ENGINEERING ISSUE: IN SITU BIOREMEDIATION OF CONTAMINATED UNSATURATED SUBSURFACE SOILS

EPA Science Inventory

An emerging technology for the remediation of unsaturated subsurface soils involves the use of microorganisms to degrade contaminants which are present in such soils. Understanding the processes which drive in situ bioremediation, as well as the effectiveness and efficiency of th...

Nitrogen removal and its relationship with the nitrogen-cycle genes and microorganisms in the horizontal subsurface flow constructed wetlands with different design parameters.

PubMed

Chen, Jun; Ying, Guang-Guo; Liu, You-Sheng; Wei, Xiao-Dong; Liu, Shuang-Shuang; He, Liang-Ying; Yang, Yong-Qiang; Chen, Fan-Rong

2017-07-03

This study aims to investigate nitrogen removal and its relationship with the nitrogen-cycle genes and microorganisms in the horizontal subsurface flow constructed wetlands (CWs) with different design parameters. Twelve mesocosm-scale CWs with four substrates and three hydraulic loading rates were set up in the outdoor. The result showed the CWs with zeolite as substrate and HLR of 20 cm/d were selected as the best choice for the TN and NH 3 -N removal. It was found that the single-stage mesocosm-scale CWs were incapable to achieve high removals of TN and NH 3 -N due to inefficient nitrification process in the systems. This was demonstrated by the lower abundance of the nitrification genes (AOA and AOB) than the denitrification genes (nirK and nirS), and the less diverse nitrification microorganisms than the denitrification microorganisms in the CWs. The results also show that microorganism community structure including nitrogen-cycle microorganisms in the constructed wetland systems was affected by the design parameters especially the substrate type. These findings show that nitrification is a limiting factor for the nitrogen removal by CWs.

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

In situ biofilm coupon device

DOEpatents

Peyton, Brent M.; Truex, Michael J.

1997-01-01

An apparatus for characterization of in-situ microbial biofilm populations in subsurface groundwater. The device permits biofilm-forming microorganisms to adhere to packing material while emplaced in a groundwater strata, so that the packing material can be later analyzed for quantity and type of microorganisms, growth rate, and nutrient requirements.

MODELING MICROBIAL TRANSPORT IN SOIL AND GROUNDWATER: MICROBIOLOGISTS CAN ASSIST IN THE DEVELOPMENT OF MODELS OF CONTAMINANT TRANSPORT

EPA Science Inventory

A large body of literature describes the processes affecting the fate of microorganisms in the subsurface environment (i.e., soil and groundwater). The fate of microorganisms depends on two main components: survival and transport. other components must be considered when determin...

In situ biofilm coupon device

DOEpatents

Peyton, B.M.; Truex, M.J.

1997-06-24

An apparatus is disclosed for characterization of in-situ microbial biofilm populations in subsurface groundwater. The device permits biofilm-forming microorganisms to adhere to packing material while emplaced in a groundwater strata, so that the packing material can be later analyzed for quantity and type of microorganisms, growth rate, and nutrient requirements. 3 figs.

Microbiological Transformations of Radionuclides in the Subsurface

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

Marshall, Matthew J.; Beliaev, Alex S.; Fredrickson, Jim K.

2010-01-04

Microorganisms are ubiquitous in subsurface environments although their populations sizes and metabolic activities can vary considerably depending on energy and nutrient inputs. As a result of their metabolic activities and the chemical properties of their cell surfaces and the exopolymers they produce, microorganisms can directly or indirectly facilitate the biotransformation of radionuclides, thus altering their solubility and overall fate and transport in the environment. Although biosorption to cell surfaces and exopolymers can be an important factor modifying the solubility of some radionuclides under specific conditions, oxidation state is often considered the single most important factor controlling their speciation and, therefore,more » environmental behavior.« less

Bioremediation of contaminated groundwater

DOEpatents

Hazen, Terry C.; Fliermans, Carl B.

1995-01-01

An apparatus and method for in situ remediation of contaminated subsurface soil or groundwater contaminated by chlorinated hydrocarbons. A nutrient fluid is selected to stimulate the growth and reproduction of indigenous subsurface microorganisms that are capable of degrading the contaminants; an oxygenated fluid is selected to create a generally aerobic environment for these microorganisms to degrade the contaminants, leaving only pockets that are anaerobic. The nutrient fluid is injected periodically while the oxygenated fluid is injected continuously and both are extracted so that both are drawn across the plume. The nutrient fluid stimulates microbial colony growth; withholding it periodicially forces the larger, healthy colony of microbes to degrade the contaminants. Treatment is continued until the subsurface concentration of contaminants is reduced to an acceptable, preselected level. The nutrient fluid can be methane and the oxygenated fluid air for stimulating production of methanotrophs to break down chlorohydrocarbons, especially trichloroethylene (TCE) and tetrachloroethylene.

Bioremediation of contaminated groundwater

DOEpatents

Hazen, T.C.; Fliermans, C.B.

1995-01-24

An apparatus and method are described for in situ remediation of contaminated subsurface soil or groundwater contaminated by chlorinated hydrocarbons. A nutrient fluid is selected to stimulate the growth and reproduction of indigenous subsurface microorganisms that are capable of degrading the contaminants. An oxygenated fluid is selected to create a generally aerobic environment for these microorganisms to degrade the contaminants, leaving only pockets that are anaerobic. The nutrient fluid is injected periodically while the oxygenated fluid is injected continuously and both are extracted so that both are drawn across the plume. The nutrient fluid stimulates microbial colony growth. Withholding it periodically forces the larger, healthy colony of microbes to degrade the contaminants. Treatment is continued until the subsurface concentration of contaminants is reduced to an acceptable, preselected level. The nutrient fluid can be methane and the oxygenated fluid air for stimulating production of methanotrophs to break down chlorohydrocarbons, especially trichloroethylene (TCE) and tetrachloroethylene. 3 figures.

Radiochemically-supported microbial communities. A potential mechanism for biocolloid production of importance to actinide transport

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

Moser, Duane P.; Hamilton-Brehm, Scott D.; Fisher, Jenny C.

The work described here revealed the presence of diverse microbial communities located across 19 subsurface sites at the NNSS/NTTR and nearby locations. Overall, the diversity of microorganisms was high for subsurface habitats and variable between sites. As of this writing, preparations are being made to combine the Illumina sequences and 16S rRNA clone libraries with other non-NNSS/NTTR well sites of Southern Nevada Regional Flow System for a publication manuscript describing our very broad landscape scale survey of subsurface microbial diversity. Isolates DRI-13 and DRI-14 remain to be fully characterized and named in accordance with the conventions established by Bergey's Manualmore » of Systematic Bacteriology. In preparation to be published, these microorganisms will be submitted to the American Type Culture Collection (ATCC) and the Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ).It is anticipated that the data resulting from this study in combination with other data sets that will allow us to produce a number of publications that will be impactful to the subsurface microbiology community.« less

MORPHOLOGICAL AND CULTURAL COMPARISON OF MICROORGANISMS IN SURFACE SOIL AND SUBSURFACE SEDIMENTS AT A PRISTINE STUDY SITE IN OKLAHOMA (JOURNAL VERSION)

EPA Science Inventory

Surface-soil and subsurface microfloras at the site of a shallow aquifer in Oklahoma were examined and compared with respect to (1) total and viable cell numbers, (2) colony and cell types that grew on various plating media, (3) cell morphologies seen in flotation films stripped ...

Nitrogen Stimulates the Growth of Subsurface Basalt-associated Microorganisms at the Western Flank of the Mid-Atlantic Ridge

PubMed Central

Zhang, Xinxu; Fang, Jing; Bach, Wolfgang; Edwards, Katrina J.; Orcutt, Beth N.; Wang, Fengping

2016-01-01

Oceanic crust constitutes the largest aquifer system on Earth, and microbial activity in this environment has been inferred from various geochemical analyses. However, empirical documentation of microbial activity from subsurface basalts is still lacking, particularly in the cool (<25°C) regions of the crust, where are assumed to harbor active iron-oxidizing microbial communities. To test this hypothesis, we report the enrichment and isolation of crust-associated microorganisms from North Pond, a site of relatively young and cold basaltic basement on the western flank of the Mid-Atlantic Ridge that was sampled during Expedition 336 of the Integrated Ocean Drilling Program. Enrichment experiments with different carbon (bicarbonate, acetate, methane) and nitrogen (nitrate and ammonium) sources revealed significant cell growth (one magnitude higher cell abundance), higher intracellular DNA content, and increased Fe3+/ΣFe ratios only when nitrogen substrates were added. Furthermore, a Marinobacter strain with neutrophilic iron-oxidizing capabilities was isolated from the basalt. This work reveals that basalt-associated microorganisms at North Pond had the potential for activity and that microbial growth could be stimulated by in vitro nitrogen addition. Furthermore, iron oxidation is supported as an important process for microbial communities in subsurface basalts from young and cool ridge flank basement. PMID:27199959

Under the sea: microbial life in volcanic oceanic crust.

PubMed

Edwards, Katrina J; Wheat, C Geoffrey; Sylvan, Jason B

2011-09-06

Exploration of the microbiology in igneous, 'hard rock' oceanic crust represents a major scientific frontier. The igneous crust harbours the largest aquifer system on Earth, most of which is hydrologically active, resulting in a substantial exchange of fluids, chemicals and microorganisms between oceanic basins and crustal reservoirs. Study of the deep-subsurface biosphere in the igneous crust is technically challenging. However, technologies have improved over the past decade, providing exciting new opportunities for the study of deep-seated marine life, including in situ and cross-disciplinary experimentation in microbiology, geochemistry and hydrogeology. In this Progress article, we describe the recent advances, available technology and remaining challenges in the study of the marine intraterrestrial microbial life that is harboured in igneous oceanic crust.

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

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.

Diagnosis of In Situ Metabolic State and Rates of Microbial Metabolism During In Situ Uranium Bioremediation with Molecular Techniques

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

Lovley, Derek R.

2012-11-28

The goal of these projects was to develop molecule tools to tract the metabolic activity and physiological status of microorganisms during in situ uranium bioremediation. Such information is important in able to design improved bioremediation strategies. As summarized below, the research was highly successful with new strategies developed for estimating in situ rates of metabolism and diagnosing the physiological status of the predominant subsurface microorganisms. This is a first not only for groundwater bioremediation studies, but also for subsurface microbiology in general. The tools and approaches developed in these studies should be applicable to the study of microbial communities inmore » a diversity of soils and sediments.« less

Aerobic microorganism for the degradation of chlorinated aliphatic hydrocarbons

DOEpatents

Fliermans, Carl B.

1989-01-01

A chlorinated aliphatic hydrocarbon-degrading microorganism, having American Type Culture Collection accession numbers ATCC 53570 and 53571, in a biologically pure culture aseptically collected from a deep subsurface habitat and enhanced, mineralizes trichloroethylene and tetrachloroethylene to HCl, H.sub.2 O and Co.sub.2 under aerobic conditions stimulated by methane, acetate, methanol, tryptone-yeast extract, propane and propane-methane.

Impact of mercury on denitrification and denitrifying microbial communities in nitrate enrichments of subsurface sediments.

PubMed

Wang, Yanping; Wiatrowski, Heather A; John, Ria; Lin, Chu-Ching; Young, Lily Y; Kerkhof, Lee J; Yee, Nathan; Barkay, Tamar

2013-02-01

The contamination of groundwater with mercury (Hg) is an increasing problem worldwide. Yet, little is known about the interactions of Hg with microorganisms and their processes in subsurface environments. We tested the impact of Hg on denitrification in nitrate reducing enrichment cultures derived from subsurface sediments from the Oak Ridge Integrated Field Research Challenge site, where nitrate is a major contaminant and where bioremediation efforts are in progress. We observed an inverse relationship between Hg concentrations and onset and rates of denitrification in nitrate enrichment cultures containing between 53 and 1.1 μM of inorganic Hg; higher Hg concentrations increasingly extended the time to onset of denitrification and inhibited denitrification rates. Microbial community complexity, as indicated by terminal restriction fragment length polymorphism (tRFLP) analysis of the 16S rRNA genes, declined with increasing Hg concentrations; at the 312 nM Hg treatment, a single tRFLP peak was detected representing a culture of Bradyrhizobium sp. that possessed the merA gene indicating a potential for Hg reduction. A culture identified as Bradyrhizobium sp. strain FRC01 with an identical 16S rRNA sequence to that of the enriched peak in the tRFLP patterns, reduced Hg(II) to Hg(0) and carried merA whose amino acid sequence has 97 % identity to merA from the Proteobacteria and Firmicutes. This study demonstrates that in subsurface sediment incubations, Hg may inhibit denitrification and that inhibition may be alleviated when Hg resistant denitrifying Bradyrhizobium spp. detoxify Hg by its reduction to the volatile elemental form.

Identification and Removal of Contaminant Sequences From Ribosomal Gene Databases: Lessons From the Census of Deep Life

PubMed Central

Sheik, Cody S.; Reese, Brandi Kiel; Twing, Katrina I.; Sylvan, Jason B.; Grim, Sharon L.; Schrenk, Matthew O.; Sogin, Mitchell L.; Colwell, Frederick S.

2018-01-01

Earth’s subsurface environment is one of the largest, yet least studied, biomes on Earth, and many questions remain regarding what microorganisms are indigenous to the subsurface. Through the activity of the Census of Deep Life (CoDL) and the Deep Carbon Observatory, an open access 16S ribosomal RNA gene sequence database from diverse subsurface environments has been compiled. However, due to low quantities of biomass in the deep subsurface, the potential for incorporation of contaminants from reagents used during sample collection, processing, and/or sequencing is high. Thus, to understand the ecology of subsurface microorganisms (i.e., the distribution, richness, or survival), it is necessary to minimize, identify, and remove contaminant sequences that will skew the relative abundances of all taxa in the sample. In this meta-analysis, we identify putative contaminants associated with the CoDL dataset, recommend best practices for removing contaminants from samples, and propose a series of best practices for subsurface microbiology sampling. The most abundant putative contaminant genera observed, independent of evenness across samples, were Propionibacterium, Aquabacterium, Ralstonia, and Acinetobacter. While the top five most frequently observed genera were Pseudomonas, Propionibacterium, Acinetobacter, Ralstonia, and Sphingomonas. The majority of the most frequently observed genera (high evenness) were associated with reagent or potential human contamination. Additionally, in DNA extraction blanks, we observed potential archaeal contaminants, including methanogens, which have not been discussed in previous contamination studies. Such contaminants would directly affect the interpretation of subsurface molecular studies, as methanogenesis is an important subsurface biogeochemical process. Utilizing previously identified contaminant genera, we found that ∼27% of the total dataset were identified as contaminant sequences that likely originate from DNA extraction and DNA cleanup methods. Thus, controls must be taken at every step of the collection and processing procedure when working with low biomass environments such as, but not limited to, portions of Earth’s deep subsurface. Taken together, we stress that the CoDL dataset is an incredible resource for the broader research community interested in subsurface life, and steps to remove contamination derived sequences must be taken prior to using this dataset. PMID:29780369

Identification and Removal of Contaminant Sequences From Ribosomal Gene Databases: Lessons From the Census of Deep Life.

PubMed

Sheik, Cody S; Reese, Brandi Kiel; Twing, Katrina I; Sylvan, Jason B; Grim, Sharon L; Schrenk, Matthew O; Sogin, Mitchell L; Colwell, Frederick S

2018-01-01

Earth's subsurface environment is one of the largest, yet least studied, biomes on Earth, and many questions remain regarding what microorganisms are indigenous to the subsurface. Through the activity of the Census of Deep Life (CoDL) and the Deep Carbon Observatory, an open access 16S ribosomal RNA gene sequence database from diverse subsurface environments has been compiled. However, due to low quantities of biomass in the deep subsurface, the potential for incorporation of contaminants from reagents used during sample collection, processing, and/or sequencing is high. Thus, to understand the ecology of subsurface microorganisms (i.e., the distribution, richness, or survival), it is necessary to minimize, identify, and remove contaminant sequences that will skew the relative abundances of all taxa in the sample. In this meta-analysis, we identify putative contaminants associated with the CoDL dataset, recommend best practices for removing contaminants from samples, and propose a series of best practices for subsurface microbiology sampling. The most abundant putative contaminant genera observed, independent of evenness across samples, were Propionibacterium , Aquabacterium , Ralstonia , and Acinetobacter . While the top five most frequently observed genera were Pseudomonas , Propionibacterium , Acinetobacter , Ralstonia , and Sphingomonas . The majority of the most frequently observed genera (high evenness) were associated with reagent or potential human contamination. Additionally, in DNA extraction blanks, we observed potential archaeal contaminants, including methanogens, which have not been discussed in previous contamination studies. Such contaminants would directly affect the interpretation of subsurface molecular studies, as methanogenesis is an important subsurface biogeochemical process. Utilizing previously identified contaminant genera, we found that ∼27% of the total dataset were identified as contaminant sequences that likely originate from DNA extraction and DNA cleanup methods. Thus, controls must be taken at every step of the collection and processing procedure when working with low biomass environments such as, but not limited to, portions of Earth's deep subsurface. Taken together, we stress that the CoDL dataset is an incredible resource for the broader research community interested in subsurface life, and steps to remove contamination derived sequences must be taken prior to using this dataset.

Some Ecological Mechanisms to Generate Habitability in Planetary Subsurface Areas by Chemolithotrophic Communities: The Ro Tinto Subsurface Ecosystem as a Model System

NASA Astrophysics Data System (ADS)

Fernández-Remolar, David C.; Gómez, Felipe; Prieto-Ballesteros, Olga; Schelble, Rachel T.; Rodríguez, Nuria; Amiols, Ricardo

2008-02-01

Chemolithotrophic communities that colonize subsurface habitats have great relevance for the astrobiological exploration of our Solar System. We hypothesize that the chemical and thermal stabilization of an environment through microbial activity could make a given planetary region habitable. The MARTE project ground-truth drilling campaigns that sampled cryptic subsurface microbial communities in the basement of the Ro Tinto headwaters have shown that acidic surficial habitats are the result of the microbial oxidation of pyritic ores. The oxidation process is exothermic and releases heat under both aerobic and anaerobic conditions. These microbial communities can maintain the subsurface habitat temperature through storage heat if the subsurface temperature does not exceed their maximum growth temperature. In the acidic solutions of the Ro Tinto, ferric iron acts as an effective buffer for controlling water pH. Under anaerobic conditions, ferric iron is the oxidant used by microbes to decompose pyrite through the production of sulfate, ferrous iron, and protons. The integration between the physical and chemical processes mediated by microorganisms with those driven by the local geology and hydrology have led us to hypothesize that thermal and chemical regulation mechanisms exist in this environment and that these homeostatic mechanisms could play an essential role in creating habitable areas for other types of microorganisms. Therefore, searching for the physicochemical expression of extinct and extant homeostatic mechanisms through physical and chemical anomalies in the Mars crust (i.e., local thermal gradient or high concentration of unusual products such as ferric sulfates precipitated out from acidic solutions produced by hypothetical microbial communities) could be a first step in the search for biological traces of a putative extant or extinct Mars biosphere.

Some ecological mechanisms to generate habitability in planetary subsurface areas by chemolithotrophic communities: the Río Tinto subsurface ecosystem as a model system.

PubMed

Fernández-Remolar, David C; Gómez, Felipe; Prieto-Ballesteros, Olga; Schelble, Rachel T; Rodríguez, Nuria; Amils, Ricardo

2008-02-01

Chemolithotrophic communities that colonize subsurface habitats have great relevance for the astrobiological exploration of our Solar System. We hypothesize that the chemical and thermal stabilization of an environment through microbial activity could make a given planetary region habitable. The MARTE project ground-truth drilling campaigns that sampled cryptic subsurface microbial communities in the basement of the Río Tinto headwaters have shown that acidic surficial habitats are the result of the microbial oxidation of pyritic ores. The oxidation process is exothermic and releases heat under both aerobic and anaerobic conditions. These microbial communities can maintain the subsurface habitat temperature through storage heat if the subsurface temperature does not exceed their maximum growth temperature. In the acidic solutions of the Río Tinto, ferric iron acts as an effective buffer for controlling water pH. Under anaerobic conditions, ferric iron is the oxidant used by microbes to decompose pyrite through the production of sulfate, ferrous iron, and protons. The integration between the physical and chemical processes mediated by microorganisms with those driven by the local geology and hydrology have led us to hypothesize that thermal and chemical regulation mechanisms exist in this environment and that these homeostatic mechanisms could play an essential role in creating habitable areas for other types of microorganisms. Therefore, searching for the physicochemical expression of extinct and extant homeostatic mechanisms through physical and chemical anomalies in the Mars crust (i.e., local thermal gradient or high concentration of unusual products such as ferric sulfates precipitated out from acidic solutions produced by hypothetical microbial communities) could be a first step in the search for biological traces of a putative extant or extinct Mars biosphere.

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.

An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers

PubMed Central

Kieft, Thomas L.; Kuloyo, Olukayode; Linage-Alvarez, Borja; van Heerden, Esta; Lindsay, Melody R.; Magnabosco, Cara; Wang, Wei; Wiggins, Jessica B.; Guo, Ling; Perlman, David H.; Kyin, Saw; Shwe, Henry H.; Harris, Rachel L.; Oh, Youmi; Yi, Min Joo; Purtschert, Roland; Slater, Greg F.; Ono, Shuhei; Wei, Siwen; Li, Long; Sherwood Lollar, Barbara; Onstott, Tullis C.

2016-01-01

Subsurface lithoautotrophic microbial ecosystems (SLiMEs) under oligotrophic conditions are typically supported by H2. Methanogens and sulfate reducers, and the respective energy processes, are thought to be the dominant players and have been the research foci. Recent investigations showed that, in some deep, fluid-filled fractures in the Witwatersrand Basin, South Africa, methanogens contribute <5% of the total DNA and appear to produce sufficient CH4 to support the rest of the diverse community. This paradoxical situation reflects our lack of knowledge about the in situ metabolic diversity and the overall ecological trophic structure of SLiMEs. Here, we show the active metabolic processes and interactions in one of these communities by combining metatranscriptomic assemblies, metaproteomic and stable isotopic data, and thermodynamic modeling. Dominating the active community are four autotrophic β-proteobacterial genera that are capable of oxidizing sulfur by denitrification, a process that was previously unnoticed in the deep subsurface. They co-occur with sulfate reducers, anaerobic methane oxidizers, and methanogens, which each comprise <5% of the total community. Syntrophic interactions between these microbial groups remove thermodynamic bottlenecks and enable diverse metabolic reactions to occur under the oligotrophic conditions that dominate in the subsurface. The dominance of sulfur oxidizers is explained by the availability of electron donors and acceptors to these microorganisms and the ability of sulfur-oxidizing denitrifiers to gain energy through concomitant S and H2 oxidation. We demonstrate that SLiMEs support taxonomically and metabolically diverse microorganisms, which, through developing syntrophic partnerships, overcome thermodynamic barriers imposed by the environmental conditions in the deep subsurface. PMID:27872277

Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales

PubMed Central

Booker, Anne E.; Borton, Mikayla A.; Daly, Rebecca A.; Welch, Susan A.; Nicora, Carrie D.; Hoyt, David W.; Wilson, Travis; Purvine, Samuel O.; Wolfe, Richard A.; Sharma, Shikha; Mouser, Paula J.; Cole, David R.; Lipton, Mary S.; Wrighton, Kelly C.

2017-01-01

ABSTRACT Hydraulic fracturing of black shale formations has greatly increased United States oil and natural gas recovery. However, the accumulation of biomass in subsurface reservoirs and pipelines is detrimental because of possible well souring, microbially induced corrosion, and pore clogging. Temporal sampling of produced fluids from a well in the Utica Shale revealed the dominance of Halanaerobium strains within the in situ microbial community and the potential for these microorganisms to catalyze thiosulfate-dependent sulfidogenesis. From these field data, we investigated biogenic sulfide production catalyzed by a Halanaerobium strain isolated from the produced fluids using proteogenomics and laboratory growth experiments. Analysis of Halanaerobium isolate genomes and reconstructed genomes from metagenomic data sets revealed the conserved presence of rhodanese-like proteins and anaerobic sulfite reductase complexes capable of converting thiosulfate to sulfide. Shotgun proteomics measurements using a Halanaerobium isolate verified that these proteins were more abundant when thiosulfate was present in the growth medium, and culture-based assays identified thiosulfate-dependent sulfide production by the same isolate. Increased production of sulfide and organic acids during the stationary growth phase suggests that fermentative Halanaerobium uses thiosulfate to remove excess reductant. These findings emphasize the potential detrimental effects that could arise from thiosulfate-reducing microorganisms in hydraulically fractured shales, which are undetected by current industry-wide corrosion diagnostics. IMPORTANCE Although thousands of wells in deep shale formations across the United States have been hydraulically fractured for oil and gas recovery, the impact of microbial metabolism within these environments is poorly understood. Our research demonstrates that dominant microbial populations in these subsurface ecosystems contain the conserved capacity for the reduction of thiosulfate to sulfide and that this process is likely occurring in the environment. Sulfide generation (also known as “souring”) is considered deleterious in the oil and gas industry because of both toxicity issues and impacts on corrosion of the subsurface infrastructure. Critically, the capacity for sulfide generation via reduction of sulfate was not detected in our data sets. Given that current industry wellhead tests for sulfidogenesis target canonical sulfate-reducing microorganisms, these data suggest that new approaches to the detection of sulfide-producing microorganisms may be necessary. PMID:28685163

Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales

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

Booker, Anne E.; Borton, Mikayla A.; Daly, Rebecca A.

ABSTRACT Hydraulic fracturing of black shale formations has greatly increased United States oil and natural gas recovery. However, the accumulation of biomass in subsurface reservoirs and pipelines is detrimental because of possible well souring, microbially induced corrosion, and pore clogging. Temporal sampling of produced fluids from a well in the Utica Shale revealed the dominance ofHalanaerobiumstrains within thein situmicrobial community and the potential for these microorganisms to catalyze thiosulfate-dependent sulfidogenesis. From these field data, we investigated biogenic sulfide production catalyzed by aHalanaerobiumstrain isolated from the produced fluids using proteogenomics and laboratory growth experiments. Analysis ofHalanaerobiumisolate genomes and reconstructed genomes frommore » metagenomic data sets revealed the conserved presence of rhodanese-like proteins and anaerobic sulfite reductase complexes capable of converting thiosulfate to sulfide. Shotgun proteomics measurements using aHalanaerobiumisolate verified that these proteins were more abundant when thiosulfate was present in the growth medium, and culture-based assays identified thiosulfate-dependent sulfide production by the same isolate. Increased production of sulfide and organic acids during the stationary growth phase suggests that fermentativeHalanaerobiumuses thiosulfate to remove excess reductant. These findings emphasize the potential detrimental effects that could arise from thiosulfate-reducing microorganisms in hydraulically fractured shales, which are undetected by current industry-wide corrosion diagnostics. IMPORTANCEAlthough thousands of wells in deep shale formations across the United States have been hydraulically fractured for oil and gas recovery, the impact of microbial metabolism within these environments is poorly understood. Our research demonstrates that dominant microbial populations in these subsurface ecosystems contain the conserved capacity for the reduction of thiosulfate to sulfide and that this process is likely occurring in the environment. Sulfide generation (also known as “souring”) is considered deleterious in the oil and gas industry because of both toxicity issues and impacts on corrosion of the subsurface infrastructure. Critically, the capacity for sulfide generation via reduction of sulfate was not detected in our data sets. Given that current industry wellhead tests for sulfidogenesis target canonical sulfate-reducing microorganisms, these data suggest that new approaches to the detection of sulfide-producing microorganisms may be necessary.« less

Anaerobic decomposition of humic substances by Clostridium from the deep subsurface

PubMed Central

Ueno, Akio; Shimizu, Satoru; Tamamura, Shuji; Okuyama, Hidetoshi; Naganuma, Takeshi; Kaneko, Katsuhiko

2016-01-01

Decomposition of humic substances (HSs) is a slow and cryptic but non-negligible component of carbon cycling in sediments. Aerobic decomposition of HSs by microorganisms in the surface environment has been well documented; however, the mechanism of anaerobic microbial decomposition of HSs is not completely understood. Moreover, no microorganisms capable of anaerobic decomposition of HSs have been isolated. Here, we report the anaerobic decomposition of humic acids (HAs) by the anaerobic bacterium Clostridium sp. HSAI-1 isolated from the deep terrestrial subsurface. The use of 14C-labelled polycatechol as an HA analogue demonstrated that the bacterium decomposed this substance up to 7.4% over 14 days. The decomposition of commercial and natural HAs by the bacterium yielded lower molecular mass fractions, as determined using high-performance size-exclusion chromatography. Fourier transform infrared spectroscopy revealed the removal of carboxyl groups and polysaccharide-related substances, as well as the generation of aliphatic components, amide and aromatic groups. Therefore, our results suggest that Clostridium sp. HSAI-1 anaerobically decomposes and transforms HSs. This study improves our understanding of the anaerobic decomposition of HSs in the hidden carbon cycling in the Earth’s subsurface. PMID:26743007

Mobility of Source Zone Heavy Metals and Radionuclides: The Mixed Roles of Fermentative Activity on Fate and Transport of U and Cr. Final Report

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

Gerlach, Robin; Peyton, Brent M.; Apel, William A.

2014-01-29

Various U. S. Department of Energy (DOE) low and medium-level radioactive waste sites contain mixtures of heavy metals, radionuclides and assorted organic materials. In addition, there are numerous sites around the world that are contaminated with a mixture of organic and inorganic contaminants. In most sites, over time, water infiltrates the wastes, and releases metals, radionuclides and other contaminants causing transport into the surrounding environment. We investigated the role of fermentative microorganisms in such sites that may control metal, radionuclide and organics migration from source zones. The project was initiated based on the following overarching hypothesis: Metals, radionuclides and othermore » contaminants can be mobilized by infiltration of water into waste storage sites. Microbial communities of lignocellulose degrading and fermenting microorganisms present in the subsurface of contaminated DOE sites can significantly impact migration by directly reducing and immobilizing metals and radionuclides while degrading complex organic matter to low molecular weight organic compounds. These low molecular weight organic acids and alcohols can increase metal and radionuclide mobility by chelation (i.e., certain organic acids) or decrease mobility by stimulating respiratory metal reducing microorganisms. We demonstrated that fermentative organisms capable of affecting the fate of Cr6+, U6+ and trinitrotoluene can be isolated from organic-rich low level waste sites as well as from less organic rich subsurface environments. The mechanisms, pathways and extent of contaminant transformation depend on a variety of factors related to the type of organisms present, the aqueous chemistry as well as the geochemistry and mineralogy. This work provides observations and quantitative data across multiple scales that identify and predict the coupled effects of fermentative carbon and electron flow on the transport of radionuclides, heavy metals and organic contaminants in the subsurface; a primary concern of the DOE Environmental Remediation Science Division (ERSD) and Subsurface Geochemical Research (SBR) Program.« less

Feldspars as a source of nutrients for microorganisms

USGS Publications Warehouse

Rogers, J.R.; Bennett, P.C.; Choi, W.J.

1998-01-01

Phosphorus and nitrogen are essential macronutrients necessary for the survival of virtually all living organisms. In groundwater systems, these nutrients can be quite scarce and can represent limiting elements for growth of subsurface microorganisms. In this study we examined silicate sources of these elements by characterizing the colonization and weathering of feldspars in situ using field microcosms. We found that in carbon-rich anoxic groundwaters where P and N are scarce, feldspars that contain inclusions of P-minerals such as apatite are preferentially colonized over similar feldspars without P. A microcline from S. Dakota, which contains 0.24% P2O5 but ,1 mmol/ g NH , was heavily colonized 1 4 and deeply weathered. A similar microcline from Ontario, which has no detectable P or NH , was barren of attached organisms and completely unweathered after one year. An- 1 4 orthoclase (0.28% P2O5, ;1 mmol/g NH ) was very heavily colonized and weathered, 1 4 whereas plagioclase specimens (,0.01% P, ,1 mmmol/g NH ) were uncolonized and 1 4 unweathered. In addition, the observed weathering rates are faster than expected based on laboratory rates. We propose that this system is particularly sensitive to the availability of P, and the native subsurface microorganisms have developed biochemical strategies to aggressively scavenge P (or some other essential nutrient such as Fe31 ) from resistant feldspars. The result of this interaction is that only minerals containing P will be signifi- cantly colonized, and these feldspars will be preferentially destroyed, as the subsurface microbial community scavenges a limiting nutrient.

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.

Chemolithotrophy in the continental deep subsurface: Sanford Underground Research Facility (SURF), USA

PubMed Central

Osburn, Magdalena R.; LaRowe, Douglas E.; Momper, Lily M.; Amend, Jan P.

2014-01-01

The deep subsurface is an enormous repository of microbial life. However, the metabolic capabilities of these microorganisms and the degree to which they are dependent on surface processes are largely unknown. Due to the logistical difficulty of sampling and inherent heterogeneity, the microbial populations of the terrestrial subsurface are poorly characterized. In an effort to better understand the biogeochemistry of deep terrestrial habitats, we evaluate the energetic yield of chemolithotrophic metabolisms and microbial diversity in the Sanford Underground Research Facility (SURF) in the former Homestake Gold Mine, SD, USA. Geochemical data, energetic modeling, and DNA sequencing were combined with principle component analysis to describe this deep (down to 8100 ft below surface), terrestrial environment. SURF provides access into an iron-rich Paleoproterozoic metasedimentary deposit that contains deeply circulating groundwater. Geochemical analyses of subsurface fluids reveal enormous geochemical diversity ranging widely in salinity, oxidation state (ORP 330 to −328 mV), and concentrations of redox sensitive species (e.g., Fe2+ from near 0 to 6.2 mg/L and Σ S2- from 7 to 2778μg/L). As a direct result of this compositional buffet, Gibbs energy calculations reveal an abundance of energy for microorganisms from the oxidation of sulfur, iron, nitrogen, methane, and manganese. Pyrotag DNA sequencing reveals diverse communities of chemolithoautotrophs, thermophiles, aerobic and anaerobic heterotrophs, and numerous uncultivated clades. Extrapolated across the mine footprint, these data suggest a complex spatial mosaic of subsurface primary productivity that is in good agreement with predicted energy yields. Notably, we report Gibbs energy normalized both per mole of reaction and per kg fluid (energy density) and find the later to be more consistent with observed physiologies and environmental conditions. Further application of this approach will significantly expand our understanding of the deep terrestrial biosphere. PMID:25429287

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

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...

ADSORPTION OF BACTERIOPHAGES ON CLAY MINERALS

EPA Science Inventory

Theability to predict the fate of microorganisms in soil is dependent on an understanding of the process of their sorption on soil and subsurface materials. Presently, we have focused on studying the thermodynamics of sorption of bacteriophages (T-2, MS-2, and

Optical fiber-mediated photosynthesis for enhanced subsurface oxygen delivery.

PubMed

Lanzarini-Lopes, Mariana; Delgado, Anca G; Guo, Yuanming; Dahlen, Paul; Westerhoff, Paul

2018-03-01

Remediation of polluted groundwater often requires oxygen delivery into subsurface to sustain aerobic bacteria. Air sparging or injection of oxygen containing solutions (e.g., hydrogen peroxide) into the subsurface are common. In this study visible light was delivered into the subsurface using radially emitting optical fibers. Phototrophic organisms grew near the optical fiber in a saturated sand column. When applying light in on-off cycles, dissolved oxygen (DO) varied from super saturation levels of >15 mg DO/L in presence of light to under-saturation (<5 mg DO/L) in absence of light. Non-photosynthetic bacteria dominated at longer radial distances from the fiber, presumably supported by soluble microbial products produced by the photosynthetic microorganisms. The dissolved oxygen variations alter redox condition changes in response to light demonstrate the potential to biologically deliver oxygen into the subsurface and support a diverse microbial community. The ability to deliver oxygen and modulate redox conditions on diurnal cycles using solar light may provide a sustainable, long term strategy for increasing dissolved oxygen levels in subsurface environments and maintaining diverse biological communities. Copyright © 2017 Elsevier Ltd. All rights reserved.

Depth Distribution and Assembly of Sulfate-Reducing Microbial Communities in Marine Sediments of Aarhus Bay

PubMed Central

Jochum, Lara M.; Chen, Xihan; Lever, Mark A.; Loy, Alexander; Jørgensen, Bo Barker; Schramm, Andreas

2017-01-01

ABSTRACT Most sulfate-reducing microorganisms (SRMs) present in subsurface marine sediments belong to uncultured groups only distantly related to known SRMs, and it remains unclear how changing geochemical zones and sediment depth influence their community structure. We mapped the community composition and abundance of SRMs by amplicon sequencing and quantifying the dsrB gene, which encodes dissimilatory sulfite reductase subunit beta, in sediment samples covering different vertical geochemical zones ranging from the surface sediment to the deep sulfate-depleted subsurface at four locations in Aarhus Bay, Denmark. SRMs were present in all geochemical zones, including sulfate-depleted methanogenic sediment. The biggest shift in SRM community composition and abundance occurred across the transition from bioturbated surface sediments to nonbioturbated sediments below, where redox fluctuations and the input of fresh organic matter due to macrofaunal activity are absent. SRM abundance correlated with sulfate reduction rates determined for the same sediments. Sulfate availability showed a weaker correlation with SRM abundances and no significant correlation with the composition of the SRM community. The overall SRM species diversity decreased with depth, yet we identified a subset of highly abundant community members that persists across all vertical geochemical zones of all stations. We conclude that subsurface SRM communities assemble by the persistence of members of the surface community and that the transition from the bioturbated surface sediment to the unmixed sediment below is a main site of assembly of the subsurface SRM community. IMPORTANCE Sulfate-reducing microorganisms (SRMs) are key players in the marine carbon and sulfur cycles, especially in coastal sediments, yet little is understood about the environmental factors controlling their depth distribution. Our results suggest that macrofaunal activity is a key driver of SRM abundance and community structure in marine sediments and that a small subset of SRM species of high relative abundance in the subsurface SRM community persists from the sulfate-rich surface sediment to sulfate-depleted methanogenic subsurface sediment. More generally, we conclude that SRM communities inhabiting the subsurface seabed assemble by the selective survival of members of the surface community. PMID:28939599

FATE OF PATHOGENIC MICROORGANISMS IN SOIL

EPA Science Inventory

In order to forecast the effect of viruses contaminating the ground water supply, sorption of pathogens on soil and subsurface materials was studied. Considering that change in free energy for the process is directly proportional to the degree of sorption, a model has been develo...

Denitrifying bioreactors for nitrate removal from tile drained cropland

USDA-ARS?s Scientific Manuscript database

Denitrification bioreactors are a promising technology for mitigation of nitrate-nitrogen (NO3-N) losses in subsurface drainage water. Bioreactors are constructed with carbon substrates, typically wood chips, to provide a substrate for denitrifying microorganisms. Researchers in Iowa found that for ...

IN-SITU BIOREMEDIATION OF GROUND WATER AND GEOLOGICAL MATERIAL: A REVIEW OF TECHNOLOGIES

EPA Science Inventory

In situ bioremediation of subsurface environments involve the use of microorganisms to convert contaminants to less harmful products and sometimes offers significant potential advantages over other remediation technologies. n order for these biodegradative processes to occur, icr...

Final Technical Report

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

Sobecky, Patricia A; Taillefert, Martial

This final technical report describes results and findings from a research project to examine the role of microbial phosphohydrolase enzymes in naturally occurring subsurface microorganisms for the purpose of promoting the immobilization of the radionuclide uranium through the production of insoluble uranium phosphate minerals. The research project investigated the microbial mechanisms and the physical and chemical processes promoting uranium biomineralization and sequestration in oxygenated subsurface soils. Uranium biomineralization under aerobic conditions can provide a secondary biobarrier strategy to immobilize radionuclides should the metal precipitates formed by microbial dissimilatory mechanisms remobilize due to a change in redox state.

Bioremediation of contaminated groundwater

DOEpatents

Hazen, T.C.; Fliermans, C.B.

1994-01-01

Disclosed is an apparatus and method for in situ remediation of contaminated subsurface soil or groundwater contaminated by chlorinated hydrocarbons. A nutrient fluid (NF) is selected to simulated the growth and reproduction of indigenous subsurface microorganisms capable of degrading the contaminants; an oxygenated fluid (OF) is selected to create an aerobic environment with anaerobic pockets. NF is injected periodically while OF is injected continuously and both are extracted so that both are drawn across the plume. NF stimulates microbial colony growth; withholding it periodically forces the larger, healthy colony of microbes to degrade the contaminants. Treatment is continued until the subsurface concentration of contaminants is acceptable. NF can be methane and OF be air, for stimulating production of methanotrophs to break down chlorohydrocarbons, especially TCE and tetrachloroethylene.

Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes.

PubMed

Long, Philip E; Williams, Kenneth H; Hubbard, Susan S; Banfield, Jillian F

2016-08-01

Microorganisms play key roles in terrestrial system processes, including the turnover of natural organic carbon, such as leaf litter and woody debris that accumulate in soils and subsurface sediments. What has emerged from a series of recent DNA sequencing-based studies is recognition of the enormous variety of little known and previously unknown microorganisms that mediate recycling of these vast stores of buried carbon in subsoil compartments of the terrestrial system. More importantly, the genome resolution achieved in these studies has enabled association of specific members of these microbial communities with carbon compound transformations and other linked biogeochemical processes-such as the nitrogen cycle-that can impact the quality of groundwater, surface water, and atmospheric trace gas concentrations. The emerging view also emphasizes the importance of organism interactions through exchange of metabolic byproducts (e.g., within the carbon, nitrogen, and sulfur cycles) and via symbioses since many novel organisms exhibit restricted metabolic capabilities and an associated extremely small cell size. New, genome-resolved information reshapes our view of subsurface microbial communities and provides critical new inputs for advanced reactive transport models. These inputs are needed for accurate prediction of feedbacks in watershed biogeochemical functioning and their influence on the climate via the fluxes of greenhouse gases, CO2, CH4, and N2O. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

Microbial Life Driving Low-Temperature Basalt Alteration in the Subsurface: Decoupling Abiotic Processes from Biologically-Mediated Rock Alteration

NASA Astrophysics Data System (ADS)

Moore, R.; Lecoeuvre, A.; Stephant, S.; Dupraz, S.; Ranchou-Peyruse, M.; Ranchou-Peyruse, A.; Gérard, E.; Ménez, B.

2017-12-01

Microorganisms are involved with specific rock alteration processes in the deep subsurface. It is a challenge to link any contribution microbial life may have on rock alteration with specific functions or phyla because many alteration features and secondary minerals produced by metabolic processes can also produce abiotically. Here, two flow-through experiments were designed to mimic the circulation of a CO2-rich fluid through crystalline basalt. In order to identify microbially-mediated alteration and be able to link it with specific metabolisms represented in the subsurface, a relatively fresh crystalline basalt substrate was subsampled, sterilized and used as the substrate for both experiments. In one experiment, the substrate was left sterile, and in the other it was inoculated with an enrichment culture derived from the same aquifer as the rock substrate. Initial results show that the inoculum contained Proteobacteria and Firmicutes, which have diverse metabolic potentials. Fluid and rock analyses before, during, and after the experiments show that mineralogy, fluid chemistry, and dissolution processes differ between the sterile and inoculated systems. In the inoculated experiment iron-rich orthopyroxenes were preferentially dissolved while in the sterile system clinopyroxenes and plagioclases both exhibited a higher degree of dissolution. Additionally, the patterns of CO2 consumption and production over the duration of both experiments is different. This suggest that in a low-temperature basalt system with microorganisms CO2 is either consumed to produce biomass, or that carbonates are produced and then subsequently preserved. This suite of results combined with molecular ecology analyses can be used to conclude that in low-temperature basalts microorganisms play an intrinsic role in rock alteration.

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

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

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.

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

Goltz, M.N.; Kawakami, B.T.; McCarty, P.L.

A full-scale study of in-situ bioremediation is being planned for implementation at Edwards Air Force Base. The bioremediation system that is being proposed has been developed over 8 years of research and testing in the laboratory and at a pilot field site located at Moffett Naval Air Station in Mountain View, California. Studies conducted at the Moffett field site have demonstrated that trichloroethylene (TCE), the contaminant found at Edwards, can be effectively biodegraded cometabolically through the introduction into the subsurface of a primary substrate and an oxygen source to support the growth and energy requirements of a native population ofmore » microorganisms. One of the main questions that needs to be answered, prior to full-scale demonstration of this technology on the Edwards TCE plume, is how best to mix a primary substrate, an oxygen source, and TCE, and subsequently get the mixture to the microorganisms. At Moffett Field, mixing of these three components was accomplished above ground, with the mixture then introduced into the subsurface through an injection well. In the full-scale demonstration, the TCE will, of course, already be in the groundwater. A major objective of the demonstration will be to investigate how a primary substrate and an oxygen source can be efficiently mixed and transported to indigenous microorganisms, in order to promote cometabolic degradation of TCE.« less

Optimization of denitrifying bioreactor performance with agricultural residue-based filter media

USDA-ARS?s Scientific Manuscript database

Denitrification bioreactors are a promising technology for mitigation of nitrate-nitrogen (NO3-N) losses in subsurface drainage water. Bioreactors are constructed with carbon substrates, typically wood chips, to provide a substrate for denitrifying microorganisms. Columns were packed with wood chips...

Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships

PubMed Central

Lau, Maggie C. Y.; Cameron, Connor; Magnabosco, Cara; Brown, C. Titus; Schilkey, Faye; Grim, Sharon; Hendrickson, Sarah; Pullin, Michael; Sherwood Lollar, Barbara; van Heerden, Esta; Kieft, Thomas L.; Onstott, Tullis C.

2014-01-01

Comparative studies on community phylogenetics and phylogeography of microorganisms living in extreme environments are rare. Terrestrial subsurface habitats are valuable for studying microbial biogeographical patterns due to their isolation and the restricted dispersal mechanisms. Since the taxonomic identity of a microorganism does not always correspond well with its functional role in a particular community, the use of taxonomic assignments or patterns may give limited inference on how microbial functions are affected by historical, geographical and environmental factors. With seven metagenomic libraries generated from fracture water samples collected from five South African mines, this study was carried out to (1) screen for ubiquitous functions or pathways of biogeochemical cycling of CH4, S, and N; (2) to characterize the biodiversity represented by the common functional genes; (3) to investigate the subsurface biogeography as revealed by this subset of genes; and (4) to explore the possibility of using metagenomic data for evolutionary study. The ubiquitous functional genes are NarV, NPD, PAPS reductase, NifH, NifD, NifK, NifE, and NifN genes. Although these eight common functional genes were taxonomically and phylogenetically diverse and distinct from each other, the dissimilarity between samples did not correlate strongly with geographical or environmental parameters or residence time of the water. Por genes homologous to those of Thermodesulfovibrio yellowstonii detected in all metagenomes were deep lineages of Nitrospirae, suggesting that subsurface habitats have preserved ancestral genetic signatures that inform the study of the origin and evolution of prokaryotes. PMID:25400621

Growth Inhibition and Stimulation of Shewanella oneidensis MR-1 by Surfactants and Calcium Polysulfide

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

Bailey, Kathryn L.; Tilton, Fred A.; Jansik, Danielle P.

2012-06-14

Foam delivery technology (FDT) uses surfactant based foam to immobilize subsurface contaminants in situ. Where traditional approaches are impractical, FDT has the potential to overcome many of the technical challenges facing the remediation of contaminated deep vadose zone environments. However, little is known about the effects these reactive chemicals may have on microorganisms inhabiting the contaminated subsurface. In addition, there are currently no standard assays to assess microbial responses to subsurface remedial treatments while these agents are under development. The objective of this study was to develop a rapid laboratory assay to assess the potential growth inhibition and/or stimulation ofmore » microorganisms following exposure to candidate FDT components. Calcium polysulfide (CPS) and several surfactants (i.e. sodium laureth sulfate (SLES), sodium dodecyl sulfate (SDS), cocamidopropyl betaine (CAPB) and NINOL40-CO) have diverse chemistries and are candidate components of FDT. Shewanella oneidensis MR-1 cultures were exposed to a range of concentrations of these chemicals to determine the minimum bactericidal concentration (MBC) and the growth and viability potential of these components. Concentrations of SDS higher than 700 {micro}M were toxic to S. oneidensis MR-1 growth over the course of four days of exposure. The relative acute toxicity order for these compounds was SDS>>CPS>>NINOL40-CO>SLES-CAPB. Dose dependent growth decreases (20 to 100 mM) were observed in the CAPB and SLES treated cultures and both CPS and NINOL 40-CO were toxic at all concentrations tested (1.45 to 7.25 mM CPS). Both SLES (20 to 100 mM) and SDS at lower concentrations (20 to 500 {micro}M) were stimulatory to S. oneidensis MR-1 indicating a capacity to be used as a carbon source. These studies also identified potentially key component characteristics, such as precipitate formation and oxygen availability, which may prove valuable in assessing the response of subsurface microorganisms. This benchtop system provides a capability to assess adverse microbial-remediation responses and contributes to the development of in situ remedial chemistries before they are deployed in the field.« less

Growth inhibition and stimulation of Shewanella oneidensis MR-1 by surfactants and calcium polysulfide.

PubMed

Bailey, Kathryn L; Tilton, Fred; Jansik, Danielle P; Ergas, Sarina J; Marshall, Matthew J; Miracle, Ann L; Wellman, Dawn M

2012-06-01

Foam delivery technology (FDT) uses surfactant based foam to immobilize subsurface contaminants in situ. Where traditional approaches are impractical, FDT has the potential to overcome many of the technical challenges facing the remediation of contaminated deep vadose zone environments. However, little is known about the effects these reactive chemicals may have on microorganisms inhabiting the contaminated subsurface. In addition, there are currently no standard assays to assess microbial responses to subsurface remedial treatments while these agents are under development. The objective of this study was to develop a rapid laboratory assay to assess the potential growth inhibition and/or stimulation of microorganisms following exposure to candidate FDT components. Calcium polysulfide (CPS) and several surfactants (i.e. sodium laureth sulfate (SLES), sodium dodecyl sulfate (SDS), cocamidopropyl betaine (CAPB) and NINOL40-CO) have diverse chemistries and are candidate components of FDT. Shewanella oneidensis MR-1 cultures were exposed to a range of concentrations of these chemicals to determine the minimum bactericidal concentration (MBC) and the growth and viability potential of these components. Concentrations of SDS higher than 700 μM were toxic to S. oneidensis MR-1 growth over the course of four days of exposure. The relative acute toxicity order for these compounds was SDS > CPS > NINOL 40-CO>SLES≥CAPB. Dose dependent growth decreases (20-100mM) were observed in the CAPB and SLES treated cultures and both CPS and NINOL 40-CO were toxic at all concentrations tested (1.45-7.25 mM CPS). Both SLES (20-100mM) and SDS at lower concentrations (20-500 μM) were stimulatory to S. oneidensis MR-1 indicating a capacity to be used as a carbon source. These studies also identified potentially key component characteristics, such as precipitate formation and oxygen availability, which may prove valuable in assessing the response of subsurface microorganisms. This benchtop system provides a capability to assess adverse microbial-remediation responses and contributes to the development of in situ remedial chemistries before they are deployed in the field. Copyright © 2012 Elsevier Inc. All rights reserved.

Evidence of biological activity in Hawaiian subsurface basalts

NASA Astrophysics Data System (ADS)

Fisk, M. R.; Storrie-Lombardi, M. C.; Douglas, S.; Popa, R.; McDonald, G.; di Meo-Savoie, C.

2003-12-01

The Hawaii Scientific Drilling Program (HSDP) cored and recovered igneous rock from the surface to a depth of 3109 m near Hilo, Hawaii. Much of the deeper parts of the hole is composed of hyaloclastite (fractured basalt glass that has been cemented in situ with secondary minerals). Some hyaloclastite units have been altered in a manner attributed to microorganisms in volcanic rocks. Samples from one such unit (1336 m to 1404 m below sea level) were examined to test the hypothesis that the alteration was associated with microorganisms. Deep ultraviolet native fluorescence and resonance Raman spectroscopy indicate that nucleic acids and aromatic amino acids are present in clay inside spherical cavities (vesicles) within basalt glass. Chemical mapping shows that phosphorus and carbon were enriched at the boundary between the clay and volcanic glass of the vesicles. Environmental scanning electron microscopy (ESEM) reveals two to three micrometer coccoid structures in these same boundaries. ESEM-linked energy dispersive spectroscopy demonstrated carbon, phosphorous, chloride, and magnesium in these bodies significantly differing from unoccupied neighboring regions of basalt. These observations taken together indicate the presence of microorganisms at the boundary between primary volcanic glass and secondary clays. Amino acids and nucleic acids were extracted from bulk samples of the hyaloclastite unit. Amino acid abundance was low, and if the amino acids are derived from microorganisms in the rock, then there are less than 100,000 cells per gram of rock. Most nucleic acid sequences extracted from the unit were closely related to sequences of Crenarchaeota collected from the subsurface of the ocean floor.

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...

Habitable periglacial landscapes in martian mid-latitudes

NASA Astrophysics Data System (ADS)

Ulrich, M.; Wagner, D.; Hauber, E.; de Vera, J.-P.; Schirrmeister, L.

2012-05-01

Subsurface permafrost environments on Mars are considered to be zones where extant life could have survived. For the identification of possible habitats it is important to understand periglacial landscape evolution and related subsurface and environmental conditions. Many landforms that are interpreted to be related to ground ice are located in the martian mid-latitudinal belts. This paper summarizes the insights gained from studies of terrestrial analogs to permafrost landforms on Mars. The potential habitability of martian mid-latitude periglacial landscapes is exemplarily deduced for one such landscape, that of Utopia Planitia, by a review and discussion of environmental conditions influencing periglacial landscape evolution. Based on recent calculations of the astronomical forcing of climate changes, specific climate periods are identified within the last 10 Ma when thaw processes and liquid water were probably important for the development of permafrost geomorphology. No periods could be identified within the last 4 Ma which met the suggested threshold criteria for liquid water and habitable conditions. Implications of past and present environmental conditions such as temperature variations, ground-ice conditions, and liquid water activity are discussed with respect to the potential survival of highly-specialized microorganisms known from terrestrial permafrost. We conclude that possible habitable subsurface niches might have been developed in close relation to specific permafrost landform morphology on Mars. These would have probably been dominated by lithoautotrophic microorganisms (i.e. methanogenic archaea).

2500 high-quality genomes reveal that the biogeochemical cycles of C, N, S and H are cross-linked by metabolic handoffs in the terrestrial subsurface

NASA Astrophysics Data System (ADS)

Anantharaman, K.; Brown, C. T.; Hug, L. A.; Sharon, I.; Castelle, C. J.; Shelton, A.; Bonet, B.; Probst, A. J.; Thomas, B. C.; Singh, A.; Wilkins, M.; Williams, K. H.; Tringe, S. G.; Beller, H. R.; Brodie, E.; Hubbard, S. S.; Banfield, J. F.

2015-12-01

Microorganisms drive the transformations of carbon compounds in the terrestrial subsurface, a key reservoir of carbon on earth, and impact other linked biogeochemical cycles. Our current knowledge of the microbial ecology in this environment is primarily based on 16S rRNA gene sequences that paint a biased picture of microbial community composition and provide no reliable information on microbial metabolism. Consequently, little is known about the identity and metabolic roles of the uncultivated microbial majority in the subsurface. In turn, this lack of understanding of the microbial processes that impact the turnover of carbon in the subsurface has restricted the scope and ability of biogeochemical models to capture key aspects of the carbon cycle. In this study, we used a culture-independent, genome-resolved metagenomic approach to decipher the metabolic capabilities of microorganisms in an aquifer adjacent to the Colorado River, near Rifle, CO, USA. We sequenced groundwater and sediment samples collected across fifteen different geochemical regimes. Sequence assembly, binning and manual curation resulted in the recovery of 2,542 high-quality genomes, 27 of which are complete. These genomes represent 1,300 non-redundant organisms comprising both abundant and rare community members. Phylogenetic analyses involving ribosomal proteins and 16S rRNA genes revealed the presence of up to 34 new phyla that were hitherto unknown. Less than 11% of all genomes belonged to the 4 most commonly represented phyla that constitute 93% of all currently available genomes. Genome-specific analyses of metabolic potential revealed the co-occurrence of important functional traits such as carbon fixation, nitrogen fixation and use of electron donors and electron acceptors. Finally, we predict that multiple organisms are often required to complete redox pathways through a complex network of metabolic handoffs that extensively cross-link subsurface biogeochemical cycles.

[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.

Recalcitrant Carbonaceous Material: A Source of Electron Donors for Anaerobic Microbial Metabolisms in the Subsurface?

NASA Astrophysics Data System (ADS)

Nixon, S. L.; Montgomery, W.; Sephton, M. A.; Cockell, C. S.

2014-12-01

More than 90% of organic material on Earth resides in sedimentary rocks in the form of kerogens; fossilized organic matter formed through selective preservation of high molecular weight biopolymers under anoxic conditions. Despite its prevalence in the subsurface, the extent to which this material supports microbial metabolisms is unknown. Whilst aerobic microorganisms are known to derive energy from kerogens within shales, utilization in anaerobic microbial metabolisms that proliferate in the terrestrial subsurface, such as microbial iron reduction, has yet to be demonstrated. Data are presented from microbial growth experiments in which kerogens and shales were supplied as the sole electron donor source for microbial iron reduction by an enrichment culture. Four well-characterized kerogens samples (representative of Types I-IV, classified by starting material), and two shale samples, were assessed. Organic analysis was carried out to investigate major compound classes present in each starting material. Parallel experiments were conducted to test inhibition of microbial iron reduction in the presence of each material when the culture was supplied with a full redox couple. The results demonstrate that iron-reducing microorganisms in this culture were unable to use kerogens and shales as a source of electron donors for energy acquisition, despite the presence of compound classes known to support this metabolism. Furthermore, the presence of these materials was found to inhibit microbial iron reduction to varying degrees, with some samples leading to complete inhibition. These results suggest that recalcitrant carbonaceous material in the terrestrial subsurface is not available for microbial iron reduction and similar metabolisms, such as sulphate-reduction. Further research is needed to investigate the inhibition exerted by these materials, and to assess whether these findings apply to other microbial consortia. These results may have significant implications for the role of anaerobic microbial metabolisms in the subsurface terrestrial carbon cycle. Kerogens are chemically similar to organic material in carbonaceous chondrites. As such, further study may provide insight into the potential availability of organic compounds for microbial metabolisms operating in the subsurface of Mars.

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.

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

Cave speleothems as repositories of microbial biosignatures

NASA Astrophysics Data System (ADS)

Miller, Ana Z.; Jurado, Valme; Pereira, Manuel F. C.; Fernández, Octavio; Calaforra, José M.; Dionísio, Amélia; Saiz-Jimenez, Cesareo

2015-04-01

The need to better understand the biodiversity, origins of life on Earth and on other planets, and the wide applications of the microbe-mineral interactions have led to a rapid expansion of interest in subsurface environments. Recently reported results indicated signs of an early wet Mars and rather recent volcanic activity which suggest that Mars's subsurface can house organic molecules or traces of microbial life, making the search for microbial life on Earth's subsurface even more compelling. Caves on Earth are windows into the subsurface that harbor a wide variety of mineral-utilizing microorganisms, which may contribute to the formation of biominerals and unusual microstructures recognized as biosignatures. These environments contain a wide variety of redox interfaces and stable physicochemical conditions, which enhance secondary mineral precipitation and microbial growth under limited organic nutrient inputs. Enigmatic microorganisms and unusual mineral features have been found associated with secondary mineral deposits or speleothems in limestone caves and lava tubes. In this study, Field Emission Scanning Electron Microscopy (FESEM) and Energy Dispersive X-ray spectroscopy (EDS) analyses were conducted on cave speleothem samples to assess microbe-mineral interactions, evaluate biogenicity, as well as to describe unusual mineral formations and microbial features. Microbial mats, extracellular polymeric substances, tubular empty sheaths, mineralized cells, filamentous fabrics, as well as "cell-sized" etch pits or microborings produced by bacterial cells were observed on minerals. These features evidence microbe-mineral interactions and may represent mineralogical signatures of life. We can thus consider that caves on Earth are plausible repositories of terrestrial biosignatures where we can look for microbial signatures. Acknowledgments: AZM acknowledges the support from the Marie Curie Intra-European Fellowship within the 7th European Community Framework Programme (PIEF-GA-2012-328689- DECAVE). The authors acknowledge the Spanish Ministry of Economy and Competitiveness (project CGL2013-41674-P) for financial support.

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

Mineral stimulation of subsurface microorganisms: release of limiting nutrients from silicates

USGS Publications Warehouse

Roger, Jennifer Roberts; Bennett, Philip C.

2004-01-01

Microorganisms play an important role in the weathering of silicate minerals in many subsurface environments, but an unanswered question is whether the mineral plays an important role in the microbial ecology. Silicate minerals often contain nutrients necessary for microbial growth, but whether the microbial community benefits from their release during weathering is unclear. In this study, we used field and laboratory approaches to investigate microbial interactions with minerals and glasses containing beneficial nutrients and metals. Field experiments from a petroleum-contaminated aquifer, where silicate weathering is substantially accelerated in the contaminated zone, revealed that phosphorus (P) and iron (Fe)-bearing silicate glasses were preferentially colonized and weathered, while glasses without these elements were typically barren of colonizing microorganisms, corroborating previous studies using feldspars. In laboratory studies, we investigated microbial weathering of silicates and the release of nutrients using a model ligand-promoted pathway. A metal-chelating organic ligand 3,4 dihydroxybenzoic acid (3,4 DHBA) was used as a source of chelated ferric iron, and a carbon source, to investigate mineral weathering rate and microbial metabolism.In the investigated aquifer, we hypothesize that microbes produce organic ligands to chelate metals, particularly Fe, for metabolic processes and also form stable complexes with Al and occasionally with Si. Further, the concentration of these ligands is apparently sufficient near an attached microorganism to destroy the silicate framework while releasing the nutrient of interest. In microcosms containing silicates and glasses with trace phosphate mineral inclusions, microbial biomass increased, indicating that the microbial community can use silicate-bound phosphate inclusions. The addition of a native microbial consortium to microcosms containing silicates or glasses with iron oxide inclusions correlated to accelerated weathering and release of Si into solution as well as the accelerated degradation of the model substrate 3,4 DHBA. We propose that silicate-bound P and Fe inclusions are bioavailable, and microorganisms may use organic ligands to dissolve the silicate matrix and access these otherwise limiting nutrients.

Effects of subsurface aeration and trinexapac-ethyl application on soil microbial communities in a creeping bentgrass putting green

USGS Publications Warehouse

Feng, Y.; Stoeckel, D.M.; Van Santen, E.; Walker, R.H.

