs) determined at 97% sequence identity. Abundant OTUs were affiliated with the Acidobacteria (35.5±2.4% and 39.2±1.2% of all classified sequences in surface and subsurface peat, respectively), Alphaproteobacteria (15.9±1.7% and 25.8±1.4%), Actinobacteria (9.5±2.0% and 10.7±0.5%), Verrucomicrobia (8.5±1.4% and 0.6±0.2%), Planctomycetes (5.8±0.4% and 9.7±0.6%), Deltaproteobacteria (7.1±0.4% and 4.4%±0.3%), and Gammaproteobacteria (6.6±0.4% and 2.1±0.1%). The taxonomic patterns of the abundant OTUs were uniform across all the subsamples taken from each peat layer. In contrast, the taxonomic patterns of rare OTUs were different from those of the abundant OTUs and varied greatly among subsamples, in both surface and subsurface peat. In addition to the bacterial taxa listed above, rare OTUs represented the following groups: Armatimonadetes, Bacteroidetes, Chlamydia, Chloroflexi, Cyanobacteria, Elusimicrobia, Fibrobacteres, Firmicutes, Gemmatimonadetes, Spirochaetes, AD3, WS1, WS4, WS5, WYO, OD1, OP3, BRC1, TM6, TM7, WPS-2, and FCPU426. OTU richness was notably higher in the surface layer (882 OTUs) than in the anoxic subsurface peat (483 OTUs), with only 96 OTUs common to both data sets. Most members of poorly studied phyla, such as the Acidobacteria, Verrucomicrobia, Planctomycetes and the candidate division TM6, showed a clear preference for growth in either oxic or anoxic conditions. Apparently, the bacterial communities in surface and subsurface layers of northern peatlands are highly diverse and taxonomically distinct, reflecting the different abiotic conditions in microhabitats within the peat profile.

Microbial monitoring during CO2 storage in deep subsurface saline aquifers in Ketzin, Germany

NASA Astrophysics Data System (ADS)

Wuerdemann, H.; Wandrey, M.; Fischer, S.; Zemke, K.; Let, D.; Zettlitzer, M.; Morozova, D.

2010-12-01

Investigations on subsurface saline aquifers have shown an active biosphere composed of diverse groups of microorganisms in the subsurface. Since microorganisms represent very effective geochemical catalysts, they may influence the process of CO2 storage significantly. In the frames of the EU Project CO2SINK a field laboratory to study CO2 storage into saline aquifer was operated. Our studies aim at monitoring of biological and biogeochemical processes and their impact on the technical effectiveness of CO2 storage technique. The interactions between microorganisms and the minerals of both the reservoir and the cap rock may cause changes to the structure and chemical composition of the rock formations, which may influence the reservoir permeability locally. In addition, precipitation and corrosion may be induced around the well affecting the casing and the casing cement. Therefore, analyses of the composition of microbial communities and its changes should contribute to an evaluation of the effectiveness and reliability of the long-term CO2 storage technique. In order to investigate processes in the deep biosphere caused by the injection of supercritical CO2, genetic fingerprinting (PCR SSCP Single-Strand-Conformation Polymorphism) and FISH (Fluorescence in situ Hybridisation) were used for identification and quantification of microorganisms. Although saline aquifers could be characterised as an extreme habitat for microorganisms due to reduced conditions, high pressure and salinity, a high number of diverse groups of microorganisms were detected with downhole sampling in the injection and observation wells at a depth of about 650m depth. Of great importance was the identification of the sulphate reducing bacteria, which are known to be involved in corrosion processes. Microbial monitoring during CO2 injection has shown that both quantity and diversity of microbial communities were strongly influenced by the CO2 injection. In addition, the indigenous microbial communities revealed a high adaptability to the changed environments after CO2 injection. In order to investigate processes in the rock substrate, long term CO2 exposure experiments on freshly drilled, pristine Ketzin reservoir core samples were accomplished for 24 months using sterile synthetic brine under in situ pressure and temperature conditions. The composition of the microbial community dominated by chemoorganotrophic bacteria and hydrogen oxidizing bacteria changed slightly under CO2 exposure. In addition, changes in porosities were observed with time. During the experiments porosity first increased due to mineral dissolution but then tend to decrease due to mineral precipitation. These mineralogical changes are consistent with changes in fluid composition during the course of the experiments that indicate notably increased K+, Ca2+, Mg2+, and SO4 2- concentrations. K+, Ca2+, Mg2+ concentrations exceeded the reservoir brine composition significantly and can be attributed to the CO2 exposure.

Where Does Amber Come from?

ERIC Educational Resources Information Center

Booth, Bibi

2005-01-01

Amber is the fossilized resin of now-extinct trees, primarily ancient conifers but also some flowering tropical trees. An aromatic, soft, sticky substance, resin in extinct trees probably served the same purposes as resin in modern trees: to protect the plant by sealing cuts and by excluding bacteria, fungi, and insects.

Triple-acting antimicrobial treatment for drug-resistant and intracellular Staphylococcus aureus

USDA-ARS?s Scientific Manuscript database

Multi-drug resistant bacteria are a persistent problem in modern health care, food safety and animal health. There is a need for new antimicrobials to replace over-used conventional antibiotics. Staphylococcus aureus (S. aureus) is a notorious pathogen for both animal and human health with multi-d...

Alternatives to antibiotics: overview and engineered peptidoglycan hydrolases that reduce resistance development

USDA-ARS?s Scientific Manuscript database

Multi-drug resistant bacteria are a persistent problem in modern health care, food safety and animal health. There is a need for new antimicrobials to replace over-used conventional antibiotics. A symposium in Paris, France, 2012 entitled “Alternatives to Antibiotics” was organized by Cyril Gay an...

Triple-acting antimicrobial treatment for drug-resistant and intracellular Staphylococcus aureus.

USDA-ARS?s Scientific Manuscript database

Multi-drug resistant bacteria are a persistent problem in modern health care, food safety and animal health. There is a need for new antimicrobials to replace over-used conventional antibiotics. Staphylococcus aureus (S. aureus) is a notorious pathogen for both animal and human health with multi-d...

Triple-acting Peptidoglycan hydrolase treatment for drug-resistant and intracellular Staphylococcus aureus

USDA-ARS?s Scientific Manuscript database

Multi-drug resistant bacteria are a persistent problem in modern health care, food safety and animal health. There is a need for new antimicrobials to replace over-used conventional antibiotics. Staphylococcus aureus (S. aureus) is a notorious pathogen for both animal and human health with multi-d...

Learning Molecular Genetics in Teacher-Led Outreach Laboratories

ERIC Educational Resources Information Center

Ben-Nun, Michal Stolarsky; Yarden, Anat

2009-01-01

Learning modern genetics is challenging and students have difficulty acquiring a coherent cognitive mental model of abstract concepts such as DNA, bacteria and enzymes. Here we investigated students' mental models of genetics through analysis and interpretation of the discourse that took place while high-school students practised hands-on…

Seasonal Patterns in Microbial Community Composition in Denitrifying Bioreactors Treating Subsurface Agricultural Drainage.

PubMed

Porter, Matthew D; Andrus, J Malia; Bartolerio, Nicholas A; Rodriguez, Luis F; Zhang, Yuanhui; Zilles, Julie L; Kent, Angela D

2015-10-01

Denitrifying bioreactors, consisting of water flow control structures and a woodchip-filled trench, are a promising approach for removing nitrate from agricultural subsurface or tile drainage systems. To better understand the seasonal dynamics and the ecological drivers of the microbial communities responsible for denitrification in these bioreactors, we employed microbial community "fingerprinting" techniques in a time-series examination of three denitrifying bioreactors over 2 years, looking at bacteria, fungi, and the denitrifier functional group responsible for the final step of complete denitrification. Our analysis revealed that microbial community composition responds to depth and seasonal variation in moisture content and inundation of the bioreactor media, as well as temperature. Using a geostatistical analysis approach, we observed recurring temporal patterns in bacterial and denitrifying bacterial community composition in these bioreactors, consistent with annual cycling. The fungal communities were more stable, having longer temporal autocorrelations, and did not show significant annual cycling. These results suggest a recurring seasonal cycle in the denitrifying bioreactor microbial community, likely due to seasonal variation in moisture content.

Antibiotic resistance monitoring: the Spanish programme. The VAV Network. Red de Vigilancia de Resistencias Antibióticas en Bacterias de Origen Veterinario.

PubMed

Moreno, M A; Domínguez, L; Teshager, T; Herrero, I A; Porrero, M C

2000-05-01

Antimicrobial resistance is a problem in modern public health and antimicrobial use and especially misuse, the most important selecting force for bacterial antibiotic resistance. As this resistance must be monitored we have designed the Spanish network 'Red de Vigilancia de Resistencias Antibióticas en Bacterias de Origen Veterinario'. This network covers the three critical points of veterinary responsibility, bacteria from sick animals, bacteria from healthy animals and bacteria from food animals. Key bacteria, antimicrobials and animal species have been defined for each of these groups along with laboratory methods for testing antimicrobial susceptibility and for data analysis and reporting. Surveillance of sick animals was first implemented using Escherichia coli as the sentinel bacterium. Surveillance of E. coli and Enterococcus faecium from healthy pigs was implemented in 1998. In July 1999, data collection on Salmonella spp. was initiated in poultry slaughterhouses. Additionally, the prevalence of vancomycin resistant E. faecium was also monitored. This network has specific topics of interest related to methods of determining resistance, analysis and reporting of data, methods of use for veterinary practitioners and collaboration with public health authorities.

Terrestrial Biomarkers for Early Life on Earth as Analogs for Possible Martian Life Forms: Examples of Minerally Replaced Bacteria and Biofilms From the 3.5 - 3.3-Ga Barberton Greenstone Belt, South Africa

NASA Technical Reports Server (NTRS)

Westall, F.; McKay, D. S.; Gibson, E. K.; deWit, M. J.; Dann, J.; Gerneke, D.; deRonde, C. E. J.

1998-01-01

The search for extraterrestrial life and especially martian life hinges on a variety of methods used to identify vestiges of what we could recognize as life, including chemical signatures, morphological fossils, and biogenic precipitates. Although the possibility of extant life on Mars (subsurface) is being considered, most exploration efforts may be directed toward the search for fossil life. Geomorphological evidence points to a warmer and wetter Mars early on in its history, a scenario that encourages comparison with the early Earth. For this reason, study of the early terrestrial life forms and environment in which they lived may provide clues as to how to search for extinct martian life. As a contribution to the early Archean database of terrestrial microfossils, we present new data on morphological fossils from the 3.5-3.3-Ga Barberton greenstone belt (BGB), South Africa. This study underlines the variety of fossil types already present in some of the oldest, best-preserved terrestrial sediments, ranging from minerally replaced bacteria and bacteria molds of vaRious morphologies (coccoid, coccobacillus, bacillus) to minerally replaced biofilm. Biofilm or extracellular polymeric substance (EPS) is produced by bacteria and appears to be more readily fossilisable than bacteria themselves. The BGB fossils occur in shallow water to subaerial sediments interbedded with volcanic lavas, the whole being deposited on oceanic crust. Penecontemporaneous silicification of sediments and volcanics resulted in the chertification of the rocks, which were later subjected to low-grade metamorphism (lower greenschist).

Occurrence and importance of anaerobic ammonium-oxidising bacteria in vegetable soils.

PubMed

Shen, Li-dong; Wu, Hong-sheng; Gao, Zhi-qiu; Xu, Xiang-hua; Chen, Tie-xi; Liu, Shuai; Cheng, Hai-xiang

2015-07-01

The quantitative importance of anaerobic ammonium oxidation (anammox) has been described in paddy fields, while the presence and importance of anammox in subsurface soil from vegetable fields have not been determined yet. Here, we investigated the occurrence and activity of anammox bacteria in five different types of vegetable fields located in Jiangsu Province, China. Stable isotope experiments confirmed the anammox activity in the examined soils, with the potential rates of 2.1 and 23.2 nmol N2 g(-1) dry soil day(-1), and the anammox accounted for 5.9-20.5% of total soil dinitrogen gas production. It is estimated that a total loss of 7.1-78.2 g N m(-2) year(-1) could be linked to the anammox process in the examined vegetable fields. Phylogenetic analyses showed that multiple co-occurring anammox genera were present in the examined soils, including Candidatus Brocadia, Candidatus Kuenenia, Candidatus Anammoxoglobus and Candidatus Jettenia, and Candidatus Brocadia appeared to be the most common anammox genus. Quantitative PCR further confirmed the presence of anammox bacteria in the examined soils, with the abundance varying from 2.8 × 10(5) to 3.0 × 10(6) copies g(-1) dry soil. Correlation analyses suggested that the soil ammonium concentration had significant influence on the activity and abundance of anammox bacteria in the examined soils. The results of our study showed the presence of diverse anammox bacteria and indicated that the anammox process could serve as an important nitrogen loss pathway in vegetable fields.

Diversity, metal resistance and uranium sequestration abilities of bacteria from uranium ore deposit in deep earth stratum.

PubMed

Islam, Ekramul; Sar, Pinaki

2016-05-01

Metal resistance and uranium (U) sequestration abilities of bacteria residing in subsurface U ore was investigated using 122 pure culture strains isolated through enrichment. The cumulative frequencies of isolates resistant to each metal tested were as follows: As(V), 74%; Zn, 58%; Ni, 53%; Cd, 47%; Cr(VI), 41%; Co, 40%; Cu, 20%; and Hg, 4%. 16S rRNA gene analysis revealed that isolated bacteria belonged to 14 genera with abundance of Arthrobacter, Microbacterium, Acinetobacter and Stenotrophomonas. Cobalt did not interfere with the growth of most of the bacterial isolates belonging to different groups while U allowed growth of four different genera of which Stenotrophomonas and Microbacterium showed high U tolerance. Interestingly, tolerance to Ni, Zn, Cu, and Hg was observed only in Microbacterium, Arthrobacter, Paenibacillus¸ and Acinetobacter, respectively. However, Microbacterium was found to be dominant when isolated from other five different metal enrichments including U. Uranium removal study showed that 84% of the test bacteria could remove more than 50mgUg(-1) dry weight from 80 or 160mgL(-1) U within 48h. In general, Microbacterium, Arthrobacter and Acinetobacter could remove a higher amount of U. High resolution transmission electron microscopy (HRTEM) study of U exposed cells revealed that accumulated U sequestered mostly around the cell periphery. The study highlights that indigenous U ore deposit bacteria have the potential to interact with U, and thus could be applied for bioremediation of U contaminated sites or wastes. Copyright © 2016 Elsevier Inc. All rights reserved.

Iron microbial mats in modern and phanerozoic environments

NASA Astrophysics Data System (ADS)

Baele, Jean-Marc; Bouvain, Frédéric; De Jong, Jeroen; Matielli, Nadine; Papier, Séverine; Préat, Alain

2008-08-01

The recognition of iron microbial mats in terrestrial environments is of great relevance for the search for extraterrestrial life, especially on mars where significant iron minerals were identified in the subsurface. Most researches focused on very ancient microbial mats (e.g. BIFs) since they formed on Earth at a time where similar conditions are supposed to have prevailed on Mars too. However, environmental proxies are often difficult to use for these deposits on Earth which, in addition, may be heavily transformed due to diagenesis or even metamorphism. Here we present modern and phanerozoic iron microbial mats occurrences illustrating the wide variety of environments in which they form, including many marine settings, ponds, creeks, caves, volcanoes, etc. Contrarily to their Precambrian counterparts, Modern and Phanerozoic deposits are usually less affected by diagenesis and the environmental conditions likely to be better constrained. Therefore, their investigation may help for the search for morphological and geochemical biosignatures (e.g. iron isotopes) in ancient iron microbial occurrences on Earth but also on other Planets. In particular, many of the case studies presented here show that microstromatolithe-like morphologies may be valuable targets for screening potential biosignatures in various rock types.

Active hematite concretion formation in modern acid saline lake sediments, Lake Brown, Western Australia

NASA Astrophysics Data System (ADS)

Bowen, Brenda Beitler; Benison, K. C.; Oboh-Ikuenobe, F. E.; Story, S.; Mormile, M. R.

2008-04-01

Concretions can provide valuable records of diagenesis and fluid-sediment interactions, however, reconstruction of ancient concretion-forming conditions can be difficult. Observation of modern hematite concretion growth in a natural sedimentary setting provides a rare glimpse of conditions at the time of formation. Spheroidal hematite-cemented concretions are actively precipitating in shallow subsurface sediments at Lake Brown in Western Australia. Lake Brown is a hypersaline (total dissolved solids up to 23%) and acidic (pH ˜ 4) ephemeral lake. The concretion host sediments were deposited between ˜ 1 and 3 ka, based on dating of stratigraphically higher and lower beds. These age constraints indicate that the diagenetic concretions formed < 3 ka, and field observations suggest that some are currently forming. These modern concretions from Lake Brown provide an example of very early diagenetic formation in acid and saline conditions that may be analogous to past conditions on Mars. Previously, the hematite concretions in the Burns formation on Mars have been interpreted as late stage diagenetic products, requiring long geologic time scales and multiple fluid flow events to form. In contrast, the Lake Brown concretions support the possibility of similar syndepositional to very early diagenetic concretion precipitation on Mars.

A urolith of biogenic dolomite - another clue in the dolomite mystery

NASA Astrophysics Data System (ADS)

Mansfield, Charles F.

1980-06-01

A male Dalmatian, Canis familiaris, produced uroliths of almost pure dolomite, 3-8 mm across, in his urinary bladder in less than 8 months at 38°C and about 1 atm. The X-ray diffractogram identified the predominant mineral as dolomite, and the sharp (01.5) peak showed it is ordered dolomite, not the disordered form, protodolomite. Geochemically and biologically plausible causes include (1) renal, respiratory, or metabolic alkalosis, (2) infection by urease-producing (urea-splitting) fungi or bacteria and (3) infection by uric acid-fermenting bacteria. Hematological, bacteriological, urological and geochemical considerations most strongly implicate infection by either anaerobic, urease-producing bacteria or anaerobic, uric acid-fermenting bacteria. The physical and chemical conditions of this urinary system more closely approximate modern and inferred ancient carbonate depositional settings than most previous laboratory experiments, especially in terms of temperature, pressure, total salinity and, possibly, biota. The presence of urease-producing and/or uric acid-fermenting bacteria in urea- and/or acid-containing sediment, such as fecal pellets and algal mats, could promote formation of authigenic dolomite or other carbonates.

Cabin air filtration: helping to protect occupants from infectious diseases.

PubMed

Bull, Karen

2008-05-01

Presentation made at the Aviation Health Conference, London, November 2006. In modern aircraft, the air in the cabin is provided by the environmental control system (ECS) and consists of approximately 50% outside air (engine 'bleed air') mixed with approximately 50% filtered, recirculated air. This paper describes how modern aircraft cabin air filters are effective at removing airborne particulate contamination (such as bacteria and viruses) from the recirculated air system. It also describes one of the technological solutions that is currently available to treat any odours or volatile organic compounds (VOCs) that may be present in the aircraft ECS.

The modern calcifying sponge Spheciospongia vesparium (Lamarck, 1815), Great Bahama Bank: Implications for ancient sponge mud-mounds

NASA Astrophysics Data System (ADS)

Neuweiler, Fritz; Burdige, David J.

2005-04-01

Modern calcified siliceous sponges from the Great Bahama Bank, living at water depth ranges of 2 to 5 m, have been proposed as likely analogues for calcified sponges in Upper Jurassic sponge "reefs" (e.g., southern Germany), or Lower Jurassic bioherms that consist of reddish, spiculiferous limestones (e.g., Broccatello Formation of the Southern Alps). Indeed, sponge-related calcification or siliceous sponge diagenesis, in general, is widely considered a key feature for the mechanisms of accretion and textural maturation in Phanerozoic sponge mounds or spiculiferous carbonate mud-mounds. Based on a revisit of the original sites on the Great Bahama Bank (NW of Andros Island) the biostratonomy of the calcifying sponge Spheciospongia vesparium (Lamarck, 1815) was explored using the patterns of fluorescent dissolved organic matter (FDOM) as revealed by the application of three-dimensional excitation-emission matrix (EEM) fluorescence spectroscopy. Geochemical sampling distinguished between FDOM that was extracted from sponge tissue and FDOM that was intimately associated with CaCO 3 (from particles due to sediment agglutination and authigenic CaCO 3), both obtained from the living sponge at the sediment surface and from the calcified sponge at the shallow subsurface (from 5 to 10 cm of depth). As expected, the sponge tissue shows highest intensities for protein-like fluorescence. However, from the surface to the subsurface, there is a loss of such relatively pristine fluorescent material in the range of 70%. Humic-like fluorescence that occurs associated with sponge tissue is relatively mature or aged, thus it most probably represents seawater FDOM taken up through active filter feeding. Relative to the sponge tissue material, the FDOM patterns associated with Ca-carbonates show much lower total fluorescence intensities, by up to two orders of magnitude. The agglutinated sedimentary carbonate particles from the surface (pellets, ooids, grapestones) exclusively show a relatively mature, humic-like fluorescence. The deeper, calcified parts of Spheciospongia, which represent a mixture of particles and authigenic CaCO 3, provided a FDOM pattern that obviously combines the mature FDOM pattern of particles with diagenetically fresh, protein-like and fulvic acid-like fluorescence. We conclude that shallow subsurface calcification of S. vesparium correlates with the initial stage of sponge biomass humification. Such a mechanism of biomass transformation, i.e., from biopolymers to geopolymers via degradation and condensation, has also been suggested for the large-scale development of carbonate (sponge) mud-mounds. Therefore, we consider the modern calcifying siliceous sponge S. vesparium (Lamarck, 1815) a potential pardigm to decipher in more detail the geologically important process of biomass-induced calcification or organomineralisation with its subsequent effect of pore water FDOM preservation and sediment lithification.

From Nanowires to Biofilms: An Exploration of Novel Mechanisms of Uranium Transformation Mediated by Geobacter Bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

REGUERA, GEMMA

2014-01-16

One promising strategy for the in situ bioremediation of radioactive groundwater contaminants that has been identified by the SBR Program is to stimulate the activity of dissimilatory metal-reducing microorganisms to reductively precipitate uranium and other soluble toxic metals. The reduction of U(VI) and other soluble contaminants by Geobacteraceae is directly dependent on the reduction of Fe(III) oxides, their natural electron acceptor, a process that requires the expression of Geobacter’s conductive pili (pilus nanowires). Expression of conductive pili by Geobacter cells leads to biofilm development on surfaces and to the formation of suspended biogranules, which may be physiological closer to biofilmsmore » than to planktonic cells. Biofilm development is often assumed in the subsurface, particularly at the matrix-well screen interface, but evidence of biofilms in the bulk aquifer matrix is scarce. Our preliminary results suggest, however, that biofilms develop in the subsurface and contribute to uranium transformations via sorption and reductive mechanisms. In this project we elucidated the mechanism(s) for uranium immobilization mediated by Geobacter biofilms and identified molecular markers to investigate if biofilm development is happening in the contaminated subsurface. The results provided novel insights needed in order to understand the metabolic potential and physiology of microorganisms with a known role in contaminant transformation in situ, thus having a significant positive impact in the SBR Program and providing novel concept to monitor, model, and predict biological behavior during in situ treatments.« less

Combined fabrication technique for high-precision aspheric optical windows

NASA Astrophysics Data System (ADS)

Hu, Hao; Song, Ci; Xie, Xuhui

2016-07-01

Specifications made on optical components are becoming more and more stringent with the performance improvement of modern optical systems. These strict requirements not only involve low spatial frequency surface accuracy, mid-and-high spatial frequency surface errors, but also surface smoothness and so on. This presentation mainly focuses on the fabrication process for square aspheric window which combines accurate grinding, magnetorheological finishing (MRF) and smoothing polishing (SP). In order to remove the low spatial frequency surface errors and subsurface defects after accurate grinding, the deterministic polishing method MRF with high convergence and stable material removal rate is applied. Then the SP technology with pseudo-random path is adopted to eliminate the mid-and-high spatial frequency surface ripples and high slope errors which is the defect for MRF. Additionally, the coordinate measurement method and interferometry are combined in different phase. Acid-etched method and ion beam figuring (IBF) are also investigated on observing and reducing the subsurface defects. Actual fabrication result indicates that the combined fabrication technique can lead to high machining efficiency on manufaturing the high-precision and high-quality optical aspheric windows.

Bacterial trajectories tracked with time-lapse video-microscopy reveal the impact of manganese biomineralization on bacterial sedimentation.

NASA Astrophysics Data System (ADS)

Kerboas, Camille; Pena, Jasquelin; De Anna, Pietro

2017-04-01

In aquatic and subsurface environments, sedimentation may influence bacterial transport. Microorganisms that carry out biomineralization reactions may exhibit distinct transport properties from non-biomineralizing organisms due an apparent increase in density caused by biomineral production. For several decades, the biomineralization of manganese (Mn) has been recognized to be a major environmental process, whereby Mn oxide (MnO2(s)) minerals participate in a plethora of biogeochemical processes including contaminant adsorption, organic matter oxidation. Typically, manganese biomineralization proceeds through the enzymatic oxidation of aqueous Mn2+ to Mn4+ and precipitation of MnO2(s) in a biofilm matrix outside the bacterial cell. Here, we present a study of the impact of biomineralization on the sedimentation properties of bacteria at small scales (over mm distances) under hydrostatic conditions. We hypothesize that bacteria will sediment faster when biomineralization is active due to encrustation of the organisms by mineral particles. To test this hypothesis, we tracked the vertical notion of individual bacteria (Pseudomonas putida GB-1) using time-lapse video-microscopy. We compared the sedimentation velocity of bacteria in the case where significant biomineralization had occurred, as inferred from bulk measurements of solid phase Mn, with the sinking velocity of bacteria grown without Mn. We calibrated the proposed method by comparing velocity measurements of sinking polystyrene micro-sphere of known density and size with Stokes law, obtaining results that were accurate within 1% of the theoretical value (29.4 nm/s). We also measured a diffusion coefficient of 7x10-13 m2/s for the particles. Following this approach, we measured the sedimentation velocity of P. putida with and without MnO2(s). Our results show that biomineralization leads to faster sedimentation of the bacteria. In natural environments, biomineralization reactions may increase the sinking velocity of bacteria and therefore contribute to the physical separation of organisms according to phenotype and give rise to localized spots of high mineralization rates.

Uncertainty in the modelling of spatial and temporal patterns of shallow groundwater flow paths: The role of geological and hydrological site information

NASA Astrophysics Data System (ADS)

Woodward, Simon J. R.; Wöhling, Thomas; Stenger, Roland

2016-03-01

Understanding the hydrological and hydrogeochemical responses of hillslopes and other small scale groundwater systems requires mapping the velocity and direction of groundwater flow relative to the controlling subsurface material features. Since point observations of subsurface materials and groundwater head are often the basis for modelling these complex, dynamic, three-dimensional systems, considerable uncertainties are inevitable, but are rarely assessed. This study explored whether piezometric head data measured at high spatial and temporal resolution over six years at a hillslope research site provided sufficient information to determine the flow paths that transfer nitrate leached from the soil zone through the shallow saturated zone into a nearby wetland and stream. Transient groundwater flow paths were modelled using MODFLOW and MODPATH, with spatial patterns of hydraulic conductivity in the three material layers at the site being estimated by regularised pilot point calibration using PEST, constrained by slug test estimates of saturated hydraulic conductivity at several locations. Subsequent Null Space Monte Carlo uncertainty analysis showed that this data was not sufficient to definitively determine the spatial pattern of hydraulic conductivity at the site, although modelled water table dynamics matched the measured heads with acceptable accuracy in space and time. Particle tracking analysis predicted that the saturated flow direction was similar throughout the year as the water table rose and fell, but was not aligned with either the ground surface or subsurface material contours; indeed the subsurface material layers, having relatively similar hydraulic properties, appeared to have little effect on saturated water flow at the site. Flow path uncertainty analysis showed that, while accurate flow path direction or velocity could not be determined on the basis of the available head and slug test data alone, the origin of well water samples relative to the material layers and site contour could still be broadly deduced. This study highlights both the challenge of collecting suitably informative field data with which to characterise subsurface hydrology, and the power of modern calibration and uncertainty modelling techniques to assess flow path uncertainty in hillslopes and other small scale systems.

Archaeal Distribution in Moonmilk Deposits from Alpine Caves and Their Ecophysiological Potential.

PubMed

Reitschuler, Christoph; Spötl, Christoph; Hofmann, Katrin; Wagner, Andreas O; Illmer, Paul

2016-04-01

(Alpine) caves are, in general, windows into the Earth's subsurface. Frequently occurring structures in caves such as moonmilk (secondary calcite deposits) offer the opportunity to study intraterrestrial microbial communities, adapted to oligotrophic and cold conditions. This is an important research field regarding the dimensions of subsurface systems and cold regions on Earth. On a methodological level, moonmilk deposits from 11 caves in the Austrian Alps were collected aseptically and investigated using a molecular (qPCR and DGGE sequencing-based) methodology in order to study the occurrence, abundance, and diversity of the prevailing native Archaea community. Furthermore, these Archaea were enriched in complex media and studied regarding their physiology, with a media selection targeting different physiological requirements, e.g. methanogenesis and ammonia oxidation. The investigation of the environmental samples showed that all moonmilk deposits were characterized by the presence of the same few habitat-specific archaeal species, showing high abundances and constituting about 50 % of the total microbial communities. The largest fraction of these Archaea was ammonia-oxidizing Thaumarchaeota, while another abundant group was very distantly related to extremophilic Euryarchaeota (Moonmilk Archaea). The archaeal community showed a depth- and oxygen-dependent stratification. Archaea were much more abundant (around 80 %), compared to bacteria, in the actively forming surface part of moonmilk deposits, decreasing to about 5 % down to the bedrock. Via extensive cultivation efforts, it was possible to enrich the enigmatic Moonmilk Archaea and also AOA significantly above the level of bacteria. The most expedient prerequisites for cultivating Moonmilk Archaea were a cold temperature, oligotrophic conditions, short incubation times, a moonmilk surface inoculum, the application of erythromycin, and anaerobic (microaerophilic) conditions. On a physiological level, it seems that methanogenesis is of marginal importance, while ammonia oxidation and a still undiscovered metabolic pathway are vital elements in the (archaeal) moonmilk biome.

Phylogenetic Diversity Analysis of Subterranean Hot Springs in Iceland

PubMed Central

Marteinsson, Viggó Thór; Hauksdóttir, Sigurbjörg; Hobel, Cédric F. V.; Kristmannsdóttir, Hrefna; Hreggvidsson, Gudmundur Oli; Kristjánsson, Jakob K.

2001-01-01

Geothermal energy has been harnessed and used for domestic heating in Iceland. In wells that are typically drilled to a depth of 1,500 to 2,000 m, the temperature of the source water is 50 to 130°C. The bottoms of the boreholes can therefore be regarded as subterranean hot springs and provide a unique opportunity to study the subterranean biosphere. Large volumes of geothermal fluid from five wells and a mixture of geothermal water from 50 geothermal wells (hot tap water) were sampled and concentrated through a 0.2-μm-pore-size filter. Cells were observed in wells RG-39 (91.4°C) and MG-18 (71.8°C) and in hot tap water (76°C), but no cells were detected in wells SN-4, SN-5 (95 to 117°C), and RV-5 (130°C). Archaea and Bacteria were detected by whole-cell fluorescent in situ hybridization. DNAs were extracted from the biomass, and small-subunit rRNA genes (16S rDNAs) were amplified by PCR using primers specific for the Archaea and Bacteria domains. The PCR products were cloned and sequenced. The sequence analysis showed 11 new operational taxonomic units (OTUs) out of 14, 3 of which were affiliated with known surface OTUs. Samples from RG-39 and hot tap water were inoculated into enrichment media and incubated at 65 and 85°C. Growth was observed only in media based on geothermal water. 16S rDNA analysis showed enrichments dominated with Desulfurococcales relatives. Two strains belonging to Desulfurococcus mobilis and to the Thermus/Deinococcus group were isolated from borehole RG-39. The results indicate that subsurface volcanic zones are an environment that provides a rich subsurface for novel thermophiles. PMID:11526029

Phylogenetic diversity analysis of subterranean hot springs in Iceland.

PubMed

Marteinsson, V T; Hauksdóttir, S; Hobel, C F; Kristmannsdóttir, H; Hreggvidsson, G O; Kristjánsson, J K

2001-09-01

Geothermal energy has been harnessed and used for domestic heating in Iceland. In wells that are typically drilled to a depth of 1,500 to 2,000 m, the temperature of the source water is 50 to 130 degrees C. The bottoms of the boreholes can therefore be regarded as subterranean hot springs and provide a unique opportunity to study the subterranean biosphere. Large volumes of geothermal fluid from five wells and a mixture of geothermal water from 50 geothermal wells (hot tap water) were sampled and concentrated through a 0.2-microm-pore-size filter. Cells were observed in wells RG-39 (91.4 degrees C) and MG-18 (71.8 degrees C) and in hot tap water (76 degrees C), but no cells were detected in wells SN-4, SN-5 (95 to 117 degrees C), and RV-5 (130 degrees C). Archaea and Bacteria were detected by whole-cell fluorescent in situ hybridization. DNAs were extracted from the biomass, and small-subunit rRNA genes (16S rDNAs) were amplified by PCR using primers specific for the Archaea and Bacteria domains. The PCR products were cloned and sequenced. The sequence analysis showed 11 new operational taxonomic units (OTUs) out of 14, 3 of which were affiliated with known surface OTUs. Samples from RG-39 and hot tap water were inoculated into enrichment media and incubated at 65 and 85 degrees C. Growth was observed only in media based on geothermal water. 16S rDNA analysis showed enrichments dominated with Desulfurococcales relatives. Two strains belonging to Desulfurococcus mobilis and to the Thermus/Deinococcus group were isolated from borehole RG-39. The results indicate that subsurface volcanic zones are an environment that provides a rich subsurface for novel thermophiles.

Quantification of Microbial Communities in Subsurface Marine Sediments of the Black Sea and off Namibia.

PubMed

Schippers, Axel; Kock, Dagmar; Höft, Carmen; Köweker, Gerrit; Siegert, Michael

2012-01-01

Organic-rich subsurface marine sediments were taken by gravity coring up to a depth of 10 m below seafloor at six stations from the anoxic Black Sea and the Benguela upwelling system off Namibia during the research cruises Meteor 72-5 and 76-1, respectively. The quantitative microbial community composition at various sediment depths was analyzed using total cell counting, catalyzed reporter deposition - fluorescence in situ hybridization (CARD-FISH) and quantitative real-time PCR (Q-PCR). Total cell counts decreased with depths from 10(9) to 10(10) cells/mL at the sediment surface to 10(7)-10(9) cells/mL below one meter depth. Based on CARD-FISH and Q-PCR analyses overall similar proportions of Bacteria and Archaea were found. The down-core distribution of prokaryotic and eukaryotic small subunit ribosomal RNA genes (16S and 18S rRNA) as well as functional genes involved in different biogeochemical processes was quantified using Q-PCR. Crenarchaeota and the bacterial candidate division JS-1 as well as the classes Anaerolineae and Caldilineae of the phylum Chloroflexi were highly abundant. Less abundant but detectable in most of the samples were Eukarya as well as the metal and sulfate-reducing Geobacteraceae (only in the Benguela upwelling influenced sediments). The functional genes cbbL, encoding for the large subunit of RuBisCO, the genes dsrA and aprA, indicative of sulfate-reducers as well as the mcrA gene of methanogens were detected in the Benguela upwelling and Black Sea sediments. Overall, the high organic carbon content of the sediments goes along with high cell counts and high gene copy numbers, as well as an equal abundance of Bacteria and Archaea.

Performance and bacterial community structure of a 10-years old constructed mangrove wetland.

PubMed

Tian, Tingting; Tam, Nora F Y; Zan, Qijie; Cheung, S G; Shin, Paul K S; Wong, Y S; Zhang, Li; Chen, Zhanghe

2017-11-30

Constructed mangrove wetland has been used for wastewater treatment but its long-term performance has not been reported. One-year monitoring of a 10-years old horizontal subsurface-flow constructed mangrove wetland consisting of three belts, two with mangrove plants and one without, revealed that the system maintained high and stable removal percentages of organic matter and nutrients, and planted belts performed better than unplanted control. Substrates in belts planted with Aegiceras corniculatum or Kandelia obovata had higher abundance of ammonifiers, nitrifiers and denitrifiers but lower total heterotrophic bacteria than unplanted substrate. Denaturing gradient gel electrophoresis showed that microbial diversity in planted substrate was significantly lower than that in unplanted one. The bacteria in substrates, irrespective to belts, were phylogenetically related to Proteobacteria (most dominant), Acidobacteria, Firmicutes, Nitrospirae, Gemmatimonadetes, Chloroflexi and Cyanobacteria. The steady performance of this 10-year old constructed mangrove wetland was affected by the abundance and diversity of bacterial community in substrate. Copyright © 2017 Elsevier Ltd. All rights reserved.

A bioenergetic basis for membrane divergence in archaea and bacteria.

PubMed

Sojo, Víctor; Pomiankowski, Andrew; Lane, Nick

2014-08-01

Membrane bioenergetics are universal, yet the phospholipid membranes of archaea and bacteria-the deepest branches in the tree of life-are fundamentally different. This deep divergence in membrane chemistry is reflected in other stark differences between the two domains, including ion pumping and DNA replication. We resolve this paradox by considering the energy requirements of the last universal common ancestor (LUCA). We develop a mathematical model based on the premise that LUCA depended on natural proton gradients. Our analysis shows that such gradients can power carbon and energy metabolism, but only in leaky cells with a proton permeability equivalent to fatty acid vesicles. Membranes with lower permeability (equivalent to modern phospholipids) collapse free-energy availability, precluding exploitation of natural gradients. Pumping protons across leaky membranes offers no advantage, even when permeability is decreased 1,000-fold. We hypothesize that a sodium-proton antiporter (SPAP) provided the first step towards modern membranes. SPAP increases the free energy available from natural proton gradients by ∼60%, enabling survival in 50-fold lower gradients, thereby facilitating ecological spread and divergence. Critically, SPAP also provides a steadily amplifying advantage to proton pumping as membrane permeability falls, for the first time favoring the evolution of ion-tight phospholipid membranes. The phospholipids of archaea and bacteria incorporate different stereoisomers of glycerol phosphate. We conclude that the enzymes involved took these alternatives by chance in independent populations that had already evolved distinct ion pumps. Our model offers a quantitatively robust explanation for why membrane bioenergetics are universal, yet ion pumps and phospholipid membranes arose later and independently in separate populations. Our findings elucidate the paradox that archaea and bacteria share DNA transcription, ribosomal translation, and ATP synthase, yet differ in equally fundamental traits that depend on the membrane, including DNA replication.

Wilcox group (Paleocene to Eocene) coals of the Sabine Uplift area, Texas and Louisiana

USGS Publications Warehouse

Hook, Robert W.; Warwick, Peter D.; SanFilipo, John R.; Warwick, Peter D.; Karlsen, Alexander K.; Merrill, Matthew D.; Valentine, Brett J.

2011-01-01

The Wilcox Group (Paleocene to Eocene) of the Sabine uplift, a structural arch in northeastern Texas and northwestern Louisiana (Figure 1), has lignite zones that approach subbituminous rank (see Chapter 4, this publication). These coals are among the highest quality resources known within the Gulf Coastal Plain because of their low ash yield and sulfur content. The surface expression of the Sabine uplift is defined by the contact between coal-bearing rocks of the Wilcox Group and overlying fluvial rocks of the Carrizo Sand, which is the basal unit of the Claiborne Group (Figures 2, 3). The Sabine uplift study area includes parts of Harrison, Marion, Nacogdoches, Panola, Rusk, Sabine, San Augustine, and Shelby Counties in Texas and Bossier, Caddo, De Soto, Natchitoches, Red River, and Sabine Parishes in Louisiana (Figure 1). Adjacent counties and parishes that include the subsurface Wilcox Group extend the regional Sabine uplift area. The Wilcox in the subsurface is underlain by the Midway Group (Figure 3), a mudstone-dominated marine sequence of Paleocene age. Quaternary alluvium and terrace deposits overlying the Wilcox Group at the surface are limited to areas of modern drainage.The total thickness of the Wilcox Group within the Sabine uplift area ranges from approximately 400 ft on outcrop to 2500 ft in subsurface (Kaiser, 1990). In a few places, the contact between the overlying Carrizo Sand and Wilcox Group is erosional, but in other places, the contact is gradational.

Degradation of spent craft brewer’s yeast by caprine rumen hyper ammonia-producing bacteria

USDA-ARS?s Scientific Manuscript database

Spent brewer’s yeast has long been included in ruminant diets as a protein supplement. However, modern craft beers often include more hops (Humulus lupulus L.) compounds than traditional recipes. These compounds include alpha and beta-acids, which are antimicrobial to the rumen hyper ammonia-produci...

ATLAS of Microorganisms from Ancient Phosphorites of Khubsugul (Mongolia)

NASA Technical Reports Server (NTRS)

Zhengallo, Elena A.; Rozanov, Alexei Yu.; Ushatinskaya, Galina T.; Hoover, Richard B.; Gerasimenko, Ludmila M.; Ragozina, Alla L.

2000-01-01

A photographic atlas of scanning electron microscope (SEM) images of Cambrian (Tommotian) microfossils from the phosphorites of Khubsugul Mongolia is presented. SEM images of modern cyanobacteria and bacteria are provided for comparison. The importance of bacterial fossils and morphological biomarkers to astrobiology and the understanding of the origin of phosphorites is considered.

Biogeography of thermophilic phototrophic bacteria belonging to Roseiflexus genus.

PubMed

Gaisin, Vasil A; Grouzdev, Denis S; Namsaraev, Zorigto B; Sukhacheva, Marina V; Gorlenko, Vladimir M; Kuznetsov, Boris B

2016-03-01

Isolated environments such as hot springs are particularly interesting for studying the microbial biogeography. These environments create an 'island effect' leading to genetic divergence. We studied the phylogeographic pattern of thermophilic anoxygenic phototrophic bacteria, belonging to the Roseiflexus genus. The main characteristic of the observed pattern was geographic and geochronologic fidelity to the hot springs within Circum-Pacific and Alpine-Himalayan-Indonesian orogenic belts. Mantel test revealed a correlation between genetic divergence and geographic distance among the phylotypes. Cluster analysis revealed a regional differentiation of the global phylogenetic pattern. The phylogeographic pattern is in correlation with geochronologic events during the break up of Pangaea that led to the modern configuration of continents. To our knowledge this is the first geochronological scenario of intercontinental prokaryotic taxon divergence. The existence of the modern phylogeographic pattern contradicts with the existence of the ancient evolutionary history of the Roseiflexus group proposed on the basis of its deep-branching phylogenetic position. These facts indicate that evolutionary rates in Roseiflexus varied over a wide range. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Cell wall elongation mode in Gram-negative bacteria is determined by peptidoglycan architecture.

PubMed

Turner, Robert D; Hurd, Alexander F; Cadby, Ashley; Hobbs, Jamie K; Foster, Simon J

2013-01-01

Cellular integrity and morphology of most bacteria is maintained by cell wall peptidoglycan, the target of antibiotics essential in modern healthcare. It consists of glycan strands, cross-linked by peptides, whose arrangement determines cell shape, prevents lysis due to turgor pressure and yet remains dynamic to allow insertion of new material, and hence growth. The cellular architecture and insertion pattern of peptidoglycan have remained elusive. Here we determine the peptidoglycan architecture and dynamics during growth in rod-shaped Gram-negative bacteria. Peptidoglycan is made up of circumferentially oriented bands of material interspersed with a more porous network. Super-resolution fluorescence microscopy reveals an unexpected discontinuous, patchy synthesis pattern. We present a consolidated model of growth via architecture-regulated insertion, where we propose only the more porous regions of the peptidoglycan network that are permissive for synthesis.

Bioactive natural products from novel microbial sources.

PubMed

Challinor, Victoria L; Bode, Helge B

2015-09-01

Despite the importance of microbial natural products for human health, only a few bacterial genera have been mined for the new natural products needed to overcome the urgent threat of antibiotic resistance. This is surprising, given that genome sequencing projects have revealed that the capability to produce natural products is not a rare feature among bacteria. Even the bacteria occurring in the human microbiome produce potent antibiotics, and thus potentially are an untapped resource for novel compounds, potentially with new activities. This review highlights examples of bacteria that should be considered new sources of natural products, including anaerobes, pathogens, and symbionts of humans, insects, and nematodes. Exploitation of these producer strains, combined with advances in modern natural product research methodology, has the potential to open the way for a new golden age of microbial therapeutics. © 2015 New York Academy of Sciences.

Rapid Bacterial Detection via an All-Electronic CMOS Biosensor

PubMed Central

Nikkhoo, Nasim; Cumby, Nichole; Gulak, P. Glenn; Maxwell, Karen L.

2016-01-01

The timely and accurate diagnosis of infectious diseases is one of the greatest challenges currently facing modern medicine. The development of innovative techniques for the rapid and accurate identification of bacterial pathogens in point-of-care facilities using low-cost, portable instruments is essential. We have developed a novel all-electronic biosensor that is able to identify bacteria in less than ten minutes. This technology exploits bacteriocins, protein toxins naturally produced by bacteria, as the selective biological detection element. The bacteriocins are integrated with an array of potassium-selective sensors in Complementary Metal Oxide Semiconductor technology to provide an inexpensive bacterial biosensor. An electronic platform connects the CMOS sensor to a computer for processing and real-time visualization. We have used this technology to successfully identify both Gram-positive and Gram-negative bacteria commonly found in human infections. PMID:27618185

34S/32S fractionation in sulfur cycles catalyzed by anaerobic bacteria

NASA Technical Reports Server (NTRS)

Fry, B.; Gest, H.; Hayes, J. M.

1988-01-01

Stable isotopic distributions in the sulfur cycle were studied with pure and mixed cultures of the anaerobic bacteria, Chlorobium vibrioforme and Desulfovibrio vulgaris. D. vulgaris and C. vibrioforme can catalyze three reactions constituting a complete anaerobic sulfur cycle: reduction of sulfate to sulfide (D. vulgaris), oxidation of sulfide to elemental sulfur (C. vibrioforme), and oxidation of sulfur to sulfate (C. vibrioforme). In all experiments, the first and last reactions favored concentration of the light 32S isotope in products (isotopic fractionation factor epsilon = -7.2 and -1.7%, respectively), whereas oxidation of sulfide favored concentration of the heavy 34S isotope in products (epsilon = +1.7%). Experimental results and model calculations suggest that elemental sulfur enriched in 34S versus sulfide may be a biogeochemical marker for the presence of sulfide-oxidizing bacteria in modern and ancient environments.

Modern water/rock reactions in Oman hyperalkaline peridotite aquifers and implications for microbial habitability

NASA Astrophysics Data System (ADS)

Miller, Hannah M.; Matter, Jürg M.; Kelemen, Peter; Ellison, Eric T.; Conrad, Mark E.; Fierer, Noah; Ruchala, Tyler; Tominaga, Masako; Templeton, Alexis S.

2016-04-01

The Samail ophiolite in Oman is undergoing modern hydration and carbonation of peridotite and may host a deep subsurface biosphere. Previous investigations of hyperalkaline fluids in Oman have focused on fluids released at surface seeps, which quickly lose their reducing character and precipitate carbonates upon contact with the O2/CO2-rich atmosphere. In this work, geochemical analysis of rocks and fluids from the subsurface provides new insights into the operative reactions in serpentinizing aquifers. Serpentinite rock and hyperalkaline fluids (pH > 10), which exhibit millimolar concentrations of Ca2+, H2 and CH4, as well as variable sulfate and nitrate, were accessed from wells situated in mantle peridotite near Ibra and studied to investigate their aqueous geochemistry, gas concentrations, isotopic signatures, mineralogy, Fe speciation and microbial community composition. The bulk mineralogy of drill cuttings is dominated by olivine, pyroxene, brucite, serpentine and magnetite. At depth, Fe-bearing brucite is commonly intermixed with serpentine, whereas near the surface, olivine and brucite are lost and increased magnetite and serpentine is detected. Micro-Raman spectroscopy reveals at least two distinct generations of serpentine present in drill cuttings recovered from several depths from two wells. Fe K-edge X-ray absorption near-edge spectroscopy (XANES) analysis of the lizardite shows a strong tetrahedral Fe coordination, suggesting a mixture of both Fe(II) and Fe(III) in the serpentine. Magnetite veins are also closely associated with this second generation serpentine, and 2-10 μm magnetite grains overprint all minerals in the drill cuttings. Thus we propose that the dissolved H2 that accumulates in the subsurface hyperalkaline fluids was evolved through low temperature oxidation and hydration of relict olivine, as well as destabilization of pre-existing brucite present in the partially serpentinized dunites and harzburgites. In particular, we hypothesize that Fe-bearing brucite is currently reacting with dissolved silica in the aquifer fluids to generate late-stage magnetite, additional serpentine and dissolved H2. Dissolved CH4 in the fluids exhibits the most isotopically heavy carbon in CH4 reported in the literature thus far. The CH4 may have formed through abiotic reduction of dissolved CO2 or through biogenic pathways under extreme carbon limitation. The methane isotopic composition may have also been modified by significant methane oxidation. 16S rRNA sequencing of DNA recovered from filtered hyperalkaline well fluids reveals an abundance of Meiothermus, Thermodesulfovibrionaceae (sulfate-reducers) and Clostridia (fermenters). The fluids also contain candidate phyla OP1 and OD1, as well as Methanobacterium (methanogen) and Methylococcus sp. (methanotroph). The composition of these microbial communities suggests that low-temperature hydrogen and methane generation, coupled with the presence of electron acceptors such as nitrate and sulfate, sustains subsurface microbial life within the Oman ophiolite.

Arsenite-oxidizing and arsenate-reducing bacteria associated with arsenic-rich groundwater in Taiwan

NASA Astrophysics Data System (ADS)

Liao, Vivian Hsiu-Chuan; Chu, Yu-Ju; Su, Yu-Chen; Hsiao, Sung-Yun; Wei, Chia-Cheng; Liu, Chen-Wuing; Liao, Chung-Min; Shen, Wei-Chiang; Chang, Fi-John

2011-04-01

Drinking highly arsenic-contaminated groundwater is a likely cause of blackfoot disease in Taiwan, but microorganisms that potentially control arsenic mobility in the subsurface remain unstudied. The objective of this study was to investigate the relevant arsenite-oxidizing and arsenate-reducing microbial community that exists in highly arsenic-contaminated groundwater in Taiwan. We cultured and identified arsenic-transforming bacteria, analyzed arsenic resistance and transformation, and determined the presence of genetic markers for arsenic transformation. In total, 11 arsenic-transforming bacterial strains with different colony morphologies and varying arsenic transformation abilities were isolated, including 10 facultative anaerobic arsenate-reducing bacteria and one strictly aerobic arsenite-oxidizing bacterium. All of the isolates exhibited high levels of arsenic resistance with minimum inhibitory concentrations of arsenic ranging from 2 to 200 mM. Strain AR-11 was able to rapidly oxidize arsenite to arsenate at concentrations relevant to environmental groundwater samples without the addition of any electron donors or acceptors. We provide evidence that arsenic-reduction activity may be conferred by the ars operon(s) that were not amplified by the designed primers currently in use. The 16S rRNA sequence analysis grouped the isolates into the following genera: Pseudomonas, Bacillus, Psychrobacter, Vibrio, Citrobacter, Enterobacter, and Bosea. Among these genera, we present the first report of the genus Psychrobacter being involved in arsenic reduction. Our results further support the hypothesis that bacteria capable of either oxidizing arsenite or reducing arsenate coexist and are ubiquitous in arsenic-contaminated groundwater.

What determines sclerobiont colonization on marine mollusk shells?

PubMed

Ochi Agostini, Vanessa; Ritter, Matias do Nascimento; José Macedo, Alexandre; Muxagata, Erik; Erthal, Fernando

2017-01-01

Empty mollusk shells may act as colonization surfaces for sclerobionts depending on the physical, chemical, and biological attributes of the shells. However, the main factors that can affect the establishment of an organism on hard substrates and the colonization patterns on modern and time-averaged shells remain unclear. Using experimental and field approaches, we compared sclerobiont (i.e., bacteria and invertebrate) colonization patterns on the exposed shells (internal and external sides) of three bivalve species (Anadara brasiliana, Mactra isabelleana, and Amarilladesma mactroides) with different external shell textures. In addition, we evaluated the influence of the host characteristics (mode of life, body size, color alteration, external and internal ornamentation and mineralogy) of sclerobionts on dead mollusk shells (bivalve and gastropod) collected from the Southern Brazilian coast. Finally, we compared field observations with experiments to evaluate how the biological signs of the present-day invertebrate settlements are preserved in molluscan death assemblages (incipient fossil record) in a subtropical shallow coastal setting. The results enhance our understanding of sclerobiont colonization over modern and paleoecology perspectives. The data suggest that sclerobiont settlement is enhanced by (i) high(er) biofilm bacteria density, which is more attracted to surfaces with high ornamentation; (ii) heterogeneous internal and external shell surface; (iii) shallow infaunal or attached epifaunal life modes; (iv) colorful or post-mortem oxidized shell surfaces; (v) shell size (<50 mm2 or >1,351 mm2); and (vi) calcitic mineralogy. Although the biofilm bacteria density, shell size, and texture are considered the most important factors, the effects of other covarying attributes should also be considered. We observed a similar pattern of sclerobiont colonization frequency over modern and paleoecology perspectives, with an increase of invertebrates occurring on textured bivalve shells. This study demonstrates how bacterial biofilms may influence sclerobiont colonization on biological hosts (mollusks), and shows how ecological relationships in marine organisms may be relevant for interpreting the fossil record of sclerobionts.

What determines sclerobiont colonization on marine mollusk shells?

PubMed Central

José Macedo, Alexandre; Muxagata, Erik; Erthal, Fernando

2017-01-01

Empty mollusk shells may act as colonization surfaces for sclerobionts depending on the physical, chemical, and biological attributes of the shells. However, the main factors that can affect the establishment of an organism on hard substrates and the colonization patterns on modern and time-averaged shells remain unclear. Using experimental and field approaches, we compared sclerobiont (i.e., bacteria and invertebrate) colonization patterns on the exposed shells (internal and external sides) of three bivalve species (Anadara brasiliana, Mactra isabelleana, and Amarilladesma mactroides) with different external shell textures. In addition, we evaluated the influence of the host characteristics (mode of life, body size, color alteration, external and internal ornamentation and mineralogy) of sclerobionts on dead mollusk shells (bivalve and gastropod) collected from the Southern Brazilian coast. Finally, we compared field observations with experiments to evaluate how the biological signs of the present-day invertebrate settlements are preserved in molluscan death assemblages (incipient fossil record) in a subtropical shallow coastal setting. The results enhance our understanding of sclerobiont colonization over modern and paleoecology perspectives. The data suggest that sclerobiont settlement is enhanced by (i) high(er) biofilm bacteria density, which is more attracted to surfaces with high ornamentation; (ii) heterogeneous internal and external shell surface; (iii) shallow infaunal or attached epifaunal life modes; (iv) colorful or post-mortem oxidized shell surfaces; (v) shell size (<50 mm2 or >1,351 mm2); and (vi) calcitic mineralogy. Although the biofilm bacteria density, shell size, and texture are considered the most important factors, the effects of other covarying attributes should also be considered. We observed a similar pattern of sclerobiont colonization frequency over modern and paleoecology perspectives, with an increase of invertebrates occurring on textured bivalve shells. This study demonstrates how bacterial biofilms may influence sclerobiont colonization on biological hosts (mollusks), and shows how ecological relationships in marine organisms may be relevant for interpreting the fossil record of sclerobionts. PMID:28902894

Isolation and Characterization of Electrochemically Active Subsurface Delftia and Azonexus Species

PubMed Central

Jangir, Yamini; French, Sarah; Momper, Lily M.; Moser, Duane P.; Amend, Jan P.; El-Naggar, Mohamed Y.

2016-01-01

Continental subsurface environments can present significant energetic challenges to the resident microorganisms. While these environments are geologically diverse, potentially allowing energy harvesting by microorganisms that catalyze redox reactions, many of the abundant electron donors and acceptors are insoluble and therefore not directly bioavailable. Extracellular electron transfer (EET) is a metabolic strategy that microorganisms can deploy to meet the challenges of interacting with redox-active surfaces. Though mechanistically characterized in a few metal-reducing bacteria, the role, extent, and diversity of EET in subsurface ecosystems remains unclear. Since this process can be mimicked on electrode surfaces, it opens the door to electrochemical techniques to enrich for and quantify the activities of environmental microorganisms in situ. Here, we report the electrochemical enrichment of microorganisms from a deep fractured-rock aquifer in Death Valley, CA, USA. In experiments performed in mesocosms containing a synthetic medium based on aquifer chemistry, four working electrodes (WEs) were poised at different redox potentials (272, 373, 472, 572 mV vs. SHE) to serve as electron acceptors, resulting in anodic currents coupled to the oxidation of acetate during enrichment. The anodes were dominated by Betaproteobacteria from the families Comamonadaceae and Rhodocyclaceae. A representative of each dominant family was subsequently isolated from electrode-associated biomass. The EET abilities of the isolated Delftia strain (designated WE1-13) and Azonexus strain (designated WE2-4) were confirmed in electrochemical reactors using WEs poised at 522 mV vs. SHE. The rise in anodic current upon inoculation was correlated with a modest increase in total protein content. Both genera have been previously observed in mixed communities of microbial fuel cell enrichments, but this is the first direct measurement of their electrochemical activity. While alternate metabolisms (e.g., nitrate reduction) by these organisms were previously known, our observations suggest that additional ‘hidden’ interactions with external electron acceptors are also possible. Electrochemical approaches are well positioned to dissect such extracellular interactions that may be prevalent in the subsurface. PMID:27242768

Thaumarchaeal ammonium oxidation and evidence for a nitrogen cycle in a subsurface radioactive thermal spring in the Austrian Central Alps.

PubMed

Gerbl, Friedrich W; Weidler, Gerhard W; Wanek, Wolfgang; Erhardt, Angelika; Stan-Lotter, Helga

2014-01-01

Previous studies had suggested the presence of ammonium oxidizing Thaumarchaeota as well as nitrite oxidizing Bacteria in the subsurface spring called Franz Josef Quelle (FJQ), a slightly radioactive thermal mineral spring with a temperature of 43.6-47°C near the alpine village of Bad Gastein, Austria. The microbiological consortium of the FJQ was investigated for its utilization of nitrogen compounds and the putative presence of a subsurface nitrogen cycle. Microcosm experiments made with samples from the spring water, containing planktonic microorganisms, or from biofilms, were used in this study. Three slightly different media, enriched with vitamins and trace elements, and two incubation temperatures (30 and 40°C, respectively) were employed. Under aerobic conditions, high rates of conversion of ammonium to nitrite, as well as nitrite to nitrate were measured. Under oxygen-limited conditions nitrate was converted to gaseous compounds. Stable isotope probing with (15)NH4Cl or ((15)NH4)2SO4as sole energy sources revealed incorporation of (15)N into community DNA. Genomic DNA as well as RNA were extracted from all microcosms. The following genes or fragments of genes were successfully amplified, cloned and sequenced by standard PCR from DNA extracts: Ammonia monooxygenase subunit A (amoA), nitrite oxidoreductase subunits A and B (nxrA and nxrB), nitrate reductase (narG), nitrite reductase (nirS), nitric oxide reductases (cnorB and qnorB), nitrous oxide reductase (nosZ). Reverse transcription of extracted total RNA and real-time PCR suggested the expression of each of those genes. Nitrogen fixation (as probed with nifH and nifD) was not detected. However, a geological origin of NH(+) 4 in the water of the FJQ cannot be excluded, considering the silicate, granite and gneiss containing environment. The data suggested the operation of a nitrogen cycle in the subsurface environment of the FJQ.

Thaumarchaeal ammonium oxidation and evidence for a nitrogen cycle in a subsurface radioactive thermal spring in the Austrian Central Alps

PubMed Central

Gerbl, Friedrich W.; Weidler, Gerhard W.; Wanek, Wolfgang; Erhardt, Angelika; Stan-Lotter, Helga

2014-01-01

Previous studies had suggested the presence of ammonium oxidizing Thaumarchaeota as well as nitrite oxidizing Bacteria in the subsurface spring called Franz Josef Quelle (FJQ), a slightly radioactive thermal mineral spring with a temperature of 43.6–47°C near the alpine village of Bad Gastein, Austria. The microbiological consortium of the FJQ was investigated for its utilization of nitrogen compounds and the putative presence of a subsurface nitrogen cycle. Microcosm experiments made with samples from the spring water, containing planktonic microorganisms, or from biofilms, were used in this study. Three slightly different media, enriched with vitamins and trace elements, and two incubation temperatures (30 and 40°C, respectively) were employed. Under aerobic conditions, high rates of conversion of ammonium to nitrite, as well as nitrite to nitrate were measured. Under oxygen-limited conditions nitrate was converted to gaseous compounds. Stable isotope probing with 15NH4Cl or (15NH4)2SO4as sole energy sources revealed incorporation of 15N into community DNA. Genomic DNA as well as RNA were extracted from all microcosms. The following genes or fragments of genes were successfully amplified, cloned and sequenced by standard PCR from DNA extracts: Ammonia monooxygenase subunit A (amoA), nitrite oxidoreductase subunits A and B (nxrA and nxrB), nitrate reductase (narG), nitrite reductase (nirS), nitric oxide reductases (cnorB and qnorB), nitrous oxide reductase (nosZ). Reverse transcription of extracted total RNA and real-time PCR suggested the expression of each of those genes. Nitrogen fixation (as probed with nifH and nifD) was not detected. However, a geological origin of NH+4 in the water of the FJQ cannot be excluded, considering the silicate, granite and gneiss containing environment. The data suggested the operation of a nitrogen cycle in the subsurface environment of the FJQ. PMID:24904540

A Microbial Oasis in the Hypersaline Atacama Subsurface Discovered by a Life Detector Chip: Implications for the Search for Life on Mars

PubMed Central

de Diego-Castilla, Graciela; Moreno-Paz, Mercedes; Blanco, Yolanda; Cruz-Gil, Patricia; Rodríguez-Manfredi, José A.; Fernández-Remolar, David; Gómez, Felipe; Gómez, Manuel J.; Rivas, Luis A.; Demergasso, Cecilia; Echeverría, Alex; Urtuvia, Viviana N.; Ruiz-Bermejo, Marta; García-Villadangos, Miriam; Postigo, Marina; Sánchez-Román, Mónica; Chong-Díaz, Guillermo; Gómez-Elvira, Javier

2011-01-01

Abstract The Atacama Desert has long been considered a good Mars analogue for testing instrumentation for planetary exploration, but very few data (if any) have been reported about the geomicrobiology of its salt-rich subsurface. We performed a Mars analogue drilling campaign next to the Salar Grande (Atacama, Chile) in July 2009, and several cores and powder samples from up to 5 m deep were analyzed in situ with LDChip300 (a Life Detector Chip containing 300 antibodies). Here, we show the discovery of a hypersaline subsurface microbial habitat associated with halite-, nitrate-, and perchlorate-containing salts at 2 m deep. LDChip300 detected bacteria, archaea, and other biological material (DNA, exopolysaccharides, some peptides) from the analysis of less than 0.5 g of ground core sample. The results were supported by oligonucleotide microarray hybridization in the field and finally confirmed by molecular phylogenetic analysis and direct visualization of microbial cells bound to halite crystals in the laboratory. Geochemical analyses revealed a habitat with abundant hygroscopic salts like halite (up to 260 g kg−1) and perchlorate (41.13 μg g−1 maximum), which allow deliquescence events at low relative humidity. Thin liquid water films would permit microbes to proliferate by using detected organic acids like acetate (19.14 μg g−1) or formate (76.06 μg g−1) as electron donors, and sulfate (15875 μg g−1), nitrate (13490 μg g−1), or perchlorate as acceptors. Our results correlate with the discovery of similar hygroscopic salts and possible deliquescence processes on Mars, and open new search strategies for subsurface martian biota. The performance demonstrated by our LDChip300 validates this technology for planetary exploration, particularly for the search for life on Mars. Key Words: Atacama Desert—Life detection—Biosensor—Biopolymers—In situ measurement. Astrobiology 11, 969–996. PMID:22149750

A microbial oasis in the hypersaline Atacama subsurface discovered by a life detector chip: implications for the search for life on Mars.

PubMed

Parro, Victor; de Diego-Castilla, Graciela; Moreno-Paz, Mercedes; Blanco, Yolanda; Cruz-Gil, Patricia; Rodríguez-Manfredi, José A; Fernández-Remolar, David; Gómez, Felipe; Gómez, Manuel J; Rivas, Luis A; Demergasso, Cecilia; Echeverría, Alex; Urtuvia, Viviana N; Ruiz-Bermejo, Marta; García-Villadangos, Miriam; Postigo, Marina; Sánchez-Román, Mónica; Chong-Díaz, Guillermo; Gómez-Elvira, Javier

2011-12-01

The Atacama Desert has long been considered a good Mars analogue for testing instrumentation for planetary exploration, but very few data (if any) have been reported about the geomicrobiology of its salt-rich subsurface. We performed a Mars analogue drilling campaign next to the Salar Grande (Atacama, Chile) in July 2009, and several cores and powder samples from up to 5 m deep were analyzed in situ with LDChip300 (a Life Detector Chip containing 300 antibodies). Here, we show the discovery of a hypersaline subsurface microbial habitat associated with halite-, nitrate-, and perchlorate-containing salts at 2 m deep. LDChip300 detected bacteria, archaea, and other biological material (DNA, exopolysaccharides, some peptides) from the analysis of less than 0.5 g of ground core sample. The results were supported by oligonucleotide microarray hybridization in the field and finally confirmed by molecular phylogenetic analysis and direct visualization of microbial cells bound to halite crystals in the laboratory. Geochemical analyses revealed a habitat with abundant hygroscopic salts like halite (up to 260 g kg(-1)) and perchlorate (41.13 μg g(-1) maximum), which allow deliquescence events at low relative humidity. Thin liquid water films would permit microbes to proliferate by using detected organic acids like acetate (19.14 μg g(-1)) or formate (76.06 μg g(-1)) as electron donors, and sulfate (15875 μg g(-1)), nitrate (13490 μg g(-1)), or perchlorate as acceptors. Our results correlate with the discovery of similar hygroscopic salts and possible deliquescence processes on Mars, and open new search strategies for subsurface martian biota. The performance demonstrated by our LDChip300 validates this technology for planetary exploration, particularly for the search for life on Mars.

Determining the specific microbial populations and their spatial distribution within the stromatolite ecosystem of Shark Bay.

PubMed

Goh, Falicia; Allen, Michelle A; Leuko, Stefan; Kawaguchi, Tomohiro; Decho, Alan W; Burns, Brendan P; Neilan, Brett A

2009-04-01

The stromatolites at Shark Bay, Western Australia, are analogues of some of the oldest evidence of life on Earth. The aim of this study was to identify and spatially characterize the specific microbial communities associated with Shark Bay intertidal columnar stromatolites. Conventional culturing methods and construction of 16S rDNA clone libraries from community genomic DNA with both universal and specific PCR primers were employed. The estimated coverage, richness and diversity of stromatolite microbial populations were compared with earlier studies on these ecosystems. The estimated coverage for all clone libraries indicated that population coverage was comprehensive. Phylogenetic analyses of stromatolite and surrounding seawater sequences were performed in ARB with the Greengenes database of full-length non-chimaeric 16S rRNA genes. The communities identified exhibited extensive diversity. The most abundant sequences from the stromatolites were alpha- and gamma-proteobacteria (58%), whereas the cyanobacterial community was characterized by sequences related to the genera Euhalothece, Gloeocapsa, Gloeothece, Chroococcidiopsis, Dermocarpella, Acaryochloris, Geitlerinema and Schizothrix. All clones from the archaeal-specific clone libraries were related to the halophilic archaea; however, no archaeal sequence was identified from the surrounding seawater. Fluorescence in situ hybridization also revealed stromatolite surfaces to be dominated by unicellular cyanobacteria, in contrast to the sub-surface archaea and sulphate-reducing bacteria. This study is the first to compare the microbial composition of morphologically similar stromatolites over time and examine the spatial distribution of specific microorganismic groups in these intertidal structures and the surrounding seawater at Shark Bay. The results provide a platform for identifying the key microbial physiology groups and their potential roles in modern stromatolite morphogenesis and ecology.

16S rRNA Gene Survey of Microbial Communities in Winogradsky Columns

PubMed Central

Rundell, Ethan A.; Banta, Lois M.; Ward, Doyle V.; Watts, Corey D.; Birren, Bruce; Esteban, David J.

2014-01-01

A Winogradsky column is a clear glass or plastic column filled with enriched sediment. Over time, microbial communities in the sediment grow in a stratified ecosystem with an oxic top layer and anoxic sub-surface layers. Winogradsky columns have been used extensively to demonstrate microbial nutrient cycling and metabolic diversity in undergraduate microbiology labs. In this study, we used high-throughput 16s rRNA gene sequencing to investigate the microbial diversity of Winogradsky columns. Specifically, we tested the impact of sediment source, supplemental cellulose source, and depth within the column, on microbial community structure. We found that the Winogradsky columns were highly diverse communities but are dominated by three phyla: Proteobacteria, Bacteroidetes, and Firmicutes. The community is structured by a founding population dependent on the source of sediment used to prepare the columns and is differentiated by depth within the column. Numerous biomarkers were identified distinguishing sample depth, including Cyanobacteria, Alphaproteobacteria, and Betaproteobacteria as biomarkers of the soil-water interface, and Clostridia as a biomarker of the deepest depth. Supplemental cellulose source impacted community structure but less strongly than depth and sediment source. In columns dominated by Firmicutes, the family Peptococcaceae was the most abundant sulfate reducer, while in columns abundant in Proteobacteria, several Deltaproteobacteria families, including Desulfobacteraceae, were found, showing that different taxonomic groups carry out sulfur cycling in different columns. This study brings this historical method for enrichment culture of chemolithotrophs and other soil bacteria into the modern era of microbiology and demonstrates the potential of the Winogradsky column as a model system for investigating the effect of environmental variables on soil microbial communities. PMID:25101630

Detection of biological uranium reduction using magnetic resonance.

PubMed

Vogt, Sarah J; Stewart, Brandy D; Seymour, Joseph D; Peyton, Brent M; Codd, Sarah L

2012-04-01

The conversion of soluble uranyl ions (UO₂²⁺) by bacterial reduction to sparingly soluble uraninite (UO₂(s)) is being studied as a way of immobilizing subsurface uranium contamination. Under anaerobic conditions, several known types of bacteria including iron and sulfate reducing bacteria have been shown to reduce U (VI) to U (IV). Experiments using a suspension of uraninite (UO₂(s)) particles produced by Shewanella putrefaciens CN32 bacteria show a dependence of both longitudinal (T₁) and transverse (T₂) magnetic resonance (MR) relaxation times on the oxidation state and solubility of the uranium. Gradient echo and spin echo MR images were compared to quantify the effect caused by the magnetic field fluctuations (T*₂) of the uraninite particles and soluble uranyl ions. Since the precipitate studied was suspended in liquid water, the effects of concentration and particle aggregation were explored. A suspension of uraninite particles was injected into a polysaccharide gel, which simulates the precipitation environment of uraninite in the extracellular biofilm matrix. A reduction in the T₂ of the gel surrounding the particles was observed. Tests done in situ using three bioreactors under different mixing conditions, continuously stirred, intermittently stirred, and not stirred, showed a quantifiable T₂ magnetic relaxation effect over the extent of the reaction. Copyright © 2011 Wiley Periodicals, Inc.

Uranium (U)-Tolerant Bacterial Diversity from U Ore Deposit of Domiasiat in North-East India and Its Prospective Utilisation in Bioremediation

PubMed Central

Kumar, Rakshak; Nongkhlaw, Macmillan; Acharya, Celin; Joshi, Santa Ram

2013-01-01

Uranium (U)-tolerant aerobic chemo-heterotrophic bacteria were isolated from the sub-surface soils of U-rich deposits in Domiasiat, North East India. The bacterial community explored at molecular level by amplified ribosomal DNA restriction analysis (ARDRA) resulted in 51 distinct phylotypes. Bacterial community assemblages at the U mining site with the concentration of U ranging from 20 to 100 ppm, were found to be most diverse. Representative bacteria analysed by 16S rRNA gene sequencing were affiliated to Firmicutes (51%), Gammaproteobacteria (26%), Actinobacteria (11%), Bacteroidetes (10%) and Betaproteobacteria (2%). Representative strains removed more than 90% and 53% of U from 100 μM and 2 mM uranyl nitrate solutions, respectively, at pH 3.5 within 10 min of exposure and the activity was retained until 24 h. Overall, 76% of characterized isolates possessed phosphatase enzyme and 53% had PIB-type ATPase genes. This study generated baseline information on the diverse indigenous U-tolerant bacteria which could serve as an indicator to estimate the environmental impact expected to be caused by mining in the future. Also, these natural isolates efficient in uranium binding and harbouring phosphatase enzyme and metal-transporting genes could possibly play a vital role in the bioremediation of metal-/radionuclide-contaminated environments. PMID:23080407

Microscale characterization of dissolved organic matter production and uptake in marine microbial mat communities

NASA Technical Reports Server (NTRS)

Paerl, H. W.; Bebout, B. M.; Joye, S. B.; Des Marais, D. J.

1993-01-01

Intertidal marine microbial mats exhibited biologically mediated uptake of low molecular weight dissolved organic matter (DOM), including D-glucose, acetate, and an L-amino acid mixture at trace concentrations. Uptake of all compounds occurred in darkness, but was frequently enhanced under natural illumination. The photosystem 2 inhibitor, 3-(3,4-dichlorophenyl)-1,1-dimethyl urea (DCMU) generally failed to inhibit light-stimulated DOM uptake. Occasionally, light plus DCMU-amended treatments led to uptake rates higher than light-incubated samples, possibly due to phototrophic bacteria present in subsurface anoxic layers. Uptake was similar with either 3H- or 14C-labeled substrates, indicating that recycling of labeled CO2 via photosynthetic fixation was not interfering with measurements of light-stimulated DOM uptake. Microautoradiographs showed a variety of pigmented and nonpigmented bacteria and, to a lesser extent, cyanobacteria and eucaryotic microalgae involved in light-mediated DOM uptake. Light-stimulated DOM uptake was often observed in bacteria associated with sheaths and mucilage surrounding filamentous cyanobacteria, revealing a close association of organisms taking up DOM with photoautotrophic members of the mat community. The capacity for dark- and light-mediated heterotrophy, coupled to efficient retention of fixed carbon in the mat community, may help optimize net production and accretion of mats, even in oligotrophic waters.

Alkane inducible proteins in Geobacillus thermoleovorans B23

PubMed Central

2009-01-01

Background Initial step of β-oxidation is catalyzed by acyl-CoA dehydrogenase in prokaryotes and mitochondria, while acyl-CoA oxidase primarily functions in the peroxisomes of eukaryotes. Oxidase reaction accompanies emission of toxic by-product reactive oxygen molecules including superoxide anion, and superoxide dismutase and catalase activities are essential to detoxify them in the peroxisomes. Although there is an argument about whether primitive life was born and evolved under high temperature conditions, thermophilic archaea apparently share living systems with both bacteria and eukaryotes. We hypothesized that alkane degradation pathways in thermophilic microorganisms could be premature and useful to understand their evolution. Results An extremely thermophilic and alkane degrading Geobacillus thermoleovorans B23 was previously isolated from a deep subsurface oil reservoir in Japan. In the present study, we identified novel membrane proteins (P16, P21) and superoxide dismutase (P24) whose production levels were significantly increased upon alkane degradation. Unlike other bacteria acyl-CoA oxidase and catalase activities were also increased in strain B23 by addition of alkane. Conclusion We first suggested that peroxisomal β-oxidation system exists in bacteria. This eukaryotic-type alkane degradation pathway in thermophilic bacterial cells might be a vestige of primitive living cell systems that had evolved into eukaryotes. PMID:19320977

Mobilization of radionuclides from uranium mill tailings and related waste materials in anaerobic environments

USGS Publications Warehouse

Landa, E.R.

2003-01-01

Specific extraction studies in our laboratory have shown that iron and manganese oxide- and alkaline earth sulfate minerals are important hosts of radium in uranium mill tailings. Iron- and sulfate-reducing bacteria may enhance the release of radium (and its analog barium) from uranium mill tailings, oil field pipe scale [a major technologically enhanced naturally occurring radioactive material (TENORM) waste], and jarosite (a common mineral in sulfuric acid processed-tailings). These research findings are reviewed and discussed in the context of nuclear waste forms (such as barium sulfate matrices), radioactive waste management practices, and geochemical environments in the Earth's surficial and shallow subsurface regions.

The State, Potential Distribution, and Biological Implications of Methane in the Martian Crust

NASA Technical Reports Server (NTRS)

Max, Michael D.; Clifford, Stephen M.

2000-01-01

The search for life on Mars has recently focused on its potential survival in deep (>2 km) subpermafrost aquifers where anaerobic bacteria, similar to those found in deep subsurface ecosystems on Earth, may have survived in an environment that has remained stable for billions of years. An anticipated by-product of this biological activity is methane. The detection of large deposits of methane gas and hydrate in the Martian cryosphere, or as emissions from deep fracture zones, would provide persuasive evidence of indigenous life and confirm the presence of a valuable in situ resource for use by future human explorers.

Experimental taphonomy of giant sulphur bacteria: implications for the interpretation of the embryo-like Ediacaran Doushantuo fossils.

PubMed

Cunningham, J A; Thomas, C-W; Bengtson, S; Marone, F; Stampanoni, M; Turner, F R; Bailey, J V; Raff, R A; Raff, E C; Donoghue, P C J

2012-05-07

The Ediacaran Doushantuo biota has yielded fossils interpreted as eukaryotic organisms, either animal embryos or eukaryotes basal or distantly related to Metazoa. However, the fossils have been interpreted alternatively as giant sulphur bacteria similar to the extant Thiomargarita. To test this hypothesis, living and decayed Thiomargarita were compared with Doushantuo fossils and experimental taphonomic pathways were compared with modern embryos. In the fossils, as in eukaryotic cells, subcellular structures are distributed throughout cell volume; in Thiomargarita, a central vacuole encompasses approximately 98 per cent cell volume. Key features of the fossils, including putative lipid vesicles and nuclei, complex envelope ornament, and ornate outer vesicles are incompatible with living and decay morphologies observed in Thiomargarita. Microbial taphonomy of Thiomargarita also differed from that of embryos. Embryo tissues can be consumed and replaced by bacteria, forming a replica composed of a three-dimensional biofilm, a stable fabric for potential fossilization. Vacuolated Thiomargarita cells collapse easily and do not provide an internal substrate for bacteria. The findings do not support the hypothesis that giant sulphur bacteria are an appropriate interpretative model for the embryo-like Doushantuo fossils. However, sulphur bacteria may have mediated fossil mineralization and may provide a potential bacterial analogue for other macroscopic Precambrian remains.

Experimental taphonomy of giant sulphur bacteria: implications for the interpretation of the embryo-like Ediacaran Doushantuo fossils

PubMed Central

Cunningham, J. A.; Thomas, C.-W.; Bengtson, S.; Marone, F.; Stampanoni, M.; Turner, F. R.; Bailey, J. V.; Raff, R. A.; Raff, E. C.; Donoghue, P. C. J.

2012-01-01

The Ediacaran Doushantuo biota has yielded fossils interpreted as eukaryotic organisms, either animal embryos or eukaryotes basal or distantly related to Metazoa. However, the fossils have been interpreted alternatively as giant sulphur bacteria similar to the extant Thiomargarita. To test this hypothesis, living and decayed Thiomargarita were compared with Doushantuo fossils and experimental taphonomic pathways were compared with modern embryos. In the fossils, as in eukaryotic cells, subcellular structures are distributed throughout cell volume; in Thiomargarita, a central vacuole encompasses approximately 98 per cent cell volume. Key features of the fossils, including putative lipid vesicles and nuclei, complex envelope ornament, and ornate outer vesicles are incompatible with living and decay morphologies observed in Thiomargarita. Microbial taphonomy of Thiomargarita also differed from that of embryos. Embryo tissues can be consumed and replaced by bacteria, forming a replica composed of a three-dimensional biofilm, a stable fabric for potential fossilization. Vacuolated Thiomargarita cells collapse easily and do not provide an internal substrate for bacteria. The findings do not support the hypothesis that giant sulphur bacteria are an appropriate interpretative model for the embryo-like Doushantuo fossils. However, sulphur bacteria may have mediated fossil mineralization and may provide a potential bacterial analogue for other macroscopic Precambrian remains. PMID:22158954

Microbial communities in the deep subsurface

NASA Astrophysics Data System (ADS)

Krumholz, Lee R.

The diversity of microbial populations and microbial communities within the earth's subsurface is summarized in this review. Scientists are currently exploring the subsurface and addressing questions of microbial diversity, the interactions among microorganisms, and mechanisms for maintenance of subsurface microbial communities. Heterotrophic anaerobic microbial communities exist in relatively permeable sandstone or sandy sediments, located adjacent to organic-rich deposits. These microorganisms appear to be maintained by the consumption of organic compounds derived from adjacent deposits. Sources of organic material serving as electron donors include lignite-rich Eocene sediments beneath the Texas coastal plain, organic-rich Cretaceous shales from the southwestern US, as well as Cretaceous clays containing organic materials and fermentative bacteria from the Atlantic Coastal Plain. Additionally, highly diverse microbial communities occur in regions where a source of organic matter is not apparent but where igneous rock is present. Examples include the basalt-rich subsurface of the Columbia River valley and the granitic subsurface regions of Sweden and Canada. These subsurface microbial communities appear to be maintained by the action of lithotrophic bacteria growing on H2 that is chemically generated within the subsurface. Other deep-dwelling microbial communities exist within the deep sediments of oceans. These systems often rely on anaerobic metabolism and sulfate reduction. Microbial colonization extends to the depths below which high temperatures limit the ability of microbes to survive. Energy sources for the organisms living in the oceanic subsurface may originate as oceanic sedimentary deposits. In this review, each of these microbial communities is discussed in detail with specific reference to their energy sources, their observed growth patterns, and their diverse composition. This information is critical to develop further understanding of subsurface geochemical processes and to develop new approaches to subsurface remediation. Résumé La diversité des populations et des communautés microbiennes dans le sol et le sous-sol est présentée dans cet article. Les chercheurs s'interrogent fréquemment sur la diversité microbienne du sous-sol, sur les interactions entre organismes et sur les mécanismes qui permettent le maintien des communautés microbiennes souterraines. Il existe des communautés microbiennes anérobies hétérotrophes dans des grès ou dans des sédiments sableux relativement perméables, à proximité de dépôts riches en matières organiques. Ces micro-organismes semblent se maintenir grâce à la consommation de composés organiques provenant des dépôts organiques voisins. Les sources de matériel organique jouant le rôle de donneur d'électrons sont constituées par des sédiments éocènes riches en lignite situés sous la plaine littorale du Texas, les schistes riches en matières organiques du Crétacé du sud-ouest des États-Unis, ainsi que les argiles contenant des matériaux organiques et des bactéries de fermentation de la plaine littorale atlantique. En outre, il existe des communautés fortement diversifiées dans des régions où aucune source de matière organique n'existe, mais où sont présentes des roches ignées. Le sous-sol riche en basalte de la vallée de la Columbia au Canada et les régions granitiques de Suède en sont des exemples. Ces communautés microbiennes souterraines semblent se maintenir par l'action de bactéries lithotrophes se développant grâce à l'hydrogène qui est produit par réactions chimiques dans le sous-sol. Il existe d'autres communautés microbiennes de profondeur dans les sédiments profonds des océans. Ces systèmes sont souvent associés à un métabolisme anérobie et à une réduction des sulfates. La colonisation microbienne s'étend jusqu'à des profondeurs où les températures élevées limitent leur capacité de survie. Les sources d'énergie pour ces organismes vivant dans les fonds des océans peuvent être les dépôts sédimentaires océaniques. Dans cette revue, chacune des communautés microbiennes est discutée en détail en se référant spécifiquement à leurs sources d'énergie, au schéma observé de leur développement et à leur composition diversifiée. Cette information est donnée de façon critique dans le but d'améliorer la compréhension des processus géochimiques intervenant dans le sous-sol et de développer de nouvelles approches pour la dépollution souterraine. Resumen En este artículo se resume la diversidad de las poblaciones y comunidades microbianas en el subsuelo. A partir de exploraciones realizadas en el subsuelo, los científicos se están cuestionando en la actualidad aspectos relativos a la diversidad microbiana, las interacciones entre los distintos microorganismos y los mecanismos para el mantenimiento de las comunidades de microbios. Se ha comprobado la presencia de comunidades microbianas anaerobias y heterótrofas en areniscas relativamente permeables y en sedimentos arenosos ubicados cerca de depósitos ricos en materia orgánica, de la cual se alimentan. Algunas fuentes de material orgánico, que actúan como donantes de electrones, son: sedimentos del Eoceno ricos en lignito, bajo la planicie costera de Texas; pizarras del Cretácico ricas en materia orgánica, al sudoeste del país y arcillas cretácicas con materia orgánica y bacterias fermentativas, en la llanura Atlántica. También existen comunidades microbianas de gran diversidad en rocas ígneas, aunque la fuente de materia orgánica no es tan evidente. Algunos ejemplos son la subsuperficie del valle del Río Columbia, rico en basaltos, y las regiones graníticas de Suecia y Canadá. Estas comunidades microbianas subsuperficiales se mantienen por la acción de bacterias litotrópicas, que crecen en ambiente de H2, generado en la subsuperficie. También existen comunidades microbianas a gran profundidad, como por ejemplo en los sedimentos oceánicos. Estos sistemas subsisten con un metabolismo anaerobio en un ambiente sulfato-reductor. La colonización microbiana se extiende hasta profundidades tales que las altas temperaturas limitan su supervivencia. Las fuentes de energía para estos organismos pueden ser los depósitos sedimentarios oceánicos. En este artículo se discute cada una de estas comunidades en detalle, en particular sus fuentes de energía, su esquema de crecimiento y la diversidad de su composición. Esta información es de gran interés para permitir un mayor entendimiento de los procesos geoquímicos en profundidad y para desarrollar nuevos métodos de rehabilitación.

Water runoff vs modern climatic warming in mountainous cryolithic zone in North-East Russia

NASA Astrophysics Data System (ADS)

Glotov, V. E.; Glotova, L. P.

2018-01-01

The article presents the results of studying the effects of current climatic warming for both surface and subsurface water runoffs in North-East Russia, where the Main Watershed of the Earth separates it into the Arctic and Pacific continental slopes. The process of climatic warming is testified by continuous weather records during 80-100 years and longer periods. Over the Arctic slope and in the northern areas of the Pacific slope, climatic warming results in a decline in a total runoff of rivers whereas the ground-water recharge becomes greater in winter low-level conditions. In the southern Pacific slope and in the Sea of Okhotsk basin, the effect of climatic warming is an overall increase in total runoff including its subsurface constituents. We believe these peculiar characters of river runoff there to be related to the cryolithic zone environments. Over the Arctic slope and the northern Pacific slope, where cryolithic zone is continuous, the total runoff has its subsurface constituent as basically resulting from discharge of ground waters hosted in seasonally thawing rocks. Warmer climatic conditions favor growth of vegetation that needs more water for the processes of evapotranspiration and evaporation from rocky surfaces in summer seasons. In the Sea of Okhotsk basin, where the cryolithic zone is discontinuous, not only ground waters in seasonally thawing layers, but also continuous taliks and subpermafrost waters participate in processes of river recharges. As a result, a greater biological productivity of vegetation cover does not have any effect on ground-water supply and river recharge processes. If a steady climate warming is provided, a continuous cryolithic zone can presumably degrade into a discontinuous and then into an island-type permafrost layer. Under such a scenario, there will be a general increase in the total runoff and its subsurface constituent. From geoecological viewpoints, a greater runoff will have quite positive effects, whereas some minor negative consequences of it can be successfully prevented.

Current status and emerging role of glutathione in food grade lactic acid bacteria

PubMed Central

2012-01-01

Lactic acid bacteria (LAB) have taken centre stage in perspectives of modern fermented food industry and probiotic based therapeutics. These bacteria encounter various stress conditions during industrial processing or in the gastrointestinal environment. Such conditions are overcome by complex molecular assemblies capable of synthesizing and/or metabolizing molecules that play a specific role in stress adaptation. Thiols are important class of molecules which contribute towards stress management in cell. Glutathione, a low molecular weight thiol antioxidant distributed widely in eukaryotes and Gram negative organisms, is present sporadically in Gram positive bacteria. However, new insights on its occurrence and role in the latter group are coming to light. Some LAB and closely related Gram positive organisms are proposed to possess glutathione synthesis and/or utilization machinery. Also, supplementation of glutathione in food grade LAB is gaining attention for its role in stress protection and as a nutrient and sulfur source. Owing to the immense benefits of glutathione, its release by probiotic bacteria could also find important applications in health improvement. This review presents our current understanding about the status of glutathione and its role as an exogenously added molecule in food grade LAB and closely related organisms. PMID:22920585

Can Computational Sediment Transport Models Reproduce the Observed Variability of Channel Networks in Modern Deltas?

NASA Astrophysics Data System (ADS)

Nesvold, E.; Mukerji, T.

2017-12-01

River deltas display complex channel networks that can be characterized through the framework of graph theory, as shown by Tejedor et al. (2015). Deltaic patterns may also be useful in a Bayesian approach to uncertainty quantification of the subsurface, but this requires a prior distribution of the networks of ancient deltas. By considering subaerial deltas, one can at least obtain a snapshot in time of the channel network spectrum across deltas. In this study, the directed graph structure is semi-automatically extracted from satellite imagery using techniques from statistical processing and machine learning. Once the network is labeled with vertices and edges, spatial trends and width and sinuosity distributions can also be found easily. Since imagery is inherently 2D, computational sediment transport models can serve as a link between 2D network structure and 3D depositional elements; the numerous empirical rules and parameters built into such models makes it necessary to validate the output with field data. For this purpose we have used a set of 110 modern deltas, with average water discharge ranging from 10 - 200,000 m3/s, as a benchmark for natural variability. Both graph theoretic and more general distributions are established. A key question is whether it is possible to reproduce this deltaic network spectrum with computational models. Delft3D was used to solve the shallow water equations coupled with sediment transport. The experimental setup was relatively simple; incoming channelized flow onto a tilted plane, with varying wave and tidal energy, sediment types and grain size distributions, river discharge and a few other input parameters. Each realization was run until a delta had fully developed: between 50 and 500 years (with a morphology acceleration factor). It is shown that input parameters should not be sampled independently from the natural ranges, since this may result in deltaic output that falls well outside the natural spectrum. Since we are interested in studying the patterns occurring in nature, ideas are proposed for how to sample computer realizations that match this distribution. By establishing a link between surface based patterns from the field with the associated subsurface structure from physics-based models, this is a step towards a fully Bayesian workflow in subsurface simulation.

Magnetic and gravity constraints on forearc upper crustal structure and composition, offshore northeast Japan

USGS Publications Warehouse

Finn, C.

1994-01-01

Marine magnetic and gravity data from the northeast Japan forearc offer insight to the subsurface structure, density and magnetization from which geologic interpretations and tectonic reconstructions can be made. Positive marine magnetic anomalies, on-land geology, drill hole data, and 2-1/2-dimensional models reveal that Kitakami plutons and possibly their associated volcanic rocks constitute part of the modern forearc basement and lie 100-150 km further east than previously thought. A method to create magnetization and density contrast maps was employed to produce a three-dimensional picture of the forearc basement rock properties averaged over a 14-km thickness. -Author

Effects of Jet Fuel Spills on the Microbial Community of Soil †

PubMed Central

Song, Hong-Gyu; Bartha, Richard

1990-01-01

Hydrocarbon residues, microbial numbers, and microbial activity were measured and correlated in loam soil contaminated by jet fuel spills resulting in 50 and 135 mg of hydrocarbon g of soil−1. Contaminated soil was incubated at 27°C either as well-aerated surface soil or as poorly aerated subsurface soil. In the former case, the effects of bioremediation treatment on residues, microbial numbers, and microbial activity were also assessed. Hydrocarbon residues were measured by quantitative gas chromatography. Enumerations included direct counts of metabolically active bacteria, measurement of mycelial length, plate counts of aerobic heterotrophs, and most probable numbers of hydrocarbon degraders. Activity was assessed by fluorescein diacetate (FDA) hydrolysis. Jet fuel disappeared much more rapidly from surface soil than it did from subsurface soil. In surface soil, microbial numbers and mycelial length were increased by 2 to 2.5 orders of magnitude as a result of jet fuel contamination alone and by 3 to 4 orders of magnitude as a result of the combination of jet fuel contamination and bioremediation. FDA hydrolysis was stimulated by jet fuel and bioremediation, but was inhibited by jet fuel alone. The latter was traced to an inhibition of the FDA assay by jet fuel biodegradation products. In subsurface soil, oxygen limitation strongly attenuated microbial responses to jet fuel. An increase in the most probable numbers of hydrocarbon degraders was accompanied by a decline in other aerobic heterotrophs, so that total plate counts changed little. The correlations between hydrocarbon residues, microbial numbers, and microbial activity help in elucidating microbial contributions to jet fuel elimination from soil. PMID:16348138

Anti-Biofilm Performance of Three Natural Products against Initial Bacterial Attachment

PubMed Central

Salta, Maria; Wharton, Julian A.; Dennington, Simon P.; Stoodley, Paul; Stokes, Keith R.