2002-01-01

The sensitivity of creeping bentgrass (Agrostis palustris Huds.) to the extreme heat found in the southeastern United States has led to the development of new greens-management methods. The purpose of this study was to examine the effects of subsurface aeration and growth regulator applications on soil microbial communities and mycorrhizal colonization rates in a creeping bentgrass putting green. Two cultivars (Crenshaw and Penncross), a growth regulator (trinexapacethyl), and subsurface aeration were evaluated in cool and warm seasons. Total bacterial counts were higher in whole (unsieved) soils than in sieved soils, indicating a richer rhizosphere soil environment. Mycorrhizal infection rates were higher in trinexapac-ethyl (TE) treated plants. High levels of hyphal colonization and relatively low arbuscule and vesicle occurrence were observed. Principal components analysis of whole-soil fatty acid methyl ester (FAME) profiles indicated that warm-season microbial populations in whole and sieved soils had similar constituents, but the populations differed in the cool season. FAME profiles did not indicate that subsurface aeration and TE application affected soil microbial community structure. This is the first reported study investigating the influences of subsurface aeration and TE application on soil microorganisms in a turfgrass putting green soil.

Biodegradation of crude oil in Arctic subsurface water from the Disko Bay (Greenland) is limited.

PubMed

Scheibye, Katrine; Christensen, Jan H; Johnsen, Anders R

2017-04-01

Biological degradation is the main process for oil degradation in a subsurface oil plume. There is, however, little information on the biodegradation potential of Arctic, marine subsurface environments. We therefore investigated oil biodegradation in microcosms at 2 °C containing Arctic subsurface seawater from the Disko Bay (Greenland) and crude oil at three concentrations of 2.5-10 mg/L. Within 71 days, the total petroleum hydrocarbon concentration decreased only by 18 ± 18% for an initial concentration of 5 mg/L. The saturated alkanes nC13-nC30 and the isoprenoids iC18-iC21 were biodegraded at all concentrations indicating a substantial potential for biodegradation of these compound classes. Polycyclic aromatic compounds (PACs) disappeared from the oil phase, but dissolution was the main process of removal. Analysis of diagnostic ratios indicated almost no PAC biodegradation except for the C1-naphthalenes. To conclude, the marine subsurface microorganisms from the Disko Bay had the potential for biodegradation of n-alkanes and isoprenoids while the metabolically complex and toxic PACs and their alkylated homologs remained almost unchanged. Copyright © 2016 Elsevier Ltd. All rights reserved.

Detection of the anaerobic dechlorinating microorganism Desulfomonile tiedjei in environmental matrices by its signature lipopolysacchride branched-long-chain hydroxy fatty acids

USGS Publications Warehouse

Ringleberg, D.B.; Townsend, G.T.; DeWeerd, K.A.; Suflita, J.M.; White, D.C.

1994-01-01

Desulfomonile tiedjei is a Gram-negative sulfate-reducing bacterium capable of catalyzing aryl reductive dehalogenation reactions. Since many toxic and persistent contaminants in the subsurface are halogenated aromatic compounds, the detection and enumeration of dehalogenating microorganisms in the environment may be a useful tool for planning and evaluating bioremediation efforts. In this study, we show that D. tiedjei contains unique lipopolysaccharide branched 3-hydroxy fatty acids, unknown as yet in other bacteria, and that it is possible to detect the bacterium in inoculated aquifer sediments based on these signature lipid biomarkers. The detection of D. tiedjeiand other dehalogenating microorganisms possessing similar cellular properties in environmental matrices may be possible by this technique. Additionally, the effect of such inoculation on dehalogenation activity is examined.

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

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

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.

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.

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.

Microbial Fossils from Terrestrial Subsurface Hydrothermal Environments: Examples and Implications for Mars

NASA Technical Reports Server (NTRS)

Hofmann, Beda A.; Farmer, Jack; Chang, Sherwood (Technical Monitor)

1997-01-01

The recognition of biological signatures in ancient epithermal deposits has special relevance for studies of early blaspheme evolution and in exploring for past life on Mars. Recently, proposals for the existence of an extensive subsurface blaspheme on Earth, dominated by chemoautotrophic microbial life, has gained prominence. However, reports of fossilized microbial remains, or biosedimentary structures (e.g. stromatolites) from the deposits of ancient subsurface systems, are rare. Microbial preservation is favoured where high population densities co-exist with rapid mineral precipitation. Near-surface epithetical systems with strong gradients in temperature and redox are good candidates for the abundant growth and fossilization of microorganisms, and are also favorable environments for the precipitation of ore minerals. Therefore, we might expect microbial remain, to be particularly well preserved in various kinds of hydrothermal and diagenetic mineral precipitates that formed below the upper temperature limit for life (approx. 120 C).

Bioremediation of uranium-contaminated groundwater: a systems approach to subsurface biogeochemistry.

PubMed

Williams, Kenneth H; Bargar, John R; Lloyd, Jonathan R; Lovley, Derek R

2013-06-01

Adding organic electron donors to stimulate microbial reduction of highly soluble U(VI) to less soluble U(IV) is a promising strategy for immobilizing uranium in contaminated subsurface environments. Studies suggest that diagnosing the in situ physiological status of the subsurface community during uranium bioremediation with environmental transcriptomic and proteomic techniques can identify factors potentially limiting U(VI) reduction activity. Models which couple genome-scale in silico representations of the metabolism of key microbial populations with geochemical and hydrological models may be able to predict the outcome of bioremediation strategies and aid in the development of new approaches. Concerns remain about the long-term stability of sequestered U(IV) minerals and the release of co-contaminants associated with Fe(III) oxides, which might be overcome through targeted delivery of electrons to select microorganisms using in situ electrodes. Copyright © 2012 Elsevier Ltd. All rights reserved.

Performance Indicators for Uranium Bioremediation in the Subsurface: Basis and Assessment

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

Long, Philip E.; Yabusaki, Steven B.

2006-12-29

The purpose of this letter report is to identify performance indicators for in situ engineered bioremediation of subsurface uranium (U) contamination. This report focuses on in situ treatment of groundwater by biostimulation of extant in situ microbial populations (see http://128.3.7.51/NABIR/generalinfo/primers_guides/03_NABIR_primer.pdf for background information on bioremediation of metals and radionuclides). The treatment process involves amendment of the subsurface with an electron donor such as acetate, lactate, ethanol or other organic compound such that in situ microorganisms mediate the reduction of U(VI) to U(IV). U(VI) precipitates as uraninite or other insoluble U phase. Uranium is thus immobilized in place by such processesmore » and is subject to reoxidation that may remobilize the reduced uranium. Related processes include augmenting the extant subsurface microbial populations, addition of electron acceptors, and introduction of chemically reducing materials such as zero-valent Fe. While metrics for such processes may be similar to those for in situ biostimulation, these related processes are not directly in the scope of this letter report.« less

Reduction of Non-CO2 Gas Emissions Through The In Situ Bioconversion of Methane

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

Scott, A R; Mukhopadhyay, B; Balin, D F

2012-09-06

The primary objectives of this research were to seek previously unidentified anaerobic methanotrophs and other microorganisms to be collected from methane seeps associated with coal outcrops. Subsurface application of these microbes into anaerobic environments has the potential to reduce methane seepage along coal outcrop belts and in coal mines, thereby preventing hazardous explosions. Depending upon the types and characteristics of the methanotrophs identified, it may be possible to apply the microbes to other sources of methane emissions, which include landfills, rice cultivation, and industrial sources where methane can accumulate under buildings. Finally, the microbes collected and identified during this researchmore » also had the potential for useful applications in the chemical industry, as well as in a variety of microbial processes. Sample collection focused on the South Fork of Texas Creek located approximately 15 miles east of Durango, Colorado. The creek is located near the subsurface contact between the coal-bearing Fruitland Formation and the underlying Pictured Cliffs Sandstone. The methane seeps occur within the creek and in areas adjacent to the creek where faulting may allow fluids and gases to migrate to the surface. These seeps appear to have been there prior to coalbed methane development as extensive microbial soils have developed. Our investigations screened more than 500 enrichments but were unable to convince us that anaerobic methane oxidation (AMO) was occurring and that anaerobic methanotrophs may not have been present in the samples collected. In all cases, visual and microscopic observations noted that the early stage enrichments contained viable microbial cells. However, as the levels of the readily substrates that were present in the environmental samples were progressively lowered through serial transfers, the numbers of cells in the enrichments sharply dropped and were eliminated. While the results were disappointing we acknowledge that anaerobic methane oxidizing (AOM) microorganisms are predominantly found in marine habitats and grow poorly under most laboratory conditions. One path for future research would be to use a small rotary rig to collect samples from deeper soil horizons, possibly adjacent to the coal-bearing horizons that may be more anaerobic.« less

Challenges to Life on Mars --- Ecological Perspective

NASA Astrophysics Data System (ADS)

Sun, H.; McKay, C.; Friedmann, I.; McDonald, G.

2003-12-01

This talk will address the habitability of Mars by considering major environmental challenges against the tolerance limits of microorganisms from extreme terrestrial environments including the Antarctic desert and permafrost. At the planet surface, the combination of low atmospheric pressure (below the triple point of water), high fluxes of ultraviolet radiation, and one or more powerful oxidants are likely to create sterilizing conditions that will be a barrier to the colonization and dispersal of microorganisms. In the subsurface below, long-term survival is dependent upon the frequency and duration of warm, metabolically active periods that are needed to repair cellular damages. Low temperature itself does little harm to microorganisms, but a long dormant period will accrue lethal dosages of ionizing radiation and amino acid racemization. It is probable that within the depth range of current sampling technologies, there are no conditions for extant life, leaving organic or inorganic fossils as the only legitimate target in the search for life on Mars.

Environmental and taxonomic bacterial diversity of anaerobic uranium(IV) bio-oxidation.

PubMed

Weber, Karrie A; Thrash, J Cameron; Van Trump, J Ian; Achenbach, Laurie A; Coates, John D

2011-07-01

Microorganisms in diverse terrestrial surface and subsurface environments can anaerobically catalyze the oxidative dissolution of uraninite. While a limited quantity (∼5 to 12 μmol liter(-1)) of uranium is oxidatively dissolved in pure culture studies, the metabolism is coupled to electron transport, providing the potential of uraninite to support indigenous microbial populations and to solubilize uranium.

Thixotropic gel for vadose zone remediation

DOEpatents

Riha, Brian D.

2012-07-03

A thixotropic gel suitable for use in subsurface bioremediation is provided along with a process of using the gel. The thixotropic gel provides a non-migrating injectable substrate that can provide below ground barrier properties. In addition, the gel components provide for a favorable environment in which certain contaminants are preferentially sequestered in the gel and subsequently remediated by either indigenous or introduced microorganisms.

Thixotropic gel for vadose zone remediation

DOEpatents

Rhia, Brian D [Augusta, GA

2011-03-01

A thixotropic gel suitable for use in subsurface bioremediation is provided along with a process of using the gel. The thixotropic gel provides a non-migrating injectable substrate that can provide below ground barrier properties. In addition, the gel components provide for a favorable environment in which certain contaminants are preferentially sequestered in the gel and subsequently remediated by either indigenous or introduced microorganisms.

Thixotropic gel for vadose zone remediation

DOEpatents

Riha, Brian D.; Looney, Brian B.

2015-10-27

A thixotropic gel suitable for use in subsurface bioremediation is provided along with a process of using the gel. The thixotropic gel provides a non-migrating injectable substrate that can provide below ground barrier properties. In addition, the gel components provide for a favorable environment in which certain contaminants are preferentially sequestered in the gel and subsequently remediated by either indigenous or introduced microorganisms.

High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sediments.

PubMed

Engelhardt, Tim; Kallmeyer, Jens; Cypionka, Heribert; Engelen, Bert

2014-07-01

Marine sediments cover two-thirds of our planet and harbor huge numbers of living prokaryotes. Long-term survival of indigenous microorganisms within the deep subsurface is still enigmatic, as sources of organic carbon are vanishingly small. To better understand controlling factors of microbial life, we have analyzed viral abundance within a comprehensive set of globally distributed subsurface sediments. Phages were detected by electron microscopy in deep (320 m below seafloor), ancient (∼14 Ma old) and the most oligotrophic subsurface sediments of the world's oceans (South Pacific Gyre (SPG)). The numbers of viruses (10(4)-10(9) cm(-3), counted by epifluorescence microscopy) generally decreased with sediment depth, but always exceeded the total cell counts. The enormous numbers of viruses indicate their impact as a controlling factor for prokaryotic mortality in the marine deep biosphere. The virus-to-cell ratios increased in deeper and more oligotrophic layers, exhibiting values of up to 225 in the deep subsurface of the SPG. High numbers of phages might be due to absorption onto the sediment matrix and a diminished degradation by exoenzymes. However, even in the oldest sediments, microbial communities are capable of maintaining viral populations, indicating an ongoing viral production and thus, viruses provide an independent indicator for microbial life in the marine deep biosphere.

Removal of microbial pathogens in a sandy gravel aquifer under forced-gradient subsurface flow conditions

NASA Astrophysics Data System (ADS)

Oudega, Thomas James; Derx, Julia; van Driezum, Inge; Cisneros, Anibal; Sommer, Regina; Kirschner, Alexander; Farnleitner, Andreas; Blaschke, Alfred Paul

2017-04-01

Subsurface media are being used around the world as a means to mitigate microbial contamination, but vary widely in their ability to remove pathogens. To help to provide accurate risk assessments of microbial contamination of groundwaters, and establish safe setback distances between receiving waters and disposal fields, this study aims to use aquifer tracer tests to evaluate the ability of subsurface media to attenuate these pathogens. The novelty of this work is the use of a variety of different tracer substances (e.g. phages, spores, microspheres, conservative tracers) together in field experiments. This will be done by means of injecting these substances under a forced gradient in a sandy gravel aquifer in Lobau, Austria. The extraction of the tracers will be monitored in a pumping well at a distrance of 50m downgradient. This will be able to provide us with insight to the characteristics of microbial transport and how the microorganisms react to the subsurface in the study site. Subsequent numerical modelling of the experiments can tell us more about quantification of subsurface processes such as attachment/detachment, inactivation and die-off of these substances. The first field experiment with conservative tracers (NaCl) has been carried out in December 2016, and subsequent tests are being planned for the next months.

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

A bioenergetics-kinetics coupled modeling study on subsurface microbial metabolism in a field biostimulation experiment

NASA Astrophysics Data System (ADS)

Jin, Q.; Zheng, Z.; Zhu, C.

2006-12-01

Microorganisms in nature conserve energy by catalyzing various geochemical reactions. To build a quantitative relationship between geochemical conditions and metabolic rates, we propose a bioenergetics-kinetics coupled modeling approach. This approach describes microbial community as a metabolic network, i.e., fermenting microbes degrade organic substrates while aerobic respirer, nitrate reducer, metal reducer, sulfate reducer, and methanogen consume the fermentation products. It quantifies the control of substrate availability and biological energy conservation on the metabolic rates using thermodynamically consistent rate laws. We applied this simulation approach to study the progress of microbial metabolism during a field biostimulation experiment conducted in Oak Ridge, Tennessee. In the experiment, ethanol was injected into a monitoring well and groundwater was sampled to monitor changes in the chemistry. With time, concentrations of ethanol and SO42- decreased while those of NH4+, Fe2+, and Mn2+ increased. The simulation results fitted well to the observation, indicating simultaneous ethanol degradation and terminal electron accepting processes. The rates of aerobic respiration and denitrification were mainly controlled by substrate concentrations while those of ethanol degradation, sulfate reduction, and methanogenesis were controlled dominantly by the energy availability. The simulation results suggested two different microbial growth statuses in the subsurface. For the functional groups with significant growth, variations with time in substrate concentrations demonstrated a typical S curve. For the groups without significant growth, initial decreases in substrate concentrations were linear with time. Injecting substrates followed by monitoring environmental chemistry therefore provides a convenient approach to characterize microbial growth in the subsurface where methods for direct observation are currently unavailable. This research was funded by the NABIR program, DOE, under grant No. DE-FG02-04ER63740 to CZ. We thank J. Istok, David Watson, and Philip Jardine for their help. The views and opinions of authors expressed herein do not necessarily state or reflect those of the DOE.

Hydrogen concentrations as an indicator of the predominant terminal electron-accepting reactions in aquatic sediments

USGS Publications Warehouse

Lovley, D.R.; Goodwin, S.

1988-01-01

Factors controlling the concentration of dissolved hydrogen gas in anaerobic sedimentary environments were investigated. Results, presented here or previously, demonstrated that, in sediments, only microorganisms catalyze the oxidation of H2 coupled to the reduction of nitrate, Mn(IV), Fe(III), sulfate, or carbon dioxide. Theoretical considerations suggested that, at steady-state conditions, H2 concentrations are primarily dependent upon the physiological characteristics of the microorganism(s) consuming the H2 and that organisms catalyzing H2 oxidation, with the reduction of a more electrochemically positive electron acceptor, can maintain lower H2 concentrations than organisms using electron acceptors which yield less energy from H2 oxidation. The H2 concentrations associated with the specified predominant terminal electron-accepting reactions in bottom sediments of a variety of surface water environments were: methanogenesis, 7-10 nM; sulfate reduction, 1-1.5 nM; Fe(III) reduction, 0.2 nM; Mn(IV) or nitrate reduction, less than 0.05 nM. Sediments with the same terminal electron acceptor for organic matter oxidation had comparable H2 concentrations, despite variations in the rate of organic matter decomposition, pH, and salinity. Thus, each terminal electron-accepting reaction had a unique range of steady-state H2 concentrations associated with it. Preliminary studies in a coastal plain aquifer indicated that H2 concentrations also vary in response to changes in the predominant terminal electron-accepting process in deep subsurface environments. These studies suggest that H2 measurements may aid in determining which terminal electron-accepting reactions are taking place in surface and subsurface sedimentary environments. ?? 1988.

Members of the Candidate Phyla Radiation are functionally differentiated by carbon and nitrogen cycling capabilities.

NASA Astrophysics Data System (ADS)

Danczak, R.; Johnston, M.; Kenah, C.; Slattery, M.; Wrighton, K. C.; Wilkins, M.

2017-12-01

The Candidate Phyla Radiation (CPR) is a recently described expansion of the tree of life that represents more than 15% of all bacterial diversity and putatively contains over 70 different phyla. Despite this broad phylogenetic variation, these microorganisms often feature limited functional diversity, with members generally characterized as obligate fermenters. Additionally, much of the data describing CPR phyla has been generated from a limited number of environments, constraining our knowledge of their functional roles and biogeographical distribution. To better understand subsurface CPR microorganisms, we sampled four groundwater wells over two years across three Ohio counties. Samples were analyzed using 16S rRNA gene amplicon and shotgun metagenomic sequencing. Amplicon results indicated that CPR members comprised 2-20% of the microbial communities, with relative abundances stable through time in Athens and Greene county samples but dynamic in Licking county groundwater. Shotgun metagenomic analyses generated 71 putative CPR genomes, representing roughly 32 known phyla and potentially two new phyla, Candidatus Brownbacteria and Candidatus Hugbacteria. While these genomes largely mirrored typical CPR metabolism, some features were previously uncharacterized. For instance, a nirK-encoded nitrite reductase was found in four of our Parcubacteria genomes and multiple CPR genomes from other studies, indicating a possibly undescribed role for these microorganisms in denitrification. Additionally, glycoside hydrolase (GH) family profiles for our genomes and over 2000 other CPR genomes were analyzed to characterize their carbon processing potential. Although common trends were present throughout the radiation, differences highlighted mechanisms that may allow microorganisms across the CPR to occupy various subsurface niches. For example, members of the Microgenomates superphylum appear to potentially degrade a wider range of carbon substrates than other CPR phyla. The CPR appear to be distributed across a range of groundwater systems and often constitute a large fraction of the microbial population. Further sampling of such environments will resolve this phylogenetically broad radiation at finer taxonomic levels and will likely solidify functional differences between phyla.

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.

Biotransformation at 10 C of di-n-butyl phthalate in subsurface microcosms

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

Chauret, C.; Inniss, W.E.; Mayfield, C.I.

1996-09-01

Di-n-butyl phthalate (DBP) was found to be transformed by microorganisms under aerobic and anaerobic conditions at 10 C in microcosms simulating the Canadian Forces Base (CFB) Borden subsurface environment. Biotransformation of DBP was observed under aerobic, nitrate-reducing, Fe(III)-reducing, and sulfate-reducing conditions. The biotransformation of DBP in the microcosms was significantly decrease3d as the redox potential was lowered, especially under sulfate-reducing conditions. However, other factors such as nutrient depletion and buildup of toxic intermediates could have affected the biotransformation rates. The highest DBP biotransformation rate (0.57 {micro}g DBP{center_dot}g sediment{sup {minus}1}{center_dot}day{sup {minus}1}) was under sulfate-reducing conditions. Biotransformation of DBP at 10 Cmore » was significantly enhanced by the addition of 10 mM NaNO{sub 3} suggesting that both the addition of nitrate and high redox conditions favor its biotransformation in subsurface environments.« less

[Search for life in deep biospheres].

PubMed

Naganuma, Takeshi

2003-12-01

The life in deep biospheres bridges conventional biology and future exobiology. This review focuses the microbiological studies from the selected deep biospheres, i.e., deep-sea hydrothermal vents, sub-hydrothermal vents, terrestrial subsurface and a sub-glacier lake. The dark biospheres facilitate the emergence of organisms and communities dependent on chemolithoautotrophy, which are overwhelmed by photoautotrophy (photosynthesis) in the surface biospheres. The life at deep-sea hydrothermal vents owes much to chemolithoautotrophy based on the oxidation of sulfide emitted from the vents. It is likely that similarly active bodies such as the Jovian satellite Europa may have hydrothermal vents and associated biological communities. Anoxic or anaerobic condition is characteristic of deep subsurface biospheres. Subsurface microorganisms exploit available oxidants, or terminal electron acceptors (TEA), for anaerobic respiration. Sulfate, nitrate, iron (III) and CO2 are the representative TEAs in the deep subsurface. 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, is about to be drill-penetrated for microbiological studies. These deep biosphere "platforms" provide new knowledge about the diversity and potential of the Earth's life. The expertise obtained from the deep biosphere expeditions will facilitate the capability of exobiologial exploration.

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

Hypotheses for Near-Surface Exchange of Methane on Mars.

PubMed

Hu, Renyu; Bloom, A Anthony; Gao, Peter; Miller, Charles E; Yung, Yuk L

2016-07-01

The Curiosity rover recently detected a background of 0.7 ppb and spikes of 7 ppb of methane on Mars. This in situ measurement reorients our understanding of the martian environment and its potential for life, as the current theories do not entail any geological source or sink of methane that varies sub-annually. In particular, the 10-fold elevation during the southern winter indicates episodic sources of methane that are yet to be discovered. Here we suggest a near-surface reservoir could explain this variability. Using the temperature and humidity measurements from the rover, we find that perchlorate salts in the regolith deliquesce to form liquid solutions, and deliquescence progresses to deeper subsurface in the season of the methane spikes. We therefore formulate the following three testable hypotheses. The first scenario is that the regolith in Gale Crater adsorbs methane when dry and releases this methane to the atmosphere upon deliquescence. The adsorption energy needs to be 36 kJ mol(-1) to explain the magnitude of the methane spikes, higher than existing laboratory measurements. The second scenario is that microorganisms convert organic matter in the soil to methane when they are in liquid solutions. This scenario does not require regolith adsorption but entails extant life on Mars. The third scenario is that deep subsurface aquifers produce the bursts of methane. Continued in situ measurements of methane and water, as well as laboratory studies of adsorption and deliquescence, will test these hypotheses and inform the existence of the near-surface reservoir and its exchange with the atmosphere. Mars-Methane-Astrobiology-Regolith. Astrobiology 16, 539-550.

Hypotheses for a Near-Surface Reservoir of Methane and Its Release on Mars

NASA Astrophysics Data System (ADS)

Hu, R.; Bloom, A. A.; Gao, P.; Miller, C. E.; Yung, Y. L.

2015-12-01

The Curiosity rover recently detected a background of 0.7 ppb and spikes of 7 ppb of methane on Mars. This in situ measurement reorients our understanding of the Martian environment and its potential for life, as the current theories do not entail any active source or sink of methane. In particular, the 10-fold elevation during the southern winter indicates episodic sources of methane that are yet to be discovered. Using the temperature and humidity measurements from the rover, we find that perchlorate salts in the regolith deliquesce to form liquid solutions, and deliquescence progresses to deeper subsurface in the season of the methane spikes. We therefore formulate the following three testable hypotheses as an attempt to explain the apparent variability of the atmospheric methane abundance. The first scenario is that the regolith in Gale Crater adsorbs methane when dry and releases this methane to the atmosphere upon deliquescence. The adsorption energy needs to be 36 kJ mol-1 to explain the magnitude of the methane spikes, higher than laboratory measurements. The second scenario is that microorganisms exist and convert organic matter in the soil to methane when they are in liquid solutions. This scenario does not require regolith adsorption. The third scenario is that deep subsurface aquifers sealed by ice or clathrate produce bursts of methane as a result of freezing and thawing of the permafrost, as the terrestrial arctic tundra. Continued monitoring of methane by Curiosity will test the existence of the near-surface reservoir and its exchange with the atmosphere.

Hypotheses for Near-Surface Exchange of Methane on Mars

NASA Astrophysics Data System (ADS)

Hu, Renyu; Bloom, A. Anthony; Gao, Peter; Miller, Charles E.; Yung, Yuk L.

2016-07-01

The Curiosity rover recently detected a background of 0.7 ppb and spikes of 7 ppb of methane on Mars. This in situ measurement reorients our understanding of the martian environment and its potential for life, as the current theories do not entail any geological source or sink of methane that varies sub-annually. In particular, the 10-fold elevation during the southern winter indicates episodic sources of methane that are yet to be discovered. Here we suggest a near-surface reservoir could explain this variability. Using the temperature and humidity measurements from the rover, we find that perchlorate salts in the regolith deliquesce to form liquid solutions, and deliquescence progresses to deeper subsurface in the season of the methane spikes. We therefore formulate the following three testable hypotheses. The first scenario is that the regolith in Gale Crater adsorbs methane when dry and releases this methane to the atmosphere upon deliquescence. The adsorption energy needs to be 36 kJ mol-1 to explain the magnitude of the methane spikes, higher than existing laboratory measurements. The second scenario is that microorganisms convert organic matter in the soil to methane when they are in liquid solutions. This scenario does not require regolith adsorption but entails extant life on Mars. The third scenario is that deep subsurface aquifers produce the bursts of methane. Continued in situ measurements of methane and water, as well as laboratory studies of adsorption and deliquescence, will test these hypotheses and inform the existence of the near-surface reservoir and its exchange with the atmosphere.

Survivability and growth kinetics of methanogenic archaea at various pHs and pressures: Implications for deep subsurface life on Mars

NASA Astrophysics Data System (ADS)

Sinha, Navita; Nepal, Sudip; Kral, Timothy; Kumar, Pradeep

2017-02-01

Life as we know it requires liquid water and sufficient liquid water is highly unlikely on the surface of present-day Mars. However, according to thermal models there is a possibility of liquid water in the deep subsurface of Mars. Thus, the martian subsurface, where the pressure and temperature is higher, could potentially provide a hospitable environment for a biosphere. Also, methane has been detected in the Mars' atmosphere. Analogous to Earth's atmospheric methane, martian methane could also be biological in origin. The carbon and energy sources for methanogenesis in the subsurface of Mars could be available by downwelling of atmospheric CO2 into the regolith and water-rock reactions such as serpentinization, respectively. Corresponding analogs of the martian subsurface on Earth might be the active sites of serpentinization at depths where methanogenic thermophilic archaea are the dominant species. Methanogens residing in Earth's hydrothermal environments are usually exposed to a variety of physiological stresses including a wide range of pressures, temperatures, and pHs. Martian geochemical models imply that the pH of probable groundwater varies from 4.96 to 9.13. In this work, we used the thermophilic methanogen, Methanothermobacter wolfeii, which grows optimally at 55oC. Therefore, a temperature of 55oC was chosen for these experiments, possibly simulating Mars' subsurface temperature. A martian geophysical model suggests depth and pressure corresponding to a temperature of 55 °C would be between 1-30 km and 100-3,000 atm respectively. Here, we have simulated Mars deep subsurface pH, pressure, and temperature conditions and have investigated the survivability, growth rate, and morphology of M. wolfeii after exposure to a wide range of pH 5-9) and pressure (1-1200 atm) at a temperature of 55 °C. Interestingly, in this study we have found that M. wolfeii was able to survive at all the pressures and pHs tested at 55 °C. In order to understand the effect of different pHs and pressures on the metabolic activities of M. wolfeii, we also calculated their growth rate by measuring methane concentration in the headspace gas samples at regular intervals. In acidic conditions, the growth rate (γ) of M. wolfeii increased with the increase in pressure. In neutral and alkaline conditions, the growth rate (γ) of M. wolfeii initially increased with pressure, but decreased upon further increase of pressure. To investigate the effect of combined pH, pressure, and temperature on the morphology of M. wolfeii, we took phase contrast images of the cells. We did not find any obvious significant alteration in the morphology of M. wolfeii cells. Methanogens, chemolithoautotrophic anaerobic microorganisms, are considered as ideal model microorganisms for Mars. In light of research presented here, we suggest that at least one methanogen, M. wolfeii, could survive in the deep subsurface environment of Mars.

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

“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

Activity and phylogenetic diversity of sulfate-reducing microorganisms in low-temperature subsurface fluids within the upper oceanic crust

PubMed Central

Robador, Alberto; Jungbluth, Sean P.; LaRowe, Douglas E.; Bowers, Robert M.; Rappé, Michael S.; Amend, Jan P.; Cowen, James P.

2015-01-01

The basaltic ocean crust is the largest aquifer system on Earth, yet the rates of biological activity in this environment are unknown. Low-temperature (<100°C) fluid samples were investigated from two borehole observatories in the Juan de Fuca Ridge (JFR) flank, representing a range of upper oceanic basement thermal and geochemical properties. Microbial sulfate reduction rates (SRR) were measured in laboratory incubations with 35S-sulfate over a range of temperatures and the identity of the corresponding sulfate-reducing microorganisms (SRM) was studied by analyzing the sequence diversity of the functional marker dissimilatory (bi)sulfite reductase (dsrAB) gene. We found that microbial sulfate reduction was limited by the decreasing availability of organic electron donors in higher temperature, more altered fluids. Thermodynamic calculations indicate energetic constraints for metabolism, which together with relatively higher cell-specific SRR reveal increased maintenance requirements, consistent with novel species-level dsrAB phylotypes of thermophilic SRM. Our estimates suggest that microbially-mediated sulfate reduction may account for the removal of organic matter in fluids within the upper oceanic crust and underscore the potential quantitative impact of microbial processes in deep subsurface marine crustal fluids on marine and global biogeochemical carbon cycling. PMID:25642212

Functional environmental proteomics: elucidating the role of a c-type cytochrome abundant during uranium bioremediation

PubMed Central

Yun, Jiae; Malvankar, Nikhil S; Ueki, Toshiyuki; Lovley, Derek R

2016-01-01

Studies with pure cultures of dissimilatory metal-reducing microorganisms have demonstrated that outer-surface c-type cytochromes are important electron transfer agents for the reduction of metals, but previous environmental proteomic studies have typically not recovered cytochrome sequences from subsurface environments in which metal reduction is important. Gel-separation, heme-staining and mass spectrometry of proteins in groundwater from in situ uranium bioremediation experiments identified a putative c-type cytochrome, designated Geobacter subsurface c-type cytochrome A (GscA), encoded within the genome of strain M18, a Geobacter isolate previously recovered from the site. Homologs of GscA were identified in the genomes of other Geobacter isolates in the phylogenetic cluster known as subsurface clade 1, which predominates in a diversity of Fe(III)-reducing subsurface environments. Most of the gscA sequences recovered from groundwater genomic DNA clustered in a tight phylogenetic group closely related to strain M18. GscA was most abundant in groundwater samples in which Geobacter sp. predominated. Expression of gscA in a strain of Geobacter sulfurreducens that lacked the gene for the c-type cytochrome OmcS, thought to facilitate electron transfer from conductive pili to Fe(III) oxide, restored the capacity for Fe(III) oxide reduction. Atomic force microscopy provided evidence that GscA was associated with the pili. These results demonstrate that a c-type cytochrome with an apparent function similar to that of OmcS is abundant when Geobacter sp. are abundant in the subsurface, providing insight into the mechanisms for the growth of subsurface Geobacter sp. on Fe(III) oxide and suggesting an approach for functional analysis of other Geobacter proteins found in the subsurface. PMID:26140532

Functional environmental proteomics: elucidating the role of a c-type cytochrome abundant during uranium bioremediation.

PubMed

Yun, Jiae; Malvankar, Nikhil S; Ueki, Toshiyuki; Lovley, Derek R

2016-02-01

Studies with pure cultures of dissimilatory metal-reducing microorganisms have demonstrated that outer-surface c-type cytochromes are important electron transfer agents for the reduction of metals, but previous environmental proteomic studies have typically not recovered cytochrome sequences from subsurface environments in which metal reduction is important. Gel-separation, heme-staining and mass spectrometry of proteins in groundwater from in situ uranium bioremediation experiments identified a putative c-type cytochrome, designated Geobacter subsurface c-type cytochrome A (GscA), encoded within the genome of strain M18, a Geobacter isolate previously recovered from the site. Homologs of GscA were identified in the genomes of other Geobacter isolates in the phylogenetic cluster known as subsurface clade 1, which predominates in a diversity of Fe(III)-reducing subsurface environments. Most of the gscA sequences recovered from groundwater genomic DNA clustered in a tight phylogenetic group closely related to strain M18. GscA was most abundant in groundwater samples in which Geobacter sp. predominated. Expression of gscA in a strain of Geobacter sulfurreducens that lacked the gene for the c-type cytochrome OmcS, thought to facilitate electron transfer from conductive pili to Fe(III) oxide, restored the capacity for Fe(III) oxide reduction. Atomic force microscopy provided evidence that GscA was associated with the pili. These results demonstrate that a c-type cytochrome with an apparent function similar to that of OmcS is abundant when Geobacter sp. are abundant in the subsurface, providing insight into the mechanisms for the growth of subsurface Geobacter sp. on Fe(III) oxide and suggesting an approach for functional analysis of other Geobacter proteins found in the subsurface.

Does Aspartic Acid Racemization Constrain the Depth Limit of the Subsurface Biosphere?

NASA Technical Reports Server (NTRS)

Onstott, T C.; Magnabosco, C.; Aubrey, A. D.; Burton, A. S.; Dworkin, J. P.; Elsila, J. E.; Grunsfeld, S.; Cao, B. H.; Hein, J. E.; Glavin, D. P.;

Does aspartic acid racemization constrain the depth limit of the subsurface biosphere?

PubMed

Onstott, T C; Magnabosco, C; Aubrey, A D; Burton, A S; Dworkin, J P; Elsila, J E; Grunsfeld, S; Cao, B H; Hein, J E; Glavin, D P; Kieft, T L; Silver, B J; Phelps, T J; van Heerden, E; Opperman, D J; Bada, J L

2014-01-01

Previous studies of the subsurface biosphere have deduced average cellular doubling times of hundreds to thousands of years based upon geochemical models. We have directly constrained the in situ average cellular protein turnover or doubling times for metabolically active micro-organisms based on cellular amino acid abundances, D/L values of cellular aspartic acid, and the in vivo aspartic acid racemization rate. Application of this method to planktonic microbial communities collected from deep fractures in South Africa yielded maximum cellular amino acid turnover times of ~89 years for 1 km depth and 27 °C and 1-2 years for 3 km depth and 54 °C. The latter turnover times are much shorter than previously estimated cellular turnover times based upon geochemical arguments. The aspartic acid racemization rate at higher temperatures yields cellular protein doubling times that are consistent with the survival times of hyperthermophilic strains and predicts that at temperatures of 85 °C, cells must replace proteins every couple of days to maintain enzymatic activity. Such a high maintenance requirement may be the principal limit on the abundance of living micro-organisms in the deep, hot subsurface biosphere, as well as a potential limit on their activity. The measurement of the D/L of aspartic acid in biological samples is a potentially powerful tool for deep, fractured continental and oceanic crustal settings where geochemical models of carbon turnover times are poorly constrained. Experimental observations on the racemization rates of aspartic acid in living thermophiles and hyperthermophiles could test this hypothesis. The development of corrections for cell wall peptides and spores will be required, however, to improve the accuracy of these estimates for environmental samples. © 2013 John Wiley & Sons Ltd.

The genome of Geobacter bemidjiensis, exemplar for the subsurface clade of Geobacter species that predominate in Fe(III)-reducing subsurface environments

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

Aklujkar, Muktak; Young, Nelson D; Holmes, Dawn

2010-01-01

Background. Geobacter species in a phylogenetic cluster known as subsurface clade 1 are often the predominant microorganisms in subsurface environments in which Fe(III) reduction is the primary electron-accepting process. Geobacter bemidjiensis, a member of this clade, was isolated from hydrocarbon-contaminated subsurface sediments in Bemidji, Minnesota, and is closely related to Geobacter species found to be abundant at other subsurface sites. This study examines whether there are significant differences in the metabolism and physiology of G. bemidjiensis compared to non-subsurface Geobacter species. Results. Annotation of the genome sequence of G. bemidjiensis indicates several differences in metabolism compared to previously sequenced non-subsurfacemore » Geobacteraceae, which will be useful for in silico metabolic modeling of subsurface bioremediation processes involving Geobacter species. Pathways can now be predicted for the use of various carbon sources such as propionate by G. bemidjiensis. Additional metabolic capabilities such as carbon dioxide fixation and growth on glucose were predicted from the genome annotation. The presence of different dicarboxylic acid transporters and two oxaloacetate decarboxylases in G. bemidjiensis may explain its ability to grow by disproportionation of fumarate. Although benzoate is the only aromatic compound that G. bemidjiensis is known or predicted to utilize as an electron donor and carbon source, the genome suggests that this species may be able to detoxify other aromatic pollutants without degrading them. Furthermore, G. bemidjiensis is auxotrophic for 4-aminobenzoate, which makes it the first Geobacter species identified as having a vitamin requirement. Several features of the genome indicated that G. bemidjiensis has enhanced abilities to respire, detoxify and avoid oxygen. Conclusion. Overall, the genome sequence of G. bemidjiensis offers surprising insights into the metabolism and physiology of Geobacteraceae in subsurface environments, compared to non-subsurface Geobacter species, such as the ability to disproportionate fumarate, more efficient oxidation of propionate, enhanced responses to oxygen stress, and dependence on the environment for a vitamin requirement. Therefore, an understanding of the activity of Geobacter species in the subsurface is more likely to benefit from studies of subsurface isolates such as G. bemidjiensis than from the non-subsurface model species studied so far.« less

Dehalogenation Activities and Distribution of Reductive Dehalogenase Homologous Genes in Marine Subsurface Sediments▿ †

PubMed Central

Futagami, Taiki; Morono, Yuki; Terada, Takeshi; Kaksonen, Anna H.; Inagaki, Fumio

2009-01-01

Halogenated organic compounds serve as terminal electron acceptors for anaerobic respiration in a diverse range of microorganisms. Here, we report on the widespread distribution and diversity of reductive dehalogenase homologous (rdhA) genes in marine subsurface sediments. A total of 32 putative rdhA phylotypes were detected in sediments from the southeast Pacific off Peru, the eastern equatorial Pacific, the Juan de Fuca Ridge flank off Oregon, and the northwest Pacific off Japan, collected at a maximum depth of 358 m below the seafloor. In addition, significant dehalogenation activity involving 2,4,6-tribromophenol and trichloroethene was observed in sediment slurry from the Nankai Trough Forearc Basin. These results suggest that dehalorespiration is an important energy-yielding pathway in the subseafloor microbial ecosystem. PMID:19749069

The Search for Carbonates on Mars

NASA Technical Reports Server (NTRS)

Farmer, Jack D.; DesMarais, David J.; Morrison, David (Technical Monitor)

1994-01-01

Liquid water is presently unstable at the Martian surface, where the mean atmospheric pressure is 6 mbar (due to CO2) and the winter diurnal temperature ranges from 150 K at the pole to 220 K at the equator. Liquid water is widely regarded as a basic requirement for living systems, suggesting that life as we know it is not possible in present surface environments on Mars. However, life may survive within "oases" where liquid water is present. Potential oases on Mars include subsurface hydrothermal systems or deeply buried aquifers where chemoautolithotrophic microorganisms may exist. Potential metabolic strategies for primary production in such environments on Mars (and for the microbial mediation of geologic processes!) encompass the full range presently known for subsurface environments on the Earth (e.g. sulphate reduction, methanogenesis, acetogenesis, etc).

Dehalogenation activities and distribution of reductive dehalogenase homologous genes in marine subsurface sediments.

PubMed

Futagami, Taiki; Morono, Yuki; Terada, Takeshi; Kaksonen, Anna H; Inagaki, Fumio

2009-11-01

Halogenated organic compounds serve as terminal electron acceptors for anaerobic respiration in a diverse range of microorganisms. Here, we report on the widespread distribution and diversity of reductive dehalogenase homologous (rdhA) genes in marine subsurface sediments. A total of 32 putative rdhA phylotypes were detected in sediments from the southeast Pacific off Peru, the eastern equatorial Pacific, the Juan de Fuca Ridge flank off Oregon, and the northwest Pacific off Japan, collected at a maximum depth of 358 m below the seafloor. In addition, significant dehalogenation activity involving 2,4,6-tribromophenol and trichloroethene was observed in sediment slurry from the Nankai Trough Forearc Basin. These results suggest that dehalorespiration is an important energy-yielding pathway in the subseafloor microbial ecosystem.

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

Subsurface soil carbon losses offset surface carbon accumulation in abandoned agricultural fields

NASA Astrophysics Data System (ADS)

Yang, Y.; Knops, J. M. H.

2017-12-01

Soil carbon is widely understood to accumulate after agricultural abandonment. However, most of the studies have been focused on shallow depths (10 to 30 cm), and there is a lack of deeper soil carbon data. It was reported that in temperate grasslands, 58% of the soil organic carbon in the first meter was stored between 20 and 100 cm, and organic matter in deeper soil might also be susceptible to agricultural disturbance. We used repeated sampling in 2001 and 2014 to directly measure rates of soil carbon change in both surface and subsurface soil in 21 abandoned agricultural fields at Cedar Creek Ecosystem Science Reserve, MN. Congruent with many other studies, we found carbon accumulated 384.2 C g/m2 in surface soil (0 - 20 cm) over the 13 years. However, we also found carbon pool declined 688.1 C g/m2 in the subsurface soil (40-100 cm), which resulted in a net total loss of soil carbon. We investigated the ecosystem carbon pools and fluxes to explore the mechanisms of the observed soil carbon changes. We found root carbon was not significantly correlated with soil carbon in any of the depth. In situ soil incubation showed nitrogen mineralization rates in subsurface soil are lower than that of surface soil. However, the estimated nitrogen and carbon output through decomposition is higher than inputs from roots, therefore leading to carbon loss in subsurface soil. These results suggest that the decomposition of soil organic matter by microorganisms in subsurface soil is significant, and should be incorporated in ecosystem carbon budget models.

Denitrifying Bacteria from the Genus Rhodanobacter Dominate Bacterial Communities in the Highly Contaminated Subsurface of a Nuclear Legacy Waste Site

PubMed Central

Green, Stefan J.; Prakash, Om; Jasrotia, Puja; Overholt, Will A.; Cardenas, Erick; Hubbard, Daniela; Tiedje, James M.; Watson, David B.; Schadt, Christopher W.; Brooks, Scott C.

2012-01-01

The effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of rRNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure and that denitrifying bacteria from the genus Rhodanobacter (class Gammaproteobacteria) dominate at low pH. The relative abundance of bacteria from this genus was positively correlated with lower-pH conditions, and these bacteria were abundant and active in the most highly contaminated areas. Other factors, such as the concentration of nitrogen species, oxygen level, and sampling season, did not appear to strongly influence the distribution of Rhodanobacter bacteria. The results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of bacterial community structure in this contaminated subsurface environment. PMID:22179233

Progress in the development of gelling agents for improved culturability of microorganisms

PubMed Central

Das, Nabajit; Tripathi, Naveen; Basu, Srijoni; Bose, Chandra; Maitra, Susmit; Khurana, Sukant

2015-01-01

Gelling agents are required for formulating both solid and semisolid media, vital for the isolation of microorganisms. Gelatin was the first gelling agent to be discovered but it soon paved the way for agar, which has far superior material qualities. Source depletion, issues with polymerase-chain-reaction and inability to sustain extermophiles etc., necessitate the need of other gelling agents. Many new gelling agents, such as xantham gum, gellan gum, carrageenan, isubgol, and guar gum have been formulated, raising the hopes for the growth of previously unculturable microorganisms. We evaluate the progress in the development of gelling agents, with the hope that our synthesis would help accelerate research in the field. PMID:26257708

Models of Micro-Organisms: Children's Knowledge and Understanding of Micro-Organisms from 7 to 14 Years Old

ERIC Educational Resources Information Center

Byrne, Jenny

2011-01-01

This paper describes the expressed models that children aged 7, 11, and 14 years have about micro-organisms and microbial activity. These were elicited using a variety of data collection techniques that complemented each other, resulting in a rich dataset, and provided information about the level of knowledge and progression of ideas across the…

Development of a Design Tool for Planning Aqueous Amendment Injection Systems

DTIC Science & Technology

2008-06-01

BIOREMresources.asp) • “Protocol for Enhanced In Situ Bioremediation Using Emulsified Edible Oil” – (search for title at http://docs.serdp-estcp.org...index.cfm) • “Protocol for In Situ Bioremediation of Chlorinated Solvents Using Edible Oil” (http://www.afcee.brooks.af.mil/products/techtrans...and acetate by common subsurface microorganisms . The H2 and acetate are then used as a carbon and energy source for anaerobic biodegradation of the

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

Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface

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

Probst, Alexander J.; Ladd, Bethany; Jarett, Jessica K.

An enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO 2-driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Genome-resolved metagenomics, single-cell genomics and geochemical analyses confirmed this hypothesis and linked microorganisms to groundwater compositions from different depths. Autotrophic Candidatus “Altiarchaeum sp.” and phylogenetically deep-branching nanoarchaea dominate the deepest groundwater. Amore » nanoarchaeon with limited metabolic capacity is inferred to be a potential symbiont of the Ca. “Altiarchaeum”. Candidate Phyla Radiation bacteria are also present in the deepest groundwater and they are relatively abundant in water from intermediate depths. During the recovery phase of the geyser, microaerophilic Fe- and S-oxidizers have high in situ genome replication rates. Autotrophic Sulfurimonas sustained by aerobic sulfide oxidation and with the capacity for N 2 fixation dominate the shallow aquifer. Overall, 104 different phylum-level lineages are present in water from these subsurface environments, with uncultivated archaea and bacteria partitioned to the deeper subsurface.« less

Phylogenetic and Functional Diversity of Microbial Communities Associated with Subsurface Sediments of the Sonora Margin, Guaymas Basin

PubMed Central

Vigneron, Adrien; Cruaud, Perrine; Roussel, Erwan G.; Pignet, Patricia; Caprais, Jean-Claude; Callac, Nolwenn; Ciobanu, Maria-Cristina; Godfroy, Anne; Cragg, Barry A.; Parkes, John R.; Van Nostrand, Joy D.; He, Zhili; Zhou, Jizhong; Toffin, Laurent

2014-01-01

Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PCR with an extensive primers set) and correlated to comprehensive geochemical data. Moreover the metabolic potentials and functional traits of the microbial community were also identified using the GeoChip functional gene microarray and metabolic rates. The active microbial community structure in the Sonora Margin sediments was related to deep subsurface ecosystems (Marine Benthic Groups B and D, Miscellaneous Crenarchaeotal Group, Chloroflexi and Candidate divisions) and remained relatively similar throughout the sediment section, despite defined biogeochemical gradients. However, relative abundances of bacterial and archaeal dominant lineages were significantly correlated with organic carbon quantity and origin. Consistently, metabolic pathways for the degradation and assimilation of this organic carbon as well as genetic potentials for the transformation of detrital organic matters, hydrocarbons and recalcitrant substrates were detected, suggesting that chemoorganotrophic microorganisms may dominate the microbial community of the Sonora Margin subsurface sediments. PMID:25099369

Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface

DOE PAGES

Probst, Alexander J.; Ladd, Bethany; Jarett, Jessica K.; ...

2018-01-29

An enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO 2-driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Genome-resolved metagenomics, single-cell genomics and geochemical analyses confirmed this hypothesis and linked microorganisms to groundwater compositions from different depths. Autotrophic Candidatus “Altiarchaeum sp.” and phylogenetically deep-branching nanoarchaea dominate the deepest groundwater. Amore » nanoarchaeon with limited metabolic capacity is inferred to be a potential symbiont of the Ca. “Altiarchaeum”. Candidate Phyla Radiation bacteria are also present in the deepest groundwater and they are relatively abundant in water from intermediate depths. During the recovery phase of the geyser, microaerophilic Fe- and S-oxidizers have high in situ genome replication rates. Autotrophic Sulfurimonas sustained by aerobic sulfide oxidation and with the capacity for N 2 fixation dominate the shallow aquifer. Overall, 104 different phylum-level lineages are present in water from these subsurface environments, with uncultivated archaea and bacteria partitioned to the deeper subsurface.« less

The Search for Sustainable Subsurface Habitats on Mars, and the Sampling of Impact Ejecta

NASA Astrophysics Data System (ADS)

Ivarsson, Magnus; Lindgren, Paula

2010-07-01

On Earth, the deep subsurface biosphere of both the oceanic and the continental crust is well known for surviving harsh conditions and environments characterized by high temperatures, high pressures, extreme pHs, and the absence of sunlight. The microorganisms of the terrestrial deep biosphere have an excellent capacity for adapting to changing geochemistry, as the alteration of the crust proceeds and the conditions of their habitats slowly change. Despite an almost complete isolation from surface conditions and the surface biosphere, the deep biosphere of the crustal rocks has endured over geologic time. This indicates that the deep biosphere is a self-sufficient system, independent of the global events that occur at the surface, such as impacts, glaciations, sea level fluctuations, and climate changes. With our sustainable terrestrial subsurface biosphere in mind, the subsurface on Mars has often been suggested as the most plausible place to search for fossil Martian life, or even present Martian life. Since the Martian surface is more or less sterile, subsurface settings are the only place on Mars where life could have been sustained over geologic time. To detect a deep biosphere in the Martian basement, drilling is a requirement. However, near future Mars sample return missions are limited by the mission's payload, which excludes heavy drilling equipment and restrict the missions to only dig the topmost meter of the Martian soil. Therefore, the sampling and analysis of Martian impact ejecta has been suggested as a way of accessing the deeper Martian subsurface without using heavy drilling equipment. Impact cratering is a natural geological process capable of excavating and exposing large amounts of rock material from great depths up to the surface. Several studies of terrestrial impact deposits show the preservation of pre-impact biosignatures, such as fossilized organisms and chemical biological markers. Therefore, if the Martian subsurface contains a record of life, it is reasonable to assume that biosignatures derived from the Martian subsurface could also be preserved in the Martian impact ejecta.

Linking Metabolism, Elemental Cycles, and Environmental Conditions in the Deep Biosphere: Growth of a Model Extremophile, Archaeoglobus fulgidus, Under High-Pressure Conditions

NASA Astrophysics Data System (ADS)

Oliver, G. C. M.; Cario, A.; Rogers, K. L.

2015-12-01

A majority of Earth's biosphere is hosted in subsurface environments where global-scale biogeochemical and energy cycles are driven by diverse microbial communities that operate on and are influenced by micro-scale environmental variables. While the subsurface hosts a variety of geochemical and geothermal conditions, elevated pressures are common to all subsurface ecosystems. Understanding how microbes adapt to and thrive in high-pressure environments is essential to linking microbial subsurface processes with global-scale cycles. Here we are using a model extremophile, Archaeoglobus fulgidus, to determine how elevated pressures affect the growth, metabolism, and physiology of subsurface microorganisms. A. fulgidus cycles carbon and sulfur via heterotrophic and autotrophic sulfate reduction in various high temperature and high-pressure niches including shallow marine vents, deep-sea hydrothermal vents, and deep oil reservoirs. Here we report the results of A. fulgidus growth experiments at optimum temperature, 83°C, and pressures up to 600 bars. Exponential growth was observed over the entire pressure range, though growth rates were diminished at 500 and 600 bars compared to ambient pressure experimental controls. At pressures up to 400 bars, cell density yields and growth rates were at least as high as ambient pressure controls. Elevated pressures and extended incubation times stimulated cell flocculation, a common stress response in this strain, and cellular morphology was affected at pressures exceeding 400 bars. These results suggest that A. fulgidus continues carbon, sulfur and energy cycling unaffected by elevated pressures up to 400 bars, representing a variety of subsurface environments. The ability of subsurface organisms to drive biogeochemical cycles at elevated pressures is a critical link between the surface and subsurface biospheres and understanding how species-scale processes operate under these conditions is a vital part of global-scale biogeochemical models.

A New Method and Mass-Spectrometric Instrument for Extraterrestrial Microbial Life Detection Using the Elemental Composition Analyses of Martian Regolith and Permafrost/Ice

NASA Astrophysics Data System (ADS)

Managadze, G. G.; Safronova, A. A.; Luchnikov, K. A.; Vorobyova, E. A.; Duxbury, N. S.; Wurz, P.; Managadze, N. G.; Chumikov, A. E.; Khamizov, R. Kh.

2017-05-01

We propose a new technique for the detection of microorganisms by elemental composition analyses of a sample extracted from regolith, permafrost, and ice of extraterrestrial bodies. We also describe the design of the ABIMAS instrument, which consists of the onboard time-of-flight laser mass-reflectron (TOF LMR) and the sample preparation unit (SPU) for biomass extraction. This instrument was initially approved to fly on board the ExoMars 2020 lander mission. The instrument can be used to analyze the elemental composition of possible extraterrestrial microbial communities and compare it to that of terrestrial microorganisms. We have conducted numerous laboratory studies to confirm the possibility of biomass identification via the following biomarkers: P/S and Ca/K ratios, and C and N abundances. We underline that only the combination of these factors will allow one to discriminate microbial samples from geological ones. Our technique has been tested experimentally in numerous laboratory trials on cultures of microorganisms and polar permafrost samples as terrestrial analogues for martian polar soils. We discuss various methods of extracting microorganisms and sample preparation. The developed technique can be used to search for and identify microorganisms in different martian samples and in the subsurface of other planets, satellites, comets, and asteroids—in particular, Europa, Ganymede, and Enceladus.

Some New Windows into Terrestrial Deep Subsurface Microbial Ecosystems

NASA Astrophysics Data System (ADS)

Moser, D. P.

2011-12-01

Over the past several years, our group has surveyed the microbial ecology and biogeochemistry of a range of fracture rock subsurface ecosystems via deep mine boreholes in South Africa, the United States, and Canada; and boreholes from surface or deeply-sourced natural springs of the U.S. Great Basin. Collectively, these mostly unexplored habitats represent a wide range of geologic provinces, host rock types, aquatic chemistries, and the vast potential for biogeographic isolation. Thus, patterns of microbial diversity are of interest from the perspective of filling a fundamental knowledge gap; and while not necessarily expected, the detection of closely related microorganisms from geographically isolated settings would be noteworthy. Across these sample sets, microbial communities were invariably very low in biomass (e.g. 10e3 - 10e4 cells per mL) and dominated by deeply-branching bacterial lineages, particularly from the phyla Firmicutes and Nitrospira. In several cases, the Firmicutes have shown very close phylogenetic affiliations to lineages detected at divergent locations. For example, one abundant lineage from a new artesian well drilled into the Furnace Creek Fault of Death Valley, CA bears a very close phylogenetic relatedness to environmental DNA sequences (SSU rRNA gene) detected in one of the world's deepest mines (Tau Tona of South Africa) and what was North America's deepest gold mine (Homestake of South Dakota). Several radioactive wells from the Nevada National Security Site have produced rRNA gene sequences very close (e.g. greater than 99% identity) to that of Desulforudis audaxviator, a rarely detected microorganism thought to subsist as a single species ecosystem on the products of radiochemical reactions in deep crustal rocks from the South African Witwatersrand Basin. These sequences, along with more distantly related sequences from the marine subsurface (ridge flank basalt and mud volcanoes) and groundwater in Europe, hint at a role in certain hydrogen-rich subsurface settings for this group. Likewise, patterns of archaeal diversity across many of our Great Basin sites suggest shared deep lineages, particularly with the phylum, Thaumarchaeota. Here we will explore the possible significance of these patterns of diversity and discuss future research plans involving high throughput molecular techniques.

Assessing the Potential for Ancient Habitable Environments in Gusev Crater, Mars

NASA Astrophysics Data System (ADS)

Des Marais, D. J.; Athena Science Team

2007-12-01

In order to be habitable for microbial life as we know it, an environment must provide nutrient elements, energy and liquid water. We assess the potential for habitable environments in the areas explored by the MER rover Spirit. These areas include the basaltic plains near Columbia Memorial Station, West Spur, Husband Hill, and the inner basin south of Husband Hill. Little aqueous activity apparently occurred in Gusev crater since the basaltic plains were emplaced in Hesperian times, therefore the basaltic plains were highly unlikely to have sustained habitable environments. The Columbia Hills, located ~3 km southeast of the landing site, are older than the surrounding basaltic plains. Aqueous processes have extensively altered bedrock in the Columbia Hills. Ferrous iron in the original, unaltered parent rock of hills materials has typically been oxidized extensively to form ferric oxides, hydroxides, and other ferric minerals. Migrating fluids have removed Ca and other cations, allowing residual Al to become relatively more abundant, and fluids added sulfates and chlorides. In subsurface environments on Earth, microorganisms can obtain key nutrients from the weathering of basalts. Materials examined in the Columbia Hills have comparable or greater abundances of these elements than do MORB. Wishstone rock and Watchtower outcrop have very high contents of phosphorous. Chemoautotrophs ("chemical- feeders" that obtain energy from inorganic chemicals) can thrive in subsurface environments. Mixing oxidized constituents from surface environments with generally more reduced constituents from subsurface rocks and thermal emanations provides energy to sustain microorganisms. Ferrous iron in parent materials in the Columbia Hills has been oxidized to form a variety of ferric minerals. On Earth, microbial processes have been documented to contribute to the production of goethite, hematite and other iron oxides. Observations by Spirit are consistent with the possibility that liquid water, nutrients and sources of chemical energy were simultaneously available to sustain habitable conditions in subsurface Columbia Hills materials at least some time in the distant (Noachian?) past. There is as yet no evidence that these conditions ever existed at the surface. Future research must seek to determine whether ancient migrating fluids in Gusev ever achieved the water activity necessary to sustain life.

The nature and function of microbial enzymes in subsurface marine sediments

NASA Astrophysics Data System (ADS)

Steen, A. D.; Schmidt, J.

2016-02-01

Isotopic and genomic evidence indicates that marine sediments contain populations of active heterotrophic microorganisms which appear to metabolize old, detrital, apparently recalcitrant organic matter. In surface communities, heterotrophs use extracellular enzymes to access complex organic matter. In subsurface sediments, in which microbial doubling times can be on the order of hundreds or thousands of years, it is not clear whether extracellular enzymes could remain stable and active long enough to constitute a 'profitable' stragtegy for accessing complex organic carbon. Here we present evidence that a wide range of extracellular enzyme are active in subsurface sediments from two different environments: the White Oak River, NC, and deep (up to 80 m) sediments of the Baltic Sea Basin recovered from IODP Expedition 347. In the White Oak River, enzymes from deeper sediments appear to be better-adapted to highly-degraded organic matter than enzymes from surface sediments. In the Baltic Sea, preliminary data suggest that enzymes related to nitrogen acquisition are preferentially expressed. By characterizing the extracellular enzymes present in marine sediments, we hope to achieve a better understanding of the mechanisms that control sedimentary organic matter remineralization and preservation.

The Astrobiology of the Subsurface: Caves and Rock Fracture Habitats on Earth, Mars and Beyond

NASA Technical Reports Server (NTRS)

Boston, Penelope J.

2017-01-01

The Astrobiology of the Subsurface: Exploring Cave Habitats on Earth, Mars and Beyond. We are using the spectacular underground landscapes of Earth caves as models for the subsurfaces of other planets. Caves have been detected on the Moon and Mars and are strongly suspected for other bodies in the Solar System including some of the ice covered Ocean Worlds that orbit gas giant planets. The caves we explore and study include many extreme conditions of relevance to planetary astrobiology exploration including high and low temperatures, gas atmospheres poisonous to humans but where exotic microbes can fluorish, highly acidic or salty fluids, heavy metals, and high background radiation levels. Some cave microorganisms eat their way through bedrock, some live in battery acid conditions, some produce unusual biominerals and rare cave formations, and many produce compounds of potential pharmaceutical and industrial significance. We study these unique lifeforms and the physical and chemical biosignatures that they leave behind. Such traces can be used to provide a Field Guide to Unknown Organisms for developing life detection space missions.

The deep, hot biosphere: Twenty-five years of retrospection.

PubMed

Colman, Daniel R; Poudel, Saroj; Stamps, Blake W; Boyd, Eric S; Spear, John R

2017-07-03

Twenty-five years ago this month, Thomas Gold published a seminal manuscript suggesting the presence of a "deep, hot biosphere" in the Earth's crust. Since this publication, a considerable amount of attention has been given to the study of deep biospheres, their role in geochemical cycles, and their potential to inform on the origin of life and its potential outside of Earth. Overwhelming evidence now supports the presence of a deep biosphere ubiquitously distributed on Earth in both terrestrial and marine settings. Furthermore, it has become apparent that much of this life is dependent on lithogenically sourced high-energy compounds to sustain productivity. A vast diversity of uncultivated microorganisms has been detected in subsurface environments, and we show that H 2 , CH 4 , and CO feature prominently in many of their predicted metabolisms. Despite 25 years of intense study, key questions remain on life in the deep subsurface, including whether it is endemic and the extent of its involvement in the anaerobic formation and degradation of hydrocarbons. Emergent data from cultivation and next-generation sequencing approaches continue to provide promising new hints to answer these questions. As Gold suggested, and as has become increasingly evident, to better understand the subsurface is critical to further understanding the Earth, life, the evolution of life, and the potential for life elsewhere. To this end, we suggest the need to develop a robust network of interdisciplinary scientists and accessible field sites for long-term monitoring of the Earth's subsurface in the form of a deep subsurface microbiome initiative.