2013-01-01

Marine bacteria contribute significantly towards the fouling consortium, both directly (modern foul release coatings fail to prevent “slime” attachment) and indirectly (biofilms often excrete chemical cues that attract macrofouling settlement). This study assessed the natural product anti-biofilm performance of an extract of the seaweed, Chondrus crispus, and two isolated compounds from terrestrial sources, (+)-usnic acid and juglone, against two marine biofilm forming bacteria, Cobetia marina and Marinobacter hydrocarbonoclasticus. Bioassays were developed using quantitative imaging and fluorescent labelling to test the natural products over a range of concentrations against initial bacterial attachment. All natural products affected bacterial attachment; however, juglone demonstrated the best anti-biofilm performance against both bacterial species at a concentration range between 5–20 ppm. In addition, for the first time, a dose-dependent inhibition (hormetic) response was observed for natural products against marine biofilm forming bacteria. PMID:24192819

Warm ocean processes and carbon cycling in the Eocene.

PubMed

John, Eleanor H; Pearson, Paul N; Coxall, Helen K; Birch, Heather; Wade, Bridget S; Foster, Gavin L

2013-10-28

Sea surface and subsurface temperatures over large parts of the ocean during the Eocene epoch (55.5-33.7 Ma) exceeded modern values by several degrees, which must have affected a number of oceanic processes. Here, we focus on the effect of elevated water column temperatures on the efficiency of the biological pump, particularly in relation to carbon and nutrient cycling. We use stable isotope values from exceptionally well-preserved planktonic foraminiferal calcite from Tanzania and Mexico to reconstruct vertical carbon isotope gradients in the upper water column, exploiting the fact that individual species lived and calcified at different depths. The oxygen isotope ratios of different species' tests are used to estimate the temperature of calcification, which we converted to absolute depths using Eocene temperature profiles generated by general circulation models. This approach, along with potential pitfalls, is illustrated using data from modern core-top assemblages from the same area. Our results indicate that, during the Early and Middle Eocene, carbon isotope gradients were steeper (and larger) through the upper thermocline than in the modern ocean. This is consistent with a shallower average depth of organic matter remineralization and supports previously proposed hypotheses that invoke high metabolic rates in a warm Eocene ocean, leading to more efficient recycling of organic matter and reduced burial rates of organic carbon.

Bioremediation process on Brazil shoreline. Laboratory experiments.

PubMed

Rosa, Anabela P; Triguis, Jorge A

2007-11-01

Bioremediation technique can be considered a promising alternative to clean oil spills using microbial processes to reduce the concentration and/or the toxicity of pollutants. To understand the importance of this work we must know that there is only little research performed to date using bioremediation techniques to clean oil spills in tropical countries. So, the main objective of this work is to analyze the behavior of a laboratory's bioremediation test using nutrients on coastal sediments. The bioremediation process is followed through geochemical analysis during the tests. This organic material is analyzed by medium pressure liquid chromatography (MPLC), gas chromatography/flame ionization detection (GC/FID) and gas chromatography/ mass spectrometry. By microbial counting, the number of total bacteria and degrading bacteria is determined during the experiments, in order to confirm the effectiveness of the bioremediation process. The seawater obtained throughout the bioremediation process is analyzed for nutrients grade (phosphate and ammonium ions) and also for its toxicity (Microtox tests) due the presence of hydrocarbons and fertilizer. The results from the geochemical analyses of the oil show a relative decrease in the saturated hydrocarbon fraction that is compensated by a relative enrichment on polar compounds. It's confirmed by the fingerprint evaluation where it is possible to see a complete reduction of the normal alkanes followed by isoprenoids. Seawater analysis done by toxicity and nutrients analysis, such as microbial counting (total and degrading bacteria), confirm the fertilizer effectiveness during the bioremediation process. Results from simulating test using NPK, a low-price plant fertilizer, suggest that it's able to stimulate the degradation process. Results from medium pressure liquid chromatography (MPLC), done at two different depths (surface and subsurface), show different behavior during the biodegradation process where the later is seen to be more susceptible to microbial attack. Data from bioremediation unit shows a bigger reduction of the saturated fraction, followed by some smaller reduction of aromatic fractions, compensated by a relative increase from polar compounds (NSO). n-C17/pristane, n-C18/ fitane and pristane/fitane rates show constant values for the unity control, different from bioremediation samples which have a significant reduction, especially on subsurface areas, where a strong fall in the rates, seen to be reduced to zero over twenty days, had occurred during the first ten days. However, sample surfaces are reduced to zero in thirty days of experiments, proving that biodegradation is better on subsurfaces. Gaseous chromatography/mass spectrometry (CG/MS) analysis shows constant values to cyclic biomarker rates and aromatic compounds, suggesting that the biodegradation process is not strong enough to reduce these composites. Microbial analysis shows a reduction on heterotrophic (total bacteria) number from control unit, probably because the bacteria uses the spill oil like carbon source and energy. However, the number increases on bioremediation unit, because it uses NPK like a biostimulator. The hydrocarbonoclastic number isn't enough on the first moment, but it's detected after 30 days and quantified in all units, showing big values especially in bioremediation. Toxicity tests confirm that NPK fertilizer does not intoxicate the shoreline during the application of the bioremediation technique. Some nutrient concentration shows high values of ammonium and phosphate per bioremediation unit, reducing by the end of the experiment. Results reached the goal, finding a proper nutrient (NPK fertilizer) to stimulate the biodegradation process, growing bacteria responsible for reducing impact-contaminated coast ambient by oil spills. Chemical analysis of oil shows a reduction in the saturated fraction with a relative enrichment in polar composites (NSO) and the aromatic fraction from oil remaining constant. Subsurface samples show more biodegradation than surface samples, probably because the first one has higher humidity. Linear alcanes are more biodegraded than isoprenoids, confirming the biodegradation susceptibility order. Saturated cyclic biomarkers and aromatic compounds show constant behavior maybe because the nutrients or time was not enough for microorganismic attack. Fertilizer does not demonstrate any toxic effects in local biota so that it does not compromise the technique applicability and the environment is not saturated by nutrients during the simulation, especially since the coastal environment is an open system affected daily by tides. Therefore, bioremediation tests can be classified as moderate, reaching level 5 in the classification scale by Peters & Moldowan (1993). The use of marine environment by the petroleum industry on exploration, production and transportation operation, transform this oil to become the most important pollutant in the oceans. Bioremediation is an important technique used to clean spilled oil impacting on shorelines, accelerating the biodegradation process by using fertilizer growing the microorganisms responsible for decontaminating the environment. We recommend confirming the efficiency of NPK nutrient used on bioremediation simulating experiments on beaches, while monitoring the chemical changes long-term. NPK fertilizer can be used to stimulate the biodegradation process on shoreline impacted by spilled oil.

Biocolloid transport in water saturated columns packed with sand

NASA Astrophysics Data System (ADS)

Syngouna, V. I.; Chrysikopoulos, C.

2010-12-01

Protection of groundwater supplies from microbial contamination necessitates a solid understanding of the factors controlling the migration and retention of pathogenic organisms (biocolloids) in the subsurface. The transport behavior of three waterborne pathogens (Escherichia coli, MS2, and ΦΧ174) was investigated using laboratory-scale columns packed with clean quartz sand. Various grain sizes and pore water velocities were examined. Though coliform bacteria and coliphages are used worldwide to indicate fecal pollution of groundwater, the various parameters controlling the transport of Escherichia coli MS2 and ΦΧ174 in the subsurface are not fully understood. In this study, the attachment behavior of Escherichia coli, MS2, and ΦΧ174 onto ultra-pure quartz sand were evaluated. The mass recoveries of the three biocolloids examined were found to be proportional to the sand size. The observed mass recoveries were in the order: Escherichia coli > ΦΧ174 > MS2. To assess the importance of biocolloid attachment, the single collector removal efficiency, and the collision efficiency were quantified using the classical colloid filtration theory. Our results indicate that the secondary energy minimum plays an important role in biocolloid deposition even for smaller biocolloid particles (e.g. viruses).

Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments.

PubMed

Hernsdorf, Alex W; Amano, Yuki; Miyakawa, Kazuya; Ise, Kotaro; Suzuki, Yohey; Anantharaman, Karthik; Probst, Alexander; Burstein, David; Thomas, Brian C; Banfield, Jillian F

2017-08-01

Geological sequestration in deep underground repositories is the prevailing proposed route for radioactive waste disposal. After the disposal of radioactive waste in the subsurface, H 2 may be produced by corrosion of steel and, ultimately, radionuclides will be exposed to the surrounding environment. To evaluate the potential for microbial activities to impact disposal systems, we explored the microbial community structure and metabolic functions of a sediment-hosted ecosystem at the Horonobe Underground Research Laboratory, Hokkaido, Japan. Overall, we found that the ecosystem hosted organisms from diverse lineages, including many from the phyla that lack isolated representatives. The majority of organisms can metabolize H 2 , often via oxidative [NiFe] hydrogenases or electron-bifurcating [FeFe] hydrogenases that enable ferredoxin-based pathways, including the ion motive Rnf complex. Many organisms implicated in H 2 metabolism are also predicted to catalyze carbon, nitrogen, iron and sulfur transformations. Notably, iron-based metabolism is predicted in a novel lineage of Actinobacteria and in a putative methane-oxidizing ANME-2d archaeon. We infer an ecological model that links microorganisms to sediment-derived resources and predict potential impacts of microbial activity on H 2 consumption and retardation of radionuclide migration.

Bacterial carbon utilization in vertical subsurface flow constructed wetlands.

PubMed

Tietz, Alexandra; Langergraber, Günter; Watzinger, Andrea; Haberl, Raimund; Kirschner, Alexander K T

2008-03-01

Subsurface vertical flow constructed wetlands with intermittent loading are considered as state of the art and can comply with stringent effluent requirements. It is usually assumed that microbial activity in the filter body of constructed wetlands, responsible for the removal of carbon and nitrogen, relies mainly on bacterially mediated transformations. However, little quantitative information is available on the distribution of bacterial biomass and production in the "black-box" constructed wetland. The spatial distribution of bacterial carbon utilization, based on bacterial (14)C-leucine incorporation measurements, was investigated for the filter body of planted and unplanted indoor pilot-scale constructed wetlands, as well as for a planted outdoor constructed wetland. A simple mass-balance approach was applied to explain the bacterially catalysed organic matter degradation in this system by comparing estimated bacterial carbon utilization rates with simultaneously measured carbon reduction values. The pilot-scale constructed wetlands proved to be a suitable model system for investigating microbial carbon utilization in constructed wetlands. Under an ideal operating mode, the bulk of bacterial productivity occurred within the first 10cm of the filter body. Plants seemed to have no significant influence on productivity and biomass of bacteria, as well as on wastewater total organic carbon removal.

Life Beneath Glacial Ice - Earth(!) Mars(?) Europa(?)

NASA Technical Reports Server (NTRS)

Allen, Carlton C.; Grasby, Stephen E.; Longazo, Teresa G.; Lisle, John T.; Beauchamp, Benoit

2002-01-01

We are investigating a set of cold springs that deposit sulfur and carbonate minerals on the surface of a Canadian arctic glacier. The spring waters and mineral deposits contain microorganisms, as well as clear evidence that biological processes mediate subglacial chemistry, mineralogy, and isotope fractionation . The formation of native sulphur and associated deposits are related to bacterially mediated reduction and oxidation of sulphur below the glacier. A non-volcanic, topography driven geothermal system, harboring a microbiological community, operates in an extremely cold environment and discharges through solid ice. Microbial life can thus exist in isolated geothermal refuges despite long-term subfreezing surface conditions. Earth history includes several periods of essentially total glaciation. lee in the near subsurface of Mars may have discharged liquid water in the recent past Cracks in the ice crust of Europa have apparently allowed the release of water to the surface. Chemolithotrophic bacteria, such as those in the Canadian springs, could have survived beneath the ice of "Snowball Earth", and life forms with similar characteristics might exist beneath the ice of Mars or Europa. Discharges of water from such refuges may have brought to the surface living microbes, as well as longlasting chemical, mineralogical, and isotopic indications of subsurface life.

Effect of Porous Media Particle Size on Bacterial Motility and Chemotaxis

NASA Astrophysics Data System (ADS)

Olson, M. S.; Smith, J. A.; Ford, R. M.; Fernandez, E. J.

2003-12-01

Many soil-inhabiting bacteria that degrade chemical contaminants are both motile and chemotactic. Chemotaxis refers to the ability of bacteria to sense pollutant concentration gradients in water and preferentially swim toward regions of high pollutant concentration, and is thought to be important in guiding subsurface microbial populations toward chemical contaminants. Bacterial motion consists of a series of smooth-swimming runs interrupted by changes in direction. In the presence of a chemical gradient, bacteria bias their frequency of changing direction and demonstrate longer run lengths in the direction of increasing attractant concentration. One concern when studying bacterial chemotaxis in porous media is that in small pores, the porous media may interrupt the extended run lengths of bacteria swimming in the direction of a positive chemical gradient. The purpose of this study is to examine how a decrease in particle size affects the motility and chemotactic response of bacteria traveling through porous media. We employ an innovative technique for noninvasive visualization of changes in bacterial density distributions in a packed column as a function of time. Paramagnetic magnetite particles are attached to the surface of Pseudomonas putida F1 cells using an antibody. Bacterial distributions within a column of glass-coated polystyrene beads are imaged using magnetic resonance imaging (MRI), with a spatial resolution of 300 μ m. Experiments are conducted with both 250-300 μ m beads and 90-150 μ m beads. Bacteria labeled with magnetite are introduced into a specially designed chromatography column packed with glass-coated polystyrene beads. Bacterial migration is monitored over time using MRI, with and without the presence of a chemical gradient of trichloroethylene (TCE). Comparisons of the motility and chemotactic transport coefficients for Pseudomonas putida F1 cells traveling through different-sized samples of porous media in the presence of TCE will be presented and discussed. Results suggest a decrease in both motility and chemotaxis in the smaller-sized porous media.

Identification of Microorganisms by Modern Analytical Techniques.

PubMed

Buszewski, Bogusław; Rogowska, Agnieszka; Pomastowski, Paweł; Złoch, Michał; Railean-Plugaru, Viorica

2017-11-01

Rapid detection and identification of microorganisms is a challenging and important aspect in a wide range of fields, from medical to industrial, affecting human lives. Unfortunately, classical methods of microorganism identification are based on time-consuming and labor-intensive approaches. Screening techniques require the rapid and cheap grouping of bacterial isolates; however, modern bioanalytics demand comprehensive bacterial studies at a molecular level. Modern approaches for the rapid identification of bacteria use molecular techniques, such as 16S ribosomal RNA gene sequencing based on polymerase chain reaction or electromigration, especially capillary zone electrophoresis and capillary isoelectric focusing. However, there are still several challenges with the analysis of microbial complexes using electromigration technology, such as uncontrolled aggregation and/or adhesion to the capillary surface. Thus, an approach using capillary electrophoresis of microbial aggregates with UV and matrix-assisted laser desorption ionization time-of-flight MS detection is presented.

Impacts of Modernizing Urban Stormwater Systems on Nutrient and Carbon Dynamics

NASA Astrophysics Data System (ADS)

Filippelli, G. M.; Jacinthe, P. A.; Druschel, G.

2015-12-01

Over 200 cities throughout the U.S. are undergoing the painful and expensive transition from Combined Sewer Outflows (CSOs) to modern stormwater systems. The infrastructure of CSOs is frequently a century old, with a design adapted to stormwater conditions of smaller, more pervious cities. Normal rainfall events of less 1 cm per hour can now exceed the CSO capacities in many urban sub-watersheds, leading to streamwater conditions that exceed human health standards for pathogens. Although much focus has been placed on the plumbing aspects of urban stormwater modernization, less has been focused on local, and indeed regional, implications of nutrient and carbon dynamic changes. Indianapolis, Indiana, with a metropolitan population of over 1 million, is a case study of CSO modernization. Most CSO systems in the city were built almost 100 years ago, and the city has experienced classic patterns of growth of impervious surface area, population growth, and enhanced use of chemical fertilizers. The result of these changes has been frequent failure of the CSO system, and release of sewage water into suburban and urban streams, rivers and reservoirs. Driven largely by modern environmental regulations, the city is now "footing the bill" for a century of poor planning and growth, with the real costs seen by ratepayers in the form of steeply growing wastewater fees. The mitigation approach to this problem is largely one of subsurface engineering on a mega scale, with less attention (i.e., money) placed on complementary land-use and nutrient management efforts on the surface. Several examples illustrate the relatively straightforward nature of changing plumbing, in contrast to the complex result of these changes on nutrient pathways, and the implications that this has on oxygenation, nutrient cycling, and carbon release/sequestration dynamics in riparian and urban reservoir systems.

Complex carbonate and clastic stratigraphy of the inner shelf off west-central Florida

DOE Office of Scientific and Technical Information (OSTI.GOV)

Locker, S.D.; Doyle, L.J.; Hine, A.C.

1990-05-01

The near surface stratigraphy (< 30 m) of the inner shelf off the west coast of Florida was investigated using high-resolution seismic, side-scan sonar, and continuous underwater video camera coverage. The simultaneous operation of all three systems provided a unique opportunity to calibrate acoustic data with actual video images of the sea floor in a geologically complex area characterized by limestone dissolution structures, hard-bottom exposures, and overlain by a limited supply of terrigenous clastics. Three principle bottom types, grass, sand, and hard-bottom mapped using video and side-scan sonographs, show a correlation with two subsurface stratigraphic zones. The nearshore subsurface zonemore » extending to 6-7 m water depth is characterized by flat or rolling strata and sinkholes that increase in size (200-1,200 m in diameter) and become more numerous further offshore. This zone is truncated by a major erosional unconformity overlain by a thin (<3 m) sequence of Holocene sediment, which together form a terrace upon which the Anclote Key barrier island formed. The offshore subsurface zone (7-11 m water depth) exhibits irregular and discontinuous high-amplitude flat or inclined reflections and few sinkholes. Offshore, extensive hard-bottom exposures are common with discontinuous sediment that occur as lenses or sand waves. The complex stratigraphy of the west Florida shelf includes outcropping Neogene limestones that have undergone dissolution during sea level lowstands. Carbonates and clastics dispersed during multiple sea level changes overlie the Neogene limestones. Dissolution styles and erosional unconformities produced bedrock topography and now control modern geological and biological processes.« less

The evolution of cave systems from the surface to subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Loucks, R.G.; Handford, C.R.

1996-01-01

Many carbonate reservoirs are the result of cave-forming processes. The origin and recognition of fractures, breccias, and sediment fills associated with paleocaves were determined through the study of modern and paleocaves systems. Cave formation and destruction are the products of near-surface processes. Near-surface processes include solutional excavation, clastic and chemical sedimentation, and collapse of cave walls and ceilings. Cave sediment is derived from inside and/or outside the system. Depositional mechanisms include suspension, tractional, mass-flow and rock-fall. Collapse of ceilings and walls from chaotic breakdown breccias. These piles can be tens of meters thick and contain large voids and variable amountsmore » of matrix. Cave-roof crackle breccia forms from stress-and tension-related fractures in cave-roof strata. As the cave-bearing strata subside into the subsurface, mechanical compaction increases and restructures the existing breccias and remaining cavities. Fracture porosity increases and breccia and vug porosity decreases. Large cavities collapse forming burial chaotic breakdown breccias. Differentially compacted strata over the collapsed chamber fracture and form burial cave-roof crackle breccias. Continued burial leads to more extensive mechanical compaction causing previously formed clasts to fracture and pack closer together. The resulting product is a rebrecciated chaotic breakdown breccia composed predominantly of small clasts. Rebrecciated blocks are often overprinted by crackling. Subsurface paleocave systems commonly have a complex history with several episodes of fracturing and brecciation. The resulting collapsed-paleocave reservoir targets are not single collapsed passages of tens of feet across, but are homogenized collapsed-cave systems hundreds to several thousand feet across.« less

The evolution of cave systems from the surface to subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Loucks, R.G.; Handford, C.R.

1996-12-31

Many carbonate reservoirs are the result of cave-forming processes. The origin and recognition of fractures, breccias, and sediment fills associated with paleocaves were determined through the study of modern and paleocaves systems. Cave formation and destruction are the products of near-surface processes. Near-surface processes include solutional excavation, clastic and chemical sedimentation, and collapse of cave walls and ceilings. Cave sediment is derived from inside and/or outside the system. Depositional mechanisms include suspension, tractional, mass-flow and rock-fall. Collapse of ceilings and walls from chaotic breakdown breccias. These piles can be tens of meters thick and contain large voids and variable amountsmore » of matrix. Cave-roof crackle breccia forms from stress-and tension-related fractures in cave-roof strata. As the cave-bearing strata subside into the subsurface, mechanical compaction increases and restructures the existing breccias and remaining cavities. Fracture porosity increases and breccia and vug porosity decreases. Large cavities collapse forming burial chaotic breakdown breccias. Differentially compacted strata over the collapsed chamber fracture and form burial cave-roof crackle breccias. Continued burial leads to more extensive mechanical compaction causing previously formed clasts to fracture and pack closer together. The resulting product is a rebrecciated chaotic breakdown breccia composed predominantly of small clasts. Rebrecciated blocks are often overprinted by crackling. Subsurface paleocave systems commonly have a complex history with several episodes of fracturing and brecciation. The resulting collapsed-paleocave reservoir targets are not single collapsed passages of tens of feet across, but are homogenized collapsed-cave systems hundreds to several thousand feet across.« less

From Ground Truth to Space: Surface, Subsurface and Remote Observations Associated with Nuclear Test Detection

NASA Astrophysics Data System (ADS)

Sussman, A. J.; Anderson, D.; Burt, C.; Craven, J.; Kimblin, C.; McKenna, I.; Schultz-Fellenz, E. S.; Miller, E.; Yocky, D. A.; Haas, D.

2016-12-01

Underground nuclear explosions (UNEs) result in numerous signatures that manifest on a wide range of temporal and spatial scales. Currently, prompt signals, such as the detection of seismic waves provide only generalized locations and the timing and amplitude of non-prompt signals are difficult to predict. As such, research into improving the detection, location, and identification of suspect events has been conducted, resulting in advancement of nuclear test detection science. In this presentation, we demonstrate the scalar variably of surface and subsurface observables, briefly discuss current capabilities to locate, detect and characterize potential nuclear explosion locations, and explain how emergent technologies and amalgamation of disparate data sets will facilitate improved monitoring and verification. At the smaller scales, material and fracture characterization efforts on rock collected from legacy UNE sites and from underground experiments using chemical explosions can be incorporated into predictive modeling efforts. Spatial analyses of digital elevation models and orthoimagery of both modern conventional and legacy nuclear sites show subtle surface topographic changes and damage at nearby outcrops. Additionally, at sites where such technology cannot penetrate vegetative cover, it is possible to use the vegetation itself as both a companion signature reflecting geologic conditions and showing subsurface impacts to water, nutrients, and chemicals. Aerial systems based on RGB imagery, light detection and ranging, and hyperspectral imaging can allow for combined remote sensing modalities to perform pattern recognition and classification tasks. Finally, more remote systems such as satellite based synthetic aperture radar and satellite imagery are other techniques in development for UNE site detection, location and characterization.

Rationalizing the permeation of polar antibiotics into Gram-negative bacteria.

PubMed

Scorciapino, Mariano Andrea; Acosta-Gutierrez, Silvia; Benkerrou, Dehbia; D'Agostino, Tommaso; Malloci, Giuliano; Samanta, Susruta; Bodrenko, Igor; Ceccarelli, Matteo

2017-03-22

The increasing level of antibiotic resistance in Gram-negative bacteria, together with the lack of new potential drug scaffolds in the pipeline, make the problem of infectious diseases a global challenge for modern medicine. The main reason that Gram-negative bacteria are particularly challenging is the presence of an outer cell-protecting membrane, which is not present in Gram-positive species. Such an asymmetric bilayer is a highly effective barrier for polar molecules. Several protein systems are expressed in the outer membrane to control the internal concentration of both nutrients and noxious species, in particular: (i) water-filled channels that modulate the permeation of polar molecules and ions according to concentration gradients, and (ii) efflux pumps to actively expel toxic compounds. Thus, besides expressing specific enzymes for drugs degradation, Gram-negative bacteria can also resist by modulating the influx and efflux of antibiotics, keeping the internal concentration low. However, there are no direct and robust experimental methods capable of measuring the permeability of small molecules, thus severely limiting our knowledge of the molecular mechanisms that ultimately control the permeation of antibiotics through the outer membrane. This is the innovation gap to be filled for Gram-negative bacteria. This review is focused on the permeation of small molecules through porins, considered the main path for the entry of polar antibiotics into Gram-negative bacteria. A fundamental understanding of how these proteins are able to filter small molecules is a prerequisite to design/optimize antibacterials with improved permeation. The level of sophistication of modern molecular modeling algorithms and the advances in new computer hardware has made the simulation of such complex processes possible at the molecular level. In this work we aim to share our experience and perspectives in the context of a multidisciplinary extended collaboration within the IMI-Translocation consortium. The synergistic combination of structural data, in vitro assays and computer simulations has proven to give new insights towards the identification and description of physico-chemical properties modulating permeation. Once similar general rules are identified, we believe that the use of virtual screening techniques will be very helpful in searching for new molecular scaffolds with enhanced permeation, and that molecular modeling will be of fundamental assistance to the optimization stage.

Rationalizing the permeation of polar antibiotics into Gram-negative bacteria

NASA Astrophysics Data System (ADS)

Scorciapino, Mariano Andrea; Acosta-Gutierrez, Silvia; Benkerrou, Dehbia; D'Agostino, Tommaso; Malloci, Giuliano; Samanta, Susruta; Bodrenko, Igor; Ceccarelli, Matteo

2017-03-01

The increasing level of antibiotic resistance in Gram-negative bacteria, together with the lack of new potential drug scaffolds in the pipeline, make the problem of infectious diseases a global challenge for modern medicine. The main reason that Gram-negative bacteria are particularly challenging is the presence of an outer cell-protecting membrane, which is not present in Gram-positive species. Such an asymmetric bilayer is a highly effective barrier for polar molecules. Several protein systems are expressed in the outer membrane to control the internal concentration of both nutrients and noxious species, in particular: (i) water-filled channels that modulate the permeation of polar molecules and ions according to concentration gradients, and (ii) efflux pumps to actively expel toxic compounds. Thus, besides expressing specific enzymes for drugs degradation, Gram-negative bacteria can also resist by modulating the influx and efflux of antibiotics, keeping the internal concentration low. However, there are no direct and robust experimental methods capable of measuring the permeability of small molecules, thus severely limiting our knowledge of the molecular mechanisms that ultimately control the permeation of antibiotics through the outer membrane. This is the innovation gap to be filled for Gram-negative bacteria. This review is focused on the permeation of small molecules through porins, considered the main path for the entry of polar antibiotics into Gram-negative bacteria. A fundamental understanding of how these proteins are able to filter small molecules is a prerequisite to design/optimize antibacterials with improved permeation. The level of sophistication of modern molecular modeling algorithms and the advances in new computer hardware has made the simulation of such complex processes possible at the molecular level. In this work we aim to share our experience and perspectives in the context of a multidisciplinary extended collaboration within the IMI-Translocation consortium. The synergistic combination of structural data, in vitro assays and computer simulations has proven to give new insights towards the identification and description of physico-chemical properties modulating permeation. Once similar general rules are identified, we believe that the use of virtual screening techniques will be very helpful in searching for new molecular scaffolds with enhanced permeation, and that molecular modeling will be of fundamental assistance to the optimization stage.

The eukaryotic cell originated in the integration and redistribution of hyperstructures from communities of prokaryotic cells based on molecular complementarity.

PubMed

Norris, Vic; Root-Bernstein, Robert

2009-06-04

In the "ecosystems-first" approach to the origins of life, networks of non-covalent assemblies of molecules (composomes), rather than individual protocells, evolved under the constraints of molecular complementarity. Composomes evolved into the hyperstructures of modern bacteria. We extend the ecosystems-first approach to explain the origin of eukaryotic cells through the integration of mixed populations of bacteria. We suggest that mutualism and symbiosis resulted in cellular mergers entailing the loss of redundant hyperstructures, the uncoupling of transcription and translation, and the emergence of introns and multiple chromosomes. Molecular complementarity also facilitated integration of bacterial hyperstructures to perform cytoskeletal and movement functions.

GC×GC-TOF-MS of Metabolites of Lake Vida Brine (Antarctica): Evidence for Past and Current Biogeochemical Processes

NASA Astrophysics Data System (ADS)

Chou, L.; Kenig, F. P. H.; Murray, A. E.; Fritsen, C. H.; Doran, P. T.

2016-12-01

Lake Vida, located in the McMurdo Dry Valleys, Antarctica, permanently encapsulates an interstitial anoxic, aphotic, cold (-13°C), brine ecosystem within 27 m of ice, and has been isolated from the environment for millennia (Murray et al. 2012; PNAS). Active, but slow-growing bacteria ( 120 yr generation time) were observed in this brine. The processes involved in the survivability of these microbes remain unclear. Thus, we attempt to elucidate the biogeochemistry of Lake Vida brine (LVBr) using metabolomics. LVBr contains high abundance of DOC (48.2±9.7 mmol•L-1). The slow metabolism of LVBr microbes allows for the accumulation of organic carbon that is inherited from a previous ecosystem, a glacial lake that occupied Lake Vida basin prior to LVBr isolation. Consequently, the presence of this legacy carbon, including dissolved metabolites, convolutes the interpretation of metabolic signals deriving from the current ecosystem. The aim of this study is to designate metabolites of LVBr as legacy, modern metabolic products, or both. A total lipid extract of LVBr was analyzed using a multi-dimensional comprehensive gas chromatography-time of flight-mass spectrometry (GC×GC-TOF-MS). Metabolites in LVBr are dominated by an altered legacy component: compounds synthesized in a previous ecosystem that was exposed to sunlight and the atmosphere. C8-C14 norisoprenoids observed in LVBr are derived from the oxidation of C40 and diatom pigments, whereas maleimides are degradation products of chlorophylls and bacteriochlorophylls. Additionally, we observe a diversity of sulfones and sulfoxides that may have resulted from microbial oxidation or abiotic oxidation of sulfur-bearing organic compounds. It is unclear if the alteration of legacy components in LVBr is enzymatically driven or is a pure abiotic diagenetic process. The production of some of the observed legacy compounds require molecular oxygen, which suggests that they were produced in an oxic environment, not within the current anoxic brine. The presence of legacy biomarkers in the metabolome of LVBr suggests that fossil biological signals from a previous environment may be convoluting in situ interpretation of modern biological studies of slow-growing microbial ecosystems such as other dry valley lakes as well as the deep subsurface biosphere.

Microbial desulfurization of coal

NASA Technical Reports Server (NTRS)

Dastoor, M. N.; Kalvinskas, J. J.

1978-01-01

Experiments indicate that several sulfur-oxidizing bacteria strains have been very efficient in desulfurizing coal. Process occurs at room temperature and does not require large capital investments of high energy inputs. Process may expand use of abundant reserves of high-sulfur bituminous coal, which is currently restricted due to environmental pollution. On practical scale, process may be integrated with modern coal-slurry transportation lines.

Bacterial Paleontology and Studies of Carbonaceous Chondrites

NASA Technical Reports Server (NTRS)

Gerasimenko, L. M.; Hoover, Richard B.; Rozanov, Alexei Y.; Zhegallo, E. A.; Zhmur, S. I.

1999-01-01

The study of the fossilization processes of modern cyanobacteria provides insights needed to recognize bacterial microfossils. The fossilization of cyanobacteria is discussed and images of recent and fossil bacteria and cyanobacteria from the Early Proterozoic to Neogene carbonaceous rocks (kerites, shungites, and black shales) and phosphorites are provided. These are compared with biomorphic microstructures and possible microfossils encountered in-situ in carbonaceous meteorites.

Practical benefits of knowing the enemy: Modern molecular tools for diagnosing the etiology of bacterial diseases and understanding the taxonomy and diversity of plant pathogenic bacteria

USDA-ARS?s Scientific Manuscript database

Knowing the identity of bacterial plant pathogens is essential to strategic and sustainable disease management. However, such identifications are linked to bacterial taxonomy, a complicated and changing discipline that depends on methods and information that often are not used by those who are diagn...

A century of phage research: bacteriophages and the shaping of modern biology.

PubMed

Keen, Eric C

2015-01-01

2015 marks the centennial of the discovery of bacteriophages, viruses that infect bacteria. Phages have been central to some of biology's most meaningful advances over the past hundred years (shown here); they greatly influence the workings of the biosphere, and are poised to play expanded roles in biomedicine, biotechnology, and ecology. © 2015 WILEY Periodicals, Inc.

The oral microbiome - an update for oral healthcare professionals.

PubMed

Kilian, M; Chapple, I L C; Hannig, M; Marsh, P D; Meuric, V; Pedersen, A M L; Tonetti, M S; Wade, W G; Zaura, E

2016-11-18

For millions of years, our resident microbes have coevolved and coexisted with us in a mostly harmonious symbiotic relationship. We are not distinct entities from our microbiome, but together we form a 'superorganism' or holobiont, with the microbiome playing a significant role in our physiology and health. The mouth houses the second most diverse microbial community in the body, harbouring over 700 species of bacteria that colonise the hard surfaces of teeth and the soft tissues of the oral mucosa. Through recent advances in technology, we have started to unravel the complexities of the oral microbiome and gained new insights into its role during both health and disease. Perturbations of the oral microbiome through modern-day lifestyles can have detrimental consequences for our general and oral health. In dysbiosis, the finely-tuned equilibrium of the oral ecosystem is disrupted, allowing disease-promoting bacteria to manifest and cause conditions such as caries, gingivitis and periodontitis. For practitioners and patients alike, promoting a balanced microbiome is therefore important to effectively maintain or restore oral health. This article aims to give an update on our current knowledge of the oral microbiome in health and disease and to discuss implications for modern-day oral healthcare.

Aptamers against pathogenic microorganisms

PubMed Central

Davydova, Anna; Vorobjeva, Maria; Pyshnyi, Dmitrii; Altman, Sidney; Vlassov, Valentin; Venyaminova, Alya

2016-01-01

Abstract An important current issue of modern molecular medicine and biotechnology is the search for new approaches to early diagnostic assays and adequate therapy of infectious diseases. One of the promising solutions to this problem might be a development of nucleic acid aptamers capable of interacting specifically with bacteria, protozoa, and viruses. Such aptamers can be used for the specific recognition of infectious agents as well as for blocking of their functions. The present review summarizes various modern SELEX techniques used in this field, and of several currently identified aptamers against viral particles and unicellular organisms, and their applications. The prospects of applying nucleic acid aptamers for the development of novel detection systems and antibacterial and antiviral drugs are discussed. PMID:26258445

Hexagonal platelet-like magnetite as a biosignature of thermophilic iron-reducing bacteria and its applications to the exploration of the modern deep, hot biosphere and the emergence of iron-reducing bacteria in early precambrian oceans.

PubMed

Li, Yi-Liang

2012-12-01

Dissimilatory iron-reducing bacteria are able to enzymatically reduce ferric iron and couple to the oxidation of organic carbon. This mechanism induces the mineralization of fine magnetite crystals characterized by a wide distribution in size and irregular morphologies that are indistinguishable from authigenic magnetite. Thermoanaerobacter are thermophilic iron-reducing bacteria that predominantly inhabit terrestrial hot springs or deep crusts and have the capacity to transform amorphous ferric iron into magnetite with a size up to 120 nm. In this study, I first characterize the formation of hexagonal platelet-like magnetite of a few hundred nanometers in cultures of Thermoanaerobacter spp. strain TOR39. Biogenic magnetite with such large crystal sizes and unique morphology has never been observed in abiotic or biotic processes and thus can be considered as a potential biosignature for thermophilic iron-reducing bacteria. The unique crystallographic features and strong ferrimagnetic properties of these crystals allow easy and rapid screening for the previous presence of iron-reducing bacteria in deep terrestrial crustal samples that are unsuitable for biological detection methods and, also, the search for biogenic magnetite in banded iron formations that deposited only in the first 2 billion years of Earth with evidence of life.

Microbial Biogeography on the Legacies of Historical Events in the Arctic Subsurface Sediments

NASA Astrophysics Data System (ADS)

Han, Dukki; Nam, Seung-Il; Hur, Hor-Gil

2017-04-01

The Arctic marine environment consists of various microbial habitats. The niche preference of microbial assemblages in the Arctic Ocean has been surveyed with the modern environmental change by oceanographic traits such as sea-ice dynamics, current circulation, and sedimentation. The North Pacific inflow from the shallow and narrow Bering Strait is highly susceptible to sea-level fluctuations, and thus the water mass exchange mediated by the history of sea-ice between the North Pacific and the Chukchi Sea in the Arctic Ocean. Over geological timescale, the climate change may provide putative evidences for ecological niche for the Arctic microbial assemblages as well as geological records in response to the paleoclimate change. In the present study, the multidisciplinary approach, based on microbiology, geology, and geochemistry, was applied to survey the microbial assemblages in the Arctic subsurface sediments and help further integrate the microbial biogeography and biogeochemical patterns in the Arctic subsurface biosphere. Our results describe microbial assemblages with high-resolution paleoceanographic records in the Chukchi Sea sediment core (ARA02B/01A-GC; 5.4 mbsf) to show the processes that drive microbial biogeographic patterns in the Arctic subsurface sediments. We found microbial habitat preferences closely linked to Holocene paleoclimate records as well as geological, geochemical, and microbiological evidence for the inference of the sulphate-methane transition zone (SMTZ) in the Chukchi Sea. Especially, the vertically distributed predominant populations of Gammaproteobacteria and Marine Group II Euryarchaeota in the ARA02B/01A-GC consistent with the patterns of the known global SMTZs and Holocene sedimentary records, suggesting that in-depth microbiological profiles integrated with geological records may be indirectly useful for reconstructing Arctic paleoclimate changes. In the earliest phase of Mid Holocene in the ARA02B/01A-GC with concentrated crenarchaeol (a unique biomarker for Marine Group I Thaumarchaea), the most abundant archaeal population was Marine Group II Euryarchaeota rather than Marine Group I Thaumarchaea, suggesting that the interpretation of archaeal tetraether lipids in subsurface sediments needs careful consideration for paleoceanography. In conclusion, our findings have important implications for the availability of microbial biogeography in the sedimentary record. The present study offers a deeper understanding of the legacies of historical events during the Holocene and implies that the survey of microbial biogeography may be an appropriate tool to monitor potential effects from the climate change in the Arctic Ocean.

Metabolic Strategies in Energy-Limited Microbial Communities in the Anoxic Subsurface (Frasassi Cave System, Italy)

NASA Astrophysics Data System (ADS)

McCauley, R. L.; Jones, D. S.; Schaperdoth, I.; Steinberg, L.; Macalady, J. L.

2010-12-01

Two major sources of energy, light and chemical potential, are available to microorganisms. However, energy is not always abundant and is often a limiting factor in microbial survival and replication. The anoxic, terrestrial subsurface offers a unique opportunity to study microorganisms and their potentially novel metabolic strategies that are relevant for understanding biogeochemistry and biosignatures as related to the non-photosynthetic, energy-limited environments on the modern and ancient Earth and elsewhere in the solar system. Geochemical data collected in a remote stratified lake 600 m below ground surface in the sulfidic Frasassi cave system (Italy) suggest that little redox energy is available for life, consistent with low signal from domain-specific FISH probes. The carbon isotope signatures of biofilms (-33‰) and DIC (-9‰) in the anoxic water suggest in situ production by lithoautotrophs using RuBisCO. 16S rDNA libraries constructed from the biofilm are dominated by diverse sulfate reducing bacteria. The remaining bacterial and archaeal clones affiliate with more than 11 major uncultivated or novel prokaryotic lineages. Diverse dsrAB gene sequences are consistent with high sulfate concentrations and undetectable or extremely low oxygen, nitrate, and iron concentrations. However, the electron donor for sulfate reduction is unclear. Methane is detectable in the anoxic water although no 16S rDNA sequences associated with known methanogens or anaerobic methane oxidizers were retrieved. mcrA gene sequences retrieved from the biofilm by cloning are not related to cultivated methanogens or to known anaerobic methane oxidizers. Non-purgable organic carbon (NPOC) is below detection limits (i.e. <42 μM acetate) suggesting that alternative electron donors or novel metabolisms may be important. A sample collected by cave divers in October 2009 was pyrosequenced at the Pennsylvania State University Genomics Core Facility using Titanium chemistry (454 Life Sciences). We retrieved more than 420,000 metagenomic reads, of which 46% have significant homology to sequences in NCBI’s non-redundant protein database and 3% could be assigned using the Clusters of Orthologous Groups of proteins (COGs) classification system. 16S (174 reads) and 23S (283 reads) rDNA sequences in the metagenome imply a phylogenetically diverse community dominated by Deltaproteobacteria and Firmicutes. We also identified 15 metagenome sequences with homology to known dsrAB genes. Further work will identify additional genes for specific energy and nutrient metabolisms in the community, as well as use comparative analyses to determine overrepresented functions that are characteristic of life in the oligotrophic, euxinic cave environment.

Water quality and diversity of yeasts from tropical lakes and rivers from the Rio Doce basin in Southeastern Brazil

PubMed Central

Medeiros, Adriana O.; Missagia, Beatriz S.; Brandão, Luciana R.; Callisto, Marcos; Barbosa, Francisco A. R.; Rosa, Carlos A.

2012-01-01

Yeast communities were assessed in 14 rivers and four lakes from the Doce River basin in Brazil, during the rainy and dry seasons of the years 2000 and 2001. Water samples were collected at the subsurface in all sites. The following physical and chemical parameters were measured: temperature, dissolved oxygen, pH, electrical conductivity, total phosphorus, ortho-phosphate, ammonium, nitrate, nitrite and total nitrogen and the counts of faecal coliforms and heterotrophic bacteria were carried out to characterize the aquatic environmental sampled. The yeast counts were higher in aquatic environments with the highest counts of coliform and heterotrophic bacteria. These environments receive a high influx of domestic and industrial waste. A total of 317 isolates identified in forty eight yeast species were recorded in the sites sampled and the specie Aureobasidium pullulans were found in eleven out of eighteen sites sampled and some opportunistic pathogens such as the yeast species Candida krusei were isolated only in the polluted rivers with a positive correlation with the biotic and abiotic parameters that indicate sewage contamination. PMID:24031990

Microbial growth and transport in saturated and unsaturated porous media

NASA Astrophysics Data System (ADS)

Hron, Pavel; Jost, Daniel; Bastian, Peter; Ippisch, Olaf

2014-05-01

There is a considerable ongoing effort aimed at understanding the behavior of microorganisms in porous media. Microbial activity is of significant interest in various environmental applications such as in situ bioremediation, protection of drinking water supplies and for subsurface geochemistry in general. The main limiting factors for bacterial growth are the availability of electron acceptors, nutrients and bio-available water. The capillary fringe, defined - in a wider sense than usual - as the region of the subsurface above the groundwater table, but still dominated by capillary rise, is a region where all these factors are abundantly available. It is thus a region where high microbial activity is to be expected. In a research unit 'Dynamic Capillary Fringes - A Multidisciplinary Approach (DyCap)' founded by the German Research Foundation (DFG), the growth of microorganisms in the capillary fringe was studied experimentally and with numerical simulations. Processes like component transport and diffusion, exchange between the liquid phase and the gas phase, microbial growth and cell attachment and detachment were incorporated into a numerical simulator. The growth of the facultative anaerobic Escherichia coli as a function of nutrient availability and oxygen concentration in the liquid phase is modeled with modified Monod-type models and modifications for the switch between aerobic and anaerobic growth. Laboratory batch experiments with aqueous solutions of bacteria have been carried out under various combinations of oxygen concentrations in the gas phase and added amounts of dissolved organic carbon to determine the growth model parameters by solution of a parameter estimation problem. For the transport of bacteria the adhesion to phase boundaries is also very important. As microorganisms are transported through porous media, they are removed from the pore fluid by physicochemical filtration (attachment to sediment grain surfaces) or are adhering to gas-water interface. The cell attachment and detachment model was based on flow-through experiments and the parameters were obtained by fitting the model to measured bacteria breakthrough curves. Experiments on bacterial growth in porous media with and without groundwater flow were performed in Hele-Shaw cells filled with quartz sands. The cell density was determined by the fluorescence of a special protein produced by the genetically modified strain of E. coli. The simulation results are compared to experimental data and different modeling approaches are discussed.

Subsurface associations of Acaryochloris-related picocyanobacteria with oil-utilizing bacteria in the Arabian Gulf water body: promising consortia in oil sediment bioremediation.

PubMed

Al-Bader, Dhia; Eliyas, Mohamed; Rayan, Rihab; Radwan, Samir

2013-04-01

Two picocyanobacterial strains related to Acaryochloris were isolated from the Arabian Gulf, 3 m below the water surface, one from the north shore and the other from the south shore of Kuwait. Both strains were morphologically, ultrastructurally, and albeit to a less extend, phylogenetically similar to Acaryochloris. However, both isolates lacked chlorophyll d and produced instead chlorophyll a, as the major photosynthetic pigment. Both picocyanobacterial isolates were associated with oil-utilizing bacteria in the magnitude of 10(5) cells g(-1). According to their 16S rRNA gene sequences, bacteria associated with the isolate from the north were affiliated to Paenibacillus sp., Bacillus pumilus, and Marinobacter aquaeolei, but those associated with the isolate from the south were affiliated to Bacillus asahii and Alcanivorax jadensis. These bacterial differences were probably due to environmental variations. In batch cultures, the bacterial consortia in the nonaxenic biomass as well as the pure bacterial isolates effectively consumed crude oil and pure aliphatic and aromatic hydrocarbons, including very high-molecular-weight compounds. Water and diethylether extracts from the phototrophic biomass enhanced growth of individual bacterial isolates and their hydrocarbon-consumption potential in batch cultures. It was concluded that these consortia could be promising in bioremediation of hydrocarbon pollutants, especially heavy sediments in the marine ecosystem.

Identifying and Quantifying the Intermediate Processes during Nitrate-Dependent Iron(II) Oxidation.