The Limits of Life in the Deep Subsurface - Implications for the Origin of Life

NASA Astrophysics Data System (ADS)

Baross, John

2013-06-01

There are very few environments on Earth where life is absent. Microbial life has proliferated into habitats that span nearly every imaginable physico-chemical variable. Only the availability of liquid water and temperature are known to prevent the growth of organisms. The other extreme physical and chemical variables, such as pH, pressure, high concentrations of solutes, damaging radiation, and toxic metals, are life-prohibiting factors for most organisms but not for all. The deep subsurface environments span all of the extreme conditions encountered by life including habitat conditions not yet explored, such as those that combine high temperature, high and low pH and extreme pressures. Some of the ``extremophile'' microorganisms inhabiting the deep subsurface environments have been shown to be among the most ``ancient'' of extant life. Their genomes and physiologies have led to a broader understanding of the geological settings of early life, the most ancient energy pathways, and the importance of water/rock interactions and tectonics in the origin and early evolution of life. The case can now be made that deep subsurface environments contributed to life's origin and provided the habitat(s) for the earliest microbial communities. However, there is much more to be done to further our understanding on the role of moderate to high pressures and temperatures on the chemical and biochemical ``steps'' leading to life, and on the evolution and physiology of both ancient and present-day subsurface microbial communities.

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.

Growth of methanogens on a Mars soil simulant.

PubMed

Kral, Timothy A; Bekkum, Curtis R; McKay, Christopher P

2004-12-01

Currently, the surface of Mars is probably too cold, too dry, and too oxidizing for life, as we know it, to exist. But the subsurface is another matter. Life forms that might exist below the surface could not obtain their energy from photosynthesis, but rather they would have to utilize chemical energy. Methanogens are one type of microorganism that might be able to survive below the surface of Mars. A potential habitat for existence of methanogens on Mars might be a geothermal source of hydrogen, possibly due to volcanic or hydrothermal activity, or the reaction of basalt and anaerobic water, carbon dioxide, which is abundant in the martian atmosphere, and of course, subsurface liquid water. We report here that certain methanogens can grow on a Mars soil simulant when supplied with carbon dioxide, molecular hydrogen, and varying amounts of water.

Sulfur/Carbonate Springs and Life in Glacial Ice

NASA Technical Reports Server (NTRS)

Allen, Carlton; Grasby, Stephen; Longazo, Teresa

2001-01-01

Ice in the near subsurface of Mars apparently discharges liquid water on occasion. Cold-tolerant microorganisms are known to exist within terrestrial glacial ice, and may be brought to the surface as a result of melting events. We are investigating a set of springs that deposit sulfur and carbonate minerals, as well as evidence of microbial life, on the surface of a glacier in the Canadian arctic. Additional information is contained in the original extended abstract.

The Oral Microbiome in Health and Its Implication in Oral and Systemic Diseases.

PubMed

Sampaio-Maia, B; Caldas, I M; Pereira, M L; Pérez-Mongiovi, D; Araujo, R

2016-01-01

The oral microbiome can alter the balance between health and disease, locally and systemically. Within the oral cavity, bacteria, archaea, fungi, protozoa, and viruses may all be found, each having a particular role, but strongly interacting with each other and with the host, in sickness or in health. A description on how colonization occurs and how the oral microbiome dynamically evolves throughout the host's life is given. In this chapter the authors also address oral and nonoral conditions in which oral microorganisms may play a role in the etiology and progression, presenting the up-to-date knowledge on oral dysbiosis as well as the known underlying pathophysiologic mechanisms involving oral microorganisms in each condition. In oral pathology, oral microorganisms are associated with several diseases, namely dental caries, periodontal diseases, endodontic infections, and also oral cancer. In systemic diseases, nonoral infections, adverse pregnancy outcomes, cardiovascular diseases, and diabetes are among the most prevalent pathologies linked with oral cavity microorganisms. The knowledge on how colonization occurs, how oral microbiome coevolves with the host, and how oral microorganisms interact with each other may be a key factor to understand diseases etiology and progression. Copyright © 2016 Elsevier Inc. All rights reserved.

A New Method and Mass-Spectrometric Instrument for Extraterrestrial Microbial Life Detection Using the Elemental Composition Analyses of Martian Regolith and Permafrost/Ice.

PubMed

Managadze, G G; Safronova, A A; Luchnikov, K A; Vorobyova, E A; Duxbury, N S; Wurz, P; Managadze, N G; Chumikov, A E; Khamizov, R Kh

2017-05-01

We propose a new technique for the detection of microorganisms by elemental composition analyses of a sample extracted from regolith, permafrost, and ice of extraterrestrial bodies. We also describe the design of the ABIMAS instrument, which consists of the onboard time-of-flight laser mass-reflectron (TOF LMR) and the sample preparation unit (SPU) for biomass extraction. This instrument was initially approved to fly on board the ExoMars 2020 lander mission. The instrument can be used to analyze the elemental composition of possible extraterrestrial microbial communities and compare it to that of terrestrial microorganisms. We have conducted numerous laboratory studies to confirm the possibility of biomass identification via the following biomarkers: P/S and Ca/K ratios, and C and N abundances. We underline that only the combination of these factors will allow one to discriminate microbial samples from geological ones. Our technique has been tested experimentally in numerous laboratory trials on cultures of microorganisms and polar permafrost samples as terrestrial analogues for martian polar soils. We discuss various methods of extracting microorganisms and sample preparation. The developed technique can be used to search for and identify microorganisms in different martian samples and in the subsurface of other planets, satellites, comets, and asteroids-in particular, Europa, Ganymede, and Enceladus. Key Words: Mass spectrometry-Life-detection instruments-Biomarkers-Earth Mars-Biomass spectra. Astrobiology 17, 448-458.

Subsurface geomicrobiology of the Iberian Pyritic Belt, a terrestrial analogue of Mars

NASA Astrophysics Data System (ADS)

Amils, Ricardo

Terrestrial subsurface geomicrobiology is a matter of growing interest on many levels. 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 early life on Earth, as well as a representation of life as it could occur in other planetary bodies, e.g., Mars. Ŕ Tinto is an unusual extreme acidic environment due to its size, constant acidic pH, high ıo concentration of heavy metals and high level of microbial diversity. Ŕ Tinto rises in the core of ıo the Iberian Pyritic Belt (IPB), one of the biggest sulfidic ore deposits in the world. Today it is clear that the extreme characteristics of Ŕ Tinto are not due to acid mine drainage resulting ıo from mining activity. To explore the hypothesis that a continuous underground reactor of chemolithotrophic microorganisms thriving in the rich sulfidic minerals of the IPB is responsible for the extreme conditions found in the river, a drilling project has been developed to detect evidence of subsurface microbial activity and potential resources to support these microbial communities in situ from retrieved cores (MARTE project). Preliminary results clearly show that there is an active subsurface geomicrobiology in the Iberian Pyritic Belt associated to places were ground waters intersects the sulfidic ore body.

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

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.

Emulsification of hydrocarbons by subsurface bacteria

USGS Publications Warehouse

Francy, D.S.; Thomas, J.M.; Raymond, R.L.; Ward, C.H.

1991-01-01

Biosurfactants have potential for use in enhancement of in situ biorestoration by increasing the bioavailability of contaminants. Microorganisms isolated from biostimulated, contaminated and uncontaminated zones at the site of an aviation fuel spill and hydrocarbon-degrading microorganisms isolated from sites contaminated with unleaded gasoline were examined for their abilities to emulsify petroleum hydrocarbons. Emulsifying ability was quantified by a method involving agitation and visual inspection. Biostimulated-zone microbes and hydrocarbon-degrading microorganisms were the best emulsifiers as compared to contaminated and uncontaminated zone microbes. Biostimulation (nutrient and oxygen addition) may have been the dominant factor which selected for and encouraged growth of emulsifiers; exposure to hydrocarbon was also important. Biostimulated microorganisms were better emulsifiers of aviation fuel (the contaminant hydrocarbon) than of heavier hydrocarbon to which they were not previously exposed. By measuring surface tension changes of culture broths, 11 out of 41 emulsifiers tested were identified as possible biosurfactant producers and two isolates produced large surface tension reductions indicating the high probability of biosurfactant production.Biosurfactants have potential for use in enhancement of in situ biorestoration by increasing the bioavailability of contaminants. Microorganisms isolated from biostimulated, contaminated and uncontaminated zones at the site of an aviation fuel spill and hydrocarbon-degrading microorganisms isolated from sites contaminated with unleaded gasoline were examined for their abilities to emulsify petroleum hydrocarbons. Emulsifying ability was quantified by a method involving agitation and visual inspection. Biostimulated-zone microbes and hydrocarbon-degrading microorganisms were the best emulsifiers as compared to contaminated and uncontaminated zone microbes. Biostimulation (nutrient and oxygen addition) may have been the dominant factor which selected for and encouraged growth of emulsifiers; exposure to hydrocarbon was also important. Biostimulated microorganisms were better emulsifiers of aviation fuel (the contaminant hydrocarbon) than of heavier hydrocarbon to which they were not previously exposed. By measuring surface tension changes of culture broths, 11 out of 41 emulsifiers tested were identified as possible biosurfactant producers and two isolates produced large surface tension reductions, indicating a high probability of biosurfactant production.

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

The deep, hot biosphere: Twenty-five years of retrospection

PubMed Central

Colman, Daniel R.; Poudel, Saroj; Stamps, Blake W.; Boyd, Eric S.; Spear, John R.

2017-01-01

Twenty-five years ago this month, Thomas Gold published a seminal manuscript suggesting the presence of a “deep, hot biosphere” in the Earth’s crust. Since this publication, a considerable amount of attention has been given to the study of deep biospheres, their role in geochemical cycles, and their potential to inform on the origin of life and its potential outside of Earth. Overwhelming evidence now supports the presence of a deep biosphere ubiquitously distributed on Earth in both terrestrial and marine settings. Furthermore, it has become apparent that much of this life is dependent on lithogenically sourced high-energy compounds to sustain productivity. A vast diversity of uncultivated microorganisms has been detected in subsurface environments, and we show that H2, CH4, and CO feature prominently in many of their predicted metabolisms. Despite 25 years of intense study, key questions remain on life in the deep subsurface, including whether it is endemic and the extent of its involvement in the anaerobic formation and degradation of hydrocarbons. Emergent data from cultivation and next-generation sequencing approaches continue to provide promising new hints to answer these questions. As Gold suggested, and as has become increasingly evident, to better understand the subsurface is critical to further understanding the Earth, life, the evolution of life, and the potential for life elsewhere. To this end, we suggest the need to develop a robust network of interdisciplinary scientists and accessible field sites for long-term monitoring of the Earth’s subsurface in the form of a deep subsurface microbiome initiative. PMID:28674200

Microbial Communities and Organic Matter Composition in Surface and Subsurface Sediments of the Helgoland Mud Area, North Sea

PubMed Central

Oni, Oluwatobi E.; Schmidt, Frauke; Miyatake, Tetsuro; Kasten, Sabine; Witt, Matthias; Hinrichs, Kai-Uwe; Friedrich, Michael W.

2015-01-01

The role of microorganisms in the cycling of sedimentary organic carbon is a crucial one. To better understand relationships between molecular composition of a potentially bioavailable fraction of organic matter and microbial populations, bacterial and archaeal communities were characterized using pyrosequencing-based 16S rRNA gene analysis in surface (top 30 cm) and subsurface/deeper sediments (30–530 cm) of the Helgoland mud area, North Sea. Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) was used to characterize a potentially bioavailable organic matter fraction (hot-water extractable organic matter, WE-OM). Algal polymer-associated microbial populations such as members of the Gammaproteobacteria, Bacteroidetes, and Verrucomicrobia were dominant in surface sediments while members of the Chloroflexi (Dehalococcoidales and candidate order GIF9) and Miscellaneous Crenarchaeota Groups (MCG), both of which are linked to degradation of more recalcitrant, aromatic compounds and detrital proteins, were dominant in subsurface sediments. Microbial populations dominant in subsurface sediments (Chloroflexi, members of MCG, and Thermoplasmata) showed strong correlations to total organic carbon (TOC) content. Changes of WE-OM with sediment depth reveal molecular transformations from oxygen-rich [high oxygen to carbon (O/C), low hydrogen to carbon (H/C) ratios] aromatic compounds and highly unsaturated compounds toward compounds with lower O/C and higher H/C ratios. The observed molecular changes were most pronounced in organic compounds containing only CHO atoms. Our data thus, highlights classes of sedimentary organic compounds that may serve as microbial energy sources in methanic marine subsurface environments. PMID:26635758

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.

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.

Carboxydotrophy potential of uncultivated Hydrothermarchaeota from the oceanic crust deep biosphere

NASA Astrophysics Data System (ADS)

Carr, S. A.; Jungbluth, S.; Rappe, M. S.; Orcutt, B.

2017-12-01

The marine sedimentary and crustal subsurface biospheres harbor many uncultured microorganisms, including those belonging to Hydrothermarchaeota, formerly known as Marine Benthic Group E. SSU rRNA sequences of Hydrothermarchaeota have been identified in marine sediments across the globe, often in low abundance. Recently, crustal fluids from two subseafloor borehole observatories located on the eastern flank of the Juan de Fuca Ridge (i.e., CORKs at IODP Holes U1362A and U1362B), were collected for single-cell and metagenomic analyses. Both techniques revealed Hydrothermarchaeota to be prevalent in this system. Collectively, single-cell amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) depict Hydrothermarchaeota as opportunists, potentially capable of dissimilative and assimilative carboxydotrophy, sulfate reduction, thiosulfate reduction, nitrate reduction, chemotaxis, and motility. We propose that this diverse suit of metabolic potential may be advantageous for the hydrologically and geochemically dynamic subsurface crustal aquifer, an environment thought to be energy and nutrient limited.

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

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.

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

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.

Natural water purification and water management by artificial groundwater recharge

PubMed Central

Balke, Klaus-Dieter; Zhu, Yan

2008-01-01

Worldwide, several regions suffer from water scarcity and contamination. The infiltration and subsurface storage of rain and river water can reduce water stress. Artificial groundwater recharge, possibly combined with bank filtration, plant purification and/or the use of subsurface dams and artificial aquifers, is especially advantageous in areas where layers of gravel and sand exist below the earth’s surface. Artificial infiltration of surface water into the uppermost aquifer has qualitative and quantitative advantages. The contamination of infiltrated river water will be reduced by natural attenuation. Clay minerals, iron hydroxide and humic matter as well as microorganisms located in the subsurface have high decontamination capacities. By this, a final water treatment, if necessary, becomes much easier and cheaper. The quantitative effect concerns the seasonally changing river discharge that influences the possibility of water extraction for drinking water purposes. Such changes can be equalised by seasonally adapted infiltration/extraction of water in/out of the aquifer according to the river discharge and the water need. This method enables a continuous water supply over the whole year. Generally, artificially recharged groundwater is better protected against pollution than surface water, and the delimitation of water protection zones makes it even more save. PMID:18357624

Geophysical Monitoring of Coupled Microbial and Geochemical Processes During Stimulated Subsurface Bioremediation

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

Williams, Kenneth H.; Kemna, Andreas; Wilkins, Michael J.

2009-08-05

Understanding how microorganisms alter their physical and chemical environment during bioremediation is hindered by our inability to resolve subsurface microbial activity with high spatial resolution. Here we demonstrate the use of a minimally invasive geophysical technique to monitor stimulated microbial activity during acetate amendment in an aquifer near Rifle, Colorado. During electrical induced polarization (IP) measurements, spatiotemporal variations in the phase response between imposed electric current and the resultant electric field correlated with changes in groundwater geochemistry accompanying stimulated iron and sulfate reduction and sulfide mineral precipitation. The magnitude of the phase response varied with measurement frequency (0.125 and 1more » Hz) andwasdependent upon the dominant metabolic process. The spectral effect was corroborated using a biostimulated column experiment containing Rifle sediments and groundwater. Fluids and sediments recovered from regions exhibiting an anomalous phase response were enriched in Fe(II), dissolved sulfide, and cell-associated FeS nanoparticles. The accumulation of mineral precipitates and electroactive ions altered the ability of pore fluids to conduct electrical charge, accounting for the anomalous IP response and revealing the usefulness of multifrequency IP measurements for monitoring mineralogical and geochemical changes accompanying stimulated subsurface bioremediation.« less

Vanadium Respiration by Geobacter metallireducens: Novel Strategy for In Situ Removal of Vanadium from Groundwater

PubMed Central

Ortiz-Bernad, Irene; Anderson, Robert T.; Vrionis, Helen A.; Lovley, Derek R.

2004-01-01

Vanadium can be an important contaminant in groundwaters impacted by mining activities. In order to determine if microorganisms of the Geobacteraceae, the predominant dissimilatory metal reducers in many subsurface environments, were capable of reducing vanadium(V), Geobacter metallireducens was inoculated into a medium in which acetate was the electron donor and vanadium(V) was the sole electron acceptor. Reduction of vanadium(V) resulted in the production of vanadium(IV), which subsequently precipitated. Reduction of vanadium(V) was associated with cell growth with a generation time of 15 h. No vanadium(V) was reduced and no precipitate was formed in heat-killed or abiotic controls. Acetate was the most effective of all the electron donors evaluated. When acetate was injected into the subsurface to enhance the growth and activity of Geobacteraceae in an aquifer contaminated with uranium and vanadium, vanadium was removed from the groundwater even more effectively than uranium. These studies demonstrate that G. metallireducens can grow via vanadium(V) respiration and that stimulating the activity of Geobacteraceae, and hence vanadium(V) reduction, can be an effective strategy for in situ immobilization of vanadium in contaminated subsurface environments. PMID:15128571

Natural water purification and water management by artificial groundwater recharge.

PubMed

Balke, Klaus-Dieter; Zhu, Yan

2008-03-01

Worldwide, several regions suffer from water scarcity and contamination. The infiltration and subsurface storage of rain and river water can reduce water stress. Artificial groundwater recharge, possibly combined with bank filtration, plant purification and/or the use of subsurface dams and artificial aquifers, is especially advantageous in areas where layers of gravel and sand exist below the earth's surface. Artificial infiltration of surface water into the uppermost aquifer has qualitative and quantitative advantages. The contamination of infiltrated river water will be reduced by natural attenuation. Clay minerals, iron hydroxide and humic matter as well as microorganisms located in the subsurface have high decontamination capacities. By this, a final water treatment, if necessary, becomes much easier and cheaper. The quantitative effect concerns the seasonally changing river discharge that influences the possibility of water extraction for drinking water purposes. Such changes can be equalised by seasonally adapted infiltration/extraction of water in/out of the aquifer according to the river discharge and the water need. This method enables a continuous water supply over the whole year. Generally, artificially recharged groundwater is better protected against pollution than surface water, and the delimitation of water protection zones makes it even more save.

Nucleic-acid characterization of the identity and activity of subsurface microorganisms

NASA Astrophysics Data System (ADS)

Madsen, E. L.

Nucleic-acid approaches to characterizing naturally occurring microorganisms in their habitats have risen to prominence during the last decade. Extraction of deoxyribonucleic-acid (DNA) and ribonucleic-acid (RNA) biomarkers directly from environmental samples provides a new means of gathering information in microbial ecology. This review article defines: (1) the subsurface habitat; (2) what nucleic-acid procedures are; and (3) the types of information nucleic-acid procedures can and cannot reveal. Recent literature examining microbial nucleic acids in the terrestrial subsurface is tabulated and reviewed. The majority of effort to date has focused upon insights into the identity and phylogeny of subsurface microorganisms afforded by analysis of their 16S rRNA genes. Given the power of nucleic-acid-based procedures and their limited application to subsurface habitats to date, many future opportunities await exploration. Au cours des derniers dix ans, les approches basées sur les acides nucléiques sont apparues et devenues essentielles pour caractériser dans leurs habitats les microorganismes existant à l'état naturel. L'extraction directe de l'ADN et de l'ARN, qui sont des biomarqueurs, d'échantillons environnementaux a fourni un nouveau moyen d'obtenir des informations sur l'écologie microbienne. Cet article synthétique définit 1) l'habitat souterrain, 2) ce que sont les procédures basées sur les acides nucléiques, 3) quel type d'informations ces procéedures peuvent et ne peuvent pas révéler. Les travaux récemment publiés concernatn les acides nucléiques microbiens dans le milieu souterrain terrestre sont catalogués et passés en revue. La majorité des efforts pour obtenir es données s'est concentrée sur l'identité et la phylogénie des microorganismes souterrains fournies par l'analyse de leurs gènes 16S rRNA. Étant donné la puissance des procédures basées sur les acides nucléiques et leur application limitée aux habitats souterrains pour obtenir des données, de nombreuses futures occasions sont dans l'attente d'explorations. Los métodos basados en ácidos nucleicos para la caracterización de microorganismos en sus propios hábitats han experimentado un gran auge en la última década. La extracción directa en muestras de los biomarcadores ácido desoxirribonucleico (ADN) y ribonucleico (ARN) supone un nuevo método para obtener información sobre ecología microbiana. En este articulo se definen: (1) el nuevo métidi para obtener información sobre ecología microbiana. En este artículo se definen: (1) el hábitat subsuperficial; (2) qué son los métodos basados en ácidos nucleicos; y (3) la información que estos métodos pueden proporcionar. Se revisa y tabula la bibliografía reciente sobre ácidos nucleicos microbianos en la subsuperficie. Hasta ahora la mayoría de estos estudios se han centrado en la identificación y filogenia de los microorganismos, mediante el análisis de sus genes 16S rRNA. Dado el potencial de las técnicas basadas en ácidos nucleicos y el hecho de que hasta ahora su aplicación a los hábitats subsuperficiales haya sido limitada, se presentan muchas opotunidades de futuro.

Environmental assessment of the potential effects of aquifer thermal energy storage systems on microorganisms in groundwater

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

Hicks, R.J.; Stewart, D.L.

1988-03-01

The primary objective of this study was to evaluate the potential environmental effects (both adverse and beneficials) of aquifer thermal energy storage (ATES) technology pertaining to microbial communities indigenous to subsurface environments (i.e., aquifers) and the propagation, movement, and potential release of pathogenic microorganisms (specifically, Legionella) within ATES systems. Seasonal storage of thermal energy in aquifers shows great promise to reduce peak demand; reduce electric utility load problems; contribute to establishing favorable economics for district heating and cooling systems; and reduce pollution from extraction, refining, and combustion of fossil fuels. However, concerns that the widespread implementation of this technology maymore » have adverse effects on biological systems indigeneous to aquifers, as well as help to propagate and release pathogenic organisms that enter thee environments need to be resolved. 101 refs., 2 tabs.« less

Life in the Ice

NASA Technical Reports Server (NTRS)

Allen, C. C.; Wainwright, N. R.; Grasby, S. E.; Harvey, R. P.

2003-01-01

The current Martian surface environment is extremely hostile to any known form of life. The combination of subfreezing temperature, low atmospheric pressure and high ultraviolet flux, combined with desiccated and possibly oxidizing soil, could destroy even the hardiest microorganisms. The Viking biology experiments are generally interpreted to indicate that the surface of Mars is currently devoid of life and organic molecules at the part-per-billion level. Speculation on the possibility of extant or preserved microbial life on Mars thus centers on refuges in some manner protected from the current surface environment, either in space or time. Terrestrial analogs include hydrothermal systems, lakes, caves and subsurface aquifers as well as more clement conditions in the distant past. We are examining the evidence for microbiology in Earth's glaciated polar regions as analogs to the polar caps of Mars. This research concerns the detection of microorganisms or their preserved remains at the surface and within polar glacial ice.

Single-cell genomics reveal metabolic strategies for microbial growth and survival in an oligotrophic aquifer

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

Wilkins, Michael J.; Kennedy, David W.; Castelle, Cindy

Bacteria from the genus Pedobacter are a major component of microbial assemblages at Hanford Site and have been shown to significantly change in abundance in response to the subsurface intrusion of Columbia River water. Here we employed single cell genomics techniques to shed light on the physiological niche of these microorganisms. Analysis of four Pedobacter single amplified genomes (SAGs) from Hanford Site sediments revealed a chemoheterotrophic lifestyle, with the potential to exist under both aerobic and microaerophilic conditions via expression of both aa 3­-type and cbb 3-type cytochrome c oxidases. These SAGs encoded a wide-range of both intra-and extra­-cellular carbohydrate-activemore » enzymes, potentially enabling the degradation of recalcitrant substrates such as xylan and chitin, and the utilization of more labile sugars such as mannose and fucose. Coupled to these enzymes, a diversity of transporters and sugar-binding molecules were involved in the uptake of carbon from the extracellular local environment. The SAGs were enriched in TonB-dependent receptors (TBDRs), which play a key role in uptake of substrates resulting from degradation of recalcitrant carbon. CRISPR-Cas mechanisms for resisting viral infections were identified in all SAGs. These data demonstrate the potential mechanisms utilized for persistence by heterotrophic microorganisms in a carbon-limited aquifer, and hint at potential linkages between observed Pedobacter abundance shifts within the 300 Area subsurface and biogeochemical shifts associated with Columbia River water intrusion.« less

Encapsulated cell bioremediation: Evaluation on the basis of particle tracer tests

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

Petrich, C.R.; Stormo, K.E.; Ralston, D.R.

1998-09-01

Microencapsulation of degradative organisms enhances microorganism survivability. The use of encapsulated cell microbeads for in situ biodegradation depends not only on microorganism survival but also on microbead transport characteristics. Two forced-gradient, recirculating-loop tracer experiments were conducted to evaluate the feasibility of encapsulated cell transport and bioremediation on the basis of polystyrene microsphere transport results. The tracer tests were conducted in a shallow, confined, unconsolidated, heterogeneous, sedimentary aquifer using bromide ion and 2 {micro}m, 5 {micro}m, and 15{micro}m microsphere tracers. Significant differences were observed in the transport of bromide solute and polystyrene microspheres. Microspheres reached peak concentrations in monitoring wells beforemore » bromide, which was thought to reflect the influence of aquifer heterogeneity. Greater decreases in microsphere C/C{sub 0} ratios were observed with distance from the injection wells than in bromide C/C{sub 0} ratios, which was attributed to particle filtration and/or settling. Several methods might be considered for introducing encapsulated cell microbeads into a subsurface environment, including direct injection into a contaminated aquifer zone, injection through a recirculating ground water flow system, or emplacement in a subsurface microbial curtain in advance of a plume. However, the in situ use of encapsulated cells in an aquifer is probably limited to aquifers containing sufficiently large pore spaces, allowing passage of at least some encapsulated cells. The use of encapsulated cells may also be limited by differences in solute and microbead transport patterns and flowpath clogging by larger encapsulated cell microbeads.« less

Degradation of atrazine and isoproturon in surface and sub-surface soil materials undergoing different moisture and aeration conditions.

PubMed

Issa, Salah; Wood, Martin

2005-02-01

The influence of different moisture and aeration conditions on the degradation of atrazine and isoproturon was investigated in environmental samples aseptically collected from surface and sub-surface zones of agricultural land. The materials were maintained at two moisture contents corresponding to just above field capacity or 90% of field capacity. Another two groups of samples were adjusted with water to above field capacity, and, at zero time, exposed to drying-rewetting cycles. Atrazine was more persistent (t(1/2) = 22-35 days) than isoproturon (t(1/2) = 5-17 days) in samples maintained at constant moisture conditions. The rate of degradation for both herbicides was higher in samples maintained at a moisture content of 90% of field capacity than in samples with higher moisture contents. The reduction in moisture content in samples undergoing desiccation from above field capacity to much lower than field capacity enhanced the degradation of isoproturon (t(1/2) = 9-12 days) but reduced the rate of atrazine degradation (t(1/2) = 23-35 days). This demonstrates the variability between different micro-organisms in their susceptibility to desiccation. Under anaerobic conditions generated in anaerobic jars, atrazine degraded much more rapidly than isoproturon in materials taken from three soil profiles (0-250 cm depth). It is suggested that some specific micro-organisms are able to survive and degrade herbicide under severe conditions of desiccation. Copyright (c) 2005 Society of Chemical Industry.

[Research progress in root rot diseases of Chinese herbal medicine and control strategy by antagonistic microorganisms].

PubMed

Gao, Fen; Ren, Xiao-xia; Wang, Meng-liang; Qin, Xue-mei

2015-11-01

In recent years, root rot diseases of Chinese herbal medicine have been posing grave threat to the development of the traditional Chinese medicine industry. This article presents a review on the occurring situation of the root rot disease, including the occurrence of the disease, the diversity of the pathogens, the regional difference in dominant pathogens,and the complexity of symptoms and a survey of the progress in bio-control of the disease using antagonistic microorganisms. The paper also discusses the existing problems and future prospects in the research.

Active Marine Subsurface Bacterial Population Composition in Low Organic Carbon Environments from IODP Expedition 320

NASA Astrophysics Data System (ADS)

Shepard, A.; Reese, B. K.; Mills, H. J.; IODP Expedition 320 Shipboard Science Party

2011-12-01

The marine subsurface environment contains abundant and active microorganisms. These microbial populations are considered integral players in the marine subsurface biogeochemical system with significance in global geochemical cycles and reservoirs. However, variations in microbial community structure, activity and function associated with the wide-ranging sedimentary and geochemical environments found globally have not been fully resolved. Integrated Ocean Drilling Program Expedition 320 recovered sediments from site U1332. Two sampling depths were selected for analysis that spanned differing lithological units in the sediment core. Sediments were composed of mostly clay with zeolite minerals at 8 meters below sea floor (mbsf). At 27 mbsf, sediments were composed of alternating clayey radiolarian ooze and nannofossil ooze. The concentration of SO42- had little variability throughout the core and the concentration of Fe2+ remained close to, or below, detection limits (0.4 μM). Total organic carbon content ranged from a low of 0.03 wt% to a high of 0.07 wt% between 6 and 30 mbsf providing an opportunity to evaluate marine subsurface microbial communities under extreme electron donor limiting conditions. The metabolically active fraction of the bacterial population was isolated by the extraction and amplification of 16S ribosomal RNA. Pyrosequencing of 16S rRNA transcripts and subsequent bioinformatic analyses provided a robust data set (15,931 total classified sequences) to characterize the community at a high resolution. As observed in other subsurface environments, the overall diversity of active bacterial populations decreased with depth. The population shifted from a diverse but evenly distributed community at approximately 8 mbsf to a Firmicutes dominated population at 27 mbsf (80% of sequences). A total of 95% of the sequences at 27 mbsf were grouped into three genera: Lactobacillus (phylum Firmicutes) at 80% of the total sequences, Marinobacter (phylum Proteobacteria) at 8%, and Formosa (phylum Bacteroidetes) at 7%. These lineages support a paradigm suggesting the importance of fermentation in the subsurface. However, this study extends the predicted range for fermentation below the shallow subsurface and into organic carbon limited marine sediments. Other previously characterized subsurface active populations from environments with higher organic carbon concentrations do not show similar levels of reduced diversity or predominance of fermentative populations. This study further emphasizes the spatial variability of microbial populations in the deep subsurface and highlights the need for continued exploration.

Effects of probiotic fermented milk on biofilms, oral microbiota, and enamel.

PubMed

Lodi, Carolina Simonetti; Oliveira, Lidiane Viana; Brighenti, Fernanda Lourenção; Delbem, Alberto Carlos Botazzo; Martinhon, Cleide Cristina Rodrigues

2015-01-01

The aim of this study was to evaluate in vitro and in vivo the effects of 2 brands of probiotic fermented milk on biofilms, oral microbiota, and enamel. For the in situ experiment, ten volunteers wore palatine devices containing four blocks of bovine dental enamel over 3 phases, during which 20% sucrose solution, Yakult® (Treatment A), and Batavito® (Treatment B) were dropped on the enamel blocks. Salivary microbial counts were obtained and biofilm samples were analyzed after each phase. For the in vivo experiment, the same ten volunteers drunk Yakult® (Treatment C) and Batavito® (Treatment D) in two phases. Saliva samples were collected for microbial analysis after each phase. The in situ study showed that in comparison with Treatment A, Treatment B resulted in fewer total cultivable anaerobes and facultative microorganisms in biofilms, higher final microhardness, lower percentage change in surface hardness, and smaller integrated subsurface enamel hardness. In the in vivo study, Treatment D resulted in a reduction in the counts of all microorganisms. The results suggested that the probiotic fermented milk Batavito®, but not Yakult®, reduced the amount of oral microorganisms and mineral loss in bovine enamel.

In-Situ Anaerobic Biosurfactant Production Process For Remediation Of DNAPL Contamination In Subsurface Aquifers

NASA Astrophysics Data System (ADS)

Albino, J. D.; Nambi, I. M.

2009-12-01

Microbial Enhanced Oil Recovery (MEOR) and remediation of aquifers contaminated with hydrophobic contaminants require insitu production of biosurfactants for mobilization of entrapped hydrophobic liquids. Most of the biosurfactant producing microorganisms produce them under aerobic condition and hence surfactant production is limited in subsurface condition due to lack of oxygen. Currently bioremediation involves expensive air sparging or excavation followed by exsitu biodegradation. Use of microorganisms which can produce biosurfactants under anaerobic conditions can cost effectively expedite the process of insitu bioremediation or mobilization. In this work, the feasibility of anaerobic biosurfactant production in three mixed anaerobic cultures prepared from groundwater and soil contaminated with chlorinated compounds and municipal sewage sludge was investigated. The cultures were previously enriched under complete anaerobic conditions in the presence of Tetrachloroethylene (PCE) for more than a year before they were studied for biosurfactant production. Biosurfactant production under anaerobic conditions was simulated using two methods: i) induction of starvation in the microbial cultures and ii) addition of complex fermentable substrates. Positive result for biosurfactant production was not observed when the cultures were induced with starvation by adding PCE as blobs which served as the only terminal electron acceptor. However, slight reduction in interfacial tension was noticed which was caused by the adherence of microbes to water-PCE interface. Biosurfactant production was observed in all the three cultures when they were fed with complex fermentable substrates and surface tension of the liquid medium was lowered below 35 mN/m. Among the fermentable substrates tested, vegetable oil yielded highest amount of biosurfactant in all the cultures. Complete biodegradation of PCE to ethylene at a faster rate was also observed when vegetable oil was amended to the microbial cultures. The microorganisms responsible for biosurfactant production was isolated and identified as Pseudomonas Sp (designated as Pseudomonas Sp ANBIOSURF-1, Gene bank no: FJ930079), Pseudomonas stutzeri (MTCC 10033), Pseudomonas Sp (MTCC 10032) from groundwater, soil and municipal sewage sludge enrichments respectively. This study confirms that biosurfactants can be produced under anaerobic conditions and also in sufficient quantities. The cultures were also able to cometabolically degrade PCE to Ethylene. The isolated microorganisms can be used for remediation of DNAPL contaminated sites by in-situ biosurfactant production.

Temperature and pressure adaptation of a sulfate reducer from the deep subsurface

PubMed Central

Fichtel, Katja; Logemann, Jörn; Fichtel, Jörg; Rullkötter, Jürgen; Cypionka, Heribert; Engelen, Bert

2015-01-01

Microbial life in deep marine subsurface faces increasing temperatures and hydrostatic pressure with depth. In this study, we have examined growth characteristics and temperature-related adaptation of the Desulfovibrio indonesiensis strain P23 to the in situ pressure of 30 MPa. The strain originates from the deep subsurface of the eastern flank of the Juan de Fuca Ridge (IODP Site U1301). The organism was isolated at 20°C and atmospheric pressure from ~61°C-warm sediments approximately 5 m above the sediment–basement interface. In comparison to standard laboratory conditions (20°C and 0.1 MPa), faster growth was recorded when incubated at in situ pressure and high temperature (45°C), while cell filamentation was induced by further compression. The maximum growth temperature shifted from 48°C at atmospheric pressure to 50°C under high-pressure conditions. Complementary cellular lipid analyses revealed a two-step response of membrane viscosity to increasing temperature with an exchange of unsaturated by saturated fatty acids and subsequent change from branched to unbranched alkyl moieties. While temperature had a stronger effect on the degree of fatty acid saturation and restructuring of main phospholipids, pressure mainly affected branching and length of side chains. The simultaneous decrease of temperature and pressure to ambient laboratory conditions allowed the cultivation of our moderately thermophilic strain. This may in turn be one key to a successful isolation of microorganisms from the deep subsurface adapted to high temperature and pressure. PMID:26500624

The efficacy of techniques for the disinfection of artificial sub-surface dentinal caries lesions and their effect on demineralization and remineralization in vitro.

PubMed

Preston, K P; Higham, S M; Smith, P W

2007-06-01

The efficacy of three techniques for the disinfection of artificial sub-surface root caries lesions and their response to subsequent episodes of de- and remineralization was investigated quantitatively in vitro. Sub-surface dentinal lesions (n=20), cut into four experimental blocks and deliberately contaminated with Streptococcus mutans, were subject to either steam autoclaving (121 degrees C, 5min), gamma irradiation (4100Gy), immersion in 0.1% (w/v) thymol-distilled water solution (24h) or reserved as a control. Next, the lesions were incubated aerobically in sterile nutrient broth for 24h at 37 degrees C and resultant cultures plated onto blood agar and neutralisation agar. Ten blocks from each experimental group were then immersed in an acidic buffer solution or exposed to artificial saliva for 5 days. Baseline changes in the mineral content and distribution of the lesions were assessed by transverse microradiography (TMR). Micro-organisms were recovered from each control block and one block treated by gamma irradiation. Steam autoclaving and immersion in a thymol solution significantly decreased (p<0.05) the amount of mineral lost from the body of lesions subject to a further acid challenge. Mineral ion uptake by lesions exposed to artificial saliva was significantly increased (p<0.05) through disinfection by steam autoclaving. Gamma irradiation proved the most acceptable method for the disinfection of sub-surface root dentine lesions having the least adverse effect on demineralization and remineralization.

Pursuing the unlimited potential of microorganisms-progress and prospect of a fermentation company.

PubMed

Arisawa, Akira; Watanabe, Azuma

2017-01-01

Production of pharmaceuticals and chemicals using microbial functions has bestowed numerous benefits onto society. The Nobel Prize awarded to Professor Ōmura, Distinguished Emeritus Professor of Kitasato University, showed the world the importance of the discovery and practical application of microorganisms. Now, increasing attention is turned toward the future path of this field. As people involved in the microorganism industry, we will review the industrial activities thus far and consider the possible future developments in this field and its potential contribution to society.

Bacterial community structure and dissolved organic matter in repeatedly flooded subsurface karst water pools.

PubMed

Shabarova, Tanja; Villiger, Jörg; Morenkov, Oleg; Niggemann, Jutta; Dittmar, Thorsten; Pernthaler, Jakob

2014-07-01

Bacterial diversity, community assembly, and the composition of the dissolved organic matter (DOM) were studied in three temporary subsurface karst pools with different flooding regimes. We tested the hypothesis that microorganisms introduced to the pools during floods faced environmental filtering toward a 'typical' karst water community, and we investigated whether DOM composition was related to floodings and the residence time of water in stagnant pools. As predicted, longer water residence consistently led to a decline of bacterial diversity. The microbial assemblages in the influx water harbored more 'exotic' lineages with large distances to known genotypes, yet these initial communities already appeared to be shaped by selective processes. β-Proteobacterial operational taxonomic units (OTUs) closely related to microbes from subsurface or surface aquatic environments were mainly responsible for the clustering of samples according to water residence time in the pools. By contrast, several Cytophagaceae and Flavobacteriaceae OTUs were related to different floodings, which were also the main determinants of DOM composition. A subset of compounds distinguishable by molecular mass and O/C content were characteristic for individual floods. Moreover, there was a transformation of DOM in stagnant pools toward smaller and more aromatic compounds, potentially also reflecting microbial utilization. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

The Astrobiology of the Subsurface: Exploring Cave Habitats on Earth, Mars and Beyond

NASA Technical Reports Server (NTRS)

Boston, Penelope Jane

2016-01-01

We are using the spectacular underground landscapes of Earth caves as models for the subsurfaces of other planets. Caves have been detected on the Moon and Mars and are strongly suspected for other bodies in the Solar System including some of the ice covered Ocean Worlds that orbit gas giant planets. The caves we explore and study include many extreme conditions of relevance to planetary astrobiology exploration including high and low temperatures, gas atmospheres poisonous to humans but where exotic microbes can flourish, highly acidic or salty fluids, heavy metals, and high background radiation levels. Some cave microorganisms eat their way through bedrock, some live in battery acid conditions, some produce unusual biominerals and rare cave formations, and many produce compounds of potential pharmaceutical and industrial significance. We study these unique lifeforms and the physical and chemical biosignatures that they leave behind. Such traces can be used to provide a "Field Guide to Unknown Organisms" for developing life detection space missions.

Prospect of life on cold planets with low atmospheric pressures

NASA Astrophysics Data System (ADS)

Pavlov, A. A.; Vdovina, M.

2009-12-01

Stable liquid water on the surface of a planet has been viewed as the major requirement for a habitable planet. Such approach would exclude planets with low atmospheric pressures and cold mean surface temperatures (like present Mars) as potential candidates for extraterrestrial life search. Here we explore a possibility of the liquid water formation in the extremely shallow (1-3 cm) subsurface layer under low atmospheric pressures (0.1-10 mbar) and low average surface temperatures (~-30 C). During brief periods of simulated daylight warming the shallow subsurface ice sublimates, the water vapor can diffuse through the porous surface layer of soil temporarily producing supersaturated conditions in the soil, which lead to the formation of liquid films. We show that non-extremophile terrestrial microorganisms (Vibrio sp.) can grow and reproduce under such conditions. The necessary conditions for metabolism and reproduction are the sublimation of ground ice through a thin layer of soil and short episodes of warm temperatures at the planetary surface.

Remote Sensing of Subsurface Microbial Transformations

NASA Astrophysics Data System (ADS)

Williams, K. H.; Ntarlagiannis, D.; Slater, L.; Long, P.; Dohnalkova, A.; Hubbard, S. S.; Banfield, J. F.

2004-12-01

Understanding how microorganisms influence the physical and chemical properties of the subsurface is hindered by our inability to detect microbial dynamics in real time with high spatial resolution. Here we have used non-invasive geophysical methods to monitor biomineralization and related processes during biostimulation at both laboratory and field scales. Alterations in saturated sediment characteristics resulting from microbe-mediated transformations were concomitant with changes in complex resistivity, spontaneous potential, and acoustic wave signatures. Variability in complex resistivity and acoustic wave amplitudes appears tied to the nucleation, growth, and development of nanoparticulate precipitates along grain surfaces and within the pore space. In contrast, time-varying spontaneous potentials appear primarily sensitive to the electrochemical gradients resulting from metabolic pathways, such as iron- and sulfate-reduction. Furthermore, they enable us to track mobile fronts of active respiration that arise due to microbial chemotaxis. In this way, geophysical data may be used to image the distribution of mineral precipitates, biomass, and biogeochemical fronts evolving over time and suggest the ability to remotely monitor contaminated aquifers undergoing bioremediation.

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

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

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.

Quantitative 3D model of light transmittance through translucent rocks applied to the hypolithic microbial community.

PubMed

Jolitz, Rebecca D; McKay, Christopher P

2013-07-01

In extreme desert environments, photosynthetic microorganisms often live on the buried undersides of translucent rocks. Computing the light level reaching these locations requires 3D modeling of a finite rock. We report on Monte Carlo calculations of skylight and sunlight transmission through a partially buried flat cylindrical rock using one billion photons per simulation. Transmitted light level drops inversely with increasing rock opacity, as expected for purely scattering media. For a half-buried rock with an extinction coefficient of 0.1 cm(-1) (opacity of 0.2), transmission at the bottom is 64 % for sunlight at a solar zenith angle of 60° and 82 % for skylight. Transmitted light level increases slowly with increasing scattering asymmetry factor of the rock independent of illumination or depth buried. Transmitted sunlight at zenith through a thick half-buried rock (opacity of 0.6) is six times brighter at the bottom than the subsurface sides. Skylight transmits equally to the subsurface sides and bottom. When the sun is not straight overhead, the sunward side of the rock is brighter than the underside of the rock. Compared to the sunlight transmitted to the bottom, transmitted sunlight inclined at 60° is 24 times brighter at the subsurface side towards the sun and 14 times brighter at the subsurface side 70° away from the sun. Transmitted sunlight emitted from zenith and skylight is uniformly bright at the bottom regardless of how deeply the rock is buried. Sunlight not at zenith transmits preferentially to the sunward bottom edge depending on the depth the rock is buried.

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.

Microbiological Methodology in Astrobiology

NASA Technical Reports Server (NTRS)

Abyzov, S. S.; Gerasimenko, L. M.; Hoover, R. B.; Mitskevich, I. N.; Mulyukin, A. L.; Poglazova, M. N.; Rozanov, A. Y.

2005-01-01

Searching for life in astromaterials to be delivered from the future missions to extraterrestrial bodies is undoubtedly related to studies of the properties and signatures of living microbial cells and microfossils on Earth. As model terrestrial analogs of Martian polar subsurface layers are often regarded the Antarctic glacier and Earth permafrost habitats where alive microbial cells preserved viability for millennia years due to entering the anabiotic state. For the future findings of viable microorganisms in samples from extraterrestrial objects, it is important to use a combined methodology that includes classical microbiological methods, plating onto nutrient media, direct epifluorescence and electron microscopy examinations, detection of the elemental composition of cells, radiolabeling techniques, PCR and FISH methods. Of great importance is to ensure authenticity of microorganisms (if any in studied samples) and to standardize the protocols used to minimize a risk of external contamination. Although the convincing evidence of extraterrestrial microbial life will may come from the discovery of living cells in astromaterials, biomorphs and microfossils must also be regarded as a target in search of life evidence bearing in mind a scenario that alive microorganisms had not be preserved and underwent mineralization. Under the laboratory conditions, processes that accompanied fossilization of cyanobacteria were reconstructed, and artificially produced cyanobacterial stromatolites resembles by their morphological properties those found in natural Earth habitats. Regarding the vital importance of distinguishing between biogenic and abiogenic signatures and between living and fossil microorganisms in analyzed samples, it is worthwhile to use some previously developed approaches based on electron microscopy examinations and analysis of elemental composition of biomorphs in situ and comparison with the analogous data obtained for laboratory microbial cultures and fossilized microorganisms. This communication will be focused on the analysis of our experience in working with ancient microorganisms and fossils and discussion of some issues that are crucial for development of the program for future finding of extraterrestrial life and its evidence.

Status and future of disease protection and grape berry quality alteration by micro-organisms in viticulture.

PubMed

Otoguro, M; Suzuki, S

2018-06-16

Grapevine is one of the most widely grown fruit crops in the world. At present, however, there is much concern regarding chemical pollution in viticulture due to the application of chemical fungicides and fertilizers. One viticultural practice to resolve this issue is the application of micro-organisms to grapevine as a substitute for chemicals. Some micro-organisms act as an enhancer of grape berry quality as well as a suppresser of disease in grapevine through their antagonistic ability and/or systemic resistance inducing ability. Herein, we review current and prospective applications of micro-organisms in viticulture. In this review, we evaluate the applicability of micro-organisms in viticulture. Micro-organisms can improve grape berry quality through grapevine disease protection and grape berry quality alteration. Because the use of micro-organisms to protect grapevine from plant diseases is safer than the use of chemical fungicides, the use of biofungicides in viticulture is expected to be enhanced by the increasing consumer concern towards chemical fungicides. Micro-organisms also modify plant secondary metabolites for use as flavours, pharmaceuticals and food additives. Studies of micro-organisms that promote polyphenol, anthocyanin and aroma compound biosynthesis are in progress with an eye to improving grape berry quality. © 2018 The Society for Applied Microbiology.

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

Sea ice, extremophiles and life on extra-terrestrial ocean worlds

NASA Astrophysics Data System (ADS)

Martin, Andrew; McMinn, Andrew

2018-01-01

The primary aim of this review is to highlight that sea-ice microbes would be capable of occupying ice-associated biological niches on Europa and Enceladus. These moons are compelling targets for astrobiological exploration because of the inferred presence of subsurface oceans that have persisted over geological timescales. Although potentially hostile to life in general, Europa and Enceladus may still harbour biologically permissive domains associated with the ice, ocean and seafloor environments. However, validating sources of free energy is challenging, as is qualifying possible metabolic processes or ecosystem dynamics. Here, the capacity for biological adaptation exhibited by microorganisms that inhabit sea ice is reviewed. These ecosystems are among the most relevant Earth-based analogues for considering life on ocean worlds because microorganisms must adapt to multiple physicochemical extremes. In future, these organisms will likely play a significant role in defining the constraints on habitability beyond Earth and developing a mechanistic framework that contrasts the limits of Earth's biosphere with extra-terrestrial environments of interest.

Effects of remediation amendments on vadose zone microorganisms

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

Miller, Hannah M.; Tilton, Fred A.

2012-08-10

Surfactant-based foam delivery technology has been studied to remediate Hanford 200 area deep vadose zone sediment. However, the surfactants and remediation amendments have an unknown effect on indigenous subsurface microorganisms. Microbial populations are important factors to consider in remediation efforts due to their potential to alter soil geochemistry. This project focuses on measuring microbial metabolic responses to remediation amendments in batch and column studies using Deep Vadose Zone Sediments. Initial studies of the microbes from Hanford 200 area deep vadose zone sediment showed surfactants sodium dodecyl sulfate (SDS) and cocamidopropyl betaine (CAPB) and remediation amendment calcium polysulfide (CPS) had nomore » affect on microbial growth using BiologTM Ecoplates. To move towards a more realistic field analog, soil columns were packed with Hanford 200 Area sediment. Once microbial growth in the column was verified by observing growth of the effluent solution on tryptic soy agar plates, remedial surfactants were injected into the columns, and the resulting metabolic diversity was measured. Results suggest surfactant sodium dodecyl sulfate (SDS) stimulates microbial growth. The soil columns were also visualized using X-ray microtomography to inspect soil packing and possibly probe for evidence of biofilms. Overall, BiologTM Ecoplates provide a rapid assay to predict effects of remediation amendments on Hanford 200 area deep vadose zone microorganisms.« less

Growth and Survivability of Microorganisms at Martian Temperatures and Pressures

NASA Astrophysics Data System (ADS)

Mickol, Rebecca Lynne

The discovery of methane in the martian atmosphere via numerous ground- and space-based sources has prompted the study of methanogens as models for life on Mars. Methanogens are microorganisms within the domain Archaea, many of which utilize carbon dioxide (CO2) and hydrogen to produce methane. The non-photosynthetic nature of methanogens indicates that they could exist in sub-surface environments, protected from harmful UV and ionizing radiation on the surface of Mars. These organisms also do not require organics, which are sparse on the planet. Additionally, the wide variety of environments we find life in on Earth, as well as evidence for liquid brines on the surface of Mars, suggest that habitable environments may still exist on the planet. However, there are a variety of conditions that any extant life on Mars would need to endure, including wide variations in temperature over one sol, a low-pressure atmosphere, and a limited availability of liquid water, among others. This dissertation encompasses various experiments that examined the ability of four species of methanogens (Methanosarcina barkeri, Methanobacterium formicicum, Methanococcus maripaludis, and Methanothermobacter wolfeii) to survive and/or grow under 1) low-pressure conditions and 2) freeze/thaw cycles. Low pressure studies include both survival and active growth experiments conducted between 7 mbar (the average surface pressure on Mars) and 143 mbar. Freeze/thaw experiments utilized short- and long-term cycles varying in temperature between the organisms' growth temperatures (22 °C, M. maripaludis; 37 °C, M. barkeri and M. formicicum; 55 °C, M. wolfeii ) and -80 °C, encompassing Mars-relevant temperature changes. As a comparison to methanogen growth and survivability, additional experiments were conducted using a non-spore-forming bacterium, Serratia liquefaciens , previously shown capable of growth at 7 mbar, 0 °C and within an anoxic CO2 atmosphere. The experiments described here assessed the survivability of S. liquefaciens exposed to martian UV irradiation within liquid brines and ices. The experiments discussed here demonstrate the ability of Earth microorganisms to withstand certain extreme conditions on Mars and suggest that the planet may contain relatively habitable microenvironments within the near subsurface.

Astrobiological aspects of Mars and human presence: pros and cons.

PubMed

Horneck, G

2008-08-01

After the realization of the International Space Station, human exploratory missions to Moon or Mars, i.e. beyond low Earth orbit, are widely considered as the next logical step of peaceful cooperation in space on a global scale. Besides the human desire to extend the window of habitability, human exploratory missions are driven by several aspects of science, technology, culture and economy. Mars is currently considered as a major target in the search for life beyond the Earth. Understanding the history of water on Mars appears to be one of the clues to the puzzle on the probability of life on Mars. On Earth microorganisms have flourished for more than 3.5 Ga and have developed strategies to cope with so-called extreme conditions (e.g., hot vents, permafrost, subsurface regions, rocks or salt crystals). Therefore, in search for life on Mars, microorganisms are the most likely candidates for a putative biota on Mars and the search for morphological or chemical signatures of life or its relics is one of the primary and most exciting goals of Mars exploration. The presence of humans on the surface of Mars will substantially increase this research potential, e.g., by supporting deep subsurface drilling and by allowing intellectual collection and sophisticated in situ analysis of samples of astrobiological interest. On the other hand, such long-duration missions beyond LEO will add a new dimension to human space flight, concerning the distance of travel, the radiation environment, the gravity levels, the duration of the mission, and the level of confinement and isolation the crew will be exposed to. This will raise the significance of several health issues, above all radiation protection, gravity related effects as well as psychological issues. Furthermore, the import of internal and external microorganisms inevitably accompanying any human mission to Mars, or brought purposely to Mars as part of a bioregenerative life support system needs careful consideration with regard to planetary protection issues. Therefore, before planning any human exploratory mission, the critical issues concerning human health and wellbeing as well as protection of Mars in its pristine condition need to be investigated.

Astrobiological Aspects of Mars and Human Presence: Pros and Cons

PubMed Central

Horneck, G

2008-01-01

After the realization of the International Space Station, human exploratory missions to Moon or Mars, i.e. beyond low Earth orbit, are widely considered as the next logical step of peaceful cooperation in space on a global scale. Besides the human desire to extend the window of habitability, human exploratory missions are driven by several aspects of science, technology, culture and economy. Mars is currently considered as a major target in the search for life beyond the Earth. Understanding the history of water on Mars appears to be one of the clues to the puzzle on the probability of life on Mars. On Earth microorganisms have flourished for more than 3.5 Ga and have developed strategies to cope with so-called extreme conditions (e.g., hot vents, permafrost, subsurface regions, rocks or salt crystals). Therefore, in search for life on Mars, microorganisms are the most likely candidates for a putative biota on Mars and the search for morphological or chemical signatures of life or its relics is one of the primary and most exciting goals of Mars exploration. The presence of humans on the surface of Mars will substantially increase this research potential, e.g., by supporting deep subsurface drilling and by allowing intellectual collection and sophisticated in situ analysis of samples of astrobiological interest. On the other hand, such long-duration missions beyond LEO will add a new dimension to human space flight, concerning the distance of travel, the radiation environment, the gravity levels, the duration of the mission, and the level of confinement and isolation the crew will be exposed to. This will raise the significance of several health issues, above all radiation protection, gravity related effects as well as psychological issues. Furthermore, the import of internal and external microorganisms inevitably accompanying any human mission to Mars, or brought purposely to Mars as part of a bioregenerative life support system needs careful consideration with regard to planetary protection issues. Therefore, before planning any human exploratory mission, the critical issues concerning human health and wellbeing as well as protection of Mars in its pristine condition need to be investigated. PMID:19048093

The 2002 NASA Faculty Fellowship Program Research Reports

NASA Technical Reports Server (NTRS)

Bland, J. (Compiler)

2003-01-01

Contents include the following: System Identification of X-33. Neural Network Advanced Ceramic Technology for Space Applications at NASA MSFC. Developing a MATLAB-Based Tool for Visualization and Transformation. Subsurface Stress Fields in Single Crystal (Anisotropic). Contacts Our Space Future: A Challenge to the Conceptual Artist Concept Art for Presentation and Education. Identification and Characterization of Extremophile Microorganisms. Significant to Astrobiology. Mathematical Investigation of Gamma Ray and Neutron. Absorption Grid Patterns for Homeland Defense-Related Fourier Imaging Systems. The Potential of Microwave Radiation for Processing Martian Soil. Fuzzy Logic Trajectory Design and Guidance for Terminal Area.

D:L-Amino Acid Modeling Reveals Fast Microbial Turnover of Days to Months in the Subsurface Hydrothermal Sediment of Guaymas Basin.

PubMed

Møller, Mikkel H; Glombitza, Clemens; Lever, Mark A; Deng, Longhui; Morono, Yuki; Inagaki, Fumio; Doll, Mechthild; Su, Chin-Chia; Lomstein, Bente A

2018-01-01

We investigated the impact of temperature on the microbial turnover of organic matter (OM) in a hydrothermal vent system in Guaymas Basin, by calculating microbial bio- and necromass turnover times based on the culture-independent D:L-amino acid model. Sediments were recovered from two stations near hydrothermal mounds (<74°C) and from one cold station (<9°C). Cell abundance at the two hydrothermal stations dropped from 10 8 to 10 6 cells cm -3 within ∼5 m of sediment depth resulting in a 100-fold lower cell number at this depth than at the cold site where numbers remained constant at 10 8 cells cm -3 throughout the recovered sediment. There were strong indications that the drop in cell abundance was controlled by decreasing OM quality. The quality of the sedimentary OM was determined by the diagenetic indicators %T AA C (percentage of total organic carbon present as amino acid carbon), %T AA N (percentage of total nitrogen present as amino acid nitrogen), aspartic acid:β-alanine ratios, and glutamic acid:γ-amino butyric acid ratios. All parameters indicated that the OM became progressively degraded with increasing sediment depth, and the OM in the hydrothermal sediment was more degraded than in the uniformly cold sediment. Nonetheless, the small community of microorganisms in the hydrothermal sediment demonstrated short turnover times. The modeled turnover times of microbial bio- and necromass in the hydrothermal sediments were notably faster (biomass: days to months; necromass: up to a few hundred years) than in the cold sediments (biomass: tens of years; necromass: thousands of years), suggesting that temperature has a significant influence on the microbial turnover rates. We suggest that short biomass turnover times are necessary for maintance of essential cell funtions and to overcome potential damage caused by the increased temperature.The reduced OM quality at the hyrothemal sites might thus only allow for a small population size of microorganisms.

Microbially catalyzed nitrate-dependent metal/radionuclide oxidation in shallow subsurface sediments

NASA Astrophysics Data System (ADS)

Weber, K.; Healy, O.; Spanbauer, T. L.; Snow, D. D.

2011-12-01

Anaerobic, microbially catalyzed nitrate-dependent metal/radionuclide oxidation has been demonstrated in a variety of sediments, soils, and groundwater. To date, studies evaluating U bio-oxidation and mobilization have primarily focused on anthropogenically U contaminated sites. In the Platte River Basin U originating from weathering of uranium-rich igneous rocks in the Rocky Mountains was deposited in shallow alluvial sediments as insoluble reduced uranium minerals. These reduced U minerals are subject to reoxidation by available oxidants, such nitrate, in situ. Soluble uranium (U) from natural sources is a recognized contaminant in public water supplies throughout the state of Nebraska and Colorado. Here we evaluate the potential of anaerobic, nitrate-dependent microbially catalyzed metal/radionuclide oxidation in subsurface sediments near Alda, NE. Subsurface sediments and groundwater (20-64ft.) were collected from a shallow aquifer containing nitrate (from fertilizer) and natural iron and uranium. The reduction potential revealed a reduced environment and was confirmed by the presence of Fe(II) and U(IV) in sediments. Although sediments were reduced, nitrate persisted in the groundwater. Nitrate concentrations decreased, 38 mg/L to 30 mg/L, with increasing concentrations of Fe(II) and U(IV). Dissolved U, primarily as U(VI), increased with depth, 30.3 μg/L to 302 μg/L. Analysis of sequentially extracted U(VI) and U(IV) revealed that virtually all U in sediments existed as U(IV). The presence of U(IV) is consistent with reduced Fe (Fe(II)) and low reduction potential. The increase in aqueous U concentrations with depth suggests active U cycling may occur at this site. Tetravalent U (U(IV)) phases are stable in reduced environments, however the input of an oxidant such as oxygen or nitrate into these systems would result in oxidation. Thus co-occurrence of nitrate suggests that nitrate could be used by bacteria as a U(IV) oxidant. Most probable number enumeration of nitrate-dependent U(IV) oxidizing microorganisms demonstrated an abundant community ranging from 1.61x104 to 2.74x104 cells g-1 sediment. Enrichments initiated verified microbial U reduction and U oxidation coupled to nitrate reduction. Sediment slurries were serially diluted and incubated over a period of eight weeks and compared to uninoculated controls. Oxidation (0-4,554 μg/L) and reduction (0-55 μg/L) of U exceeded uninoculated controls further providing evidence of a U biogeochemical cycling in these subsurface sediments. The oxidation of U(IV) could contribute to U mobilization in the groundwater and result in decreased water quality. Not only could nitrate serve as an oxidant, but Fe(III) could also contribute to U mobilization. Nitrate-dependent Fe(II) oxidation is an environmentally ubiquitous process facilitated by a diversity of microorganisms. Additional research is necessary in order to establish a role of biogenic Fe(III) oxides in U geochemical cycling at this site. These microbially mediated processes could also have a confounding effect on uranium mobility in subsurface environments.

Using Bacterial Surrogates to Assess Pathogen Transport in the Subsurface: Laboratory and Field Indications of Co-Transport Considerations

NASA Astrophysics Data System (ADS)

Emelko, M.; Stimson, J. R.; McLellan, N. L.; Mesquita, M.

2009-12-01

Prediction of the transport and fate of colloids and nanoparticles in porous media environments remains challenging because factors such as experimental scale, subsurface heterogeneity, and variable flow paths and fluxes have made it difficult to relate laboratory outcomes to field performance. Moreover, field studies have been plagued with inadequate consideration of ground water flow, reliance on unproven “surrogate” parameters, non-detects at the extraction well, and limited sampling. Riverbank filtration (RBF) is an example of an application for which some predictive capacity regarding colloid transport is desirable. RBF is a relatively low-cost, natural water treatment technology in which surface water contaminants are removed or degraded as the infiltrating water flows from a surface source to abstraction wells. RBF has been used for water treatment for at least 200 years and its potential to provide a significant barrier to microorganisms has been demonstrated. Assignment of microbial treatment credits for RBF remains a regulatory challenge because strategies for demonstrating effective subsurface filtration of organisms are not standardized. The potential passage of Giardia lamblia and Cryptosporidium parvum through RBF systems is of particular regulatory concern because these pathogens are known to be resistant to conventional disinfection processes. The transport or relatively small, pathogenic viruses through RBF systems is also a common concern. To comply with the U.S. Long Term 2 Enhanced Surface Water Treatment Rule, utilities with sufficiently high levels of Cryptosporidium oocysts in their source water must amend existing treatment by choosing from a ‘‘toolbox’’ of technologies, including RBF. Aerobic bacterial spores have been evaluated and proposed by some as surrogates for evaluating drinking water treatment plant performance; they also have been proposed as potential surrogates for Cryptosporidium removal during subsurface filtration processes such as RBF. Here, duplicate column studies were conducted to evaluate the transport of nano- and micro-sized polystyrene micropsheres, aerobic spores of Bacillus subtilis, PR772 bacteriophage, and pathogenic Salmonella typhimurium bacteria in a well-sorted fine sand (d 50 = 0.6 mm). A field validation experiment investigating transport of 1.5 µm polystyrene micropsheres and aerobic spores in and RBF system comprised of unconsolidated silty sand, gravel, and boulders was conducted. The column studies demonstrated that the presence of the aerobic spores resulted in increased removal of 4.5 µm microspheres from< 2 log to ~4 log, and 1.5 µm microsphere removal from <0.5 log to ~1 log removal. Microscopic examination of the samples also revealed extensive clumping of microspheres and microorganisms during the experiments conducted with aerobic spores. A field trial during which microspheres and spores of B. subtilis were injected into the subsurface provided corroborating evidence of a co-transport effect of aerobic spores by demonstrating ~1.6 log increase in 1.5 µm microsphere removal in the presence of aerobic spores.

Effects of Hydraulic Frac Fluids on Subsurface Microbial Communities in Gas Shales

NASA Astrophysics Data System (ADS)

Jiménez, Núria; Krüger, Martin

2014-05-01

Shale gas is being considered as a complementary energy resource to coal or other fossil fuels. The exploitation of unconventional gas reservoirs requires the use of advanced drilling techniques and hydraulic stimulation (fracking). During fracking operations, large amounts of fluids (fresh water, proppants and chemical additives) are injected at high pressures into the formations, to produce fractures and fissures, and thus to release gas from the source rock into the wellbore. The injected fluids partly remain in the formation, while about 20 to 40% of the originally injected fluid flows back to the surface, together with formation waters, sometimes containing dissolved hydrocarbons, high salt concentrations, etc. The overall production operation will likely affect and be affected by subsurface microbial communities associated to the shale formations. On the one hand microbial activity (like growth, biofilm formation) can cause unwanted processes like corrosion, clogging, etc. On the other hand, the introduction of frac fluids could either enhance microbial growth or cause toxicity to the shale-associated microbial communities. To investigate the potential impacts of changing environmental reservoir conditions, like temperature, salinity, oxgen content and pH, as well as the introduction of frac or geogenic chemicals on subsurface microbial communities, laboratory experiments under in situ conditions (i.e. high temperatures and pressures) are being conducted. Enrichment cultures with samples from several subsurface environments (e.g. shale and coal deposits, gas reservoirs, geothermal fluids) have been set up using a variety of carbon sources, including hydrocarbons and typical frac chemicals. Classical microbiological and molecular analysis are used to determine changes in the microbial abundance, community structure and function after the exposure to different single frac chemicals, "artificial" frac fluids or production waters. On the other hand, potential transformation reactions of frac or geogenic chemicals by subsurface microbiota and their lifetime are investigated. In our "fracking simulation" experiments, an increasing number of hydrocarbon-degrading or halophilic microorganisms is to be expected after exposure of subsurface communities to artificial production waters. Whereas the introduction of freshwater and of easily biodegradable substrates might favor the proliferation of fast-growing generalistic heterotrophs in shale-associated communities. Nevertheless toxicity of some of the frac components cannot be excluded.

Energy Requirements of Hydrogen-utilizing Microbes: A Boundary Condition for Subsurface Life

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.; Alperin, Marc J.; Albert, Daniel B.; Martens, Christopher S.

2003-01-01

Microbial ecosystems based on the energy supplied by water-rock chemistry carry particular significance in the context of geo- and astrobiology. With no direct dependence on solar energy, lithotrophic microbes could conceivably penetrate a planetary crust to a depth limited only by temperature or pressure constraints (several kilometers or more). The deep lithospheric habitat is thereby potentially much greater in volume than its surface counterpart, and in addition offers a stable refuge against inhospitable surface conditions related to climatic or atmospheric evolution (e.g., Mars) or even high-energy impacts (e.g., early in Earth's history). The possibilities for a deep microbial biosphere are, however, greatly constrained by life s need to obtain energy at a certain minimum rate (the maintenance energy requirement) and of a certain minimum magnitude (the energy quantum requirement). The mere existence of these requirements implies that a significant fraction of the chemical free energy available in the subsurface environment cannot be exploited by life. Similar limits may also apply to the usefulness of light energy at very low intensities or long wavelengths. Quantification of these minimum energy requirements in terrestrial microbial ecosystems will help to establish a criterion of energetic habitability that can significantly constrain the prospects for life in Earth's subsurface, or on other bodies in the solar system. Our early work has focused on quantifying the biological energy quantum requirement for methanogenic archaea, as representatives of a plausible subsurface metabolism, in anoxic sediments (where energy availability is among the most limiting factors in microbial population growth). In both field and laboratory experiments utilizing these sediments, methanogens retain a remarkably consistent free energy intake, in the face of fluctuating environmental conditions that affect energy availability. The energy yields apparently required by methanogens in these sediment systems for sustained metabolism are about half that previously thought necessary. Lowered energy requirements would imply that a correspondingly greater proportion of the planetary subsurface could represent viable habitat for microorganisms.

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.

[Evolution of pathogenic micro-organisms as a challenge for medicine].

PubMed

Vaara, Martti

2009-01-01

Successful parasitic micro-organisms are able to adapt to the circumstances of the host's organ system, and it is usually not expedient for them to kill their host. Under selection pressure, the evolution of micro-organisms is vastly quicker that that of man. The selection pressure brought about by rapid ecological changes and alterations associated with human action provides for the development of new, dangerous pathogens and transformation of familiar pathogens to become more dangerous. Progress in molecular biology has thus far not yielded as many new tools for the treatment of infectious diseases as the hopes were in the early 2000's.

Rediscovering Acetate Metabolism: Its Potential Sources and Utilization for Biobased Transformation into Value-Added Chemicals.

PubMed

Lim, Hyun Gyu; Lee, Ji Hoon; Noh, Myung Hyun; Jung, Gyoo Yeol

2018-04-25

One of the great advantages of microbial fermentation is the capacity to convert various carbon compounds into value-added chemicals. In this regard, there have been many efforts to engineer microorganisms to facilitate utilization of abundant carbon sources. Recently, the potential of acetate as a feedstock has been discovered; efforts have been made to produce various biochemicals from acetate based on understanding of its metabolism. In this review, we discuss the potential sources of acetate and summarized the recent progress to improve acetate utilization with microorganisms. Furthermore, we also describe representative studies that engineered microorganisms for the production of biochemicals from acetate.

Using electrokinetic phenomena and electrical resistance tomography to characterize the movement of subsurface fluids

DOEpatents

Ramirez, Abelardo L.; Cooper, John F.; Daily, William D.

1996-01-01

This invention relates generally to the remote detections of subsurface liquid contaminants using in combination a geophysical technique known as ERT and an EKS. Electrokinetic transport is used to enhance the ability of electrical resistance tomography (ERT) to detect position and movement of subsurface contaminant liquids, particles or ions. ERT images alone are difficult to interpret because of natural inhomogeneities in soil composition and electrical properties. By subtracting two or more ERT images obtained before and after field induced movement, a high contrast image of a plume of distinct electrokinetic properties can be seen. The invention is applicable to important subsurface characterization problems including, as examples, (1) detection of liquid-saturated plumes of contaminants such as those associated with leaks from underground storage tanks containing hazardous concentrated electrolytes, (2) detection and characterization of soils contaminated with organic pollutants such as droplets of gasoline; and (3) monitoring the progress of electrokinetic containment or clean up of underground contamination.

Using electrokinetic phenomena and electrical resistance tomography to characterize the movement of subsurface fluids

DOEpatents

Ramirez, A.L.; Cooper, J.F.; Daily, W.D.

1996-02-27

This invention relates generally to the remote detections of subsurface liquid contaminants using in combination a geophysical technique known as ERT and an EKS. Electrokinetic transport is used to enhance the ability of electrical resistance tomography (ERT) to detect position and movement of subsurface contaminant liquids, particles or ions. ERT images alone are difficult to interpret because of natural inhomogeneities in soil composition and electrical properties. By subtracting two or more ERT images obtained before and after field induced movement, a high contrast image of a plume of distinct electrokinetic properties can be seen. The invention is applicable to important subsurface characterization problems including, as examples, (1) detection of liquid-saturated plumes of contaminants such as those associated with leaks from underground storage tanks containing hazardous concentrated electrolytes, (2) detection and characterization of soils contaminated with organic pollutants such as droplets of gasoline; and (3) monitoring the progress of electrokinetic containment or clean up of underground contamination. 1 fig.

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir

PubMed Central

Freedman, Adam J.E.; Tan, BoonFei

2017-01-01

Summary Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO2 reservoirs, which serve as analogs for the long‐term fate of sequestered scCO2, harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO2‐water separators at a natural scCO2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO2 and N2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. The existence of a microbial ecosystem associated with the McElmo Dome scCO2 reservoir indicates that potential impacts of the deep biosphere on CO2 fate and transport should be taken into consideration as a component of GCS planning and modelling. PMID:28229521

Subsurface metagenomes uncover a vast repertoire of hypervariable proteins encoded by genetic elements in uncultivated organisms and viruses

NASA Astrophysics Data System (ADS)

Paul, B. G.; Burstein, D.; Castelle, C. J.; Banfield, J. F.; Valentine, D. L.; Miller, J. F.; Ghosh, P.; Handa, S.; Arambula, D.; Czornyj, E.; Thomas, B. C.

2016-12-01

Uncultivated microorganisms primarily account for the remarkable diversity harbored in subsurface environments and represent an expansive subset of the current Tree of Life. Recent metagenomic efforts to investigate subsurface biomes have unveiled an array of bacterial and archaeal candidate phyla, whose members have minimal genomes and an apparent host-dependent existence. Still, little is known about the adaptive strategies that mediate host interactions in these organisms or their viruses. Genomic features known as diversity-generating retroelements (DGRs), which guide variability into targeted genes, were recently discovered in two single-cell genomes of uncultivated nanoarchaea, and independently in the genome of a marine virus from methane seep sediments. These prodigious drivers of protein hypervariability were first identified as the key force behind phage tail fiber diversification for binding different host receptors. Since their discovery, approximately 500 new DGRs have been found across a wide range of bacterial genomes representing various niches. We identified an unexpected 1136 distinct diversifiers from a single groundwater environment in reconstructed microbial genomes and genome fragments. The newly detected DGRs - predominantly linked to members of the candidate phyla radiation (CPR) - appear to target genes associated with cell-cell attachment, signaling, and transcription regulation. These findings suggest that targeted protein diversification may have an important role in regulating symbiotic or parasitic associations in groundwater microbiomes.

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir: Microbial life in the deep carbonated biosphere

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

Freedman, Adam J. E.; Tan, BoonFei; Thompson, Janelle R.

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected super-critical (sc) CO 2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO 2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO 2 harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO 2- water separators at a natural scCO 2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four membersmore » of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO 2 and N 2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. In conclusion, the existence of a microbial ecosystem associated with the McElmo Dome scCO 2 reservoir indicates that potential impacts of the deep biosphere on CO 2 fate and transport should be taken into consideration as a component of GCS planning and modelling.« less

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir: Microbial life in the deep carbonated biosphere

DOE PAGES

Freedman, Adam J. E.; Tan, BoonFei; Thompson, Janelle R.

2017-05-02

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected super-critical (sc) CO 2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO 2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO 2 harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO 2- water separators at a natural scCO 2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four membersmore » of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO 2 and N 2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. In conclusion, the existence of a microbial ecosystem associated with the McElmo Dome scCO 2 reservoir indicates that potential impacts of the deep biosphere on CO 2 fate and transport should be taken into consideration as a component of GCS planning and modelling.« less

Deep-Subsurface Marine Methane Hydrate Microbial Communities: Who's There and What Are They Doing?

NASA Astrophysics Data System (ADS)

Colwell, F.; Reed, D.; Fujita, Y.; Delwiche, M.; Blackwelder, D.; Uchida, T.; Fujii, T.; Lu, H.

2001-12-01

Natural gas hydrates are crystalline deposits of freshwater and primarily methane. They are estimated to represent a potentially vast reservoir of energy. Relatively little is known regarding microbial communities surrounding deep [>100 meters below sea floor (mbsf)] hydrate-bearing sediments. Deep sediment cores were collected in zones above, within, and below the hydrate bearing strata in an accretionary prism off the coast of Japan. Microorganisms were characterized using cultivation- and non-cultivation-based microbiological techniques to better understand the role that they play in the production and distribution of methane in gas hydrates. Direct counts show cell density at 105 cells/g throughout the hydrate strata. Lipid and 16S rDNA analyses indicate that diverse bacterial and archaeal microorganisms are represented throughout the strata. Acetate and hydrogen were utilized as an energy source for methane-producing microorganisms from each sediment depth. Although the methanogenic biomarker coenzyme M was not present above the detection limit in any of the samples, cloning and characterization of amplified 16S ribosomal RNA genes indicated the presence of methanogenic microorganisms related to the Methanobacteriales and Methanococcales. In addition, archaeal clones closely related to the hyperthermophilic Pyrodictiales were detected. Analysis of eubacterial clones indicated a more diverse eubacterial community compared to the archaea, including members from the groups of cyanobacteria, proteobacteria, gram positive bacteria, and flexibacter-cytophaga-bacteriodes. This study suggests that the diversity of microbial communities associated with the presence of methane in gas hydrate-rich deep marine sediments is greater than previously estimated.

Microbially Induced Calcite Precipitation (MICP) - A Technology for Managing Flow and Transport in Porous and Fractured Media

NASA Astrophysics Data System (ADS)

Phillips, A. J.; Hiebert, R.; Kirksey, J.; Lauchnor, E. G.; Rothman, A.; Spangler, L.; Esposito, R.; Gerlach, R.; Cunningham, A. B.

2014-12-01

Certain microorganisms e.g., Sporosarcina pasteurii contribute enzymes that catalyze reactions which in the presence of calcium, can create saturation conditions favorable for calcium carbonate precipitation (microbially-induced calcium carbonate precipitation (MICP)). MICP can be used for a number of engineering applications including securing geologic storage of CO2 or other fluids by sealing fractures, improving wellbore integrity, and stabilizing fractured and unstable porous media. MICP treatment has the advantage of the use of small microorganisms, ~2μm, suggesting applicability to treatment of small aperture fractures not accessible to traditional treatments, for example the use of fine cement. The promotion of MICP in the subsurface is a complex reactive transport problem coupling microbial, abiotic (geochemical), geomechanical and hydrodynamic processes. In the laboratory, MICP has been demonstrated to cement together heavily fractured shale and reduce the permeability of fractures in shale and sandstone cores up to five orders of magnitude under both ambient and subsurface relevant pressure conditions (Figure 1). Most recently, a MICP fracture treatment field study was performed at a well at the Southern Company Gorgas Steam Generation Plant (Alabama) (Figure 1). The Fayetteville Sandstone at approximately 1120' below ground surface was hydraulically fractured prior to MICP treatment. After 4 days of injection of 24 calcium pulses and 6 microbial inoculations, injectivity of brine into the formation was significantly reduced. The experiment also resulted in a reduction in pressure decay which is a measure of improved wellbore integrity. These promising results suggest the potential for MICP treatment to seal fractured pathways at the field scale to improve the long-term security of geologically-stored carbon dioxide or prevent leakage of shale gas or hydraulic fracturing fluids into functional overlying aquifers, reducing environmental impacts.

Resistance of Terrestrial Microbial Communities to Impack of Physical Conditinos of Subsurface Layers of Martian Regolith

NASA Astrophysics Data System (ADS)

Cheptsov, V. S.; Vorobyova, E. A.

2017-05-01

Currently, astrobiology is focused on Mars as one of the most perspective objects in the Solar System to search for microbial life. It was assumed that the putative biosphere of Mars could be cryopreserved and had been stored for billions of years in anabiotic state like microbial communities of Arctic and Antarctic permafrost deposits have been preserved till now for millions of years. In this case microbial cells should be not able to repair the damages or these processes have to be significantly depressed, and the main factor causing cell's death should be ionizing radiation. In a series of experiments we simulated the effects of combination of physical factors known as characteristics of the Martian regolith (and close to the space environment) on the natural microbial communities inhabiting xerophytic harsh habitats with extreme temperature conditions: polar permafrost and desert soils. The aim of the study was to examine the cumulative effect of factors (gamma radiation, low temperature, low pressure) to assess the possibility of metabolic reactions, and to find limits of the viability of natural microbial communities after exposure to the given conditions. It was found that microbial biomarkers could be reliably detected in soil samples after radiation dose accumulation up to 1 MGy (not further investigated) in combination with exposure to low temperature and low pressure. Resistance to extremely high doses of radiation in simulated conditions proves that if there was an Earth-like biosphere on the early Mars microorganisms could survive in the surface or subsurface layers of the Martian regolith for more than tens of millions of years after climate change. The study gives also some new grounds for the approval of transfer of viable microorganisms in space.

Reactive Oxygen Species are Ubiquitous along Subsurface Redox Gradients

NASA Astrophysics Data System (ADS)

Nico, P. S.; Yuan, X.; Davis, J. A.; Dwivedi, D.; Williams, K. H.; Bhattacharyya, A.; Fox, P. M.

2016-12-01

Reactive oxygen species (hydroxyl radical, superoxide, hydrogen peroxide, etc.) are known to be important intermediates in many biological and earth system processes. They have been particularly well studied in the realms of atmospheric chemistry and aquatic photochemistry. However, recently there is increasing evidence that they are also present in impactful quantities in dark systems as a result of both biotic and abiotic reactions. Herein we will present a complementary suite of laboratory and field studies examining the presence and production of hydrogen peroxide under relevant subsurface conditions. The laboratory work examines the redox cycling between reduced organic matter, molecular oxygen, and Fe which results in not only the production of hydrogen peroxide and oxidation of organic functional groups but also the maintenance of steady-state concentration of Fe(II) under fully oxygenated aqueous conditions. The field studies involve three distinct locations, namely a shallow subsurface aquifer, a hyporheic zone redox gradient across a river meander, and a hillside shale seep. In all cases detectable quantities (tens of nanomolar) of hydrogen peroxide were measured. In general, concentrations peak under transitional redox conditions where there is the simultaneous presence of reduced Fe, organic matter, and at least trace dissolved oxygen. Many, but not all, of the observed dynamics in hydrogen peroxide production can be reproduced by a simple kinetic model representing the reactions between Fe, organic matter, and molecular oxygen, but many questions remain regarding the role of microorganisms and other redox active chemical species in determining the detected hydrogen peroxide concentrations. The consistent detection of hydrogen peroxide at these disparate locations supports the hypothesis that hydrogen peroxide, and by extension, the entire suite of reactive oxygen species are ubiquitous along subsurface redox gradients.

Pacific Northwest Laboratory annual report for 1992 to the DOE Office of Energy Research

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

Grove, L.K.

1993-03-01

The 1992 Annual Report from Pacific Northwest Laboratory (PNL) to the US Department of Energy (DOE) describes research in environment and health conducted during fiscal year 1992. This report consists of four volumes oriented to particular segments of the PNL program, describing research performed for the DOE Office of Health and Environmental Research in the Office of Energy Research. The parts of the 1992 Annual Report are: Biomedical Sciences; Environmental Sciences; Atmospheric Sciences; and Physical Sciences. This Report is Part II: Environmental Sciences. Included in this report are developments in Subsurface Science, Terrestrial Science, Laboratory-Directed Research and Development, Interactions withmore » Educational Institutions, Technology Transfer, Publications, and Presentations. The research is directed toward developing a fundamental understanding of subsurface and terrestrial systems as a basis for both managing these critical resources and addressing environmental problems such as environmental restoration and global change. The Technology Transfer section of this report describes a number of examples in which fundamental research is laying the groundwork for the technology needed to resolve important environmental problems. The Interactions with Educational Institutions section of the report illustrates the results of a long-term, proactive program to make PNL facilities available for university and preuniversity education and to involve educational institutions in research programs. The areas under investigation include the effect of geochemical and physical phenomena on the diversity and function of microorganisms in deep subsurface environments, ways to address subsurface heterogeneity, and ways to determine the key biochemical and physiological pathways (and DNA markers) that control nutrient, water, and energy dynamics in arid ecosystems and the response of these systems to disturbance and climatic change.« less

Pacific Northwest Laboratory annual report for 1992 to the DOE Office of Energy Research. Part 2, Environmental sciences

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

Grove, L.K.; Wildung, R.E.

1993-03-01

The 1992 Annual Report from Pacific Northwest Laboratory (PNL) to the US Department of Energy (DOE) describes research in environment and health conducted during fiscal year 1992. This report consists of four volumes oriented to particular segments of the PNL program, describing research performed for the DOE Office of Health and Environmental Research in the Office of Energy Research. The parts of the 1992 Annual Report are: Biomedical Sciences; Environmental Sciences; Atmospheric Sciences; and Physical Sciences. This Report is Part 2: Environmental Sciences. Included in this report are developments in Subsurface Science, Terrestrial Science, Laboratory-Directed Research and Development, Interactions withmore » Educational Institutions, Technology Transfer, Publications, and Presentations. The research is directed toward developing a fundamental understanding of subsurface and terrestrial systems as a basis for both managing these critical resources and addressing environmental problems such as environmental restoration and global change. The Technology Transfer section of this report describes a number of examples in which fundamental research is laying the groundwork for the technology needed to resolve important environmental problems. The Interactions with Educational Institutions section of the report illustrates the results of a long-term, proactive program to make PNL facilities available for university and preuniversity education and to involve educational institutions in research programs. The areas under investigation include the effect of geochemical and physical phenomena on the diversity and function of microorganisms in deep subsurface environments, ways to address subsurface heterogeneity, and ways to determine the key biochemical and physiological pathways (and DNA markers) that control nutrient, water, and energy dynamics in arid ecosystems and the response of these systems to disturbance and climatic change.« less

Selective phylogenetic analysis targeting 16S rRNA genes of hyperthermophilic archaea in the deep-subsurface hot biosphere.

PubMed

Kimura, Hiroyuki; Ishibashi, Jun-Ichiro; Masuda, Harue; Kato, Kenji; Hanada, Satoshi

2007-04-01

International drilling projects for the study of microbial communities in the deep-subsurface hot biosphere have been expanded. Core samples obtained by deep drilling are commonly contaminated with mesophilic microorganisms in the drilling fluid, making it difficult to examine the microbial community by 16S rRNA gene clone library analysis. To eliminate mesophilic organism contamination, we previously developed a new method (selective phylogenetic analysis [SePA]) based on the strong correlation between the guanine-plus-cytosine (G+C) contents of the 16S rRNA genes and the optimal growth temperatures of prokaryotes, and we verified the method's effectiveness (H. Kimura, M. Sugihara, K. Kato, and S. Hanada, Appl. Environ. Microbiol. 72:21-27, 2006). In the present study we ascertained SePA's ability to eliminate contamination by archaeal rRNA genes, using deep-sea hydrothermal fluid (117 degrees C) and surface seawater (29.9 degrees C) as substitutes for deep-subsurface geothermal samples and drilling fluid, respectively. Archaeal 16S rRNA gene fragments, PCR amplified from the surface seawater, were denatured at 82 degrees C and completely digested with exonuclease I (Exo I), while gene fragments from the deep-sea hydrothermal fluid remained intact after denaturation at 84 degrees C because of their high G+C contents. An examination using mixtures of DNAs from the two environmental samples showed that denaturation at 84 degrees C and digestion with Exo I completely eliminated archaeal 16S rRNA genes from the surface seawater. Our method was quite useful for culture-independent community analysis of hyperthermophilic archaea in core samples recovered from deep-subsurface geothermal environments.

New Bio-Indicators for Long Term Natural Attenuation of Monoaromatic Compounds in Deep Terrestrial Aquifers.

PubMed

Aüllo, Thomas; Berlendis, Sabrina; Lascourrèges, Jean-François; Dessort, Daniel; Duclerc, Dominique; Saint-Laurent, Stéphanie; Schraauwers, Blandine; Mas, Johan; Patriarche, Delphine; Boesinger, Cécile; Magot, Michel; Ranchou-Peyruse, Anthony

2016-01-01

Deep subsurface aquifers despite difficult access, represent important water resources and, at the same time, are key locations for subsurface engineering activities for the oil and gas industries, geothermal energy, and CO2 or energy storage. Formation water originating from a 760 m-deep geological gas storage aquifer was sampled and microcosms were set up to test the biodegradation potential of BTEX by indigenous microorganisms. The microbial community diversity was studied using molecular approaches based on 16S rRNA genes. After a long incubation period, with several subcultures, a sulfate-reducing consortium composed of only two Desulfotomaculum populations was observed able to degrade benzene, toluene, and ethylbenzene, extending the number of hydrocarbonoclastic-related species among the Desulfotomaculum genus. Furthermore, we were able to couple specific carbon and hydrogen isotopic fractionation during benzene removal and the results obtained by dual compound specific isotope analysis (C = -2.4‰ ± 0.3‰; H = -57‰ ± 0.98‰; AKIEC: 1.0146 ± 0.0009, and AKIEH: 1.5184 ± 0.0283) were close to those obtained previously in sulfate-reducing conditions: this finding could confirm the existence of a common enzymatic reaction involving sulfate-reducers to activate benzene anaerobically. Although we cannot assign the role of each population of Desulfotomaculum in the mono-aromatic hydrocarbon degradation, this study suggests an important role of the genus Desulfotomaculum as potential biodegrader among indigenous populations in subsurface habitats. This community represents the simplest model of benzene-degrading anaerobes originating from the deepest subterranean settings ever described. As Desulfotomaculum species are often encountered in subsurface environments, this study provides some interesting results for assessing the natural response of these specific hydrologic systems in response to BTEX contamination during remediation projects.

Environmental Assessment for Selection and Operation of the Proposed Field Research Centers for the Natural and Accelerated Bioremediation Research (NABIR) Program

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

N /A

2000-04-18

The US Department of Energy (DOE) Office of Biological and Environmental Research (OBER), within the Office of Science (SC), proposes to add a Field Research Center (FRC) component to the existing Natural and Accelerated Bioremediation Research (NABIR) Program. The NABIR Program is a ten-year fundamental research program designed to increase the understanding of fundamental biogeochemical processes that would allow the use of bioremediation approaches for cleaning up DOE's contaminated legacy waste sites. An FRC would be integrated with the existing and future laboratory and field research and would provide a means of examining the fundamental biogeochemical processes that influence bioremediationmore » under controlled small-scale field conditions. The NABIR Program would continue to perform fundamental research that might lead to promising bioremediation technologies that could be demonstrated by other means in the future. For over 50 years, DOE and its predecessor agencies have been responsible for the research, design, and production of nuclear weapons, as well as other energy-related research and development efforts. DOE's weapons production and research activities generated hazardous, mixed, and radioactive waste products. Past disposal practices have led to the contamination of soils, sediments, and groundwater with complex and exotic mixtures of compounds. This contamination and its associated costs and risks represents a major concern to DOE and the public. The high costs, long duration, and technical challenges associated with remediating the subsurface contamination at DOE sites present a significant need for fundamental research in the biological, chemical, and physical sciences that will contribute to new and cost-effective solutions. One possible low-cost approach for remediating the subsurface contamination of DOE sites is through the use of a technology known as bioremediation. Bioremediation has been defined as the use of microorganisms to biodegrade or biotransform hazardous organic contaminants to environmentally safe levels in soils, subsurface materials, water, sludges, and residues.. While bioremediation technology is promising, DOE managers and non-DOE scientists have recognized that the fundamental scientific information needed to develop effective bioremediation technologies for cleanup of the legacy waste sites is lacking in many cases. DOE believes that field-based research is needed to realize the full potential of bioremediation. The Department of Energy faces a unique set of challenges associated with cleaning up waste at its former weapons production and research sites. These sites contain complex mixtures of contaminants in the subsurface, including radioactive compounds. In many cases, the fundamental field-based scientific information needed to develop safe and effective remediation and cleanup technologies is lacking. DOE needs fundamental research on the use of microorganisms and their products to assist DOE in the decontamination and cleanup of its legacy waste sites. The existing NABIR program to-date has focused on fundamental scientific research in the laboratory. Because subsurface hydrologic and geologic conditions at contaminated DOE sites cannot easily be duplicated in a laboratory, however, the DOE needs a field component to permit existing and future laboratory research results to be field-tested on a small scale in a controlled outdoor setting. Such field-testing needs to be conducted under actual legacy waste field conditions representative of those that DOE is most in need of remediating. Ideally, these field conditions should be as representative as practicable of the types of subsurface contamination conditions that resulted from legacy wastes from the nuclear weapons program activities. They should also be representative of the types of hydrologic and geologic conditions that exist across the DOE complex.« less

Hydrogeology and human health

USDA-ARS?s Scientific Manuscript database

Over the past 50 years, significant progress has been made in improving our understanding of the extent and potential consequences of groundwater contamination, with research advancing on several fronts including groundwater sampling methods, laboratory detection methods, subsurface transport (and m...

The thermal impact of subsurface building structures on urban groundwater resources - A paradigmatic example.

PubMed

Epting, Jannis; Scheidler, Stefan; Affolter, Annette; Borer, Paul; Mueller, Matthias H; Egli, Lukas; García-Gil, Alejandro; Huggenberger, Peter

2017-10-15

Shallow subsurface thermal regimes in urban areas are increasingly impacted by anthropogenic activities, which include infrastructure development like underground traffic lines as well as industrial and residential subsurface buildings. In combination with the progressive use of shallow geothermal energy systems, this results in the so-called subsurface urban heat island effect. This article emphasizes the importance of considering the thermal impact of subsurface structures, which commonly is underestimated due to missing information and of reliable subsurface temperature data. Based on synthetic heat-transport models different settings of the urban environment were investigated, including: (1) hydraulic gradients and conductivities, which result in different groundwater flow velocities; (2) aquifer properties like groundwater thickness to aquitard and depth to water table; and (3) constructional features, such as building depths and thermal properties of building structures. Our results demonstrate that with rising groundwater flow velocities, the heat-load from building structures increase, whereas down-gradient groundwater temperatures decrease. Thermal impacts on subsurface resources therefore have to be related to the permeability of aquifers and hydraulic boundary conditions. In regard to the urban settings of Basel, Switzerland, flow velocities of around 1 md -1 delineate a marker where either down-gradient temperature deviations or heat-loads into the subsurface are more relevant. Furthermore, no direct thermal influence on groundwater resources should be expected for aquifers with groundwater thicknesses larger 10m and when the distance of the building structure to the groundwater table is higher than around 10m. We demonstrate that measuring temperature changes down-gradient of subsurface structures is insufficient overall to assess thermal impacts, particularly in urban areas. Moreover, in areas which are densely urbanized, and where groundwater flow velocities are low, appropriate measures for assessing thermal impacts should specifically include a quantification of heat-loads into the subsurface which result in a more diffuse thermal contamination of urban groundwater resources. Copyright © 2017 Elsevier B.V. All rights reserved.

Single cell genomic study of Dehalococcoidites in deep sea sediments of Peru Margin 1230

NASA Astrophysics Data System (ADS)

Kaster, A.; Meyer-Blackwell, K.; Spormann, A. M.

2013-12-01

Dehalogenating Chloroflexi, such as Dehalococcoidites Dhc were originally discovered as the key microorganisms mediating reductive dehalogenation of the prevalent groundwater contaminants tetrachloroethene and trichloroethene. Molecular and genomic studies on their key enzymes for energy conservation, reductive dehalogenases rdh, have provided evidence for ubiquitous horizontal gene transfer. A pioneering study by Futagami et al. discovered novel putative rdh phylotypes in sediments from the Pacific, revealing an unknown and surprising abundance of rdh genes in pristine habitats. The frequent detection of Dhc-related 16S rRNA genes from these environments implied the occurrence of dissimilatory dehalorespiration in marine subsurface sediments, however, pristine Dhc could never be linked to this activity. Despite being ubiquitous in those environments, metabolic life style or ecological function of Dhc in the absence of anthropogenic contaminants is still completely unknown. We therefore analyzed a non-contaminated deep sea sediment sample of the Peru Margin 1230 site by a single cell genomic (SGC) approach. We present for the first time data on three single Dhc cells, helping to elucidate their role in the poorly understood oligotrophic marine sub-surface environment.

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

Brownlow, D.T.; Escude, S.; Johanneson, O.H.

The 1500 Area at Kelly Air Force Base (AFB) was the site of a subsurface release of approximately 1,000 gallons of JP-4 jet fuel. Preliminary studies found evidence of hydrocarbon contamination extending from 10 feet below ground surface (bgs) down to the shallow water table, at 20 to 25 feet bgs. In June of 1993, Kelly AFB authorized the installation and evaluation of a bioventing system at this site to aid in the cleanup of the hydrocarbon contaminated soils. The purpose of the bioventing system is to aerate subsurface soils within and immediately surrounding the release area, in order tomore » stimulate in-situ biological activity and enhance the natural bioremediation capacity of the soil. Augmenting oxygen to the indigenous soil microorganisms promotes the aerobic metabolism of fuel hydrocarbons in the soil. In vadose zone soils exhibiting relatively good permeability, bioventing has proven to be a highly cost effective remediation technology for treating fuel contaminated soils. In November, 1993, a Start-Up Test program consisting of an In-Situ Respiration Test (ISRT) and an Air Permeability Test was performed at the 1500 Area Spill Site.« less

Method of degrading pollutants in soil

DOEpatents

Hazen, Terry C.; Lopez-De-Victoria, Geralyne

1994-01-01

A method and system for enhancing the motility of microorganisms by placing an effective amount of chlorinated hydrocarbons, preferably chlorinated alkenes, and most preferably trichloroethylene in spaced relation to the microbes so that the surprisingly strong, monomodal, chemotactic response of the chlorinated hydrocarbon on subsurface microbes can draw the microbes away from or towards and into a substance, as desired. In remediation of groundwater pollution, for example, TCE can be injected into the plume to increase the population of microbes at the plume whereby the plume can be more quickly degraded. A TCE-degrading microbe, such as Welchia alkenophilia, can be used to degrade the TCE following the degradation of the original pollutant.

Subsurface site conditions and geology in the San Fernando earthquake area

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

Duke, C.M.; Johnson, J.A.; Kharraz, Y.

1971-12-01

The report presents the progress to date in establishing the facts about dynamic subsurface properties and geological features in the area affected by the San Fernando earthquake of February 9, 1971. Special emphasis is given to the locations of accelerographs, seismoscopes and Seismological Field Survey aftershock instruments. Thirty shallow geophysical surveys were made for determination of S and P velocities, with damping measured at some sites. Deep velocity data were obtained from geophysical surveys by others. Soil Mechanics and water well borings by others were utilized. Published and ongoing geological studies were applied. Results are presented in the form ofmore » five geological cross-sections, nine subsurface exploration models extending through basement complex to depths of 14,000 feet, a general geologic map, the shallow geophysical surveys, and selected data on damping.« less

Host-microbe interactions in distal airways: relevance to chronic airway diseases.

PubMed

Martin, Clémence; Burgel, Pierre-Régis; Lepage, Patricia; Andréjak, Claire; de Blic, Jacques; Bourdin, Arnaud; Brouard, Jacques; Chanez, Pascal; Dalphin, Jean-Charles; Deslée, Gaetan; Deschildre, Antoine; Gosset, Philippe; Touqui, Lhousseine; Dusser, Daniel

2015-03-01

This article is the summary of a workshop, which took place in November 2013, on the roles of microorganisms in chronic respiratory diseases. Until recently, it was assumed that lower airways were sterile in healthy individuals. However, it has long been acknowledged that microorganisms could be identified in distal airway secretions from patients with various respiratory diseases, including cystic fibrosis (CF) and non-CF bronchiectasis, chronic obstructive pulmonary disease, asthma and other chronic airway diseases (e.g. post-transplantation bronchiolitis obliterans). These microorganisms were sometimes considered as infectious agents that triggered host immune responses and contributed to disease onset and/or progression; alternatively, microorganisms were often considered as colonisers, which were considered unlikely to play roles in disease pathophysiology. These concepts were developed at a time when the identification of microorganisms relied on culture-based methods. Importantly, the majority of microorganisms cannot be cultured using conventional methods, and the use of novel culture-independent methods that rely on the identification of microorganism genomes has revealed that healthy distal airways display a complex flora called the airway microbiota. The present article reviews some aspects of current literature on host-microbe (mostly bacteria and viruses) interactions in healthy and diseased airways, with a special focus on distal airways. Copyright ©ERS 2015.

Anaerobic ethylene glycol degradation by microorganisms in poplar and willow rhizospheres.

PubMed

Carnegie, D; Ramsay, J A

2009-07-01

Although aerobic degradation of ethylene glycol is well documented, only anaerobic biodegradation via methanogenesis or fermentation has been clearly shown. Enhanced ethylene glycol degradation has been demonstrated by microorganisms in the rhizosphere of shallow-rooted plants such as alfalfa and grasses where conditions may be aerobic, but has not been demonstrated in the deeper rhizosphere of poplar or willow trees where conditions are more likely to be anaerobic. This study evaluated ethylene glycol degradation under nitrate-, and sulphate-reducing conditions by microorganisms from the rhizosphere of poplar and willow trees planted in the path of a groundwater plume containing up to 1.9 mol l(-1) (120 g l(-1)) ethylene glycol and, the effect of fertilizer addition when nitrate or sulphate was provided as a terminal electron acceptor (TEA). Microorganisms in these rhizosphere soils degraded ethylene glycol using nitrate or sulphate as TEAs at close to the theoretical stoichiometric amounts required for mineralization. Although the added nitrate or sulphate was primarily used as TEA, TEAs naturally present in the soil or CO(2) produced from ethylene glycol degradation were also used, demonstrating multiple TEA usage. Anaerobic degradation produced acetaldehyde, less acetic acid, and more ethanol than under aerobic conditions. Although aerobic degradation rates were faster, close to 100% disappearance was eventually achieved anaerobically. Degradation rates under nitrate-reducing conditions were enhanced upon fertilizer addition to achieve rates similar to aerobic degradation with up to 19.3 mmol (1.20 g) of ethylene glycol degradation l(-1) day(-1) in poplar soils. This is the first study to demonstrate that microorganisms in the rhizosphere of deep rooted trees like willow and poplar can anaerobically degrade ethylene glycol. Since anaerobic biodegradation may significantly contribute to the phytoremediation of ethylene glycol in the deeper subsurface, the need for "pump and treat" or an aerobic treatment would be eliminated, hence reducing the cost of treatment.

Subsurface-channeling-like energy loss structure of the skipping motion on an ionic crystal.

PubMed

Villette, J; Borisov, A G; Khemliche, H; Momeni, A; Roncin, P

2000-10-09

The skipping motion of Ne+ ions in grazing scattering from the LiF(001) surface is studied for velocity below 0.1 a.u. with a time-of-flight technique. It is demonstrated that suppression of electronic excitation and dominance of optical phonon excitation in the projectile stopping results in an odd 1,3,5,... progression of the energy loss peaks, a feature usually ascribed to subsurface channeling. The experimental findings are well reproduced by parameter-free model calculations where thermal vibrations are the dominant cause for the ion trapping and detrapping.

PERMEABLE REACTIVE BARRIERS FOR REMEDIATION OF INORGANIC CONTAMINANTS

EPA Science Inventory

The permeable reactive barrier (PRB) technology is an in-situ approach for groundwater remediation that couples subsurface flow management with a passive chemical or biochemical treatment zone. The development and application of the PRB technology has progressed over the last de...

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...

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.

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir.

PubMed

Freedman, Adam J E; Tan, BoonFei; Thompson, Janelle R

2017-06-01

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO 2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO 2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO 2 , harbor a 'deep carbonated biosphere' with carbon cycling potential. We sampled subsurface fluids from scCO 2 -water separators at a natural scCO 2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO 2 and N 2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. The existence of a microbial ecosystem associated with the McElmo Dome scCO 2 reservoir indicates that potential impacts of the deep biosphere on CO 2 fate and transport should be taken into consideration as a component of GCS planning and modelling. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Application of rumen microorganisms for anaerobic bioconversion of lignocellulosic biomass.

PubMed

Yue, Zheng-Bo; Li, Wen-Wei; Yu, Han-Qing

2013-01-01

Rumen in the mammalian animals is a natural cellulose-degrading system and the microorganisms inside have been found to be able to effectively digest lignocellulosic biomass. Furthermore, methane or volatile fatty acids, which could be further converted to other biofuels, are the two major products in such a system. This paper offers an overview of recent development in the application of rumen microorganisms for lignocellulosic biomass conversion. Application of recent molecular tools in the analysis of rumen microbial community, progress in the development of artificial rumen reactors, the latest research results about characterizing rumen-dominated anaerobic digestion process and energy products are summarized. Also, the potential application of such a rumen-dominated process is discussed. Copyright © 2012 Elsevier Ltd. All rights reserved.

Contamination and restoration of groundwater aquifers.

PubMed Central

Piver, W T

1993-01-01

Humans are exposed to chemicals in contaminated groundwaters that are used as sources of drinking water. Chemicals contaminate groundwater resources as a result of waste disposal methods for toxic chemicals, overuse of agricultural chemicals, and leakage of chemicals into the subsurface from buried tanks used to hold fluid chemicals and fuels. In the process, both the solid portions of the subsurface and the groundwaters that flow through these porous structures have become contaminated. Restoring these aquifers and minimizing human exposure to the parent chemicals and their degradation products will require the identification of suitable biomarkers of human exposure; better understandings of how exposure can be related to disease outcome; better understandings of mechanisms of transport of pollutants in the heterogeneous structures of the subsurface; and field testing and evaluation of methods proposed to restore and cleanup contaminated aquifers. In this review, progress in these many different but related activities is presented. PMID:8354172

Modeling Vertical Flow Treatment Wetland Hydraulics to Optimize Treatment Efficiency

DTIC Science & Technology

2011-03-24

ammonia, such as landfill leachate and food processing wastes (Kadlec and Wallace, 2009). Figure 2: Typical Horizontal Subsurface Flow Treatment...51(9): 165-171, 2005. Williams, J.B. Phytoremediation in wetland ecosystems: Progress, problems, and potential. Critical Reviews in Plant Sciences

Isoprenoid quinones resolve the stratification of microbial redox processes in a biogeochemical continuum from the photic zone to deep anoxic sediments of the Black Sea.

PubMed

Becker, Kevin W; Elling, Felix J; Schröder, Jan M; Lipp, Julius S; Goldhammer, Tobias; Zabel, Matthias; Elvert, Marcus; Overmann, Jörg; Hinrichs, Kai-Uwe

2018-03-09

The stratified water column of the Black Sea serves as a model ecosystem for studying the interactions of microorganisms with major biogeochemical cycles. Here we provide detailed analysis of isoprenoid quinones to study microbial redox processes in the ocean. In a continuum from the photic zone through the chemocline into deep anoxic sediments of the southern Black Sea, diagnostic quinones and inorganic geochemical parameters indicate niche segregation between redox processes and corresponding shifts in microbial community composition. Quinones specific for oxygenic photosynthesis and aerobic respiration dominate oxic waters, while quinones associated with thaumarchaeal ammonia-oxidation and bacterial methanotrophy, respectively, dominate a narrow interval in suboxic waters. Quinone distributions indicate highest metabolic diversity within the anoxic zone, with anoxygenic photosynthesis being a major process in its photic layer. In the dark anoxic layer, quinone profiles indicate occurrence of bacterial sulfur and nitrogen cycling, archaeal methanogenesis, and archaeal methanotrophy. Multiple novel ubiquinone isomers, possibly originating from unidentified intra-aerobic anaerobes, occur in this zone. The respiration modes found in the anoxic zone continue into shallow subsurface sediments, but quinone abundances rapidly decrease within the upper 50 cm below sea floor, reflecting the transition to lower energy availability. In the deep subseafloor sediments, quinone distributions and geochemical profiles indicate archaeal methanogenesis/methanotrophy and potentially bacterial fermentative metabolisms. We observed that sedimentary quinone distributions track lithology, which supports prior hypotheses that deep biosphere community composition and metabolisms are determined by environmental conditions during sediment deposition. Importance Microorganisms play crucial roles in global biogeochemical cycles. Yet, we have only a fragmentary understanding of the diversity of microorganisms and their metabolisms, as the majority remains uncultured. Thus, culture-independent approaches are critical for determining microbial diversity and active metabolic processes. In order to resolve the stratification of microbial communities in the Black Sea, we comprehensively analyzed redox process-specific isoprenoid quinone biomarkers in a unique continuous record from the photic zone through the chemocline into anoxic subsurface sediments. We describe an unprecedented quinone diversity that allowed us to detect distinct biogeochemical processes including oxygenic photosynthesis, archaeal ammonia oxidation, aerobic methanotrophy and anoxygenic photosynthesis in defined geochemical zones. Copyright © 2018 American Society for Microbiology.

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.

Impact of CO 2 on the Evolution of Microbial Communities Exposed to Carbon Storage Conditions, Enhanced Oil Recovery, and CO 2 Leakage

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

Gulliver, Djuna; Gregory, Kelvin B.; Lowry, Gregorgy V.

Geologic carbon storage (GCS) is a crucial part of a proposed mitigation strategy to reduce the anthropogenic carbon dioxide (CO 2) emissions to the atmosphere. During this process, CO 2 is injected as super critical carbon dioxide (SC-CO 2) in confined deep subsurface storage units, such as saline aquifers and depleted oil reservoirs. The deposition of vast amounts of CO 2 in subsurface geologic formations could unintentionally lead to CO 2 leakage into overlying freshwater aquifers. Introduction of CO 2 into these subsurface environments will greatly increase the CO 22 concentration and will create CO 2 concentration gradients that drivemore » changes in the microbial communities present. While it is expected that altered microbial communities will impact the biogeochemistry of the subsurface, there is no information available on how CO 2 gradients will impact these communities. The overarching goal of this project is to understand how CO 2 exposure will impact subsurface microbial communities at temperatures and pressures that are relevant to GCS and CO 2 leakage scenarios. To meet this goal, unfiltered, aqueous samples from a deep saline aquifer, a depleted oil reservoir, and a fresh water aquifer were exposed to varied concentrations of CO 2 at reservoir pressure and temperature. The microbial ecology of the samples was examined using molecular, DNA-based techniques. The results from these studies were also compared across the sites to determine any existing trends. Results reveal that increasing CO 2 leads to decreased DNA concentrations regardless of the site, suggesting that microbial processes will be significantly hindered or absent nearest the CO 2 injection/leakage plume where CO 2 concentrations are highest. At CO 2 exposures expected downgradient from the CO 2 plume, selected microorganisms emerged as dominant in the CO 2 exposed conditions. Results suggest that the altered microbial community was site specific and highly dependent on pH. The site-dependent results suggest a limited ability to predict the emerging dominant species for other CO 2 exposed environments. This study improves the understanding of how a subsurface microbial community may respond to conditions expected from GCS and CO 2 leakage. This is the first step for understanding how a CO 2-altered microbial community may impact injectivity, permanence of stored CO 2, and subsurface water quality. Future work with microbial communities from new subsurface sites would increase the current understanding of this project. Additionally, incorporation of metagenomic methods would increase understanding of potential microbial processes that may be prevalent in CO 2 exposed environments.« less

Impact of CO 2 on the Evolution of Microbial Communities Exposed to Carbon Storage Conditions, Enhanced Oil Recovery, and CO 2 Leakage

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

Gulliver, Djuna M.; Gregory, Kelvin B.; Lowry, Gregory V.

Geologic carbon storage (GCS) is a crucial part of a proposed mitigation strategy to reduce the anthropogenic carbon dioxide (CO 2) emissions to the atmosphere. During this process, CO 2 is injected as super critical carbon dioxide (SC-CO 2) in confined deep subsurface storage units, such as saline aquifers and depleted oil reservoirs. The deposition of vast amounts of CO 2 in subsurface geologic formations could unintentionally lead to CO 2 leakage into overlying freshwater aquifers. Introduction of CO 2 into these subsurface environments will greatly increase the CO 2 concentration and will create CO 2 concentration gradients that drivemore » changes in the microbial communities present. While it is expected that altered microbial communities will impact the biogeochemistry of the subsurface, there is no information available on how CO 2 gradients will impact these communities. The overarching goal of this project is to understand how CO 2 exposure will impact subsurface microbial communities at temperatures and pressures that are relevant to GCS and CO 2 leakage scenarios. To meet this goal, unfiltered, aqueous samples from a deep saline aquifer, a depleted oil reservoir, and a fresh water aquifer were exposed to varied concentrations of CO 2 at reservoir pressure and temperature. The microbial ecology of the samples was examined using molecular, DNA-based techniques. The results from these studies were also compared across the sites to determine any existing trends. Results reveal that increasing CO 2 leads to decreased DNA concentrations regardless of the site, suggesting that microbial processes will be significantly hindered or absent nearest the CO 2 injection/leakage plume where CO 2 concentrations are highest. At CO 2 exposures expected downgradient from the CO 2 plume, selected microorganisms emerged as dominant in the CO 2 exposed conditions. Results suggest that the altered microbial community was site specific and highly dependent on pH. The site-dependent results suggest a limited ability to predict the emerging dominant species for other CO 2-exposed environments. This study improves the understanding of how a subsurface microbial community may respond to conditions expected from GCS and CO 2 leakage. This is the first step for understanding how a CO 2-altered microbial community may impact injectivity, permanence of stored CO 2, and subsurface water quality. Future work with microbial communities from new subsurface sites would increase the current understanding of this project. Additionally, incorporation of metagenomic methods would increase understanding of potential microbial processes that may be prevalent in CO 2 exposed environments.« less

Quantification of microbial activity in subsurface environments using a hydrogenase enzyme assay

NASA Astrophysics Data System (ADS)

Adhikari, R. R.; Nickel, J.; Kallmeyer, J.

2012-04-01

The subsurface biosphere is the largest microbial ecosystem on Earth. Despite its large size and extensive industrial exploitation, very little is known about the role of microbial activity in the subsurface. Subsurface microbial activity plays a fundamental role in geochemical cycles of carbon and other biologically important elements. How the indigenous microbial communities are supplied with energy is one of the most fundamental questions in subsurface research. It is still an enigma how these communities can survive with such recalcitrant carbon over geological time scales. Despite its usually very low concentration, hydrogen is an important element in subsurface environments. Heterotrophic and chemoautotrophic microorganisms use hydrogen in their metabolic pathways; they either obtain protons from the radiolysis of water and/or cleavage of hydrogen generated by the alteration of basaltic crust, or they dispose of protons by formation of water. Hydrogenase (H2ase) is a ubiquitous intracellular enzyme that catalyzes the interconversion of molecular hydrogen and/or water into protons and electrons. The protons are used for the synthesis of ATP, thereby coupling energy-generating metabolic processes to electron acceptors such as carbon dioxide or sulfate. H2ase activity can therefore be used as a measure for total microbial activity as it targets a key metabolic compound rather than a specific turnover process. Using a highly sensitive tritium assay we measured H2ase enzyme activity in the organic-rich sediments of Lake Van, a saline, alkaline lake in eastern Turkey and in marine subsurface sediments of the Barents Sea. Additionally, sulfate reduction rates (SRRs) were measured to compare the results of the H2ase enzyme assay with the quantitatively most important electron acceptor process. H2ase activity was found at all sites, measured values and distribution of activity varied widely with depth and between sites. At the Lake Van sites H2ase activity ranged from ca. 20 mmol H2 cm-3 d-1 close to the sediment-water interface to 0.5 mmol H2 cm-3 d-1 at a depth of 0.8 m. In samples from the Barents Sea H2ase activity ranged between 0.1 to 2.5 mmol H2 cm-3 d-1 down to a depth of 1.60 m. At all sites the SRR profile followed the H2ase activity profile until SRR declined to values close to the minimum detection limit (~10 pmol cm-3 d-1). H2ase activity increased again after SRR declined, indicating that other microbial processes are becoming quantitatively more important. The H2ase and SRR data show that our assay has a potential to become a valuable tool to measure total subsurface microbial activity.

Monitoring microbial growth and activity using spectral induced polarization and low-field nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Zhang, Chi; Keating, Kristina; Revil, Andre

2015-04-01

Microbes and microbial activities in the Earth's subsurface play a significant role in shaping subsurface environments and are involved in environmental applications such as remediation of contaminants in groundwater and oil fields biodegradation. Stimulated microbial growth in such applications could cause wide variety of changes of physical/chemical properties in the subsurface. It is critical to monitor and determine the fate and transportation of microorganisms in the subsurface during such applications. Recent geophysical studies demonstrate the potential of two innovative techniques, spectral induced polarization (SIP) and low-field nuclear magnetic resonance (NMR), for monitoring microbial growth and activities in porous media. The SIP measures complex dielectric properties of porous media at low frequencies of exciting electric field, and NMR studies the porous structure of geologic media and characterizes fluids subsurface. In this laboratory study, we examined both SIP and NMR responses from bacterial growth suspension as well as suspension mixed with silica sands. We focus on the direct contribution of microbes to the SIP and NMR signals in the absence of biofilm formation or biomineralization. We used Zymomonas mobilis and Shewanella oneidensis (MR-1) for SIP and NMR measurements, respectively. The SIP measurements were collected over the frequency range of 0.1 - 1 kHz on Z. mobilis growth suspension and suspension saturated sands at different cell densities. SIP data show two distinct peaks in imaginary conductivity spectra, and both imaginary and real conductivities increased as microbial density increased. NMR data were collected using both CPMG pulse sequence and D-T2 mapping to determine the T2-distribution and diffusion properties on S. oneidensis suspension, pellets (live and dead), and suspension mixed with silica sands. NMR data show a decrease in the T2-distribution in S. oneidensis suspension saturated sands as microbial density increase. A clear distinction in the T2-distribution and D-T2 plots between live and dead cell pellets was also observed. These results will provide a basis for understanding the effect of microbes within geologic media on SIP and low-field NMR measurements. This research suggests that both SIP and NMR have the potential to monitor microbial growth and activities in the subsurface and could provide spatiotemporal variations in bacterial abundance in porous media.

Textiles for protection against microorganism

NASA Astrophysics Data System (ADS)

Sauperl, O.

2016-04-01

Concerning micro-organisms such as bacteria, viruses and fungi, there is a huge progress in the development of textile materials and procedures which should effectively protect against these various pathogens. In this sense there is especially problematic hospital environment, where it is necessary to take into account properly designed textile material which, when good selected and composed, act as a good barrier against transfer of micro-organisms through material mainly in its wet state. Respect to this it is necessary to be familiar with the rules regarding selection of the input material, the choice of proper yarn construction, the choice of the proper weaving mode, the rules regarding selection of antimicrobial-active compound suitable for (eco-friendly) treatment, and the choice of the most appropriate test method by which it is possible objectively to conclude on the reduction of selected microorganism. As is well known, fabrics are three-dimensional structures with void and non-void areas. Therefore, the physical-chemical properties of the textile material/fabric, the surface characteristics together with the shape of microorganism, and the carriers' characteristics contribute to control the transfer of microorganism through textile material. Therefore, careful planning of textile materials and treatment procedure with the compound which is able to reduce micro-organism satisfactory is particularly important, especially due to the fact that in hospital environment population with impaired immune system is mainly presented.

Microbial production and oxidation of methane in deep subsurface

NASA Astrophysics Data System (ADS)

Kotelnikova, Svetlana

2002-10-01

The goal of this review is to summarize present studies on microbial production and oxidation of methane in the deep subterranean environments. Methane is a long-living gas causing the "greenhouse" effect in the planet's atmosphere. Earlier, the deep "organic carbon poor" subsurface was not considered as a source of "biogenic" methane. Evidence of active methanogenesis and presence of viable methanogens including autotrophic organisms were obtained for some subsurface environments including water-flooded oil-fields, deep sandy aquifers, deep sea hydrothermal vents, the deep sediments and granitic groundwater at depths of 10 to 2000 m below sea level. As a rule, the deep subterranean microbial populations dwell at more or less oligotrophic conditions. Molecular hydrogen has been found in a variety of subsurface environments, where its concentrations were significantly higher than in the tested surface aquatic environments. Chemolithoautotrophic microorganisms from deep aquifers that could grow on hydrogen and carbon dioxide can act as primary producers of organic carbon, initiating heterotrophic food chains in the deep subterranean environments independent of photosynthesis. "Biogenic" methane has been found all over the world. On the basis of documented occurrences, gases in reservoirs and older sediments are similar and have the isotopic character of methane derived from CO 2 reduction. Groundwater representing the methanogenic end member are characterized by a relative depletion of dissolved organic carbon (DOC) in combination with an enrichment in 13C in inorganic carbon, which is consistent with the preferential reduction of 12CO 2 by autotrophic methanogens or acetogens. The isotopic composition of methane formed via CO 2 reduction is controlled by the δ13C of the original CO 2 substrate. Literature data shows that CH 4 as heavy as -40‰ or -50‰ can be produced by the microbial reduction of isotopically heavy CO 2. Produced methane may be oxidized microbially to carbon dioxide. Microbial methane oxidation is a biogeochemical process that limits the release of methane, a greenhouse gas from anaerobic environments. Anaerobic methane oxidation plays an important role in marine sediments. Similar processes may take place in deep subsurface and thus fuel the deep microbial community. Organisms or consortia responsible for anaerobic methane oxidation have not yet been cultured, although diverse aerobic methanotrophs have been isolated from a variety of underground niches. The presence of aerobic methanotrophs in the anoxic subsurface remains to be explained. The presence of methane in the deep subsurface have been shown all over the world. The flux of gases between the deep subsurface and the atmosphere is driven by the concentration gradient from depth to the atmosphere. However, methane is consumed by methanotrophs on the way of its evolution in oxidized environments and is transformed to organic form, available for further microbial processing. When the impact of subsurface environments to global warming is estimated, it is necessary to take into account the activity of methane-producing Archaea and methane-oxidizing biofilters in groundwater. Microbial production and oxidation of methane is involved in the carbon cycle in the deep subsurface environments.

Discrete Fracture Network Modeling and Simulation of Subsurface Transport for the Topopah Springs and Lava Flow Aquifers at Pahute Mesa, FY 15 Progress Report

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

Makedonska, Nataliia; Kwicklis, Edward Michael; Birdsell, Kay Hanson

This progress report for fiscal year 2015 (FY15) describes the development of discrete fracture network (DFN) models for Pahute Mesa. DFN models will be used to upscale parameters for simulations of subsurface flow and transport in fractured media in Pahute Mesa. The research focuses on modeling of groundwater flow and contaminant transport using DFNs generated according to fracture characteristics observed in the Topopah Spring Aquifer (TSA) and the Lava Flow Aquifer (LFA). This work will improve the representation of radionuclide transport processes in large-scale, regulatory-focused models with a view to reduce pessimistic bounding approximations and provide more realistic contaminant boundarymore » calculations that can be used to describe the future extent of contaminated groundwater. Our goal is to refine a modeling approach that can translate parameters to larger-scale models that account for local-scale flow and transport processes, which tend to attenuate migration.« less

Time-Distance Helioseismology

NASA Technical Reports Server (NTRS)

Duvall, Thomas L., Jr.

2010-01-01

Time-distance helioseismology is a method of ambient noise imaging using the solar oscillations. The basic realization that led to time-distance helioseismology was that the temporal cross correlation of the signals at two 'surface' (or photospheric) locations should show a feature at the time lag corresponding to the subsurface travel time between the locations. The temporal cross correlation, as a function of the location separation, is the Fourier transform of the spatio-temporal power spectrum of the solar oscillations, a commonly used function in helioseismology. It is therefore likely the characteristic ridge structure of the correlation function had been seen before without appreciation of its significance. Travel times are measured from the cross correlations. The times are sensitive to a number of important subsurface solar phenomena. These include sound speed variations, flows, and magnetic fields. There has been much interesting progress in the 17 years since the first paper on this subject (Duvall et al., Nature, 1993, 362, 430-432). This progress will be reviewed in this paper.

JPRS Report, Soviet Union KOMMUNIST No 8, May 1987.

DTIC Science & Technology

1987-09-08

degrees and chemical pollution at close to maximally admissible concentrations, fish and microorganism can survive; their combined effect, however, is... can preserve and increase the humanistic values of civilization and display historical initiatives in the main areas of social progress. Broad...future, we can proper answer the challenge of the time and so that socialist society indeed become the embodiment of everything that is progressive and

Regolith Volatile Recovery at Simulated Lunar Environments

NASA Technical Reports Server (NTRS)

Kleinhenz, Julie; Paulsen, Gale; Zacny, Kris; Schmidt, Sherry; Boucher, Dale

2016-01-01

Lunar Polar Volatiles: Permanently shadowed craters at the lunar poles contain water, 5 wt according to LCROSS. Interest in water for ISRU applications. Desire to ground truth water using surface prospecting e.g. Resource Prospector and RESOLVE. How to access subsurface water resources and accurately measure quantity. Excavation operations and exposure to lunar environment may affect the results. Volatile capture tests: A series a ground based dirty thermal vacuum tests are being conducted to better understand the subsurface sampling operations. Sample removal and transfer. Volatiles loss during sampling operations. Concept of operations, Instrumentation. This presentation is a progress report on volatiles capture results from these tests with lunar polar drill prototype hardware.

Method of degrading pollutants in soil

DOEpatents

Hazen, T.C.; Lopez-De-Victoria, G.

1994-07-05

Disclosed are a method and system for enhancing the motility of microorganisms. This is accomplished by placing an effective amount of chlorinated hydrocarbons, preferably chlorinated alkenes, and most preferably trichloroethylene in spaced relation to the microbes so that the surprisingly strong, monomodal, chemotactic response of the chlorinated hydrocarbon on subsurface microbes can draw the microbes away from or towards and into a substance, as desired. In remediation of groundwater pollution, for example, TCE can be injected into the plume to increase the population of microbes at the plume whereby the plume can be more quickly degraded. A TCE-degrading microbe, such as Welchia alkenophilia, can be used to degrade the TCE following the degradation of the original pollutant. 5 figures.

Recent Advances in Microbial Single Cell Genomics Technology and Applications

NASA Astrophysics Data System (ADS)

Stepanauskas, R.

2016-02-01

Single cell genomics is increasingly utilized as a powerful tool to decipher the metabolic potential, evolutionary histories and in situ interactions of environmental microorganisms. This transformative technology recovers extensive information from cultivation-unbiased samples of individual, unicellular organisms. Thus, it does not require data binning into arbitrary phylogenetic or functional groups and therefore is highly compatible with agent-based modeling approaches. I will present several technological advances in this field, which significantly improve genomic data recovery from individual cells and provide direct linkages between cell's genomic and phenotypic properties. I will also demonstrate how these new technical capabilities help understanding the metabolic potential and viral infections of the "microbial dark matter" inhabiting aquatic and subsurface environments.

Diverse arsenic- and iron-cycling microbial communities in arsenic-contaminated aquifers used for drinking water in Bangladesh.