PubMed

Jamieson, James; Prommer, Henning; Kaksonen, Anna H; Sun, Jing; Siade, Adam J; Yusov, Anna; Bostick, Benjamin

2018-05-15

Microbially driven nitrate-dependent iron (Fe) oxidation (NDFO) in subsurface environments has been intensively studied. However, the extent to which Fe(II) oxidation is biologically catalyzed remains unclear because no neutrophilic iron-oxidizing and nitrate reducing autotroph has been isolated to confirm the existence of an enzymatic pathway. While mixotrophic NDFO bacteria have been isolated, understanding the process is complicated by simultaneous abiotic oxidation due to nitrite produced during denitrification. In this study, the relative contributions of biotic and abiotic processes during NDFO were quantified through the compilation and model-based interpretation of previously published experimental data. The kinetics of chemical denitrification by Fe(II) (chemodenitrification) were assessed, and compelling evidence was found for the importance of organic ligands, specifically exopolymeric substances secreted by bacteria, in enhancing abiotic oxidation of Fe(II). However, nitrite alone could not explain the observed magnitude of Fe(II) oxidation, with 60-75% of overall Fe(II) oxidation attributed to an enzymatic pathway for investigated strains: Acidovorax ( A.) strain BoFeN1, 2AN, A. ebreus strain TPSY, Paracoccus denitrificans Pd 1222, and Pseudogulbenkiania sp. strain 2002. By rigorously quantifying the intermediate processes, this study eliminated the potential for abiotic Fe(II) oxidation to be exclusively responsible for NDFO and verified the key contribution from an additional, biological Fe(II) oxidation process catalyzed by NDFO bacteria.

Subsurface intake systems: Green choice for improving feed water quality at SWRO desalination plants, Jeddah, Saudi Arabia.

PubMed

Dehwah, Abdullah H A; Missimer, Thomas M

2016-01-01

An investigation of three seawater reverse osmosis facilities located along the shoreline of the Red Sea of Saudi Arabia that use well intake systems showed that the pumping-induced flow of raw seawater through a coastal aquifer significantly improves feed water quality. A comparison between the surface seawater and the discharge from the wells shows that turbidity, algae, bacteria, total organic carbon, most fractions of natural organic matter (NOM), and particulate and colloidal transparent exopolymer particles (TEP) have significant reductions in concentration. Nearly all of the algae, up to 99% of the bacteria, between 84 and 100% of the biopolymer fraction of NOM, and a high percentage of the TEP were removed during transport. The data suggest that the flowpath length and hydraulic retention time in the aquifer play the most important roles in removal of the organic matter. Since the collective concentrations of bacteria, biopolymers, and TEP in the intake seawater play important roles in the biofouling of SWRO membranes, the observed reductions suggest that the desalination facilities that use well intakes systems will have a potentially lower fouling rate compared to open-ocean intake systems. Furthermore, well intake system intakes also reduce the need for chemical usage during complex pretreatment systems required for operation of SWRO facilities using open-ocean intakes and reduce environmental impacts. Copyright © 2015 Elsevier Ltd. All rights reserved.

Multiresistant opportunistic pathogenic bacteria isolated from polluted rivers and first detection of nontuberculous mycobacteria in the Algerian aquatic environment.

PubMed

Djouadi, Lydia Neïla; Selama, Okba; Abderrahmani, Ahmed; Bouanane-Darenfed, Amel; Abdellaziz, Lamia; Amziane, Meriam; Fardeau, Marie-Laure; Nateche, Farida

2017-08-01

Opportunistic infections constitute a major challenge for modern medicine mainly because the involved bacteria are usually multiresistant to antibiotics. Most of these bacteria possess remarkable ability to adapt to various ecosystems, including those exposed to anthropogenic activities. This study isolated and identified 21 multiresistant opportunistic bacteria from two polluted rivers, located in Algiers. Cadmium, lead, and copper concentrations were determined for both water samples to evaluate heavy metal pollution. High prevalence of Enterobacteria and non-fermentative Gram-negative rods was found and a nontuberculous Mycobacterium (NTM) strain was isolated. To the best of our knowledge, this is the first detection of NTM in the Algerian environment. The strains were tested for their resistance against 34 antibiotics and 8 heavy metals. Multiple antibiotics and heavy metals resistance was observed in all isolates. The two most resistant strains, identified as Acinetobacter sp. and Citrobacter freundii, were submitted to plasmid curing to determine if resistance genes were plasmid or chromosome encoded. Citrobacter freundii strain P18 showed a high molecular weight plasmid which seems to code for resistance to zinc, lead, and tetracycline, at the same time. These findings strongly suggest that anthropized environments constitute a reservoir for multiresistant opportunistic bacteria and for circulating resistance genes.

Curiously modern DNA for a "250 million-year-old" bacterium.

PubMed

Nickle, David C; Learn, Gerald H; Rain, Matthew W; Mullins, James I; Mittler, John E

2002-01-01

Studies of ancient DNA have attracted considerable attention in scientific journals and the popular press. Several of the more extreme claims for ancient DNA have been questioned on biochemical grounds (i.e., DNA surviving longer than expected) and evolutionary grounds (i.e., nucleotide substitution patterns not matching theoretical expectations for ancient DNA). A recent letter to Nature from Vreeland et al. (2000), however, tops all others with respect to age and condition of the specimen. These researchers extracted and cultured a bacterium from an inclusion body from what they claim is a 250 million-year (Myr)-old salt crystal. If substantiated, this observation could fundamentally alter views about bacterial physiology, ecology and evolution. Here we report on molecular evolutionary analyses of the 16S rDNA from this specimen. We find that 2-9-3 differs from a modern halophile, Salibacillus marismortui, by just 3 unambiguous bp in 16S rDNA, versus the approximately 59 bp that would be expected if these bacteria evolved at the same rate as other bacteria. We show, using a Poisson distribution, that unless it can be shown that S. marismortui evolves 5 to 10 times more slowly than other bacteria for which 16S rDNA substitution rates have been established, Vreeland et al.'s claim would be rejected at the 0.05 level. Also, a molecular clock test and a relative rates test fail to substantiate Vreeland et al.'s claim that strain 2-9-3 is a 250-Myr-old bacterium. The report of Vreeland et al. thus falls into a long series of suspect ancient DNA studies.

Frosty Polygons

NASA Technical Reports Server (NTRS)

2004-01-01

16 January 2004 Looking somewhat like a roadmap, this 3 km (1.9 mi) wide view of a cratered plain in the martian south polar region shows a plethora of cracks that form polygonal patterns. This Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image is located near 78.9oS, 357.3oW. Polygons such as these, where they are found on Earth, would be indicators of the presence of subsurface ice. Whether the same is true for Mars is uncertain. What is certain is that modern, seasonal frost on the surface enhances the appearance of the polygons as the frost persists longer in the cracks than on adjacent plains. This southern springtime image is illuminated by sunlight from the upper left.

Investigation on Microbial Dissolution of Uranium (VI) from Autunite Mineral - 13421

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sepulveda, Paola; Katsenovich, Yelena; Lagos, Leonel

2013-07-01

Precipitating autunite minerals by polyphosphate injection was identified as a feasible remediation strategy for sequestering uranium in contaminated groundwater and soil in situ at the Hanford Site. Autunite stability under vadose and saturated zone environmental conditions can help to determine the long-term effectiveness of this remediation strategy. The Arthrobacter bacteria are one of the most common groups in soils and are found in large numbers in Hanford soil as well as other subsurface environments contaminated with radionuclides. Ubiquitous in subsurface microbial communities, these bacteria can play a significant role in the dissolution of minerals and the formation of secondary minerals.more » The main objective of this investigation was to study the bacterial interactions under oxidizing conditions with uranium (VI); study the potential role of bicarbonate, which is an integral complexing ligand for U(VI) and a major ion in groundwater compositions; and present data from autunite dissolution experiments using Arthrobacter strain G968, a less U(VI)-tolerant strain. Sterile 100 mL glass mixed reactors served as the major bioreactor for initial experimentation. These autunite-containing bioreactors were injected with bacterial cells after the autunite equilibrated with the media solution amended with 0 mM, 3 mM 5 mM and 10 mM concentrations of bicarbonate. G968 Arthrobacter cells in the amount of 10{sup 6} cells/mL were injected into the reactors after 27 days, giving time for the autunite to reach steady state. Abiotic non-carbonate controls were kept without bacterial inoculation to provide a control for the biotic samples. Samples of the solution were analyzed for dissolved U(VI) by means of kinetic phosphorescence analyzer KPA-11 (Chemcheck Instruments, Richland, WA). Analysis showed that as [HCO{sub 3}{sup -}] increases, a diminishing trend on the effect of bacteria on autunite leaching is observed. Viability of cells was conducted after 24 hours of cell incubation with the appropriate uranium and bicarbonate concentration treatment. As expected, the cells started to reduce after day 41 due to the nutritional exhaustion of the media. Moreover, viable bacteria accounted for more than 94% in the presence of 10 mM bicarbonate. Experiments showed that despite differences between the G975 and the G968 bacterial strains resistance to U(VI), in the presence of bicarbonate ions they are able to dissolute uranium from autunite mineral at the same capacity. The effect of both bacterial strains on autunite dissolution is reduced as the concentration of bicarbonate increases while the increase in soluble U(VI) concentration induced by G968 and G975 is dwarfed, for larger [HCO{sub 3}{sup -}]. (authors)« less

Field Deployment for In-situ Metal and Radionuclide Stabilization by Microbial Metabolites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Turick, C. E.; Knox, A. S.; Dixon, K. L.

2005-09-26

A novel biotechnology is reported here that was demonstrated at SRS that facilitates metal and actinide immobilization by incorporating the physiology and ecology of indigenous bacteria. This technology is based on our previous work with pyomelanin-producing bacteria isolated from SRS soils. Through tyrosine supplementation, overproduction of pyomelanin was achieved, which lead ultimately to metal and actinide immobilization, both in-vitro and in-situ. Pyomelanin is a recalcitrant microbial pigment and a humic type compound in the class of melanin pigments. Pyomelanin has electron shuttling and metal chelation capabilities and thus accelerates the bacterial reduction and/or immobilization of metals. Pyomelanin is produced outsidemore » the cell and either diffuses away or attaches to the cell surface. In either case, the reduced pyomelanin is capable of transferring electrons to metals as well as chelating metals. Because of its recalcitrance and redox cycling properties, pyomelanin molecules can be used over and over again for metal transformation. When produced in excess, pyomelanin produced by one bacterial species can be used by other species for metal reduction, thereby extending the utility of pyomelanin and further accelerating metal immobilization rates. Soils contaminated with Ni and U were the focus of this study in order to develop in-situ, metal bioimmobilization technologies. We have demonstrated pyomelanin production in soil from the Tims Branch area of SRS as a result of tyrosine amendments. These results were documented in laboratory soil column studies and field deployment studies. The amended soils demonstrated increased redox behavior and sequestration capacity of U and transition metals following pyomelanin production. Treatments incorporating tyrosine and lactate demonstrated the highest levels of pyomelanin production. In order to determine the potential use of this technology at other areas of SRS, pyomelanin producing bacteria were also quantified from metal contaminated soils at TNX and D areas of SRS. A bacterial culture collection from subsurface studies near P Area of SRS were also evaluated for pyomelanin production. Bacterial densities of pyomelanin producers were determined to be >10{sup 6} cells/g soil at TNX and D areas. In addition, approximately 25% of isolates from P area demonstrated pyomelanin production in the presence of tyrosine. Biogeochemical activity is an ongoing and dynamic process due, in part, to bacterial activity in the subsurface. Bacteria contribute significantly to biotransformation of metals and radionuclides. An understanding and application of the mechanisms of metal and radionuclide reduction offers tremendous potential for development into bioremedial processes and technologies. This report demonstrates the application of recent advances in bacterial physiology and soil ecology for future bioremediation activities involving metal and actinide immobilization.« less

Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions

DOE PAGES

Kwon, Man Jae; O’Loughlin, Edward J.; Boyanov, Maxim I.; ...

2016-01-22

Although iron- and sulfate-reducing bacteria in subsurface environments have crucial roles in biogeochemical cycling of C, Fe, and S, how specific electron donors impact the compositional structure and activity of native iron- and/or sulfate-reducing communities is largely unknown. To understand this better, we created bicarbonate-buffered batch systems in duplicate with three different electron donors (acetate, lactate, or glucose) paired with ferrihydrite and sulfate as the electron acceptors and inoculated them with subsurface sediment as the microbial inoculum. Sulfate and ferrihydrite reduction occurred simultaneously and were faster with lactate than with acetate. 16S rRNA-based sequence analysis of the communities over timemore » revealed that Desulfotomaculum was the major driver for sulfate reduction coupled with propionate oxidation in lactate-amended incubations. The reduction of sulfate resulted in sulfide production and subsequent abiotic reduction of ferrihydrite. In contrast, glucose promoted faster reduction of ferrihydrite, but without reduction of sulfate. Interestingly, the glucose-amended incubations led to two different biogeochemical trajectories among replicate bottles that resulted in distinct coloration (white and brown). The two outcomes in geochemical evolution might be due to the stochastic evolution of the microbial communities or subtle differences in the initial composition of the fermenting microbial community and its development via the use of different glucose fermentation pathways available within the community. Synchrotron-based x-ray analysis indicated that siderite and amorphous Fe(II) were formed in the replicate bottles with glucose, while ferrous sulfide and vivianite were formed with lactate or acetate. As a result, these data sets reveal that use of different C utilization pathways projects significant changes in microbial community composition over time that uniquely impact both the geochemistry and mineralogy of subsurface environments.« less

A Limited Microbial Consortium Is Responsible for Extended Bioreduction of Uranium in a Contaminated Aquifer ▿†

PubMed Central

Gihring, Thomas M.; Zhang, Gengxin; Brandt, Craig C.; Brooks, Scott C.; Campbell, James H.; Carroll, Susan; Criddle, Craig S.; Green, Stefan J.; Jardine, Phil; Kostka, Joel E.; Lowe, Kenneth; Mehlhorn, Tonia L.; Overholt, Will; Watson, David B.; Yang, Zamin; Wu, Wei-Min; Schadt, Christopher W.

2011-01-01

Subsurface amendments of slow-release substrates (e.g., emulsified vegetable oil [EVO]) are thought to be a pragmatic alternative to using short-lived, labile substrates for sustained uranium bioimmobilization within contaminated groundwater systems. Spatial and temporal dynamics of subsurface microbial communities during EVO amendment are unknown and likely differ significantly from those of populations stimulated by soluble substrates, such as ethanol and acetate. In this study, a one-time EVO injection resulted in decreased groundwater U concentrations that remained below initial levels for approximately 4 months. Pyrosequencing and quantitative PCR of 16S rRNA from monitoring well samples revealed a rapid decline in groundwater bacterial community richness and diversity after EVO injection, concurrent with increased 16S rRNA copy levels, indicating the selection of a narrow group of taxa rather than a broad community stimulation. Members of the Firmicutes family Veillonellaceae dominated after injection and most likely catalyzed the initial oil decomposition. Sulfate-reducing bacteria from the genus Desulforegula, known for long-chain fatty acid oxidation to acetate, also dominated after EVO amendment. Acetate and H2 production during EVO degradation appeared to stimulate NO3−, Fe(III), U(VI), and SO42− reduction by members of the Comamonadaceae, Geobacteriaceae, and Desulfobacterales. Methanogenic archaea flourished late to comprise over 25% of the total microbial community. Bacterial diversity rebounded after 9 months, although community compositions remained distinct from the preamendment conditions. These results demonstrated that a one-time EVO amendment served as an effective electron donor source for in situ U(VI) bioreduction and that subsurface EVO degradation and metal reduction were likely mediated by successive identifiable guilds of organisms. PMID:21764967

A limited microbial consortium is responsible for extended bioreduction of uranium in a contaminated aquifer.

PubMed

Gihring, Thomas M; Zhang, Gengxin; Brandt, Craig C; Brooks, Scott C; Campbell, James H; Carroll, Susan; Criddle, Craig S; Green, Stefan J; Jardine, Phil; Kostka, Joel E; Lowe, Kenneth; Mehlhorn, Tonia L; Overholt, Will; Watson, David B; Yang, Zamin; Wu, Wei-Min; Schadt, Christopher W

2011-09-01

Subsurface amendments of slow-release substrates (e.g., emulsified vegetable oil [EVO]) are thought to be a pragmatic alternative to using short-lived, labile substrates for sustained uranium bioimmobilization within contaminated groundwater systems. Spatial and temporal dynamics of subsurface microbial communities during EVO amendment are unknown and likely differ significantly from those of populations stimulated by soluble substrates, such as ethanol and acetate. In this study, a one-time EVO injection resulted in decreased groundwater U concentrations that remained below initial levels for approximately 4 months. Pyrosequencing and quantitative PCR of 16S rRNA from monitoring well samples revealed a rapid decline in groundwater bacterial community richness and diversity after EVO injection, concurrent with increased 16S rRNA copy levels, indicating the selection of a narrow group of taxa rather than a broad community stimulation. Members of the Firmicutes family Veillonellaceae dominated after injection and most likely catalyzed the initial oil decomposition. Sulfate-reducing bacteria from the genus Desulforegula, known for long-chain fatty acid oxidation to acetate, also dominated after EVO amendment. Acetate and H(2) production during EVO degradation appeared to stimulate NO(3)(-), Fe(III), U(VI), and SO(4)(2-) reduction by members of the Comamonadaceae, Geobacteriaceae, and Desulfobacterales. Methanogenic archaea flourished late to comprise over 25% of the total microbial community. Bacterial diversity rebounded after 9 months, although community compositions remained distinct from the preamendment conditions. These results demonstrated that a one-time EVO amendment served as an effective electron donor source for in situ U(VI) bioreduction and that subsurface EVO degradation and metal reduction were likely mediated by successive identifiable guilds of organisms.

Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kwon, Man Jae; O’Loughlin, Edward J.; Boyanov, Maxim I.

Although iron- and sulfate-reducing bacteria in subsurface environments have crucial roles in biogeochemical cycling of C, Fe, and S, how specific electron donors impact the compositional structure and activity of native iron- and/or sulfate-reducing communities is largely unknown. To understand this better, we created bicarbonate-buffered batch systems in duplicate with three different electron donors (acetate, lactate, or glucose) paired with ferrihydrite and sulfate as the electron acceptors and inoculated them with subsurface sediment as the microbial inoculum. Sulfate and ferrihydrite reduction occurred simultaneously and were faster with lactate than with acetate. 16S rRNA-based sequence analysis of the communities over timemore » revealed that Desulfotomaculum was the major driver for sulfate reduction coupled with propionate oxidation in lactate-amended incubations. The reduction of sulfate resulted in sulfide production and subsequent abiotic reduction of ferrihydrite. In contrast, glucose promoted faster reduction of ferrihydrite, but without reduction of sulfate. Interestingly, the glucose-amended incubations led to two different biogeochemical trajectories among replicate bottles that resulted in distinct coloration (white and brown). The two outcomes in geochemical evolution might be due to the stochastic evolution of the microbial communities or subtle differences in the initial composition of the fermenting microbial community and its development via the use of different glucose fermentation pathways available within the community. Synchrotron-based x-ray analysis indicated that siderite and amorphous Fe(II) were formed in the replicate bottles with glucose, while ferrous sulfide and vivianite were formed with lactate or acetate. As a result, these data sets reveal that use of different C utilization pathways projects significant changes in microbial community composition over time that uniquely impact both the geochemistry and mineralogy of subsurface environments.« less

Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions.

PubMed

Kwon, Man Jae; O'Loughlin, Edward J; Boyanov, Maxim I; Brulc, Jennifer M; Johnston, Eric R; Kemner, Kenneth M; Antonopoulos, Dionysios A

2016-01-01

Although iron- and sulfate-reducing bacteria in subsurface environments have crucial roles in biogeochemical cycling of C, Fe, and S, how specific electron donors impact the compositional structure and activity of native iron- and/or sulfate-reducing communities is largely unknown. To understand this better, we created bicarbonate-buffered batch systems in duplicate with three different electron donors (acetate, lactate, or glucose) paired with ferrihydrite and sulfate as the electron acceptors and inoculated them with subsurface sediment as the microbial inoculum. Sulfate and ferrihydrite reduction occurred simultaneously and were faster with lactate than with acetate. 16S rRNA-based sequence analysis of the communities over time revealed that Desulfotomaculum was the major driver for sulfate reduction coupled with propionate oxidation in lactate-amended incubations. The reduction of sulfate resulted in sulfide production and subsequent abiotic reduction of ferrihydrite. In contrast, glucose promoted faster reduction of ferrihydrite, but without reduction of sulfate. Interestingly, the glucose-amended incubations led to two different biogeochemical trajectories among replicate bottles that resulted in distinct coloration (white and brown). The two outcomes in geochemical evolution might be due to the stochastic evolution of the microbial communities or subtle differences in the initial composition of the fermenting microbial community and its development via the use of different glucose fermentation pathways available within the community. Synchrotron-based x-ray analysis indicated that siderite and amorphous Fe(II) were formed in the replicate bottles with glucose, while ferrous sulfide and vivianite were formed with lactate or acetate. These data sets reveal that use of different C utilization pathways projects significant changes in microbial community composition over time that uniquely impact both the geochemistry and mineralogy of subsurface environments.

Energy Gradients Structure Microbial Communities Across Sediment Horizons in Deep Marine Sediments of the South China Sea

PubMed Central

Graw, Michael F.; D'Angelo, Grace; Borchers, Matthew; Thurber, Andrew R.; Johnson, Joel E.; Zhang, Chuanlun; Liu, Haodong; Colwell, Frederick S.

2018-01-01

The deep marine subsurface is a heterogeneous environment in which the assembly of microbial communities is thought to be controlled by a combination of organic matter deposition, electron acceptor availability, and sedimentology. However, the relative importance of these factors in structuring microbial communities in marine sediments remains unclear. The South China Sea (SCS) experiences significant variability in sedimentation across the basin and features discrete changes in sedimentology as a result of episodic deposition of turbidites and volcanic ashes within lithogenic clays and siliceous or calcareous ooze deposits throughout the basin's history. Deep subsurface microbial communities were recently sampled by the International Ocean Discovery Program (IODP) at three locations in the SCS with sedimentation rates of 5, 12, and 20 cm per thousand years. Here, we used Illumina sequencing of the 16S ribosomal RNA gene to characterize deep subsurface microbial communities from distinct sediment types at these sites. Communities across all sites were dominated by several poorly characterized taxa implicated in organic matter degradation, including Atribacteria, Dehalococcoidia, and Aerophobetes. Sulfate-reducing bacteria comprised only 4% of the community across sulfate-bearing sediments from multiple cores and did not change in abundance in sediments from the methanogenic zone at the site with the lowest sedimentation rate. Microbial communities were significantly structured by sediment age and the availability of sulfate as an electron acceptor in pore waters. However, microbial communities demonstrated no partitioning based on the sediment type they inhabited. These results indicate that microbial communities in the SCS are structured by the availability of electron donors and acceptors rather than sedimentological characteristics. PMID:29696012

Profiling defect depth in composite materials using thermal imaging NDE

NASA Astrophysics Data System (ADS)

Obeidat, Omar; Yu, Qiuye; Han, Xiaoyan

2018-04-01

Sonic Infrared (IR) NDE, is a relatively new NDE technology; it has been demonstrated as a reliable and sensitive method to detect defects. SIR uses ultrasonic excitation with IR imaging to detect defects and flaws in the structures being inspected. An IR camera captures infrared radiation from the target for a period of time covering the ultrasound pulse. This period of time may be much longer than the pulse depending on the defect depth and the thermal properties of the materials. With the increasing deployment of composites in modern aerospace and automobile structures, fast, wide-area and reliable NDE methods are necessary. Impact damage is one of the major concerns in modern composites. Damage can occur at a certain depth without any visual indication on the surface. Defect depth information can influence maintenance decisions. Depth profiling relies on the time delays in the captured image sequence. We'll present our work on the defect depth profiling by using the temporal information of IR images. An analytical model is introduced to describe heat diffusion from subsurface defects in composite materials. Depth profiling using peak time is introduced as well.

Investigating Microbe-Mineral Interactions: Recent Advances in X-Ray and Electron Microscopy and Redox-Sensitive Methods

NASA Astrophysics Data System (ADS)

Miot, Jennyfer; Benzerara, Karim; Kappler, Andreas

2014-05-01

Microbe-mineral interactions occur in diverse modern environments, from the deep sea and subsurface rocks to soils and surface aquatic environments. They may have played a central role in the geochemical cycling of major (e.g., C, Fe, Ca, Mn, S, P) and trace (e.g., Ni, Mo, As, Cr) elements over Earth's history. Such interactions include electron transfer at the microbe-mineral interface that left traces in the rock record. Geomicrobiology consists in studying interactions at these organic-mineral interfaces in modern samples and looking for traces of past microbe-mineral interactions recorded in ancient rocks. Specific tools are required to probe these interfaces and to understand the mechanisms of interaction between microbes and minerals from the scale of the biofilm to the nanometer scale. In this review, we focus on recent advances in electron microscopy, in particular in cryoelectron microscopy, and on a panel of electrochemical and synchrotron-based methods that have recently provided new understanding and imaging of the microbe-mineral interface, ultimately opening new fields to be explored.

Novel Protein Folding Pathways for Protein Salvage and Recycling

DTIC Science & Technology

2013-08-26

cooperative protein folding and unfolding reactions. Archaea are primitive microorganisms placed by most taxonomic criteria at the base of the Tree of...Life. The Archaea have many molecular properties that are found universally in modern lineages of both Bacteria and Archaea , and many species are...specialized for survival and growth in extreme conditions, including at or above the normal boiling point of water. These hyperthermophilic archaea

Functional diversity of microbial communities in pristine aquifers inferred by PLFA- and sequencing-based approaches

NASA Astrophysics Data System (ADS)

Schwab, Valérie F.; Herrmann, Martina; Roth, Vanessa-Nina; Gleixner, Gerd; Lehmann, Robert; Pohnert, Georg; Trumbore, Susan; Küsel, Kirsten; Totsche, Kai U.

2017-05-01

Microorganisms in groundwater play an important role in aquifer biogeochemical cycles and water quality. However, the mechanisms linking the functional diversity of microbial populations and the groundwater physico-chemistry are still not well understood due to the complexity of interactions between surface and subsurface. Within the framework of Hainich (north-western Thuringia, central Germany) Critical Zone Exploratory of the Collaborative Research Centre AquaDiva, we used the relative abundances of phospholipid-derived fatty acids (PLFAs) to link specific biochemical markers within the microbial communities to the spatio-temporal changes of the groundwater physico-chemistry. The functional diversities of the microbial communities were mainly correlated with groundwater chemistry, including dissolved O2, Fet and NH4+ concentrations. Abundances of PLFAs derived from eukaryotes and potential nitrite-oxidizing bacteria (11Me16:0 as biomarker for Nitrospira moscoviensis) were high at sites with elevated O2 concentration where groundwater recharge supplies bioavailable substrates. In anoxic groundwaters more rich in Fet, PLFAs abundant in sulfate-reducing bacteria (SRB), iron-reducing bacteria and fungi increased with Fet and HCO3- concentrations, suggesting the occurrence of active iron reduction and the possible role of fungi in meditating iron solubilization and transport in those aquifer domains. In more NH4+-rich anoxic groundwaters, anammox bacteria and SRB-derived PLFAs increased with NH4+ concentration, further evidencing the dependence of the anammox process on ammonium concentration and potential links between SRB and anammox bacteria. Additional support of the PLFA-based bacterial communities was found in DNA- and RNA-based Illumina MiSeq amplicon sequencing of bacterial 16S rRNA genes, which showed high predominance of nitrite-oxidizing bacteria Nitrospira, e.g. Nitrospira moscoviensis, in oxic aquifer zones and of anammox bacteria in more NH4+-rich anoxic groundwater. Higher relative abundances of sequence reads in the RNA-based datasets affiliated with iron-reducing bacteria in more Fet-rich groundwater supported the occurrence of active dissimilatory iron reduction. The functional diversity of the microbial communities in the biogeochemically distinct groundwater assemblages can be largely attributed to the redox conditions linked to changes in bioavailable substrates and input of substrates with the seepage. Our results demonstrate the power of complementary information derived from PLFA-based and sequencing-based approaches.

Constraining the redox landscape of the mid-Proterozoic oceans: new insights from the carbonate uranium isotope record

NASA Astrophysics Data System (ADS)

Gilleaudeau, G. J.; Kaufman, A. J.; Luo, G.; Romaniello, S. J.; Zhang, F.; Kah, L. C.; Azmy, K.; Bartley, J. K.; Sahoo, S. K.; Knoll, A. H.; Anbar, A. D.

2017-12-01

The redox landscape of the global oceans during the prolonged period between the Great Oxidation Event (GOE) and the Neoproterozoic Oxygenation Event (NOE) is a topic of considerable debate. Data from local redox proxies such as iron speciation suggest largely ferruginous conditions in the subsurface oceans (with the exception of one report of oxic subsurface waters) and a variable degree of euxinia in shallow shelf and epeiric sea environments. There is general consensus that anoxia was more widespread than in the modern ocean, but quantifying the degree of seafloor anoxia is challenging given that most redox proxies are inherently local and/or based on the relatively sparse black shale record. Here, we present new uranium (U) isotope data from carbonate rocks than span the mid-Proterozoic Eon. U-isotopes operate as a proxy for seafloor anoxia because the δ238U value of seawater is largely controlled by the size of the anoxic/euxinic U sink, which preferentially removes isotopically heavy 238U, leaving the oceans enriched in 235U. Our compilation of data from mid-Proterozoic successions reveals δ238U values similar to modern seawater (-0.39 ± 0.19 ‰ [1 s.d.] for the Gaoyuzhuang, Angmaat, El Mreiti, Vazante, and Turukhansk successions spanning 1.5 to 0.9 Ga). Given the potential for an isotopic offset between carbonate minerals and seawater of up to 0.3 ‰, we suggest that mid-Proterozoic seawater had a δ238U value generally between -0.4 and -0.7 ‰, which is lower than modern seawater, but higher than has been inferred for intervals of expanded anoxia elsewhere in Earth history. These results are consistent with recently published U-isotope data from the 1.36 Ga Velkerri Formation, and suggest that large portions of the seafloor may have been covered by at least weakly oxygenated waters during the mid-Proterozoic Eon. Uncertainty remains, however, because the isotopic effects of the non-euxinic anoxic sink are poorly constrained. Nonetheless, our data suggest that euxinia was spatially restricted and that suboxic to oxic conditions may have been more widespread than previously thought. Future work should seek to reconcile possible interpretations of our data with recent pO2 estimates to provide a more holistic view of mid-Proterozoic redox conditions.

Stable carbon isotopes of HCO3- in oil-field waters-implications for the origin of CO2

USGS Publications Warehouse

Carothers, W.W.; Kharaka, Y.K.

1980-01-01

The ??13C values of dissolved HCO3- in 75 water samples from 15 oil and gas fields (San Joaquin Valley, Calif., and the Houston-Galveston and Corpus Christi areas of Texas) were determined to study the sources of CO2 of the dissolved species and carbonate cements that modify the porosity and permeability of many petroleum reservoir rocks. The reservoir rocks are sandstones which range in age from Eocene through Miocene. The ??13C values of total HCO3- indicate that the carbon in the dissolved carbonate species and carbonate cements is mainly of organic origin. The range of ??13C values for the HCO3- of these waters is -20-28 per mil relative to PDB. This wide range of ??13C values is explained by three mechanisms. Microbiological degradation of organic matter appears to be the dominant process controlling the extremely low and high ??13C values of HCO3- in the shallow production zones where the subsurface temperatures are less than 80??C. The extremely low ??13C values (< -10 per mil) are obtained in waters where concentrations of SO42- are more than 25 mg/l and probably result from the degradation of organic acid anions by sulfate-reducing bacteria (SO42- + CH3COO- ??? 2HCO3- + HS-). The high ??13C values probably result from the degradation of these anions by methanogenic bacteria (CH3COO- + H2O ai HCO3- + CH4). Thermal decarboxylation of short-chain aliphatic acid anions (principally acetate) to produce CO2 and CH4 is probably the major source of CO2 for production zones with subsurface temperatures greater than 80??C. The ??13C values of HCO3- for waters from zones with temperatures greater than 100??C result from isotopic equilibration between CO2 and CH4. At these high temperatures, ??13C values of HCO3- decrease with increasing temperatures and decreasing concentrations of these acid anions. ?? 1980.

Effect of growth conditions and staining procedure upon the subsurface transport and attachment behaviors of a groundwater protist

USGS Publications Warehouse

Harvey, R.W.; Mayberry, N.; Kinner, N.E.; Metge, D.W.; Novarino, F.

2002-01-01

The transport and attachment behaviors of Spumella guttula (Kent), a nanoflagellate (protist) found in contaminated and uncontaminated aquifer sediments in Cape Cod, Mass., were assessed in flowthrough and static columns and in a field injection-and-recovery transport experiment involving an array of multilevel samplers. Transport of S. guttula harvested from low-nutrient (10 mg of dissolved organic carbon per liter), slightly acidic, granular (porous) growth media was compared to earlier observations involving nanoflagellates grown in a traditional high-nutrient liquid broth. In contrast to the highly retarded (retardation factor of ???3) subsurface transport previously reported for S. guttula, the peak concentration of porous-medium-grown S. guttula traveled concomitantly with that of a conservative (bromide) tracer. About one-third of the porous-medium-grown nanoflagellates added to the aquifer were transported at least 2.8 m downgradient, compared to only ???2% of the broth-grown nanoflagellates. Flowthrough column studies revealed that a vital (hydroethidine [HE]) staining procedure resulted in considerably less attachment (more transport) of S. guttula in aquifer sediments than did a staining-and-fixation procedure involving 4???,6???-diamidino-2-phenylindole (DAPI) and glutaraldehyde. The calculated collision efficiency (???10-2. for porous-medium-grown, DAPI-stained nanoflagellates) was comparable to that observed earlier for the indigenous community of unattached ground-water bacteria that serve as prey. The attachment of HE-labeled S. guttula onto aquifer sediment grains was independent of pH (over the range from pH 3 to 9) suggesting a primary attachment mechanism that may be fundamentally different from that of their prey bacteria, which exhibit sharp decreases in fractional attachment with increasing pH. The high degree of mobility of S. guttula in the aquifer sediments has important ecological implications for the protistan community within the temporally changing plume of organic contaminants in the Cape Cod aquifer.

Isolation of sulfate-reducing bacteria from the terrestrial deep subsurface and description of Desulfovibrio cavernae sp. nov.

PubMed

Sass, Henrik; Cypionka, Heribert

2004-09-01

Deep subsurface sandstones in the area of Berlin (Germany) located 600 to 1060 m below the surface were examined for the presence of viable microorganisms. The in situ temperatures at the sampling sites ranged from 37 to 45 degrees C. Investigations focussed on sulfate-reducing bacteria able to grow on methanol and triethylene glycol, which are added as chemicals to facilitate the long-term underground storage of natural gas. Seven strains were isolated from porewater brines in the porous sandstone. Three of them were obtained with methanol (strains H1M, H3M, and B1M), three strains with triethylene glycol (strains H1T, B1T, and B2T) and one strain with a mixture of lactate, acetate and butyrate (strain H1-13). Due to phenotypic properties six isolates could be identified as members of the genus Desulfovibrio, and strain B2T as a Desulfotomaculum. The salt tolerance and temperature range for growth indicated that the isolates originated from the indigenous deep subsurface sandstones. They grew in mineral media reflecting the in situ ionic composition of the different brines, which contained 1.5 to 190 g NaCl x l(-1) and high calcium and magnesium concentrations. The Desulfovibrio strains grew at temperatures between 20 and 50 degrees C, while the Desulfotomaculum strain was thermophilic and grew between 30 and 65 degrees C. The strains utilized a broad spectrum of electron donors and acceptors. They grew with carbon compounds like lactate, pyruvate, formate, n-alcohols (C1-C5), glycerol, ethylene glycol, malate, succinate, and fumarate. Some strains even utilized glucose as electron donor and carbon source. All strains were able to use sulfate, sulfite and nitrate as electron acceptors. Additionally, three Desulfovibrio strains reduced manganese oxide, the Desulfotomaculum strain reduced manganese oxide, iron oxide, and elemental sulfur. The 16S rRNA analysis revealed that the isolates belong to three different species. The strains H1T, H3M and B1M could be identified as Desulfovibrio indonesiensis, and strain B2T as Desulfotomaculum geothermicum. The other Desulfovibrio strains (H1M, H1-13, and B1T) showed identical 16S rDNA sequences and similarities as low as 93% to their closest relative, Desulfovibrio aminophilusT. Therefore, these isolates were assigned to a new species, Desulfovibrio cavernae sp. nov., with strain H1M as the type strain.

Growth of the acidophilic iron-sulfur bacterium Acidithiobacillus ferrooxidans under Mars-like geochemical conditions

NASA Astrophysics Data System (ADS)

Bauermeister, Anja; Rettberg, Petra; Flemming, Hans-Curt

2014-08-01

The question of life on Mars has been in focus of astrobiological research for several decades, and recent missions in orbit or on the surface of the planet are constantly expanding our knowledge on Martian geochemistry. For example, massive stratified deposits have been identified on Mars containing sulfate minerals and iron oxides, which suggest the existence of acidic aqueous conditions in the past, similar to acidic iron- and sulfur-rich environments on Earth. Acidophilic organisms thriving in such habitats could have been an integral part of a possibly widely extinct Martian ecosystem, but remains might possibly even exist today in protected subsurface niches. The chemolithoautotrophic strain Acidithiobacillus ferrooxidans was selected as a model organism to study the metabolic capacities of acidophilic iron-sulfur bacteria, especially regarding their ability to grow with in situ resources that could be expected on Mars. The experiments were not designed to accurately simulate Martian physical conditions (except when certain single parameters such as oxygen partial pressure were considered), but rather the geochemical environment that can be found on Mars. A. ferrooxidans could grow solely on the minerals contained in synthetic Mars regolith mixtures with no added nutrients, using either O2 as an external electron acceptor for iron oxidation, or H2 as an external electron donor for iron reduction, and thus might play important roles in the redox cycling of iron on Mars. Though the oxygen partial pressure of the Martian atmosphere at the surface was not sufficient for detectable iron oxidation and growth of A. ferrooxidans during short-term incubation (7 days), alternative chemical O2-generating processes in the subsurface might yield microhabitats enriched in oxygen, which principally are possible under such conditions. The bacteria might also contribute to the reductive dissolution of Fe3+-containing minerals like goethite and hematite, which are characterized by a high thermodynamic stability. Even in a desiccated environment, A. ferrooxidans survived for one week under simulated Martian shallow subsurface conditions (6 hPa, -20 °C, 0.13% O2) in the form of dried biofilms without loss of viability. Low temperature and low oxygen pressure were favorable to survival. Thus, the acidophilic iron-sulfur bacterium A. ferrooxidans may be considered a plausible candidate of a potential Martian food web based on its metabolic capacities. As an autotroph it would be located at the base of such a food web, providing organic carbon.

A Review of Phage Therapy against Bacterial Pathogens of Aquatic and Terrestrial Organisms.

PubMed

Doss, Janis; Culbertson, Kayla; Hahn, Delilah; Camacho, Joanna; Barekzi, Nazir

2017-03-18

Since the discovery of bacteriophage in the early 1900s, there have been numerous attempts to exploit their innate ability to kill bacteria. The purpose of this report is to review current findings and new developments in phage therapy with an emphasis on bacterial diseases of marine organisms, humans, and plants. The body of evidence includes data from studies investigating bacteriophage in marine and land environments as modern antimicrobial agents against harmful bacteria. The goal of this paper is to present an overview of the topic of phage therapy, the use of phage-derived protein therapy, and the hosts that bacteriophage are currently being used against, with an emphasis on the uses of bacteriophage against marine, human, animal and plant pathogens.

Microbial safety in space

NASA Astrophysics Data System (ADS)

Krooneman, Janneke; Harmsen, Hermie; Landini, Paolo; Zinn, Manfred; Munaut, Françoise; van der Meer, Walter; Beimfohr, Claudia; Reichert, Bas; Preuß, Andrea

2005-10-01

Microbial hygiene is important in our daily lives; preventing and combating microbial infections is increasingly important in society. In hospitals, strict monitoring and control is exercised for people and infrastructure alike. In modern buildings, air-conditioning system are screened for harmful bacteria such as Legionella. More recently, concerns about SARS (virus) and anthrax (bacteria) have added pressure on the scientific community to come up with adequate monitoring and control techniques to assure microbial hygiene. Additionally, the use of biotechnological recycling and cleaning processes for sustainability brings the need for reliable monitoring tools and preventive or riks-reducing strategies. In the manned space environment, similar problems need to be solved and efforts have already been made to study the behaviour of micro-organisms and microbial hygiene onboard space stations.

A really useful pathogen, Agrobacterium tumefaciens.

PubMed

Yuan, Ze-Chun; Williams, Mary

2012-10-01

Bacteria of the genus Agrobacterium are very useful and unusual plant pathogens. Through a rare inter-kingdom DNA transfer, the bacteria move some of their genes into their host's genome, thereby inducing the host cells to proliferate and produce opines, nutrients sources for the pathogen. Agrobacterium's ability to transfer DNA makes can be adapted to introduce other genes, such as those encoding useful traits, into plant genomes. The development of Agrobacterium as a tool to transform plants is a landmark event in modern plant biology. This lecture provides an introduction to Agrobacterium tumefaciens and related species, focusing on their modes of pathogenicity, their usefulness as tools for plant transformation, and their use as a model for the study of plant-pathogen interactions.

Continuous 'Passive' Registration of Non-Point Contaminant Loads Via Agricultural Subsurface Drain Tubes

NASA Astrophysics Data System (ADS)

Rozemeijer, J.; Jansen, S.; de Jonge, H.; Lindblad Vendelboe, A.

2014-12-01

Considering their crucial role in water and solute transport, enhanced monitoring and modeling of agricultural subsurface tube drain systems is important for adequate water quality management. For example, previous work in lowland agricultural catchments has shown that subsurface tube drain effluent contributed up to 80% of the annual discharge and 90-92% of the annual NO3 loads from agricultural fields towards the surface water. However, existing monitoring techniques for flow and contaminant loads from tube drains are expensive and labor-intensive. Therefore, despite the unambiguous relevance of this transport route, tube drain monitoring data are scarce. The presented study aimed developing a cheap, simple, and robust method to monitor loads from tube drains. We are now ready to introduce the Flowcap that can be attached to the outlet of tube drains and is capable of registering total flow, contaminant loads, and flow-averaged concentrations. The Flowcap builds on the existing SorbiCells, a modern passive sampling technique that measures average concentrations over longer periods of time (days to months) for various substances. By mounting SorbiCells in our Flowcap, a flow-proportional part of the drain effluent is sampled from the main stream. Laboratory testing yielded good linear relations (R-squared of 0.98) between drainage flow rates and sampling rates. The Flowcap was tested in practice for measuring NO3 loads from two agricultural fields and one glasshouse in the Netherlands. The Flowcap registers contaminant loads from tube drains without any need for housing, electricity, or maintenance. This enables large-scale monitoring of non-point contaminant loads via tube drains, which would facilitate the improvement of contaminant transport models and would yield valuable information for the selection and evaluation of mitigation options to improve water quality.

Genomic variation of subseafloor archaeal and bacterial populations from venting fluids at the Mid-Cayman Rise

NASA Astrophysics Data System (ADS)

Anderson, R. E.; Eren, A. M.; Stepanauskas, R.; Huber, J. A.; Reveillaud, J.

2015-12-01

Deep-sea hydrothermal vent systems serve as windows to a dynamic, gradient-dominated deep biosphere that is home to a wide diversity of archaea, bacteria, and viruses. Until recently the majority of these microbial lineages were uncultivated, resulting in a poor understanding of how the physical and geochemical context shapes microbial evolution in the deep subsurface. By comparing metagenomes, metatranscriptomes and single-cell genomes between geologically distinct vent fields, we can better understand the relationship between the environment and the evolution of subsurface microbial communities. An ideal setting in which to use this approach is the Mid-Cayman Rise, located on the world's deepest and slowest-spreading mid-ocean ridge, which hosts both the mafic-influenced Piccard and ultramafic-influenced Von Damm vent fields. Previous work has shown that Von Damm has higher taxonomic and metabolic diversity than Piccard, consistent with geochemical model expectations, and the fluids from all vents are enriched in hydrogen (Reveillaud et al., submitted). Mapping of both metagenomes and metatranscriptomes to a combined assembly showed very little overlap among the Von Damm samples, indicating substantial variability that is consistent with the diversity of potential metabolites in this ultramafic vent field. In contrast, the most consistently abundant and active lineage across the Piccard samples was Sulfurovum, a sulfur-oxidizing chemolithotroph that uses nitrate or oxygen as an electron acceptor. Moreover, analysis of point mutations within individual lineages suggested that Sulfurovumat Piccard is under strong selection, whereas microbial genomes at Von Damm were more variable. These results are consistent with the hypothesis that the subsurface environment at Piccard supports the emergence of a dominant lineage that is under strong selection pressure, whereas the more geochemically diverse microbial habitat at Von Damm creates a wider variety of stable ecological niches, facilitating higher diversity both within and between microbial lineages. By examining how the environment is imprinted into microbial genomes, we hope to gain insight into how subsurface microbial communities co-evolve with their environment in both the present and the deep past.

Tracing microbiota changes in yamahai-moto, the traditional Japanese sake starter.

PubMed

Koyanagi, Takashi; Nakagawa, Akira; Kiyohara, Masashi; Matsui, Hiroshi; Tsuji, Atsushi; Barla, Florin; Take, Harumi; Katsuyama, Yoko; Tokuda, Koji; Nakamura, Shizuo; Minami, Hiromichi; Enomoto, Toshiki; Katayama, Takane; Kumagai, Hidehiko

2016-01-01

Sake is made from steamed rice, malted rice, and water. Sake production begins with the preparation of a small-scale starter (moto); the quality of moto significantly influences the flavor and richness of sake. In the traditional starter, yamahai-moto, the growth of naturally occurring lactic acid bacteria represses the putrefactive micro-organisms, whereas in the modern starter, sokujo-moto, this is achieved by adding lactic acid. In this study, the successive change in bacterial flora of yamahai-moto was analyzed by pyrosequencing 16S ribosomal RNA genes. Lactobacillus was dominant throughout the process (93-98%). Nitrate-reducing bacteria that have been generally assumed to be the first colonizers of yamahai-moto were scarcely found in the early stage, but Lactobacillus acidipiscis dominated. Lactobacillus sakei drastically increased in the middle stage. This is the first report, though one case study, to show how the early stage microbiota in Japanese yamahai-moto is varyingly controlled without nitrate-reducing bacteria using next-generation sequencing.

Chemotrophic Microbial Mats and Their Potential for Preservation in the Rock Record

NASA Astrophysics Data System (ADS)

Bailey, Jake V.; Orphan, Victoria J.; Joye, Samantha B.; Corsetti, Frank A.

2009-11-01

Putative microbialites are commonly regarded to have formed in association with photosynthetic microorganisms, such as cyanobacteria. However, many modern microbial mat ecosystems are dominated by chemotrophic bacteria and archaea. Like phototrophs, filamentous sulfur-oxidizing bacteria form large mats at the sediment/water interface that can act to stabilize sediments, and their metabolic activities may mediate the formation of marine phosphorites. Similarly, bacteria and archaea associated with the anaerobic oxidation of methane (AOM) catalyze the precipitation of seafloor authigenic carbonates. When preserved, lipid biomarkers, isotopic signatures, body fossils, and lithological indicators of the local depositional environment may be used to identify chemotrophic mats in the rock record. The recognition of chemotrophic communities in the rock record has the potential to transform our understanding of ancient microbial ecologies, evolution, and geochemical conditions. Chemotrophic microbes on Earth occupy naturally occurring interfaces between oxidized and reduced chemical species and thus may provide a new set of search criteria to target life-detection efforts on other planets.