PubMed

Hassan, Zahid; Sultana, Munawar; van Breukelen, Boris M; Khan, Sirajul I; Röling, Wilfred F M

2015-04-01

Subsurface removal of arsenic by injection with oxygenated groundwater has been proposed as a viable technology for obtaining 'safe' drinking water in Bangladesh. While the oxidation of ferrous iron to solid ferric iron minerals, to which arsenic adsorbs, is assumed to be driven by abiotic reactions, metal-cycling microorganisms may potentially affect arsenic removal. A cultivation-independent survey covering 24 drinking water wells in several geographical regions in Bangladesh was conducted to obtain information on microbial community structure and diversity in general, and on specific functional groups capable of the oxidation or reduction of arsenic or iron. Each functional group, targeted by either group-specific 16S rRNA or functional gene amplification, occurred in at least 79% of investigated samples. Putative arsenate reducers and iron-oxidizing Gallionellaceae were present at low diversity, while more variation in potentially arsenite-oxidizing microorganisms and iron-reducing Desulfuromonadales was revealed within and between samples. Relations between community composition on the one hand and hydrochemistry on the other hand were in general not evident, apart from an impact of salinity on iron-cycling microorganisms. Our data suggest widespread potential for a positive contribution of arsenite and iron oxidizers to arsenic removal upon injection with oxygenated water, but also indicate a potential risk for arsenic re-mobilization by anaerobic arsenate and iron reducers once injection is halted. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Omics and multi-omics approaches to study the biosynthesis of secondary metabolites in microorganisms.

PubMed

Palazzotto, Emilia; Weber, Tilmann

2018-04-12

Natural products produced by microorganisms represent the main source of bioactive molecules. The development of high-throughput (omics) techniques have importantly contributed to the renaissance of new antibiotic discovery increasing our understanding of complex mechanisms controlling the expression of biosynthetic gene clusters (BGCs) encoding secondary metabolites. In this context this review highlights recent progress in the use and integration of 'omics' approaches with focuses on genomics, transcriptomics, proteomics metabolomics meta-omics and combined omics as powerful strategy to discover new antibiotics. Copyright © 2018 Elsevier Ltd. All rights reserved.

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.

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.

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.

Biotechnological approaches for the production of polyhydroxyalkanoates in microorganisms and plants - a review.

PubMed

Suriyamongkol, Pornpa; Weselake, Randall; Narine, Suresh; Moloney, Maurice; Shah, Saleh

2007-01-01

The increasing effect of non-degradable plastic wastes is a growing concern. Polyhydroxyalkanoates (PHAs), macromolecule-polyesters naturally produced by many species of microorganisms, are being considered as a replacement for conventional plastics. Unlike petroleum-derived plastics that take several decades to degrade, PHAs can be completely bio-degraded within a year by a variety of microorganisms. This biodegradation results in carbon dioxide and water, which return to the environment. Attempts based on various methods have been undertaken for mass production of PHAs. Promising strategies involve genetic engineering of microorganisms and plants to introduce production pathways. This challenge requires the expression of several genes along with optimization of PHA synthesis in the host. Although excellent progress has been made in recombinant hosts, the barriers to obtaining high quantities of PHA at low cost still remain to be solved. The commercially viable production of PHA in crops, however, appears to be a realistic goal for the future.

Seasonal dynamics in colored dissolved organic matter in the Mediterranean Sea: Patterns and drivers

NASA Astrophysics Data System (ADS)

Xing, Xiaogang; Claustre, Hervé; Wang, Haili; Poteau, Antoine; D`Ortenzio, Fabrizio

2014-01-01

Two autonomous profiling “Bio-Argo” floats were deployed in the northwestern and eastern sub-basins of the Mediterranean Sea in 2008. They recorded at high vertical (1 m) and temporal (5 day) resolution, the vertical distribution and seasonal variation of colored dissolved organic matter (CDOM), as well as of chlorophyll-a concentration and hydrological variables. The CDOM standing stock presented a clear seasonal dynamics with the progressive summer formation and winter destruction of subsurface CDOM maxima (YSM, for Yellow Substance Maximum). It was argued that subsurface CDOM is a by-product of phytoplankton, based on two main characteristics, (1) the YSM was located at the same depth than the deep chlorophyll maximum (DCM) and (2) the CDOM increased in summer parallels the decline in chlorophyll-a. These observations suggested an indirect but tight coupling between subsurface CDOM and phytoplankton via microbial activity or planktonic foodweb interactions. Moreover, the surface CDOM variations observed both by floats and MODIS displayed different seasonal dynamics from what recorded at subsurface one. This implies that CDOM standing stock can be hardly detected by satellite. It is worthnoting that surface CDOM was found to be more related to the sea surface temperature (SST) than chlorophyll-a concentration, suggesting its physical origin, in contrast to the biological origin of YSM and subsurface standing stocks.

A new solar cycle model including meridional circulation

NASA Technical Reports Server (NTRS)

Wang, Y.-M.; Sheeley, N. R., Jr.; Nash, A. G.

1991-01-01

A kinematic model is presented for the solar cycle which includes not only the transport of magnetic flux by supergranular diffusion and a poleward bulk flow at the sun's surface, but also the effects of turbulent diffusion and an equatorward 'return flow' beneath the surface. As in the earlier models of Babcock and Leighton, the rotational shearing of a subsurface poloidal field generates toroidal flux that erupts at the surface in the form of bipolar magnetic regions. However, such eruptions do not result in any net loss of toroidal flux from the sun (as assumed by Babcock and Leighton); instead, the large-scale toroidal field is destroyed both by 'unwinding' as the local poloidal field reverses its polarity, and by diffusion as the toroidal flux is transported equatorward by the subsurface flow and merged with its opposite hemisphere counterpart. The inclusion of meridional circulation allows stable oscillations of the magnetic field, accompanied by the equatorward progression of flux eruptions, to be achieved even in the absence of a radial gradient in the angular velocity. An illustrative case in which a subsurface flow speed of order 1 m/s and subsurface diffusion rate of order 10 sq km/s yield 22-yr oscillations in qualitative agreement with observations.

In Situ Field Sequencing and Life Detection in Remote (79°26'N) Canadian High Arctic Permafrost Ice Wedge Microbial Communities.

PubMed

Goordial, J; Altshuler, Ianina; Hindson, Katherine; Chan-Yam, Kelly; Marcolefas, Evangelos; Whyte, Lyle G

2017-01-01

Significant progress is being made in the development of the next generation of low cost life detection instrumentation with much smaller size, mass and energy requirements. Here, we describe in situ life detection and sequencing in the field in soils over laying ice wedges in polygonal permafrost terrain on Axel Heiberg Island, located in the Canadian high Arctic (79°26'N), an analog to the polygonal permafrost terrain observed on Mars. The life detection methods used here include (1) the cryo-iPlate for culturing microorganisms using diffusion of in situ nutrients into semi-solid media (2) a Microbial Activity Microassay (MAM) plate (BIOLOG Ecoplate) for detecting viable extant microorganisms through a colourimetric assay, and (3) the Oxford Nanopore MinION for nucleic acid detection and sequencing of environmental samples and the products of MAM plate and cryo-iPlate. We obtained 39 microbial isolates using the cryo-iPlate, which included several putatively novel strains based on the 16S rRNA gene, including a Pedobacter sp. (96% closest similarity in GenBank) which we partially genome sequenced using the MinION. The MAM plate successfully identified an active community capable of L-serine metabolism, which was used for metagenomic sequencing with the MinION to identify the active and enriched community. A metagenome on environmental ice wedge soil samples was completed, with base calling and uplink/downlink carried out via satellite internet. Validation of MinION sequencing using the Illumina MiSeq platform was consistent with the results obtained with the MinION. The instrumentation and technology utilized here is pre-existing, low cost, low mass, low volume, and offers the prospect of equipping micro-rovers and micro-penetrators with aggressive astrobiological capabilities. Since potentially habitable astrobiology targets have been identified (RSLs on Mars, near subsurface water ice on Mars, the plumes and oceans of Europa and Enceladus), future astrobiology missions will certainly target these areas and there is a need for direct life detection instrumentation.

Modern Subsurface Bacteria in Pristine 2.7 Ga-Old Fossil Stromatolite Drillcore Samples from the Fortescue Group, Western Australia

PubMed Central

Gérard, Emmanuelle; Moreira, David; Philippot, Pascal; Van Kranendonk, Martin J.; López-García, Purificación

2009-01-01

Background Several abiotic processes leading to the formation of life-like signatures or later contamination with actual biogenic traces can blur the interpretation of the earliest fossil record. In recent years, a large body of evidence showing the occurrence of diverse and active microbial communities in the terrestrial subsurface has accumulated. Considering the time elapsed since Archaean sedimentation, the contribution of subsurface microbial communities postdating the rock formation to the fossil biomarker pool and other biogenic remains in Archaean rocks may be far from negligible. Methodology/Principal Findings In order to evaluate the degree of potential contamination of Archean rocks by modern microorganisms, we looked for the presence of living indigenous bacteria in fresh diamond drillcores through 2,724 Myr-old stromatolites (Tumbiana Formation, Fortescue Group, Western Australia) using molecular methods based on the amplification of small subunit ribosomal RNA genes (SSU rDNAs). We analyzed drillcore samples from 4.3 m and 66.2 m depth, showing signs of meteoritic alteration, and also from deeper “fresh” samples showing no apparent evidence for late stage alteration (68 m, 78.8 m, and 99.3 m). We also analyzed control samples from drilling and sawing fluids and a series of laboratory controls to establish a list of potential contaminants introduced during sample manipulation and PCR experiments. We identified in this way the presence of indigenous bacteria belonging to Firmicutes, Actinobacteria, and Alpha-, Beta-, and Gammaproteobacteria in aseptically-sawed inner parts of drillcores down to at least 78.8 m depth. Conclusions/Significance The presence of modern bacterial communities in subsurface fossil stromatolite layers opens the possibility that a continuous microbial colonization had existed in the past and contributed to the accumulation of biogenic traces over geological timescales. This finding casts shadow on bulk analyses of early life remains and makes claims for morphological, chemical, isotopic, and biomarker traces syngenetic with the rock unreliable in the absence of detailed contextual analyses at microscale. PMID:19396360

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

New Bio-Indicators for Long Term Natural Attenuation of Monoaromatic Compounds in Deep Terrestrial Aquifers

PubMed Central

Aüllo, Thomas; Berlendis, Sabrina; Lascourrèges, Jean-François; Dessort, Daniel; Duclerc, Dominique; Saint-Laurent, Stéphanie; Schraauwers, Blandine; Mas, Johan; Patriarche, Delphine; Boesinger, Cécile; Magot, Michel; Ranchou-Peyruse, Anthony

2016-01-01

Deep subsurface aquifers despite difficult access, represent important water resources and, at the same time, are key locations for subsurface engineering activities for the oil and gas industries, geothermal energy, and CO2 or energy storage. Formation water originating from a 760 m-deep geological gas storage aquifer was sampled and microcosms were set up to test the biodegradation potential of BTEX by indigenous microorganisms. The microbial community diversity was studied using molecular approaches based on 16S rRNA genes. After a long incubation period, with several subcultures, a sulfate-reducing consortium composed of only two Desulfotomaculum populations was observed able to degrade benzene, toluene, and ethylbenzene, extending the number of hydrocarbonoclastic–related species among the Desulfotomaculum genus. Furthermore, we were able to couple specific carbon and hydrogen isotopic fractionation during benzene removal and the results obtained by dual compound specific isotope analysis (𝜀C = -2.4‰ ± 0.3‰; 𝜀H = -57‰ ± 0.98‰; AKIEC: 1.0146 ± 0.0009, and AKIEH: 1.5184 ± 0.0283) were close to those obtained previously in sulfate-reducing conditions: this finding could confirm the existence of a common enzymatic reaction involving sulfate-reducers to activate benzene anaerobically. Although we cannot assign the role of each population of Desulfotomaculum in the mono-aromatic hydrocarbon degradation, this study suggests an important role of the genus Desulfotomaculum as potential biodegrader among indigenous populations in subsurface habitats. This community represents the simplest model of benzene-degrading anaerobes originating from the deepest subterranean settings ever described. As Desulfotomaculum species are often encountered in subsurface environments, this study provides some interesting results for assessing the natural response of these specific hydrologic systems in response to BTEX contamination during remediation projects. PMID:26904000

Microbial colonization in diverse surface soil types in Surtsey and diversity analysis of its subsurface microbiota

NASA Astrophysics Data System (ADS)

Marteinsson, V.; Klonowski, A.; Reynisson, E.; Vannier, P.; Sigurdsson, B. D.; Ólafsson, M.

2015-02-01

Colonization of life on Surtsey has been observed systematically since the formation of the island 50 years ago. Although the first colonisers were prokaryotes, such as bacteria and blue-green algae, most studies have been focused on the settlement of plants and animals but less on microbial succession. To explore microbial colonization in diverse soils and the influence of associated vegetation and birds on numbers of environmental bacteria, we collected 45 samples from different soil types on the surface of the island. Total viable bacterial counts were performed with the plate count method at 22, 30 and 37 °C for all soil samples, and the amount of organic matter and nitrogen (N) was measured. Selected samples were also tested for coliforms, faecal coliforms and aerobic and anaerobic bacteria. The subsurface biosphere was investigated by collecting liquid subsurface samples from a 181 m borehole with a special sampler. Diversity analysis of uncultivated biota in samples was performed by 16S rRNA gene sequences analysis and cultivation. Correlation was observed between nutrient deficits and the number of microorganisms in surface soil samples. The lowest number of bacteria (1 × 104-1 × 105 cells g-1) was detected in almost pure pumice but the count was significantly higher (1 × 106-1 × 109 cells g-1) in vegetated soil or pumice with bird droppings. The number of faecal bacteria correlated also to the total number of bacteria and type of soil. Bacteria belonging to Enterobacteriaceae were only detected in vegetated samples and samples containing bird droppings. The human pathogens Salmonella, Campylobacter and Listeria were not in any sample. Both thermophilic bacteria and archaea 16S rDNA sequences were found in the subsurface samples collected at 145 and 172 m depth at 80 and 54 °C, respectively, but no growth was observed in enrichments. The microbiota sequences generally showed low affiliation to any known 16S rRNA gene sequences.

Microbial colonisation in diverse surface soil types in Surtsey and diversity analysis of its subsurface microbiota

NASA Astrophysics Data System (ADS)

Marteinsson, V.; Klonowski, A.; Reynisson, E.; Vannier, P.; Sigurdsson, B. D.; Ólafsson, M.

2014-09-01

Colonisation of life on Surtsey has been observed systematically since the formation of the island 50 years ago. Although the first colonisers were prokaryotes, such as bacteria and blue-green algae, most studies have been focusing on settlement of plants and animals but less on microbial succession. To explore microbial colonization in diverse soils and the influence of associate vegetation and birds on numbers of environmental bacteria, we collected 45 samples from different soils types on the surface of the island. Total viable bacterial counts were performed with plate count at 22, 30 and 37 °C for all soils samples and the amount of organic matter and nitrogen (N) was measured. Selected samples were also tested for coliforms, faecal coliforms aerobic and anaerobic bacteria. The deep subsurface biosphere was investigated by collecting liquid subsurface samples from a 182 m borehole with a special sampler. Diversity analysis of uncultivated biota in samples was performed by 16S rRNA gene sequences analysis and cultivation. Correlation was observed between N deficits and the number of microorganisms in surface soils samples. The lowest number of bacteria (1 × 104-1 × 105 g-1) was detected in almost pure pumice but the count was significant higher (1 × 106-1 × 109 g-1) in vegetated soil or pumice with bird droppings. The number of faecal bacteria correlated also to the total number of bacteria and type of soil. Bacteria belonging to Enterobacteriaceae were only detected in vegetated and samples containing bird droppings. The human pathogens Salmonella, Campylobacter and Listeria were not in any sample. Both thermophilic bacteria and archaea 16S rDNA sequences were found in the subsurface samples collected at 145 m and 172 m depth at 80 °C and 54 °C, respectively, but no growth was observed in enrichments. The microbiota sequences generally showed low affiliation to any known 16S rRNA gene sequences.

Ionic liquid-tolerant microorganisms and microbial communities for lignocellulose conversion to bioproducts

DOE PAGES

Yu, Chaowei; Simmons, Blake A.; Singer, Steven W.; ...

2016-11-12

Chemical and physical pretreatment of biomass is a critical step in the conversion of lignocellulose to biofuels and bioproducts. Ionic liquid (IL) pretreatment has attracted significant attention due to the unique ability of certain ILs to solubilize some or all components of the plant cell wall. However, these ILs inhibit not only the enzyme activities but also the growth and productivity of microorganisms used in downstream hydrolysis and fermentation processes. While pretreated biomass can be washed to remove residual IL and reduce inhibition, extensive washing is costly and not feasible in large-scale processes. IL-tolerant microorganisms and microbial communities have beenmore » discovered from environmental samples and studies begun to elucidate mechanisms of IL tolerance. The discovery of IL tolerance in environmental microbial communities and individual microbes has lead to the proposal of molecular mechanisms of resistance. Here, we review recent progress on discovering IL-tolerant microorganisms, identifying metabolic pathways and mechanisms of tolerance, and engineering microorganisms for IL tolerance. Research in these areas will yield new approaches to overcome inhibition in lignocellulosic biomass bioconversion processes and increase opportunities for the use of ILs in biomass pretreatment.« less

Ionic liquid-tolerant microorganisms and microbial communities for lignocellulose conversion to bioproducts.

PubMed

Yu, Chaowei; Simmons, Blake A; Singer, Steven W; Thelen, Michael P; VanderGheynst, Jean S

2016-12-01

Chemical and physical pretreatment of biomass is a critical step in the conversion of lignocellulose to biofuels and bioproducts. Ionic liquid (IL) pretreatment has attracted significant attention due to the unique ability of certain ILs to solubilize some or all components of the plant cell wall. However, these ILs inhibit not only the enzyme activities but also the growth and productivity of microorganisms used in downstream hydrolysis and fermentation processes. While pretreated biomass can be washed to remove residual IL and reduce inhibition, extensive washing is costly and not feasible in large-scale processes. IL-tolerant microorganisms and microbial communities have been discovered from environmental samples and studies begun to elucidate mechanisms of IL tolerance. The discovery of IL tolerance in environmental microbial communities and individual microbes has lead to the proposal of molecular mechanisms of resistance. In this article, we review recent progress on discovering IL-tolerant microorganisms, identifying metabolic pathways and mechanisms of tolerance, and engineering microorganisms for IL tolerance. Research in these areas will yield new approaches to overcome inhibition in lignocellulosic biomass bioconversion processes and increase opportunities for the use of ILs in biomass pretreatment.

Ionic liquid-tolerant microorganisms and microbial communities for lignocellulose conversion to bioproducts

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

Yu, Chaowei; Simmons, Blake A.; Singer, Steven W.

Chemical and physical pretreatment of biomass is a critical step in the conversion of lignocellulose to biofuels and bioproducts. Ionic liquid (IL) pretreatment has attracted significant attention due to the unique ability of certain ILs to solubilize some or all components of the plant cell wall. However, these ILs inhibit not only the enzyme activities but also the growth and productivity of microorganisms used in downstream hydrolysis and fermentation processes. While pretreated biomass can be washed to remove residual IL and reduce inhibition, extensive washing is costly and not feasible in large-scale processes. IL-tolerant microorganisms and microbial communities have beenmore » discovered from environmental samples and studies begun to elucidate mechanisms of IL tolerance. The discovery of IL tolerance in environmental microbial communities and individual microbes has lead to the proposal of molecular mechanisms of resistance. Here, we review recent progress on discovering IL-tolerant microorganisms, identifying metabolic pathways and mechanisms of tolerance, and engineering microorganisms for IL tolerance. Research in these areas will yield new approaches to overcome inhibition in lignocellulosic biomass bioconversion processes and increase opportunities for the use of ILs in biomass pretreatment.« less

A subsurface Fe-silicate weathering microbiome

NASA Astrophysics Data System (ADS)

Napieralski, S. A.; Buss, H. L.; Roden, E. E.

2017-12-01

Traditional models of microbially mediated weathering of primary Fe-bearing minerals often invoke organic ligands (e.g. siderophores) used for nutrient acquisition. However, it is well known that the oxidation of Fe(II) governs the overall rate of Fe-silicate mineral dissolution. Recent work has demonstrated the ability of lithtrophic iron oxidizing bacteria (FeOB) to grow via the oxidation of structural Fe(II) in biotite as a source of metabolic energy with evidence suggesting a direct enzymatic attack on the mineral surface. This process necessitates the involvement of dedicated outer membrane proteins that interact with insoluble mineral phases in a process known as extracellular electron transfer (EET). To investigate the potential role FeOB in a terrestrial subsurface weathering system, samples were obtained from the bedrock-saprolite interface (785 cm depth) within the Rio Icacos Watershed of the Luquillo Mountains in Puerto Rico. Prior geochemical evidence suggests the flux of Fe(II) from the weathering bedrock supports a robust lithotrophic microbial community at depth. Current work confirms the activity of microorganism in situ, with a marked increase in ATP near the bedrock-saprolite interface. Regolith recovered from the interface was used as inoculum to establish enrichment cultures with powderized Fe(II)-bearing minerals serving as the sole energy source. Monitoring of the Fe(II)/Fe(total) ratio and ATP generation suggests growth of microorganisms coupled to the oxidation of mineral bound Fe(II). Analysis of 16S rRNA gene and shotgun metagenomic libraries from in situ and enrichment culture samples lends further support to FeOB involvement in the weathering process. Multiple metagenomic bins related to known FeOB, including Betaproteobacteria genera, contain homologs to model EET systems, including Cyc2 and MtoAB. Our approach combining geochemistry and metagenomics with ongoing microbiological and genomic characterization of novel isolates obtained from enrichment cultures provides insight into the role of FeOB in Fe(II)-mineral alteration as well as furthering our understanding of the biotic reactions contributing the globally important biogeochemical phenomenon of chemical weathering.

Isolation and characterization of a CO2-tolerant Lactobacillus strain from Crystal Geyser, Utah, U.S.A.

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

Santillan, Eugenio-Felipe U.; Shanahan, Timothy M.; Omelon, Christopher R.

2015-07-23

When CO 2 is sequestered into the deep subsurface, changes to the subsurface microbial community will occur. Capnophiles, microorganisms that grow in CO 2-rich environments, are some organisms that may be selected for under the new environmental conditions. To determine whether capnophiles comprise an important part of CO 2-rich environments, an isolate from Crystal Geyser, Utah, U.S.A., a CO 2- rich spring considered a carbon sequestration analog, was characterized. The isolate was cultured under varying CO 2, pH, salinity, and temperature, as well as different carbon substrates and terminal electron acceptors (TEAs) to elucidate growth conditions and metabolic activity. Designatedmore » CG-1, the isolate is related (99%) to Lactobacillus casei in 16S rRNA gene identity, growing at PCO 2 between 0 and 1.0 MPa. Growth is inhibited at 2.5 MPa, but stationary phase cultures exposed to this pressure survive beyond 5 days. At 5.0 MPa, survival is at least 24 h. CG-1 grows in neutral pH, 0.25 M NaCl, and between 25° and 45°C and consumes glucose, lactose, sucrose, or crude oil, likely performing lactic acid fermentation. Fatty acid profiles between 0.1 and 1.0 MPa suggests decreases in cell size and increases in membrane rigidity. Transmission electron microscopy reveals rod shaped bacteria at 0.1 MPa. At 1.0 MPa, cells are smaller, amorphous, and produce abundant capsular material. Its ability to grow in environments regardless of the presence of CO 2 suggests we have isolated an organism that is more capnotolerant than capnophilic. Results also show that microorganisms are capable of surviving the stressful conditions created by the introduction of CO 2 for sequestration. Furthermore, our ability to culture an environmental isolate indicates that organisms found in CO 2 environments from previous genomic and metagenomics studies are viable, metabolizing, and potentially affecting the surrounding environment.« less

Isolation and characterization of a CO2-tolerant Lactobacillus strain from Crystal Geyser, Utah, U.S.A.

NASA Astrophysics Data System (ADS)

Santillan, Eugenio Felipe; Shanahan, Timothy; Omelon, Christopher; Major, Jonathan; Bennett, Philip

2015-07-01

When CO2 is sequestered into the deep subsurface, changes to the subsurface microbial community will occur. Capnophiles, microorganisms that grow in CO2-rich environments, are some organisms that may be selected for under the new environmental conditions. To determine whether capnophiles comprise an important part of CO2-rich environments, an isolate from Crystal Geyser, Utah, U.S.A., a CO2- rich spring considered a carbon sequestration analogue, was characterized. The isolate was cultured under varying CO2, pH, salinity, and temperature, as well as different carbon substrates and terminal electron acceptors (TEAs) to elucidate growth conditions and metabolic activity. Designated CG-1, the isolate is related (99%) to Lactobacillus casei in 16S rRNA gene identity, growing at PCO2 between 0 to 1.0 MPa. Growth is inhibited at 2.5 MPa, but stationary phase cultures exposed to this pressure survive beyond 5 days. At 5.0 MPa, survival is at least 24 hours. CG-1 grows in neutral pH, 0.25 M NaCl, and between 25° to 45°C andconsumes glucose, lactose, sucrose, or crude oil, likely performing lactic acid fermentation. Fatty acid profiles between 0.1 MPa to 1.0 MPa suggests decreases in cell size and increases in membrane rigidity. Transmission electron microscopy reveals rod shaped bacteria at 0.1 MPa. At 1.0 MPa, cells are smaller, amorphous, and produce abundant capsular material. Its ability to grow in environments regardless of the presence of CO2 suggests we have isolated an organism that is more capnotolerant than capnophilic. Results also show that microorganisms are capable of surviving the stressful conditions created by the introduction of CO2 for sequestration. Furthermore, our ability to culture an environmental isolate indicates that organisms found in CO2 environments from previous genomic and metagenomics studies are viable, metabolizing, and potentially affecting the surrounding environment.

Microorganisms in extreme environments with a view to astrobiology in the outer solar system

NASA Astrophysics Data System (ADS)

Seckbach, Joseph; Chela-Flores, Julian

2015-09-01

We review the various manifestations of the evolution of life in extreme environments. We review those aspects of extremophiles that are most relevant for astrobiology. We are aware that geothermal energy triggering sources of heat in oceanic environments are not unique to our planet, a fact that was exposed by the Voyager mission images of volcanic activity on Io, the Jovian moon. Such activity exceeded by far what was known form terrestrial geology. The science of astrobiology has considered the possible presence of several moon oceans in the vicinity of both giant gas and icy planets. These watery environments include, not only Europa (strongly suggested by data from the Galileo mission), but the Voyager flybys exposed, not only the unusual geothermal activity on Io, but also the possible presence of subsurface oceans and some geothermal activity on the Neptune's moon Triton. More recently, calculations of Hussmann and coworkers with available data do not exclude that even Uranus moons may be candidates for bearing subsurface oceans. These possibilities invite a challenge that we gladly welcome, of preliminary discussions of habitability of extremophiles in so far novel environments for the science of astrobiology. Nevertheless, such exploration is currently believed to be feasible with the new generations of missions suggested for the time window of 2030 - 2040, or even earlier. We are envisaging, not only the current exploration of the moons of Saturn, but in the coming years we expect to go beyond to Uranus and Neptune to include dwarf planets and trans-neptunian worlds. Consequently, it is necessary to begin questioning whether the Europa-like conditions for the evolution of microorganisms are repeatable elsewhere. At present three new missions are in the process of being formulated, including the selection of payloads that will be necessary for the exploration of the various so far unexplored moons.

Biofilm development in a hotspot of mixing between shallow and deep groundwater in a fractured aquifer: field evidence from joint flow, chemical and microbiological measurements

NASA Astrophysics Data System (ADS)

Bochet, O.; Dufresne, A.; Pédrot, M.; Chatton, E.; Labasque, T.; Ben Maamar, S.; Burté, L.; de la Bernardie, J.; Guihéneuf, N.; Lavenant, N.; Petton, C.; Bour, O.; Aquilina, L.; Le Borgne, T.

2015-12-01

Biofilms play a major role in controlling the fluxes and reactivity of chemical species transported in hydro-logical systems. Micro-organisms require both electron donors and electron acceptors for cellular growth, proliferation and maintenance of their metabolic functions. The mechanisms controlling these reactions derive from the interactions occurring at the micro-scale that depend on mineral compositions, the biota of subsurface environment, but also fluid mixing, which determines the local concentrations of nutriments, electron donors and electron acceptors. Hence, mixing zones between oxygen and nutriment rich shallow groundwater and mineralized deep groundwater are often considered as potential hotspots of microbial activity, although relatively few field data document flow distributions, transport properties, chemical gradients and micro-organisms distributions across these mixing interfaces. Here we investigate the origin of a localized biofilm development observed in the fractured granite aquifer at the Ploemeur observatory (H+ network hplus.ore.fr).This biofilm composed of ferro-oxidizing bacteria is observed in an 130m deep artesian well. Borehole video logs show an important colonization of the well by the biofilm in the shallower part (0 to 60m), while it is inexistent in the deeper part (60 to 130m). As flow is localized in a few deep and shallow fractures, we presume that the spatial distribution of biofilm is controlled by mixing between shallow and deep groundwater. To verify this hypothesis we conducted a field campaign with joint characterization of the flow and chemical composition of water flowing from the different fractures, as well as the microbiological composition of the biofilm at different depth, using pyrosequencing techniques. We will discuss in this presentation the results of this interdisciplinary dataset and their implications for the occurrence of hotspots of microbiological activity in the subsurface.

CHARACTERIZATION OF TRAVELING WAVES AND ANALYTICAL ESTIMATION OF POLLUTANT REMOVAL IN ONE-DIMENSIONAL SUBSURFACE BIOREMEDIATION MODELING. (R824785)

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...

Selective Phylogenetic Analysis Targeted at 16S rRNA Genes of Thermophiles and Hyperthermophiles in Deep-Subsurface Geothermal Environments

PubMed Central

Kimura, Hiroyuki; Sugihara, Maki; Kato, Kenji; Hanada, Satoshi

2006-01-01

Deep-subsurface samples obtained by deep drilling are likely to be contaminated with mesophilic microorganisms in the drilling fluid, and this could affect determination of the community structure of the geothermal microflora using 16S rRNA gene clone library analysis. To eliminate possible contamination by PCR-amplified 16S rRNA genes from mesophiles, a combined thermal denaturation and enzyme digestion method, based on a strong correlation between the G+C content of the 16S rRNA gene and the optimum growth temperatures of most known prokaryotic cultures, was used prior to clone library construction. To validate this technique, hot spring fluid (76°C) and river water (14°C) were used to mimic a deep-subsurface sample contaminated with drilling fluid. After DNA extraction and PCR amplification of the 16S rRNA genes from individual samples separately, the amplified products from river water were observed to be denatured at 82°C and completely digested by exonuclease I (Exo I), while the amplified products from hot spring fluid remained intact after denaturation at 84°C and enzyme digestion with Exo I. DNAs extracted from the two samples were mixed and used as a template for amplification of the 16S rRNA genes. The amplified rRNA genes were denatured at 84°C and digested with Exo I before clone library construction. The results indicated that the 16S rRNA gene sequences from the river water were almost completely eliminated, whereas those from the hot spring fluid remained. PMID:16391020

Biogeographic congruency among bacterial communities from terrestrial sulfidic springs

PubMed Central

Headd, Brendan; Engel, Annette S.

2014-01-01

Terrestrial sulfidic springs support diverse microbial communities by serving as stable conduits for geochemically diverse and nutrient-rich subsurface waters. Microorganisms that colonize terrestrial springs likely originate from groundwater, but may also be sourced from the surface. As such, the biogeographic distribution of microbial communities inhabiting sulfidic springs should be controlled by a combination of spring geochemistry and surface and subsurface transport mechanisms, and not necessarily geographic proximity to other springs. We examined the bacterial diversity of seven springs to test the hypothesis that occurrence of taxonomically similar microbes, important to the sulfur cycle, at each spring is controlled by geochemistry. Complementary Sanger sequencing and 454 pyrosequencing of 16S rRNA genes retrieved five proteobacterial classes, and Bacteroidetes, Chlorobi, Chloroflexi, and Firmicutes phyla from all springs, which suggested the potential for a core sulfidic spring microbiome. Among the putative sulfide-oxidizing groups (Epsilonproteobacteria and Gammaproteobacteria), up to 83% of the sequences from geochemically similar springs clustered together. Abundant populations of Hydrogenimonas-like or Sulfurovum-like spp. (Epsilonproteobacteria) occurred with abundant Thiothrix and Thiofaba spp. (Gammaproteobacteria), but Arcobacter-like and Sulfurimonas spp. (Epsilonproteobacteria) occurred with less abundant gammaproteobacterial populations. These distribution patterns confirmed that geochemistry rather than biogeography regulates bacterial dominance at each spring. Potential biogeographic controls were related to paleogeologic sedimentation patterns that could control long-term microbial transport mechanisms that link surface and subsurface environments. Knowing the composition of a core sulfidic spring microbial community could provide a way to monitor diversity changes if a system is threatened by anthropogenic processes or climate change. PMID:25250021

Trace Metals in Groundwater & the Vadose Zone Calcite: In Situ Containment & Stabilization of Strontium-90 & Other Divalent Metals & Radionuclides at Arid West DOE

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

Smith, Robert W.

2004-12-01

Radionuclide and metal contaminants such as strontium-90 are present beneath U.S. Department of Energy (DOE) lands in both the groundwater (e.g., 100-N area at Hanford, WA) and vadose zone (e.g., Idaho Nuclear Technology and Engineering Center at the Idaho National Engineering and Environmental Laboratory). In situ containment and stabilization of these contaminants is a cost-effective treatment strategy. However, implementing in situ containment and stabilization approaches requires definition of the mechanisms that control contaminant sequestration. We are investigating the in situ immobilization of radionuclides or contaminant metals (e.g., strontium-90) by their facilitated co-precipitation with calcium carbonate in groundwater and vadose zonemore » systems. Our facilitated approach, shown schematically in Figure 1, relies upon the hydrolysis of introduced urea to cause the acceleration of calcium carbonate precipitation (and trace metal co-precipitation) by increasing pH and alkalinity. Subsurface urea hydrolysis is catalyzed by the urease enzyme, which may be either introduced with the urea or produced in situ by ubiquitous subsurface urea hydrolyzing microorganisms. Because the precipitation process tends to be irreversible and many western aquifers are saturated with respect to calcite, the co-precipitated metals and radionuclides will be effectively removed from the aqueous phase over the long-term. Another advantage of the ureolysis approach is that the ammonium ions produced by the reaction can exchange with radionuclides sorbed to subsurface minerals, thereby enhancing the availability of the radionuclides for re-capture in a more stable solid phase (co-precipitation rather than adsorption).« less

Microbial community assembly patterns under incipient conditions in a basaltic soil system

NASA Astrophysics Data System (ADS)

Sengupta, A.; Stegen, J.; Alves Meira Neto, A.; Wang, Y.; Chorover, J.; Troch, P. A. A.; Maier, R. M.

2017-12-01

In sub-surface environments, the biotic components are critically linked to the abiotic processes. However, there is limited understanding of community establishment, functional associations, and community assembly processes of such microbes in sub-surface environments. This study presents the first analysis of microbial signatures in an incipient terrestrial basalt soil system conducted under controlled conditions. A sub-meter scale sampling of a soil mesocosm revealed the contrasting distribution patterns of simple soil parameters such as bulk density and electrical conductivity. Phylogenetic analysis of 16S rRNA gene indicated the presence of a total 40 bacterial and archaeal phyla, with high relative abundance of Actinobacteria on the surface and highest abundance of Proteobacteria throughout the system. Community diversity patterns were inferred to be dependent on depth profile and average water content in the system. Predicted functional gene analysis suggested mixotrophy lifestyles with both autotrophic and heterotrophic metabolisms, likelihood of a unique salt tolerant methanogenic pathway with links to novel Euryarchea, signatures of an incomplete nitrogen cycle, and predicted enzymes of extracellular iron (II) to iron (III) conversion followed by intracellular uptake, transport and regulation. Null modeling revealed microbial community assembly was predominantly governed by variable selection, but the influence of the variable selection did not show systematic spatial structure. The presence of significant heterogeneity in predicted functions and ecologically deterministic shifts in community composition in a homogeneous incipient basalt highlights the complexity exhibited by microorganisms even in the simplest of environmental systems. This presents an opportunity to further develop our understanding of how microbial communities establish, evolve, impact, and respond in sub-surface environments.

Reduction of hexavalent chromium by the thermophilic methanogen Methanothermobacter thermautotrophicus

NASA Astrophysics Data System (ADS)

Singh, Rajesh; Dong, Hailiang; Liu, Deng; Zhao, Linduo; Marts, Amy R.; Farquhar, Erik; Tierney, David L.; Almquist, Catherine B.; Briggs, Brandon R.

2015-01-01

Despite significant progress on iron reduction by thermophilic microorganisms, studies on their ability to reduce toxic metals are still limited, despite their common co-existence in high temperature environments (up to 70 °C). In this study, Methanothermobacter thermautotrophicus, an obligate thermophilic methanogen, was used to reduce hexavalent chromium. Experiments were conducted in a growth medium with H2/CO2 as substrate with various Cr6+ concentrations (0.2, 0.4, 1, 3, and 5 mM) in the form of potassium dichromate (K2Cr2O7). Time-course measurements of aqueous Cr6+ concentrations using 1,5-diphenylcarbazide colorimetric method showed complete reduction of the 0.2 and 0.4 mM Cr6+ solutions by this methanogen. However, much lower reduction extents of 43.6%, 13.0%, and 3.7% were observed at higher Cr6+ concentrations of 1, 3 and 5 mM, respectively. These lower extents of bioreduction suggest a toxic effect of aqueous Cr6+ to cells at this concentration range. At these higher Cr6+ concentrations, methanogenesis was inhibited and cell growth was impaired as evidenced by decreased total cellular protein production and live/dead cell ratio. Likewise, Cr6+ bioreduction rates decreased with increased initial concentrations of Cr6+ from 13.3 to 1.9 μM h-1. X-ray absorption near-edge structure (XANES) spectroscopy revealed a progressive reduction of soluble Cr6+ to insoluble Cr3+ precipitates, which was confirmed as amorphous chromium hydroxide by selected area electron diffraction pattern. However, a small fraction of reduced Cr occurred as aqueous Cr3+. Scanning and transmission electron microscope observations of M. thermautotrophicus cells after Cr6+ exposure suggest both extra- and intracellular chromium reduction mechanisms. Results of this study demonstrate the ability of M. thermautotrophicus cells to reduce toxic Cr6+ to less toxic Cr3+ and its potential application in metal bioremediation, especially at high temperature subsurface radioactive waste disposal sites, where the temperature may reach ∼70 °C.

Pinellas County, Florida Site Environmental Restoration Project Semiannual Progress Report for the 4.5 Acre Site June through November 2016 January 2017

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

Survochak, Scott; Daniel, Joe

This Pinellas County, Florida, Site Environmental Restoration Project Semiannual Progress Report for the 4.5 Acre Site describes environmental restoration activities for the 4.5 Acre Site located in Pinellas County, Largo, Florida (Figure 1). The former U.S. Department of Energy (DOE) Pinellas Plant facility consisted of the 4.5 Acre Site and what is now the STAR Center (Young - Rainey Science, Technology, and Research Center). Both the 4.5 Acre Site and the STAR Center are part of the overall Pinellas County, Florida, Site (Figure 2). The 4.5 Acre Site is located immediately northwest of the STAR Center, in the northeast quartermore » of Section 13, Township 30 South, Range 15 East. DOE owned this parcel from 1957 to 1972, at which time it was sold to a private landowner. During the period of DOE ownership, the property was used for the disposal of drums of waste resins and solvents. As a result of this practice, the surficial aquifer was impacted by volatile organic compounds (VOCs)—trichloroethene (TCE), cis-1,2-dichloroethene (cDCE), trans-1,2-dichloroethene (tDCE), vinyl chloride (VC), and benzene. Detailed background information for the site is contained in the Long-Term Surveillance and Maintenance Plan for the Pinellas Site (DOE 2016). That document and other site-related documents can be accessed at this website: http://www.lm.doe.gov/Pinellas/Sites.aspx. Recent remediation activities consist of the injection of emulsified soybean oil and the microorganism Dehalococcoides mccartyi (formerly known as Dehalococcoides ethenogenes) into the subsurface in February 2010 and again in July 2013 to enhance contaminant biodegradation (hereafter described as bioinjection). Monitoring the performance of these actions, in the form of monitoring well sampling, is ongoing.« less

Use of immunomagnetic separation for the detection of Desulfovibrio vulgaris from environmental samples

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

Chakraborty, R.; Hazen, T.C.; Joyner, D.C.

2011-04-15

Immunomagnetic separation (IMS) has proved highly efficient for recovering microorganisms from heterogeneous samples. Current investigation targeted the separation of viable cells of the sulfate-reducing bacterium, Desulfovibrio vulgaris. Streptavidin-coupled paramagnetic beads and biotin labeled antibodies raised against surface antigens of this microorganism were used to capture D. vulgaris cells in both bioreactor grown laboratory samples and from extremely low-biomass environmental soil and subsurface drilling samples. Initial studies on detection, recovery efficiency and viability for IMS were performed with laboratory grown D. vulgaris cells using various cell densities. Efficiency of cell isolation and recovery (i.e., release of the microbial cells from themore » beads following separation) was followed by microscopic imaging and acridine orange direct counts (AODC). Excellent recovery efficiency encouraged the use of IMS to capture Desulfovibrio spp. cells from low-biomass environmental samples. The environmental samples were obtained from a radionuclide-contaminated site in Germany and the chromium (VI)-contaminated Hanford site, an ongoing bioremediation project of the U.S. Department of Energy. Field deployable IMS technology may greatly facilitate environmental sampling and bioremediation process monitoring and enable transcriptomics and proteomics/metabolomics-based studies directly on cells collected from the field.« less

Utilization of agricultural wastes for production of ethanol. Progress report, October 1979-May 1980

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

Singh, B.

1980-05-01

The project proposes to develop methods to utilize agricultural wastes, especially cottonseed hulls and peanut shells to produce ethanol. Initial steps will involve development of methods to break down cellulose to a usable form of substrates for chemical or biological digestion. The process of ethanol production will consist of (a) preparatory step to separate fibrous (cellulose) and non-fibrous (non-cellulosic compounds). The non-cellulosic residues which may include grains, fats or other substrates for alcoholic fermentation. The fibrous residues will be first pre-treated to digest cellulose with acid, alkali, and sulfur dioxide gas or other solvents. (b) The altered cellulose will bemore » digested by suitable micro-organisms and cellulose enzymes before alcoholic fermentation. The digester and fermentative unit will be specially designed to develop a prototype for pilot plant for a continuous process. The first phase of the project will be devoted toward screening of a suitable method for cellulose modification, separation of fibrous and non-fibrous residues, the micro-organism and enzyme preparations. Work is in progress on: the effects of various microorganisms on the degree of saccharification; the effects of higher concentrations of acids, alkali, and EDTA on efficiency of microbial degradation; and the effects of chemicals on enzymatic digestion.« less

Influence of dissimilatory metal reduction on fate of organic and metal contaminants in the subsurface

NASA Astrophysics Data System (ADS)

Lovley, Derek R.; Anderson, Robert T.

Dissimilatory Fe(III)-reducing microorganisms have the ability to destroy organic contaminants under anaerobic conditions by oxidizing them to carbon dioxide. Some Fe(III)-reducing microorganisms can also reductively dechlorinate chlorinated contaminants. Fe(III)-reducing microorganisms can reduce a variety of contaminant metals and convert them from soluble forms to forms that are likely to be immobilized in the subsurface. Studies in petroleum-contaminated aquifers have demonstrated that Fe(III)-reducing microorganisms can be effective agents in removing aromatic hydrocarbons from groundwater under anaerobic conditions. Laboratory studies have demonstrated the potential for Fe(III)-reducing microorganisms to remove uranium from contaminated groundwaters. The activity of Fe(III)-reducing microorganisms can be stimulated in several ways to enhance organic contaminant oxidation and metal reduction. Molecular analyses in both field and laboratory studies have demonstrated that microorganisms of the genus Geobacter become dominant members of the microbial community when Fe(III)-reducing conditions develop as the result of organic contamination, or when Fe(III) reduction is artificially stimulated. These results suggest that further understanding of the ecophysiology of Geobacter species would aid in better prediction of the natural attenuation of organic contaminants under anaerobic conditions and in the design of strategies for the bioremediation of subsurface metal contamination. Des micro-organismes simulant la réduction du fer ont la capacité de détruire des polluants organiques dans des conditions anérobies en les oxydant en dioxyde de carbone. Certains micro-organismes réducteurs de fer peuvent aussi dé-chlorer par réduction des polluants chlorés. Des micro-organismes réducteurs de fer peuvent réduire tout un ensemble de métaux polluants et les faire passer de formes solubles à des formes qui sont susceptibles d'être immobilisées dans le milieu souterrain. Des études d'aquifères pollués par du pétrole ont montré que des micro-organismes réducteurs de fer peuvent être des agents efficaces pour éliminer les hydrocarbures aromatiques des eaux souterraines dans des conditions anérobies. Des études en laboratoire ont montré que des micro-organismes réducteurs de fer avaient la capacité d'éliminer l'uranium d'eaux souterraines polluées. L'activité de micro-organismes réducteurs de fer peut être stimulée de différentes manières pour augmenter l'oxydation de polluants organiques et la réduction de métaux. Des analyses moléculaires concernant des études de terrain et de laboratoire ont montré que des micro-organismes du genre Geobacter deviennent les membres dominants de la communauté microbienne quand les conditions de réduction en Fe(III) sont réalisées à la suite d'une pollution organique, ou lorsque la réduction en Fe(III) est stimulée artificiellement. Ces résultats laissent penser que des connaissances supplémentaires sur l'écophysiologie des espèces Geobacter devraient aider à une meilleure prédiction de la diminution naturelle des teneurs en polluants organiques dans des conditions anérobies, ainsi qu'à la définition de stratégies de dépollution biologique de pollutions souterraines par les métaux. Algunos microorganismos Fe(III)-reductores son capaces de destruir selectivamente determinados contaminantes orgánicos en condiciones anaerobias, oxidándolos a dióxido de carbono. Otros de estos microorganismos Fe(III)-reductores pueden reducir, bien compuestos clorados, bien una gran variedad de metales, que dejan de ser solubles y se inmovilizan en el subsuelo. Estudios realizados en acuéferos contaminados por petróleo muestran que los microorganismos Fe(III)-reductores pueden ser unos agentes muy eficientes para eliminar los hidrocarburos aromáticos de las aguas subterráneas en condiciones anaerobias, mientras que estudios de laboratorio muestran el potencial de estos microorganismos para eliminar uranio. La actividad de los microorganismos Fe(III)-reductores se puede estimular para conseguir una mayor eficiencia en la oxidación de contaminantes orgánicos y en la reducción de metales. Diversos análisis moleculares en estudios de campo y de laboratorio muestran que los microorganismos del género Geobacter se convierten en los miembros dominantes de la comunidad microbiana cuando se desarrollan condiciones Fe(III)-reductoras, bien como resultado de la contaminación orgánica, bien por estimulación artificial. En consecuencia, se hace necesario un mayor entendimiento de la ecofisiologéa de los microorganismos del género Geobacter para mejorar las predicciones sobre atenuación natural de los contaminantes orgánicos bajo condiciones anaerobias y para el diseño de estrategias de biorremediación del subsuelo en los casos de contaminación por metales.

STATE WATER RESOURCES RESEARCH INSTITUTE PROGRAM: GROUND WATER RESEARCH.

USGS Publications Warehouse

Burton, James S.; ,

1985-01-01

This paper updates a review of the accomplishments of the State Water Resources Research Program in ground water contamination research. The aim is to assess the progress made towards understanding the mechanisms of ground water contamination and based on this understanding, to suggest procedures for the prevention and control of ground water contamination. The following research areas are covered: (1) mechanisms of organic contaminant transport in the subsurface environment; (2) bacterial and viral contamination of ground water from landfills and septic tank systems; (3) fate and persistence of pesticides in the subsurface; (4) leachability and transport of ground water pollutants from coal production and utilization; and (5) pollution of ground water from mineral mining activities.

Subsurface Grain Morphology Reconstruction by Differential Aperture X-ray Microscopy

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

Eisenlohr, Philip; Shanthraj, Pratheek; Vande Kieft, Brendan R.

A multistep, non-destructive grain morphology reconstruction methodology that is applicable to near-surface volumes is developed and tested on synthetic grain structures. This approach probes the subsurface crystal orientation using differential aperture x-ray microscopy on a sparse grid across the microstructure volume of interest. Resulting orientation data are clustered according to proximity in physical and orientation space and used as seed points for an initial Voronoi tessellation to (crudely) approximate the grain morphology. Curvature-driven grain boundary relaxation, simulated by means of the Voronoi implicit interface method, progressively improves the reconstruction accuracy. The similarity between bulk and readily accessible surface reconstruction errormore » provides an objective termination criterion for boundary relaxation.« less

Characterization on White Etching Layer Formed During Ceramic Milling of Inconel 718

NASA Astrophysics Data System (ADS)

Kruk, A.; Wusatowska-Sarnek, A. M.; Ziętara, M.; Jemielniak, K.; Siemiątkowski, Z.; Czyrska-Filemonowicz, A.

2018-03-01

A comprehensive characterization of the near surface formed during the interrupted high-speed dry ceramic milling of IN718 was performed using light imaging, SEM/EDX, TEM and nano-hardness methods. It was found out that even an initial cut by a fresh tool creates a sub-surface alteration roughly 20 µm deep. The depth of altered sub-surface progressively changed to a roughly 40 µm when the tool reached an approximately half of its life, and almost 60 µm at the tool's end of the life. In the last two cases, the visible WEL (utilizing a light microscope) of the thickness roughly 6 and 15 µm was created, respectively. The outermost layer of the deformed subsurface was found to be for all three cases approximately 1.5 µm thick and composed of dynamically recrystallized γ phase grains with the average diameter of approximately 150 nm. This layer was free of δ phase and γ' or γ″ precipitates. It was followed by a plastically deformed zone.

Mini-review: Inhibition of biofouling by marine microorganisms.

PubMed

Dobretsov, Sergey; Abed, Raeid M M; Teplitski, Max

2013-01-01

Any natural or artificial substratum exposed to seawater is quickly fouled by marine microorganisms and later by macrofouling species. Microfouling organisms on the surface of a substratum form heterogenic biofilms, which are composed of multiple species of heterotrophic bacteria, cyanobacteria, diatoms, protozoa and fungi. Biofilms on artificial structures create serious problems for industries worldwide, with effects including an increase in drag force and metal corrosion as well as a reduction in heat transfer efficiency. Additionally, microorganisms produce chemical compounds that may induce or inhibit settlement and growth of other fouling organisms. Since the last review by the first author on inhibition of biofouling by marine microbes in 2006, significant progress has been made in the field. Several antimicrobial, antialgal and antilarval compounds have been isolated from heterotrophic marine bacteria, cyanobacteria and fungi. Some of these compounds have multiple bioactivities. Microorganisms are able to disrupt biofilms by inhibition of bacterial signalling and production of enzymes that degrade bacterial signals and polymers. Epibiotic microorganisms associated with marine algae and invertebrates have a high antifouling (AF) potential, which can be used to solve biofouling problems in industry. However, more information about the production of AF compounds by marine microorganisms in situ and their mechanisms of action needs to be obtained. This review focuses on the AF activity of marine heterotrophic bacteria, cyanobacteria and fungi and covers publications from 2006 up to the end of 2012.

How the microbiota shapes rheumatic diseases.

PubMed

Van de Wiele, Tom; Van Praet, Jens T; Marzorati, Massimo; Drennan, Michael B; Elewaut, Dirk

2016-07-01

The human gut harbours a tremendously diverse and abundant microbial community that correlates with, and even modulates, many health-related processes. The mucosal interfaces are particularly active sites of microorganism-host interplay. Growing insight into the characteristic composition and functionality of the mucosal microbiota has revealed that the microbiota is involved in mucosal barrier integrity and immune function. This involvement affects proinflammatory and anti-inflammatory processes not only at the epithelial level, but also at remote sites such as the joints. Here, we review the role of the gut microbiota in shaping local and systemic immune responses and how disturbances in the host-microorganism interplay can potentially affect the development and progression of rheumatic diseases. Increasing our understanding of how to promote host-microorganism homeostasis could therefore reveal novel strategies for the prevention or alleviation of rheumatic disease.

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.

Mechanisms for Electron Transfer Through Pili to Fe(III) Oxide in Geobacter

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

Lovley, Derek R.

The purpose of these studies was to aid the Department of Energy in its goal of understanding how microorganisms involved in the bioremediation of metals and radionuclides sustain their activity in the subsurface. This information is required in order to incorporate biological processes into decision making for environmental remediation and long-term stewardship of contaminated sites. The proposed research was designed to elucidate the mechanisms for electron transfer to Fe(III) oxides in Geobacter species because Geobacter species are abundant dissimilatory metal-reducing microorganisms in a diversity of sites in which uranium is undergoing natural attenuation via the reduction of soluble U(VI) tomore » insoluble U(IV) or when this process is artificially stimulated with the addition of organic electron donors. This study investigated the novel, but highly controversial, concept that the final conduit for electron transfer to Fe(III) oxides are electrically conductive pili. The specific objectives were to: 1) further evaluate the conductivity along the pili of Geobacter sulfurreducens and related organisms; 2) determine the mechanisms for pili conductivity; and 3) investigate the role of pili in Fe(III) oxide reduction. The studies demonstrated that the pili of G. sulfurreducens are conductive along their length. Surprisingly, the pili possess a metallic-like conductivity similar to that observed in synthetic organic conducting polymers such as polyaniline. Detailed physical analysis of the pili, as well as studies in which the structure of the pili was genetically modified, demonstrated that the metallic-like conductivity of the pili could be attributed to overlapping pi-pi orbitals of aromatic amino acids. Other potential mechanisms for conductivity, such as electron hopping between cytochromes associated with the pili were definitively ruled out. Pili were also found to be essential for Fe(III) oxide reduction in G. metallireducens. Ecological studies demonstrated that electron conduction along pili is a better strategy for Fe(III) oxide reduction under conditions found in the subsurface than producing an electron shuttle. The role of pili in uranium reduction was also elucidated. Our results are the first example of metallic-like conductivity in a biological protein and represent a paradigm shift in the understanding of long-range biological electron transport. The results are of importance not only for understanding subsurface microbial processes involved in the mobility of metal contaminants and carbon cycling, but also make a basic contribution to microbiology and the emerging field of bioelectronics.« less

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.

Integrating real-time subsurface hydrologic monitoring with empirical rainfall thresholds to improve landslide early warning

USGS Publications Warehouse

Mirus, Benjamin B.; Becker, Rachel E.; Baum, Rex L.; Smith, Joel B.

2018-01-01

Early warning for rainfall-induced shallow landsliding can help reduce fatalities and economic losses. Although these commonly occurring landslides are typically triggered by subsurface hydrological processes, most early warning criteria rely exclusively on empirical rainfall thresholds and other indirect proxies for subsurface wetness. We explore the utility of explicitly accounting for antecedent wetness by integrating real-time subsurface hydrologic measurements into landslide early warning criteria. Our efforts build on previous progress with rainfall thresholds, monitoring, and numerical modeling along the landslide-prone railway corridor between Everett and Seattle, Washington, USA. We propose a modification to a previously established recent versus antecedent (RA) cumulative rainfall thresholds by replacing the antecedent 15-day rainfall component with an average saturation observed over the same timeframe. We calculate this antecedent saturation with real-time telemetered measurements from five volumetric water content probes installed in the shallow subsurface within a steep vegetated hillslope. Our hybrid rainfall versus saturation (RS) threshold still relies on the same recent 3-day rainfall component as the existing RA thresholds, to facilitate ready integration with quantitative precipitation forecasts. During the 2015–2017 monitoring period, this RS hybrid approach has an increase of true positives and a decrease of false positives and false negatives relative to the previous RA rainfall-only thresholds. We also demonstrate that alternative hybrid threshold formats could be even more accurate, which suggests that further development and testing during future landslide seasons is needed. The positive results confirm that accounting for antecedent wetness conditions with direct subsurface hydrologic measurements can improve thresholds for alert systems and early warning of rainfall-induced shallow landsliding.

BOUNDS ON SUBSURFACE MERCURY FLUX FROM THE SULPHUR BANK MERCURY MINE, LAKE COUNTY, CALIFORNIA

EPA Science Inventory

The Sulphur Bank Mercury Mine (SBMM) in Lake County, California has been identified as a significant source of mercury to Clear Lake. The mine was operated from the 1860s through the 1950's. Mining started with surface operations, progressed to shaft mining, and later to open p...

The role of subsurface flow in hillslope and streambank erosion: A review of status and research needs

USDA-ARS?s Scientific Manuscript database

Sediment is the most common cause of stream impairment. Great progress has been made in understanding processes of soil erosion due to surface runoff and incorporating these in prediction technologies. However, in many landscapes the dominant source of sediment is derived from mass wasting of hillsl...

Diversity and Composition of Sulfate-Reducing Microbial Communities Based on Genomic DNA and RNA Transcription in Production Water of High Temperature and Corrosive Oil Reservoir

PubMed Central

Li, Xiao-Xiao; Liu, Jin-Feng; Zhou, Lei; Mbadinga, Serge M.; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

2017-01-01

Deep subsurface petroleum reservoir ecosystems harbor a high diversity of microorganisms, and microbial influenced corrosion is a major problem for the petroleum industry. Here, we used high-throughput sequencing to explore the microbial communities based on genomic 16S rDNA and metabolically active 16S rRNA analyses of production water samples with different extents of corrosion from a high-temperature oil reservoir. Results showed that Desulfotignum and Roseovarius were the most abundant genera in both genomic and active bacterial communities of all the samples. Both genomic and active archaeal communities were mainly composed of Archaeoglobus and Methanolobus. Within both bacteria and archaea, the active and genomic communities were compositionally distinct from one another across the different oil wells (bacteria p = 0.002; archaea p = 0.01). In addition, the sulfate-reducing microorganisms (SRMs) were specifically assessed by Sanger sequencing of functional genes aprA and dsrA encoding the enzymes adenosine-5′-phosphosulfate reductase and dissimilatory sulfite reductase, respectively. Functional gene analysis indicated that potentially active Archaeoglobus, Desulfotignum, Desulfovibrio, and Thermodesulforhabdus were frequently detected, with Archaeoglobus as the most abundant and active sulfate-reducing group. Canonical correspondence analysis revealed that the SRM communities in petroleum reservoir system were closely related to pH of the production water and sulfate concentration. This study highlights the importance of distinguishing the metabolically active microorganisms from the genomic community and extends our knowledge on the active SRM communities in corrosive petroleum reservoirs. PMID:28638372

Identification of subsurface microorganisms at Yucca Mountain; Third quarterly report, January 1, 1994--March 31, 1994

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

Stetzenbach, L.D.

1994-05-01

Bacteria isolated from ground water samples taken from 31 springs during 1993 were collected and processed according to procedures described in earlier reports. These procedures required aseptic collection of surface water samples in sterile screw-capped containers, transportation to the HRC microbiology laboratory, and culture by spread plating onto R2A medium. The isolates were further processed for identification using a gas chromatographic analysis of fatty acid methyl esters (FAME) extracted from cell membranes. This work generated a presumptive identification of 113 bacterial species distributed among 45 genera using a database obtained from Microbial ID, Inc., Newark, Delaware (MIDI). A preliminary examinationmore » of the FAME data was accomplished using cluster analysis and principal component analysis software obtained from MIDI. Typically, bacterial strains that cluster at less than 10 Euclidian distance units have fatty acid patterns consistent among members of the same species. Thus an organism obtained from one source can be recognized if it is isolated again from the same or any other source. This makes it possible to track the distribution of organisms and monitor environmental conditions or fluid transport mechanisms. Microorganisms are seldom found as monocultures in natural environments. They are more likely to be closely associated with other genera with complementary metabolic requirements. An understanding of the indigenous microorganism population is useful in understanding subtle changes in the environment. However, classification of environmental organisms using traditional methods is not ideal because differentiation of species with small variations or genera with very similar taxonomic characteristics is beyond the capabilities of traditional microbiological methods.« less

Modern Approach to Medical Diagnostics - the Use of Separation Techniques in Microorganisms Detection.

PubMed

Chylewska, Agnieszka; Ogryzek, M; Makowski, Mariusz

2017-10-23

New analytical and molecular methods for microorganisms are being developed on various features of identification i.e. selectivity, specificity, sensitivity, rapidity and discrimination of the viable cell. The presented review was established following the current trends in improved pathogens separation and detection methods and their subsequent use in medical diagnosis. This contribution also focuses on the development of analytical and biological methods in the analysis of microorganisms, with special attention paid to bio-samples containing microbes (blood, urine, lymph, wastewater). First, the paper discusses microbes characterization, their structure, surface, properties, size and then it describes pivotal points in the bacteria, viruses and fungi separation procedure obtained by researchers in the last 30 years. According to the above, detection techniques can be classified into three categories, which were, in our opinion, examined and modified most intensively during this period: electrophoretic, nucleic-acid-based, and immunological methods. The review covers also the progress, limitations and challenges of these approaches and emphasizes the advantages of new separative techniques in selective fractionating of microorganisms. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

On the relative role of meridional convergence and downwelling motion during the heat buildup leading to El Niño events

NASA Astrophysics Data System (ADS)

Ballester, Joan; Bordoni, Simona; Petrova, Desislava; Rodó, Xavier

2015-04-01

Despite steady progress in the understanding of El Niño-Southern Oscillation (ENSO) in the past decades, questions remain on the exact mechanisms leading to the onset of El Niño (EN) events. Several authors have highlighted how the subsurface heat buildup in the western tropical Pacific and the recharged phase in equatorial heat content are intrinsic elements of ENSO variability, leading to those changes in zonal wind stress, sea surface temperature and thermocline tilt that characterize the growing and mature phases of EN. Here we use an ensemble of ocean and atmosphere assimilation products to identify the mechanisms contributing to the heat buildup that precedes EN events by about 18-24 months on average. Anomalous equatorward subsurface mass convergence due to meridional Sverdrup transport is found to be an important mechanism of thermocline deepening near and to the east of the dateline. In the warm pool, instead, surface horizontal convergence and downwelling motion have a leading role in subsurface warming, since equatorward mass convergence is weaker and counterbalanced by subsurface zonal divergence. The picture emerging from our results highlights the complexity of the three dimensional dynamic and thermodynamic structure of the tropical Pacific during the heat buildup leading to EN events.

Development of radon-222 as a natural tracer for monitoring the remediation of NAPL contamination in the subsurface. 1998 annual progress report

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

Semprini, L.; Istok, J.

'The objective of this research is to develop a unique method of using naturally occurring radon-222 as a tracer for locating and quantitatively describing the presence of subsurface NAPL contamination. The research will evaluate using radon as an inexpensive, yet highly accurate, means of detecting NAPL contamination and assessing the effectiveness of NAPL remediation. Laboratory, field, and modeling studies are being performed to evaluate this technique, and to develop methods for its successful implementation in practice. This report summarizes work that has been accomplished after 1-year of a 3-year project. The research to date has included radon tracer tests inmore » physical aquifer models (PAMs) and field studies at Site 300 of the Lawrence Livermore National Laboratory, CA, and Site 100D at Hanford DOE Facility, WA. The PAM tests have evaluated the ability of radon as a tracer to monitor the remediation of TCE NAPL contamination using surfactant treatment, and oxidation with permanganate. The surfactant tests were performed in collaboration with Dr. Jack Istok and Dr. Jennifer Field and their EMSP project ``In-situ, Field-Scale Evaluation of Surfactant Enhanced DNAPL Recovery Using a Single-Well-Push-Pull Test.'''' This collaboration enabled the EMSP radon project to make rapid progress. The PAM surfactant tests were performed in a radial flow geometry to simulate the push-pull-method that is being developed for surfactant field tests. The radon tests were easily incorporated into these experiments, since they simply rely on measuring the natural radon present in the subsurface fluids. Two types of radon tests were performed: (1) static tests where radon was permitted to build-up to steady-state concentrations in the pore fluids and the groundwater concentrations were monitored, and (2) dynamic tests were the radon response during push-pull surfactant tests was measured. Both methods were found to be useful in determining how NAPL remediation was progressing.'« less

Looking For a Needle in the Haystack: Deciphering Indigenous 1.79 km Deep Subsurface Microbial Communities from Drilling Mud Contaminants Using 454 Pyrotag Sequencing

NASA Astrophysics Data System (ADS)

Dong, Y.; Cann, I.; Mackie, R.; Price, N.; Flynn, T. M.; Sanford, R.; Miller, P.; Chia, N.; Kumar, C. G.; Kim, P.; Sivaguru, M.; Fouke, B. W.

2010-12-01

Knowledge of the composition, structure and activity of microbial communities that live in deeply buried sedimentary rocks is fundamental to the future of subsurface biosphere stewardship as it relates to hydrocarbon exploration and extraction, carbon sequestration, gas storage and groundwater management. However, the study of indigenous subsurface microorganisms has been limited by the technical challenges of collecting deep formation water samples that have not been heavily contaminated by the mud used to drill the wells. To address this issue, a “clean-sampling method” deploying the newly developed Schlumberger Quicksilver MDT probe was used to collect a subsurface sample at a depth of 1.79 km (5872 ft) from an exploratory well within Cambrian-age sandstones in the Illinois Basin. This yielded a formation water sample that was determined to have less than 4% drilling mud contamination based on tracking changes in the aqueous geochemistry of the formation water during ~3 hours of pumping at depth prior to sample collection. A suite of microscopy and culture-independent molecular analyses were completed using the DNA extracted from microbial cells in the formation water, which included 454 amplicon pyrosequencing that targeted the V1-V3 hypervariable region of bacterial 16S rRNA gene sequences. Results demonstrated an extremely low diversity microbial community living in formation water at 1.79 km-depth. More than 95 % of the total V1-V3 pyrosequencing reads (n=11574) obtained from the formation water were affiliated with a halophilic γ-proteobacterium and most closely related to the genus Halomonas. In contrast, about 3 % of the V1-V3 sequences in the drilling mud library (n=13044) were classified as genus Halomonas but were distinctly different and distantly related to the formation water Halomonas detected at 1.79 km-depth. These results were consistent with those obtained using a suite of other molecular screens (e.g., Terminal-Restriction Fragment Length Polymorphism (T-RFLP) and the initial full length 16S rRNA amplicon libraries) and bioinformatic analyses (e.g., 16S rRNA and Open Reading Frame (ORF) calls established from the 454 metagenomic community analyses). Functional pathway modeling is underway to evaluate the adaptation of this indigenous microbial community to the hydrologic and geologic history of the deep subsurface environment of the Illinois Basin.

Molecular ecology of hydrothermal vent microbial communities.

PubMed

Jeanthon, C

2000-02-01

The study of the structure and diversity of hydrothermal vent microbial communities has long been restricted to the morphological description of microorganisms and the use of enrichment culture-based techniques. Until recently the identification of the culturable fraction required the isolation of pure cultures followed by testing for multiple physiological and biochemical traits. However, peculiar inhabitants of the hydrothermal ecosystem such as the invertebrate endosymbionts and the dense microbial mat filaments have eluded laboratory cultivation. Substantial progress has been achieved in recent years in techniques for the identification of microorganisms in natural environments. Application of molecular approaches has revealed the existence of unique and previously unrecognized microorganisms. These have provided fresh insight into the ecology, diversity and evolution of mesophilic and thermophilic microbial communities from the deep-sea hydrothermal ecosystem. This review reports the main discoveries made through the introduction of these powerful techniques in the study of deep-sea hydrothermal vent microbiology.

Trash to treasure: production of biofuels and commodity chemicals via syngas fermenting microorganisms.

PubMed

Latif, Haythem; Zeidan, Ahmad A; Nielsen, Alex T; Zengler, Karsten

2014-06-01

Fermentation of syngas is a means through which unutilized organic waste streams can be converted biologically into biofuels and commodity chemicals. Despite recent advances, several issues remain which limit implementation of industrial-scale syngas fermentation processes. At the cellular level, the energy conservation mechanism of syngas fermenting microorganisms has not yet been entirely elucidated. Furthermore, there was a lack of genetic tools to study and ultimately enhance their metabolic capabilities. Recently, substantial progress has been made in understanding the intricate energy conservation mechanisms of these microorganisms. Given the complex relationship between energy conservation and metabolism, strain design greatly benefits from systems-level approaches. Numerous genetic manipulation tools have also been developed, paving the way for the use of metabolic engineering and systems biology approaches. Rational strain designs can now be deployed resulting in desirable phenotypic traits for large-scale production. Copyright © 2013 Elsevier Ltd. All rights reserved.

[Progress in synthetic biology of pinocembrin].

PubMed

Guo, Lei; Kong, Jianqiang

2015-04-01

Pinocembrin, belonging to flavanons, was isolated from various plants. Pinocembrin has a variety of pharmacological activities, such as neuroprotective effect, antimicrobial activity, and antioxidant efficacy. Pinocembrin was approved as class I drugs to its phase II clinical trial by CFDA in 2009, mainly used for the treatment of ischemic stroke. As a promising compound, the manufacturing technologies of pinocembrin, including chemical synthesis, extraction from plant and synthetic biology, have attracted many attentions. Compared with the first two technologies, synthetic biology has many advantages, such as environment-friendly and low-cost. Construction of biosynthetic pathway in microorganism offers promising results for large scale pinocembrin production by fermentation after taking lots of effective strategies. This article reviews some of recent strategies in microorganisms to improve the yield, with focus on the selection of appropriate the key enzyme sources, the supply of precursors and cofactors by microorganisms, the choice of substance and the level of the key enzyme expression.

Subsurface Grain Morphology Reconstruction by Differential Aperture X-ray Microscopy

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

Eisenlohr, Philip; Shanthraj, Pratheek; Vande Kieft, Brendan R.

A multistep, non-destructive grain morphology reconstruction methodology that is applicable to near-surface volumes is developed and tested on synthetic grain structures. This approach probes the subsurface crystal orientation using differential aperture X-ray microscopy (DAXM) on a sparse grid across the microstructure volume of interest. Resulting orientation data is clustered according to proximity in physical and orientation space and used as seed points for an initial Voronoi tessellation to (crudely) approximate the grain morphology. Curvature-driven grain boundary relaxation, simulated by means of the Voronoi Implicit Interface Method (VIIM), progressively improves the reconstruction accuracy. The similarity between bulk and readily accessible surfacemore » reconstruction error provides an objective termination criterion for boundary relaxation.« less

THE ROLE OF MICROORGANISMS IN ELEMENTAL MERCURY FORMATION IN NATURAL WATERS. (R824778)

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...

KINETICS OF PCB DECHLORINATION BY HUDSON RIVER, NEW YORK, USA, SEDIMENT MICROORGANISMS. (R825449)

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...

RAPID DETECTION OF MICROORGANISMS USING 5S RRNA SPECIFIC MOLECULAR BEACONS. (R825354)

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...

Gut microbiota, epigenetic modification and colorectal cancer

PubMed Central

Rezasoltani, Sama; Asadzadeh-Aghdaei, Hamid; Nazemalhosseini-Mojarad, Ehsan; Dabiri, Hossein; Ghanbari, Reza; Zali, Mohammad Reza

2017-01-01

Micro-organisms contain 90% of cells in human body and trillions foreign genes versus less than 30 thousand of their own. The human colon host various species of microorganisms, appraised at more than 1014 microbiota and contained of over a thousand species. Although each one’s profile is separable, the relative abundance and distribution of bacterial species is the same between healthy ones, causing conservation of each person’s overall health. Germline DNA mutations have been attributed to the less than 5% of CRC occurrence while more than 90% is associated with the epigenetic regulation. The most ubiquitous environmental factor in epigenetic modification is gut microbiota. Disruptive changes in the gut microbiome strongly contributed to the improvement of colorectal cancer. Gut microbiota may play critical role in progression of CRC via their metabolite or their structural component interacting with host intestinal epithelial cell (IEC). Herein we discuss the mechanism of epigenetic modification and its implication in CRC development, progression even metastasis by gut microbiota induction. PMID:29213996

A minimalistic microbial food web in an excavated deep subsurface clay rock.

PubMed

Bagnoud, Alexandre; de Bruijn, Ino; Andersson, Anders F; Diomidis, Nikitas; Leupin, Olivier X; Schwyn, Bernhard; Bernier-Latmani, Rizlan

2016-01-01

Clay rocks are being considered for radioactive waste disposal, but relatively little is known about the impact of microbes on the long-term safety of geological repositories. Thus, a more complete understanding of microbial community structure and function in these environments would provide further detail for the evaluation of the safety of geological disposal of radioactive waste in clay rocks. It would also provide a unique glimpse into a poorly studied deep subsurface microbial ecosystem. Previous studies concluded that microorganisms were present in pristine Opalinus Clay, but inactive. In this work, we describe the microbial community and assess the metabolic activities taking place within borehole water. Metagenomic sequencing and genome-binning of a porewater sample containing suspended clay particles revealed a remarkably simple heterotrophic microbial community, fueled by sedimentary organic carbon, mainly composed of two organisms: a Pseudomonas sp. fermenting bacterium growing on organic macromolecules and releasing organic acids and H2, and a sulfate-reducing Peptococcaceae able to oxidize organic molecules to CO(2). In Opalinus Clay, this microbial system likely thrives where pore space allows it. In a repository, this may occur where the clay rock has been locally damaged by excavation or in engineered backfills. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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.

Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes.

PubMed

Graham, Emily B; Crump, Alex R; Resch, Charles T; Fansler, Sarah; Arntzen, Evan; Kennedy, David W; Fredrickson, Jim K; Stegen, James C

2017-04-01

Subsurface groundwater-surface water mixing zones (hyporheic zones) have enhanced biogeochemical activity, but assembly processes governing subsurface microbiomes remain a critical uncertainty in understanding hyporheic biogeochemistry. To address this obstacle, we investigated (a) biogeographical patterns in attached and waterborne microbiomes across three hydrologically-connected, physicochemically-distinct zones (inland hyporheic, nearshore hyporheic and river); (b) assembly processes that generated these patterns; (c) groups of organisms that corresponded to deterministic changes in the environment; and (d) correlations between these groups and hyporheic metabolism. All microbiomes remained dissimilar through time, but consistent presence of similar taxa suggested dispersal and/or common selective pressures among zones. Further, we demonstrated a pronounced impact of deterministic assembly in all microbiomes as well as seasonal shifts from heterotrophic to autotrophic microorganisms associated with increases in groundwater discharge. The abundance of one statistical cluster of organisms increased with active biomass and respiration, revealing organisms that may strongly influence hyporheic biogeochemistry. Based on our results, we propose a conceptualization of hyporheic zone metabolism in which increased organic carbon concentrations during surface water intrusion support heterotrophy, which succumbs to autotrophy under groundwater discharge. These results provide new opportunities to enhance microbially-explicit ecosystem models describing hyporheic zone biogeochemistry and its influence over riverine ecosystem function. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

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

Use of an uncertainty analysis for genome-scale models as a prediction tool for microbial growth processes in subsurface environments.

PubMed

Klier, Christine

2012-03-06

The integration of genome-scale, constraint-based models of microbial cell function into simulations of contaminant transport and fate in complex groundwater systems is a promising approach to help characterize the metabolic activities of microorganisms in natural environments. In constraint-based modeling, the specific uptake flux rates of external metabolites are usually determined by Michaelis-Menten kinetic theory. However, extensive data sets based on experimentally measured values are not always available. In this study, a genome-scale model of Pseudomonas putida was used to study the key issue of uncertainty arising from the parametrization of the influx of two growth-limiting substrates: oxygen and toluene. The results showed that simulated growth rates are highly sensitive to substrate affinity constants and that uncertainties in specific substrate uptake rates have a significant influence on the variability of simulated microbial growth. Michaelis-Menten kinetic theory does not, therefore, seem to be appropriate for descriptions of substrate uptake processes in the genome-scale model of P. putida. Microbial growth rates of P. putida in subsurface environments can only be accurately predicted if the processes of complex substrate transport and microbial uptake regulation are sufficiently understood in natural environments and if data-driven uptake flux constraints can be applied.

The biogeochemical fate of nickel during microbial ISA degradation; implications for nuclear waste disposal.

PubMed

Kuippers, Gina; Boothman, Christopher; Bagshaw, Heath; Ward, Michael; Beard, Rebecca; Bryan, Nicholas; Lloyd, Jonathan R

2018-06-08

Intermediate level radioactive waste (ILW) generally contains a heterogeneous range of organic and inorganic materials, of which some are encapsulated in cement. Of particular concern are cellulosic waste items, which will chemically degrade under the conditions predicted during waste disposal, forming significant quantities of isosaccharinic acid (ISA), a strongly chelating ligand. ISA therefore has the potential to increase the mobility of a wide range of radionuclides via complex formation, including Ni-63 and Ni-59. Although ISA is known to be metabolized by anaerobic microorganisms, the biodegradation of metal-ISA complexes remains unexplored. This study investigates the fate of a Ni-ISA complex in Fe(III)-reducing enrichment cultures at neutral pH, representative of a microbial community in the subsurface. After initial sorption of Ni onto Fe(III)oxyhydroxides, microbial ISA biodegradation resulted in >90% removal of the remaining Ni from solution when present at 0.1 mM, whereas higher concentrations of Ni proved toxic. The microbial consortium associated with ISA degradation was dominated by close relatives to Clostridia and Geobacter species. Nickel was preferentially immobilized with trace amounts of biogenic amorphous iron sulfides. This study highlights the potential for microbial activity to help remove chelating agents and radionuclides from the groundwater in the subsurface geosphere surrounding a geodisposal facility.

Assessment of a Hydroxyapatite Permeable Reactive Barrier to Remediate Uranium at the Old Rifle Site Colorado.

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

Moore, Robert C.; Szecsody, James; Rigali, Mark J.

We have performed an initial evaluation and testing program to assess the effectiveness of a hydroxyapatite (Ca10(PO4)6(OH)2) permeable reactive barrier and source area treatment to decrease uranium mobility at the Department of Energy (DOE) former Old Rifle uranium mill processing site in Rifle, western Colorado. Uranium ore was processed at the site from the 1940s to the 1970s. The mill facilities at the site as well as the uranium mill tailings previously stored there have all been removed. Groundwater in the alluvial aquifer beneath the site still contains elevated concentrations of uranium, and is currently used for field tests tomore » study uranium behavior in groundwater and investigate potential uranium remediation technologies. The technology investigated in this work is based on in situ formation of apatite in sediment to create a subsurface apatite PRB and also for source area treatment. The process is based on injecting a solution containing calcium citrate and sodium into the subsurface for constructing the PRB within the uranium plume. As the indigenous sediment micro-organisms biodegrade the injected citrate, the calcium is released and reacts with the phosphate to form hydroxyapatite (precipitate). This paper reports on proof-of-principle column tests with Old Rifle sediment and synthetic groundwater.« less

Comparison of Bacterial Diversity in Azorean and Hawai’ian Lava Cave Microbial Mats

PubMed Central

MARSHALL HATHAWAY, JENNIFER J.; GARCIA, MATTHEW G.; BALASCH, MONICA MOYA; SPILDE, MICHAEL N.; STONE, FRED D.; DAPKEVICIUS, MARIA DE LURDES N. E.; AMORIM, ISABEL R.; GABRIEL, ROSALINA; BORGES, PAULO A. V.; NORTHUP, DIANA E.

2015-01-01

Worldwide, lava caves host colorful microbial mats. However, little is known about the diversity of these microorganisms, or what role they may play in the subsurface ecosystem. White and yellow microbial mats were collected from four lava caves each on the Azorean island of Terceira and the Big Island of Hawai’i, to compare the bacterial diversity found in lava caves from two widely separated archipelagos in two different oceans at different latitudes. Scanning electron microscopy of mat samples showed striking similarities between Terceira and Hawai’ian microbial morphologies. 16S rRNA gene clone libraries were constructed to determine the diversity within these lava caves. Fifteen bacterial phyla were found across the samples, with more Actinobacteria clones in Hawai’ian communities and greater numbers of Acidobacteria clones in Terceira communities. Bacterial diversity in the subsurface was correlated with a set of factors. Geographical location was the major contributor to differences in community composition (at the OTU level), together with differences in the amounts of organic carbon, nitrogen and copper available in the lava rock that forms the cave. These results reveal, for the first time, the similarity among the extensive bacterial diversity found in lava caves in two geographically separate locations and contribute to the current debate on the nature of microbial biogeography. PMID:26924866

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

Hydraulic fracturing offers view of microbial life in the deep terrestrial subsurface.

PubMed

Mouser, Paula J; Borton, Mikayla; Darrah, Thomas H; Hartsock, Angela; Wrighton, Kelly C

2016-11-01

Horizontal drilling and hydraulic fracturing are increasingly used for recovering energy resources in black shales across the globe. Although newly drilled wells are providing access to rocks and fluids from kilometer depths to study the deep biosphere, we have much to learn about microbial ecology of shales before and after 'fracking'. Recent studies provide a framework for considering how engineering activities alter this rock-hosted ecosystem. We first provide data on the geochemical environment and microbial habitability in pristine shales. Next, we summarize data showing the same pattern across fractured shales: diverse assemblages of microbes are introduced into the subsurface, eventually converging to a low diversity, halotolerant, bacterial and archaeal community. Data we synthesized show that the shale microbial community predictably shifts in response to temporal changes in geochemistry, favoring conservation of key microorganisms regardless of inputs, shale location or operators. We identified factors that constrain diversity in the shale and inhibit biodegradation at the surface, including salinity, biocides, substrates and redox. Continued research in this engineered ecosystem is required to assess additive biodegradability, quantify infrastructure biocorrosion, treat wastewaters that return to the surface and potentially enhance energy production through in situ methanogenesis. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

ANNUAL REPORT FOR ENVIRONMENTAL MANAGEMENT SCIENCE PROGRAM PROJECT NUMBER 87016 CO-PRECIPITATION OF TRACE METALS IN GROUNDWATER AND VADOSE ZONE CALCITE: IN SITU CONTAINMENT AND STABILIZATION OF STRONTIUM-90 AND OTHER DIVALENT METALS AND RADIONUCLIDES AT ARID WESTERN DOE SITES

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

Smith, Robert W.; Fujita, Yoshiko; Ferris, F. Grant

2003-06-15

Radionuclide and metal contaminants such as 90Sr are present beneath U.S. Department of Energy (DOE) lands in both the groundwater (e.g., 100-N area at Hanford, WA) and vadose zone (e.g., Idaho Nuclear Technology and Engineering Center at the Idaho National Engineering and Environmental Laboratory). In situ containment and stabilization of these contaminants is a cost-effective treatment strategy. However, implementing in situ containment and stabilization approaches requires definition of the mechanisms that control contaminant sequestration. We are investigating the in situ immobilization of radionuclides or contaminant metals (e.g., 90Sr) by their facilitated co-precipitation with calcium carbonate in groundwater and vadose zonemore » systems. Our facilitated approach, shown schematically in Figure 1, relies upon the hydrolysis of introduced urea to cause the acceleration of calcium carbonate precipitation (and trace metal co-precipitation) by increasing pH and alkalinity. Subsurface urea hydrolysis is catalyzed by the urease enzyme, which may be either introduced with the urea or produced in situ by ubiquitous subsurface urea hydrolyzing microorganisms. Because the precipitation process tends to be irreversible and many western aquifers are saturated with respect to calcite, the coprecipitated metals and radionuclides will be effectively removed from the aqueous phase over the long-term. Another advantage of the ureolysis approach is that the ammonium ions produced by the reaction can exchange with radionuclides sorbed to subsurface minerals, thereby enhancing the availability of the radionuclides for re-capture in a more stable solid phase (co-precipitation rather than adsorption).« less

Seasonal Progression and Interannual Variability of Nutrient and Chlorophyll-a Distributions in the Northern Gulf of Alaska, 1998-2010

NASA Astrophysics Data System (ADS)

Trahanovsky, K.; Whitledge, T. E.

2016-02-01

We examined nutrient and chlorophyll-a (chl) concentrations from bottle samples collected from 0-50 m depth in the Northern Gulf of Alaska along the Seward Line transect on 56 cruises from 1998-2010. We computed monthly average concentrations of macronutrients (N, P, and Si) and chlorophyll-a by depth at four major stations along the transect to describe the regular seasonal progression of the nutricline and typical water column distributions of chlorophyll-a in this seasonally productive, downwelling coastal zone. The across-shelf transect displayed two different patterns of seasonal progression clearly associated with the Alaska Coastal Current (ACC) and Alaskan Stream (AS) current systems. The annual cycle of nutrient drawdown and replenishment is remarkably consistent from year to year within each system and is well correlated with chl measurements. The spring bloom begins earlier and nutrient depletion is sustained longer in the near-shore ACC then in the AS system centered over the shelf break. Chlorophyll-a concentrations frequently peak at 10-20m depth in both systems during July through October, as nutrients remain depleted in the top 10m. Subsurface nutrients (20 - 50 m depth) begin to recover between July and August and then experience a secondary drawdown between August and October, consistent with higher chl levels observed during the fall bloom. Interannual variability in the progression of the nutricline and the relative contribution of subsurface chl to total chl is presented. Physical data demonstrate increasing stratification in this region due to climate change; the implications for nutrient dynamics and primary production are discussed.

A Torino Scale for Europa and Icy Satellites: A Potential Means for Evaluating the Impact Cratering's Contribution to an Icy Shell's Energy Budget

NASA Astrophysics Data System (ADS)

Bierhaus, E. B.

2017-11-01

Impacts on Europa mix surface and subsurface material, introduce fracturing, and at progressively larger sizes, result in deeper melting (and mixing) within the ice shell. The largest sizes punch through the ice, providing a direct, albeit temporary, conduit between the ocean and the surface.

The Cartridge Theory: a description of the functioning of horizontal subsurface flow constructed wetlands for wastewater treatment, based on modelling results.

PubMed

Samsó, Roger; García, Joan

2014-03-01

Despite the fact that horizontal subsurface flow constructed wetlands have been in operation for several decades now, there is still no clear understanding of some of their most basic internal functioning patterns. To fill this knowledge gap, on this paper we present what we call "The Cartridge Theory". This theory was derived from simulation results obtained with the BIO_PORE model and explains the functioning of urban wastewater treatment wetlands based on the interaction between bacterial communities and the accumulated solids leading to clogging. In this paper we start by discussing some changes applied to the biokinetic model implemented in BIO_PORE (CWM1) so that the growth of bacterial communities is consistent with a well-known population dynamics models. This discussion, combined with simulation results for a pilot wetland system, led to the introduction of "The Cartridge Theory", which states that the granular media of horizontal subsurface flow wetlands can be assimilated to a generic cartridge which is progressively consumed (clogged) with inert solids from inlet to outlet. Simulations also revealed that bacterial communities are poorly distributed within the system and that their location is not static but changes over time, moving towards the outlet as a consequence of the progressive clogging of the granular media. According to these findings, the life-span of constructed wetlands corresponds to the time when bacterial communities are pushed as much towards the outlet that their biomass is not anymore sufficient to remove the desirable proportion of the influent pollutants. Copyright © 2013 Elsevier B.V. All rights reserved.

Iatrogenic Damage to the Periodontium Caused by Periodontal Treatment Procedures

PubMed Central

Latheef, P; Sirajuddin, Syed; Gundapaneni, Veenadharini; MN, Kumuda; Apine, Ashwini

2015-01-01

Periodontitis is an inflammatory disease affecting the periodontium i.e. the tissues that surround and support the teeth. Periodontitis manifests as progressive loss of the alveolar bone around the teeth, and if left untreated, can cause loosening and subsequent loss of teeth. Periodontitis is initiated by microorganisms that adhere to and grow on the tooth's surfaces, besides an over -aggressive immune response against these microorganisms. The primary goal of periodontal therapy is to preserve the natural dentition by accomplishing and preserving a healthy functional periodontium. Many treatment modalities have been introduced to improve the therapeutic result of periodontal treatment which may also damage the periodontiumiatrogenically. PMID:26312087

Recent research progress on microbial L-asparaginases.

PubMed

Zuo, Shaohua; Zhang, Tao; Jiang, Bo; Mu, Wanmeng

2015-02-01

L-Asparaginases (EC 3.5.1.1) are enzymes that catalyze the hydrolysis of L-asparagine to L-aspartic acid and found in a variety of organisms from microorganisms to mammals. However, they are mainly expressed and produced by microorganisms. Microbial L-asparaginases have received sustained attention due to their irreplaceable role in the therapy of acute lymphoblastic leukemia and for their inhibition of acrylamide formation during food processing. In this article, we review the application of microbial L-asparaginases in medical treatments and acrylamide mitigation. In addition, we describe in detail recent advances in the existing sources, purification, production, properties, molecular modification, and immobilization of L-asparaginase.

Technical progress report of biological research on the Volcanic Island Surtsey and its environs for the period 1965--1978

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

Fridriksson, S.

Progress is reported on the following research projects: changes in shoreline and surface of the island due to volcanic activity; colonization of microorganisms, algae, lichens, and vascular plants; introduction of insects and other arthropods by wind, water, and man; transport of invertebrates to the island by flotsam of the sea; species and nesting habits of birds on the island; behavior of seals on beaches of the island; and future trends of Surtsey ecosystems. (HLW)

Beneficial Uses Program progress report, period ending December 31, 1976. [Gamma inactivation of microorganisms in sewage sludge

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

Not Available

1977-03-01

Progress is reported on a comprehensive program to develop the necessary technologies for cost/beneficial uses of existing and future surplus radioactive materials. The major portion of the work was concentrated on the testing of the effectiveness of ..gamma.. sources for the processing of sewage sludge to inactivate enteric viruses and bacteria and the subsequent testing of the biological effects of the treated sludge when used as fertilizer or additives to animal feeds.

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.

Geotechnical sensing using electromagnetic attenuation between radio transceivers

NASA Astrophysics Data System (ADS)

Ghazanfari, Ehsan; Pamukcu, Sibel; Yoon, Suk-Un; Suleiman, Muhannad T.; Cheng, Liang

2012-12-01

Monitoring the onset of a geo-event such as the intrusion of a chemical plume or a slow progressive mass slide that results in marked changes in the physical properties of the host soil could be potentially accomplished using a distributed network of embedded radio transceivers. This paper introduces a new concept of subsurface geo-event monitoring, which takes advantage of the spatial and temporal variations in signal strength of electromagnetic (EM) waves transmitted within the net of distributed radios within a sensing area. Results of experiments in the laboratory and the field demonstrated that variations in EM signal strength could be used to detect physical changes in the subsurface. Changes in selected physical properties of host soil including water content, density, and formation of discontinuities could be discerned from the changes in the signal strength of the transmitted wave between embedded radio transceivers. Good agreement was observed between a theoretical model and the experimental results for inter-transceiver distances less than 55 cm. These results demonstrated a viable new approach for distributed sensing and monitoring of subsurface hazards for civil infrastructure within a networked domain of radio transceivers.

The Microbiology of Subsurface, Salt-Based Nuclear Waste Repositories: Using Microbial Ecology, Bioenergetics, and Projected Conditions to Help Predict Microbial Effects on Repository Performance

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

Swanson, Juliet S.; Cherkouk, Andrea; Arnold, Thuro

This report summarizes the potential role of microorganisms in salt-based nuclear waste repositories using available information on the microbial ecology of hypersaline environments, the bioenergetics of survival under high ionic strength conditions, and “repository microbiology” related studies. In areas where microbial activity is in question, there may be a need to shift the research focus toward feasibility studies rather than studies that generate actual input for performance assessments. In areas where activity is not necessary to affect performance (e.g., biocolloid transport), repository-relevant data should be generated. Both approaches will lend a realistic perspective to a safety case/performance scenario that willmore » most likely underscore the conservative value of that case.« less

Powering microbes with electricity: direct electron transfer from electrodes to microbes.

PubMed

Lovley, Derek R

2011-02-01

The discovery of electrotrophs, microorganisms that can directly accept electrons from electrodes for the reduction of terminal electron acceptors, has spurred the investigation of a wide range of potential applications. To date, only a handful of pure cultures have been shown to be capable of electrotrophy, but this process has also been inferred in many studies with undefined consortia. Potential electron acceptors include: carbon dioxide, nitrate, metals, chlorinated compounds, organic acids, protons and oxygen. Direct electron transfer from electrodes to cells has many advantages over indirect electrical stimulation of microbial metabolism via electron shuttles or hydrogen production. Supplying electrons with electrodes for the bioremediation of chlorinated compounds, nitrate or toxic metals may be preferable to adding organic electron donors or hydrogen to the subsurface or bioreactors. The most transformative application of electrotrophy may be microbial electrosynthesis in which carbon dioxide and water are converted to multi-carbon organic compounds that are released extracellularly. Coupling photovoltaic technology with microbial electrosynthesis represents a novel photosynthesis strategy that avoids many of the drawbacks of biomass-based strategies for the production of transportation fuels and other organic chemicals. The mechanisms for direct electron transfer from electrodes to microorganisms warrant further investigation in order to optimize envisioned applications. © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.

Activation of CO2-reducing methanogens in oil reservoir after addition of nutrient.

PubMed

Yang, Guang-Chao; Zhou, Lei; Mbadinga, Serge Maurice; You, Jing; Yang, Hua-Zhen; Liu, Jin-Feng; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

2016-12-01

Nutrient addition as part of microbial enhanced oil recovery (MEOR) operations have important implications for more energy recovery from oil reservoirs, but very little is known about the in situ response of microorganisms after intervention. An analysis of two genes as biomarkers, mcrA encoding the key enzyme in methanogenesis and fthfs encoding the key enzyme in acetogenesis, was conducted during nutrient addition in oil reservoir. Clone library data showed that dominant mcrA sequences changed from acetoclastic (Methanosaetaceae) to CO 2 -reducing methanogens (Methanomicrobiales and Methanobacteriales), and the authentic acetogens affiliated to Firmicutes decreased after the intervention. Principal coordinates analysis (PCoA) and Jackknife environment clusters revealed evidence on the shift of the microbial community structure among the samples. Quantitative analysis of methanogens via qPCR showed that Methanobacteriales and Methanomicrobiales increased after nutrient addition, while acetoclastic methanogens (Methanosaetaceae) changed slightly. Nutrient treatment activated native CO 2 -reducing methanogens in oil reservoir. The high frequency of Methanobacteriales and Methanomicrobiales (CO 2 -reducers) after nutrient addition in this petroleum system suggested that CO 2 -reducing methanogenesis was involved in methane production. The nutrient addition could promote the methane production. The results will likely improve strategies of utilizing microorganisms in subsurface environments. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Isolation of Geobacter species from diverse sedimentary environments

USGS Publications Warehouse

Coaxes, J.D.; Phillips, E.J.P.; Lonergan, D.J.; Jenter, H.; Lovley, D.R.

1996-01-01

In an attempt to better understand the microorganisms responsible for Fe(III) reduction in sedimentary environments, Fe(III)-reducing microorganisms were enriched for and isolated from freshwater aquatic sediments, a pristine deep aquifer, and a petroleum-contaminated shallow aquifer. Enrichments were initiated with acetate or toluene as the electron donor and Fe(III) as the electron acceptor. Isolations were made with acetate or benzoate. Five new strains which could obtain energy for growth by dissimilatory Fe(III) reduction were isolated. All five isolates are gram- negative strict anaerobes which grow with acetate as the electron donor and Fe(III) as the electron acceptor. Analysis of the 16S rRNA sequence of the isolated organisms demonstrated that they all belonged to the genus Geobacter in the delta subdivision of the Proteobacteria. Unlike the type strain, Geobacter metallireducens, three of the five isolates could use H2 as an electron donor fur Fe(III) reduction. The deep subsurface isolate is the first Fe(III) reducer shown to completely oxidize lactate to carbon dioxide, while one of the freshwater sediment isolates is only the second Fe(III) reducer known that can oxidize toluene. The isolation of these organisms demonstrates that Geobacter species are widely distributed in a diversity of sedimentary environments in which Fe(III) reduction is an important process.

Lack of correlation of desiccation and radiation tolerance in microorganisms from diverse extreme environments tested under anoxic conditions

PubMed Central

Bohmeier, Maria; Perras, Alexandra K; Schwendner, Petra; Rabbow, Elke; Moissl-Eichinger, Christine; Cockell, Charles S; Vannier, Pauline; Marteinsson, Viggo T; Monaghan, Euan P; Ehrenfreund, Pascale; Garcia-Descalzo, Laura; Gómez, Felipe; Malki, Moustafa; Amils, Ricardo; Gaboyer, Frédéric; Westall, Frances; Cabezas, Patricia; Walter, Nicolas; Rettberg, Petra

2018-01-01

Abstract Four facultative anaerobic and two obligate anaerobic bacteria were isolated from extreme environments (deep subsurface halite mine, sulfidic anoxic spring, mineral-rich river) in the frame MASE (Mars Analogues for Space Exploration) project. The isolates were investigated under anoxic conditions for their survivability after desiccation up to 6 months and their tolerance to ionizing radiation up to 3000 Gy. The results indicated that tolerances to both stresses are strain-specific features. Yersinia intermedia MASE-LG-1 showed a high desiccation tolerance but its radiation tolerance was very low. The most radiation-tolerant strains were Buttiauxella sp. MASE-IM-9 and Halanaerobium sp. MASE-BB-1. In both cases, cultivable cells were detectable after an exposure to 3 kGy of ionizing radiation, but cells only survived desiccation for 90 and 30 days, respectively. Although a correlation between desiccation and ionizing radiation resistance has been hypothesized for some aerobic microorganisms, our data showed that there was no correlation between tolerance to desiccation and ionizing radiation, suggesting that the physiological basis of both forms of tolerances is not necessarily linked. In addition, these results indicated that facultative and obligate anaerobic organisms living in extreme environments possess varied species-specific tolerances to extremes. PMID:29474542

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

Goltz, M.N.; Hopkins, G.D.; Kawakami, B.T.

A trichloroethylene (TCE) ground water plume at Edwards AFB in Southern California is being used to demonstrate in situ aerobic cometabolic bioremediation in the field. The bioremediation system that will be demonstrated at Edwards was developed over nine years of research and testing in the laboratory and at a pilot field site located at Moffett Federal Airfield in Mountain View, California. Studies conducted at the Moffett field site have demonstrated that TCE can be effectively biodegraded cometabolically through the introduction into the subsurface of a primary substrate and an oxygen source to support the growth and energy requirements of amore » native population of microorganisms. A system to demonstrate the feasibility of in situ aerobic cometabolic bioremediation is presently being constructed at Edwards, using an area of the plume having TCE concentrations ranging up to 1 mg/L. A major objective of the Edwards study will be to investigate how a primary substrate and an oxygen source can be efficiently mixed and transported to indigenous microorganisms, in order to promote cometabolic degradation of TCE. In this presentation, the earlier studies at Moffett, as well as the preliminary modeling work and site characterization which have been conducted in preparation for the Edwards demonstration, will be presented. In addition, problems encountered and lessons learned bringing an innovative technology from the laboratory to the field will be discussed.« less

Mineralogical controls on surface colonization by sulfur-metabolizing microbial communities

NASA Astrophysics Data System (ADS)

Jones, A. A.; Bennett, P.

2012-12-01

When characterizing microbial diversity and the microbial ecosystem of the shallow subsurface the mineral matrix is generally assumed to be homogenous and unreactive. We report here experimental evidence that microorganisms colonize rock surfaces according to the rock's chemistry and the organism's metabolic requirements and tolerances. We investigated this phenomenon using laboratory biofilm reactors with both a pure culture of sulfur-oxidizing Thiothrix unzii and a mixed environmental sulfur-metabolizing community from Lower Kane, Cave, WY, USA. Reactors contained rock and mineral chips (calcite, albite, microcline, quartz, chert, Madison Limestone (ML), Madison Dolostone (MD), and basalt) amended with one of the two inoculants. Biomass of attached microorganisms on each mineral surface was quantified. The 16S rRNA of attached microbial communities were compared using Roche FLX and Titanium 454 next generation pyrosequencing. A primary controlling factor on taxonomy of attached microorganisms in both pure and mixed culture experiments was mineral buffering capacity. In mixed culture experiments acid-buffering carbonates were preferentially colonized by neutrophilic sulfur-oxidizing microorganisms (~18% to ~27% of microorganisms), while acidophilic sulfur-oxidizing microorganisms colonized non-buffering quartz exclusively (~46% of microorganisms). The nutrient content of the rock was a controlling factor on biomass accumulation, with neutrophilic organisms selecting between carbonate surfaces of equivalent buffer capacities according to the availability of phosphate. Dry biomass on ML was 17.8 ± 2.3 mg/cm2 and MD was 20.6 ± 6.8 mg/cm2; while nutrient poor calcite accumulated 2.4 ± 0.3 mg/cm2. Biomass accumulation was minimal on non-buffering nutrient-limited surfaces. These factors are countered by the competitive exclusion of some populations. A pure culture of T. unzii preferentially colonizes carbonates while a very closely related Thiothrix spp is excluded from these same rock samples in a mixed culture. Diversity analysis reveals that ML, MD, and calcite have >98% of sequences belonging to shared OTUs. The carbonates have <3% of sequences belonging to OTUs shared with any silicate mineral surface with the exception of basalt (~85% similarity). These four surfaces were host to the least diverse microbial communities, suggesting that competitive exclusion of microorganisms not adapted to these surfaces is a controlling variable on taxonomy. Furthermore, the microorganisms on basalt reveal an unique association between Thiothrix unzii (often found in mid-ocean ridge environments) and basalt, where it excludes other sulfur oxidizers and accumulates the highest non-carbonate biomass in both pure (3.5 ± 1.0 mg/cm2) and mixed culture (5.4 ± 1.4 mg/cm2) experiments. This association suggests that adaptations to specific rocks may be retained even when the organism is displaced from an ancestral rock/mineral surface habitat. Combined, these variables (buffering capacity, nutrient availability, competitive exclusion, tolerance of surface geochemistry, and latent adaptations) affect biomass density, local diversity, and global diversity of the attached communities on mineral and rock surfaces and suggest that different populations are more tolerant of, and more competitive on, specific rock/mineral types.

Degradation of the Herbicide Metolachlor in Drummer Soil Under Different Redox Conditions

USDA-ARS?s Scientific Manuscript database

Understanding the role of microorganisms and effect of soil environmental conditions on herbicide fate is critical for stewardship of herbicide use in cropping systems. As compared to the modernized perceptions of soil redox status, diminutive progress has been made in characterizing the impact of a...

Detecting contaminating microorganism in human food and water from Raman mapping through biofilms

USDA-ARS?s Scientific Manuscript database

Detecting microbial growth can help experts determine how to prevent the outbreaks especially if human food or water has been contaminated. Biofilms are a group of microbial cells that can either grow on living surfaces or surrounding themselves as they progress. Biofilms are not necessarily uniform...

Marine Subsurface Microbial Communities Across a Hydrothermal Gradient in Okinawa Trough Sediments

NASA Astrophysics Data System (ADS)

Brandt, L. D.; Hser Wah Saw, J.; Ettema, T.; House, C. H.

2015-12-01

IODP Expedition 331 to the Okinawa backarc basin provided an opportunity to study the microbial stratigraphy within the sediments surrounding a hydrothermal vent. The Okinawa backarc basin is a sedimented region of the seafloor located on a continental margin, and also hosts a hydrothermal network within the subsurface. Site C0014 within the Iheya North hydrothermal field is located 450 m east of the active vent and has a surface temperature of 5°C with no evidence of hydrothermal alteration within the top 10 meters below sea floor (mbsf). Temperature increases with depth at an estimated rate of 3°C/m and transitions from non-hydrothermal margin sediments to a hydrothermally altered regime below 10 mbsf. In this study, we utilized deep 16S rRNA sequencing of DNA from IODP Expedition 331 Site C0014 sediment horizons in order to assess diversity throughout the sediment column as well as determine the potential limits of the biosphere. Analysis of the amplicon data shows a shift over 15 mbsf from a heterogeneous community of cosmopolitan marine subsurface taxa toward an archaeal-dominated community in the deepest horizons of the predicted biosphere. Notably, the phylum Chloroflexi represents a substantial taxon through most horizons, where it appears to be replaced below 10 mbsf by punctuations of thermophilic and methanotrophic Archaea and Miscellaneous Crenarchaeotic Group abundances. DNA from the aforementioned transition horizons was further analyzed using metagenomic sequencing. Preliminary taxonomic analysis of the metagenomic data agrees well with amplicon data in capturing the shift in relative abundance of Archaea increasing with depth. Additionally, reverse gyrase, a gene found exclusively in hyperthermophilic microorganisms, was recovered only in the metagenome of the deepest horizon. A BLAST search of this protein sequence against the GenBank non-redudnant protein database produced top hits with reverse gyrase from Thermococcus and Pyrococcus, which are known thermophiles. Up until now, thermophiles and hyperthermophiles have been studied in cultured hydrothermal vent fluid samples, or have been identified from 16S rRNA taxonomic analyses. These recovered genes provide direct evidence for a pervasive subsurface hyperthermophilic biosphere in off-axis hydrothermal sediments.

ANME-2D Archaea Catalyze Methane Oxidation in Deep Subsurface Sediments Independent of Nitrate Reduction

NASA Astrophysics Data System (ADS)

Hernsdorf, A. W.; Amano, Y.; Suzuki, Y.; Ise, K.; Thomas, B. C.; Banfield, J. F.

2015-12-01

Terrestrial sediments are an important global reservoir for methane. Microorganisms in the deep subsurface play a critical role in the methane cycle, yet much remains to be learned about their diversity and metabolisms. To provide more comprehensive insight into the microbiology of the methane cycle in the deep subsurface, we conducted a genome-resolved study of samples collected from the Horonobe Underground Research Laboratory (HURL), Japan. Groundwater samples were obtained from three boreholes from a depth range of between 140 m and 250 m in two consecutive years. Groundwater was filtered and metagenomic DNA extracted and sequenced, and the sequence data assembled. Based on the sequences of phylogenetically informative genes on the assembled fragments, we detected a high degree of overlap in community composition across a vertical transect within one borehole at the two sampling times. However, there was comparatively little similarity observed among communities across boreholes. Spatial and temporal abundance patterns were used in combination with tetranucleotide signatures of assembled genome fragments to bin the data and reconstruct over 200 unique draft genomes, of which 137 are considered to be of high quality (>90% complete). The deepest samples from one borehole were highly dominated by an archaeon identified as ANME-2D; this organism was also present at lower abundance in all other samples from that borehole. Also abundant in these microbial communities were novel members of the Gammaproteobacteria, Saccharibacteria (TM7) and Tenericute phyla. Notably, a ~2 Mbp draft genome for the ANME-2D archaeon was reconstructed. As expected, the genome encodes all of the genes predicted to be involved in the reverse methanogenesis pathway. In contrast with the previously reported ANME2-D genome, the HURL ANME-2D genome lacks the capacity to reduce nitrate. However, we identified many multiheme cytochromes with closest similarity to those of the known Fe-reducing/oxidizing archaeon Ferroglobus placidus. Thus, we suggest that ANME2-D may couple methane oxidation to reduction of ferric iron minerals in the sediment and may be generally important as a link between the iron and methane cycles in deep subsurface environments. Such information has important implications for modeling the global carbon cycle.

Cultivating the Deep Subsurface Microbiome

NASA Astrophysics Data System (ADS)

Casar, C. P.; Osburn, M. R.; Flynn, T. M.; Masterson, A.; Kruger, B.

2017-12-01

Subterranean ecosystems are poorly understood because many microbes detected in metagenomic surveys are only distantly related to characterized isolates. Cultivating microorganisms from the deep subsurface is challenging due to its inaccessibility and potential for contamination. The Deep Mine Microbial Observatory (DeMMO) in Lead, SD however, offers access to deep microbial life via pristine fracture fluids in bedrock to a depth of 1478 m. The metabolic landscape of DeMMO was previously characterized via thermodynamic modeling coupled with genomic data, illustrating the potential for microbial inhabitants of DeMMO to utilize mineral substrates as energy sources. Here, we employ field and lab based cultivation approaches with pure minerals to link phylogeny to metabolism at DeMMO. Fracture fluids were directed through reactors filled with Fe3O4, Fe2O3, FeS2, MnO2, and FeCO3 at two sites (610 m and 1478 m) for 2 months prior to harvesting for subsequent analyses. We examined mineralogical, geochemical, and microbiological composition of the reactors via DNA sequencing, microscopy, lipid biomarker characterization, and bulk C and N isotope ratios to determine the influence of mineralogy on biofilm community development. Pre-characterized mineral chips were imaged via SEM to assay microbial growth; preliminary results suggest MnO2, Fe3O4, and Fe2O3 were most conducive to colonization. Solid materials from reactors were used as inoculum for batch cultivation experiments. Media designed to mimic fracture fluid chemistry was supplemented with mineral substrates targeting metal reducers. DNA sequences and microscopy of iron oxide-rich biofilms and fracture fluids suggest iron oxidation is a major energy source at redox transition zones where anaerobic fluids meet more oxidizing conditions. We utilized these biofilms and fluids as inoculum in gradient cultivation experiments targeting microaerophilic iron oxidizers. Cultivation of microbes endemic to DeMMO, a system locally dominated by unclassified and candidate phyla, has the potential to yield novel subsurface organisms with unique physiologies. We intend to further utilize subsurface isolates to probe the effects of geochemical perturbations on biosignatures in future studies, thus broadening our understanding of subterranean ecosystems.

Intracellular subsurface imaging using a hybrid shear-force feedback/scanning quantitative phase microscopy technique

NASA Astrophysics Data System (ADS)

Edward, Kert

Quantitative phase microscopy (QPM) allows for the imaging of translucent or transparent biological specimens without the need for exogenous contrast agents. This technique is usually applied towards the investigation of simple cells such as red blood cells which are typically enucleated and can be considered to be homogenous. However, most biological cells are nucleated and contain other interesting intracellular organelles. It has been established that the physical characteristics of certain subsurface structures such as the shape and roughness of the nucleus is well correlated with onset and progress of pathological conditions such as cancer. Although the acquired quantitative phase information of biological cells contains surface information as well as coupled subsurface information, the latter has been ignored up until now. A novel scanning quantitative phase imaging system unencumbered by 2pi ambiguities is hereby presented. This system is incorporated into a shear-force feedback scheme which allows for simultaneous phase and topography determination. It will be shown how subsequent image processing of these two data sets allows for the extraction of the subsurface component in the phase data and in vivo cell refractometry studies. Both fabricated samples and biological cells ranging from rat fibroblast cells to malaria infected human erythrocytes were investigated as part of this research. The results correlate quite well with that obtained via other microscopy techniques.

Triaxial Measurement Method for Analysis of Residual Stress after High Feed Milling by X-Ray Diffraction

NASA Astrophysics Data System (ADS)

Čuma, Matúš; Török, Jozef; Telišková, Monika

2016-12-01

Surface integrity is a broad term which includes various quality factors affecting the functional properties of parts. Residual stress is one of these factors. Machining generates residual stresses in the surface and subsurface layers of the structural elements. X-ray diffractometry is a non-destructive method applicable for the measurement of residual stresses in surface and subsurface layers of components. The article is focused on the non-destructive progressive method of triaxial measurement of residual stress after machining the surface of sample by high feed milling technology. Significance of triaxial measuring is the capability of measuring in different angles so it is possible to acquire stress tensor containing normal and shear stress components acting in the spot of measuring, using a Cartesian coordinate system.

Nature's Helpers: Using Microorganisms to Remove Trichloroethene (TCE) from Groundwater

NASA Astrophysics Data System (ADS)

Delgado, A. G.; Krajmlanik-Brown, R.; Fajardo-Williams, D.; Halloum, I.

2015-12-01

Organic chlorinated solvents, such as perchloroethene (PCE) and trichloroethene (TCE), are toxic pollutants threatening ground water quality worldwide and present at many superfund sites. Bioremediation using microorganisms is a promising, green, efficient, and sustainable approach to remove PCE and TCE contamination from soil and groundwater. Under anaerobic conditions, specialized microorganisms (dechlorinators) can reduce these chlorinated ethenes to ethene, an innocuous product, and gain energy for growth by a process known as reductive dechlorination. Dechlorinators are most often present in the environment and in dechlorinating cultures alongside other microbes such as fermenters, methanogens, and acetogens. Fermenters, methanogens, and acetogens syntrophically provide essential nutrients and growth factors to dechlorinators, most specifically to the only members able to reduce TCE all the way to ethene: Dehalococcoides; unfortunately, they also compete with dechlorinators for electron donors. My laboratory devises reductive chlorination platforms to study competition and syntrophy among Dehalococcoides, and other microbes to optimize remediation reactions and transport in the subsurface. We look at competing processes present as part of the natural soil chemistry and microbiology and address these challenges through a combination of enrichment techniques, molecular microbial ecology (deep sequencing), water chemistry, and electron balances. We have applied knowledge gathered in my laboratory to: 1) enrich microbial dechlorinating cultures capable of some of the fastest rates of TCE to ethene dechlorination ever reported, and 2) successfully design and operate three different continuous dechlorinating reactor types. We attribute our successful reactor operations to our multidisciplinary approach which links microbiology and engineering. Our reactors produce robust dechlorinating cultures used for in-situ bioaugmentation of PCE and TCE at contaminated sites. The results gathered to date provide a fundamental understanding of the role of homoacetogens and methanogens in electron and carbon flow in dechlorinating consortia.

Nitrate-Dependent Iron Oxidation: A Potential Mars Metabolism

PubMed Central

Price, Alex; Pearson, Victoria K.; Schwenzer, Susanne P.; Miot, Jennyfer; Olsson-Francis, Karen

2018-01-01

This work considers the hypothetical viability of microbial nitrate-dependent Fe2+ oxidation (NDFO) for supporting simple life in the context of the early Mars environment. This draws on knowledge built up over several decades of remote and in situ observation, as well as recent discoveries that have shaped current understanding of early Mars. Our current understanding is that certain early martian environments fulfill several of the key requirements for microbes with NDFO metabolism. First, abundant Fe2+ has been identified on Mars and provides evidence of an accessible electron donor; evidence of anoxia suggests that abiotic Fe2+ oxidation by molecular oxygen would not have interfered and competed with microbial iron metabolism in these environments. Second, nitrate, which can be used by some iron oxidizing microorganisms as an electron acceptor, has also been confirmed in modern aeolian and ancient sediment deposits on Mars. In addition to redox substrates, reservoirs of both organic and inorganic carbon are available for biosynthesis, and geochemical evidence suggests that lacustrine systems during the hydrologically active Noachian period (4.1–3.7 Ga) match the circumneutral pH requirements of nitrate-dependent iron-oxidizing microorganisms. As well as potentially acting as a primary producer in early martian lakes and fluvial systems, the light-independent nature of NDFO suggests that such microbes could have persisted in sub-surface aquifers long after the desiccation of the surface, provided that adequate carbon and nitrates sources were prevalent. Traces of NDFO microorganisms may be preserved in the rock record by biomineralization and cellular encrustation in zones of high Fe2+ concentrations. These processes could produce morphological biosignatures, preserve distinctive Fe-isotope variation patterns, and enhance preservation of biological organic compounds. Such biosignatures could be detectable by future missions to Mars with appropriate instrumentation. PMID:29616015

A national-scale assessment of micro-organic contaminants in groundwater of England and Wales.

PubMed

Manamsa, Katya; Crane, Emily; Stuart, Marianne; Talbot, John; Lapworth, Dan; Hart, Alwyn

2016-10-15

A large variety of micro-organic (MO) compounds is used in huge quantities for a range of purposes (e.g. manufacturing, food production, healthcare) and is now being frequently detected in the aquatic environment. Interest in the occurrence of MO contaminants in the terrestrial and aquatic environments continues to grow, as well as in their environmental fate and potential toxicity. However, the contamination of groundwater resources by MOs has a limited evidence base compared to other freshwater resources. Of particular concern are newly 'emerging contaminants' such as pharmaceuticals and lifestyle compounds, particularly those with potential endocrine disrupting properties. While groundwater often has a high degree of protection from pollution due to physical, chemical and biological attenuation processes in the subsurface compared to surface aquatic environments, trace concentrations of a large range of compounds are still detected in groundwater and in some cases may persist for decades due to the long residence times of groundwater systems. This study provides the first national-scale assessment of micro-organic compounds in groundwater in England and Wales. A large set of monitoring data was analysed to determine the relative occurrence and detected concentrations of different groups of compounds and to determine relationships with land-use, aquifer type and groundwater vulnerability. MOs detected including emerging compounds such as caffeine, DEET, bisphenol A, anti-microbial agents and pharmaceuticals as well as a range of legacy contaminants including chlorinated solvents and THMs, petroleum hydrocarbons, pesticides and other industrial compounds. There are clear differences in MOs between land-use types, particularly for urban-industrial and natural land-use. Temporal trends of MO occurrence are assessed but establishing long-term trends is not yet possible. Copyright © 2016 British Geological Survey, NERC. Published by Elsevier B.V. All rights reserved.

Nitrate-Dependent Iron Oxidation: A Potential Mars Metabolism.

PubMed

Price, Alex; Pearson, Victoria K; Schwenzer, Susanne P; Miot, Jennyfer; Olsson-Francis, Karen

2018-01-01

This work considers the hypothetical viability of microbial nitrate-dependent Fe 2+ oxidation (NDFO) for supporting simple life in the context of the early Mars environment. This draws on knowledge built up over several decades of remote and in situ observation, as well as recent discoveries that have shaped current understanding of early Mars. Our current understanding is that certain early martian environments fulfill several of the key requirements for microbes with NDFO metabolism. First, abundant Fe 2+ has been identified on Mars and provides evidence of an accessible electron donor; evidence of anoxia suggests that abiotic Fe 2+ oxidation by molecular oxygen would not have interfered and competed with microbial iron metabolism in these environments. Second, nitrate, which can be used by some iron oxidizing microorganisms as an electron acceptor, has also been confirmed in modern aeolian and ancient sediment deposits on Mars. In addition to redox substrates, reservoirs of both organic and inorganic carbon are available for biosynthesis, and geochemical evidence suggests that lacustrine systems during the hydrologically active Noachian period (4.1-3.7 Ga) match the circumneutral pH requirements of nitrate-dependent iron-oxidizing microorganisms. As well as potentially acting as a primary producer in early martian lakes and fluvial systems, the light-independent nature of NDFO suggests that such microbes could have persisted in sub-surface aquifers long after the desiccation of the surface, provided that adequate carbon and nitrates sources were prevalent. Traces of NDFO microorganisms may be preserved in the rock record by biomineralization and cellular encrustation in zones of high Fe 2+ concentrations. These processes could produce morphological biosignatures, preserve distinctive Fe-isotope variation patterns, and enhance preservation of biological organic compounds. Such biosignatures could be detectable by future missions to Mars with appropriate instrumentation.

Model for the prediction of subsurface strata movement due to underground mining

NASA Astrophysics Data System (ADS)

Cheng, Jianwei; Liu, Fangyuan; Li, Siyuan

2017-12-01

The problem of ground control stability due to large underground mining operations is often associated with large movements and deformations of strata. It is a complicated problem, and can induce severe safety or environmental hazards either at the surface or in strata. Hence, knowing the subsurface strata movement characteristics, and making any subsidence predictions in advance, are desirable for mining engineers to estimate any damage likely to affect the ground surface or subsurface strata. Based on previous research findings, this paper broadly applies a surface subsidence prediction model based on the influence function method to subsurface strata, in order to predict subsurface stratum movement. A step-wise prediction model is proposed, to investigate the movement of underground strata. The model involves a dynamic iteration calculation process to derive the movements and deformations for each stratum layer; modifications to the influence method function are also made for more precise calculations. The critical subsidence parameters, incorporating stratum mechanical properties and the spatial relationship of interest at the mining level, are thoroughly considered, with the purpose of improving the reliability of input parameters. Such research efforts can be very helpful to mining engineers’ understanding of the moving behavior of all strata over underground excavations, and assist in making any damage mitigation plan. In order to check the reliability of the model, two methods are carried out and cross-validation applied. One is to use a borehole TV monitor recording to identify the progress of subsurface stratum bedding and caving in a coal mine, the other is to conduct physical modelling of the subsidence in underground strata. The results of these two methods are used to compare with theoretical results calculated by the proposed mathematical model. The testing results agree well with each other, and the acceptable accuracy and reliability of the proposed prediction model are thus validated.

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.

Where microorganisms meet rocks in the Earth's Critical Zone

NASA Astrophysics Data System (ADS)

Akob, D. M.; Küsel, K.

2011-12-01

The Critical Zone (CZ) is the Earth's outer shell where all the fundamental physical, chemical, and biological processes critical for sustaining life occur and interact. As microbes in the CZ drive many of these biogeochemical cycles, understanding their impact on life-sustaining processes starts with an understanding of their biodiversity. In this review, we summarize the factors controlling where terrestrial CZ microbes (prokaryotes and micro-eukaryotes) live and what is known about their diversity and function. Microbes are found throughout the CZ, down to 5 km below the surface, but their functional roles change with depth due to habitat complexity, e.g. variability in pore spaces, water, oxygen, and nutrients. Abundances of prokaryotes and micro-eukaryotes decrease from 1010 or 107 cells g soil-1 or rock-1, or ml water-1 by up to eight orders of magnitude with depth. Although symbiotic mycorrhizal fungi and free-living decomposers have been studied extensively in soil habitats, where they occur up to 103 cells g soil-1, little is known regarding their identity or impact on weathering in the deep subsurface. The relatively low abundance of micro-eukaryotes in the deep subsurface suggests that they are limited in space, nutrients, are unable to cope with oxygen limitations, or some combination thereof. Since deep regions of the CZ have limited access to recent photosynthesis-derived carbon, microbes there depend on deposited organic material or a chemolithoautotrophic metabolism that allows for a complete food chain, independent from the surface, although limited energy flux means cell growth may take tens to thousands of years. Microbes are found in all regions of the CZ and can mediate important biogeochemical processes, but more work is needed to understand how microbial populations influence the links between different regions of the CZ and weathering processes. With the recent development of "omics" technologies, microbial ecologists have new methods that can be used to link the composition and function of in situ microbial communities. In particular, these methods can be used to search for new metabolic pathways that are relevant to biogeochemical nutrient cycling and determine how the activity of microorganisms can affect transport of carbon, particulates, and reactive gases between and within CZ regions.

Light-energy conversion in engineered microorganisms.

PubMed

Johnson, Ethan T; Schmidt-Dannert, Claudia

2008-12-01

Increasing interest in renewable resources by the energy and chemical industries has spurred new technologies both to capture solar energy and to develop biologically derived chemical feedstocks and fuels. Advances in molecular biology and metabolic engineering have provided new insights and techniques for increasing biomass and biohydrogen production, and recent efforts in synthetic biology have demonstrated that complex regulatory and metabolic networks can be designed and engineered in microorganisms. Here, we explore how light-driven processes may be incorporated into nonphotosynthetic microbes to boost metabolic capacity for the production of industrial and fine chemicals. Progress towards the introduction of light-driven proton pumping or anoxygenic photosynthesis into Escherichia coli to increase the efficiency of metabolically-engineered biosynthetic pathways is highlighted.

Biofilm development in a hotspot of mixing between shallow and deep groundwater in a fractured aquifer: field evidence from joint flow, chemical and microbiological characterization

NASA Astrophysics Data System (ADS)

Bochet, Olivier; Le Borgne, Tanguy; Pédrot, Mathieu; Labasque, Thierry; Lavenant, Nicolas; Petton, Christophe; Dufresne, Alexis; Ben Maamar, Sarah; Chatton, Eliot; De la Bernardie, Jérôme; Aquilina, Luc

2015-04-01

Biofilm development in a hotspot of mixing between shallow and deep groundwater in a fractured aquifer: field evidence from joint flow, chemical and microbiological characterization Olivier Bochet1, Tanguy Le Borgne1, Mathieu Pédrot1, Thierry Labasque1, Nicolas Lavenant1, Christophe Petton1, Alexis Dufresne2,Sarah Ben Maamar1-2, Eliot Chatton1, Jérôme de la Bernardie1, Luc Aquilina1 1: Géosciences Rennes, CNRS UMR 6118, Université de Rennes 1, Campus de Beaulieu bât 14B, Rennes, France 2: Ecobio, CNRS UMR 6553, Université de Rennes 1, Campus de Beaulieu, bât 14, Rennes, France Biofilms play a major role in controlling the fluxes and reactivity of chemical species transported in hydrological systems. Their development can have either positive impacts on groundwater quality (e.g. attenuation of contaminants under natural or stimulated conditions), or possible negative effects on subsurface operations (e.g. bio-clogging of geothermal dipoles or artificial recharge systems). Micro-organisms require both electron donors and electron acceptors for cellular growth, proliferation and maintenance of their metabolic functions. The mechanisms controlling these reactions derive from the interactions occurring at the micro-scale that depend on mineral compositions, the biota of subsurface environment, but also fluid mixing, which determines the local concentrations of nutriments, electron donors and electron acceptors. Hence, mixing zones between oxygen and nutriment rich shallow groundwater and mineralized deep groundwater are often considered as potential hotspots of microbial activity, although relatively few field data document flow distributions, transport properties, chemical gradients and micro-organisms distributions across these mixing interfaces. Here we investigate the origin of a localized biofilm development observed in the fractured granite aquifer at the Ploemeur observatory (H+ network hplus.ore.fr).This biofilm composed of ferro-oxidizing bacteria is observed in an 130m deep artesian well. Borehole video logs show an important colonization of the well by the biofilm in the shallower part (0 to 60m), while it is inexistent in the deeper part (60 to 130m). As flow is localized in a few deep and shallow fractures, we presume that the spatial distribution of biofilm is controlled by mixing between shallow and deep groundwater. To verify this hypothesis we conducted a field campaign with joint characterization of the flow and chemical composition of water flowing from the different fractures, as well as the microbiological composition of the biofilm at different depth, using pyrosequencing techniques. We will discuss in this presentation the results of this interdisciplinary dataset and their implications for the occurrence of hotspots of microbiological activity in the subsurface.