The Prehistory of Antibiotic Resistance.

PubMed

Perry, Julie; Waglechner, Nicholas; Wright, Gerard

2016-06-01

Antibiotic resistance is a global problem that is reaching crisis levels. The global collection of resistance genes in clinical and environmental samples is the antibiotic "resistome," and is subject to the selective pressure of human activity. The origin of many modern resistance genes in pathogens is likely environmental bacteria, including antibiotic producing organisms that have existed for millennia. Recent work has uncovered resistance in ancient permafrost, isolated caves, and in human specimens preserved for hundreds of years. Together with bioinformatic analyses on modern-day sequences, these studies predict an ancient origin of resistance that long precedes the use of antibiotics in the clinic. Understanding the history of antibiotic resistance is important in predicting its future evolution. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

Genetic and functional properties of uncultivated thermophilic crenarchaeotes from a subsurface gold mine as revealed by analysis of genome fragments.

PubMed

Nunoura, Takuro; Hirayama, Hisako; Takami, Hideto; Oida, Hanako; Nishi, Shinro; Shimamura, Shigeru; Suzuki, Yohey; Inagaki, Fumio; Takai, Ken; Nealson, Kenneth H; Horikoshi, Koki

2005-12-01

Within a phylum Crenarchaeota, only some members of the hyperthermophilic class Thermoprotei, have been cultivated and characterized. In this study, we have constructed a metagenomic library from a microbial mat formation in a subsurface hot water stream of the Hishikari gold mine, Japan, and sequenced genome fragments of two different phylogroups of uncultivated thermophilic Crenarchaeota: (i) hot water crenarchaeotic group (HWCG) I (41.2 kb), and (ii) HWCG III (49.3 kb). The genome fragment of HWCG I contained a 16S rRNA gene, two tRNA genes and 35 genes encoding proteins but no 23S rRNA gene. Among the genes encoding proteins, several genes for putative aerobic-type carbon monoxide dehydrogenase represented a potential clue with regard to the yet unknown metabolism of HWCG I Archaea. The genome fragment of HWCG III contained a 16S/23S rRNA operon and 44 genes encoding proteins. In the 23S rRNA gene, we detected a homing-endonuclease encoding a group I intron similar to those detected in hyperthermophilic Crenarchaeota and Bacteria, as well as eukaryotic organelles. The reconstructed phylogenetic tree based on the 23S rRNA gene sequence reinforced the intermediate phylogenetic affiliation of HWCG III bridging the hyperthermophilic and non-thermophilic uncultivated Crenarchaeota.

Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages

DOE PAGES

Hug, Laura A.; Thomas, Brian C.; Sharon, Itai; ...

2015-07-22

Nitrogen, sulfur and carbon fluxes in the terrestrial subsurface are determined by the intersecting activities of microbial community members, yet the organisms responsible are largely unknown. Metagenomic methods can identify organisms and functions, but genome recovery is often precluded by data complexity. To address this limitation, we developed subsampling assembly methods to re-construct high-quality draft genomes from complex samples. Here, we applied these methods to evaluate the interlinked roles of the most abundant organisms in biogeochemical cycling in the aquifer sediment. Community proteomics confirmed these activities. The eight most abundant organisms belong to novel lineages, and two represent phyla withmore » no previously sequenced genome. Four organisms are predicted to fix carbon via the Calvin Benson Bassham, Wood Ljungdahl or 3-hydroxyproprionate/4-hydroxybutarate pathways. The profiled organisms are involved in the network of denitrification, dissimilatory nitrate reduction to ammonia, ammonia oxidation and sulfate reduction/oxidation, and require substrates supplied by other community members. An ammonium-oxidizing Thaumarchaeote is the most abundant community member, despite low ammonium concentrations in the groundwater. Finally, this organism likely benefits from two other relatively abundant organisms capable of producing ammonium from nitrate, which is abundant in the groundwater. Overall, dominant members of the microbial community are interconnected through exchange of geochemical resources.« less

“Altiarchaeales”: Uncultivated Archaea from the Subsurface

PubMed Central

Probst, Alexander J.; Moissl-Eichinger, Christine

2015-01-01

Due to the limited cultivability of the vast majority of microorganisms, researchers have applied environmental genomics and other state-of-the-art technologies to gain insights into the biology of uncultivated Archaea and bacteria in their natural biotope. In this review, we summarize the scientific findings on a recently proposed order-level lineage of uncultivated Archaea called Altiarchaeales, which includes “Candidatus Altiarchaeum hamiconexum” as the most well-described representative. Ca. A. hamiconexum possesses a complex biology: thriving strictly anaerobically, this microorganism is capable of forming highly-pure biofilms, connecting the cells by extraordinary cell surface appendages (the “hami”) and has other highly unusual traits, such as a double-membrane-based cell wall. Indicated by genomic information from different biotopes, the Altiarchaeales seem to proliferate in deep, anoxic groundwater of Earth’s crust bearing a potentially very important function: carbon fixation. Although their net carbon fixation rate has not yet been determined, they appear as highly abundant organisms in their biotopes and may thus represent an important primary producer in the subsurface. In sum, the research over more than a decade on Ca. A. hamiconexum has revealed many interesting features of its lifestyle, its genomic information, metabolism and ultrastructure, making this archaeon one of the best-studied uncultivated Archaea in the literature. PMID:25984733

Effects of manure-application practices on curli production by Escherichia coli transported through soil

NASA Astrophysics Data System (ADS)

Truhlar, A. M.; Salvucci, A. E.; Siler, J. D.; Richards, B. K.; Geohring, L.; Walter, M. T.; Hay, A. G.

2014-12-01

The release of Escherichia coli into the environment from untreated manure can pose a threat to human health. Environmental survival of E. coli has been linked to extracellular fibers called curli. We investigated the effect of manure management (surface application followed by incorporation versus immediate incorporation) on the relative abundance of curli-producing E. coli in subsurface drainage effluent. Samples were collected from three dairy farms. The proportion of curli-producing E. coli in the manure storage facilities was uniform across the farms. However, the abundance of curli-producing E. coli was much greater (P < 0.05) in the tile drains of farms performing surface application of manure than in the tile drain of the farm that incorporated manure. This field result was corroborated by controlled soil column experiments; the abundance of curli-producing E. coli in soil column effluents was greater (P < 0.05) when manure was surface-applied than when it was incorporated. Our findings suggest selection pressures resulting from the different manure application methods affected curli production by E. coli isolates transported through soil. Given the importance of curli production in pathogenesis, this work highlights the effect that manure management strategies may have on pathogenesis-associated phenotypes of bacteria in agricultural subsurface runoff.

Riboflavin-mediated RDX transformation in the presence of Shewanella putrefaciens CN32 and lepidocrocite.

PubMed

Bae, Sungjun; Lee, Yoonhwa; Kwon, Man Jae; Lee, Woojin

2014-06-15

The potential of riboflavin for the reductive degradation of a cyclic nitramine, hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), was investigated in the presence of lepidocrocite and/or Shewanella putrefaciens CN32. RDX reduction by CN32 alone or CN32 with lepidocrocite was insignificant, while 110 μM RDX was completely reduced by CN32 with riboflavin in 78 h. The transformation products identified included nitroso metabolites, formaldehyde, and ammonium, indicating the ring cleavage of RDX. UV and visible light analysis revealed that riboflavin was microbially reduced by CN32, and that the reduced riboflavin was linked to the complete degradation of RDX. In the presence of both CN32 and lepidocrocite (γ-FeOOH), 100 μM-riboflavin increased the rate and extent of Fe(II) production as well as RDX reduction. An abiotic study also showed that Fe(II)-riboflavin complex, and Fe(II) adsorbed on lepidocrocite, reduced RDX by 48% and 21%, respectively. The findings in this study suggest that riboflavin-mediated RDX degradation pathways in subsurface environments are diverse and complex. However, riboflavin, either from bacteria or exogenous sources, can significantly increase RDX degradation. This will provide a sustainable clean-up option for explosive-contaminated subsurface environments. Copyright © 2014 Elsevier B.V. All rights reserved.

Microbially Mediated Kinetic Sulfur Isotope Fractionation: Reactive Transport Modeling Benchmark

NASA Astrophysics Data System (ADS)

Wanner, C.; Druhan, J. L.; Cheng, Y.; Amos, R. T.; Steefel, C. I.; Ajo Franklin, J. B.

2014-12-01

Microbially mediated sulfate reduction is a ubiquitous process in many subsurface systems. Isotopic fractionation is characteristic of this anaerobic process, since sulfate reducing bacteria (SRB) favor the reduction of the lighter sulfate isotopologue (S32O42-) over the heavier isotopologue (S34O42-). Detection of isotopic shifts have been utilized as a proxy for the onset of sulfate reduction in subsurface systems such as oil reservoirs and aquifers undergoing uranium bioremediation. Reactive transport modeling (RTM) of kinetic sulfur isotope fractionation has been applied to field and laboratory studies. These RTM approaches employ different mathematical formulations in the representation of kinetic sulfur isotope fractionation. In order to test the various formulations, we propose a benchmark problem set for the simulation of kinetic sulfur isotope fractionation during microbially mediated sulfate reduction. The benchmark problem set is comprised of four problem levels and is based on a recent laboratory column experimental study of sulfur isotope fractionation. Pertinent processes impacting sulfur isotopic composition such as microbial sulfate reduction and dispersion are included in the problem set. To date, participating RTM codes are: CRUNCHTOPE, TOUGHREACT, MIN3P and THE GEOCHEMIST'S WORKBENCH. Preliminary results from various codes show reasonable agreement for the problem levels simulating sulfur isotope fractionation in 1D.

Spatial Distribution of an Uranium-Respiring Betaproteobacterium at the Rifle, CO Field Research Site

PubMed Central

Koribanics, Nicole M.; Tuorto, Steven J.; Lopez-Chiaffarelli, Nora; McGuinness, Lora R.; Häggblom, Max M.; Williams, Kenneth H.; Long, Philip E.; Kerkhof, Lee J.

2015-01-01

The Department of Energy’s Integrated Field-Scale Subsurface Research Challenge Site (IFRC) at Rifle, Colorado was created to address the gaps in knowledge on the mechanisms and rates of U(VI) bioreduction in alluvial sediments. Previous studies at the Rifle IFRC have linked microbial processes to uranium immobilization during acetate amendment. Several key bacteria believed to be involved in radionuclide containment have been described; however, most of the evidence implicating uranium reduction with specific microbiota has been indirect. Here, we report on the cultivation of a microorganism from the Rifle IFRC that reduces uranium and appears to utilize it as a terminal electron acceptor for respiration with acetate as electron donor. Furthermore, this bacterium constitutes a significant proportion of the subsurface sediment community prior to biostimulation based on TRFLP profiling of 16S rRNA genes. 16S rRNA gene sequence analysis indicates that the microorganism is a betaproteobacterium with a high similarity to Burkholderia fungorum. This is, to our knowledge, the first report of a betaproteobacterium capable of uranium respiration. Our results indicate that this microorganism occurs commonly in alluvial sediments located between 3-6 m below ground surface at Rifle and may play a role in the initial reduction of uranium at the site. PMID:25874721

Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments

PubMed Central

Hernsdorf, Alex W; Amano, Yuki; Miyakawa, Kazuya; Ise, Kotaro; Suzuki, Yohey; Anantharaman, Karthik; Probst, Alexander; Burstein, David; Thomas, Brian C; Banfield, Jillian F

2017-01-01

Geological sequestration in deep underground repositories is the prevailing proposed route for radioactive waste disposal. After the disposal of radioactive waste in the subsurface, H2 may be produced by corrosion of steel and, ultimately, radionuclides will be exposed to the surrounding environment. To evaluate the potential for microbial activities to impact disposal systems, we explored the microbial community structure and metabolic functions of a sediment-hosted ecosystem at the Horonobe Underground Research Laboratory, Hokkaido, Japan. Overall, we found that the ecosystem hosted organisms from diverse lineages, including many from the phyla that lack isolated representatives. The majority of organisms can metabolize H2, often via oxidative [NiFe] hydrogenases or electron-bifurcating [FeFe] hydrogenases that enable ferredoxin-based pathways, including the ion motive Rnf complex. Many organisms implicated in H2 metabolism are also predicted to catalyze carbon, nitrogen, iron and sulfur transformations. Notably, iron-based metabolism is predicted in a novel lineage of Actinobacteria and in a putative methane-oxidizing ANME-2d archaeon. We infer an ecological model that links microorganisms to sediment-derived resources and predict potential impacts of microbial activity on H2 consumption and retardation of radionuclide migration. PMID:28350393

Changes in bacteria recoverable from subsurface volcanic rock samples during storage at 4{degrees}C

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haldeman, D.L.; Amy, P.S.; White, D.C.

1994-08-01

The abundance of viable microorganisms recovered from deep subsurface volcanic rock samples increased after rock perturbation and storage for 1 week at 4{degrees}C, while the diversity and evenness of recoverable heterotrophic bacterial communities generally decreased. One sample of each morphologically distinct colony type, recovered both before and after storage of U12n rock samples, was purified and characterized by fatty acid methyl ester (MIDI) and API rapid NFT strips. As determined by MIDI cluster analysis, the composition of the recoverable microbial communities changed with storage of rock samples; some groups of organisms were recovered only before, only after, or at bothmore » sample times. In general, the isolates recovered only after storage of rock samples had a greater ability to utilize the carbohydrates included in API test strips and had faster generation times than isolates recovered only on initial plating. The nutritional versatility and faster growth rates of organisms recovered in higher proportions after sample storage provide evidence that some microbial community changes may be due to the proliferation of a few bacterial types. However, because some new genera are recovered only after storage, the possibility also exists that dormant bacterial types are resuscitated during sample perturbation and storage. 30 refs., 1 fig., 5 tabs.« less

Spatial distribution of an uranium-respiring betaproteobacterium at the Rifle, CO field research site

DOE PAGES

Koribanics, Nicole M.; Tuorto, Steven J.; Lopez-Chiaffarelli, Nora; ...

2015-04-13

The Department of Energy’s Integrated Field-Scale Subsurface Research Challenge Site (IFRC) at Rifle, Colorado was created to address the gaps in knowledge on the mechanisms and rates of U(VI) bioreduction in alluvial sediments. Previous studies at the Rifle IFRC have linked microbial processes to uranium immobilization during acetate amendment. Several key bacteria believed to be involved in radionuclide containment have been described; however, most of the evidence implicating uranium reduction with specific microbiota has been indirect. Here, we report on the cultivation of a microorganism from the Rifle IFRC that reduces uranium and appears to utilize it as a terminalmore » electron acceptor for respiration with acetate as electron donor. Furthermore, this bacterium constitutes a significant proportion of the subsurface sediment community prior to biostimulation based on TRFLP profiling of 16S rRNA genes. 16S rRNA gene sequence analysis indicates that the microorganism is a betaproteobacterium with a high similarity to Burkholderia fungorum. This is, to our knowledge, the first report of a betaproteobacterium capable of uranium respiration. Our results indicate that this microorganism occurs commonly in alluvial sediments located between 3-6 m below ground surface at Rifle and may play a role in the initial reduction of uranium at the site.« less

Predominance of Viable Spore-Forming Piezophilic Bacteria in High-Pressure Enrichment Cultures from ~1.5 to 2.4 km-Deep Coal-Bearing Sediments below the Ocean Floor

PubMed Central

Fang, Jiasong; Kato, Chiaki; Runko, Gabriella M.; Nogi, Yuichi; Hori, Tomoyuki; Li, Jiangtao; Morono, Yuki; Inagaki, Fumio

2017-01-01

Phylogenetically diverse microorganisms have been observed in marine subsurface sediments down to ~2.5 km below the seafloor (kmbsf). However, very little is known about the pressure-adapted and/or pressure-loving microorganisms, the so called piezophiles, in the deep subseafloor biosphere, despite that pressure directly affects microbial physiology, metabolism, and biogeochemical processes of carbon and other elements in situ. In this study, we studied taxonomic compositions of microbial communities in high-pressure incubated sediment, obtained during the Integrated Ocean Drilling Program (IODP) Expedition 337 off the Shimokita Peninsula, Japan. Analysis of 16S rRNA gene-tagged sequences showed that members of spore-forming bacteria within Firmicutes and Actinobacteria were predominantly detected in all enrichment cultures from ~1.5 to 2.4 km-deep sediment samples, followed by members of Proteobacteria, Acidobacteria, and Bacteroidetes according to the sequence frequency. To further study the physiology of the deep subseafloor sedimentary piezophilic bacteria, we isolated and characterized two bacterial strains, 19R1-5 and 29R7-12, from 1.9 and 2.4 km-deep sediment samples, respectively. The isolates were both low G+C content, gram-positive, endospore-forming and facultative anaerobic piezophilic bacteria, closely related to Virgibacillus pantothenticus and Bacillus subtilis within the phylum Firmicutes, respectively. The optimal pressure and temperature conditions for growth were 20 MPa and 42°C for strain 19R1-5, and 10 MPa and 43°C for strain 29R7-12. Bacterial (endo)spores were observed in both the enrichment and pure cultures examined, suggesting that these piezophilic members were derived from microbial communities buried in the ~20 million-year-old coal-bearing sediments after the long-term survival as spores and that the deep biosphere may host more abundant gram-positive spore-forming bacteria and their spores than hitherto recognized. PMID:28220112

Predominance of Viable Spore-Forming Piezophilic Bacteria in High-Pressure Enrichment Cultures from ~1.5 to 2.4 km-Deep Coal-Bearing Sediments below the Ocean Floor.

PubMed

Fang, Jiasong; Kato, Chiaki; Runko, Gabriella M; Nogi, Yuichi; Hori, Tomoyuki; Li, Jiangtao; Morono, Yuki; Inagaki, Fumio

2017-01-01

Phylogenetically diverse microorganisms have been observed in marine subsurface sediments down to ~2.5 km below the seafloor (kmbsf). However, very little is known about the pressure-adapted and/or pressure-loving microorganisms, the so called piezophiles, in the deep subseafloor biosphere, despite that pressure directly affects microbial physiology, metabolism, and biogeochemical processes of carbon and other elements in situ . In this study, we studied taxonomic compositions of microbial communities in high-pressure incubated sediment, obtained during the Integrated Ocean Drilling Program (IODP) Expedition 337 off the Shimokita Peninsula, Japan. Analysis of 16S rRNA gene-tagged sequences showed that members of spore-forming bacteria within Firmicutes and Actinobacteria were predominantly detected in all enrichment cultures from ~1.5 to 2.4 km-deep sediment samples, followed by members of Proteobacteria, Acidobacteria, and Bacteroidetes according to the sequence frequency. To further study the physiology of the deep subseafloor sedimentary piezophilic bacteria, we isolated and characterized two bacterial strains, 19R1-5 and 29R7-12, from 1.9 and 2.4 km-deep sediment samples, respectively. The isolates were both low G+C content, gram-positive, endospore-forming and facultative anaerobic piezophilic bacteria, closely related to Virgibacillus pantothenticus and Bacillus subtilis within the phylum Firmicutes, respectively. The optimal pressure and temperature conditions for growth were 20 MPa and 42°C for strain 19R1-5, and 10 MPa and 43°C for strain 29R7-12. Bacterial (endo)spores were observed in both the enrichment and pure cultures examined, suggesting that these piezophilic members were derived from microbial communities buried in the ~20 million-year-old coal-bearing sediments after the long-term survival as spores and that the deep biosphere may host more abundant gram-positive spore-forming bacteria and their spores than hitherto recognized.

Significant Association between Sulfate-Reducing Bacteria and Uranium-Reducing Microbial Communities as Revealed by a Combined Massively Parallel Sequencing-Indicator Species Approach▿ †

PubMed Central

Cardenas, Erick; Wu, Wei-Min; Leigh, Mary Beth; Carley, Jack; Carroll, Sue; Gentry, Terry; Luo, Jian; Watson, David; Gu, Baohua; Ginder-Vogel, Matthew; Kitanidis, Peter K.; Jardine, Philip M.; Zhou, Jizhong; Criddle, Craig S.; Marsh, Terence L.; Tiedje, James M.

2010-01-01

Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 μM and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared. PMID:20729318

Significant association between sulfate-reducing bacteria and uranium-reducing microbial communities as revealed by a combined massively parallel sequencing-indicator species approach.

PubMed

Cardenas, Erick; Wu, Wei-Min; Leigh, Mary Beth; Carley, Jack; Carroll, Sue; Gentry, Terry; Luo, Jian; Watson, David; Gu, Baohua; Ginder-Vogel, Matthew; Kitanidis, Peter K; Jardine, Philip M; Zhou, Jizhong; Criddle, Craig S; Marsh, Terence L; Tiedje, James M

2010-10-01

Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 μM and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared.

The effect of bicarbonate on the microbial dissolution of autunite mineral in the presence of gram-positive bacteria.

PubMed

Sepulveda-Medina, Paola M; Katsenovich, Yelena P; Wellman, Dawn M; Lagos, Leonel E

2015-06-01

Bacteria are key players in the processes that govern fate and transport of contaminants. The uranium release from Na and Ca-autunite by Arthrobacter oxydans strain G968 was evaluated in the presence of bicarbonate ions. This bacterium was previously isolated from Hanford Site soil and in earlier prescreening tests demonstrated low tolerance to U(VI) toxicity compared to other A. oxydans isolates. Experiments were conducted using glass serum bottles as mixed bioreactors and sterile 6-well cell culture plates with inserts separating bacteria cells from mineral solids. Reactors containing phosphorus-limiting media were amended with bicarbonate ranging between 0 and 10 mM and meta-autunite solids to provide a U(VI) concentration of 4.4 mmol/L. Results showed that in the presence of bicarbonate, A. oxydans G968 was able to enhance the release of U(VI) from Na and Ca autunite at the same capacity as other A. oxydans isolates with relatively high tolerance to U(VI). The effect of bacterial strains on autunite dissolution decreases as the concentration of bicarbonate increases. The results illustrate that direct interaction between the bacteria and the mineral is not necessary to result in U(VI) biorelease from autunite. The formation of secondary calcium-phosphate mineral phases on the surface of the mineral during the dissolution can ultimately reduce the natural autunite mineral contact area, which bacterial cells can access. This thereby reduces the concentration of uranium released into the solution. This study provides a better understanding of the interactions between meta-autunite and microbes in conditions mimicking arid and semiarid subsurface environments of western U.S. Copyright © 2015 Elsevier Ltd. All rights reserved.

Geomicrobiology of High-Level Nuclear Waste-Contaminated Vadose Sediments at the Hanford Site, Washington State

PubMed Central

Fredrickson, James K.; Zachara, John M.; Balkwill, David L.; Kennedy, David; Li, Shu-mei W.; Kostandarithes, Heather M.; Daly, Michael J.; Romine, Margaret F.; Brockman, Fred J.

2004-01-01

Sediments from a high-level nuclear waste plume were collected as part of investigations to evaluate the potential fate and migration of contaminants in the subsurface. The plume originated from a leak that occurred in 1962 from a waste tank consisting of high concentrations of alkali, nitrate, aluminate, Cr(VI), 137Cs, and 99Tc. Investigations were initiated to determine the distribution of viable microorganisms in the vadose sediment samples, probe the phylogeny of cultivated and uncultivated members, and evaluate the ability of the cultivated organisms to survive acute doses of ionizing radiation. The populations of viable aerobic heterotrophic bacteria were generally low, from below detection to ∼104 CFU g−1, but viable microorganisms were recovered from 11 of 16 samples, including several of the most radioactive ones (e.g., >10 μCi of 137Cs/g). The isolates from the contaminated sediments and clone libraries from sediment DNA extracts were dominated by members related to known gram-positive bacteria. Gram-positive bacteria most closely related to Arthrobacter species were the most common isolates among all samples, but other phyla high in G+C content were also represented, including Rhodococcus and Nocardia. Two isolates from the second-most radioactive sample (>20 μCi of 137Cs g−1) were closely related to Deinococcus radiodurans and were able to survive acute doses of ionizing radiation approaching 20 kGy. Many of the gram-positive isolates were resistant to lower levels of gamma radiation. These results demonstrate that gram-positive bacteria, predominantly from phyla high in G+C content, are indigenous to Hanford vadose sediments and that some are effective at surviving the extreme physical and chemical stress associated with radioactive waste. PMID:15240306

Geochemical controls on microbial nitrate-dependent U(IV) oxidation

USGS Publications Warehouse

Senko, John M.; Suflita, Joseph M.; Krumholz, Lee R.

2005-01-01

After reductive immobilization of uranium, the element may be oxidized and remobilized in the presence of nitrate by the activity of dissimilatory nitrate-reducing bacteria. We examined controls on microbially mediated nitrate-dependent U(IV) oxidation in landfill leachate-impacted subsurface sediments. Nitrate-dependent U(IV)-oxidizing bacteria were at least two orders of magnitude less numerous in these sediments than glucose- or Fe(II)-oxidizing nitrate-reducing bacteria and grew more slowly than the latter organisms, suggesting that U(IV) is ultimately oxidized by Fe(III) produced by nitrate-dependent Fe(II)-oxidizing bacteria or by oxidation of Fe(II) by nitrite that accumulates during organotrophic dissimilatory nitrate reduction. We examined the effect of nitrate and reductant concentration on nitrate-dependent U(IV) oxidation in sediment incubations and used the initial reductive capacity (RDC = [reducing equivalents] - [oxidizing equivalents]) of the incubations as a unified measurement of the nitrate or reductant concentration. When we lowered the RDC with progressively higher nitrate concentrations, we observed a corresponding increase in the extent of U(IV) oxidation, but did not observe this relationship between RDC and U(IV) oxidation rate, especially when RDC > 0, suggesting that nitrate concentration strongly controls the extent, but not the rate of nitrate-dependent U(IV) oxidation. On the other hand, when we raised the RDC in sediment incubations with progressively higher reductant (acetate, sulfide, soluble Fe(II), or FeS) concentrations, we observed progressively lower extents and rates of nitrate-dependent U(IV) oxidation. Acetate was a relatively poor inhibitor of nitrate-dependent U(IV) oxidation, while Fe(II) was the most effective inhibitor. Based on these results, we propose that it may be possible to predict the stability of U(IV) in a bioremediated aquifer based on the geochemical characteristics of that aquifer.

The Effect of Bicarbonate on the Microbial Dissolution of Autunite Mineral in the Presence of Gram-Positive Bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sepulveda-Medina, Paola; Katsenovich, Yelena; Wellman, Dawn M.

Bacteria are key players in the processes that govern fate and transport of contaminants. The uranium release from Na and Ca-autunite by Arthrobacter oxydans strain G968 was evaluated in the presence of bicarbonate ions. This bacterium was previously isolated from Hanford Site soil and in earlier prescreening tests demonstrated low tolerance to U(VI) toxicity compared to other A.oxydans isolates. Experiments were conducted using glass serum bottles as mixed bioreactors and sterile 6-well cell culture plates with inserts separating bacteria cells from mineral solids. Reactors containing phosphorus-limiting media were amended with bicarbonate ranging between 0-10 mM and metaautunite solids to providemore » a U(VI) concentration of 4.4 mmol/L. Results showed that in the presence of bicarbonate, A.oxydans G968 was able to enhance the release of U(VI) from Na and Ca autunite at the same capacity as other A.oxydans isolates with relatively high tolerance to U(VI). The effect of bacterial strains on autunite dissolution decreases as the concentration of bicarbonate increases. The results illustrate that direct interaction between the bacteria and the mineral is not necessary to result in U (VI) biorelease from autunite. The formation of secondary calcium-phosphate mineral phases on the surface of the mineral during the dissolution can ultimately reduce the natural autunite mineral contact area, which bacterial cells can access. This thereby reduces the concentration of uranium released into the solution. This study provides a better understanding of the interactions between meta-autunite and microbes in conditions mimicking arid and semiarid subsurface environments of western U.S.« less

Subsurface Density Structure of Taurus Littrow Valley Using Apollo 17 Gravity Data

NASA Astrophysics Data System (ADS)

Urbancic, N.; Ghent, R. R.; Johnson, C.; Stanley, S.; Hatch, D.; Carroll, K. A.; Williamson, M. C.; Garry, W. B.; Talwani, M.

2016-12-01

The Traverse Gravimeter Experiment (TGE) from the Apollo 17 mission was the first and only successful gravity survey on the surface of the Moon, revealing the local gravity field at Taurus Littrow Valley (TLV). Satellite surveys are resolution-limited due to their altitudes, making the TGE dataset a novel tool to probe the near-surface, fine-scale (<1 km) subsurface density structure of the Moon. TLV is hypothesized to be a basalt-filled graben oriented radial to Serenitatis basin. Talwani et al. [Apollo 17 Preliminary Science Report, 13 (1973)] used 2D correction and modelling techniques to derive a 1 km thickness for the subsurface basalt, assuming a rectangular geometry and densities derived from Apollo samples. We used modern 3D correction and modelling techniques and recent high-resolution Lunar Reconnaisance Orbiter topographic and image datasets to reinvestigate the subsurface structure of TLV, assuming a trapezoidal geometry for the valley. Updated topographic maps led to significant improvements in the accuracy of free-air, Bouguer and terrain corrections applied to the data. To determine the underlying geometry for TLV, we tested a range of possible thicknesses (T), dips (θ) and positions for the graben fill. We found that the thickness and position used by Talwani et al. represent the best fit to the data, but with walls that dip 30°. From sensitivity analyses we quantified the effect that different noise levels have on determining the correct model parameters. We found that less than 4 mgal noise in the gravity measurements is required to determine the valley position to within 1 km. At the noise level from the TGE data of ˜3.1 mgal, for an input model with θ=90° and a T=1 km, there will be a range in model dips and thicknesses, with θ=45-90° and T=0.9-1.1 km. Even for noise levels of 1 mgal, the range in parameters is θ=72-90° and T=0.95-1.05 km. These noise constraints are crucial for informing the design of future lunar gravimetry experiments.

Biomarkers: d13C and d15N Distribution Tightly Coupled to Nutrient Dynamics and Viral Lysing in a Microbial Mat From Death Valley, California

NASA Astrophysics Data System (ADS)

Hewson, I.; Archer, R.; Mahaffey, C.; Scott, J.; Tsapin, A.

2002-12-01

Extrapolations into ancient biomes make many assumptions and inferences regarding life modes and environmental habitat. While definition of a stromatolite as an extinct microbial biome by petrographic analysis is promising, Life interacts with is environment, actively manipulating energy flow across chemical disequilibria gradients, harvesting energy crucial for physiological maintenance and reproduction. Such structuring of communities in turn, leaves specific chemical/isotopic imprints related to physiological processes of prokaryotic communities specific to each oxidation/redox horizon. We examine stable isotopic d13C signals (d13C and d15N) as potential biomarkers reflecting bacterial physiology and microbial community nutrient-energy dynamics. While isotopes may reveal ancient chemical structuring of microbial mats, we also turn to invoking viral lysing of bacterial hosts in nutrient cycling within modern extreme environments as well as ancient stromatic structures of early Earth. Our records of d13C indicate extreme enrichment(-12%) for Corg in our extant mat due to CO2 limitation across a hypersaline diffusive barrier at the mat's surface. d15N is lowest at the mat's surface (indicating N2- fixation) where nitrogen- fixing cyanobacteria Microcoleus sp. are present . Viruses are extremely abundant in the microbial mat, exceeding bacterial abundances by a factor of ten. The ratio of viruses to bacteria was very high (VBR = 39 ñ 10) compared with abundances in marine sediments. Distribution of viruses closely follows distribution of bacteria, suggesting bacteria as primary hosts. The ratio of viruses to bacteria is inversely correlated to the concentration of organic C suggesting virus abundance is responsive to host substrate availability. High ratios of viruses to bacteria in mid-mat horizons (2.5 - 3.7 cm) above increasing levels of d13C in deeper horizons, coupled with a lack of increase in bacteria, suggests that viral lysis contributes to significant downward organic C (polysaccaride exudates) transport within the mat. Subsequent accumulation of d13C as well as heavier d15N in deeper sediment(denitrification)horizons elucidates tight nutrient coupling between evaporite substrate, nitrogen fixing primary producers and downcore zones of active denitrification and sulphate reduction. Discrepencies between d13C of ancient stromatolites (in line with C-3 photosynthetic pathways) and modern analogues (Badwater, CA) suggest a migration of microbial mats towards more extreme environments through time. A methodology for isotopically testing environmental and physiological responses in the geological record is presented here.

Remediation of TCE-contaminated groundwater using nanocatalyst and bacteria.

PubMed

Kang, Ser Ku; Seo, Hyunhee; Sun, Eunyoung; Kim, Inseon; Roh, Yul

2011-08-01

The objective of this study was to develop and evaluate the remediation of trichloroethene (TCE)-contaminated groundwater using both a nanocatalyst (bio-Zn-magnetite) and bacterium (similar to Clostridium quinii) in anoxic environments. Of the 7 nanocatalysts tested, bio-Zn-magnetite showed the highest TCE dechlorination efficiency, with an average of ca. 90% within 8 days in a batch experiment. The column tests confirmed that the application of bio-Zn-magnetite in combination with the bacterium achieved high degradation efficiency (ca. 90%) of TCE within 5 days compared to the nanocatalyst only, which degraded only 30% of the TCE. These results suggest that the application of a nanocatalyst and the bacterium have potential for the remediation of TCE-contaminated groundwater in subsurface environments.

Mathematical Modelling of Bacterial Populations in Bio-remediation Processes

NASA Astrophysics Data System (ADS)

Vasiliadou, Ioanna A.; Vayenas, Dimitris V.; Chrysikopoulos, Constantinos V.

2011-09-01

An understanding of bacterial behaviour concerns many field applications, such as the enhancement of water, wastewater and subsurface bio-remediation, the prevention of environmental pollution and the protection of human health. Numerous microorganisms have been identified to be able to degrade chemical pollutants, thus, a variety of bacteria are known that can be used in bio-remediation processes. In this study the development of mathematical models capable of describing bacterial behaviour considered in bio-augmentation plans, such as bacterial growth, consumption of nutrients, removal of pollutants, bacterial transport and attachment in porous media, is presented. The mathematical models may be used as a guide in designing and assessing the conditions under which areas contaminated with pollutants can be better remediated.

Strain of alcaligenes latus bacteria used for the decomposition of polychlorinated biphenyls

DOEpatents

Dyadischev, Nikolai Romanovich; Zharikov, Gennady Alekseevich; Kapranov, Vladimir Vladimirovich

2001-09-11

Alcaligenes latus bacterial strain TXD-13 VKPM B 75-05 is capable of degrading polychlorinated biphenyls (PCBs). The strain may be employed to detoxicate environment media and PCB-containing industrial waste. To produce biomass, the strain is incubated on media which contain carbon sources, nitrogen sources and mineral salts. The strain is cultivated by a subsurface method up to a titer from 6.0.multidot.10.sup.8 to 2.0.times.10.sup.9 cells per cu cm. The produced biomass is used for degrading PCBs in concentrations from 10.sup.7 to 10.sup.8 cells per cu cm. The strain ensures from 35 to 50% reduction in PCB content in soil and water.

Microbial Life Under Extreme Energy Limitation

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.; Jorgensen, Bo Barker

2013-01-01

A great number of the bacteria and archaea on Earth are found in subsurface environments in a physiological state that is poorly represented or explained by laboratory cultures. Microbial cells in these very stable and oligotrophic settings catabolize 104- to 106-fold more slowly than model organisms in nutrient-rich cultures, turn over biomass on timescales of centuries to millennia rather than hours to days, and subsist with energy fluxes that are 1,000-fold lower than the typical culture-based estimates of maintenance requirements. To reconcile this disparate state of being with our knowledge of microbial physiology will require a revised understanding of microbial energy requirements, including identifying the factors that comprise true basal maintenance and the adaptations that might serve to minimize these factors.

In situ thermally enhanced biodegradation of petroleum fuel hydrocarbons and halogenated organic solvents

DOEpatents

Taylor, Robert T.; Jackson, Kenneth J.; Duba, Alfred G.; Chen, Ching-I

1998-01-01

An in situ thermally enhanced microbial remediation strategy and a method for the biodegradation of toxic petroleum fuel hydrocarbon and halogenated organic solvent contaminants. The method utilizes nonpathogenic, thermophilic bacteria for the thermal biodegradation of toxic and carcinogenic contaminants, such as benzene, toluene, ethylbenzene and xylenes, from fuel leaks and the chlorinated ethenes, such as trichloroethylene, chlorinated ethanes, such as 1,1,1-trichloroethane, and chlorinated methanes, such as chloroform, from past solvent cleaning practices. The method relies on and takes advantage of the pre-existing heated conditions and the array of delivery/recovery wells that are created and in place following primary subsurface contaminant volatilization efforts via thermal approaches, such as dynamic underground steam-electrical heating.

In situ thermally enhanced biodegradation of petroleum fuel hydrocarbons and halogenated organic solvents

DOEpatents

Taylor, R.T.; Jackson, K.J.; Duba, A.G.; Chen, C.I.

1998-05-19

An in situ thermally enhanced microbial remediation strategy and a method for the biodegradation of toxic petroleum fuel hydrocarbon and halogenated organic solvent contaminants are described. The method utilizes nonpathogenic, thermophilic bacteria for the thermal biodegradation of toxic and carcinogenic contaminants, such as benzene, toluene, ethylbenzene and xylenes, from fuel leaks and the chlorinated ethenes, such as trichloroethylene, chlorinated ethanes, such as 1,1,1-trichloroethane, and chlorinated methanes, such as chloroform, from past solvent cleaning practices. The method relies on and takes advantage of the pre-existing heated conditions and the array of delivery/recovery wells that are created and in place following primary subsurface contaminant volatilization efforts via thermal approaches, such as dynamic underground steam-electrical heating. 21 figs.

Genetic Analysis of Stress Responses in Soil Bacteria for Enhanced Bioremediation of Mixed Contaminants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wong, Kwong-Kwok

In order to realize the full potential of bioremediation, an understanding of microbial community and individual bacterial responses to the stresses encountered at contaminated sites is needed. Knowledge about genetic responses of soil and subsurface bacteria to environmental stresses, which include low nutrients, low oxygen, and mixed pollutants, will allow extrapolation of basic principles to field applications, either using indigenous bacteria or genetically engineered microorganisms. Defining bacterial responses to those stresses presents an opportunity for improving bioremediation strategies, both with indigenous populations and genetically-engineered microbes, and should contribute to environmental management and restoration actions that would reduce the cost andmore » time required to achieve OEM's clean up goals. Stress-inducible genes identified in this project can be used as molecular probes for monitoring performance of indigenous bacteria as well as the effectiveness of bioremediation strategies being employed. Knowledge of survival and catabolic plasmid stability of indigenous bacteria will be needed for devising the most effective bioremediation strategy. In addition, stress-inducible regulatory elements identified in this project will be useful for creating genetically-engineered microorganisms which are able to degrade hazardous wastes under stress conditions at contaminated sites. One of the model organisms, Deinococcus radiodurans, is a stress-resistant bacterium. Thus, in addition to serving as a model for gene regulation in Gram-positive organisms, it may have specific application at aerobic DOE sites where combinations of contaminants produce a particularly stressful environment. Similarly, the use of Sphingomonas F199, isolated from a depth of 407 m at the Savannah River site (Fredrickson et al., 1991), may have relevance to deep subsurface bioremediation applications, where indigenous or engineered microorganisms adapted to the that environment are needed. In addition, F199 contains aromatic oxygenases that are relevant to degradation of contaminants at that site and is representative of a large class of similar organisms from Savannah River Identification of the genes responsive to different stresses encountered at contaminated sites will provide a basic understanding of stress responses in soil bacteria and can lead to improved strategies for bioremediation. Enhanced in situ removal of hazardous wastes by stimulating growth of indigenous bacteria with nutrients or electron acceptors such as oxygen has been demonstrated. However, how much and how often to apply these supplements has largely been determined empirically. As a result, a controlled, reproducible, and properly managed degradation of pollutants in the environment is difficult to achieve. Genes inducible by low nutrient and low oxygen conditions can serve as markers for determining the minimal amount of supplements needed. The disappearance and reappearance of such stress responses will determine how much and when nutrients and oxygen are needed to be applied or reapplied. Similar applications of stress-inducible markers are already being applied in bacterial cultures in solution (Selifonova and Eaton, 1996). Stress responses induced by pollutants also have potential use as a biological index for the performance of indigenous bacteria during bioremediation as well as a microbiological risk assessment index for environmental pollutants. For instance, measurement of the stress responses of contaminant-degrading microorganisms would provide information complementary to measurement of enzymatic activity. This more complete picture of the physiological state of the desired organisms can be used to predict their performance. Finally, prior knowledge of the stress responses of competing bacteria could be used to predict their environmental competitiveness. Promoters from stress inducible genes will facilitate the construction of genetically engineered microorganisms in which the expression of the catabolic genes is uncoupled from both microbial growth and the utilization of the pollutant as the carbon source. The application of genetically engineered organisms in bioremediation requires the design of gene expression systems that function under environmental conditions and are cost effective. The promoter, the genetic regulatory element that directs the use of the gene, plays the central role in gene expression systems. The ideal promoter for environmental applications should possess two qualities: (1) it does not require the addition of exogenous compounds for activation, and (2) it is active under nutrient-limited conditions and not dependent on cell growth for activity. Promoters that are expressed constitutively meet the first quality. However, such promoters usually require active cell growth for expression and thus incur the increased cost of constant nutrient addition.« less

Hyporheic flow and transport processes: mechanisms, models, and biogeochemical implications

USGS Publications Warehouse

Boano, Fulvio; Harvey, Judson W.; Marion, Andrea; Packman, Aaron I.; Revelli, Roberto; Ridolfi, Luca; Anders, Wörman

2014-01-01

Fifty years of hyporheic zone research have shown the important role played by the hyporheic zone as an interface between groundwater and surface waters. However, it is only in the last two decades that what began as an empirical science has become a mechanistic science devoted to modeling studies of the complex fluid dynamical and biogeochemical mechanisms occurring in the hyporheic zone. These efforts have led to the picture of surface-subsurface water interactions as regulators of the form and function of fluvial ecosystems. Rather than being isolated systems, surface water bodies continuously interact with the subsurface. Exploration of hyporheic zone processes has led to a new appreciation of their wide reaching consequences for water quality and stream ecology. Modern research aims toward a unified approach, in which processes occurring in the hyporheic zone are key elements for the appreciation, management, and restoration of the whole river environment. In this unifying context, this review summarizes results from modeling studies and field observations about flow and transport processes in the hyporheic zone and describes the theories proposed in hydrology and fluid dynamics developed to quantitatively model and predict the hyporheic transport of water, heat, and dissolved and suspended compounds from sediment grain scale up to the watershed scale. The implications of these processes for stream biogeochemistry and ecology are also discussed."

Subsurface Structure Interpretation Beneath of Mt. Pandan Based on Gravity Data

NASA Astrophysics Data System (ADS)

Santoso, D.; Wahyudi, E. J.; Alawiyah, S.; Nugraha, A. D.; Widiyantoro, S.; Kadir, W. G. A.; Supendi, P.; Wiyono, S.; Zulkafriza

2017-04-01

Mt. Pandan is one of the volcano that state as dormant volcano. On the other hand, Smyth et al. (2008) defined that Mt. Pandan is an active volcano. This volcano is apart a volcanic chain in Java island which is trending east-west along the island. This volcanic chain known as present day volcanic arc. Mt. Wilis is located in the south and it relatively much bigger compare to Mt. Pandan. There were earthquakes activity experienced in the surrounding Mt. Pandan area in the past several years. This event is interesting, because Mt. Pandan is not classify as the active volcano according to the list of volcanoes in Indonesia. On the otherhand Smyth et. al. (2008) mentioned that G. Pandan as modern volcanic which is located in Kendeng Zone of East Java. Gravity measurement around Mt. Pandan area was done in order to understand subsurface structure of Mt. Pandan. Gravity interpretation results shows that there is a low density structure beneath Mt. Pandan. It could be interpreted as existing of magma body below the surface. Some indication of submagmatic activities were found as hot spring and warm ground. Therefore it could be concluded that there is a possibility of magmatic activity below the Mt. Pandan.

Application of Geodetic Techniques for Antenna Positioning in a Ground Penetrating Radar Method

NASA Astrophysics Data System (ADS)

Mazurkiewicz, Ewelina; Ortyl, Łukasz; Karczewski, Jerzy

2018-03-01

The accuracy of determining the location of detectable subsurface objects is related to the accuracy of the position of georadar traces in a given profile, which in turn depends on the precise assessment of the distance covered by an antenna. During georadar measurements the distance covered by an antenna can be determined with a variety of methods. Recording traces at fixed time intervals is the simplest of them. A method which allows for more precise location of georadar traces is recording them at fixed distance intervals, which can be performed with the use of distance triggers (such as a measuring wheel or a hip chain). The search for methods eliminating these discrepancies can be based on the measurement of spatial coordinates of georadar traces conducted with the use of modern geodetic techniques for 3-D location. These techniques include above all a GNSS satellite system and electronic tachymeters. Application of the above mentioned methods increases the accuracy of space location of georadar traces. The article presents the results of georadar measurements performed with the use of geodetic techniques in the test area of Mydlniki in Krakow. A satellite receiver Leica system 1200 and a electronic tachymeter Leica 1102 TCRA were integrated with the georadar equipment. The accuracy of locating chosen subsurface structures was compared.

Hyporheic flow and transport processes: Mechanisms, models, and biogeochemical implications

NASA Astrophysics Data System (ADS)

Boano, F.; Harvey, J. W.; Marion, A.; Packman, A. I.; Revelli, R.; Ridolfi, L.; Wörman, A.

2014-12-01

Fifty years of hyporheic zone research have shown the important role played by the hyporheic zone as an interface between groundwater and surface waters. However, it is only in the last two decades that what began as an empirical science has become a mechanistic science devoted to modeling studies of the complex fluid dynamical and biogeochemical mechanisms occurring in the hyporheic zone. These efforts have led to the picture of surface-subsurface water interactions as regulators of the form and function of fluvial ecosystems. Rather than being isolated systems, surface water bodies continuously interact with the subsurface. Exploration of hyporheic zone processes has led to a new appreciation of their wide reaching consequences for water quality and stream ecology. Modern research aims toward a unified approach, in which processes occurring in the hyporheic zone are key elements for the appreciation, management, and restoration of the whole river environment. In this unifying context, this review summarizes results from modeling studies and field observations about flow and transport processes in the hyporheic zone and describes the theories proposed in hydrology and fluid dynamics developed to quantitatively model and predict the hyporheic transport of water, heat, and dissolved and suspended compounds from sediment grain scale up to the watershed scale. The implications of these processes for stream biogeochemistry and ecology are also discussed.

Effective Detection of Sub-Surface Archeological Features from Laser Scanning Point Clouds and Imagery Data

NASA Astrophysics Data System (ADS)

Fryskowska, A.; Kedzierski, M.; Walczykowski, P.; Wierzbicki, D.; Delis, P.; Lada, A.

2017-08-01

The archaeological heritage is non-renewable, and any invasive research or other actions leading to the intervention of mechanical or chemical into the ground lead to the destruction of the archaeological site in whole or in part. For this reason, modern archeology is looking for alternative methods of non-destructive and non-invasive methods of new objects identification. The concept of aerial archeology is relation between the presence of the archaeological site in the particular localization, and the phenomena that in the same place can be observed on the terrain surface form airborne platform. One of the most appreciated, moreover, extremely precise, methods of such measurements is airborne laser scanning. In research airborne laser scanning point cloud with a density of 5 points/sq. m was used. Additionally unmanned aerial vehicle imagery data was acquired. Test area is located in central Europe. The preliminary verification of potentially microstructures localization was the creation of digital terrain and surface models. These models gave an information about the differences in elevation, as well as regular shapes and sizes that can be related to the former settlement/sub-surface feature. The paper presents the results of the detection of potentially sub-surface microstructure fields in the forestry area.

Organic waste impact of capture-based Atlantic bluefin tuna aquaculture at an exposed site in the Mediterranean Sea

NASA Astrophysics Data System (ADS)

Vezzulli, Luigi; Moreno, Mariapaola; Marin, Valentina; Pezzati, Elisabetta; Bartoli, Marco; Fabiano, Mauro

2008-06-01

A variety of pelagic and benthic parameters were measured at an aquaculture farm used for the fattening of Atlantic bluefin tuna ( Thunnus thynnus) which is located at an exposed site (700 m from the coast, average bottom depth of 45 m and average current speed of 6 cm s -1) in the Mediterranean Sea. The objective was to test whether modern off-shore tuna fattening industries can exert a sustainable organic waste impact on the receiving environment as has been reported for the offshore culture of more traditional Mediterranean species such as sparids. In the water column, the concentration of phytopigments, organic matter, heterotrophic bacteria and the taxonomic abundance of mesozooplankton (at the species level) were assessed. In the sediment, we assessed the concentration of reduced sulphur pools, phytopigments, organic matter, heterotrophic bacteria and the taxonomic abundance of meiofauna (at the taxa level) and nematodes (at the genus level). For most parameters, we found no substantial differences between farm and control sites. Deviations of farm values from control values, when they occurred, were small and did not indicate any significant impact on either the pelagic and benthic environment. Deviations were more apparent in the benthic compartment where lower redox potential values, higher bacterial production rates and a change in nematode genus composition pointed out to early changes in the sediment's metabolism. In addition, indigenous potential pathogenic bacteria showed higher concentration at the fish farm stations and were a warning of an undesirable event that may become established following aquaculture practice in oligotrophic environments. The overall data from this study provide extensive experimental evidence to support the sustainability of modern offshore farming technology in minimizing the hypertrophic-dystrophic risks associated with the rapidly-expanding tuna-fattening industry in the Mediterranean Sea.

A Proteomic and Lipidomic Characterization of Bradyrhizobium diazoefficiens Membranes Under Microaerobic Conditions

NASA Astrophysics Data System (ADS)

Tookmanian, E. M.; Neubauer, C.; Newman, D. K.

2016-12-01

Hopanoids are a class of sterol-like molecules found in modern bacterial membranes. Remarkably, they can leave behind carbon skeletons (hopanes) that persist for millions of years. Previously, hopanes were thought to be biomarkers of cyanobacteria, and thus, indirectly, the evolution of oxygen. As our understanding of the biosynthetic pathway of hopanoids has improved, we have learned that oxygen is not required for hopanoid biosynthesis and that many different bacteria have the genetic potential to synthesize hopanoids. These facts motivate a deeper understanding of the distribution and role(s) of hopanoids in bacteria. Bioinformatic approaches revealed that a subgroup of bacteria that synthesize hopanoids have symbiotic relationships with plants. These symbioses often take the form of root nodules, which have a unique microenvironment including microaerobic conditions to promote nitrogen fixation. We utilized the legume symbiont Bradyrhizobium diazoefficiens to investigate the molecular composition of membranes through lipidomic and proteomic studies. A B. diazoefficiens mutant lacking the C-2 hopanoid methylase (ΔhpnP) was previously shown to have a growth defect compared to wildtype under microaerobic conditions, whereas a mutant unable to synthesize C35 hopanoids (ΔhpnH) failed to grow entirely. Because these different hopanoid classes impact the fitness of this organism under nodule-like growth conditions, we sought to determine how these classes affect the rest of the membrane. Here, we present how the presence or absence of specific hopanoid classes alters the membrane proteome and lipidome of B. diazoefficiens; this information provides clues regarding their cellular function. By constraining the roles hopanoids play in modern niches, we hope to identify conserved biochemical functions that will advance our interpretations of the hopane rock record.

Formation of Deep Sea Umber Deposits Linked to Microbial Metal Oxidation at the South Atlantic Ridge

NASA Astrophysics Data System (ADS)

Peng, Xiaotong; Ta, Kaiwen; Chen, Shun; Zhang, Lijuan; Xu, Hengchao

2015-04-01

Umber deposits are important metalliferous deposits, which occur in off-axis half-graben structures at ancient and modern ocean floor. The genesis of umber deposits has remained controversial for several decades. Recently, microbial Fe(II) oxidation associated with low-temperature diffuse venting has been identified as a key process for the formation of umber deposits, but the exact biochemical mechanisms involved to the precipitation of Mn oxides and co-precipitation of Fe oxyhydroxides and Mn oxides in umber deposits still remain unknown. Here, we used nano secondary ion mass spectrometer, synchrotron-based X-ray absorption spectroscopy, electron microscopy, and molecular techniques to demonstrate the coexistence of two types of metal-oxidizing bacteria within deep-sea hydrothermal umber deposits at the South Atlantic Ridge, where we found unique spheroids composed of biogenic Fe oxyhydroxides and Mn oxides in the deposits. Our data suggest that Fe oxyhydroxides and Mn oxides are metabolic by-products of lithotrophic Fe(II)-oxidizing bacteria and heterotrophic Mn(II)-oxidizing bacteria, respectively. The hydrothermal vents fuel lithotrophic Fe(II)-oxidizing bacteria, which constitute a trophic base that may support the activities of heterotrophic Mn(II)-oxidizing bacteria. The biological origin of umber deposits underscore the importance of geomicrobiologcial interaction in triggering the formation of deep-sea deposits, with important implications for the generation of submarine Mn deposits and crusts.

Coping with antibiotic resistance: combining nanoparticles with antibiotics and other antimicrobial agents.

PubMed

Allahverdiyev, Adil M; Kon, Kateryna Volodymyrivna; Abamor, Emrah Sefik; Bagirova, Malahat; Rafailovich, Miriam

2011-11-01

The worldwide escalation of bacterial resistance to conventional medical antibiotics is a serious concern for modern medicine. High prevalence of multidrug-resistant bacteria among bacteria-based infections decreases effectiveness of current treatments and causes thousands of deaths. New improvements in present methods and novel strategies are urgently needed to cope with this problem. Owing to their antibacterial activities, metallic nanoparticles represent an effective solution for overcoming bacterial resistance. However, metallic nanoparticles are toxic, which causes restrictions in their use. Recent studies have shown that combining nanoparticles with antibiotics not only reduces the toxicity of both agents towards human cells by decreasing the requirement for high dosages but also enhances their bactericidal properties. Combining antibiotics with nanoparticles also restores their ability to destroy bacteria that have acquired resistance to them. Furthermore, nanoparticles tagged with antibiotics have been shown to increase the concentration of antibiotics at the site of bacterium-antibiotic interaction, and to facilitate binding of antibiotics to bacteria. Likewise, combining nanoparticles with antimicrobial peptides and essential oils generates genuine synergy against bacterial resistance. In this article, we aim to summarize recent studies on interactions between nanoparticles and antibiotics, as well as other antibacterial agents to formulate new prospects for future studies. Based on the promising data that demonstrated the synergistic effects of antimicrobial agents with nanoparticles, we believe that this combination is a potential candidate for more research into treatments for antibiotic-resistant bacteria.

Integration of organohalide-respiring bacteria and nanoscale zero-valent iron (Bio-nZVI-RD): A perfect marriage for the remediation of organohalide pollutants?

PubMed

Wang, Shanquan; Chen, Siyuan; Wang, Yu; Low, Adrian; Lu, Qihong; Qiu, Rongliang

2016-12-01

Due to massive production and improper handling, organohalide compounds are widely distributed in subsurface environments, primarily in anoxic groundwater, soil and sediment. Compared to traditional pump-and-treat or dredging-and-disposal treatments, in situ remediation employing abiotic or biotic reductive dehalogenation represents a sustainable and economic solution for the removal of organohalide pollutants. Both nanoscale zero-valent iron (nZVI) and organohalide-respiring bacteria remove halogens through reductive dehalogenation and have been extensively studied and successfully applied for the in situ remediation of chloroethenes and other organohalide pollutants. nZVI and microbial reductive dehalogenation (Bio-RD) complement each other to boost reductive dehalogenation efficiency, suggesting that the integration of nZVI with Bio-RD (Bio-nZVI-RD) may constitute an even more promising strategy for the in situ remediation of organohalide pollutants. In this review, we first provide an overview of the current literature pertaining to nZVI- and organohalide-respiring bacteria-mediated reductive dehalogenation of organohalide pollutants and compare the pros and cons of individual treatment methods. We then highlight recent studies investigating the implementation of Bio-nZVI-RD to achieve rapid and complete dehalogenation and discuss the halogen removal mechanism of Bio-nZVI-RD and its prospects for future remediation applications. In summary, the use of Bio-nZVI-RD facilitates opportunities for the effective in situ remediation of a wide range of organohalide pollutants. Copyright © 2016 Elsevier Inc. All rights reserved.

Constraints on mechanisms and rates of anaerobic oxidation of methane by microbial consortia: process-based modeling of ANME-2 archaea and sulfate reducing bacteria interactions

NASA Astrophysics Data System (ADS)

Orcutt, B.; Meile, C.

2008-11-01

Anaerobic oxidation of methane (AOM) is the main process responsible for the removal of methane generated in Earth's marine subsurface environments. However, the biochemical mechanism of AOM remains elusive. By explicitly resolving the observed spatial arrangement of methanotrophic archaea and sulfate reducing bacteria found in consortia mediating AOM, potential intermediates involved in the electron transfer between the methane oxidizing and sulfate reducing partners were investigated via a consortium-scale reaction transport model that integrates the effect of diffusional transport with thermodynamic and kinetic controls on microbial activity. Model simulations were used to assess the impact of poorly constrained microbial characteristics such as minimum energy requirements to sustain metabolism and cell specific rates. The role of environmental conditions such as the influence of methane levels on the feasibility of H2, formate and acetate as intermediate species, and the impact of the abundance of intermediate species on pathway reversal were examined. The results show that higher production rates of intermediates via AOM lead to increased diffusive fluxes from the methane oxidizing archaea to sulfate reducing bacteria, but the build-up of the exchangeable species can cause the energy yield of AOM to drop below that required for ATP production. Comparison to data from laboratory experiments shows that under the experimental conditions of Nauhaus et al. (2007), none of the potential intermediates considered here is able to support metabolic activity matching the measured rates.

Impact of clay minerals on sulfate-reducing activity in aquifers

USGS Publications Warehouse

Wong, D.; Suflita, J.M.; McKinley, J.P.; Krumholz, L.R.

2004-01-01

Previous studies have shown that sulfate-reduction activity occurs in a heterogeneous manner throughout the terrestrial subsurface. Low-activity regions are often observed in the presence of clay minerals. Here we report that clays inhibit sulfate reduction activity in sediments and in a pure culture of Desulfovibriovulgaris. Clay minerals including bentonite and kaolinite inhibited sulfate reduction by 70–90% in sediments. Intact clays and clay colloids or soluble components, capable of passing through a 0.2-µm filter, were also inhibitory to sulfate-reducing bacteria. Other adsorbent materials, including anion or cation exchangers and a zeolite, did not inhibit sulfate reduction in sediments, suggesting that the effect of clays was not due to their cation-exchange capacity. We observed a strong correlation between the Al2O3content of clays and their relative ability to inhibit sulfate reduction in sediments (r2 = 0.82). This suggested that inhibition might be a direct effect of Al3+ (aq) on the bacteria. We then tested pure aluminum oxide (Al2O3) and showed it to act in a similar manner to clay. As dissolved aluminum is known to be toxic to a variety of organisms at low concentrations, our results suggest that the effects of clay on sulfate-reducing bacteria may be directly due to aluminum. Thus, our experiments provide an explanation for the lack of sulfate-reduction activity in clay-rich regions and presents a mechanism for the effect.

Nitrogen isotopic composition of enameloid-bound organic matter from modern and fossil shark teeth

NASA Astrophysics Data System (ADS)

Kast, E.; Wang, X. T.; Kim, S.; Kocsis, L.; Sigman, D. M.

2016-12-01

The nitrogen isotopic composition of fossil organic matter has been used to reconstruct ocean biogeochemical conditions in the past, and there is the potential for such investigations to be extended to trophic and ecological processes. Organic matter trapped within biogenic minerals is of particular interest for this purpose because of relatively good preservation and specificity when compared to bulk sedimentary organic matter. The approach for measuring mineral bound organic matter δ15N previously applied to diatoms, foraminifera, and coral skeleton has been adapted for use with tooth apatite, with reproducibility within 0.25‰ for modern and fossil shark enameloid. Studies of modern shark enameloid bound δ15N (δ15NEB) show substantial variability ( 3‰) between individuals of a single species and in some cases among teeth from a given individual. δ15NEB is affected by the isotopic composition of nutrient supply, which is a primary determinant of the δ15N at the base of the food web, and progressive 15N enrichment with trophic level due to the metabolism and excretion of low-δ15N N. Among modern shark species studied, patterns in δ15NEB appear to primarily reflect regional variations in subsurface nitrate δ15N, with the trophic effect as a secondary signal, in part because trophic level does not vary greatly across the studied shark species (or, indeed, across many shark species). Teeth from individual jaws can show trends in δ15NEB with the age of the tooth, possibly representing a dietary shift or seasonal migration. The modern measurements suggest that, with care, enameloid bound δ15N can be used to reconstruct past nutrient cycling dynamics. In this context, measurements will be presented of δ15NEB from fossil shark teeth of various Cenozoic ages from the Atlantic basin.

Mortality risk factors show similar trends in modern and historic populations exposed to plague.

PubMed

Rubini, Mauro; Gualdi-Russo, Emanuela; Manzon, Vanessa S; Rinaldo, Natascia; Bianucci, Raffaella

2016-05-31

Plague has been responsible for two major historic pandemics (6th-8th century CE; 14th-19th century CE) and a modern one. The recent Malagasy plague outbreaks raised new concerns on the deadly potential of the plague-causing bacteria Yersinia pestis. Between September 2014 and April 2015, outbreaks of bubonic and pneumonic plague hit the Malagasy population. Two hundred and sixty-three cases, including 71 deaths, have been reported in 16 different districts with a case fatality rate of 27%. The scope of our study was to ascertain whether the risk factors for health in modern-day populations exposed to plague and in ancient populations that faced the two historic pandemics varied or remained substantially unaltered. The risk of mortality of the Malagasy population with those obtained from the reconstruction of three samples of European populations exposed to the historic pandemics was contrasted. The evidence shows that the risks of death are not uniform across age neither in modern nor in historic populations exposed to plague and shows precise concentrations in specific age groups (children between five and nine years of age and young adults). Although in the post-antibiotic era, the fatality rates have drastically reduced, both modern and historic populations were exposed to the same risk factors that are essentially represented by a low standard of environmental hygiene, poor nutrition, and weak health systems.

Antimicrobial Nanomaterials Derived from Natural Products—A Review

PubMed Central

Wang, Ji; Vermerris, Wilfred

2016-01-01

Modern medicine has relied heavily on the availability of effective antibiotics to manage infections and enable invasive surgery. With the emergence of antibiotic-resistant bacteria, novel approaches are necessary to prevent the formation of biofilms on sensitive surfaces such as medical implants. Advances in nanotechnology have resulted in novel materials and the ability to create novel surface topographies. This review article provides an overview of advances in the fabrication of antimicrobial nanomaterials that are derived from biological polymers or that rely on the incorporation of natural compounds with antimicrobial activity in nanofibers made from synthetic materials. The availability of these novel materials will contribute to ensuring that the current level of medical care can be maintained as more bacteria are expected to develop resistance against existing antibiotics. PMID:28773379

Antimicrobial nanomaterials derived from natural products—A review

DOE PAGES

Wang, Ji; Vermerris, Wilfred

2016-03-30

Modern medicine has relied heavily on the availability of effective antibiotics to manage infections and enable invasive surgery. With the emergence of antibiotic-resistant bacteria, novel approaches are necessary to prevent the formation of biofilms on sensitive surfaces such as medical implants. Advances in nanotechnology have resulted in novel materials and the ability to create novel surface topographies. This review article provides an overview of advances in the fabrication of antimicrobial nanomaterials that are derived from biological polymers or that rely on the incorporation of natural compounds with antimicrobial activity in nanofibers made from synthetic materials. Furthermore, the availability of thesemore » novel materials will contribute to ensuring that the current level of medical care can be maintained as more bacteria are expected to develop resistance against existing antibiotics.« less

Antimicrobial nanomaterials derived from natural products—A review

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Ji; Vermerris, Wilfred

Modern medicine has relied heavily on the availability of effective antibiotics to manage infections and enable invasive surgery. With the emergence of antibiotic-resistant bacteria, novel approaches are necessary to prevent the formation of biofilms on sensitive surfaces such as medical implants. Advances in nanotechnology have resulted in novel materials and the ability to create novel surface topographies. This review article provides an overview of advances in the fabrication of antimicrobial nanomaterials that are derived from biological polymers or that rely on the incorporation of natural compounds with antimicrobial activity in nanofibers made from synthetic materials. Furthermore, the availability of thesemore » novel materials will contribute to ensuring that the current level of medical care can be maintained as more bacteria are expected to develop resistance against existing antibiotics.« less

Occurence of sulfate- and iron-reducing bacteria in stratal waters of the Romashkinskoe oil field

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nazina, T.N.; Ivanova, A.E.; Goulbeva, O.V.

1995-03-01

The occurrence of microorganisms and the rates of terminal biogenic processes-sulfate reduction and methane synthesis-were studied in stratial waters in bed 302 of the Bashkir Carboniferous deposit at the Romashkinskoe oil field. It was shown that bed 302 was a dynamic, highly reduced ecosystem containing sulfates and hydrogen sulfide in considerable concentrations, in which active biogenic processes occurred. Sulfate reduction was a dominating anaerobic process by which the transformation of organic matter occurred. The sulfate-reducing microflora was diverse and characterized by a wide range of metabolic potentials. Enrichment cultures capable of oxidizing many organic substances, such as benzoate, acetate, ethanol,more » or lactate, at the expense of reduction of sulfates and ferric ion were isolated from 302. It was suggested that the sulfate-reducing microflora might be responsible not only for sulfate reduction in the stratum but also for mobilization of some insoluble iron oxides in the oil-bearing rock. These findings indicate that bacteria carrying out dissimilatory reduction of sulfate and iron can contribute to the geochemistry of organic and mineral compounds in subsurface ecosystems. 24 refs., 2 figs., 6 tabs.« less

[Identification of new conserved and variable regions in the 16S rRNA gene of acetic acid bacteria and acetobacteraceae family].

PubMed

Chakravorty, S; Sarkar, S; Gachhui, R

2015-01-01

The Acetobacteraceae family of the class Alpha Proteobacteria is comprised of high sugar and acid tolerant bacteria. The Acetic Acid Bacteria are the economically most significant group of this family because of its association with food products like vinegar, wine etc. Acetobacteraceae are often hard to culture in laboratory conditions and they also maintain very low abundances in their natural habitats. Thus identification of the organisms in such environments is greatly dependent on modern tools of molecular biology which require a thorough knowledge of specific conserved gene sequences that may act as primers and or probes. Moreover unconserved domains in genes also become markers for differentiating closely related genera. In bacteria, the 16S rRNA gene is an ideal candidate for such conserved and variable domains. In order to study the conserved and variable domains of the 16S rRNA gene of Acetic Acid Bacteria and the Acetobacteraceae family, sequences from publicly available databases were aligned and compared. Near complete sequences of the gene were also obtained from Kombucha tea biofilm, a known Acetobacteraceae family habitat, in order to corroborate the domains obtained from the alignment studies. The study indicated that the degree of conservation in the gene is significantly higher among the Acetic Acid Bacteria than the whole Acetobacteraceae family. Moreover it was also observed that the previously described hypervariable regions V1, V3, V5, V6 and V7 were more or less conserved in the family and the spans of the variable regions are quite distinct as well.

Facies dimensions within carbonate reservoirs - guidelines from satellite images of modern analogs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harris, P.M.; Kowalik, W.S.

1995-08-01

Modern analogs illustrate the distribution of carbonate facies within an overall depositional setting and can be an integral part of a subsurface geologic model in indicating the dimensions, trend, and interrelationships of facies that might be related to reservoir and non-reservoir distribution. Satellite images from several modern carbonate areas depict the geologic characteristics that can be expected in ancient shallow-water settings. Isolated carbonate platforms- the Bahamas, Caicos Platform in the British West Indies, Chinchorro Bank offshore of Yucatan, and portions of the Belize area; Ramp-style shelf-to-basin transitions - Abu Dhabi and northern Yucatan; Rimmed shelf margins - South Florida, portionsmore » of Belize, and the Great Barrier Reef of Australia; Broad, deep shelf lagoons - the Great Barrier Reef and Belize; Reef variability - South Florida, the Bahamas, Caicos, Northern Yucatan, and Abu Dhabi; Shallow lagoon/tidal flat settings - South Florida, the Bahamas, Caicos, Northern Yucatan, Shark Bay in Western Australia, Abu Dhabi; Mixed carbonate and siliciclastic depostion - South Florida, Belize, the Great Barrier Reef, Shark Bay and Abu Dhabi. The geologic framework as illustrated by these areas is important at the development scale where lateral variation of porosity and permeability, i.e. reservoir quality, is commonly tied to facies changes and facies dimensions are required as input to reservoir models. The geologic framework is essential at the exploration scale for reservoir facies prediction and stratigraphic play concepts which are related directly to depositional facies patterns.« less

Results and interpretation of exploratory drilling near the Picacho Fault, south-central Arizona

USGS Publications Warehouse

Holzer, Thomas L.

1978-01-01

Modern surface faulting along the Picacho fault, east of Picacho, Arizona, has been attributed to ground-water withdrawal. In September 1977, three exploratory test holes were drilled 5 km east of Picacho and across the Picacho fault to investigate subsurface conditions and the mechanism of the faulting. The holes were logged by conventional geophysical and geologic methods. Piezometers were set in each hole and have been monitored since September 1977. The drilling indicates that the unconsolidated alluvium beneath the surface fault is approximately 310 m thick. Drilling and piezometer data and an associated seismic refraction survey indicate that the modern faulting is coincident with a preexisting, high-angle, normal fault that offsets units within the alluvium as well as the underlying bedrock. Piezometer and neutron log data indicate that the preexisting fault behaves as a partial ground-water barrier. Monitoring of the piezometers indicates that the magnitude of the man-induced difference in water level across the preexisting fault is seasonal in nature, essentially disappearing during periods of water-level recovery. The magnitude of the seasonal difference in water level, however, appears to be sufficient to account for the modern fault offset by localized differential compaction caused by a difference in water level across the preexisting fault. In addition, repeated level surveys since September 1977 of bench marks across the surface fault and near the piezometers have indicated fault movement that corresponds to fluctuations of water level.

Application of adenosine triphosphate-driven bioluminescence for quantification of plaque bacteria and assessment of oral hygiene in children.

PubMed

Fazilat, Shahram; Sauerwein, Rebecca; McLeod, Jennifer; Finlayson, Tyler; Adam, Emilia; Engle, John; Gagneja, Prashant; Maier, Tom; Machida, Curtis A

2010-01-01

Dentistry has undergone a shift in caries management toward prevention and improved oral hygiene and diagnosis. Caries prevention now represents one of the most important aspects of modern dental practice. The purpose of this cross-sectional study was to demonstrate the use of adenosine triphosphate- (ATP-) driven bioluminescence as an innovative tool for the rapid chairside enumeration of oral bacteria (including plague streptococci) and assessment of oral hygiene and caries risk. Thirty-three pediatric patients (7- to 12-year-old males and females) were examined, and plague specimens, in addition to stimulated saliva, were collected from representative teeth within each quadrant. Oral specimens (n=150 specimens) were assessed by plating on enriched and selective agars, to enumerate total bacteria and streptococci, and subjected to adenosine triphosphate- (ATP-) driven bioluminescence determinations using a luciferase-based assay system. Statistical correlations, linking ATP values to numbers of total bacteria, oral streptococci and mutans streptococci, yielded highly significant r values of 0.854, 0.840, and 0.796, respectively Our clinical data is consistent with the hypothesis that ATP measurements have a strong statistical association with bacterial number in plague and saliva specimens, including numbers for oral streptococci, and may be used as a potential assessment tool for oral hygiene and caries risk in children.

Magnetotactic bacteria and magnetosomes - Scope and challenges.

PubMed

Jacob, Jobin John; Suthindhiran, K

2016-11-01

Geomagnetism aided navigation has been demonstrated by certain organisms which allows them to identify a particular location using magnetic field. This attractive technique to recognize the course was earlier exhibited in numerous animals, for example, birds, insects, reptiles, fishes and mammals. Magnetotactic bacteria (MTB) are one of the best examples for magnetoreception among microorganisms as the magnetic mineral functions as an internal magnet and aid the microbe to move towards the water columns in an oxic-anoxic interface (OAI). The ability of MTB to biomineralize the magnetic particles (magnetosomes) into uniform nano-sized, highly crystalline structure with uniform magnetic properties has made the bacteria an important topic of research. The superior properties of magnetosomes over chemically synthesized magnetic nanoparticles made it an attractive candidate for potential applications in microbiology, biophysics, biochemistry, nanotechnology and biomedicine. In this review article, the scope of MTB, magnetosomes and its challenges in research and industrial application have been discussed in brief. This article mainly focuses on the application based on the magnetotactic behaviour of MTB and magnetosomes in different areas of modern science. Copyright © 2016 Elsevier B.V. All rights reserved.

Purification and culture characteristics of 36 benthic marine diatoms isolated from the Solthörn tidal flat (Southern North Sea).

PubMed

Scholz, Bettina

2014-08-01

Marine benthic diatoms growing in biofilms on sediment surfaces generally occur associated with heterotrophic bacteria, whereas modern molecular techniques and analyses of species-specific physiology create a demand for axenic cultures. Numerous benthic diatoms were isolated from surface sediments during a monitoring of the Solthörn tidal flat (southern North Sea, Germany) from May 2008 to May 2009. Of these, around 50% could be purified from the accompanying heterotrophic bacteria using different antibiotics combined with physical separation methods (vortexing, ultrasound). Overall, seven different antibiotics were tested at different concentrations, and a best working protocol was developed. The axenic strains were stable on average for only around 15 months, indicating a symbiotic interaction between the benthic diatoms and the associated bacteria. While most short-term effects during the purification process were restricted to differences in growth rates among xenic and axenic diatom strains, long-term cultivation led to distinct changes in cell volumes and growth characteristics of the axenic strains. © 2014 Phycological Society of America.

Microorganisms as tracers in groundwater injection and recovery experiments: A review

USGS Publications Warehouse

Harvey, R.W.

1997-01-01

Modern day injection and recovery techniques designed to examine the transport behavior of microorganisms in groundwater have evolved from experiments conducted in the late 1800s, in which bacteria that form red or yellow pigments were used to trace flow paths through karst and fractured- rock aquifers. A number of subsequent groundwater hydrology studies employed bacteriophage that can be injected into aquifers at very high concentrations (e g., 1013 phage ml-1) and monitored through many log units of dilution to follow groundwater flow paths for great distances, particularly in karst terrain. Starting in the 1930s, microbial indicators of fecal contamination (particularly coliform bacteria and their coliphages) were employed as tracers to determine potential migration of pathogens in groundwater. Several injection and recovery experiments performed in the 1990s employed indigenous groundwater microorganisms (both cultured and uncultured) that are better able to survive under in situ conditions. Better methods for labeling native bacteria (e.g by stable isotope labeling or inserting genetic markers; such as the ability to cause ice nucleation) are being developed that will not compromise the organisms' viability during the experimental time course.

Minute tubular forms in soil

NASA Technical Reports Server (NTRS)

Casida, L. E., Jr.; Liu, K.-C.

1979-01-01

Large numbers of long, straight, flattened structures were observed during an electron-microscope study of bacteriophage in aqueous extracts. These structures were called tubules and ranged in width from 10 to 50 nm. Materials and methods were discussed relative to extraction of tubules from soil, electron microscopy, quantitation of tubules in filtrate suspension, tests performed on tubules, plaque formation, and nutrient amendments. It is found that all of the tubules recovered from soil are broken at one or both ends. They are present in surface soils but not in a subsurface sample. Their numbers decrease during bacterial multiplication in soil or broth-containing soil. The tubules appear to be composed of protein that could be disintegrated to liberate nonprotein fibers. A possible clue to the nature of the tubules is their apparent relation to soil bacteria.

Low upper limit to methane abundance on Mars.

PubMed

Webster, Christopher R; Mahaffy, Paul R; Atreya, Sushil K; Flesch, Gregory J; Farley, Kenneth A

2013-10-18

By analogy with Earth, methane in the Martian atmosphere is a potential signature of ongoing or past biological activity. During the past decade, Earth-based telescopic observations reported "plumes" of methane of tens of parts per billion by volume (ppbv), and those from Mars orbit showed localized patches, prompting speculation of sources from subsurface bacteria or nonbiological sources. From in situ measurements made with the Tunable Laser Spectrometer (TLS) on Curiosity using a distinctive spectral pattern specific to methane, we report no detection of atmospheric methane with a measured value of 0.18 ± 0.67 ppbv corresponding to an upper limit of only 1.3 ppbv (95% confidence level), which reduces the probability of current methanogenic microbial activity on Mars and limits the recent contribution from extraplanetary and geologic sources.

Phytoextraction, phytotransformation and rhizodegradation of ibuprofen associated with Typha angustifolia in a horizontal subsurface flow constructed wetland.

PubMed

Li, Yifei; Zhang, Jiefeng; Zhu, Guibing; Liu, Yu; Wu, Bing; Ng, Wun Jern; Appan, Adhityan; Tan, Soon Keat

2016-10-01

Widespread occurrence of trace pharmaceutical residues in aquatic environments is of great concerns due to the potential chronic toxicity of certain pharmaceuticals including ibuprofen on aquatic organisms even at environmental levels. In this study, the phytoextraction, phytotransformation and rhizodegradation of ibuprofen associated with Typha angustifolia were investigated in a horizontal subsurface flow constructed wetland system. The experimental wetland system consisted of a planted bed with Typha angustifolia and an unplanted bed (control) to treat ibuprofen-loaded wastewater (∼107.2 μg L(-1)). Over a period of 342 days, ibuprofen was accumulated in leaf sheath and lamina tissues at a mean concentration of 160.7 ng g(-1), indicating the occurrence of the phytoextraction of ibuprofen. Root-uptake ibuprofen was partially transformed to ibuprofen carboxylic acid, 2-hydroxy ibuprofen and 1-hydroxy ibuprofen which were found to be 1374.9, 235.6 and 301.5 ng g(-1) in the sheath, respectively, while they were 1051.1, 693.6 and 178.7 ng g(-1) in the lamina. The findings from pyrosequencing analysis of the rhizosphere bacteria suggest that the Dechloromonas sp., the Clostridium sp. (e.g. Clostridium saccharobutylicum), the order Sphingobacteriales, and the Cytophaga sp. in the order Cytophagales were most probably responsible for the rhizodegradation of ibuprofen. Copyright © 2016 Elsevier Ltd. All rights reserved.

Detecting Microbially Induced Calcite Precipitation in a Model Well-Bore Using Downhole Low-Field NMR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kirkland, Catherine M.; Zanetti, Sam; Grunewald, Elliot

Microbially induced calcite precipitation (MICP) has been widely researched recently due to its relevance for subsurface engineering applications including sealing leakage pathways and permeability modification. These applications of MICP are inherently difficult to monitor nondestructively in time and space. Nuclear magnetic resonance (NMR) can characterize the pore size distributions, porosity, and permeability of subsurface formations. This investigation used a low-field NMR well-logging probe to monitor MICP in a sand-filled bioreactor, measuring NMR signal amplitude and T 2 relaxation over an 8 day experimental period. Following inoculation with the ureolytic bacteria, Sporosarcina pasteurii, and pulsed injections of urea and calcium substrate,more » the NMR measured water content in the reactor decreased to 76% of its initial value. T 2 relaxation distributions bifurcated from a single mode centered about approximately 650 ms into a fast decaying population ( T 2 less than 10 ms) and a larger population with T 2 greater than 1000 ms. The combination of changes in pore volume and surface minerology accounts for the changes in the T 2 distributions. Destructive sampling confirmed final porosity was approximately 88% of the original value. Here, these results indicate the low-field NMR well-logging probe is sensitive to the physical and chemical changes caused by MICP in a laboratory bioreactor.« less

Detecting Microbially Induced Calcite Precipitation in a Model Well-Bore Using Downhole Low-Field NMR

DOE PAGES

Kirkland, Catherine M.; Zanetti, Sam; Grunewald, Elliot; ...

2016-12-20

Microbially induced calcite precipitation (MICP) has been widely researched recently due to its relevance for subsurface engineering applications including sealing leakage pathways and permeability modification. These applications of MICP are inherently difficult to monitor nondestructively in time and space. Nuclear magnetic resonance (NMR) can characterize the pore size distributions, porosity, and permeability of subsurface formations. This investigation used a low-field NMR well-logging probe to monitor MICP in a sand-filled bioreactor, measuring NMR signal amplitude and T 2 relaxation over an 8 day experimental period. Following inoculation with the ureolytic bacteria, Sporosarcina pasteurii, and pulsed injections of urea and calcium substrate,more » the NMR measured water content in the reactor decreased to 76% of its initial value. T 2 relaxation distributions bifurcated from a single mode centered about approximately 650 ms into a fast decaying population ( T 2 less than 10 ms) and a larger population with T 2 greater than 1000 ms. The combination of changes in pore volume and surface minerology accounts for the changes in the T 2 distributions. Destructive sampling confirmed final porosity was approximately 88% of the original value. Here, these results indicate the low-field NMR well-logging probe is sensitive to the physical and chemical changes caused by MICP in a laboratory bioreactor.« less

Mineralization of Bacteria in Terrestrial Basaltic Rocks: Comparison With Possible Biogenic Features in Martian Meteorite Allan Hills 84001

NASA Technical Reports Server (NTRS)

Thomas-Keprta, K. L.; McKay, D. S.; Wentworth, S. J.; Stevens, T. O.; Taunton, A. E.; Allen, C. C.; Gibson, E. K., Jr.; Romanek, C. S.

1998-01-01

The identification of biogenic features altered by diagenesis or mineralization is important in determining whether specific features in terrestrial rocks and in meteorites may have a biogenic origin. Unfortunately, few studies have addressed the formation of biogenic features in igneous rocks, which may be important to these phenomena, including the controversy over possible biogenic features in basaltic martian meteorite ALH84001. To explore the presence of biogenic features in igneous rocks, we examined microcosms growing in basaltic small-scale experimental growth chambers or microcosms. Microbial communities were harvested from aquifers of the Columbia River Basalt (CRB) group and grown in a microcosm containing unweathered basalt chips and groundwater (technique described in. These microcosms simulated natural growth conditions in the deep subsurface of the CRB, which should be a good terrestrial analog for any putative martian subsurface ecosystem that may have once included ALH84001. Here we present new size measurements and photomicrographs comparing the putative martian fossils to biogenic material in the CRB microcosms. The range of size and shapes of the biogenic features on the CRB microcosm chips overlaps with and is similar to those on ALH84001 chips. Although this present work does not provide evidence for the biogenicity of ALH84001 features, we believe that, based on criteria of size, shape, and general morphology, a biogenic interpretation for the ALH84001 features remains plausible.

Culturable prokaryotic diversity of deep, gas hydrate sediments: first use of a continuous high-pressure, anaerobic, enrichment and isolation system for subseafloor sediments (DeepIsoBUG)

PubMed Central

Parkes, R John; Sellek, Gerard; Webster, Gordon; Martin, Derek; Anders, Erik; Weightman, Andrew J; Sass, Henrik

2009-01-01

Deep subseafloor sediments may contain depressurization-sensitive, anaerobic, piezophilic prokaryotes. To test this we developed the DeepIsoBUG system, which when coupled with the HYACINTH pressure-retaining drilling and core storage system and the PRESS core cutting and processing system, enables deep sediments to be handled without depressurization (up to 25 MPa) and anaerobic prokaryotic enrichments and isolation to be conducted up to 100 MPa. Here, we describe the system and its first use with subsurface gas hydrate sediments from the Indian Continental Shelf, Cascadia Margin and Gulf of Mexico. Generally, highest cell concentrations in enrichments occurred close to in situ pressures (14 MPa) in a variety of media, although growth continued up to at least 80 MPa. Predominant sequences in enrichments were Carnobacterium, Clostridium, Marinilactibacillus and Pseudomonas, plus Acetobacterium and Bacteroidetes in Indian samples, largely independent of media and pressures. Related 16S rRNA gene sequences for all of these Bacteria have been detected in deep, subsurface environments, although isolated strains were piezotolerant, being able to grow at atmospheric pressure. Only the Clostridium and Acetobacterium were obligate anaerobes. No Archaea were enriched. It may be that these sediment samples were not deep enough (total depth 1126–1527 m) to obtain obligate piezophiles. PMID:19694787

Heterotrophic potential of Atribacteria from deep marine Antarctic sediment

NASA Astrophysics Data System (ADS)

Carr, S. A.; Orcutt, B.; Mandernack, K. W.; Spear, J. R.

2015-12-01

Bacteria belonging to the newly classified candidate phylum "Atribacteria" (formerly referred to as "OP9" and "JS1") are common in anoxic methane-rich sediments. However, the metabolic functions and biogeochemical role of these microorganisms in the subsurface remains unrealized due to the lack of pure culture representatives. This study observed a steady increase of Atribacteria-related sequences with increasing sediment depth throughout the methane-rich zone of the Adélie Basin, Antarctica (according to a 16S rRNA gene survey). To explore the functional potential of Atribacteria in this basin, samples from various depths (14, 25 and 97 meters below seafloor), were subjected to metagenomic sequencing. Additionally, individual cells were separated from frozen, unpreserved sediment for whole genome amplification. The successful isolation and sequencing of a single-amplified Atribacteria genome from these unpreserved sediments demonstrates a future use of single cell techniques with previously collected and frozen sediments. Our resulting single-cell amplified genome, combined with metagenomic interpretations, provides our first insights to the functional potential of Atribacteria in deep subsurface settings. As observed for non-marine Atribacteria, genomic analyses suggest a heterotrophic metabolism, with Atribacteria potentially producing fermentation products such as acetate, ethanol and CO2. These products may in turn support methanogens within the sediment microbial community and explain the frequent occurrence of Atribacteria in anoxic methane-rich sediments.

Evidence for marine origin and microbial-viral habitability of sub-zero hypersaline aqueous inclusions within permafrost near Barrow, Alaska.

PubMed

Colangelo-Lillis, J; Eicken, H; Carpenter, S D; Deming, J W

2016-05-01

Cryopegs are sub-surface hypersaline brines at sub-zero temperatures within permafrost; their global extent and distribution are unknown. The permafrost barrier to surface and groundwater advection maintains these brines as semi-isolated systems over geological time. A cryopeg 7 m below ground near Barrow, Alaska, was sampled for geochemical and microbiological analysis. Sub-surface brines (in situtemperature of -6 °C, salinity of 115 ppt), and an associated sediment-infused ice wedge (melt salinity of 0.04 ppt) were sampled using sterile technique. Major ionic concentrations in the brine corresponded more closely to other (Siberian) cryopegs than to Standard seawater or the ice wedge. Ionic ratios and stable isotope analysis of water conformed to a marine or brackish origin with subsequent Rayleigh fractionation. The brine contained ∼1000× more bacteria than surrounding ice, relatively high viral numbers suggestive of infection and reproduction, and an unusually high ratio of particulate to dissolved extracellular polysaccharide substances. A viral metagenome indicated a high frequency of temperate viruses and limited viral diversity compared to surface environments, with closest similarity to low water activity environments. Interpretations of the results underscore the isolation of these underexplored microbial ecosystems from past and present oceans. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt

PubMed Central

Jungbluth, Sean P; Bowers, Robert M; Lin, Huei-Ting; Cowen, James P; Rappé, Michael S

2016-01-01

Although little is known regarding microbial life within our planet's rock-hosted deep subseafloor biosphere, boreholes drilled through deep ocean sediment and into the underlying basaltic crust provide invaluable windows of access that have been used previously to document the presence of microorganisms within fluids percolating through the deep ocean crust. In this study, the analysis of 1.7 million small subunit ribosomal RNA genes amplified and sequenced from marine sediment, bottom seawater and basalt-hosted deep subseafloor fluids that span multiple years and locations on the Juan de Fuca Ridge flank was used to quantitatively delineate a subseafloor microbiome comprised of distinct bacteria and archaea. Hot, anoxic crustal fluids tapped by newly installed seafloor sampling observatories at boreholes U1362A and U1362B contained abundant bacterial lineages of phylogenetically unique Nitrospirae, Aminicenantes, Calescamantes and Chloroflexi. Although less abundant, the domain Archaea was dominated by unique, uncultivated lineages of marine benthic group E, the Terrestrial Hot Spring Crenarchaeotic Group, the Bathyarchaeota and relatives of cultivated, sulfate-reducing Archaeoglobi. Consistent with recent geochemical measurements and bioenergetic predictions, the potential importance of methane cycling and sulfate reduction were imprinted within the basalt-hosted deep subseafloor crustal fluid microbial community. This unique window of access to the deep ocean subsurface basement reveals a microbial landscape that exhibits previously undetected spatial heterogeneity. PMID:26872042

Surfactant-Enhanced Size-Excluded Transport of Bacteria Through Unsaturated Porous Media.

NASA Astrophysics Data System (ADS)

Zhu, J.

2017-12-01

US domestic waste water is rich in surfactants because of the intensive usage of surfactants-containing household product. It results in a surfactants presence environment when this untreated waste water released into subsurface. It was reported that surfactants enhance the colloidal transport in porous media, which have significant effect on issues such as subsurface pathogens contamination and biodegradation. In this study, soil column experiments were conducted. The soil column was remained unsaturated and with a steady flow passing through it. Escherichia coli K-12 transported in the soil column and its breakthrough data was collected in presence of surfactant anionic surfactant linear alkylbenzene sulfonate (LAS) concentration range over 0, 0.25, 0.5, 0.75, 1, and 2 times Critical Micelle Concentration (CMC). It was found that the increase in LAS concentration greatly increases breakthrough concentration C/C0 and decreases breakthrough time tb until LAS concentration reaches 1 xCMC. Numerical models were built simulating and investigating this phenomenon. The goodness of model fitting was greatly improved by adding exclusion factor into the model, which indicated that the presence of surfactant might enhance the exclusion effect. The relationships between LAS concentration and the two coefficients, deposition rate coefficient k and exclusion effect coefficient θim, were found can be fitted by a quasi-Langmuir equation. And the model validation with observed data showed that the model has an acceptable reliability.

Profile of selected bacterial counts and Salmonella prevalence on raw poultry in a poultry slaughter establishment.

PubMed

James, W O; Williams, W O; Prucha, J C; Johnston, R; Christensen, W

1992-01-01

The USDA Food Safety and Inspection Service determined populations of bacteria on poultry during processing at a slaughter plant in Puerto Rico in November and December 1987. The plant was selected because of its management's willingness to support important changes in equipment and processing procedures. The plant was representative of modern slaughter facilities. Eight-hundred samples were collected over 20 consecutive 8-hour days of operation from 5 sites in the processing plant. Results indicated that slaughter, dressing, and chilling practices significantly decreased the bacterial contamination on poultry carcasses, as determined by counts of aerobic bacteria, Enterobacteriaceae, and Escherichia coli. Salmonella was not enumerated; rather, it was determined to be present or absent by culturing almost the entire rinse. The prevalence of Salmonella in the study decreased during evisceration, then increased during immersion chilling.

Microbial DNA; a possible tracer of groundwater

NASA Astrophysics Data System (ADS)

Sugiyama, Ayumi; Segawa, Takuya; Furuta, Tsuyumi; Nagaosa, Kazuyo; Tsujimura, Maki; Kato, Kenji

2017-04-01

Though chemical analysis of groundwater shows an averaged value of chemistry of the examined water which was blended by various water with different sources and routes in subsurface environment, microbial DNA analysis may suggest the place where they originated, which may give information of the source and transport routes of the water examined. A huge amount of groundwater is stored in lava layer with maximum depth of 300m in Mt. Fuji (3,776m asl ), the largest volcanic mountain in Japan. Although the density of prokaryotes was low in the examined groundwater of Mt. Fuji, thermophilic prokaryotes as Thermoanaerobacterales, Gaiellales and Thermoplasmatales were significantly detected. They are optimally adapted to the temperature higher than 40oC. This finding suggests that at least some of the source of the examined groundwater was subsurface environment with 600m deep or greater, based on a temperature gradient of 4oC/100m and temperature of spring water ranges from 10 to 15oC in the foot of Mt. Fuji. This depth is far below the lava layer. Thus, the groundwater is not simply originated from the lava layer. In addition to those findings, we observed a very fast response of groundwater just a couple of weeks after the heavy rainfall exceeding 2 or 300 mm/event in Mt. Fuji. The fast response was suggested by a sharp increase in bacterial abundance in spring water located at 700m in height in the west foot of Mt. Fuji, where the average recharge elevation of groundwater was estimated to be 1,500m - 1,700m (Kato et. al. EGU 2016). This increase was mainly provided by soil bacteria as Burkholderiales, which might be detached from soil by strengthened subsurface flow caused by heavy rainfall. This suggests that heavy rainfall promotes shallow subsurface flow contributing to the discharge in addition to the groundwater in the deep aquifer. Microbial DNA, thus could give information about the route of the examined groundwater, which was never elucidated by analysis of chemical materials dissolved in groundwater. Though viral particle was employed as a tracer to chase the movement of groundwater, it doesn't tell the chemical and physical environmental condition where the particle was incorporated into groundwater. Thus, we propose microbial DNA as a new tracer to track the route of groundwater.