Yucca Mountain Project Subsurface Facilities Design

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

A. Linden; R.S. Saunders; R.J. Boutin

2002-11-19

Four units of the Topopah Springs formation (volcanic tuff) are considered for the proposed repository: the upper lithophysal, the middle non-lithophysal, the lower lithophysal, and the lower non-lithophysal. Yucca Mountain was recently designated the site for a proposed repository to dispose of spent nuclear fuel and high-level radioactive waste. Work is proceeding to advance the design of subsurface facilities to accommodate emplacing waste packages in the proposed repository. This paper summarized recent progress in the design of subsurface layout of the proposed repository. The original Site Recommendation (SR) concept for the subsurface design located the repository largely within the lowermore » lithophysal zone (approximately 73%) of the Topopah The Site Recommendation characterized area suitable for emplacement consisted of the primary upper block, the lower block and the southern upper block extension. The primary upper block accommodated the mandated 70,000 metric tons of heavy metal (MTHM) at a 1.45 kW/m hear heat load. Based on further study of the Site Recommendation concept, the proposed repository siting area footprint was modified to make maximum use of available site characterization data, and thus, reduce uncertainties associated with performance assessment. As a result of this study, a modified repository footprint has been proposed and is presently being review for acceptance by the DOE. A panel design concept was developed to reduce overall costs and reduce the overall emplacement schedule. This concept provides flexibility to adjust the proposed repository subsurface layout with time, as it makes it unnecessary to ''commit'' to development of a large single panel at the earliest stages of construction. A description of the underground layout configuration and influencing factors that affect the layout configuration are discussed in the report.« less

Effect of Lesion Baseline Severity and Mineral Distribution on Remineralization and Progression of Human and Bovine Dentin Caries Lesions.

PubMed

Lippert, Frank; Churchley, David; Lynch, Richard J

2015-01-01

The aims of this laboratory study were to compare the effects of lesion baseline severity, mineral distribution and substrate on remineralization and progression of caries lesions created in root dentin. Lesions were formed in dentin specimens prepared from human and bovine dentin using three protocols, each utilizing three demineralization periods to create lesions of different mineral distributions (subsurface, moderate softening, extreme softening) and severity within each lesion type. Lesions were then either remineralized or demineralized further and analyzed using transverse microradiography. At lesion baseline, no differences were found between human and bovine dentin for integrated mineral loss (x0394;Z). Differences in mineral distribution between lesion types were apparent. Human dentin lesions were more prone to secondary demineralization (x0394;x0394;Z) than bovine dentin lesions, although there were no differences in x0394;L. Likewise, smaller lesions were more susceptible to secondary demineralization than larger ones. Subsurface lesions were more acid-resistant than moderately and extremely softened lesions. After remineralization, differences between human and bovine dentin lesions were not apparent for x0394;x0394;Z although bovine dentin lesions showed greater reduction in lesion depth L. For lesion types, responsiveness to remineralization (x0394;x0394;Z) was in the order extremely softened>moderately softened>subsurface. More demineralized lesions exhibited greater remineralization than shallower ones. In summary, some differences exist between human and bovine dentin and their relative responsiveness to de- and remineralization. These differences, however, were overshadowed by the effects of lesion baseline mineral distribution and severity. Thus, bovine dentin appears to be a suitable substitute for human dentin in mechanistic root caries studies. © 2015 S. Karger AG, Basel.

Xylose fermentation to ethanol. A review

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

McMillan, J D

1993-01-01

The past several years have seen tremendous progress in the understanding of xylose metabolism and in the identification, characterization, and development of strains with improved xylose fermentation characteristics. A survey of the numerous microorganisms capable of directly fermenting xylose to ethanol indicates that wild-type yeast and recombinant bacteria offer the best overall performance in terms of high yield, final ethanol concentration, and volumetric productivity. The best performing bacteria, yeast, and fungi can achieve yields greater than 0.4 g/g and final ethanol concentrations approaching 5%. Productivities remain low for most yeast and particularly for fungi, but volumetric productivities exceeding 1.0 g/L-hmore » have been reported for xylose-fermenting bacteria. In terms of wild-type microorganisms, strains of the yeast Pichia stipitis show the most promise in the short term for direct high-yield fermentation of xylose without byproduct formation. Of the recombinant xylose-fermenting microorganisms developed, recombinant E. coli ATTC 11303 (pLOI297) exhibits the most favorable performance characteristics reported to date.« less

Xylose fermentation to ethanol

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

McMillan, J.D.

1993-01-01

The past several years have seen tremendous progress in the understanding of xylose metabolism and in the identification, characterization, and development of strains with improved xylose fermentation characteristics. A survey of the numerous microorganisms capable of directly fermenting xylose to ethanol indicates that wild-type yeast and recombinant bacteria offer the best overall performance in terms of high yield, final ethanol concentration, and volumetric productivity. The best performing bacteria, yeast, and fungi can achieve yields greater than 0.4 g/g and final ethanol concentrations approaching 5%. Productivities remain low for most yeast and particularly for fungi, but volumetric productivities exceeding 1.0 g/L-hmore » have been reported for xylose-fermenting bacteria. In terms of wild-type microorganisms, strains of the yeast Pichia stipitis show the most promise in the short term for direct high-yield fermentation of xylose without byproduct formation. Of the recombinant xylose-fermenting microorganisms developed, recombinant E. coli ATTC 11303 (pLOI297) exhibits the most favorable performance characteristics reported to date.« less

Gene-Based Detection of Microorganisms in Environmental Samples Using PCR

NASA Technical Reports Server (NTRS)

Glass, John I.; Lefkowitz, Elliot J.; Cassell, Gail H.; Wechser, Mark; Taylor, Theresa B.; Albin, Michael; Paszko-Kolva, Christine; Roman, Monsi C.

1997-01-01

Contaminating microorganisms pose a serious potential risk to the crew's well being and water system integrity aboard the International Space Station (ISS). We are developing a gene-based microbial monitor that functions by replicating specific segments of DNA as much as 10(exp 12) x. Thus a single molecule of DNA can be replicated to detectable levels, and the kinetics of that molecule's accumulation can be used to determine the original concentration of specific microorganisms in a sample. Referred to as the polymerase chain reaction (PCR), this enzymatic amplification of specific segments of the DNA or RNA from contaminating microbes offers the promise of rapid, sensitive, quantitative detection and identification of bacteria, fungi, viruses, and parasites. We envision a small instrument capable of assaying an ISS water sample for 48 different microbes in a 24 hour period. We will report on both the developments in the chemistry necessary for the PCR assays to detect microbial contaminants in ISS water, and on progress towards the miniaturization and automation of the instrumentation.

Candida spp. in periodontal disease: a brief review.

PubMed

Sardi, Janaina C O; Duque, Cristiane; Mariano, Flávia S; Peixoto, Iza T A; Höfling, José F; Gonçalves, Reginaldo B

2010-06-01

Although the main reservoir of Candida spp. is believed to be the buccal mucosa, these microorganisms can coaggregate with bacteria in subgingival biofilm and adhere to epithelial cells. Such interactions are associated with the capacity of Candida spp. to invade gingival conjunctive tissue, and may be important in the microbial colonization that contributes to progression of oral alterations caused by diabetes mellitus, some medications, and immunosuppressive diseases such as AIDS. In addition, immune deficiency can result in proliferation of Candida spp. and germination of forms that are more virulent and have a higher capacity to adhere to and penetrate cells in host tissues. The virulence factors of Candida spp. increase host susceptibility to proliferation of these microorganisms and are likely to be important in the study of periodontal disease. Herein, we briefly review the literature pertaining to the role of Candida spp. in periodontal disease, and consider the main virulence factors, the host immune response to these microorganisms, and the effect of concomitant immunosuppressive conditions.

GROWTH OF A DEHALOCOCCOIDES-LIKE MICROORGANISM ON VINYL CHLORIDE AND CIS-DICHLOROETHENE AS ELECTRON ACCEPTORS AS DETERMINED BY COMPETITIVE PCR. (R828772)

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...

[Research Progress in Technology of Using Soil Micro-organisms to Generate Electricity and Its Potential Applications].

PubMed

Deng, Huan; Xue, Hong-jing; Jiang, Yun-bin; Zhong, Wen-hui

2015-10-01

Microbial fuel cells ( microbial fuel cells, MFCs) are devices in which micro-organisms convert chemical energy into electrical power. Soil has electrogenic bacteria and organic substrates, thus can generate electrical current in MFCs. Soil MFCs can be operated and applied to real-time and continuously monitor soil pollution, remove soil pollutants and to reduce methane emitted from flooded rice paddy, without energy consumption and the application of chemical reagents to the soil. Instead, the operation of soil MFCs generates small amount of electrical power. Therefore, soil MFCs are useful in the development of environment-friendly technology for monitoring and remediating soil pollution, which have potential value for applications in the domain of environmental science and engineering. However, much of advanced technology hasn't been applied into soil MFCs since the studies on soil MFCs was not started until recently. This paper summarized the research progress in related to soil MFCs combining with the frontier of MFCs technology, and brought forward the possible direction in studies on soil MFCs.

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.

Effects of timber harvesting on the lag time of a Caspar Creek watershed...a study in progress

Treesearch

Karen D. Hardison

1982-01-01

Researchers are not agreed on the effects of logging on lag time. Numerous studies have shown that the use of heavy equipment in logging operations can cause soil compaction. Also, associated roads alter natural drainage patterns by concentrating runoff and interrupting subsurface flow. As a result these researchers say, less infiltration into the soil takes place...

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

Wrighton, Kelly C.; Castelle, Cindy; Wilkins, Michael J.

Fermentation-based metabolism is an important ecosystem function often associated with environments rich in organic carbon, such as wetlands, sewage sludge, and the mammalian gut. The diversity of microorganisms and pathways involved in carbon and hydrogen cycling in sediments and aquifers and the impacts of these processes on other biogeochemical cycles remain poorly understood. Here we used metagenomics and proteomics to characterize microbial communities sampled from an aquifer adjacent to the Colorado River at Rifle, Colorado, USA, and document interlinked microbial roles in geochemical cycling. The organic carbon content in the aquifer was elevated via two acetate-based biostimulation treatments. Samples weremore » collected at three time points, with the objective of extensive genome recovery to enable metabolic reconstruction of the community. Fermentative community members include genomes from a new phylum (ACD20), phylogenetically novel members of the Chloroflexi and Bacteroidetes, as well as candidate phyla genomes (OD1, BD1-5, SR1, WWE3, ACD58, TM6, PER, and OP11). These organisms have the capacity to produce hydrogen, acetate, formate, ethanol, butyrate, and lactate, activities supported by proteomic data. The diversity and expression of hydrogenases suggests the importance of hydrogen currency in the subsurface. Our proteogenomic data further indicate the consumption of fermentation intermediates by Proteobacteria can be coupled to nitrate, sulfate, and iron reduction. Thus, fermentation carried out by previously unstudied members of sediment microbial communities may be an important driver of diverse subsurface biogeochemical cycles.« less

Evidence for Seismogenic Hydrogen Gas, a Potential Microbial Energy Source on Earth and Mars

NASA Astrophysics Data System (ADS)

McMahon, Sean; Parnell, John; Blamey, Nigel J. F.

2016-09-01

The oxidation of molecular hydrogen (H2) is thought to be a major source of metabolic energy for life in the deep subsurface on Earth, and it could likewise support any extant biosphere on Mars, where stable habitable environments are probably limited to the subsurface. Faulting and fracturing may stimulate the supply of H2 from several sources. We report the H2 content of fluids present in terrestrial rocks formed by brittle fracturing on fault planes (pseudotachylites and cataclasites), along with protolith control samples. The fluids are dominated by water and include H2 at abundances sufficient to support hydrogenotrophic microorganisms, with strong H2 enrichments in the pseudotachylites compared to the controls. Weaker and less consistent H2 enrichments are observed in the cataclasites, which represent less intense seismic friction than the pseudotachylites. The enrichments agree quantitatively with previous experimental measurements of frictionally driven H2 formation during rock fracturing. We find that conservative estimates of current martian global seismicity predict episodic H2 generation by Marsquakes in quantities useful to hydrogenotrophs over a range of scales and recurrence times. On both Earth and Mars, secondary release of H2 may also accompany the breakdown of ancient fault rocks, which are particularly abundant in the pervasively fractured martian crust. This study strengthens the case for the astrobiological investigation of ancient martian fracture systems.

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.

Mineral Ecology: Surface Specific Colonization and Geochemical Drivers of Biofilm Accumulation, Composition, and Phylogeny

PubMed Central

Jones, Aaron A.; Bennett, Philip C.

2017-01-01

This study tests the hypothesis that surface composition influences microbial community structure and growth of biofilms. We used laboratory biofilm reactors (inoculated with a diverse subsurface community) to explore the phylogenetic and taxonomic variability in microbial communities as a function of surface type (carbonate, silicate, aluminosilicate), media pH, and carbon and phosphate availability. Using high-throughput pyrosequencing, we found that surface type significantly controlled ~70–90% of the variance in phylogenetic diversity regardless of environmental pressures. Consistent patterns also emerged in the taxonomy of specific guilds (sulfur-oxidizers/reducers, Gram-positives, acidophiles) due to variations in media chemistry. Media phosphate availability was a key property associated with variation in phylogeny and taxonomy of whole reactors and was negatively correlated with biofilm accumulation and α-diversity (species richness and evenness). However, mineral-bound phosphate limitations were correlated with less biofilm. Carbon added to the media was correlated with a significant increase in biofilm accumulation and overall α-diversity. Additionally, planktonic communities were phylogenetically distant from those in biofilms. All treatments harbored structurally (taxonomically and phylogenetically) distinct microbial communities. Selective advantages within each treatment encouraged growth and revealed the presence of hundreds of additional operational taxonomix units (OTU), representing distinct consortiums of microorganisms. Ultimately, these results provide evidence that mineral/rock composition significantly influences microbial community structure, diversity, membership, phylogenetic variability, and biofilm growth in subsurface communities. PMID:28400754

Development of a biomarker for Geobacter activity and strain composition: Proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI)

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

Wilkins, M.J.; Callister, S.J.; Miletto, M.

2010-02-15

Monitoring the activity of target microorganisms during stimulated bioremediation is a key problem for the development of effective remediation strategies. At the US Department of Energy's Integrated Field Research Challenge (IFRC) site in Rifle, CO, the stimulation of Geobacter growth and activity via subsurface acetate addition leads to precipitation of U(VI) from groundwater as U(IV). Citrate synthase (gltA) is a key enzyme in Geobacter central metabolism that controls flux into the TCA cycle. Here, we utilize shotgun proteomic methods to demonstrate that the measurement of gltA peptides can be used to track Geobacter activity and strain evolution during in situmore » biostimulation. Abundances of conserved gltA peptides tracked Fe(III) reduction and changes in U(VI) concentrations during biostimulation, whereas changing patterns of unique peptide abundances between samples suggested sample-specific strain shifts within the Geobacter population. Abundances of unique peptides indicated potential differences at the strain level between Fe(III)-reducing populations stimulated during in situ biostimulation experiments conducted a year apart at the Rifle IFRC. These results offer a novel technique for the rapid screening of large numbers of proteomic samples for Geobacter species and will aid monitoring of subsurface bioremediation efforts that rely on metal reduction for desired outcomes.« less

Development of a biomarker for Geobacter activity and strain composition; Proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI).

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

Wilkins, Michael J.; Callister, Stephen J.; Miletto, Marzia

2011-01-01

Monitoring the activity of target microorganisms during stimulated bioremediation is a key problem for the development of effective remediation strategies. At the U.S. Department of Energy’s Integrated Field Research Challenge (IFRC) site in Rifle, CO, the stimulation of Geobacter growth and activity via subsurface acetate addition leads to precipitation of U(VI) from groundwater as U(IV). Citrate synthase (gltA) is a key enzyme in Geobacter central metabolism that controls flux into the TCA cycle. Here, we utilize shotgun proteomic methods to demonstrate that the measurement of gltA peptides can be used to track Geobacter activity and strain evolution during in situmore » biostimulation. Abundances of conserved gltA peptides tracked Fe(III) reduction and changes in U(VI) concentrations during biostimulation, whereas changing patterns of unique peptide abundances between samples suggested sample-specific strain shifts within the Geobacter population. Abundances of unique peptides indicated potential differences at the strain level between Fe(III)-reducing populations stimulated during in situ biostimulation experiments conducted a year apart at the Rifle IFRC. These results offer a novel technique for the rapid screening of large numbers of proteomic samples for Geobacter species and will aid monitoring of subsurface bioremediation efforts that rely on metal reduction for desired outcomes.« less

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.

Something new from something old? Fracking stimulated microbial processes

NASA Astrophysics Data System (ADS)

Wrighton, K. C.; Daly, R. A.; Hoyt, D.; Trexler, R.; McRae, J.; Wilkins, M.; Mouser, P. J.

2015-12-01

Hydraulic fracturing, colloquially known as "fracking", is employed for effective gas and oil recovery in deep shales. This process injects organisms and liquids from the surface into the deep subsurface (~2500 m), exposing microorganisms to high pressures, elevated temperatures, chemical additives, and brine-level salinities. Here we use assembly-based metagenomics to create a metabolic blueprint from an energy-producing Marcellus shale well over a 328-day period. Using this approach we ask the question: What abiotic and biotic factors drive microbial metabolism and thus biogeochemical cycling during natural gas extraction? We found that after 49 days, increased salinity in produced waters corresponded to a shift in the microbial community, with only organisms that encode salinity adaptations detected. We posit that organic compatible solutes, produced by organisms adapting to increased salinity, fuels a methylamine-driven ecosystem in fractured shale. This metabolic network ultimately results in biogenic methane production from members of Methanohalophilus and Methanolobus. Proton NMR validated these genomic hypotheses, with mono-methylamine being highest in the input material, but detected throughout the sampling. Beyond abiotic constraints, our genomic investigations revealed that viruses can be linked to key members of the microbial community, potentially releasing methylamine osmoprotectants and impacting bacterial strain variation. Collectively our results indicate that adaptation to high salinity, metabolism in the absence of oxidized electron acceptors, and viral predation are controlling factors mediating microbial community metabolism during hydraulic fracturing of the deep subsurface.

Electrokinetic-enhanced bioremediation of organic contaminants: a review of processes and environmental applications.

PubMed

Gill, R T; Harbottle, M J; Smith, J W N; Thornton, S F

2014-07-01

There is current interest in finding sustainable remediation technologies for the removal of contaminants from soil and groundwater. This review focuses on the combination of electrokinetics, the use of an electric potential to move organic and inorganic compounds, or charged particles/organisms in the subsurface independent of hydraulic conductivity; and bioremediation, the destruction of organic contaminants or attenuation of inorganic compounds by the activity of microorganisms in situ or ex situ. The objective of the review is to examine the state of knowledge on electrokinetic bioremediation and critically evaluate factors which affect the up-scaling of laboratory and bench-scale research to field-scale application. It discusses the mechanisms of electrokinetic bioremediation in the subsurface environment at different micro and macroscales, the influence of environmental processes on electrokinetic phenomena and the design options available for application to the field scale. The review also presents results from a modelling exercise to illustrate the effectiveness of electrokinetics on the supply electron acceptors to a plume scale scenario where these are limiting. Current research needs include analysis of electrokinetic bioremediation in more representative environmental settings, such as those in physically heterogeneous systems in order to gain a greater understanding of the controlling mechanisms on both electrokinetics and bioremediation in those scenarios. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

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

Oil biodegradation. Water droplets in oil are microhabitats for microbial life.

PubMed

Meckenstock, Rainer U; von Netzer, Frederick; Stumpp, Christine; Lueders, Tillmann; Himmelberg, Anne M; Hertkorn, Norbert; Schmitt-Kopplin, Philipp; Harir, Mourad; Hosein, Riad; Haque, Shirin; Schulze-Makuch, Dirk

2014-08-08

Anaerobic microbial degradation of hydrocarbons, typically occurring at the oil-water transition zone, influences the quality of oil reservoirs. In Pitch Lake, Trinidad and Tobago--the world's largest asphalt lake--we found that microorganisms are metabolically active in minuscule water droplets (1 to 3 microliters) entrapped in oil. Pyrotag sequencing of individual droplet microbiomes revealed complex methanogenic microbial communities actively degrading the oil into a diverse range of metabolites, as shown by nuclear magnetic resonance and Fourier transform ion cyclotron resonance mass spectrometry. High salinity and water-stable isotopes of the droplets indicate a deep subsurface origin. The 13.5% water content and the large surface area of the droplets represent an underestimated potential for biodegradation of oil away from the oil-water transition zone. Copyright © 2014, American Association for the Advancement of Science.

Mars polar cap: a habitat for elementary life1

NASA Astrophysics Data System (ADS)

Wallis, M. K.; Wickramasinghe, N. C.

2009-04-01

Ices in the Martian polar caps are potential habitats for various species of microorganisms. Salts in the ice and biological anti-freeze polymers maintain liquid in cracks in the ices far below 0°C, possibly down to the mean 220-240 K. Sub-surface microbial life is shielded from ultraviolet (UV) radiation, but could potentially be activated on south-facing slopes under the midday, midsummer Sun. Such life would be limited by low levels of vapour, little transport of nutrients, low light levels below a protective dirt-crust, frost accumulation at night and in shadows, and little if any active translocation of organisms. As in the Antarctic and in permafrost, movement to new habitats depends on geo-climatic changes, which for Mars's north polar cap occur on a 50 000 year scale, except for rare meteorite impacts.

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.

Human recombinant lysosomal enzymes produced in microorganisms.

PubMed

Espejo-Mojica, Ángela J; Alméciga-Díaz, Carlos J; Rodríguez, Alexander; Mosquera, Ángela; Díaz, Dennis; Beltrán, Laura; Díaz, Sergio; Pimentel, Natalia; Moreno, Jefferson; Sánchez, Jhonnathan; Sánchez, Oscar F; Córdoba, Henry; Poutou-Piñales, Raúl A; Barrera, Luis A

2015-01-01

Lysosomal storage diseases (LSDs) are caused by accumulation of partially degraded substrates within the lysosome, as a result of a function loss of a lysosomal protein. Recombinant lysosomal proteins are usually produced in mammalian cells, based on their capacity to carry out post-translational modifications similar to those observed in human native proteins. However, during the last years, a growing number of studies have shown the possibility to produce active forms of lysosomal proteins in other expression systems, such as plants and microorganisms. In this paper, we review the production and characterization of human lysosomal proteins, deficient in several LSDs, which have been produced in microorganisms. For this purpose, Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris, Yarrowia lipolytica, and Ogataea minuta have been used as expression systems. The recombinant lysosomal proteins expressed in these hosts have shown similar substrate specificities, and temperature and pH stability profiles to those produced in mammalian cells. In addition, pre-clinical results have shown that recombinant lysosomal enzymes produced in microorganisms can be taken-up by cells and reduce the substrate accumulated within the lysosome. Recently, metabolic engineering in yeasts has allowed the production of lysosomal enzymes with tailored N-glycosylations, while progresses in E. coli N-glycosylations offer a potential platform to improve the production of these recombinant lysosomal enzymes. In summary, microorganisms represent convenient platform for the production of recombinant lysosomal proteins for biochemical and physicochemical characterization, as well as for the development of ERT for LSD. Copyright © 2015 Elsevier Inc. All rights reserved.

Reduction of hexavalent chromium by the thermophilic methanogen Methanothermobacter thermautotrophicus

DOE PAGES

Singh, Rajesh; Dong, Hailiang; Liu, Deng; ...

2014-10-22

Despite the significant progress on iron reduction by thermophilic microorganisms, studies on their ability to reduce toxic metals are still limited, despite their common co-existence in high temperature environments (up to 70°C). In this study, Methanothermobacter thermautotrophicus, an obligate thermophilic methanogen, was used to reduce hexavalent chromium. Experiments were conducted in a growth medium with H 2/CO 2 as substrate with various Cr 6+ concentrations (0.2, 0.4, 1, 3, and 5 mM) in the form of potassium dichromate (K 2Cr 2O 7). Time-course measurements of aqueous Cr 6+ concentrations with the 1, 5-diphenylcarbazide colorimetric method showed complete reduction of themore » 0.2 and 0.4 mM Cr 6+ solutions by this methanogen. However, much lower reduction extents of 43.6%, 13.0%, and 3.7% were observed at higher Cr 6+ concentrations of 1, 3 and 5 mM, respectively. These lower extents of bioreduction suggest a toxic effect of aqueous Cr 6+ to cells at this concentration range. At these higher Cr 6+ concentrations, methanogenesis was inhibited and cell growth was impaired as evidenced by decreased total cellular protein production and live/dead cell ratio. Likewise, Cr 6+ bioreduction rates decreased with increased initial concentrations of Cr 6+ from 13.3 to1.9 μM h ₋1. X-ray absorption near-edge structure (XANES) spectroscopy revealed a progressive reduction of soluble Cr 6+ to insoluble Cr 3+ precipitates, which was confirmed as amorphous chromium hydroxide by X-ray diffraction and selected area electron diffraction pattern. However, a small fraction of reduced Cr occurred as aqueous Cr 3+. Scanning and transmission electron microscope observations of M. thermautotrophicus cells after Cr 6+ exposure suggest both extra- and intracellular chromium reduction mechanisms. Results of this study demonstrate the ability of M. thermautotrophicus cells to reduce toxic Cr 6+ to less toxic Cr 3+ and its potential application in metal bioremediation, especially at high temperature subsurface radioactive waste disposal sites, where the temperature may reach ~70°C.« less

Subsurface high resolution definition of subsurface heterogeneity for understanding the biodynamics of natural field systems: Advancing the ability for scaling to field conditions. 1998 annual progress report

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

Majer, E.L.; Brockman, F.J.

1998-06-01

'This research is an integrated physical (geophysical and hydrologic) and microbial study using innovative geophysical imaging and microbial characterization methods to identify key scales of physical heterogeneities that affect the biodynamics of natural subsurface environments. Data from controlled laboratory and in-situ experiments at the INEEL Test Area North (TAN) site are being used to determine the dominant physical characteristics (lithologic, structural, and hydrologic) that can be imaged in-situ and correlated with microbial properties. The overall goal of this research is to contribute to the understanding of the interrelationships between transport properties and spatially varying physical, chemical, and microbiological heterogeneity. Themore » outcome will be an improved understanding of the relationship between physical and microbial heterogeneity, thus facilitating the design of bioremediation strategies in similar environments. This report summarizes work as of May 1998, the second year of the project. This work is an extension of basic research on natural heterogeneity first initiated within the DOE/OHER Subsurface Science Program (SSP) and is intended to be one of the building blocks of an integrated and collaborative approach with an INEEL/PNNL effort aimed at understanding the effect of physical heterogeneity on transport properties and biodynamics in natural systems. The work is closely integrated with other EMSP projects at INEEL (Rick Colwell et al.) and PNNL (Fred Brockman and Jim Fredrickson).'« less

Succession in the petroleum reservoir microbiome through an oil field production lifecycle.

PubMed

Vigneron, Adrien; Alsop, Eric B; Lomans, Bartholomeus P; Kyrpides, Nikos C; Head, Ian M; Tsesmetzis, Nicolas

2017-09-01

Subsurface petroleum reservoirs are an important component of the deep biosphere where indigenous microorganisms live under extreme conditions and in isolation from the Earth's surface for millions of years. However, unlike the bulk of the deep biosphere, the petroleum reservoir deep biosphere is subject to extreme anthropogenic perturbation, with the introduction of new electron acceptors, donors and exogenous microbes during oil exploration and production. Despite the fundamental and practical significance of this perturbation, there has never been a systematic evaluation of the ecological changes that occur over the production lifetime of an active offshore petroleum production system. Analysis of the entire Halfdan oil field in the North Sea (32 producing wells in production for 1-15 years) using quantitative PCR, multigenic sequencing, comparative metagenomic and genomic bins reconstruction revealed systematic shifts in microbial community composition and metabolic potential, as well as changing ecological strategies in response to anthropogenic perturbation of the oil field ecosystem, related to length of time in production. The microbial communities were initially dominated by slow growing anaerobes such as members of the Thermotogales and Clostridiales adapted to living on hydrocarbons and complex refractory organic matter. However, as seawater and nitrate injection (used for secondary oil production) delivered oxidants, the microbial community composition progressively changed to fast growing opportunists such as members of the Deferribacteres, Delta-, Epsilon- and Gammaproteobacteria, with energetically more favorable metabolism (for example, nitrate reduction, H 2 S, sulfide and sulfur oxidation). This perturbation has profound consequences for understanding the microbial ecology of the system and is of considerable practical importance as it promotes detrimental processes such as reservoir souring and metal corrosion. These findings provide a new conceptual framework for understanding the petroleum reservoir biosphere and have consequences for developing strategies to manage microbiological problems in the oil industry.

Engineering biofuel tolerance in non-native producing microorganisms.

PubMed

Jin, Hu; Chen, Lei; Wang, Jiangxin; Zhang, Weiwen

2014-01-01

Large-scale production of renewable biofuels through microbiological processes has drawn significant attention in recent years, mostly due to the increasing concerns on the petroleum fuel shortages and the environmental consequences of the over-utilization of petroleum-based fuels. In addition to native biofuel-producing microbes that have been employed for biofuel production for decades, recent advances in metabolic engineering and synthetic biology have made it possible to produce biofuels in several non-native biofuel-producing microorganisms. Compared to native producers, these non-native systems carry the advantages of fast growth, simple nutrient requirements, readiness for genetic modifications, and even the capability to assimilate CO2 and solar energy, making them competitive alternative systems to further decrease the biofuel production cost. However, the tolerance of these non-native microorganisms to toxic biofuels is naturally low, which has restricted the potentials of their application for high-efficiency biofuel production. To address the issues, researches have been recently conducted to explore the biofuel tolerance mechanisms and to construct robust high-tolerance strains for non-native biofuel-producing microorganisms. In this review, we critically summarize the recent progress in this area, focusing on three popular non-native biofuel-producing systems, i.e. Escherichia coli, Lactobacillus and photosynthetic cyanobacteria. Copyright © 2014 Elsevier Inc. All rights reserved.

Salivary proteins and microbiota as biomarkers for early childhood caries risk assessment

PubMed Central

Hemadi, Abdullah S; Huang, Ruijie; Zhou, Yuan; Zou, Jing

2017-01-01

Early childhood caries (ECC) is a term used to describe dental caries in children aged 6 years or younger. Oral streptococci, such as Streptococcus mutans and Streptococcus sorbrinus, are considered to be the main etiological agents of tooth decay in children. Other bacteria, such as Prevotella spp. and Lactobacillus spp., and fungus, that is, Candida albicans, are related to the development and progression of ECC. Biomolecules in saliva, mainly proteins, affect the survival of oral microorganisms by multiple innate defensive mechanisms, thus modulating the oral microflora. Therefore, the protein composition of saliva can be a sensitive indicator for dental health. Resistance or susceptibility to caries may be significantly correlated with alterations in salivary protein components. Some oral microorganisms and saliva proteins may serve as useful biomarkers in predicting the risk and prognosis of caries. Current research has generated abundant information that contributes to a better understanding of the roles of microorganisms and salivary proteins in ECC occurrence and prevention. This review summarizes the microorganisms that cause caries and tooth-protective salivary proteins with their potential as functional biomarkers for ECC risk assessment. The identification of biomarkers for children at high risk of ECC is not only critical for early diagnosis but also important for preventing and treating the disease. PMID:29125139

Phage Therapy and Photodynamic Therapy: Low Environmental Impact Approaches to Inactivate Microorganisms in Fish Farming Plants

PubMed Central

Almeida, Adelaide; Cunha, Ângela; Gomes, Newton C.M.; Alves, Eliana; Costa, Liliana; Faustino, Maria A.F.

2009-01-01

Owing to the increasing importance of aquaculture to compensate for the progressive worldwide reduction of natural fish and to the fact that several fish farming plants often suffer from heavy financial losses due to the development of infections caused by microbial pathogens, including multidrug resistant bacteria, more environmentally-friendly strategies to control fish infections are urgently needed to make the aquaculture industry more sustainable. The aim of this review is to briefly present the typical fish farming diseases and their threats and discuss the present state of chemotherapy to inactivate microorganisms in fish farming plants as well as to examine the new environmentally friendly approaches to control fish infection namely phage therapy and photodynamic antimicrobial therapy. PMID:19841715

Super-long Anabiosis of Ancient Microorganisms in Ice and Terrestrial Models for Development of Methods to Search for Life on Mars, Europa and other Planetary Bodies

NASA Technical Reports Server (NTRS)

Abyzov, S. S.; Duxbury, N. S.; Bobin, N. E.; Fukuchi, M.; Hoover, R. B.; Kanda, H.; Mitskevich, I. N.; Mulyukin, A. L.; Naganuma, T.; Poglazova, M. N.;

Siderophore production and facilitated uptake of iron plutonium in p. putida.

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

Boukhalfa, H.; Lack, J. G.; Reilly, S. D.

2003-01-01

Bioremediation is a very attractive alternative for restoration of contaminated soil and ground water . This is particularly true for radionuclide contamination, which tends to be low in concentration and distributed over large surface areas . Microorganisms, through their natural metabolism, produce a large variety of organic molecules of different size and functionality . These molecules interact with contaminants present in the microbe's environment . Through these interactions bio-molecules can solubilize, oxidize, reduce or precipitate major metal contaminant in soils and ground water . We are studying these interaction for actinides and common soil subsurface bacteria . One focus hasmore » been on siderophores, small molecules that have great affinity for hard metal ions, and their potential to affect the distribution and mobility of actinide contaminants . The metal siderophores assembly can be recognized and taken up by micro-organisms through their interference with their iron uptake system . The first step in the active iron transport consists of Fe(III)-siderophore recognition by membrane receptors, which requires specific stereo orientation of the Fe(III)-siderophore complex . Recent investigations have shown that siderophores can form strong complexes with a large variety of toxic metals and may mediate their introduction inside the cell . We have previously shown that a Puhydroxamate siderophore assembly is recognized and taken up by the Microbacterium flavescens (JG-9). However, it is not clear if Pu-siderophore assemblies of other siderophores are also recognized.« less

Microbial Growth under Supercritical CO2

PubMed Central

Peet, Kyle C.; Freedman, Adam J. E.; Hernandez, Hector H.; Britto, Vanya; Boreham, Chris; Ajo-Franklin, Jonathan B.

2015-01-01

Growth of microorganisms in environments containing CO2 above its critical point is unexpected due to a combination of deleterious effects, including cytoplasmic acidification and membrane destabilization. Thus, supercritical CO2 (scCO2) is generally regarded as a sterilizing agent. We report isolation of bacteria from three sites targeted for geologic carbon dioxide sequestration (GCS) that are capable of growth in pressurized bioreactors containing scCO2. Analysis of 16S rRNA genes from scCO2 enrichment cultures revealed microbial assemblages of varied complexity, including representatives of the genus Bacillus. Propagation of enrichment cultures under scCO2 headspace led to isolation of six strains corresponding to Bacillus cereus, Bacillus subterraneus, Bacillus amyloliquefaciens, Bacillus safensis, and Bacillus megaterium. Isolates are spore-forming, facultative anaerobes and capable of germination and growth under an scCO2 headspace. In addition to these isolates, several Bacillus type strains grew under scCO2, suggesting that this may be a shared feature of spore-forming Bacillus spp. Our results provide direct evidence of microbial activity at the interface between scCO2 and an aqueous phase. Since microbial activity can influence the key mechanisms for permanent storage of sequestered CO2 (i.e., structural, residual, solubility, and mineral trapping), our work suggests that during GCS microorganisms may grow and catalyze biological reactions that influence the fate and transport of CO2 in the deep subsurface. PMID:25681188

[Cobalt(III)-EDTA] - Reduction by Thermophilic Methanogen Methanothermobacter Thermautotrophicus

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

Singh, Rajesh; Dong, Hailiang; Liu, Deng

2015-06-30

Cobalt is a metal contaminant at high temperature radioactive waste disposal sites. In previous studies have largely focused on mesophilic microorganisms to remediate cobalt, despite the presence of thermophilic microorganisms at such sites. In this study,Methanothermobacter thermautotrophicus, a thermophilic methanogen, was used to reduce Co(III) in the form of [Co(III)–EDTA] -. Bioreduction experiments were conducted in a growth medium with H 2/CO 2 as a growth substrate at initial Co(III) concentrations of 1, 2, 4, 7, and 10 mM. At low Co(III) concentrations (< 4 mM), a complete reduction was observed within a week. Wet chemistry, X-ray absorption near-edge structuremore » (XANES) and electron paramagnetic resonance (EPR) analyses were all consistent in revealing the reduction kinetics. But, at higher concentrations (7 and 10 mM) the reduction extents only reached 69.8% and 48.5%, respectively, likely due to the toxic effect of Co(III) to the methanogen cells as evidenced by a decrease in total cellular protein at these Co(III) concentrations. Methanogenesis was inhibited by Co(III) bioreduction, possibly due to impaired cell growth and electron diversion from CO 2 to Co(III). Overall, our results demonstrated the ability of M. thermautotrophicus to reduce Co(III) to Co(II) and its potential application for remediating 60Co contaminant at high temperature subsurface radioactive waste disposal sites.« less

Metaproteomics Identifies the Protein Machinery Involved in Metal and Radionuclide Reduction in Subsurface Microbiomes and Elucidates Mechanisms and U(VI) Reduction Immobilization

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

Pfiffner, Susan M.; Löffler, Frank; Ritalahti, Kirsti

The overall goal for this funded project was to develop and exploit environmental metaproteomics tools to identify biomarkers for monitoring microbial activity affecting U speciation at U-contaminated sites, correlate metaproteomics profiles with geochemical parameters and U(VI) reduction activity (or lack thereof), elucidate mechanisms contributing to U(VI) reduction, and provide remediation project managers with additional information to make science-based site management decisions for achieving cleanup goals more efficiently. Although significant progress has been made in elucidating the microbiology contribution to metal and radionuclide reduction, the cellular components, pathway(s), and mechanisms involved in U trans-formation remain poorly understood. Recent advances in (meta)proteomicsmore » technology enable detailed studies of complex samples, including environmental samples, which differ between sites and even show considerable variability within the same site (e.g., the Oak Ridge IFRC site). Additionally, site-specific geochemical conditions affect microbial activity and function, suggesting generalized assessment and interpretations may not suffice. This research effort integrated current understanding of the microbiology and biochemistry of U(VI) reduction and capitalize on advances in proteomics technology made over the past few years. Field-related analyses used Oak Ridge IFRC field ground water samples from locations where slow-release substrate biostimulation has been implemented to accelerate in situ U(VI) reduction rates. Our overarching hypothesis was that the metabolic signature in environmental samples, as deciphered by the metaproteome measurements, would show a relationship with U(VI) reduction activity. Since metaproteomic and metagenomic characterizations were computationally challenging and time-consuming, we used a tiered approach that combines database mining, controlled laboratory studies, U(VI) reduction activity measurements, phylogenetic analyses, and gene expression studies to support the metaproteomics characterizations. Growth experiments of target microorganisms (Anaeromyxobacter, Shewanella, Geobacter) revealed tremendous respiratory versatility, as evidenced by the ability to utilize a range of electron donors (e.g. acetate, hydrogen, pyruvate, lactate, succinate, formate) and electron acceptors (e.g. nitrate, fumarate, halogenated phenols, ferric iron, nitrous oxide, etc.). In particular, the dissimilatory metabolic reduction of metals, including radionuclides, by target microorganisms spurred interest for in situ bioremediation of contaminated soils and sediments. Distinct c-type cytochrome expression patterns were observed in target microorganisms grown with the different electron acceptors. For each target microorganism, the core proteome covered almost all metabolic pathways represented by their corresponding pan-proteomes. Unique proteins were detected for each target microorganism, and their expression and possible functionalities were linked to specific growth conditions through proteomics measurements. Optimization of the proteomic tools included in-depth comprehensive metagenomic and metaproteomic analyses on a limited number of samples. The optimized metaproteomic analyses were then applied to Oak Ridge IFRC field samples from the slow-release substrate biostimulation. Metaproteomic analysis and pathway mapping results demonstrated the distinct effects of metal and non-metal growth conditions on the proteome expression. With these metaproteomic tools, we identified which previously hypothetical metabolic pathways were active during the analyzed time points of the slow release substrate biostimulation. Thus, we demonstrated the utility of these tools for site assessment, efficient implementation of bioremediation and long-term monitoring. This research of detailed protein analysis linked with metal reduction activity did (1) show that c-type cytochrome isoforms, previously associated with radionuclide reduction activity, are suitable biomarkers, (2) identify new biomarker targets for site assessment and bioremediation monitoring, and (3) provide new information about specific proteins and mechanisms involved in U(VI) reduction and immobilization. This expanded metagenomic and metaproteomic toolbox contributed to implementing science-driven site management with broad benefits to the DOE mission.« less

Microbiological and biochemical aspects of Camembert-type cheeses depend on atmospheric composition in the ripening chamber.

PubMed

Leclercq-Perlat, M-N; Picque, D; Riahi, H; Corrieu, G

2006-08-01

Camembert-type cheeses were prepared from pasteurized milk seeded with Kluyveromyces lactis, Geotrichum candidum, Penicillium camemberti, and Brevibacterium aurantiacum. Microorganism growth and biochemical dynamics were studied in relation to ripening chamber CO(2) atmospheric composition using 31 descriptors based on kinetic data. The chamber ripening was carried out under 5 different controlled atmospheres: continuously renewed atmosphere, periodically renewed atmosphere, no renewed atmosphere, and 2 for which CO(2) was either 2% or 6%. All microorganism dynamics depended on CO(2) level. Kluyveromyces lactis was not sensitive to CO(2) during its growth phases, but its death did depend on it. An increase of CO(2) led to a significant improvement in G. candidum. Penicillium camemberti mycelium development was enhanced by 2% CO(2). The equilibrium between P. camemberti and G. candidum populations was disrupted in favor of the yeast when CO(2) was higher than 4%. Growth of B. aurantiacum depended more on O(2) than on CO(2). Two ripening progressions were observed in relation to the presence of CO(2) at the beginning of ripening: in the presence of CO(2), the ripening was fast-slow, and in the absence of CO(2), it was slow-fast. The underrind was too runny if CO(2) was equal to or higher than 6%. The nitrogen substrate progressions were slightly related to ripening chamber CO(2) and O(2) levels. During chamber ripening, the best atmospheric condition to produce an optimum between microorganism growth, biochemical dynamics, and cheese appearance was a constant CO(2) level close to 2%.

Systems metabolic engineering: the creation of microbial cell factories by rational metabolic design and evolution.

PubMed

Furusawa, Chikara; Horinouchi, Takaaki; Hirasawa, Takashi; Shimizu, Hiroshi

2013-01-01

It is widely acknowledged that in order to establish sustainable societies, production processes should shift from petrochemical-based processes to bioprocesses. Because bioconversion technologies, in which biomass resources are converted to valuable materials, are preferable to processes dependent on fossil resources, the former should be further developed. The following two approaches can be adopted to improve cellular properties and obtain high productivity and production yield of target products: (1) optimization of cellular metabolic pathways involved in various bioprocesses and (2) creation of stress-tolerant cells that can be active even under severe stress conditions in the bioprocesses. Recent progress in omics analyses has facilitated the analysis of microorganisms based on bioinformatics data for molecular breeding and bioprocess development. Systems metabolic engineering is a new area of study, and it has been defined as a methodology in which metabolic engineering and systems biology are integrated to upgrade the designability of industrially useful microorganisms. This chapter discusses multi-omics analyses and rational design methods for molecular breeding. The first is an example of the rational design of metabolic networks for target production by flux balance analysis using genome-scale metabolic models. Recent progress in the development of genome-scale metabolic models and the application of these models to the design of desirable metabolic networks is also described in this example. The second is an example of evolution engineering with omics analyses for the creation of stress-tolerant microorganisms. Long-term culture experiments to obtain the desired phenotypes and omics analyses to identify the phenotypic changes are described here.

Septic implantation syndrome in dogs and cats: a distinct pattern of endophthalmitis with lenticular abscess.

PubMed

Bell, Cynthia M; Pot, Simon A; Dubielzig, Richard R

2013-05-01

To summarize the clinical and pathologic findings in a group of dogs and cats with progressive clinical ocular disease, which were diagnosed with suppurative endophthalmitis and lens capsule rupture. Twenty cats and forty-six dogs that underwent unilateral enucleation or evisceration for intractable uveitis and/or glaucoma. Biopsy submission requests and microscopic case material were evaluated for clinical and histological features, including history of ocular trauma, duration of ocular disease, pattern of inflammation, and the presence of intralenticular microorganisms. The median duration for cats and dogs was 6 and 5 weeks, respectively. A history of trauma was reported for four (20%) cats and 18 (39%) dogs. All confirmed cases of trauma-three in cats and 14 in dogs-were caused by a cat scratch. Microscopically, all cases had suppurative endophthalmitis centered on the lens, lens capsule rupture, cataract, and lenticular abscess. Infectious organisms were identified by Gram stain within the lens of 14 (70%) cats and 30 (65%) dogs. Gram-positive cocci were seen most commonly. Male cats were overrepresented as compared to females. There were no apparent gender, age or breed predilections in dogs. A unique pattern of slowly progressive or delayed-onset endophthalmitis with lens capsule rupture, lenticular abscess, and frequently intralenticular microorganisms is associated with traumatic penetration of the globe and lens capsule. The term Septic Implantation Syndrome (SIS) is favored in lieu of 'phacoclastic uveitis' to avoid confusion with phacolytic uveitis and to clearly implicate the role of intralenticular microorganisms in the pathogenesis. © 2012 American College of Veterinary Ophthalmologists.

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.

Deep subsurface life in Bengal Fan sediments (IODP Exp. 354)

NASA Astrophysics Data System (ADS)

Adhikari, R. R.; Heuer, V. B.; Elvert, M.; Kallmeyer, J.; Kitte, J. A.; Wörmer, L.; Hinrichs, K. U.

2017-12-01

We collected Bengal Fan sediment samples along a 8°N transect during International Ocean Discovery Program Expedition 354 (February - March 2015, Singapore - Colombo, Sri Lanka) to study subseafloor life in this, as yet unstudied, area. Among other biogeochemical parameters, we quantified microbial biomass by analyzing prokaryotic cells using epifluorescence microscopy after detaching cells from the sediment, and bacterial endospores by analyzing the diagnostic biomarker dipicolinic acid (DPA) by detection of fluorescence of the terbium-DPA complex. To gain understanding of total microbial activity, we quantified hydrogen utilization potential of hydrogenase enzymes, which are ubiquitous in subsurface microorganisms, by using a tritium assay. We measured highest cell concentrations of ca. 108 cells g-1 in shallow sediments close to the seafloor. These concentrations are one to two orders of magnitude lower than in most marine continental margin settings [1]. Similar to the global trend [1], cell concentrations decreased with depth according to a power-law function. Endospore concentrations scattered between ca. 105 and 107 cells g-1 sediment at all sites and depths. We could not observe a clear relationship of endospore concentration and sediment depth; instead, it appears to be linked to lithology and total organic carbon content. Bulk Hydrogenase enzyme activity ranged from nmolar to μmolar range of H2 g-1d-1. Similar to previous observations [2], per-cell hydrogen utilization depends on vertical biogeochemical zones, which could be due to the differences in hydrogen utilization requirements/efficiency of the respective metabolic processes such as sulfate reduction, methanogenesis, fermentation etc. Bengal fan is highly dynamic due to channel and levee systems and the sediments are dominated by turbidites, thick sand layers and hemipelagic deposits, which may control biogeochemical zonation. Based on our microbial biomass and activity data, we suggest that the nature, quality and origin of sedimentary material influence the deep subsurface life. [1] Kallmeyer et al., (2012) PNAS 109(40), 16213-16216 [2] Adhikari et al., (2016) Frontiers in Microbiology 7:8

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

Application of an in-situ soil sampler for assessing subsurface biogeochemical dynamics in a diesel-contaminated coastal site during soil flushing operations.

PubMed

Kwon, Man Jae; O'Loughlin, Edward J; Ham, Baknoon; Hwang, Yunho; Shim, Moojoon; Lee, Soonjae

2018-01-15

Subsurface biogeochemistry and contaminant dynamics during the remediation of diesel-contamination by in-situ soil flushing were investigated at a site located in a coastal region. An in-situ sampler containing diesel-contaminated soils separated into two size fractions (<0.063- and <2-mm) was utilized in two monitoring wells: DH1 (located close to the injection and extraction wells for in-situ soil flushing) and DH2 (located beyond sheet piles placed to block the transport of leaked diesel). Total petroleum hydrocarbon (TPH) concentrations and biogeochemical properties were monitored both in soil and groundwater for six months. A shift occurred in the groundwater type from Ca-HCO 3 to Na-Cl due to seawater intrusion during intense pumping, while the concentrations of Ni, Cu, Co, V, Cr, and Se increased substantially following surfactant (TWEEN 80) injection. The in-situ sampler with fine particles was more sensitive to variations in conditions during the remedial soil flushing process. In both wells, soil TPH concentrations in the <0.063-mm fraction were much higher than those in the <2-mm fraction. Increases in soil TPH in DH1 were consistent with the expected outcomes following well pumping and surfactant injection used to enhance TPH extraction. However, the number of diesel-degrading microorganisms decreased after surfactant injection. 16S-rRNA gene-based analysis also showed that the community composition and diversity depended on both particle size and diesel contamination. The multidisciplinary approach to the contaminated site assessments showed that soil flushing with surfactant enhanced diesel extraction, but negatively impacted in-situ diesel biodegradation as well as groundwater quality. The results also suggest that the in-situ sampler can be an effective monitoring tool for subsurface biogeochemistry as well as contaminant dynamics. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

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.

Reactivation of Deep Subsurface Microbial Community in Response to Methane or Methanol Amendment

PubMed Central

Rajala, Pauliina; Bomberg, Malin

2017-01-01

Microbial communities in deep subsurface environments comprise a large portion of Earth’s biomass, but the microbial activity in these habitats is largely unknown. Here, we studied how microorganisms from two isolated groundwater fractures at 180 and 500 m depths of the Outokumpu Deep Drillhole (Finland) responded to methane or methanol amendment, in the presence or absence of sulfate as an additional electron acceptor. Methane is a plausible intermediate in the deep subsurface carbon cycle, and electron acceptors such as sulfate are critical components for oxidation processes. In fact, the majority of the available carbon in the Outokumpu deep biosphere is present as methane. Methanol is an intermediate of methane oxidation, but may also be produced through degradation of organic matter. The fracture fluid samples were incubated in vitro with methane or methanol in the presence or absence of sulfate as electron acceptor. The metabolic response of microbial communities was measured by staining the microbial cells with fluorescent redox sensitive dye combined with flow cytometry, and DNA or cDNA-derived amplicon sequencing. The microbial community of the fracture zone at the 180 m depth was originally considerably more respiratory active and 10-fold more numerous (105 cells ml-1 at 180 m depth and 104 cells ml-1 at 500 m depth) than the community of the fracture zone at the 500 m. However, the dormant microbial community at the 500 m depth rapidly reactivated their transcription and respiration systems in the presence of methane or methanol, whereas in the shallower fracture zone only a small sub-population was able to utilize the newly available carbon source. In addition, the composition of substrate activated microbial communities differed at both depths from original microbial communities. The results demonstrate that OTUs representing minor groups of the total microbial communities play an important role when microbial communities face changes in environmental conditions. PMID:28367144

A simple model for remineralization of subsurface lesions in tooth enamel

NASA Astrophysics Data System (ADS)

Christoffersen, J.; Christoffersen, M. R.; Arends, J.

1982-12-01

A model for remineralization of subsurface lesions in tooth enamel is presented. The important assumption on which the model is based is that the rate-controlling process is the crystal surface process by which ions are incorporated in the crystallites; that is, the transport of ions through small holes in the so-called intact surface layer does not influence the rate of mineral uptake at the crystal surface. Further, the density of mineral in the lesion is assumed to increase down the lesion, when the remineralization process is started. It is shown that the dimension of the initial holes in the enamel surface layer must be larger than the dimension of the individual crystallites in order to prevent the formation of arrested lesions. Theoretical expressions for the progress of remineralization are given. The suggested model emphasizes the need for measurements of mineral densities in the lesion, prior to, and during the lesion repair.

Europa's shallow subsurface: lakes, layers and life? (Invited)

NASA Astrophysics Data System (ADS)

Schmidt, B. E.; Soderlund, K. M.; Gooch, B. T.; Blankenship, D. D.

2013-12-01

With an icy exterior covering a global ocean, Europa has long been a target of interest in the search for life beyond Earth. A critical question related to the habitability of this icy world is: how does the ice shell recycle? Recent detection of shallow subsurface water lenses or "lakes" joins the evidence that implies Europa is currently active, recycling its ice shell. This new perspective has important astrobiological implications. At a surface age of 40-90 Myr, and about 50% covered by chaos terrain, Europa's resurfacing rate is likely to be very high if water does play a significant role in their formation. Because of the vigor of overturn implied if chaos does form by the collapse of ice above subsurface lenses, it is likely that surface and subsurface materials are well-mixed within the largest and deepest lenses, providing a mechanism for bringing oxidants and other surface contaminants to the deeper ice shell where it can reach the ocean by convective or compositional effects. The timescales over which large lenses refreeze (a few hundred thousand years) are large compared to the timescales for vertical transport (a few tens of thousands of years), while the timescales for smaller lenses are comparable to or shorter than convective timescales but involving smaller impurity loads than for larger more well-mixed sources. Melt lenses are intriguing potential habitats, particularly the larger features. Moreover, their formation likely requires the existence of impurities within the upper ice shell that may be sources of energy for microorganisms. Geomorphic evidence also exists for brine percolation that can disperse fluids both vertically and horizontally through pores and fractures. This process, observed in terrestrial ice shelves, may preserve liquid water within the ice matrix over many kilometers from the source. Horizontal transport of material may produce interconnectivity between distinct regions of Europa, providing a pathway for transferring nutrients and biomass, thus preserving habitable conditions within the ice over a longer duration. From this point of view, we evaluate the habitability of Europa's ice and ocean in light of active processes, including the lifetime of liquid reservoirs, vertical and horizontal material transport, and the resurfacing rate of the body that may be responsible both for reenergizing and destroying shallow habitats.

Zones of life in the subsurface of hydrothermal vents: A synthesis

NASA Astrophysics Data System (ADS)

Larson, B. I.; Houghton, J.; Meile, C. D.

2011-12-01

Subsurface microbial communities in Mid-ocean Ridge (MOR) hydrothermal systems host a wide array of unique metabolic strategies, but the spatial distribution of biogeochemical transformations is poorly constrained. Here we present an approach that reexamines chemical measurements from diffuse fluids with models of convective transport to delineate likely reaction zones. Chemical data have been compiled from bare basalt surfaces at a wide array of mid-ocean ridge systems, including 9°N, East Pacific Rise, Axial Seamount, Juan de Fuca, and Lucky Strike, Mid-Atlantic Ridge. Co-sampled end-member fluid from Ty (EPR) was used to constrain reaction path models that define diffuse fluid compositions as a function of temperature. The degree of mixing between hot vent fluid (350 deg. C) and seawater (2 deg. C) governs fluid temperature, Fe-oxide mineral precipitation is suppressed, and aqueous redox reactions are prevented from equilibrating, consistent with sluggish kinetics. Quartz and pyrite are predicted to precipitate, consistent with field observations. Most reported samples of diffuse fluids from EPR and Axial Seamount fall along the same predicted mixing line only when pyrite precipitation is suppressed, but Lucky Strike fluids do not follow the same trend. The predicted fluid composition as a function of temperature is then used to calculate the free energy available to autotrophic microorganisms for a variety of catabolic strategies in the subsurface. Finally, the relationships between temperature and free energy is combined with modeled temperature fields (Lowell et al., 2007 Geochem. Geophys., Geosys.) over a 500 m x 500 m region extending downward from the seafloor and outward from the high temperature focused hydrothermal flow to define areas that are energetically most favorable for a given metabolic process as well as below the upper temperature limit for life (~120 deg. C). In this way, we can expand the relevance of geochemical model predictions of bioenergetics by predicting functionally-defined 'Zones of Life' and placing them spatially within the boundary of the 120 deg. C isotherm, estimating the extent of subsurface biosphere beneath mid-ocean ridge hydrothermal systems. Preliminary results indicate that methanogenesis yields the most energy per kg of vent fluid, consistent with the elevated CH4(aq) seen at all three sites, but may be constrained by temperatures too hot for microbial life while available energy from the oxidation of Fe(II) peaks near regions of the crust that are more hospitable.

Flux analysis and metabolomics for systematic metabolic engineering of microorganisms.

PubMed

Toya, Yoshihiro; Shimizu, Hiroshi

2013-11-01

Rational engineering of metabolism is important for bio-production using microorganisms. Metabolic design based on in silico simulations and experimental validation of the metabolic state in the engineered strain helps in accomplishing systematic metabolic engineering. Flux balance analysis (FBA) is a method for the prediction of metabolic phenotype, and many applications have been developed using FBA to design metabolic networks. Elementary mode analysis (EMA) and ensemble modeling techniques are also useful tools for in silico strain design. The metabolome and flux distribution of the metabolic pathways enable us to evaluate the metabolic state and provide useful clues to improve target productivity. Here, we reviewed several computational applications for metabolic engineering by using genome-scale metabolic models of microorganisms. We also discussed the recent progress made in the field of metabolomics and (13)C-metabolic flux analysis techniques, and reviewed these applications pertaining to bio-production development. Because these in silico or experimental approaches have their respective advantages and disadvantages, the combined usage of these methods is complementary and effective for metabolic engineering. Copyright © 2013 Elsevier Inc. All rights reserved.

Use of PRD1 bacteriophage in groundwater viral transport, inactivation, and attachment studies

USGS Publications Warehouse

Harvey, Ronald W.; Ryan, Joseph N.

2004-01-01

PRD1, an icosahedra-shaped, 62 nm (diameter), double-stranded DNA bacteriophage with an internal membrane, has emerged as an important model virus for studying the manner in which microorganisms are transported through a variety of groundwater environments. The popularity of this phage for use in transport studies involving geologic media is due, in part, to its relative stability over a range of temperatures and low degree of attachment in aquifer sediments. Laboratory and field investigations employing PRD1 are leading to a better understanding of viral attachment and transport behaviors in saturated geologic media and to improved methods for describing mathematically subsurface microbial transport at environmentally significant field scales. Radioisotopic labeling of PRD1 is facilitating additional information about the nature of viral interactions with solid surfaces in geologic media, the importance of iron oxide surfaces, and allowing differentiation between inactivation and attachment in field-scale tracer tests.

Influence of irrigation and weathering reactions on the composition of percolates from retorted oil shale in field lysimeters

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

Garland, T. R.; Wildung, R. E.; Harbert, H. P.

1979-04-01

Major cations, anions, trace elements and dissolved organic C were measured in percolate from retorted oil shale collected from irrigated lysimeters in the field at Anvil Points, Colorado, over a two year period. The investigations indicated that chemical equilibrium was not established over the monitoring period and major changes occurred in percolate composition as a function of applied water volume and water residence time in the shale. Field and laboratory studies indicated that several factors contributed to changes in the chemistry of the shale on weathering, including recarbonization of the surface horizons with atmospheric CO/sub 2/ and the activities ofmore » microorganisms in surface and subsurface horizons. However, the principal mechanism responsible for the decreases in pH and salt concentrations appeared to be the conversion of major quantities of sulfide in the retorted shale to sulfate through a thiosulfate intermediate.« less

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

Joel E. Kostka

This project represented a joint effort between Oak Ridge National Laboratory (ORNL), the University of Tennessee (UT), and Florida State University (FSU). ORNL served as the lead in-stitution with Dr. A.V. Palumbo responsible for project coordination, integration, and deliver-ables. In situ uranium bioremediation is focused on biostimulating indigenous microorganisms through a combination of pH neutralization and the addition of large amounts of electron donor. Successful biostimulation of U(VI) reduction has been demonstrated in the field and in the laboratory. However, little data is available on the dynamics of microbial populations capable of U(VI) reduction, and the differences in the microbialmore » community dynamics between proposed electron donors have not been explored. In order to elucidate the potential mechanisms of U(VI) reduction for optimization of bioremediation strategies, structure-function relationships of microbial populations were investigated in microcosms of subsurface materials cocontaminated with radionuclides and nitrate from the Oak Ridge Field Research Center (ORFRC), Oak Ridge, Tennessee.« less

Current progress of targetron technology: development, improvement and application in metabolic engineering.