Modern stromatolites in a saline maar in the Western District of Victoria, Australia: a possible analogue for Precambrian marine carbonates

NASA Astrophysics Data System (ADS)

Lynch, J. E.; Wallace, M. W.

2011-12-01

Stromatolites and thrombolites are microbially-mediated, sedimentary structures of various size and morphology, found throughout the rock record. Although they do not always contain fossils of microbial cells, ancient stromatolitic structures are considered biogenic in origin and, therefore, evidence of early life. Modern, living stromatolites are found in lacustrine and marine environments and can provide a window in which to observe some of Earth's earliest biological processes. However, secular variation in marine chemistry over geological time means that modern marine settings are not always the best analogues for ancient carbonates. This study describes the occurrence of modern stromatolites in a saline, alkaline maar in Victoria, Australia. Dolomite is a principle carbonate mineral precipitating from this lake, an unusual and poorly understood occurrence in modern environments, but one that was common in the Precambrian. The peculiar lacustrine chemistry in this volcanic region may, therefore, provide a better analogue for Precambrian marine carbonates than modern marine environments. Several types of stromatolites/thrombolites are observed occurring around this maar. Living thrombolites grow just below the shoreline to ~60 cm below the surface of the water. They are nucleating on the cemented surfaces of older lake carbonates, as well as cattle skulls and fence wires that have become submerged. Distinct microbial mats are observed, the uppermost being cyanobacteria, followed by purple sulfur bacteria, and underlain by sulfate reducing bacteria. Older exposed stromatolites are more consolidated and have a more clearly defined laminated and columnar morphology. The thickness ranges from a few to 15 cm and each column is up to a centimeter in diameter. Together these give the surface of the rock a "bubbly" appearance. Along the shore, a sandy-gravel composed of stromatolite remnants has formed, indicating that wind-generated surface waves of substantial strength to break apart stomatolites can form in the lake. The next bench contains mudstone layers with clasts of basalt and olivine from the surrounding volcanic tuff, but lacks stromatolitic features. Visible ostrocod shells are abundant in these layers, perhaps suggesting that microorganisms could not compete with grazers at this time to form mats of sufficient size to form stromatolites. Finally, a bench lying about 1.8 m above the current water level is a carbonate rock containing small cavities (mm to a few cm in size) in which cements have formed. Also present are ooids of ~1-2 cm diameter. The mineralogy of these cements, ooids, and stromatolites will be determined by XRD and SEM. These data will be combined with an assessment of microbial 16S rRNA gene phylogeny in order to interpret the stromatolite morphogenesis of this unique lake. By studying stromatolite morphogenesis and microbial ecology in a modern dolomite-precipitating saline maar, we hope to gain a better understanding of the factors that controlled ancient stromatolite morphogenesis; and to examine the extent to which microorganisms versus the environment drive these processes.

Geochemical Influence on Microbial Communities at CO2-Leakage Analog Sites.

PubMed

Ham, Baknoon; Choi, Byoung-Young; Chae, Gi-Tak; Kirk, Matthew F; Kwon, Man Jae

2017-01-01

Microorganisms influence the chemical and physical properties of subsurface environments and thus represent an important control on the fate and environmental impact of CO 2 that leaks into aquifers from deep storage reservoirs. How leakage will influence microbial populations over long time scales is largely unknown. This study uses natural analog sites to investigate the long-term impact of CO 2 leakage from underground storage sites on subsurface biogeochemistry. We considered two sites with elevated CO 2 levels (sample groups I and II) and one control site with low CO 2 content (group III). Samples from sites with elevated CO 2 had pH ranging from 6.2 to 4.5 and samples from the low-CO 2 control group had pH ranging from 7.3 to 6.2. Solute concentrations were relatively low for samples from the control group and group I but high for samples from group II, reflecting varying degrees of water-rock interaction. Microbial communities were analyzed through clone library and MiSeq sequencing. Each 16S rRNA analysis identified various bacteria, methane-producing archaea, and ammonia-oxidizing archaea. Both bacterial and archaeal diversities were low in groundwater with high CO 2 content and community compositions between the groups were also clearly different. In group II samples, sequences classified in groups capable of methanogenesis, metal reduction, and nitrate reduction had higher relative abundance in samples with relative high methane, iron, and manganese concentrations and low nitrate levels. Sequences close to Comamonadaceae were abundant in group I, while the taxa related to methanogens, Nitrospirae , and Anaerolineaceae were predominant in group II. Our findings provide insight into subsurface biogeochemical reactions that influence the carbon budget of the system including carbon fixation, carbon trapping, and CO 2 conversion to methane. The results also suggest that monitoring groundwater microbial community can be a potential tool for tracking CO 2 leakage from geologic storage sites.

Removal of antibiotics and antibiotic resistance genes from domestic sewage by constructed wetlands: Effect of flow configuration and plant species.

PubMed

Chen, Jun; Ying, Guang-Guo; Wei, Xiao-Dong; Liu, You-Sheng; Liu, Shuang-Shuang; Hu, Li-Xin; He, Liang-Ying; Chen, Zhi-Feng; Chen, Fan-Rong; Yang, Yong-Qiang

2016-11-15

This study aims to investigate the removal of antibiotics and antibiotic resistance genes (ARGs) in raw domestic wastewater by various mesocosm-scale constructed wetlands (CWs) with different flow configurations or plant species including the constructed wetland with or without plant. Six mesocosm-scale CWs with three flow types (surface flow, horizontal subsurface flow and vertical subsurface flow) and two plant species (Thaliadealbata Fraser and Iris tectorum Maxim) were set up in the outdoor. 8 antibiotics including erythromycin-H2O (ETM-H2O), monensin (MON), clarithromycin (CTM), leucomycin (LCM), sulfamethoxazole (SMX), trimethoprim (TMP), sulfamethazine (SMZ) and sulfapyridine (SPD) and 12 genes including three sulfonamide resistance genes (sul1, sul2 and sul3), four tetracycline resistance genes (tetG, tetM, tetO and tetX), two macrolide resistance genes (ermB and ermC), two chloramphenicol resistance genes (cmlA and floR) and 16S rRNA (bacteria) were determined in different matrices (water, particle, substrate and plant phases) from the mesocosm-scale systems. The aqueous removal efficiencies of total antibiotics ranged from 75.8 to 98.6%, while those of total ARGs varied between 63.9 and 84.0% by the mesocosm-scale CWs. The presence of plants was beneficial to the removal of pollutants, and the subsurface flow CWs had higher pollutant removal than the surface flow CWs, especially for antibiotics. According to the mass balance analysis, the masses of all detected antibiotics during the operation period were 247,000, 4920-10,600, 0.05-0.41 and 3500-60,000μg in influent, substrate, plant and effluent of the mesocosm-scale CWs. In the CWs, biodegradation, substrate adsorption and plant uptake all played certain roles in reducing the loadings of nutrients, antibiotics and ARGs, but biodegradation was the most important process in the removal of these pollutants. Copyright © 2016 Elsevier B.V. All rights reserved.

Geochemical Influence on Microbial Communities at CO2-Leakage Analog Sites

PubMed Central

Ham, Baknoon; Choi, Byoung-Young; Chae, Gi-Tak; Kirk, Matthew F.; Kwon, Man Jae

2017-01-01

Microorganisms influence the chemical and physical properties of subsurface environments and thus represent an important control on the fate and environmental impact of CO2 that leaks into aquifers from deep storage reservoirs. How leakage will influence microbial populations over long time scales is largely unknown. This study uses natural analog sites to investigate the long-term impact of CO2 leakage from underground storage sites on subsurface biogeochemistry. We considered two sites with elevated CO2 levels (sample groups I and II) and one control site with low CO2 content (group III). Samples from sites with elevated CO2 had pH ranging from 6.2 to 4.5 and samples from the low-CO2 control group had pH ranging from 7.3 to 6.2. Solute concentrations were relatively low for samples from the control group and group I but high for samples from group II, reflecting varying degrees of water-rock interaction. Microbial communities were analyzed through clone library and MiSeq sequencing. Each 16S rRNA analysis identified various bacteria, methane-producing archaea, and ammonia-oxidizing archaea. Both bacterial and archaeal diversities were low in groundwater with high CO2 content and community compositions between the groups were also clearly different. In group II samples, sequences classified in groups capable of methanogenesis, metal reduction, and nitrate reduction had higher relative abundance in samples with relative high methane, iron, and manganese concentrations and low nitrate levels. Sequences close to Comamonadaceae were abundant in group I, while the taxa related to methanogens, Nitrospirae, and Anaerolineaceae were predominant in group II. Our findings provide insight into subsurface biogeochemical reactions that influence the carbon budget of the system including carbon fixation, carbon trapping, and CO2 conversion to methane. The results also suggest that monitoring groundwater microbial community can be a potential tool for tracking CO2 leakage from geologic storage sites. PMID:29170659

Biological CO2 conversion to acetate in subsurface coal-sand formation using a high-pressure reactor system.

PubMed

Ohtomo, Yoko; Ijiri, Akira; Ikegawa, Yojiro; Tsutsumi, Masazumi; Imachi, Hiroyuki; Uramoto, Go-Ichiro; Hoshino, Tatsuhiko; Morono, Yuki; Sakai, Sanae; Saito, Yumi; Tanikawa, Wataru; Hirose, Takehiro; Inagaki, Fumio

2013-01-01

Geological CO2 sequestration in unmineable subsurface oil/gas fields and coal formations has been proposed as a means of reducing anthropogenic greenhouse gasses in the atmosphere. However, the feasibility of injecting CO2 into subsurface depends upon a variety of geological and economic conditions, and the ecological consequences are largely unpredictable. In this study, we developed a new flow-through-type reactor system to examine potential geophysical, geochemical and microbiological impacts associated with CO2 injection by simulating in-situ pressure (0-100 MPa) and temperature (0-70°C) conditions. Using the reactor system, anaerobic artificial fluid and CO2 (flow rate: 0.002 and 0.00001 ml/min, respectively) were continuously supplemented into a column comprised of bituminous coal and sand under a pore pressure of 40 MPa (confined pressure: 41 MPa) at 40°C for 56 days. 16S rRNA gene analysis of the bacterial components showed distinct spatial separation of the predominant taxa in the coal and sand over the course of the experiment. Cultivation experiments using sub-sampled fluids revealed that some microbes survived, or were metabolically active, under CO2-rich conditions. However, no methanogens were activated during the experiment, even though hydrogenotrophic and methylotrophic methanogens were obtained from conventional batch-type cultivation at 20°C. During the reactor experiment, the acetate and methanol concentration in the fluids increased while the δ(13)Cacetate, H2 and CO2 concentrations decreased, indicating the occurrence of homo-acetogenesis. 16S rRNA genes of homo-acetogenic spore-forming bacteria related to the genus Sporomusa were consistently detected from the sandstone after the reactor experiment. Our results suggest that the injection of CO2 into a natural coal-sand formation preferentially stimulates homo-acetogenesis rather than methanogenesis, and that this process is accompanied by biogenic CO2 conversion to acetate.

Biological CO2 conversion to acetate in subsurface coal-sand formation using a high-pressure reactor system

PubMed Central

Ohtomo, Yoko; Ijiri, Akira; Ikegawa, Yojiro; Tsutsumi, Masazumi; Imachi, Hiroyuki; Uramoto, Go-Ichiro; Hoshino, Tatsuhiko; Morono, Yuki; Sakai, Sanae; Saito, Yumi; Tanikawa, Wataru; Hirose, Takehiro; Inagaki, Fumio

2013-01-01

Geological CO2 sequestration in unmineable subsurface oil/gas fields and coal formations has been proposed as a means of reducing anthropogenic greenhouse gasses in the atmosphere. However, the feasibility of injecting CO2 into subsurface depends upon a variety of geological and economic conditions, and the ecological consequences are largely unpredictable. In this study, we developed a new flow-through-type reactor system to examine potential geophysical, geochemical and microbiological impacts associated with CO2 injection by simulating in-situ pressure (0–100 MPa) and temperature (0–70°C) conditions. Using the reactor system, anaerobic artificial fluid and CO2 (flow rate: 0.002 and 0.00001 ml/min, respectively) were continuously supplemented into a column comprised of bituminous coal and sand under a pore pressure of 40 MPa (confined pressure: 41 MPa) at 40°C for 56 days. 16S rRNA gene analysis of the bacterial components showed distinct spatial separation of the predominant taxa in the coal and sand over the course of the experiment. Cultivation experiments using sub-sampled fluids revealed that some microbes survived, or were metabolically active, under CO2-rich conditions. However, no methanogens were activated during the experiment, even though hydrogenotrophic and methylotrophic methanogens were obtained from conventional batch-type cultivation at 20°C. During the reactor experiment, the acetate and methanol concentration in the fluids increased while the δ13Cacetate, H2 and CO2 concentrations decreased, indicating the occurrence of homo-acetogenesis. 16S rRNA genes of homo-acetogenic spore-forming bacteria related to the genus Sporomusa were consistently detected from the sandstone after the reactor experiment. Our results suggest that the injection of CO2 into a natural coal-sand formation preferentially stimulates homo-acetogenesis rather than methanogenesis, and that this process is accompanied by biogenic CO2 conversion to acetate. PMID:24348470

Microbiology of Ultrabasic Groundwaters of the Coast Range Ophiolite, California

NASA Astrophysics Data System (ADS)

Schrenk, M. O.; Brazelton, W. J.; Twing, K. I.; Kubo, M.; Cardace, D.; Hoehler, T. M.; McCollom, T. M.

2013-12-01

Upon exposure to water, ultramafic rocks characteristic of the Earth's mantle undergo a process known as serpentinization. These water-rock reactions lead to highly reducing conditions and some of the highest pH values reported in nature. In contrast to alkaline soda lakes, actively serpentinizing environments exposed on land are commonly associated with low salinity freshwaters, imparting unique challenges upon their resident microbial communities. These environments are especially prevalent along continental margins, and cover extensive portions of the west coast of North America. Most studies of serpentinizing environments have focused upon springs that emanate from fractures in the subsurface. Here, we present microbiological data from a series of groundwater wells associated with active serpentinization in the California Coast Range, an ophiolite complex near Lower Lake, California. Waters from ultrabasic wells had lower microbial cell concentrations and diversity than were found in moderate pH wells in the same area. Bacteria consistently made up a higher proportion of the microbial communities compared to Archaea as determined by qPCR. High pH wells were dominated by taxa within the Betaproteobacteria and Clostridia, whereas moderate pH wells predominantly contained common soil taxa related to Gammaproteobacteria and Bacilli. Multivariate statistical analyses incorporating key environmental parameters supported these observations and also highlighted correlations between the high-pH taxa and the abundance of hydrogen and methane gas. Similarly, colony forming units of alkaliphilic microorganisms were consistently 1-2 orders of magnitude higher in the ultrabasic wells and were taxonomically distinct from the moderate pH groundwaters. Together, these results show that distinct populations inhabit subsurface environments associated with active serpentinization, consistent with previous observations, and suggest that Betaproteobacteria and Clostridia probably play significant roles in the microbiology of these ecosystems. The low diversity microbial communities of serpentinizing subsurface habitats are likely sustained by the high hydrogen and methane fluxes that emanate from such systems and further investigations will directly test their roles in mediating biogeochemical cycles in these environments.

Fungal and Prokaryotic Activities in the Marine Subsurface Biosphere at Peru Margin and Canterbury Basin Inferred from RNA-Based Analyses and Microscopy

PubMed Central

Pachiadaki, Maria G.; Rédou, Vanessa; Beaudoin, David J.; Burgaud, Gaëtan; Edgcomb, Virginia P.

2016-01-01

The deep sedimentary biosphere, extending 100s of meters below the seafloor harbors unexpected diversity of Bacteria, Archaea, and microbial eukaryotes. Far less is known about microbial eukaryotes in subsurface habitats, albeit several studies have indicated that fungi dominate microbial eukaryotic communities and fungal molecular signatures (of both yeasts and filamentous forms) have been detected in samples as deep as 1740 mbsf. Here, we compare and contrast fungal ribosomal RNA gene signatures and whole community metatranscriptomes present in sediment core samples from 6 and 95 mbsf from Peru Margin site 1229A and from samples from 12 and 345 mbsf from Canterbury Basin site U1352. The metatranscriptome analyses reveal higher relative expression of amino acid and peptide transporters in the less nutrient rich Canterbury Basin sediments compared to the nutrient rich Peru Margin, and higher expression of motility genes in the Peru Margin samples. Higher expression of genes associated with metals transporters and antibiotic resistance and production was detected in Canterbury Basin sediments. A poly-A focused metatranscriptome produced for the Canterbury Basin sample from 345 mbsf provides further evidence for active fungal communities in the subsurface in the form of fungal-associated transcripts for metabolic and cellular processes, cell and membrane functions, and catalytic activities. Fungal communities at comparable depths at the two geographically separated locations appear dominated by distinct taxa. Differences in taxonomic composition and expression of genes associated with particular metabolic activities may be a function of sediment organic content as well as oceanic province. Microscopic analysis of Canterbury Basin sediment samples from 4 and 403 mbsf produced visualizations of septate fungal filaments, branching fungi, conidiogenesis, and spores. These images provide another important line of evidence supporting the occurrence and activity of fungi in the deep subseafloor biosphere. PMID:27375571

Delving into the Deep Biosphere

NASA Astrophysics Data System (ADS)

Grim, S. L.; Sogin, M. L.; Boetius, A.; Briggs, B. R.; Brazelton, W. J.; D'Hondt, S. L.; Edwards, K. J.; Fisk, M. R.; Gaidos, E.; Gralnick, J.; Hinrichs, K.; Lazar, C.; Lavalleur, H.; Lever, M. A.; Marteinsson, V.; Moser, D. P.; Orcutt, B.; Pedersen, K.; Popa, R.; Ramette, A.; Schrenk, M. O.; Sylvan, J. B.; Smith, A. R.; Teske, A.; Walsh, E. A.; Colwell, F. S.

2013-12-01

The Census of Deep Life organized an international survey of microbial community diversity in terrestrial and marine deep subsurface environments. Habitats included subsurface continental fractured rock aquifers, volcanic and metamorphic subseafloor sedimentary units from the open ocean, subsurface oxic and anoxic sediments and underlying basaltic oceanic crust, and their overlying water columns. Our survey employed high-throughput pyrosequencing of the hypervariable V4-V6 16S rRNA gene of bacteria and archaea. We detected 1292 bacterial genera representing 40 phyla, and 99 archaeal genera from 30 phyla. Of these, a core group of thirteen bacterial genera occurred in every environment. A genus of the South African Goldmine Group (Euryarchaeota) was always present whenever archaea were detected. Members of the rare biosphere in one system often represented highly abundant taxa in other environments. Dispersal could account for this observation but mechanisms of transport remain elusive. Ralstonia (Betaproteobacteria) represented highly abundant taxa in marine communities and terrestrial rock, but generally low abundance organisms in groundwater. Some of these taxa could represent sample contamination, and their extensive distribution in several systems requires further assessment. An unknown Sphingobacteriales (Bacteroidetes) genus, Stenotrophomonas (Gammaproteobacteria), Acidovorax and Aquabacterium (both Betaproteobacteria), a Chlorobiales genus, and a TM7 genus were in the core group as well but more prevalent in terrestrial environments. Similarly, Bacillus (Firmicutes), a new cyanobacterial genus, Bradyrhizobium and Sphingomonas (both Alphaproteobacteria), a novel Acidobacteriaceae genus, and Variovorax (Betaproteobacteria) frequently occurred in marine systems but represented low abundance taxa in other environments. Communities tended to cluster by biome and material, and many genera were unique to systems. For example, certain Rhizobiales (Alphaproteobacteria) only occurred in groundwater, and select Firmicutes and actinobacterial taxa were specific to rock environments. We continue to investigate the ecological and physiological context of these organisms. By combining deep sequencing of microbial communities and geochemical and physical evaluations of their environments, we bring to light the diversity and scope of the deep biosphere and insight into the factors that determine the nature of these communities.

Metabolic potential of a Novel Gram-Negative, Spore-forming, and Putatively Sulfate-Reducing Bacterium in the Continental Subsurface

NASA Astrophysics Data System (ADS)

Lau, C. Y. M.; Becraft, E. D.; Cason, E. D.; Borgonie, G.; Kieft, T. L.; Li, L.; van Heerden, E.; Jarett, J.; Woyke, T.; Stepanauskas, R.; Onstott, T. C.

2017-12-01

Anaerobic sulfate reduction is among the most thermodynamically favorable biochemical reactions in the deep subsurface environments. Phylogenetically and functionally diverse sulfate-reducing bacteria (SRB) within Deltaproteobacteria and Firmicutes have been reported. However, only few of them have been isolated in pure cultures for detailed physiological characterization. Previous studies showed that fracture fluid samples from the 1 km-deep borehole DR5IPC (Driefontein gold mine, South Africa) harbored novel SRB, as indicated by the low percentages (84% and 90%) of identity of the 16S ribosomal RNA clone sequences to known SRB. To overcome the challenge of low cultivability, we employed next-generation sequencing to unveil the metabolic potential of these novel SRB. Metagenomic assembly and binning yielded seven >50% complete genomes including a methylotrophic SRB belonging to Deltaproteobacteria (DR5_3) and two draft genomes representing an uncultivated phylum, tentatively "Driefonteinae" (DR5_4 and DR5_5). They accounted for 3%, 2% and 18% of all metagenomic reads. Three single-cell assembled genomes (SAGs) sharing 99% of average nucleotide identity (ANI) with DR5_5 were obtained. Analysis of the protein-coding genes in DR5_5 and related SAGs indicated that "Driefonteinae" possesses dissimilatory sulfite reductase genes (dsrAB), suggesting that sulfate would be the terminal electron acceptor. Whereas it may use diverse electron acceptors such as carbon monoxide, acetate, lactate and formate. A near-complete collection of genes for Wood-Ljungdahl pathway and genes for partial pentose phosphate pathway, glycolysis and tricarboxylic acid cycle further showed that "Driefonteinae" may live a mixotrophic life style. It is evident that archaeal genes related to methanogens were acquired through horizontal gene transfer. Phenotypically, "Driefonteinae" has a Gram-negative cell wall and flagella. The ability of forming spores would enable this microorganism to endure adverse conditions. Genomic analysis has provided an invaluable avenue to reveal novel microbial players in the subsurface sulfur cycle.

The Ability of Microbial Community of Lake Baikal Bottom Sediments Associated with Gas Discharge to Carry Out the Transformation of Organic Matter under Thermobaric Conditions

PubMed Central

Bukin, Sergei V.; Pavlova, Olga N.; Manakov, Andrei Y.; Kostyreva, Elena A.; Chernitsyna, Svetlana M.; Mamaeva, Elena V.; Pogodaeva, Tatyana V.; Zemskaya, Tamara I.

2016-01-01

The ability to compare the composition and metabolic potential of microbial communities inhabiting the subsurface sediment in geographically distinct locations is one of the keys to understanding the evolution and function of the subsurface biosphere. Prospective areas for study of the subsurface biosphere are the sites of hydrocarbon discharges on the bottom of the Lake Baikal rift, where ascending fluxes of gas-saturated fluids and oil from deep layers of bottom sediments seep into near-surface sediment. The samples of surface sediments collected in the area of the Posolskaya Bank methane seep were cultured for 17 months under thermobaric conditions (80°C, 5 MPa) with the addition of complementary organic substrate, and a different composition for the gas phase. After incubation, the presence of intact cells of microorganisms, organic matter transformation and the formation of oil biomarkers was confirmed in the samples, with the addition of Baikal diatom alga Synedra acus detritus, and gas mixture CH4:H2:CO2. Taxonomic assignment of the 16S rRNA sequence data indicates that the predominant sequences in the enrichment were Sphingomonas (55.3%), Solirubrobacter (27.5%) and Arthrobacter (16.6%). At the same time, in heat-killed sediment and in sediment without any additional substrates, which were cultivated in a CH4 atmosphere, no geochemical changes were detected, nor the presence of intact cells and 16S rRNA sequences of Bacteria and Archaea. This data may suggest that the decomposition of organic matter under culturing conditions could be performed by microorganisms from low-temperature sediment layers. One possible explanation of this phenomenon is migration of the representatives of the deep thermophilic community through fault zones in the near surface sediment layers, together with gas-bearing fluids. PMID:27242716

Fungal and Prokaryotic Activities in the Marine Subsurface Biosphere at Peru Margin and Canterbury Basin Inferred from RNA-Based Analyses and Microscopy.

PubMed

Pachiadaki, Maria G; Rédou, Vanessa; Beaudoin, David J; Burgaud, Gaëtan; Edgcomb, Virginia P

2016-01-01

The deep sedimentary biosphere, extending 100s of meters below the seafloor harbors unexpected diversity of Bacteria, Archaea, and microbial eukaryotes. Far less is known about microbial eukaryotes in subsurface habitats, albeit several studies have indicated that fungi dominate microbial eukaryotic communities and fungal molecular signatures (of both yeasts and filamentous forms) have been detected in samples as deep as 1740 mbsf. Here, we compare and contrast fungal ribosomal RNA gene signatures and whole community metatranscriptomes present in sediment core samples from 6 and 95 mbsf from Peru Margin site 1229A and from samples from 12 and 345 mbsf from Canterbury Basin site U1352. The metatranscriptome analyses reveal higher relative expression of amino acid and peptide transporters in the less nutrient rich Canterbury Basin sediments compared to the nutrient rich Peru Margin, and higher expression of motility genes in the Peru Margin samples. Higher expression of genes associated with metals transporters and antibiotic resistance and production was detected in Canterbury Basin sediments. A poly-A focused metatranscriptome produced for the Canterbury Basin sample from 345 mbsf provides further evidence for active fungal communities in the subsurface in the form of fungal-associated transcripts for metabolic and cellular processes, cell and membrane functions, and catalytic activities. Fungal communities at comparable depths at the two geographically separated locations appear dominated by distinct taxa. Differences in taxonomic composition and expression of genes associated with particular metabolic activities may be a function of sediment organic content as well as oceanic province. Microscopic analysis of Canterbury Basin sediment samples from 4 and 403 mbsf produced visualizations of septate fungal filaments, branching fungi, conidiogenesis, and spores. These images provide another important line of evidence supporting the occurrence and activity of fungi in the deep subseafloor biosphere.

The Ability of Microbial Community of Lake Baikal Bottom Sediments Associated with Gas Discharge to Carry Out the Transformation of Organic Matter under Thermobaric Conditions.

PubMed

Bukin, Sergei V; Pavlova, Olga N; Manakov, Andrei Y; Kostyreva, Elena A; Chernitsyna, Svetlana M; Mamaeva, Elena V; Pogodaeva, Tatyana V; Zemskaya, Tamara I

2016-01-01

The ability to compare the composition and metabolic potential of microbial communities inhabiting the subsurface sediment in geographically distinct locations is one of the keys to understanding the evolution and function of the subsurface biosphere. Prospective areas for study of the subsurface biosphere are the sites of hydrocarbon discharges on the bottom of the Lake Baikal rift, where ascending fluxes of gas-saturated fluids and oil from deep layers of bottom sediments seep into near-surface sediment. The samples of surface sediments collected in the area of the Posolskaya Bank methane seep were cultured for 17 months under thermobaric conditions (80°C, 5 MPa) with the addition of complementary organic substrate, and a different composition for the gas phase. After incubation, the presence of intact cells of microorganisms, organic matter transformation and the formation of oil biomarkers was confirmed in the samples, with the addition of Baikal diatom alga Synedra acus detritus, and gas mixture CH4:H2:CO2. Taxonomic assignment of the 16S rRNA sequence data indicates that the predominant sequences in the enrichment were Sphingomonas (55.3%), Solirubrobacter (27.5%) and Arthrobacter (16.6%). At the same time, in heat-killed sediment and in sediment without any additional substrates, which were cultivated in a CH4 atmosphere, no geochemical changes were detected, nor the presence of intact cells and 16S rRNA sequences of Bacteria and Archaea. This data may suggest that the decomposition of organic matter under culturing conditions could be performed by microorganisms from low-temperature sediment layers. One possible explanation of this phenomenon is migration of the representatives of the deep thermophilic community through fault zones in the near surface sediment layers, together with gas-bearing fluids.

Lunar and Planetary Science XXXV: Astrobiology: Analogs and Applications to the Search for Life

NASA Technical Reports Server (NTRS)

2004-01-01

The session "Astrobiology: Analogs and Applications to the Search for Life" included the folowing reports:The Search for Life on Mars Using Macroscopically Visible Microbial Mats (Stromatolites) in 3.5/3.3 Ga Cherts from the Pilbara in Australia and Barberton in South Africa as Analogues; Life in a Mars Analog: Microbial Activity Associated with Carbonate Cemented Lava Breccias from NW Spitsbergen; Groundwater-fed Iron-rich Microbial Mats in a Freshwater Creek: Growth Cycles and Fossilization Potential of Microbial Features; Episodic Fossilization of Microorganisms on an Annual Timescale in an Anthropogenically Modified Natural Environment: Geochemical Controls and Implications for Astrobiology; Proterozoic Microfossils and Their Implications for Recognizing Life on Mars; Microbial Alteration of Volcanic Glass in Modern and Ancient Oceanic Crust as a Proxy for Studies of Extraterrestrial Material ; Olivine Alteration on Earth and Mars; Searching for an Acidic Aquifer in the R!o Tinto Basin. First Geobiology Results of MARTE Project; In-Field Testing of Life Detection Instruments and Protocols in a Mars Analogue Arctic Environment; Habitability of the Shallow Subsurface on Mars: Clues from the Meteorites; Mars Analog Rio Tinto Experiment (MARTE): 2003 Drilling Campaign to Search for a Subsurface Biosphere at Rio Tinto Spain; Characterization of the Organic Matter in an Archean Chert (Warrawoona, Australia); and The Solfatara Crater, Italy: Characterization of Hydrothermal Deposits, Biosignatures and Their Astrobiological Implication.

Water use efficiency of different sugarcane genotypes irrigated by a subsurface drip irrigation system

NASA Astrophysics Data System (ADS)

Silva, A. L. B. O.; Pires, R. C. M.; Ribeiro, R. V.; Machado, E. C.; Rolim, G. S.; Magalhães Filho, J. R.; Marchiori, P. E. R.

2012-04-01

The biofuel production is a growing concern on modern society due to the agricultural sustainability, in which both food and energy supplying should be take into account. The agroclimatic zoning indicates that sugarcane expansion in Brazil can only take place in marginal lands, where water deficit occurs and irrigation is necessary. The aim of this work was to evaluate water consumption and the water use efficiency of two sugarcane genotypes irrigated by a subsurface drip irrigation system. The field experiment was carried out in Campinas SP Brazil, with IACSP95-5000 and SP79-1011 varieties. Those varieties have different canopy characteristics and development, with IACSP95-5000 being more responsive to soil water availability and presenting higher light interception when compared to SP79-1011. Crop evapotranspiration (ETc) was calculated through field water balance from August 2010 to March 2011. Soil water content was evaluated by using a capacitance probe, sampling different depths in soil profile until 1-m. IACSP95-5000 had higher water consumption than SP79-1011. The mean ETc value of IACSP95-5000 was 5.0 mm day-1, whereas SP79-1011 showed 3.7 mm day-1. ETc values were positively correlated to biomass production, with IACSP95-5000 exhibiting higher growth and water use efficiency than SP79-1011.

Constraints on mechanisms and rates of anaerobic oxidation of methane by microbial consortia: process-based modeling of ANME-2 archaea and sulfate reducing bacteria interactions

NASA Astrophysics Data System (ADS)

Orcutt, B.; Meile, C.

2008-05-01

Anaerobic oxidation of methane (AOM) is the main process responsible for the removal of methane generated in Earth's marine subsurface environments. However, the biochemical mechanism of AOM remains elusive. By explicitly resolving the observed spatial arrangement of methanotrophic archaea and sulfate reducing bacteria found in consortia mediating AOM, potential intermediates involved in the electron transfer between the methane oxidizing and sulfate reducing partners were investigated via a consortium-scale reaction transport model that integrates the effect of diffusional transport with thermodynamic and kinetic controls on microbial activity. Model simulations were used to assess the impact of poorly constrained microbial characteristics such as minimum energy requirements to sustain metabolism, substrate affinity and cell specific rates. The role of environmental conditions such as the influence of methane levels on the feasibility of H2, formate and acetate as intermediate species, and the impact of the abundance of intermediate species on pathway reversal was examined. The results show that higher production rates of intermediates via AOM lead to increased diffusive fluxes from the methane oxidizing archaea to sulfate reducing bacteria, but the build-up of the exchangeable species causes the energy yield of AOM to drop below that required for ATP production. Comparison to data from laboratory experiments shows that under the experimental conditions of Nauhaus et al. (2007), neither hydrogen nor formate is exchanged fast enough between the consortia partners to achieve measured rates of metabolic activity, but that acetate exchange might support rates that approach those observed.

Enhanced U(VI) release from autunite mineral by aerobic Arthrobacter sp. in the presence of aqueous bicarbonate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Katsenovich, Yelena P.; Carvajal, Denny A.; Wellman, Dawn M.

2012-05-01

The bacterial effect on U(VI) release from the autunite mineral (Ca[(UO2)(PO4)]2•3H2O) was investigated to provide a more comprehensive understanding of the important microbiological processes affecting autunite stability within subsurface bicarbonate-bearing environments. Experiments were performed in a culture of the Arthrobacter oxydans G975 strain, herein referred to as G975, a soil bacterium previously isolated from Hanford Site soil. 91 mg of autunite powder and 50 mL of phosphorous-limiting sterile media were amended with bicarbonate (ranging between 1 and 10 mM) in glass reactor bottles and inoculated with the G975 strain after the dissolution of autunite was at steady state. SEM observationsmore » indicated that G975 formed a biofilm on the autunite surface and penetrated the mineral cleavages. The mineral surface colonization by bacteria tended to increase concomitantly with bicarbonate concentrations. Additionally, a sterile culture-ware with inserts was used in non-contact dissolution experiments where autunite and bacteria cells were kept separately. The data suggest that G975 bacteria is able to enhance the release of U(VI) from autunite without direct contact with the mineral. In the presence of bicarbonate, the damage to bacterial cells caused by U(VI) toxicity was reduced, yielding similar values for total organic carbon (TOC) degradation and cell density compared to U(VI)-free controls. The presence of active bacterial cells greatly enhanced the release of U(VI) from autunite in bicarbonate-amended media.« less

Enhanced U(VI) release from autunite mineral by aerobic Arthrobacter sp. in the presence of aqueous bicarbonate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Katsenovich, Yelena; Carvajal, Denny A.; Wellman, Dawn M.

2012-04-20

The bacterial effect on U(VI) leaching from the autunite mineral (Ca[(UO{sub 2})(PO{sub 4})]{sub 2} {center_dot} 3H{sub 2}O) was investigated to provide a more comprehensive understanding into important microbiological processes affecting autunite stability within subsurface bicarbonate-bearing environments. Experiments were performed in a culture of G975 Arthrobacter oxydans strain, herein referred to as G975, a soil bacterium previously isolated from Hanford Site soil. 91 mg of autunite powder and 50 mL of phosphorus-limiting sterile media were amended with bicarbonate ranging between 1-10 mM in glass reactor bottles and inoculated with G975 strain after the dissolution of autunite was at steady state. SEMmore » observations indicated G975 formed a biofilm on the autunite surface and penetrated the mineral cleavages. The mineral surface colonization by bacteria tended to increase concomitantly with bicarbonate concentrations. Additionally, a sterile cultureware with inserts was used in non-contact bioleaching experiments where autunite and bacteria cells were kept separately. The data suggest the G975 bacteria is able to enhance U(VI) leaching from autunite without the direct contact with the mineral. In the presence of bicarbonate, the damage to bacterial cells caused by U(VI) toxicity was reduced, yielding similar values for total organic carbon (TOC) degradation and cell density compared to U(VI)-free controls. The presence of active bacterial cells greatly enhanced the U(VI) bioleaching from autunite in bicarbonate-amended media.« less

Adaptive Wavelet Modeling of Geophysical Data

NASA Astrophysics Data System (ADS)

Plattner, A.; Maurer, H.; Dahmen, W.; Vorloeper, J.

2009-12-01

Despite the ever-increasing power of modern computers, realistic modeling of complex three-dimensional Earth models is still a challenging task and requires substantial computing resources. The overwhelming majority of current geophysical modeling approaches includes either finite difference or non-adaptive finite element algorithms, and variants thereof. These numerical methods usually require the subsurface to be discretized with a fine mesh to accurately capture the behavior of the physical fields. However, this may result in excessive memory consumption and computing times. A common feature of most of these algorithms is that the modeled data discretizations are independent of the model complexity, which may be wasteful when there are only minor to moderate spatial variations in the subsurface parameters. Recent developments in the theory of adaptive numerical solvers have the potential to overcome this problem. Here, we consider an adaptive wavelet based approach that is applicable to a large scope of problems, also including nonlinear problems. To the best of our knowledge such algorithms have not yet been applied in geophysics. Adaptive wavelet algorithms offer several attractive features: (i) for a given subsurface model, they allow the forward modeling domain to be discretized with a quasi minimal number of degrees of freedom, (ii) sparsity of the associated system matrices is guaranteed, which makes the algorithm memory efficient, and (iii) the modeling accuracy scales linearly with computing time. We have implemented the adaptive wavelet algorithm for solving three-dimensional geoelectric problems. To test its performance, numerical experiments were conducted with a series of conductivity models exhibiting varying degrees of structural complexity. Results were compared with a non-adaptive finite element algorithm, which incorporates an unstructured mesh to best fit subsurface boundaries. Such algorithms represent the current state-of-the-art in geoelectrical modeling. An analysis of the numerical accuracy as a function of the number of degrees of freedom revealed that the adaptive wavelet algorithm outperforms the finite element solver for simple and moderately complex models, whereas the results become comparable for models with spatially highly variable electrical conductivities. The linear dependency of the modeling error and the computing time proved to be model-independent. This feature will allow very efficient computations using large-scale models as soon as our experimental code is optimized in terms of its implementation.

AIDA - from Airborne Data Inversion to In-Depth Analysis

NASA Astrophysics Data System (ADS)

Meyer, U.; Goetze, H.; Schroeder, M.; Boerner, R.; Tezkan, B.; Winsemann, J.; Siemon, B.; Alvers, M.; Stoll, J. B.

2011-12-01

The rising competition in land use especially between water economy, agriculture, forestry, building material economy and other industries often leads to irreversible deterioration in the water and soil system (as salinization and degradation) which results in a long term damage of natural resources. A sustainable exploitation of the near subsurface by industry, economy and private households is a fundamental demand of a modern society. To fulfill this demand, a sound and comprehensive knowledge on structures and processes of the near subsurface is an important prerequisite. A spatial survey of the usable underground by aerogeophysical means and a subsequent ground geophysics survey targeted at special locations will deliver essential contributions within short time that make it possible to gain the needed additional knowledge. The complementary use of airborne and ground geophysics as well as the validation, assimilation and improvement of current findings by geological and hydrogeological investigations and plausibility tests leads to the following key questions: a) Which new and/or improved automatic algorithms (joint inversion, data assimilation and such) are useful to describe the structural setting of the usable subsurface by user specific characteristics as i.e. water volume, layer thicknesses, porosities etc.? b) What are the physical relations of the measured parameters (as electrical conductivities, magnetic susceptibilities, densities, etc.)? c) How can we deduce characteristics or parameters from the observations which describe near subsurface structures as ground water systems, their charge, discharge and recharge, vulnerabilities and other quantities? d) How plausible and realistic are the numerically obtained results in relation to user specific questions and parameters? e) Is it possible to compile material flux balances that describe spatial and time dependent impacts of environmental changes on aquifers and soils by repeated airborne surveys? In order to follow up these questions raised the project aims to achieve the following goals: a) Development of new and expansion of existent inversion strategies to improve structural parameter information on different space and time scales. b) Development, modification, and tests for a multi-parameter inversion (joint inversion). c) Development of new quantitative approaches in data assimilation and plausibility studies. d) Compilation of optimized work flows for fast employment by end users. e) Primary goal is to solve comparable society related problems (as salinization, erosion, contamination, degradation etc.) in regions within Germany and abroad by generalization of project results.

Final Technical Report: Viral Infection of Subsurface Microorganisms and Metal/Radionuclide Transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weber, Karrie A.; Bender, Kelly S.; Li, Yusong

Microbially mediated metabolisms have been identified as a significant factor either directly or indirectly impacting the fate and transport of heavy metal/radionuclide contaminants. To date microorganisms have been isolated from contaminated environments. Examination of annotated finished genome sequences of many of these subsurface isolates from DOE sites, revealed evidence of prior viral infection. To date the role that viruses play influencing microbial mortality and the resulting community structure which directly influences biogeochemical cycling in soils and sedimentary environments remains poorly understood. The objective of this exploratory study was to investigate the role of viral infection of subsurface bacteria and themore » formation of contaminant-bearing viral particles. This objective was approached by examining the following working hypotheses: (i) subsurface microorganisms are susceptible to viral infections by the indigenous subsurface viral community, and (ii) viral surfaces will adsorb heavy metals and radionuclides. Our results have addressed basic research needed to accomplish the BER Long Term Measure to provide sufficient scientific understanding such that DOE sites would be able to incorporate coupled physical, chemical and biological processes into decision making for environmental remediation or natural attenuation and long-term stewardship by establishing viral-microbial relationships on the subsequent fate and transport of heavy metals and radionuclides. Here we demonstrated that viruses play a significant role in microbial mortality and community structure in terrestrial subsurface sedimentary systems. The production of viral-like particles within subsurface sediments in response to biostimulation with dissolved organic carbon and a terminal electron acceptor resulted in the production of viral-like particles. Organic carbon alone did not result in significant viral production and required the addition of a terminal electron acceptor (nitrate), indicating that nutrients are not limiting viral production, but rather substrates that can be converted into energy for host metabolism. Our results also revealed that cell abundance was not correlated to the mineralization of organic carbon, but rather viruses were positively correlated with carbon mineralization. This is a result of viral-mediated cell lysis and demonstrates that viruses are sensitive indicators of microbial activity. Viruses as an indicator of microbial activity was not unique to batch culture studies as results obtained from an in situ field experiment conducted at the DOE Old Rifle Field site. This study revealed that viral abundance increased in response to the injection of oxygenated groundwater and influx of dissolved organic carbon whereas cell abundance changes were minimal. However, the extent to which viral-mediated cell lysis alters organic matter pools subsequently influencing microbial community structure and biogeochemical function remains a critical question in subsurface biogeochemical cycling. The production of significant numbers of viruses in groundwater has implications for nanoparticulate metal as well as carbon transport in groundwater. We have demonstrated that the virus surface is reactive and will adsorb heavy metals. Thus viruses can promote colloidal contaminant mobility. Interestingly, the presence of heavy metals has a positive effect on infectivity of the phage, increasing phage infection which could lead to further production of viruses. Together, the results indicate that the sorption of metals to the surface of viruses could not only contribute to nanoparticulate metal as well as carbon transport but could also enhance infectivity further contributing to cell lysis which could subsequently influence biogeochemical cycling. As more viruses infect host microbial populations the high concentration of metals would enhance infection, resulting in cell lysis, and decreasing the metabolically active host population while yielding greater numbers of viruses capable of transporting contaminats. Additional studies will be necessary to further establish the potential relationship(s) between viruses, cells, carbon, and metals/radionuclides to provide sufficient scientific understanding to incorporate coupled physical, chemical, and biological processes into agent based and reactive transport models.« less

Molecular Probes: A Tool for Studying Toxicity of VOCs to P.Putida F1

NASA Astrophysics Data System (ADS)

Singh, R.; Olson, M. S.

2007-12-01

Volatile Organic Compounds (VOCs) are of great concern in ground water remediation, and are generally present in the form of NAPLs in subsurface environments. Among the various treatment technologies, in situ bioremediation is one of the most effective and low-cost treatment options. Many soil bacteria are reported to degrade these organic contaminants via metabolism (using them as a source of carbon to derive energy) or co- metabolism up to certain concentrations. However, larger concentrations of these contaminants are toxic to bacteria. Thus, in order to achieve successful bioremediation, it is important to determine the optimal concentrations of various contaminants that is beneficial for the activity and survival of degrading bacteria. The purpose of this study is to develop a novel method for toxicity analyses of VOC contaminants to the soil bacteria that degrade them. The present study is based on a two-color fluorescence assay of bacterial viability which facilitates actual counting of live and dead bacteria. Pseudomonas putida F1 cells were labeled with a LIVE/DEAD® BacLightTM bacterial viability kit (Invitrogen), which consists of a mixture of two dyes, SYTO 9 and propidium iodide, each with a different ability to penetrate healthy bacterial cells. Live cells stain green whereas propidium iodide (red dye) only penetrates cells with compromised membranes that are considered dead or dying. Stained cells were exposed to different concentrations of trichloroethylene (TCE) and toluene in sealed vials. Change in the concentrations of green and red cells were monitored over the time using fluorescence microscopy. UTHSCSA ImageTool software was used to count the live and dead cells in the images. It was observed that live (green) cell concentrations decreased and dead/damaged (red) cell concentrations increased over time when cells were exposed to TCE. No significant changes were observed in control experiments. Death rate constants calculated based on live cell disappearance and dead/damaged cell appearance were found to be approximately equal for TCE. Results will be presented in terms of dose response and death rate curves. Death rate constants and minimum inhibitory concentrations for survival of P. Putida F1 exposed to TCE and toluene will be compared.

Detecting Organic Compounds Released from Iron Oxidizing Bacteria using Sample Analysis at Mars (SAM) Like Instrument Protocols

NASA Technical Reports Server (NTRS)

Glavin, D. P.; Popa, R.; Martin, M. G.; Freissinet, C.; Fisk, M. R.; Dworkin, J. P.; Mahaffy, P. R.

2012-01-01

Mars is a planet of great interest for Astrobiology since its past environmental conditions are thought to have been favourable for the emergence life. At present, the Red Planet is extremely cold and dry and the surface is exposed to intense UV and ionizing radiation, conditions generally considered to be incompatible with life as we know it on Earth. It was proposed that the shallow subsurface of Mars, where temperatures can be above freezing and liquid water can exist on rock surfaces, could harbor chemolithoautotrophic bacteria such as the iron oxidizing microorganism Pseudomonas sp. HerB. The Mars Science Laboratory (MSL) mission will provide the next opportunity to carry out in situ measurements for organic compounds of possible biological origin on Mars. One instrument onboard MSL, called the Sample Analysis at Mars (SAM) instrument suite, will carry out a broad and sensitive search for organic compounds in surface samples using either high temperature pyrolysis or chemical extraction followed by gas chromatography mass spectrometry. We present gas chromatograph mass spectrometer (GC/MS) data on crushed olivine rock powders that have been inoculated with Pseudomonas sp. HerB at different concentrations ranging from approx 10(exp 2) to 10(exp 7) cells per gram. The inoculated olivine samples were heated under helium carrier gas flow at 500 C and the pyrolysis products concentrated using a SAM-like hydrocarbon trap set at -20 C followed by trap heating and analysis by GC/Ms. In addition, the samples were also extracted using a low temperature "one-pot" chemical extraction technique using N-methyl, N-(tert-butyldimethylsilyl) trifluoroacetamide (MTBSTFA) as the silylating agent prior to GC/MS analysis. We identified several aldehydes, thiols, and alkene nitriles after pyrolysis GC/MS analysis of the bacteria that were not found in the olivine control samples that had not been inoculated with bacteria. The distribution of pyrolysis products extracted from the bacteria was clearly distinct from similar GC/MS analyses of the carbonaceous meteorite Murchison that was dominated by sulfur containing aromatic compounds. A similar comparison, if organic compounds are detected by SAM on Mars, could be useful to help discriminate between meteoritic or biological origins.

Evaluation of nutrient removal efficiency and microbial enzyme activity in a baffled subsurface-flow constructed wetland system

Treesearch

Lihua Cui; Ying Ouyang; Wenjie Gu; Weozhi Yang; Qiaoling Xu

2013-01-01

In this study, the enzyme activities and their relationships to domestic wastewater purification are investigated in four different types of subsurface-flow constructed wetlands (CWs), namely the traditional horizontal subsurface-flow, horizontal baffled subsurface-flow, vertical baffled subsurface-flow, and composite baffled subsurface-flow CWs. Results showed that...

Pleistocene hydrology of North America: The role of ice sheets in reorganizing groundwater flow systems

NASA Astrophysics Data System (ADS)

Person, Mark; McIntosh, Jennifer; Bense, Victor; Remenda, V. H.

2007-09-01

While the geomorphic consequences of Pleistocene megafloods have been known for some time, it has been only in the past 2 decades that hydrogeologists and glaciologists alike have begun to appreciate the important impact that ice sheet-aquifer interactions have had in controlling subsurface flow patterns, recharge rates, and the distribution of fresh water in confined aquifer systems across North America. In this paper, we document the numerous lines of geochemical, isotopic, and geomechanical evidence of ice sheet hydrogeology across North America. We also review the mechanical, thermal, and hydrologic processes that control subsurface fluid migration beneath ice sheets. Finite element models of subsurface fluid flow, permafrost formation, and ice sheet loading are presented to investigate the coupled nature of transport processes during glaciation/deglaciation. These indicate that recharge rates as high as 10 times modern values occurred as the Laurentide Ice Sheet overran the margins of sedimentary basins. The effects of ice sheet loading and permafrost formation result in complex transient flow patterns within aquifers and confining units alike. Using geochemical and environmental isotopic data, we estimate that the volume of glacial meltwater emplaced at the margins of sedimentary basins overrun by the Laurentide Ice Sheet totals about 3.7 × 104 km3, which is about 0.2% of the volume of the Laurentide Ice Sheet. Subglacial infiltration estimates based on continental-scale hydrologic models are even higher (5-10% of meltwater generated). These studies in sum call into question the widely held notion that groundwater flow patterns within confined aquifer systems are controlled primarily by the water table configuration during the Pleistocene. Rather, groundwater flow patterns were likely much more complex and transient in nature than has previously been thought. Because Pleistocene recharge rates are believed to be highly variable, these studies have profound implications for water resource managers charged with determining sustainable pumping rates from confined aquifers that host ice sheet meltwater.

Accelerating Subsurface Transport Simulation on Heterogeneous Clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Villa, Oreste; Gawande, Nitin A.; Tumeo, Antonino

Reactive transport numerical models simulate chemical and microbiological reactions that occur along a flowpath. These models have to compute reactions for a large number of locations. They solve the set of ordinary differential equations (ODEs) that describes the reaction for each location through the Newton-Raphson technique. This technique involves computing a Jacobian matrix and a residual vector for each set of equation, and then solving iteratively the linearized system by performing Gaussian Elimination and LU decomposition until convergence. STOMP, a well known subsurface flow simulation tool, employs matrices with sizes in the order of 100x100 elements and, for numerical accuracy,more » LU factorization with full pivoting instead of the faster partial pivoting. Modern high performance computing systems are heterogeneous machines whose nodes integrate both CPUs and GPUs, exposing unprecedented amounts of parallelism. To exploit all their computational power, applications must use both the types of processing elements. For the case of subsurface flow simulation, this mainly requires implementing efficient batched LU-based solvers and identifying efficient solutions for enabling load balancing among the different processors of the system. In this paper we discuss two approaches that allows scaling STOMP's performance on heterogeneous clusters. We initially identify the challenges in implementing batched LU-based solvers for small matrices on GPUs, and propose an implementation that fulfills STOMP's requirements. We compare this implementation to other existing solutions. Then, we combine the batched GPU solver with an OpenMP-based CPU solver, and present an adaptive load balancer that dynamically distributes the linear systems to solve between the two components inside a node. We show how these approaches, integrated into the full application, provide speed ups from 6 to 7 times on large problems, executed on up to 16 nodes of a cluster with two AMD Opteron 6272 and a Tesla M2090 per node.« less

Seismic reflection imaging with conventional and unconventional sources

NASA Astrophysics Data System (ADS)

Quiros Ugalde, Diego Alonso

This manuscript reports the results of research using both conventional and unconventional energy sources as well as conventional and unconventional analysis to image crustal structure using reflected seismic waves. The work presented here includes the use of explosions to investigate the Taiwanese lithosphere, the use of 'noise' from railroads to investigate the shallow subsurface of the Rio Grande rift, and the use of microearthquakes to image subsurface structure near an active fault zone within the Appalachian mountains. Chapter 1 uses recordings from the land refraction and wide-angle reflection component of the Taiwan Integrated Geodynamic Research (TAIGER) project. The most prominent reflection feature imaged by these surveys is an anomalously strong reflector found in northeastern Taiwan. The goal of this chapter is to analyze the TAIGER recordings and to place the reflector into a geologic framework that fits with the modern tectonic kinematics of the region. Chapter 2 uses railroad traffic as a source for reflection profiling within the Rio Grande rift. Here the railroad recordings are treated in an analogous way to Vibroseis recordings. These results suggest that railroad noise in general can be a valuable new tool in imaging and characterizing the shallow subsurface in environmental and geotechnical studies. In chapters 3 and 4, earthquakes serve as the seismic imaging source. In these studies the methodology of Vertical Seismic Profiling (VSP) is borrowed from the oil and gas industry to develop reflection images. In chapter 3, a single earthquake is used to probe a small area beneath Waterboro, Maine. In chapter 4, the same method is applied to multiple earthquakes to take advantage of the increased redundancy that results from multiple events illuminating the same structure. The latter study demonstrates how dense arrays can be a powerful new tool for delineating, and monitoring temporal changes of deep structure in areas characterized by significant seismic activity.

How to Manage and Control Healthcare Associated Infections

NASA Astrophysics Data System (ADS)

Wijaya, L.

2018-03-01

Healthcare associated infections (HAI) are the major complications of modern medical therapy. The most important HAIs are related to invasive devices including central line- associated bloodstream infections (CLABSI), catheter-associated urinary tract infections (CAUTI), ventilator-associated pneumonia (VAP) and surgical-site infections (SSI). Excessive use of antibiotics has also led to the emergence and the global dissemination of antibiotic resistant bacteria over the last few decades. Reducing HAIs will involve a multi-modal approach to infection control practices as well as antibiotic stewardship program.

[Biotechnological potential of methylotrophic bacteria: a review of current status and future prospects].

PubMed

Trotsenko, Iu A; Doronina, N V; Khmelenina, V N

2005-01-01

Major results of the authors' findings on the implementation of biotechnological potential of aerobic methylobacteria and methanotrophs for obtaining forage proteins, biopolymers (polybutyrate and polysaccharides), enzymes (oxidoreductases), and bioprotectors (ectoin), as well as for degrading toxic C1 and Cn compounds have been reviewed. Unique features of the structural and functional organization of the metabolism of extremophilic (tolerant) methylotrophs are discussed, with a view for their prospective use in various fields of modern biotechnology, including biocatalysis and nanotechnology.

Green synthesis of silver nanoparticles using leaf extract of medicinally potent plant Saraca indica: a novel study

NASA Astrophysics Data System (ADS)

Perugu, Shyam; Nagati, Veerababu; Bhanoori, Manjula

2016-06-01

Eco-friendly silver nanoparticles (AgNPs) have various applications in modern biotechnology for better outcomes and benefits to the society. In the present study, we report an eco-friendly synthesis of silver nanoparticles using Saraca indica leaf extract. Characterization of S. indica silver nanoparticles (SAgNPs) was carried out by Fourier transform infrared spectroscopy, scanning electron microscopy, energy dispersive spectrometry, Zeta potential, and transmission electron microscopy. SAgNPs showed antimicrobial activity against Gram-negative and Gram-positive bacteria.

Bog iron formation in the Nassawango Creek watershed, Maryland, USA

USGS Publications Warehouse

Bricker, O.P.; Newell, Wayne L.; Simon, N.S.; ,

2004-01-01

The Nassawango bog ores in the modern environment for surficial geochemical processes were studied. The formation of Nassawango bog ores was suggested to be due to inorganic oxidation when groundwater rich in ferrous iron emerges into the oxic, surficial environment. It was suggested that the process, providing a phosphorus sink, may be an unrecognized benefit for mitigating nutrient loading from agricultural lands. It is found that without the effect of iron fixing bacteria, bog deposites could not form at significant rates.

Variable scale channel avulsion history using fan architecture and stratigraphy, and sediment provenance of Sutlej-Yamuna fans in northwest Gangetic plains during Late Quaternary

NASA Astrophysics Data System (ADS)

Singh, Ajit; Gupta, Sanjeev; Sinha, Rajiv; Densmore, Alexander; Buylaert, Jan-Pieter; Carter, Andrew; Van-Dijk, Wout M.; Joshi, Suneel; Nayak, Nibedita; Mason, Philippa J.; Kumar, Dewashish; Mondal, Setbandhu; Murray, Andrew; Rai, Shiv P.; Shekhar, Shashank

2016-04-01

Channel avulsion during fan development controls distribution and deposition of channel sandbodies and hence alluvial architecture of a fan system. Variable scale spatio-temporal information of fluvial responses to past climate changes is stored in these channel sandbodies. Further these channel sandbodies form fluvial aquifers in alluvial fans and therefore understanding of alluvial architecture and stratigraphy of a fan is crucial for development of groundwater management strategies. In this study we used multiple approaches to map subsurface fluvial aquifer architecture and alluvial stratigraphy, and to estimate sediment provenance using U-Pb dating of detrital zircon grains of Sutlej-Yamuna fan system in northwest India. Satellite imagery based geomorphic mapping shows two large fan system with interfan area. The fan surfaces show presence of major and minor paleochannels. 2D resistivity tomography along several transects across fan surfaces shows distinct layers with contrasting resistivity values. These geo-electric facies corresponds to presence of channel sandbodies beneath surface signature of paleochannels and finer floodplain deposits useful to demarcate lateral extent of subsurface channel sandbodies. A more detailed subsurface stratigraphy using ~50m deep sediment cores and their luminescence ages from across fan surface shows presence of multi-storey sandbodies (MSB) separated by floodplain fines. Within the MSB, individual channel deposits are identified by presence of channel scour surfaces located at coarse sand overlying fine sand layer. Depositional ages of MSB's ranges from ~81 ka (late MIS5) to ~15 ka (MIS2) with major depositional break during MIS3 in parts of the fans. Sediment aggradation rate varies laterally across fan surface as well as vertically down the depth with an average rate of 0.54 mm/year. Fluvial channel persistence for studied time interval (about last 81 ka BP) shows major depositional breaks (and possible incision) at ~41 ka (mid MIS3) and ~31 ka (late MIS3). U-Pb age patterns of detrital zircon grains from cores located at paleochannels on the fan system show prominent age peaks at ~480 Ma and ~1800 Ma that respectively corresponds to modern Sutlej and Yamuna rivers. Luminescence ages of these samples suggest that major channel activity of Sutlej river at its fan system ceased around ~15 ka (post last-glacial maxima) and thereafter it avulsed to its modern course. Our surface study results clearly show that alluvial fan system have well developed longitudinal channel sandbodies that may or may not have surface expression in the form of paleochannel and/or longitudinal ridges. However our geophysical studies show that such channel sandbodies can be delineated in shallow surface on the basis of characteristic resistivity values. The subsurface stratigraphy results show development of MSB possibly due to series of small scale (intravalley) avulsion punctuated by large scale (intervalley) avulsion across the fan surface. Our provenance studies clearly identifies two major large scale channel avulsions of Sutlej and Yamuna rivers. Our study has importance for groundwater management policies in this water-stressed agricultural hotspot of India. Thus, understanding the variability in sand body stratigraphy, channel avulsion history, and aggradation rates is important for understanding aquifer geometry of alluvial fan system.

Subsurface dolomite formation during post-depositional flow of sulphate-bearing fluids from underlying salt giants: Early Pliocene example at DSDP Leg 42A, Site 374, Ionian Abyssal Plain

NASA Astrophysics Data System (ADS)

McKenzie, Judith A.; Evans, Nick; Hodell, David; Aloisi, Giovanni; Vasconcelos, Crisogono

2017-04-01

Deciphering exact mechanisms for the formation of massive dolomite deposits has long been an enigma in sedimentary geology. The recognition that microbes can play a role in the dolomite precipitation process has added a new dimension to the study of the origin of dolomite formations in both shallow and deep-water environments. This scientific advance has evolved, particularly, through the investigation of dolomite-containing, organic-rich hemipelagic sediments cored on various continental margins during DSDP and ODP drilling campaigns, as well as intensive evaluations of modern hypersaline dolomite-precipitating environments with complementary culture experiments conducted in the laboratory. For example, the association of an active subsurface microbial community in contact with underlying brines of unknown origin leading to in situ dolomite precipitation has been observed in a Quaternary sequence of hemi-pelagic, organic carbon-rich sediments drilled on the Peru Margin, ODP Leg 201, Site 1229 (1). Specifically, it can be concluded that the long-term activity of subsurface microbes can be maintained by post-depositional flow of sulfate-bearing fluids from underlying large-scale evaporite deposits, or salt giants, promoting in situ dolomite precipitation. Another example of dolomite precipitation directly associated with the underlying Messinian salt giant was found at DSDP Leg 42A, Site 374 in the Ionian Abyssal Plain. Deep-sea drilling recovered a lowermost Pliocene sequence of diagenetically altered sediment (Unit II) separating the overlying Pliocene open-marine deposits (Unit I) and the underlying end Messinian dolomitic mudstone with gypsum layers (Unit III). The lower portion of this altered interval contained in Core 11, Section 2 (378.0 - 381.5 mbsf) comprises a dolomicrite with an unusual crystal morphology (2). The original interstitial water geochemical profiles indicate that a saline brine is diffusing upwards from below and into the dolomicrite sequence. There appears to be on-going bacterial sulfate reduction in this boundary zone between the evaporitic and normal pelagic sediments with a significant decrease in sulfate concentrations, whereas the chloride profile remains constant. It was concluded that the earliest Pliocene marine sediments of Unit II had been dolomitized after burial as a consequence of ionic migration across a steep Mg-concentration gradient (3). However, with the addition of a microbial factor into the study of the dolomite precipitation process, an alternate interpretation is possible. We propose that, at the location of DSDP Leg 42A, Site 374, modern subsurface dolomite precipitation is ongoing and the site is a "natural laboratory" in which to investigate the microbial phenomenon in the context of a giant evaporite deposit. This actualistic example may provide a new model for the origin of massive dolomite deposits associated with other salt giants in the rock record. (1) Meister, P., et al., 2007. Sedimentology, 54, 1007-1031. (2) Bernoulli, D. & Mélières, F., 1978. In: Hsü, K., Montadert, L. et al., 1978. Initial Reports of the Deep Sea Drilling Project, Volume 42, Part 1, 621-633. (3) McDuff, R.E., et al., 1978. In: Hsü, K., Montadert, L. et al., 1978. Initial Reports of the Deep Sea Drilling Project, Volume 42, Part 1, 561-568.

Detection and cultivation of indigenous microorganisms in Mesozoic claystone core samples from the Opalinus Clay Formation (Mont Terri Rock Laboratory)

NASA Astrophysics Data System (ADS)

Mauclaire, L.; McKenzie, J. A.; Schwyn, B.; Bossart, P.

Although microorganisms have been isolated from various deep-subsurface environments, the persistence of microbial activity in claystones buried to great depths and on geological time scales has been poorly studied. The presence of in-situ microbial life in the Opalinus Clay Formation (Mesozoic claystone, 170 million years old) at the Mont Terri Rock Laboratory, Canton Jura, Switzerland was investigated. Opalinus Clay is a host rock candidate for a radioactive waste repository. Particle tracer tests demonstrated the uncontaminated nature of the cored samples, showing their suitability for microbiological investigations. To determine whether microorganisms are a consistent and characteristic component of the Opalinus Clay Formation, two approaches were used: (i) the cultivation of indigenous micoorganisms focusing mainly on the cultivation of sulfate-reducing bacteria, and (ii) the direct detection of molecular biomarkers of bacteria. The goal of the first set of experiments was to assess the presence of cultivable microorganisms within the Opalinus Clay Formation. After few months of incubation, the number of cell ranged from 0.1 to 2 × 10 3 cells ml -1 media. The microorganisms were actively growing as confirmed by the observation of dividing cells, and detection of traces of sulfide. To avoid cultivation bias, quantification of molecular biomarkers (phospholipid fatty acids) was used to assess the presence of autochthonous microorganisms. These molecules are good indicators of the presence of living cells. The Opalinus Clay contained on average 64 ng of PLFA g -1 dry claystone. The detected microbial community comprises mainly Gram-negative anaerobic bacteria as indicated by the ratio of iso/anteiso phospholipids (about 2) and the detection of large amount of β-hydroxy substituted fatty acids. The PLFA composition reveals the presence of specific functional groups of microorganisms in particular sulfate-reducing bacteria ( Desulfovibrio, Desulfobulbus, and Desulfobacter). This study demonstrates that microorganisms are a characteristic component of the unperturbed Opalinus Clay Formation.

The patterns of bacterial community and relationships between sulfate-reducing bacteria and hydrochemistry in sulfate-polluted groundwater of Baogang rare earth tailings.

PubMed

An, Xinli; Baker, Paul; Li, Hu; Su, Jianqiang; Yu, Changping; Cai, Chao

2016-11-01

Microorganisms are the primary agents responsible for the modification, degradation, and/or detoxification of pollutants, and thus, they play a major role in their natural attenuation; yet, little is known about the structure and diversity of the subsurface community and relationships between microbial community and groundwater hydrochemistry. In this study, denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) allowed a comparative microbial community analysis of sulfate-contaminated groundwater samples from nine different wells in the region of Baogang rare earth tailings. Using real-time PCR, the abundance of total bacteria and the sulfate-reducing genes of aprA and dsrB were quantified. Statistical analyses showed a clear distinction of the microbial community diversity between the contaminated and uncontaminated samples, with Proteobacteria being the most dominant members of the microbial community. SO 4 2- concentrations exerted a significant effect on the variation of the bacterial community (P < 0.05), with higher concentrations of sulfate reducing the microbial diversity (H' index), indicating that human activity (e.g., mining industries) was a possible factor disturbing the structure of the bacterial community. Quantitative analysis of the functional genes showed that the proportions of dsrB to total bacteria were 0.002-2.85 %, and the sulfate-reducing bacteria (SRB) were predominant within the prokaryotic community in the groundwater. The uncontaminated groundwater with low sulfate concentration harbored higher abundance of SRB than that in the polluted samples, while no significant correlation was observed between sulfate concentrations and SRB abundances in this study, suggesting other environmental factors possibly contributed to different distributions and abundances of SRB in the different sites. The results should facilitate expanded studies to identify robust microbe-environment interactions and provide a strong foundation for qualitative exploration of the bacterial diversity in rare earth tailings groundwater that might ultimately be incorporated into the remediation of environmental contamination.

Geochemical features of the ore-bearing medium in uranium deposits in the Khiagda ore field

NASA Astrophysics Data System (ADS)

Kochkin, B. T.; Solodov, I. N.; Ganina, N. I.; Rekun, M. L.; Tarasov, N. N.; Shugina, G. A.; Shulik, L. S.

2017-09-01

The Neogene uranium deposits of the Khiagda ore field (KOF) belong to the paleovalley variety of the hydrogene type and differ from other deposits of this genetic type in the geological and geochemical localization conditions. The contemporary hydrogeochemical setting and microbiological composition of ore-bearing medium are discussed. The redox potential of the medium (Eh is as low as-400 mV) is much lower than those established at other hydrogenic deposits, both ancient Late Mesozoic and young Late Alpine, studied with the same methods in Russia, Uzbekistan, and southern Kazakhstan. The pH of subsurface water (6.86-8.13) differs in significant fluctuations both between neighboring deposits and within individual ore lodes. Hydrogen-forming and denitrifying bacteria are predominant in microbiological populations, whereas sulfate-reducing bacteria are low-active. The consideration of these factors allowed us to describe the mechanism of uranium ore conservation as resulting from the development of the cryolithic zone, which isolates ore lodes from the effect of the external medium. Carbonated water supplied from the basement along fault zones also participates in the formation of the present-day hydrogeochemical setting. Based on the features of the ore-bearing medium, we propose a method of borehole in situ acid leaching to increase the efficiency of mining in the Khiagda ore field.

Coliform bacteria removal from sewage in constructed wetlands planted with Mentha aquatica.

PubMed

Avelar, Fabiana F; de Matos, Antonio T; de Matos, Mateus P; Borges, Alisson C

2014-08-01

The present study evaluated the performance of the species Mentha aquatica in constructed wetlands of horizontal subsurface flow (CW-HSSF) with regard to the removal of coliforms bacteria in an effluent from the primary treatment of sewage as well as to obtain adjustment parameters of the bacterial decay kinetic model along the length of the CW-HSSF. Therefore, four CW-HSSFs measuring 24.0 m x 1.0 m x 0.35 m were built and filled with number 0 gravel as the support medium to a height of 0.20m. Two of the CW-HSSFs were planted with the species M. aquatica, while the other two remained uncultivated. Cultivation of M. aquatica in CW-HSSF resulted in total coliforms (TC) and Escherichia coli (EC) removals from 0.9 to 1.3 log units greater than those obtained in the uncultivated experimental plots, for the hydraulic retention times (HRTs) of 4.5 and 6.0 days. For HRT ranged from 1.5 to 6.0 days, the highest removal efficiencies in counts of TC and EC were obtained when using longer HRT. The mathematical models evaluated showed good fit to average counts of TC and EC highlighting the modified first-order kinetic model with the inclusion of the power parameter in the HRT variable.

Hydrogeology and quality of ground water in the Boone Formation and Cotter Dolomite in karst terrain of northwestern Boone County, Arkansas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leidy, V.A.; Morris, E.E.

1991-01-01

Shallow groundwater flow systems in karst terrain of northwestern Boone County, Arkansas, are particularly susceptible to contamination. The potential for groundwater contamination probably is greater in the northern one-half of the study area where there are more photolineaments and presumably subsurface fractures. Groundwater samples from 17 springs discharging from the Boone Formation and 17 wells completed in the Cotter Dolomite were analyzed to determine ambient groundwater quality and to document water quality variations. The chemical constituents in groundwater generally did not exceed US Environmental Protection Agency primary or secondary maximum contaminant levels. However, fecal coliform and fecal streptococcus bacteria weremore » detected in most springs and in three wells. One spring, located near an abandoned wood-treatment plant (a designated Superfund site), had maximum iron, manganese, lead, and pentachlorophenol concentration that exceeded US Environmental Protection Agency's primary or secondary maximum contamination levels for drinking water. Water samples collected from selected springs emerging from the Boone Formation exhibited an overall decrease in specific conductance and total alkalinity, calcium, magnesium, sodium, and chloride concentrations and an overall increase in nitrate, fecal coliform, and fecal streptococcus bacteria concentrations 3 to 8 hours after a rainstorm.« less

Novel Bacterial Proteins and Lipids Reveal the Diversity of Triterpenoid Biomarker Synthesis

NASA Astrophysics Data System (ADS)

Wei, J. H.; Banta, A. B.; Gill, C. C. C.; Giner, J. L.; Welander, P. V.

2017-12-01

Lipids preserved in sediments and rocks function as organic biomarkers providing evidence for the types of organisms that lived in ancient environments. We use a combined approach utilizing comparative genomics, molecular biology, and lipid analysis to discover novel cyclic triteprenoid lipids and their biosynthetic pathways in bacteria. Here, we present two cases of bacterial synthesis of pentacylic triterpenols previously thought to be indicative of eukaryotes, which address current incongruities in the fossil record. Cyclic triterpenoid lipids, such as hopanoids and sterols, are generally associated with bacteria and eukaryotes, respectively. The pentacyclic triterpenoid tetrahymanol, first discovered in the ciliate Tetrahymena pyriformis, and its diagenetic product gammacerane, have been previously interpreted as markers for eukaryotes and linked to water column stratification. Yet the occurrence of tetrahymanol in bacteria implies our knowledge of extant tetrahymanol producers is not complete. Through comparative genomics we identified a new gene required for tetrahymanol synthesis in the bacterium Methylomicrobium alcaliphilum. This gene encodes a novel enzyme, Tetrahymanol synthase (THS), that synthesizes tetrahymanol from the hopanoid diploptene demonstrating a pathway for tetrahymanol production in bacteria distinct from that in eukaryotes. We bionformatically identified THS homologs in 104 bacterial genomes and 472 metagenomes, implying a great diversity of tetrahymanol producers. Lipids of the arborane class, such as iso-arborinol, are commonly found in modern angiosperms. Arobranes are synthesized by the enzyme oxidosqualene cyclase (OSC), which in plants can form both tetra and pentacyclic molecules. While bacteria are known to produce tetracyclic sterol compounds, bacterial synthesis of pentacyclic arborane class triterpenols of this class were previously undiscovered. We have identified a bacterium, Eudoraea adriatica, whose OSC synthesizes arborinols, specifically the novel compounds Eudoraenol and Adriaticol. Discovery of these compounds in bacteria also sheds light on the occurrence of arboranes in Permian sediments predating the angiosperm fossil record, further demonstrating bacteria as a potential source for other orphan biomarkers.

Types and prevalence of extended-spectrum beta-lactamase producing Enterobacteriaceae in poultry.

PubMed

Saliu, Eva-Maria; Vahjen, Wilfried; Zentek, Jürgen

2017-06-01

For several billion years, bacteria have developed mechanisms to resist antibacterial substances. In modern time, antibiotics are frequently used in veterinary and human medicine for prevention and treatment of diseases, globally still also for their growth promoting effects as feed additives. This complex situation has evolved in accelerating development and prevalence of multi-drug resistant bacteria in livestock and people. Extended-spectrum beta-lactamase (ESBL) producing bacteria are resistant to a wide range of ß-lactam antibiotics. They are currently considered as one of the main threats for the treatment of infections in humans and animals. In livestock and animal products, poultry and poultry products show the highest prevalence of ESBL-producers with CTX-M-1, TEM-52 and SHV-12 being the most common ESBL-types in poultry. Escherichia coli and Salmonella spp. are the bacteria in poultry, which carry ESBL-genes most frequently. ESBL-producing bacteria are present at every level of the poultry production pyramid and can be detected even in the meconium of newly hatched chicks. The environment close to poultry barns shows high prevalence rates of these bacteria and contributes to an ongoing infection pressure with further ESBL-types. Probiotics have been shown to successfully reduce ESBL-producers in chicken, as well as ESBL-gene transfer. Other feed additives, such as zinc and copper, increase the prevalence of ESBL-producing bacteria when fed to animals. To our best knowledge, this is the first publication presenting a comparative overview of the prevalence of ESBL-types using data from different countries. To reduce the hazard for public health from poultry carrying high numbers of ESBL-producers, preventive measurements must include the surrounding environment and avoidance of antibiotic usage at all levels of the production pyramid. The first results, of the research on the impact of feed additives on the spread of ESBL-genes, indicate the diet as a further, possible magnitude of influence.

Origins and ages of fracture fluids in the South African Crust

NASA Astrophysics Data System (ADS)

Heard, A. W.; Warr, O.; Borgonie, G.; Linage-Alvarez, B.; Kuloyo, O.; Magnabosco, C.; Lau, M.; Erasmus, M.; Cason, E. D.; van Heerden, E.; Kieft, T. L.; Mabry, J.; Onstott, T. C.; Sherwood Lollar, B.; Ballentine, C. J.

2017-12-01

Crustal fracture fluids can remain isolated for millions (Myr) to billions of years (Gyr), and contain information on paleohydrogeology, subsurface ecology, and conservative components that may elucidate the atmospheric evolution of the early Earth [1-3]. Stable isotope analyses of water combined with isotopic analyses of the dissolved noble gases provide insight into the history of aqueous fracture fluids. We report stable isotope and noble gas data for fracture fluids from 5 different sites in the Witwatersrand Basin and Bushveld Igneous Province, South Africa. We determine radiogenic noble gas residence times ranging from thousands of years to tens of millions of years. The oldest sample, from Masimong Mine, has a water stable isotopic composition close to the global meteoric water line (GMWL), indicating its preservation in the crust and making it one of the oldest recorded paleometeoric waters. The δ2H and δ18O of water in this sample and similar age samples from the same mining district [1,4] require isotopically depleted groundwater recharge compared to modern precipitation. This could reflect a recharge regime at a higher paleolatitude, elevation, or with higher rainfall, established up to tens of Myr ago, and perhaps similar to the recharge regime in the modern Lesotho Highlands [5]. These data suggest that groundwater isotopes may provide useful paleoclimatic information for many Myr. As hypothesized, such paleometeoric water samples lack 124-128Xe enrichments reported from Gyr age groundwaters discovered on the Canadian Shield [3] and in Archean fluid inclusions [6], providing an important control set and reaffirming that those samples record the evolution of ancient atmospheric Xe rather than subsurface alteration. [1] Lippmann, J. et al. (2003) GCA 67, 4597-4619. [2] Lin, L.-H. (2006) et al. Science 314, 479-482. [3] Holland, G. et al. (2013) Nature 497, 357-360. [4] Lippmann-Pipke, J. et al. (2011) Chem. Geol. 283, 287-296. [5] West, A. G. et al. (2014) J. Geochem. Explor. 145, 213-222. [6] Pujol, M. et al. (2011) EPSL 308,298-306.

Building a viable decollement geometry for the Central Nepal Himalaya through integrating surface geology, thermochronology and data from the 2015 Gorkha Earthquake

NASA Astrophysics Data System (ADS)

Ghoshal, S.; McQuarrie, N.; Robinson, D. M.; Olree, E.; Valentino, C.; Olsen, J.

2017-12-01

Recent field mapping in the Central Himalaya revealed a marked change in the location and orientation of exposed Greater Himalayan rocks around the epicenter of the April 2015 Gorkha earthquake, arguing for a lateral structure in the Main Himalayan Thrust (MHT). The earthquake provided new insight into the geometry of the MHT, but left the position and depth of the mid-crustal ramp in dispute. Combining new field data with existing thermochronometric data from the region emphasizes that both the mapped geology and young cooling ages step abruptly southward from east to west, immediately adjacent to the earthquake epicenter. The distribution of cooling ages is strongly influenced by the location of ramps in the decollement surface, as the vertical component of uplift concentrates exhumation over the ramp, producing the youngest ages there. We propose that the existence and location of frontal and lateral ramps can be evaluated using the regional distribution of thermochronometric ages. Sequentially deformed cross-sections present a model of how structurally induced uplift varies in time and space, as well as a predicted geometry of the active, modern fault. We created new balanced cross-sections, constrained by surface geology and the proposed decollement geometries. For an accurate representation of the subsurface, the geometries must reproduce cooling ages measured at the surface. Each cross section was sequentially deformed, allowing for flexure and erosion. The resulting displacement field was used to predict cooling ages for muscovite 40Ar/39Ar, zircon (U-Th)/He, and apatite fission-track, using the thermokinematic model Pecube. The different closure temperatures for these systems allow them to represent different times and locations of exhumation driven by evolving fault geometries. The modeled cooling ages are the cumulative effect of the entire deformational sequence. However, the ages are particularly sensitive to the modern active decollement fault geometry, allowing us to evaluate the different proposed cross-section geometries, and identify the best match to the regional distribution of cooling ages. We argue that this final geometry is the most accurate representation of the subsurface, being constrained by surface geology, thermochronological ages, and data from the earthquake.

Four-year bacterial monitoring in the International Space Station-Japanese Experiment Module "Kibo" with culture-independent approach.

PubMed

Ichijo, Tomoaki; Yamaguchi, Nobuyasu; Tanigaki, Fumiaki; Shirakawa, Masaki; Nasu, Masao

2016-01-01

Studies on the relationships between humans and microbes in space habitation environments are critical for success in long-duration space missions, to reduce potential hazards to the crew and the spacecraft infrastructure. We performed microbial monitoring in the Japanese Experiment Module "Kibo", a part of the International Space Station, for 4 years after its completion, and analyzed samples with modern molecular microbiological techniques. Sampling was performed in September 2009, February 2011, and October 2012. The surface of the incubator, inside the door of the incubator, an air intake, air diffuser, and handrail were selected as sampling sites. Sampling was performed using the optimized swabbing method. Abundance and phylogenetic affiliation of bacteria on the interior surfaces of Kibo were determined by quantitative PCR and pyrosequencing, respectively. Bacteria in the phyla Proteobacteria (γ-subclass) and Firmicutes were frequently detected on the interior surfaces in Kibo. Families Staphylococcaceae and Enterobacteriaceae were dominant. Most bacteria detected belonged to the human microbiota; thus, we suggest that bacterial cells are transferred to the surfaces in Kibo from the astronauts. Environmental bacteria such as Legionella spp. were also detected. From the data on bacterial abundance and phylogenetic affiliation, Kibo has been microbiologically well maintained; however, the microbial community structure in Kibo may change with prolonged stay of astronauts. Continuous monitoring is required to obtain information on changes in the microbial community structure in Kibo.

Rapid shift and millennial-scale variations in Holocene North Pacific Intermediate Water ventilation.

PubMed

Lembke-Jene, Lester; Tiedemann, Ralf; Nürnberg, Dirk; Gong, Xun; Lohmann, Gerrit

2018-05-22

The Pacific hosts the largest oxygen minimum zones (OMZs) in the world ocean, which are thought to intensify and expand under future climate change, with significant consequences for marine ecosystems, biogeochemical cycles, and fisheries. At present, no deep ventilation occurs in the North Pacific due to a persistent halocline, but relatively better-oxygenated subsurface North Pacific Intermediate Water (NPIW) mitigates OMZ development in lower latitudes. Over the past decades, instrumental data show decreasing oxygenation in NPIW; however, long-term variations in middepth ventilation are potentially large, obscuring anthropogenic influences against millennial-scale natural background shifts. Here, we use paleoceanographic proxy evidence from the Okhotsk Sea, the foremost North Pacific ventilation region, to show that its modern oxygenated pattern is a relatively recent feature, with little to no ventilation before six thousand years ago, constituting an apparent Early-Middle Holocene (EMH) threshold or "tipping point." Complementary paleomodeling results likewise indicate a warmer, saltier EMH NPIW, different from its modern conditions. During the EMH, the Okhotsk Sea switched from a modern oxygenation source to a sink, through a combination of sea ice loss, higher water temperatures, and remineralization rates, inhibiting ventilation. We estimate a strongly decreased EMH NPIW oxygenation of ∼30 to 50%, and increased middepth Pacific nutrient concentrations and carbon storage. Our results ( i ) imply that under past or future warmer-than-present conditions, oceanic biogeochemical feedback mechanisms may change or even switch direction, and ( ii ) provide constraints on the high-latitude North Pacific's influence on mesopelagic ventilation dynamics, with consequences for large oceanic regions. Copyright © 2018 the Author(s). Published by PNAS.

Piscivory in a Miocene Cetotheriidae of Peru: first record of fossilized stomach content for an extinct baleen-bearing whale

NASA Astrophysics Data System (ADS)

Collareta, Alberto; Landini, Walter; Lambert, Olivier; Post, Klaas; Tinelli, Chiara; Di Celma, Claudio; Panetta, Daniele; Tripodi, Maria; Salvadori, Piero A.; Caramella, Davide; Marchi, Damiano; Urbina, Mario; Bianucci, Giovanni

2015-12-01

Instead of teeth, modern mysticetes bear hair-fringed keratinous baleen plates that permit various bulk-filtering predation techniques (from subsurface skimming to lateral benthic suction and engulfment) devoted to various target prey (from small invertebrates to schooling fish). Current knowledge about the feeding ecology of extant cetaceans is revealed by stomach content analyses and observations of behavior. Unfortunately, no fossil stomach contents of ancient mysticetes have been described so far; the investigation of the diet of fossil baleen whales, including the Neogene family Cetotheriidae, remains thus largely speculative. We report on an aggregate of fossil fish remains found within a mysticete skeleton belonging to an undescribed late Miocene (Tortonian) cetotheriid from the Pisco Formation (Peru). Micro-computed tomography allowed us to interpret it as the fossilized content of the forestomach of the host whale and to identify the prey as belonging to the extant clupeiform genus Sardinops. Our discovery represents the first direct evidence of piscivory in an ancient edentulous mysticete. Since among modern mysticetes only Balaenopteridae are known to ordinarily consume fish, this fossil record may indicate that part of the cetotheriids experimented some degree of balaenopterid-like engulfment feeding. Moreover, this report corresponds to one of the geologically oldest records of Sardinops worldwide, occurring near the Tortonian peak of oceanic primary productivity and cooling phase. Therefore, our discovery evokes a link between the rise of Cetotheriidae; the setup of modern coastal upwelling systems; and the radiation of epipelagic, small-sized, schooling clupeiform fish in such highly productive environments.

Piscivory in a Miocene Cetotheriidae of Peru: first record of fossilized stomach content for an extinct baleen-bearing whale.

PubMed

Collareta, Alberto; Landini, Walter; Lambert, Olivier; Post, Klaas; Tinelli, Chiara; Di Celma, Claudio; Panetta, Daniele; Tripodi, Maria; Salvadori, Piero A; Caramella, Davide; Marchi, Damiano; Urbina, Mario; Bianucci, Giovanni

2015-12-01

Instead of teeth, modern mysticetes bear hair-fringed keratinous baleen plates that permit various bulk-filtering predation techniques (from subsurface skimming to lateral benthic suction and engulfment) devoted to various target prey (from small invertebrates to schooling fish). Current knowledge about the feeding ecology of extant cetaceans is revealed by stomach content analyses and observations of behavior. Unfortunately, no fossil stomach contents of ancient mysticetes have been described so far; the investigation of the diet of fossil baleen whales, including the Neogene family Cetotheriidae, remains thus largely speculative. We report on an aggregate of fossil fish remains found within a mysticete skeleton belonging to an undescribed late Miocene (Tortonian) cetotheriid from the Pisco Formation (Peru). Micro-computed tomography allowed us to interpret it as the fossilized content of the forestomach of the host whale and to identify the prey as belonging to the extant clupeiform genus Sardinops. Our discovery represents the first direct evidence of piscivory in an ancient edentulous mysticete. Since among modern mysticetes only Balaenopteridae are known to ordinarily consume fish, this fossil record may indicate that part of the cetotheriids experimented some degree of balaenopterid-like engulfment feeding. Moreover, this report corresponds to one of the geologically oldest records of Sardinops worldwide, occurring near the Tortonian peak of oceanic primary productivity and cooling phase. Therefore, our discovery evokes a link between the rise of Cetotheriidae; the setup of modern coastal upwelling systems; and the radiation of epipelagic, small-sized, schooling clupeiform fish in such highly productive environments.

Ochre Bathing of the Bearded Vulture: A Bio-Mimetic Model for Early Humans towards Smell Prevention and Health

PubMed Central

Tributsch, Helmut

2016-01-01

Simple Summary The once widespread bearded vulture (Gypaetus barbatus) has the habit of bathing its polluted feathers and skin in red iron oxide-ochre-tainted water puddles. Primitive man may have tried to find out why: ochre is active in sunlight producing aggressive chemical species. They can kill viruses and bacteria and convert smelly organic substances into volatile neutral carbon dioxide gas. There is consequently a sanitary reason for the vulture’s habit of bathing in red ochre mud and this explains why prehistoric people included ochre use into their habits and rituals. Abstract Since primordial times, vultures have been competing with man for animal carcasses. One of these vultures, the once widespread bearded vulture (Gypaetus barbatus), has the habit of bathing its polluted feathers and skin in red iron oxide - ochre - tainted water puddles. Why? Primitive man may have tried to find out and may have discovered its advantages. Red ochre, which has accompanied human rituals and everyday life for more than 100,000 years, is not just a simple red paint for decoration or a symbol for blood. As modern experiments demonstrate, it is active in sunlight producing aggressive chemical species. They can kill viruses and bacteria and convert smelly organic substances into volatile neutral carbon dioxide gas. In this way, ochre can in sunlight sterilize and clean the skin to provide health and comfort and make it scentless, a definitive advantage for nomadic meat hunters. This research thus also demonstrates a sanitary reason for the vulture’s habit of bathing in red ochre mud. Prehistoric people have therefore included ochre use into their rituals, especially into those in relation to birth and death. Significant ritual impulses during evolution of man may thus have developed bio-mimetically, inspired from the habits of a vulture. It is discussed how this health strategy could be developed to a modern standard helping to fight antibiotics-resistant bacteria in hospitals. PMID:26784238

Controls on O2 Production in Cyanobacterial Mats and Implications for Earth's Oxygenation

NASA Astrophysics Data System (ADS)

Dick, Gregory J.; Grim, Sharon L.; Klatt, Judith M.

2018-05-01

Cyanobacterial mats are widely assumed to have been globally significant hot spots of biogeochemistry and evolution during the Archean and Proterozoic, but little is known about their quantitative contributions to global primary productivity or Earth's oxygenation. Modern systems show that mat biogeochemistry is the outcome of concerted activities and intimate interactions between various microbial metabolisms. Emerging knowledge of the regulation of oxygenic and sulfide-driven anoxygenic photosynthesis by versatile cyanobacteria, and their interactions with sulfur-oxidizing bacteria and sulfate-reducing bacteria, highlights how ecological and geochemical processes can control O2 production in cyanobacterial mats in unexpected ways. This review explores such biological controls on O2 production. We argue that the intertwined effects of light availability, redox geochemistry, regulation and competition of microbial metabolisms, and biogeochemical feedbacks result in emergent properties of cyanobacterial mat communities that are all critical yet largely overlooked mechanisms to potentially explain the protracted nature of Earth's oxygenation.

Cooperative Bacterial Growth Dynamics Predict the Evolution of Antibiotic Resistance

NASA Astrophysics Data System (ADS)

Artemova, Tatiana; Gerardin, Ylaine; Hsin-Jung Li, Sophia; Gore, Jeff

2011-03-01

Since the discovery of penicillin, antibiotics have been our primary weapon against bacterial infections. Unfortunately, bacteria can gain resistance to penicillin by acquiring the gene that encodes beta-lactamase, which inactivates the antibiotic. However, mutations in this gene are necessary to degrade the modern antibiotic cefotaxime. Understanding the conditions that favor the spread of these mutations is a challenge. Here we show that bacterial growth in beta-lactam antibiotics is cooperative and that the nature of this growth determines the conditions in which resistance evolves. Quantitative analysis of the growth dynamics predicts a peak in selection at very low antibiotic concentrations; competition between strains confirms this prediction. We also find significant selection at higher antibiotic concentrations, close to the minimum inhibitory concentrations of the strains. Our results argue that an understanding of the evolutionary forces that lead to antibiotic resistance requires a quantitative understanding of the evolution of cooperation in bacteria.

Bisphosphocins: novel antimicrobials for enhanced killing of drug-resistant and biofilm-forming bacteria.

PubMed

Wong, Jonathan P; DiTullio, Paul; Parkinson, Steve

2015-01-01

The global prevalence of antibiotic resistance and the threat posed by drug-resistant superbugs are a leading challenge confronting modern medicine in the 21st century. However, the progress on the development of novel antibiotics to combat this problem is severely lagging. A more concerted effort to develop novel therapeutic agents with robust activity and unique mechanisms of action will be needed to overcome the problem of drug resistance. Furthermore, biofilm forming bacteria are known to be increasingly resistant to the actions of antibiotics and are a leading cause of mortality or morbidity in nosocomial infections. Bisphosphocins (also scientifically known as nubiotics) are novel small protonated deoxynucleotide molecules, and exert their antibacterial activity by depolarization of the bacterial cell membrane, causing bacterial cell death. Bisphosphocins may represent an effective weapon against antibiotic-resistant and biofilm-forming pathogenic bacteria. Preclinical efficacy studies in animals have shown that the compounds are safe and, efficacious against various bacterial infections, including drug-resistant pathogens. In vitro biochemical analysis confirmed that the bactericidal activity of bisphosphocins is mediated by depolarization of the bacterial cell membrane, and these compounds are better able to penetrate through bacterial biofilm and kill the biofilm encased bacteria. This article will cover the structure, mode of action, safety, efficacy and the current state of development of bisphosphocins. Together, the information presented here will present a strong case for bisphosphocins to be considered for use as new weapons to complement the existing arsenal of antimicrobial drugs and as a first line defence against drug-resistant and biofilm-forming bacteria.

Multi-Disciplinary Approach to Trace Contamination of Streams and Beaches

USGS Publications Warehouse

Nickles, James

2008-01-01

Concentrations of fecal-indicator bacteria in urban streams and ocean beaches in and around Santa Barbara occasionally can exceed public-health standards for recreation. The U.S. Geological Survey (USGS), working with the City of Santa Barbara, has used multi-disciplinary science to trace the sources of the bacteria. This research is helping local agencies take steps to improve recreational water quality. The USGS used an approach that combined traditional hydrologic and microbiological data, with state-of-the-art genetic, molecular, and chemical tracer analysis. This research integrated physical data on streamflow, ground water, and near-shore oceanography, and made extensive use of modern geophysical and isotopic techniques. Using those techniques, the USGS was able to evaluate the movement of water and the exchange of ground water with near-shore ocean water. The USGS has found that most fecal bacteria in the urban streams came from storm-drain discharges, with the highest concentrations occurring during storm flow. During low streamflow, the concentrations varied as much as three-fold, owing to variable contribution of non-point sources such as outdoor water use and urban runoff to streamflow. Fecal indicator bacteria along ocean beaches were from both stream discharge to the ocean and from non-point sources such as bird fecal material that accumulates in kelp and sand at the high-tide line. Low levels of human-specific Bacteroides, suggesting fecal material from a human source, were consistently detected on area beaches. One potential source, a local sewer line buried beneath the beach, was found not to be responsible for the fecal bacteria.