PubMed

Liu, Ya-Jun; Zhang, Jie; Cui, Gu-Zhen; Cui, Qiu

2015-06-01

Targetrons are mobile group II introns that can recognize their DNA target sites by base-pairing RNA-DNA interactions with the aid of site-specific binding reverse transcriptases. Targetron technology stands out from recently developed gene targeting methods because of the flexibility, feasibility, and efficiency, and is particularly suitable for the genetic engineering of difficult microorganisms, including cellulolytic bacteria that are considered promising candidates for biomass conversion via consolidated bioprocessing. Along with the development of the thermotargetron method for thermophiles, targetron technology becomes increasingly important for the metabolic engineering of industrial microorganisms aiming at biofuel/chemical production. To summarize the current progress of targetron technology and provide new insights on the use of the technology, this paper reviews the retrohoming mechanisms of both mesophilic and thermophilic targetron methods based on various group II introns, investigates the improvement of targetron tools for high target efficiency and specificity, and discusses the current applications in the metabolic engineering for bacterial producers. Although there are still intellectual property and technical restrictions in targetron applications, we propose that targetron technology will contribute to both biochemistry research and the metabolic engineering for industrial productions. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Design and development of synthetic microbial platform cells for bioenergy

PubMed Central

Lee, Sang Jun; Lee, Sang-Jae; Lee, Dong-Woo

2013-01-01

The finite reservation of fossil fuels accelerates the necessity of development of renewable energy sources. Recent advances in synthetic biology encompassing systems biology and metabolic engineering enable us to engineer and/or create tailor made microorganisms to produce alternative biofuels for the future bio-era. For the efficient transformation of biomass to bioenergy, microbial cells need to be designed and engineered to maximize the performance of cellular metabolisms for the production of biofuels during energy flow. Toward this end, two different conceptual approaches have been applied for the development of platform cell factories: forward minimization and reverse engineering. From the context of naturally minimized genomes,non-essential energy-consuming pathways and/or related gene clusters could be progressively deleted to optimize cellular energy status for bioenergy production. Alternatively, incorporation of non-indigenous parts and/or modules including biomass-degrading enzymes, carbon uptake transporters, photosynthesis, CO2 fixation, and etc. into chassis microorganisms allows the platform cells to gain novel metabolic functions for bioenergy. This review focuses on the current progress in synthetic biology-aided pathway engineering in microbial cells and discusses its impact on the production of sustainable bioenergy. PMID:23626588

Effects of Potassium Permanganate Oxidation on Subsurface Microbial Activity

NASA Technical Reports Server (NTRS)

Rowland, Martin A.; Brubaker, Gaylen R.; Westray, Mark; Morris, Damon; Kohler, Keisha; McCool, Alex (Technical Monitor)

2001-01-01

In situ chemical oxidation has the potential for degrading large quantities of organic contaminants and can be more effective and timely than traditional ex situ treatment methods. However, there is a need to better characterize the potential effects of this treatment on natural processes. This study focuses on potential inhibition to anaerobic dechlorination of trichloroethene (TCE) in soils from a large manufacturing facility as a result of in situ oxidation using potassium permanganate (KMn04)Previous microcosm studies established that natural attenuation occurs on-site and that it is enhanced by the addition of ethanol to the system. A potential remediation scheme for the site involves the use of potassium permanganate to reduce levels of TCE in heavily contaminated areas, then to inject ethanol into the system to "neutralize" excess oxidant and enhance microbial degradation. However, it is currently unknown whether the exposure of indigenous microbial populations to potassium permanganate may adversely affect biological reductive dechlorination by these microorganisms. Consequently, additional microcosm studies were conducted to evaluate this remediation scheme and assess the effect of potassium permanganate addition on biological reductive dechlorination of TCE. Samples of subsurface soil and groundwater were collected from a TCE-impacted area of the site. A portion of the soil was pretreated with nutrients and ethanol to stimulate microbial activity, while the remainder of the soil was left unamended. Soil/groundwater microcosms were prepared in sealed vials using the nutrient-amended and unamended soils, and the effects of potassium permanganate addition were evaluated using two permanganate concentrations (0.8 and 2.4 percent) and two contact times (1 and 3 weeks). TCE was then re-added to each microcosm and TCE and dichloroethene (DCE) concentrations were monitored to determine the degree to which microbial dechlorination occurred following chemical oxidation. Evidence of microbial degradation was generally detected within four weeks after TCE addition. Increases in DCE concentrations were consistent with decreases in TCE. The concentration of TCE in the nutrient-amended samples exposed to 2.4% KMnO4 for one week degraded somewhat more slowly than the samples exposed to the 0.8% KMnO4. The rates of degradation did not correlate with the length of KMn04 exposure for the nutrient-amended microcosms. Microbial degradation of TCE in the unamended microcosms was generally similar to that observed in the nutrient-amended microcosms. One treatment condition (unamended, one week exposure, 2.4% KMnO4) was exposed to elevated levels of ethanol and showed little evidence of degradation. It is suspected that the high levels of ethanol were toxic to the microorganisms. The results of the study indicate that exposure of indigenous soil and groundwater microbial populations to KMnO4 at concentrations of 0.8 to 2.4% do not impair the ability of the microbial populations to dechlorinate TCE. Consequently, the combination of chemical oxidation followed by enhanced biological reductive dechlorination appears to be a viable remedial strategy for highly-impacted subsurface areas of the site.

The hidden face of academic researches on classified highly pathogenic microorganisms.

PubMed

Devaux, Christian A

2015-01-01

Highly pathogenic microorganisms and toxins are manipulated in academic laboratories for fundamental research purposes, diagnostics, drugs and vaccines development. Obviously, these infectious pathogens represent a potential risk for human and/or animal health and their accidental or intentional release (biosafety and biosecurity, respectively) is a major concern of governments. In the past decade, several incidents have occurred in laboratories and reported by media causing fear and raising a sense of suspicion against biologists. Some scientists have been ordered by US government to leave their laboratory for long periods of time following the occurrence of an incident involving infectious pathogens; in other cases laboratories have been shut down and universities have been forced to pay fines and incur a long-term ban on funding after gross negligence of biosafety/biosecurity procedures. Measures of criminal sanctions have also been taken to minimize the risk that such incidents can reoccur. As United States and many other countries, France has recently strengthened its legal measures for laboratories' protection. During the past two decades, France has adopted a series of specific restriction measures to better protect scientific discoveries with a potential economic/social impact and prevent their misuse by ill-intentioned people without affecting the progress of science through fundamental research. French legal regulations concerning scientific discoveries have progressively strengthened since 2001, until the publication in November 2011 of a decree concerning the "PPST" (for "Protection du Potentiel Scientifique et Technique de la nation", the protection of sensitive scientific data). Following the same logic of protection of sensitive scientific researches, regulations were also adopted in an order published in April 2012 concerning the biology and health field. The aim was to define the legal framework that precise the conditions for authorizing microorganisms and toxins experimentation in France; these regulations apply for any operation of production, manufacturing, transportation, import, export, possession, supply, transfer, acquisition and use of highly pathogenic microorganisms and toxins, referred to as "MOT" (for "MicroOrganismes et Toxines hautement pathogènes") by the French law. Finally, laboratories conducting researches on such infectious pathogens are henceforth classified restricted area or ZRR (for "Zone à Régime Restrictif"), according an order of July 2012. In terms of economic protection, biosafety and biosecurity, these regulations represent an undeniable progress as compared to the previous condition. However, the competitiveness of research laboratories handling MOTs is likely to suffer the side effects of these severe constraints. For example research teams working on MOTs can be drastically affected both by (i) the indirect costs generated by the security measure to be applied; (ii) the working time devoted to samples recording; (iii) the establishment of traceability and reporting to national security agency ANSM, (iv) the latency period required for staff members being officially authorized to conduct experiments on MOTs; (v) the consequent reduced attractiveness for recruiting new trainees whose work would be significantly hampered by theses administrative constraints; and (vi) the limitations in the exchange of material with external laboratories and collaborators. Importantly, there is a risk that French academic researchers gradually abandon research on MOTs in favor of other projects that are less subject to legal restrictions. This would reduce the acquisition of knowledge in the field of MOTs which, in the long term, could be highly detrimental to the country by increasing its vulnerability to natural epidemics due to pathogenic microorganisms that are classified as MOTs and, by reducing its preparedness against possible bioterrorist attacks that would use such microorganisms. Copyright © 2014 Elsevier B.V. All rights reserved.

Development of novel drugs from marine surface associated microorganisms.

PubMed

Penesyan, Anahit; Kjelleberg, Staffan; Egan, Suhelen

2010-03-01

While the oceans cover more than 70% of the Earth's surface, marine derived microbial natural products have been largely unexplored. The marine environment is a habitat for many unique microorganisms, which produce biologically active compounds ("bioactives") to adapt to particular environmental conditions. For example, marine surface associated microorganisms have proven to be a rich source for novel bioactives because of the necessity to evolve allelochemicals capable of protecting the producer from the fierce competition that exists between microorganisms on the surfaces of marine eukaryotes. Chemically driven interactions are also important for the establishment of cross-relationships between microbes and their eukaryotic hosts, in which organisms producing antimicrobial compounds ("antimicrobials"), may protect the host surface against over colonisation in return for a nutrient rich environment. As is the case for bioactive discovery in general, progress in the detection and characterization of marine microbial bioactives has been limited by a number of obstacles, such as unsuitable culture conditions, laborious purification processes, and a lack of de-replication. However many of these limitations are now being overcome due to improved microbial cultivation techniques, microbial (meta-) genomic analysis and novel sensitive analytical tools for structural elucidation. Here we discuss how these technical advances, together with a better understanding of microbial and chemical ecology, will inevitably translate into an increase in the discovery and development of novel drugs from marine microbial sources in the future.

The Characterization of Psychrophilic Microorganisms and their potentially useful Cold-Active Glycosidases Final Progress Report

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

Brenchly, Jean E.

Our studies of novel, cold-loving microorganisms have focused on two distinct extreme environments. The first is an ice core sample from a 120,000 year old Greenland glacier. The results of this study are particularly exciting and have been highlighted with press releases and additional coverage. The first press release in 2004 was based on our presentation at the General Meeting of the American Society for Microbiology and was augmented by coverage of our publication (Appl. Environ. Microbiol. 2005. Vol. 71:7806) in the Current Topics section of the ASM news journal, “Microbe.” Of special interest for this report was the isolationmore » of numerous, phylogenetically distinct and potentially novel ultrasmall microorganisms. The detection and isolation of members of the ultrasmall population is significant because these cells pass through 0.2 micron pore filters that are generally used to trap microorganisms from environmental samples. Thus, analyses by other investigators that examined only cells captured on the filters would have missed a significant portion of this population. Only a few ultrasmall isolates had been obtained prior to our examination of the ice core samples. Our development of a filtration enrichment and subsequent cultivation of these organisms has added extensively to the collection of, and knowledge about, this important population in the microbial world.« less

Photoacoustic microscopy of human teeth

NASA Astrophysics Data System (ADS)

Rao, Bin; Cai, Xin; Favazza, Christopher; Yao, Junjie; Li, Li; Duong, Steven; Liaw, Lih-Huei; Holtzman, Jennifer; Wilder-Smith, Petra; Wang, Lihong V.

2011-03-01

Photoacoustic microscopy (PAM) utilizes short laser pulses to deposit energy into light absorbers and sensitively detects the ultrasonic waves the absorbers generate in response. PAM directly renders a three-dimensional spatial distribution of sub-surface optical absorbers. Unlike other optical imaging technologies, PAM features label-free optical absorption contrast and excellent imaging depths. Standard dental imaging instruments are limited to X-ray and CCD cameras. Subsurface optical dental imaging is difficult due to the highly-scattering enamel and dentin tissue. Thus, very few imaging methods can detect dental decay or diagnose dental pulp, which is the innermost part of the tooth, containing the nerves, blood vessels, and other cells. Here, we conducted a feasibility study on imaging dental decay and dental pulp with PAM. Our results showed that PAM is sensitive to the color change associated with dental decay. Although the relative PA signal distribution may be affected by surface contours and subsurface reflections from deeper dental tissue, monitoring changes in the PA signals (at the same site) over time is necessary to identify the progress of dental decay. Our results also showed that deep-imaging, near-infrared (NIR) PAM can sensitively image blood in the dental pulp of an in vitro tooth. In conclusion, PAM is a promising tool for imaging both dental decay and dental pulp.

Monitoring of Gasoline-ethanol Degradation In Undisturbed Soil

NASA Astrophysics Data System (ADS)

Österreicher-Cunha, P.; Nunes, C. M. F.; Vargas, E. A.; Guimarães, J. R. D.; Costa, A.

Environmental contamination problems are greatly emphasised nowadays because of the direct threat they represent for human health. Traditional remediation methods fre- quently present low efficiency and high costs; therefore, biological treatment is being considered as an accessible and efficient alternative for soil and water remediation. Bioventing, commonly used to remediate petroleum hydrocarbon spills, stimulates the degradation capacity of indigenous microorganisms by providing better subsur- face oxygenation. In Brazil, gasoline and ethanol are mixed (78:22 v/v); some authors indicate that despite gasoline high degradability, its degradation in subsurface is hin- dered by the presence of much more rapidly degrading ethanol. Contaminant distribu- tion and degradation in the subsurface can be monitored by several physical, chemical and microbiological methodologies. This study aims to evaluate and follow the degra- dation of a gasoline-ethanol mixture in a residual undisturbed tropical soil from Rio de Janeiro. Bioventing was used to enhance microbial degradation. Shifts in bacte- rial culturable populations due to contamination and treatment effects were followed by conventional microbiology methods. Ground Penetrating Radar (GPR) measure- ments, which consist of the emission of electro-magnetic waves into the soil, yield a visualisation of contaminant degradation because of changes in soil conductivity due to microbial action on the pollutants. Chemical analyses will measure contaminant residue in soil. Our results disclosed contamination impact as well as bioventing stim- ulation on soil culturable heterotrophic bacterial populations. This multidisciplinary approach allows for a wider evaluation of processes occurring in soil.

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

Evidence for Seismogenic Hydrogen Gas, a Potential Microbial Energy Source on Earth and Mars.

PubMed

McMahon, Sean; Parnell, John; Blamey, Nigel J F

2016-09-01

The oxidation of molecular hydrogen (H2) is thought to be a major source of metabolic energy for life in the deep subsurface on Earth, and it could likewise support any extant biosphere on Mars, where stable habitable environments are probably limited to the subsurface. Faulting and fracturing may stimulate the supply of H2 from several sources. We report the H2 content of fluids present in terrestrial rocks formed by brittle fracturing on fault planes (pseudotachylites and cataclasites), along with protolith control samples. The fluids are dominated by water and include H2 at abundances sufficient to support hydrogenotrophic microorganisms, with strong H2 enrichments in the pseudotachylites compared to the controls. Weaker and less consistent H2 enrichments are observed in the cataclasites, which represent less intense seismic friction than the pseudotachylites. The enrichments agree quantitatively with previous experimental measurements of frictionally driven H2 formation during rock fracturing. We find that conservative estimates of current martian global seismicity predict episodic H2 generation by Marsquakes in quantities useful to hydrogenotrophs over a range of scales and recurrence times. On both Earth and Mars, secondary release of H2 may also accompany the breakdown of ancient fault rocks, which are particularly abundant in the pervasively fractured martian crust. This study strengthens the case for the astrobiological investigation of ancient martian fracture systems. Deep biosphere-Faults-Fault rocks-Seismic activity-Hydrogen-Mars. Astrobiology 16, 690-702.

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

ENVIRONMENTALMANAGEMENT SCIENCE PROGRAM PROJECT NUMBER 87016 CO-PRECIPITATION OF TRACEMETALS INGROUNDWATER AND VADOSE ZONE CALCITE: IN SITU CONTAINMENT AND STABILIZATION OF STRONTIUM-90 ANDOTHER DIVALENT METALS AND RADIONUCLIDES AT ARIDWESTERN DOE SITES

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

Ferris, F. Grant; Fujita, Yoshiko; Smith, Robert W.

2004-06-15

Radionuclide and metal contaminants are present in the vadose zone and groundwater throughout the U.S. Department of Energy (DOE) weapons complex. In situ containment and stabilization of these contaminants in vadose zones or groundwater is a cost-effective treatment strategy. Our facilitated approach relies upon the hydrolysis of introduced urea to cause the acceleration of calcium carbonate precipitation (and trace metal coprecipitation) by increasing groundwater pH and alkalinity (Fujita et al., 2000; Warren et al., 2001). Subsurface urea hydrolysis is catalyzed by the urease enzyme, which may be either introduced with the urea or produced in situ by ubiquitous subsurface ureamore » hydrolyzing microorganisms. Because the precipitation processes are irreversible and many western aquifers are saturated with respect to calcite, the co-precipitated metals and radionuclides will be effectively removed from groundwater. The rate at which trace metals are incorporated into calcite is a function of calcite precipitation kinetics, adsorption interactions between the calcite surface and the trace metal in solution (Zachara et al., 1991), solid solution properties of the trace metal in calcite (Tesoriero and Pankow, 1996), and also the surfaces upon which the calcite is precipitating. A fundamental understanding of the coupling of calcite precipitation and trace metal partitioning, and how this occurs in aquifers and vadose environments is lacking. This report summarizes work undertaken during the second year of this project.« less

Microbial transformations of arsenic: Mobilization from glauconitic sediments to water

USGS Publications Warehouse

Mumford, Adam C.; Barringer, Julia L.; Benzel, William M.; Reilly, Pamela A.; Young, L.Y.

2012-01-01

In the Inner Coastal Plain of New Jersey, arsenic (As) is released from glauconitic sediment to carbon- and nutrient-rich shallow groundwater. This As-rich groundwater discharges to a major area stream. We hypothesize that microbes play an active role in the mobilization of As from glauconitic subsurface sediments into groundwater in the Inner Coastal Plain of New Jersey. We have examined the potential impact of microbial activity on the mobilization of arsenic from subsurface sediments into the groundwater at a site on Crosswicks Creek in southern New Jersey. The As contents of sediments 33–90 cm below the streambed were found to range from 15 to 26.4 mg/kg, with siderite forming at depth. Groundwater beneath the streambed contains As at concentrations up to 89 μg/L. Microcosms developed from site sediments released 23 μg/L of As, and active microbial reduction of As(V) was observed in microcosms developed from site groundwater. DNA extracted from site sediments was amplified with primers for the 16S rRNA gene and the arsenate respiratory reductase gene, arrA, and indicated the presence of a diverse anaerobic microbial community, as well as the presence of potential arsenic-reducing bacteria. In addition, high iron (Fe) concentrations in groundwater and the presence of iron-reducing microbial genera suggests that Fe reduction in minerals may provide an additional mechanism for release of associated As, while arsenic-reducing microorganisms may serve to enhance the mobility of As in groundwater at this site.

Long term impacts of CMC/nZVI amendment injection on organohalide-respiring microbial communities at a chlorinated solvent field site

NASA Astrophysics Data System (ADS)

Kocur, C. M.; Lomheim, L.; Boparai, H. K.; Chowdhury, A. I.; Weber, K.; Austrins, L. M.; Sleep, B.; O'Carroll, D. M.; Edwards, E.

2014-12-01

Injection of carboxymethyl-cellulose stabilized nanoscale Zero Valent Iron (CMC/nZVI) has received significant attention in the last decade as an emerging alternative for in-situ remediation of chlorinated solvents and other recalcitrant compounds. There has also been some indication that injection of nZVI will create conditions that will stimulate in-situ microbial populations, leading to further contaminant degradation. Carboxy-methyl cellulose (CMC) is commonly used for nZVI synthesis as it provides steric stabilization for the nanoparticles, however, the CMC is equally important as a subsurface amendment as it may act as a fermentable substrate for microorganisms in-situ. In this study, microbial communities were monitored over a 2.5 year period following the injection of CMC/nZVI at a chlorinated solvent remediation site. Dehalococcoides spp. genetic markers and vinyl chloride reductase genes (vcrA) were targeted in the 16s RNA using quantitative polymerase chain reaction (qPCR). This analysis was complimented with a suite of aqueous chlorinated ethene, ethane, and methane compounds to monitor degradation. Following the injection of CMC/nZVI a decline of parent chlorinated compound concentrations was observed as well as the emergence of daughter products. A period of abiotic nZVI oxidation is believed to be responsible for a portion of the degradation at the site, however, a prolonged period of contaminant degradation followed and is believed to be the result of organohalide-respiring microorganisms native to the site. Further analysis was performed on the microbial samples using 454 pyrotag sequencing of amplified 16S rRNA genes to obtain the genetic profile of the microbial community. Of particular interest within this large genomic profile is the characterization of the stable population of important organohalide-respiring microorganisms on site. Results suggest that there is a distinctly different response in the organohalide-respiring microbial community in areas of the site where CMC/nZVI amendments were injected compared to a background response.

Microbial acceleration of aerobic pyrite oxidation at circumneutral pH.

PubMed

Percak-Dennett, E; He, S; Converse, B; Konishi, H; Xu, H; Corcoran, A; Noguera, D; Chan, C; Bhattacharyya, A; Borch, T; Boyd, E; Roden, E E

2017-09-01

Pyrite (FeS 2 ) is the most abundant sulfide mineral on Earth and represents a significant reservoir of reduced iron and sulfur both today and in the geologic past. In modern environments, oxidative transformations of pyrite and other metal sulfides play a key role in terrestrial element partitioning with broad impacts to contaminant mobility and the formation of acid mine drainage systems. Although the role of aerobic micro-organisms in pyrite oxidation under acidic-pH conditions is well known, to date there is very little known about the capacity for aerobic micro-organisms to oxidize pyrite at circumneutral pH. Here, we describe two enrichment cultures, obtained from pyrite-bearing subsurface sediments, that were capable of sustained cell growth linked to pyrite oxidation and sulfate generation at neutral pH. The cultures were dominated by two Rhizobiales species (Bradyrhizobium sp. and Mesorhizobium sp.) and a Ralstonia species. Shotgun metagenomic sequencing and genome reconstruction indicated the presence of Fe and S oxidation pathways in these organisms, and the presence of a complete Calvin-Benson-Bassham CO 2 fixation system in the Bradyrhizobium sp. Oxidation of pyrite resulted in thin (30-50 nm) coatings of amorphous Fe(III) oxide on the pyrite surface, with no other secondary Fe or S phases detected by electron microscopy or X-ray absorption spectroscopy. Rates of microbial pyrite oxidation were approximately one order of magnitude higher than abiotic rates. These results demonstrate the ability of aerobic microbial activity to accelerate pyrite oxidation and expand the potential contribution of micro-organisms to continental sulfide mineral weathering around the time of the Great Oxidation Event to include neutral-pH environments. In addition, our findings have direct implications for the geochemistry of modern sedimentary environments, including stimulation of the early stages of acid mine drainage formation and mobilization of pyrite-associated metals. © 2017 John Wiley & Sons Ltd.

Plutonium Interactions with Pseudomonas sp. and its Extracellular Polymeric Substances (Sorption and Reduction of Plutonium by Bacterial Extracellular Polymeric Substances)

DOE PAGES

Boggs, Mark A.; Jiao, Yongqin; Dai, Zurong; ...

2016-09-30

Safe and effective nuclear waste disposal, as well as accidental radionuclide releases, necessitates our understanding of the fate of radionuclides in the environment, including their interaction with microorganisms. We examined the sorption of Pu(IV) and Pu(V) toPseudomonassp. strain EPS-1W, an aerobic bacterium isolated from plutonium (Pu) contaminated groundwater collected in the United States at the Nevada National Security Site (NNSS), Nevada. We compared Pu sorption to cells with and without bound extracellular polymeric substances (EPS). Wild type cells with intact EPS sorbed Pu(V) more effectively than cells with EPS removed. In contrast, cells with and without EPS showed the samemore » sorption affinity for Pu(IV).In vitroexperiments with extracted EPS revealed rapid reduction of Pu(V) to Pu(IV). Transmission Electron Microscopy indicated that 2-3 nm nanocrystalline Pu(IV)O 2formed on cells equilibrated with high concentrations of Pu(IV) but not Pu(V). Thus, EPS, while facilitating Pu(V) reduction, inhibit the formation of nanocrystalline Pu(IV) precipitates. ImportanceOur results indicate that EPS are an effective reductant for Pu(V) and sorbent for Pu(IV), and may impact Pu redox cycling and mobility in the environment. Additionally, the resulting Pu morphology associated with EPS will depend on the concentration and initial Pu oxidation state. While our results are not directly applicable to the Pu transport situation at the NNSS, the results suggest that, in general, stationary microorganisms and biofilms will tend to limit the migration of Pu and provide an important Pu retardation mechanism in the environment. In a broader sense, our results along with a growing body of literature highlight the important role of microorganisms as producers of redox-active organic ligands and therefore as modulators of radionuclide redox transformations and complexation in the subsurface.« less

Plutonium Interactions with Pseudomonas sp. and its Extracellular Polymeric Substances (Sorption and Reduction of Plutonium by Bacterial Extracellular Polymeric Substances)

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

Boggs, Mark A.; Jiao, Yongqin; Dai, Zurong

Safe and effective nuclear waste disposal, as well as accidental radionuclide releases, necessitates our understanding of the fate of radionuclides in the environment, including their interaction with microorganisms. We examined the sorption of Pu(IV) and Pu(V) toPseudomonassp. strain EPS-1W, an aerobic bacterium isolated from plutonium (Pu) contaminated groundwater collected in the United States at the Nevada National Security Site (NNSS), Nevada. We compared Pu sorption to cells with and without bound extracellular polymeric substances (EPS). Wild type cells with intact EPS sorbed Pu(V) more effectively than cells with EPS removed. In contrast, cells with and without EPS showed the samemore » sorption affinity for Pu(IV).In vitroexperiments with extracted EPS revealed rapid reduction of Pu(V) to Pu(IV). Transmission Electron Microscopy indicated that 2-3 nm nanocrystalline Pu(IV)O 2formed on cells equilibrated with high concentrations of Pu(IV) but not Pu(V). Thus, EPS, while facilitating Pu(V) reduction, inhibit the formation of nanocrystalline Pu(IV) precipitates. ImportanceOur results indicate that EPS are an effective reductant for Pu(V) and sorbent for Pu(IV), and may impact Pu redox cycling and mobility in the environment. Additionally, the resulting Pu morphology associated with EPS will depend on the concentration and initial Pu oxidation state. While our results are not directly applicable to the Pu transport situation at the NNSS, the results suggest that, in general, stationary microorganisms and biofilms will tend to limit the migration of Pu and provide an important Pu retardation mechanism in the environment. In a broader sense, our results along with a growing body of literature highlight the important role of microorganisms as producers of redox-active organic ligands and therefore as modulators of radionuclide redox transformations and complexation in the subsurface.« less

A Holographic Microscope for Detection of Microorganisms on Icy Worlds

NASA Astrophysics Data System (ADS)

Lindensmith, C. A.; Nadeau, J. L.; Deming, J. W.; Showalter, G. M.; Rider, S.; Bedrossian, M.

2015-12-01

Holography is a well-established imaging technique that uses the interference of light to record and reproduce three-dimensional images of objects. Its use began in the 1960s with the invention of the laser. Digital holographic microscopy (DHM) has several advantages over ordinary imaging microscopy which make it ideal for field and astrobiology use, including no need for focus or scanning so that instruments are readily made autonomous. DHM can produce simultaneous bright-field and quantitative phase-contrast images of the same field, providing additional information about transparent objects, e.g., refractive index and/or thickness; thus it inherently supports effective label-free imaging. We have built a fieldable DHM for detection of microorganisms in bodies of water and in brines collected from sea ice. Ice that appears solid to the eye contains interconnected brine-filled microscopic pores and veins which are occupied by populations of prokaryotes and eukaryotes. The presence of life in "solid" ice has important implications for exploration of icy worlds, where it is unlikely that the first missions will be able to access the subsurface oceans. Using this new instrument, we examined several dozen samples from three different sites around Nuuk, Greenland. In all samples, mixed populations of both prokaryotic and eukaryotic microorganisms were observed. Many of the organisms were motile immediately upon extraction from sea ice, and others became motile after warming or addition of sugars and/or amino acids. Meaningful motility was readily distinguished from turbulence or fluid flow. The spatial resolution of the instrument was better than 1 μm, leading to unambiguous recognition of subcellular structures in eukaryotes, including nuclei and chloroplasts. We present mission scenrios for both orbiters and landers in which DHM may be used as a valuable complement to chemical-based life detection techniques for discovery of cellular life on icy worlds.

Habitability of Mars: hyperthermophiles in permafrost

NASA Astrophysics Data System (ADS)

Gilichinsky, David; Rivkina, Elizaveta; Vishnivetskaya, Tatiana; Felipe, Gomez; Mironov, Vasilii; Blamey, Jenny; Ramos, Miguel; Ángel de Pablo, Miguel; Castro, Miguel; Boehmwald, Freddy

This is a first microbiological study of volcanic permafrost carried out on Kluchevskaya volcano group (Kamchatka Peninsula) and Deception Island (Antarctica). By culture-and culture-independent methods we showed the presence of viable hyper(thermophilic) microorganisms and their genes within volcanic permafrost. The optimal temperature for sulfide producing bacteria was 65, whereas acetogens and methanogens were able to produce acetate and methane at temperatures up to 75o C, while sulphur-reducers showed optimal growth at 85-92o C. Hy-per(thermophiles) were never found in permafrost outside the volcanic areas before. The only way they are to appear within a frozen material is a concurrent deposition during the eruption, together with products associated with volcano heated subsurface geothermal oases. The elo-quent evidence to the hypothesis is the presence among clones of the sequences affiliated with (hyper)thermophilic bacteria, both, aerobic and anaerobic, in the environmental DNA derived from ashes freshly deposited on snow in close proximity to volcano Shiveluch (Kamchatka) and aerobic bacteria incubated at 80o C from ashes freshly deposited on the top of Llaima Vol-cano glacier (Andes). Thus, in the areas of active volcanism the catastrophic geological events transports the life from the depths to the surface and this life from high-temperature ecological niches might survive in permafrost over a long period of time. The results obtained give insights for habitability of Mars. Terrestrial permafrost represents a possible ecosystem for Mars as an Earth-like cryogenic planet. But permafrost on Earth and Mars vary in age, from a few million years on Earth to a few billion years on Mars. Because such difference in age, the longevity of life forms preserved within terrestrial permafrost may only serve as an approximate model for Mars. On the other hand, numerous ancient extinct volcanoes are known on Mars. Their past eruptions periodically burn-through the frozen strata by magma fluxes and formed the thermal and water oases. Simultaneously, products of eruptions (lava, rock debris, scoria, ash) lift from the depths to the surface and freeze. The age of these permanently frozen volcanic deposits is much younger than the age of surrounding permafrost, and the age of youngest volcanoes date back to few million -few dozen million years. It is reasonable to expect to find here the youngest permafrost of the age close to that one on Earth, and analogously to the Earth (even if the recent Mars is a sterile planet), inhabited by viable life forms coming from the depths. This is why the terrestrial hyper(thermophilic) psychrotolerant microbial inhabitants of the vol-canic permafrost might serve as a model for hypothesis of existing microorganisms, that may probably be found in permafrost around young Martian volcanoes. For free of oxygen Martian subsurface with inaccessible organic matter these microorganisms should be chemolithotrophic anaerobes with mechanisms to assimilate CO2 .

Natural attenuation of chlorinated-hydrocarbon contamination at Fort Wainwright, Alaska; a hydrogeochemical and microbiological investigation workplan

USGS Publications Warehouse

McCarthy, Kathleen A.; Lilly, Michael R.; Braddock, Joan F.; Hinzman, Larry D.

1998-01-01

Natural attenuation processes include biological degradation, by which microorganisms break down contaminants into simpler product compounds; adsorption of contaminants to soil particles, which decreases the mass of contaminants dissolved in ground water; and dispersion, which decreases dissolved contaminant concentrations through dilution. The primary objectives of this study are to (1) assess the degree to which such natural processes are attenuating chlorinated-hydrocarbon contamination in ground water, and (2) evaluate the effects of ground-water/surface-water interactions on natural-attenuation processes in the area of the former East and West Quartermasters Fueling Systems for Fort Wainwright, Alaska. The study will include investigations of the hydrologic, geochemical, and microbiological processes occurring at this site that influence the transport and fate of chlorinated hydrocarbons in ground water. To accomplish these objectives, a data-collection program has been initiated that includes measurements of water-table elevations and the stage of the Chena River; measurements of vertical temperature profiles within the subsurface; characterization of moisture distribution and movement in the unsaturated zone; collection of ground-water samples for determination of both organic and inorganic chemical constituents; and collection of ground-water samples for enumeration of microorganisms and determination of their potential to mineralize contaminants. We will use results from the data-collection program described above to refine our conceptual model of hydrology and contaminant attenuation at this site. Measurements of water-table elevations and river stage will help us to understand the magnitude and direction of ground-water flow and how changes in the stage of the Chena River affect ground-water flow. Because ambient ground water and surface water typically have different temperature characteristics, temperature monitoring will likely provide further insight into ground-water/surface-water interactions in the subsurface. Characterization of the unsaturated zone will improve our understanding of interactions among ground water, the unsaturated zone, and the atmosphere. The interactions likely of importance to this study include the migration of water, dissolved contaminants, nutrients, and gases (oxygen, carbon dioxide, and methane) between the saturated and unsaturated zones. We will use the results of ground-water chemical analyses to determine the spatial and temporal distribution of (1) chlorinated-hydrocarbon contaminants and their degradation products, (2) oxidation-reduction indicators, (3) nutrients, and (4) major ground-water ions. These water-quality data will provide insight into ground-water flow directions, interactions between ground water and surface water, attenuation of contaminant concentrations caused by dispersion, and intrinsic microbiological processes. Microbiological analyses will indicate whether microorganisms at the site are capable of degrading the contaminants of interest, and will allow us to estimate their potential to attenuate existing contamination. Physical and chemical data interpreted as part of the analysis of ground water and surface water mixing will improve our understanding of the relationship between water quality and contaminant source mixing.

[The state of the art research findings on the relationship between chronic periodontitis and Alzheimer's disease: a review].

PubMed

Qian, X S; Ge, S

2018-04-09

Along with the development of periodontal medicine, there is a growing number of evidence showing that periodontitis could influence systemic health. Periodontitis is a chronic inflammatory disease caused by microbial infection mediated by dental plaque. Periodontal pathogenic microorganisms and its toxic products can disseminate through the blood stream or may cause the host immune response, which may lead to pathological changes of cerebral vessels and brain tissues to establish connection with Alzheimer's disease (AD). AD is a progressive neurodegenerative disease characterized by progressive memory loss, language and cognitive dysfunction. This article reviewed the association between chronic periodontitis and AD.

[Bacteremia associated with mycotic aneurysm of the transversal aortic arch and myocarditis caused by Salmonella enteritidis].

PubMed

Martínez-Martínez, L; Mesa, E; Rodríguez, J E; Sánchez, M P; Ugarte, J; Algora Weber, A; Dámaso, D; Daza, R M; Mendaza, P

1989-02-01

A 60-year-old male with diabetes mellitus had Salmonella enteritidis bacteremia associated with mycotic aneurysm of the transverse aortic arc and myocarditis. Antibiotic therapy with ampicillin and chloramphenicol was ineffective despite the fact that the microorganism was sensitive in vitro to those antimicrobials, and the patient had a progressive clinical deterioration which culminated in death.

Dissolved Organic Matter in Groundwater: a Shadow of its Former Self

NASA Astrophysics Data System (ADS)

Chapelle, F.

2017-12-01

The occurrence and dynamics of dissolved organic matter (DOM) are fundamentally different between ground- and surface water systems. The most obvious difference is that primary production, an important source of DOM to many surface waters, it is wholly absent from groundwater systems. Because of that, the composition and bioavailability of DOM is functionally linked to its residence time within the subsurface. While sorption/desorption processes segregate chemical fractions of DOM in both ground- and surface water systems, their effects are magnified by the much higher sediment/water mass ratio characteristic of groundwater systems. These differences, which often act in concert with each other, explain many observed characteristics of DOM in groundwater systems including (1) the low and nearly uniform DOM concentrations (0.5-1.0 mg/L) characteristic of many aquifers, (2) the progressive loss of carbohydrate and amino acid DOM and the enrichment of aromatic DOM, with increasing aquifer residence time (3) the progressive loss of VIS/UV absorption capacity (color) of DOM with increasing aquifer residence time, (4) the negative correlation between dissolved oxygen concentrations and DOM bioavailability, and (5) the positive correlation between DOM bioavailability and the final products of anoxic redox processes. Thus, while the principal sources of DOM to many groundwater systems are surface-derived, the dynamics unique to subsurface environments tend to render that DOM a shadow of its former self.

Analysis of microbial communities in the oil reservoir subjected to CO2-flooding by using functional genes as molecular biomarkers for microbial CO2 sequestration

PubMed Central

Liu, Jin-Feng; Sun, Xiao-Bo; Yang, Guang-Chao; Mbadinga, Serge M.; Gu, Ji-Dong; Mu, Bo-Zhong

2015-01-01

Sequestration of CO2 in oil reservoirs is considered to be one of the feasible options for mitigating atmospheric CO2 building up and also for the in situ potential bioconversion of stored CO2 to methane. However, the information on these functional microbial communities and the impact of CO2 storage on them is hardly available. In this paper a comprehensive molecular survey was performed on microbial communities in production water samples from oil reservoirs experienced CO2-flooding by analysis of functional genes involved in the process, including cbbM, cbbL, fthfs, [FeFe]-hydrogenase, and mcrA. As a comparison, these functional genes in the production water samples from oil reservoir only experienced water-flooding in areas of the same oil bearing bed were also analyzed. It showed that these functional genes were all of rich diversity in these samples, and the functional microbial communities and their diversity were strongly affected by a long-term exposure to injected CO2. More interestingly, microorganisms affiliated with members of the genera Methanothemobacter, Acetobacterium, and Halothiobacillus as well as hydrogen producers in CO2 injected area either increased or remained unchanged in relative abundance compared to that in water-flooded area, which implied that these microorganisms could adapt to CO2 injection and, if so, demonstrated the potential for microbial fixation and conversion of CO2 into methane in subsurface oil reservoirs. PMID:25873911

Methanogenic degradation kinetics of phenolic compounds in aquifer-derived microcosms

USGS Publications Warehouse

Godsy, E.M.; Goerlitz, D.F.; Grbic-Galic, D.

1992-01-01

In this segment of a larger multidisciplinary study of the movement and fate of creosote derived compounds in a sand-and-gravel aquifer, we present evidence that the methanogenic degradation of the major biodegradable phenolic compounds and concomitant microbial growth in batch microcosms derived from contaminated aquifer material can be described using Monod kinetics. Substrate depletion and bacterial growth curves were fitted to the Monod equations using nonlinear regression analysis. The method of Marquardt was used for the determination of parameter values that best fit the experimental data by minimizing the residual sum of squares. The Monod kinetic constants (??max, Ks, Y, and kd) that describe phenol, 2-, 3-, and 4-methylphenol degradation and concomitant microbial growth were determined under conditions that were substantially different from those previously reported for microcosms cultured from sewage sludge. The Ks values obtained in this study are approximately two orders of magnitude lower than values obtained for the anaerobic degradation of phenol in digesting sewage sludge, indicating that the aquifer microorganisms have developed enzyme systems that are adapted to low nutrient conditions. The values for kd are much less than ??max, and can be neglected in the microcosms. The extremely low Y values, approximately 3 orders of magnitude lower than for the sewage sludge derived cultures, and the very low numbers of microorganisms in the aquifer derived microcosms suggest that these organisms use some unique strategies to survive in the subsurface environment. ?? 1992 Kluwer Academic Publishers.

Enrichment of a microbial culture capable of reductive debromination of the flame retardant tetrabromobisphenol-A, and identification of the intermediate metabolites produced in the process.

PubMed

Arbeli, Ziv; Ronen, Zeev

2003-12-01

Tetrabromobisphenol-A is a reactive flame retardant used in the production of many plastic polymers. In previous research, it was demonstrated that anaerobic microorganisms from contaminated sediment debrominate tetrabromobisphenol-A to bisphenol-A, but an enrichment culture was not established. The current study was carried out to identify the intermediate metabolites in this process and to determine the factors facilitating enrichment of debrominating microorganisms. During the enrichment process in an anaerobic semi-continuous batch reactor, tetrabromobisphenol-A debromination gradually slowed down with concurrent accumulation of three intermediate products. These compounds were tentatively identified using GC-MS as tri-, di-, and mono-brominated bisphenol-A. GC-MS and HPLC analyses showed one dominant metabolite of dibromobisphenol-A, and NMR analysis identified it as 2,2'-dibromobisphenol-A. Addition of sterile sediment (15% wt/wt) to the reactor stimulated debromination of tetrabromobisphenol-A. Furthermore, different solid amendments such as surface soil and pulverized gray chalk from the site subsurface (100 m below ground) were also stimulating agents. We conclude that organic matter is involved in stimulation since the stimulation effect of the sediment, soil and gray chalk was abolished after it was heat-treated to 550 degrees C. Our study suggests that the debrominating culture requires some organic components found in the sediment, soil, and chalk in order to sustain activity and perhaps to survive. The possible mechanisms of stimulation by these solids are discussed.

Microbial Substrate Use at Sites of Continental Serpentinization: The Tablelands, NL, CAD and the Cedars, CA, USA

NASA Astrophysics Data System (ADS)

Morrill, P. L.; Rietze, A.; Kohl, L.; Miles, S.; Kavanagh, H.; Cox, A.; Brazelton, W. J.; Ishii, S.; Sherwood Lollar, B.; Schrenk, M. O.; Nealson, K. H.; Ziegler, S. E.; Ono, S.; Wang, D. T.; Lang, S. Q.; Cumming, E.

2014-12-01

Ultra-basic reducing springs at continental sites of serpentinization act as portals into the biogeochemistry of a subsurface ultramafic environment rich in hydrogen and methane gases. Field data and results from substrate addition microcosm experiments will be presented from two contrasting continental sites of serpentinization: the Tablelands, NL, CAN and The Cedars, CA, USA both Phanerozoic in age. These continental sites share geochemical characteristics that make these environments challenging for life, such as high pH, low Eh, scarce electron acceptors, and limited dissolved inorganic carbon for autotrophic growth. However, microbiological analyses have demonstrated that life does indeed exist in these environments. While environmental genomic studies indicated the potential metabolic capabilities of microorganisms in the sites, actual microbial metabolic activities in these environments remain unknown. To expand the understanding of biogeochemistry of the sites, we are conducting studies focusing on chemical and isotopic measurements, carbon substrate utilization, energy sources, and metabolic pathways of the microorganisms. Thus far, in situ geochemical data suggests that the methane from the Tablelands is primarily non-microbial, while the methane from The Cedars likely has some microbial contributions. To date, substrate addition microcosm experiments show no microbial production of methane from Tablelands' water and sediments. However, microbial carbon monoxide utilization has been observed in Tableland microcosms, but not in The Cedars microcosms. These results demonstrate how geochemistry and substrate addition experiments can be complementary for the determination of the processes favored at these continental sites of serpentinization.

Biological transformations of 1,2-dichloroethane in subsurface soils and groundwater

NASA Astrophysics Data System (ADS)

Klečka, G. M.; Carpenter, C. L.; Gonsior, S. J.

1998-10-01

The ability of naturally occurring microorganisms to biodegrade 1,2-dichloroethane was examined in soil/water microcosms prepared using aquifer material obtained from manufacturing sites in Louisiana and Texas with known histories of exposure to the compound, as well as in aquifer samples taken from a site in Oklahoma with no known history of 1,2-dichloroethane contamination. Biotransformation of 1,2-dichloroethane was noted under methanogenic or sulfate reducing conditions in all samples. Under anaerobic conditions, 1,2-dichloroethane was transformed to ethylene in a single step via reductive dihaloelimination. No other metabolites were detected in the reaction mixtures. Microbial adaptation appeared to be required for biotransformation of 1,2-dichloroethane. Lag periods ranging from 7 to 8 weeks preceded degradation in microcosms prepared with aquifer material from the Texas and Oklahoma sites. In contrast, no lag period was evident prior to biotransformation in microcosms prepared from the Louisiana manufacturing site, which is consistent with field evidence for natural biological attenuation in situ based on analysis of the groundwater chemistry. Aerobic biodegradation of 1,2-dichloroethane to carbon dioxide was also observed after 13 weeks in aquifer material from the Louisiana site, but was not evident in samples from the Texas or Oklahoma sites following 18 weeks of incubation. The ability of naturally occurring microorganisms to degrade 1,2-dichloroethane has bearing on assessments of the fate and lifetime of the compound in the environment, as well as having potential application in the remediation of contaminated groundwater.

[Increasing incidence of community-acquired pneumonia caused by atypical microorganisms].

PubMed

Tazón-Varela, M A; Alonso-Valle, H; Muñoz-Cacho, P; Gallo-Terán, J; Piris-García, X; Pérez-Mier, L A

2017-09-01

Knowing the most common microorganisms in our environment can help us to make proper empirical treatment decisions. The aim is to identify those microorganisms causing community-acquired pneumonia. An observational, descriptive and prospective study was conducted, including patients over 14 years with a clinical and radiographic diagnosis of community-acquired pneumonia during a 383 consecutive day period. A record was made of sociodemographic variables, personal history, prognostic severity scales, progress, and pathogenic agents. The aetiological diagnosis was made using blood cultures, detection of Streptococcus pneumoniae and Legionella pneumophila urinary antigens, sputum culture, influenza virus and Streptococcus pyogenes detection. Categorical variables are presented as absolute values and percentages, and continuous variables as their means and standard deviations. Of the 287 patients included in the study (42% women, mean age 66±22 years), 10.45% died and 70% required hospital admission. An aetiological diagnosis was achieved in 43 patients (14.98%), with 16 microorganisms found in 59 positive samples. The most frequently isolated pathogen was Streptococcus pneumonia (24/59, 41%), followed by gram-negative enteric bacilli, Klebsiella pneumonia, Escherichia coli, Serratia marcescens and Enterobacter cloacae isolated in 20% of the samples (12/59), influenza virus (5/59, 9%), methicillin-resistant Staphylococcus aureus (3/59, 5%), Pseudomonas aeruginosa (2/59, 3%), Moraxella catarrhalis (2/59, 3%), Legionella pneumophila (2/59, 3%), and Haemophilus influenza (2/59, 3%). Polymicrobial infections accounted for 14% (8/59). A high percentage of atypical microorganisms causing community-acquired pneumonia were found. Copyright © 2016 Sociedad Española de Médicos de Atención Primaria (SEMERGEN). Publicado por Elsevier España, S.L.U. All rights reserved.

Distinguishing Indigenous from Contaminating Microorganisms in Rock Samples from a Deep Au Mine in South Africa

NASA Technical Reports Server (NTRS)

Onstott, T. C.; Moser, D. P.; Fredrickson, J. K.; Pfiffner, S. M.; Phelps, T. J.; White, D. C.; Peacock, A.; Balkwill, D.; Hoover, R. B.; Krumholz, L.;

Why Earth cryopegs are interesting to astrobiologists?

NASA Astrophysics Data System (ADS)

Rivkina, Elizaveta; Spirina, Elena; Demidov, Nikita; Shcherbakova, Viktoria; Yoshikawa, Kenji; Gilichinsky, David

The lenses of perennially overcooled water brines (cryopegs) derived from ancient marine sedi-ments and sandwiched within permafrost 10 to 120,000 years ago after the placeArctic Ocean regressions. In these lenses freezing is prevented by freezing-point depression due to the dis-solved salt and they remain liquid at the in situ temperatures down to -11oC as a result of their high sodium-chloride concentration (3-5 mol/l). Cryopegs make up the only habitat on Earth that is characterized by permanently subzero temperatures, high salinity, and isolation from the influence of external factors during geological time. During last years the biodiversity of cryopeg's indigenous microbial community along the Arctic coast of placePlaceNamePolar PlaceTypeOcean (Kara and placeEast Siberian Sea, placePla-ceNameJamal PlaceTypePeninsula and placePlaceTypeCape PlaceNameBarrow) were studied and the new species representing the different genera have been isolated and described. There were found both aerobic and anaerobic microorganisms: Psychrobacters, Sulfate-reducers, Clostridia, etc. The isolated bacteria grew at subzero temperatures, and were also tolerant to salt concentra-tions up to metricconverterProductID3 M3 M NaCl. The microorganisms detected in cryopegs are halophilic and psychrophilic organisms at the same time. The microbial activity detected in cryopegs (14C-labeled glucose consumption) at temperatures as low as metricconverterProductID-15?C-15C-15° C documents the fact that subzero temper-atures themselves do not exclude biochemical reactions. In situ microbial activity and survival of microorganisms in a low-temperature high-salt aquatic environment on a geological time scale indicates the special type of microbial adaptation. From the astrobiological perspective, mineral-enriched brines provide the only opportunity for free water within the Martian subsurface permafrost, formed when Mars became dry and cold. These brines, just as terrestrial cryopegs, may contain microorganisms adapted to low tem-perature and high salinity. The halotolerant and halophilic, psychrophilic and psychrotrophic microbial community within Arctic water brines, represent the model of a plausible prototype for Martian microbial life. Based on the maps of temperature and salt distribution on the surface of Mars, areas most favorable for existence of cryopegs may be detected.

Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model.

PubMed

Fang, Yilin; Scheibe, Timothy D; Mahadevan, Radhakrishnan; Garg, Srinath; Long, Philip E; Lovley, Derek R

2011-03-25

The activity of microorganisms often plays an important role in dynamic natural attenuation or engineered bioremediation of subsurface contaminants, such as chlorinated solvents, metals, and radionuclides. To evaluate and/or design bioremediated systems, quantitative reactive transport models are needed. State-of-the-art reactive transport models often ignore the microbial effects or simulate the microbial effects with static growth yield and constant reaction rate parameters over simulated conditions, while in reality microorganisms can dynamically modify their functionality (such as utilization of alternative respiratory pathways) in response to spatial and temporal variations in environmental conditions. Constraint-based genome-scale microbial in silico models, using genomic data and multiple-pathway reaction networks, have been shown to be able to simulate transient metabolism of some well studied microorganisms and identify growth rate, substrate uptake rates, and byproduct rates under different growth conditions. These rates can be identified and used to replace specific microbially-mediated reaction rates in a reactive transport model using local geochemical conditions as constraints. We previously demonstrated the potential utility of integrating a constraint-based microbial metabolism model with a reactive transport simulator as applied to bioremediation of uranium in groundwater. However, that work relied on an indirect coupling approach that was effective for initial demonstration but may not be extensible to more complex problems that are of significant interest (e.g., communities of microbial species and multiple constraining variables). Here, we extend that work by presenting and demonstrating a method of directly integrating a reactive transport model (FORTRAN code) with constraint-based in silico models solved with IBM ILOG CPLEX linear optimizer base system (C library). The models were integrated with BABEL, a language interoperability tool. The modeling system is designed in such a way that constraint-based models targeting different microorganisms or competing organism communities can be easily plugged into the system. Constraint-based modeling is very costly given the size of a genome-scale reaction network. To save computation time, a binary tree is traversed to examine the concentration and solution pool generated during the simulation in order to decide whether the constraint-based model should be called. We also show preliminary results from the integrated model including a comparison of the direct and indirect coupling approaches and evaluated the ability of the approach to simulate field experiment. Published by Elsevier B.V.

Microbial enzymes: industrial progress in 21st century.

PubMed

Singh, Rajendra; Kumar, Manoj; Mittal, Anshumali; Mehta, Praveen Kumar

2016-12-01

Biocatalytic potential of microorganisms have been employed for centuries to produce bread, wine, vinegar and other common products without understanding the biochemical basis of their ingredients. Microbial enzymes have gained interest for their widespread uses in industries and medicine owing to their stability, catalytic activity, and ease of production and optimization than plant and animal enzymes. The use of enzymes in various industries (e.g., food, agriculture, chemicals, and pharmaceuticals) is increasing rapidly due to reduced processing time, low energy input, cost effectiveness, nontoxic and eco-friendly characteristics. Microbial enzymes are capable of degrading toxic chemical compounds of industrial and domestic wastes (phenolic compounds, nitriles, amines etc.) either via degradation or conversion. Here in this review, we highlight and discuss current technical and scientific involvement of microorganisms in enzyme production and their present status in worldwide enzyme market.

Production of anthocyanins in metabolically engineered microorganisms: Current status and perspectives.

PubMed

Zha, Jian; Koffas, Mattheos A G

2017-12-01

Microbial production of plant-derived natural products by engineered microorganisms has achieved great success thanks to large extend to metabolic engineering and synthetic biology. Anthocyanins, the water-soluble colored pigments found in terrestrial plants that are responsible for the red, blue and purple coloration of many flowers and fruits, are extensively used in food and cosmetics industry; however, their current supply heavily relies on complex extraction from plant-based materials. A promising alternative is their sustainable production in metabolically engineered microbes. Here, we review the recent progress on anthocyanin biosynthesis in engineered bacteria, with a special focus on the systematic engineering modifications such as selection and engineering of biosynthetic enzymes, engineering of transportation, regulation of UDP-glucose supply, as well as process optimization. These promising engineering strategies will facilitate successful microbial production of anthocyanins in industry in the near future.

The future is now: single-cell genomics of bacteria and archaea

PubMed Central

Blainey, Paul C.

2013-01-01

Interest in the expanding catalog of uncultivated microorganisms, increasing recognition of heterogeneity among seemingly similar cells, and technological advances in whole-genome amplification and single-cell manipulation are driving considerable progress in single-cell genomics. Here, the spectrum of applications for single-cell genomics, key advances in the development of the field, and emerging methodology for single-cell genome sequencing are reviewed by example with attention to the diversity of approaches and their unique characteristics. Experimental strategies transcending specific methodologies are identified and organized as a road map for future studies in single-cell genomics of environmental microorganisms. Over the next decade, increasingly powerful tools for single-cell genome sequencing and analysis will play key roles in accessing the genomes of uncultivated organisms, determining the basis of microbial community functions, and fundamental aspects of microbial population biology. PMID:23298390

Progression of methanogenic degradation of crude oil in the subsurface

USGS Publications Warehouse

Bekins, B.A.; Hostettler, F.D.; Herkelrath, W.N.; Delin, G.N.; Warren, E.; Essaid, H.I.

2005-01-01

Our results show that subsurface crude-oil degradation rates at a long-term research site were strongly influenced by small-scale variations in hydrologic conditions. The site is a shallow glacial outwash aquifer located near Bemidji in northern Minnesota that became contaminated when oil spilled from a broken pipeline in August 1979. In the study area, separate-phase oil forms a subsurface oil body extending from land surface to about 1 m (3.3 ft) below the 6-8-m (20-26 ft)-deep water table. Oil saturation in the sediments ranges from 10-20% in the vadose zone to 30-70% near the water table. At depths below 2 m (6.6 ft), degradation of the separate-phase crude oil occurs under methanogenic conditions. The sequence of methanogenic alkane degradation depletes the longer chain n-alkanes before the shorter chain n-alkanes, which is opposite to the better known aerobic sequence. The rates of degradation vary significantly with location in the subsurface. Oil-coated soils within 1.5 m (5 ft) of land surface have experienced little degradation where soil water saturation is less than 20%. Oil located 2-8 m (6.6-26 ft) below land surface in areas of higher recharge has been substantially degraded. The best explanation for the association between recharge and enhanced degradation seems to be increased downward transport of microbial growth nutrients to the oil body. This is supported by observations of greater microbial numbers at higher elevations in the oil body and significant decreases with depth in nutrient concentrations, especially phosphorus. Our results suggest that environmental effects may cause widely diverging degradation rates in the same spill, calling into question dating methods based on degradation state. Copyright ?? 2005. The American Association of Petroleum Geologists/Division of Environmental Geosciences. All rights reserved.

[Formation of microbial biofilms in causative agents of acute and chronic pyelonephritis].

PubMed

Lagun, L V; Atanasova, Iu V; Tapal'skiĭ, D V

2013-01-01

Study the intensity of formation of microbial biofilms by Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus strains isolated during various forms of pyelonephritis. 150 clinical isolates of microorganisms isolated from urine ofpatientswith acute and chronic pyelonephritiswere included into the study. Determination of intensity of film-formation was carried out by staining of the formed biofilms by crystal violet with consequent extraction of the dye and measurement of its concentration in washout solution. Among causative agents ofpyelonephritis P. aeruginosa isolates had the maximum film-forming ability. The intensity of biofilm formation of these isolates was 2-3 time higher than staphylococcus and enterobacteria strains. Strains isolated from patients with chronic pyelonephritis by ability to form biofilms significantly surpassed strains isolated from acute pyelonephritis patients. A higher ability to form microbial biofilms for microorganisms--causative agents of pyelonephritis progressing against the background ofurolithiasis was noted. The ability to form biofilms is determined by both causative agent species and character of the infectious process in which this microorganism participates. Intensive formation of biofilms by E. coli, P. aeruginosa, K. pneumoniae, S. aureus clinical isolates may be an important factor of chronization of urinary tract infections.

Genomic and metagenomic challenges and opportunities for bioleaching: a mini-review.

PubMed

Cárdenas, Juan Pablo; Quatrini, Raquel; Holmes, David S

2016-09-01

High-throughput genomic technologies are accelerating progress in understanding the diversity of microbial life in many environments. Here we highlight advances in genomics and metagenomics of microorganisms from bioleaching heaps and related acidic mining environments. Bioleaching heaps used for copper recovery provide significant opportunities to study the processes and mechanisms underlying microbial successions and the influence of community composition on ecosystem functioning. Obtaining quantitative and process-level knowledge of these dynamics is pivotal for understanding how microorganisms contribute to the solubilization of copper for industrial recovery. Advances in DNA sequencing technology provide unprecedented opportunities to obtain information about the genomes of bioleaching microorganisms, allowing predictive models of metabolic potential and ecosystem-level interactions to be constructed. These approaches are enabling predictive phenotyping of organisms many of which are recalcitrant to genetic approaches or are unculturable. This mini-review describes current bioleaching genomic and metagenomic projects and addresses the use of genome information to: (i) build metabolic models; (ii) predict microbial interactions; (iii) estimate genetic diversity; and (iv) study microbial evolution. Key challenges and perspectives of bioleaching genomics/metagenomics are addressed. Copyright © 2016 The Author(s). Published by Elsevier Masson SAS.. All rights reserved.

The Effects of Mineral Matrices and Extraction Method on Quantification of Bacterial Phospholipid Fatty Acids.

NASA Astrophysics Data System (ADS)

Ford, S. E.; McKelvie, J. R. M.; Sherwood Lollar, B.; Slater, G. F.

2017-12-01

Understanding the distribution, abundances and metabolic activities of microbial life in the subsurface is fundamental to our understanding of biogeochemical cycling on Earth. Given that the most likely environments for life to still exist, or be preserved, on other planets and moons in the solar system are in the subsurface, a better understanding of subsurface life on Earth is also a key factor in our ability to search for life beyond the Earth. While we have made progress in investigating life in the continental subsurface in recent years, significant challenges remain. In particular, the low biomass abundance, heterogeneous distribution of biomass, and the potential for matrix effects during sampling and analysis mean that further development and optimization of methods to study subsurface life are needed. Phospholipid fatty acids (PLFA) are a useful biosignature of extant, viable microbial communities that are applied in a wide range of environments. Here we test the sensitivity of two methods of PLFA analysis (modified Bligh and Dyer, Microwave Assisted Extraction) to detect known numbers of cells doped into two distinct matrices (bentonite, crushed granite). Samples were prepared by adding known cellular concentrations of Basciullus subtilis subtilis (ATCC 6051) to crushed bentonite, or to granite, respectively, to create dilution series. Samples were extracted for PLFA using a dichloromethane-methanol modified Bligh & Dyer (mBD) or Microwave Assisted Extraction (MAE) and then quantified using GC - MS and GC - FID. Pure culture extractions yielded a linearly decreasing trend to the level of the process blank. The ratio of cells to PLFA for this trend was 2.4x104 +/- 1.9x104 cells/pmol at the lower end of the generic range of 2 to 6 x105 cells/pmol. For bentonite the PLFA results were lower than for the pure culture. PLFA results for bentonite followed a linear trend at higher concentrations, but departed from this at low concentrations indicating the potential for interference for low biomass samples. The ratio of cells to PLFA for the bentonite was to 6.2x104 +/- 4.5x104 cells/pmol, at the upper end of generic range. Ongoing comparison of the efficiency of microwave extraction and the effect of different matrices (e.g. granite) aims to optimize detection of PLFA for low biomass samples relevant to subsurface systems.

Small County: Development of a Virtual Environment for Instruction in Geological Characterization of Petroleum Reservoirs

NASA Astrophysics Data System (ADS)

Banz, B.; Bohling, G.; Doveton, J.

2008-12-01

Traditional programs of geological education continue to be focused primarily on the evaluation of surface or near-surface geology accessed at outcrops and shallow boreholes. However, most students who graduate to careers in geology work almost entirely on subsurface problems, interpreting drilling records and petrophysical logs from exploration and production wells. Thus, college graduates commonly find themselves ill-prepared when they enter the petroleum industry and require specialized training in drilling and petrophysical log interpretation. To aid in this training process, we are developing an environment for interactive instruction in the geological aspects of petroleum reservoir characterization employing a virtual subsurface closely reflecting the geology of the US mid-continent, in the fictional setting of Small County, Kansas. Stochastic simulation techniques are used to generate the subsurface characteristics, including the overall geological structure, distributions of facies, porosity, and fluid saturations, and petrophysical logs. The student then explores this subsurface by siting exploratory wells and examining drilling and petrophysical log records obtained from those wells. We are developing the application using the Eclipse Rich Client Platform, which allows for the rapid development of a platform-agnostic application while providing an immersive graphical interface. The application provides an array of views to enable relevant data display and student interaction. One such view is an interactive map of the county allowing the student to view the locations of existing well bores and select pertinent data overlays such as a contour map of the elevation of an interesting interval. Additionally, from this view a student may choose the site of a new well. Another view emulates a drilling log, complete with drilling rate plot and iconic representation of examined drill cuttings. From here, students are directed to stipulate subsurface lithology and interval tops as they progress through the drilling operation. Once the interpretation process is complete, the student is guided through an exercise emulating a drill stem test and then is prompted to decide on perforation intervals. The application provides a graphical framework by which the student is guided through well site selection, drilling data interpretation, and well completion or dry-hole abandonment, creating a tight feedback loop by which the student gains an over-arching view of drilling logistics and the subsurface data evaluation process.

First steps in experimental cancer evolution

PubMed Central

Taylor, Tiffany B; Johnson, Louise J; Jackson, Robert W; Brockhurst, Michael A; Dash, Philip R

2013-01-01

Evolutionary processes play a central role in the development, progression and response to treatment of cancers. The current challenge facing researchers is to harness evolutionary theory to further our understanding of the clinical progression of cancers. Central to this endeavour will be the development of experimental systems and approaches by which theories of cancer evolution can be effectively tested. We argue here that the experimental evolution approach – whereby evolution is observed in real time and which has typically employed microorganisms – can be usefully applied to cancer. This approach allows us to disentangle the ecological causes of natural selection, identify the genetic basis of evolutionary changes and determine their repeatability. Cell cultures used in cancer research share many of the desirable traits that make microorganisms ideal for studying evolution. As such, experimental cancer evolution is feasible and likely to give great insight into the selective pressures driving the evolution of clinically destructive cancer traits. We highlight three areas of evolutionary theory with importance to cancer biology that are amenable to experimental evolution: drug resistance, social evolution and resource competition. Understanding the diversity, persistence and evolution of cancers is vital for treatment and drug development, and an experimental evolution approach could provide strategic directions and focus for future research. PMID:23745144

Phenotypic characterization of Aspergillus niger and Candida albicans grown under simulated microgravity using a three-dimensional clinostat.

PubMed

Yamazaki, Takashi; Yoshimoto, Maki; Nishiyama, Yayoi; Okubo, Yoichiro; Makimura, Koichi

2012-07-01

The living and working environments of spacecraft become progressively contaminated by a number of microorganisms. A large number of microorganisms, including pathogenic microorganisms, some of which are fungi, have been found in the cabins of space stations. However, it is not known how the characteristics of microorganisms change in the space environment. To predict how a microgravity environment might affect fungi, and thus how their characteristics could change on board spacecraft, strains of the pathogenic fungi Aspergillus niger and Candida albicans were subjected to on-ground tests in a simulated microgravity environment produced by a three-dimensional (3D) clinostat. These fungi were incubated and cultured in a 3D clinostat in a simulated microgravity environment. No positive or negative differences in morphology, asexual reproductive capability, or susceptibility to antifungal agents were observed in cultures grown under simulated microgravity compared to those grown in normal earth gravity (1 G). These results strongly suggest that a microgravity environment, such as that on board spacecraft, allows growth of potentially pathogenic fungi that can contaminate the living environment for astronauts in spacecraft in the same way as they contaminate residential areas on earth. They also suggest that these organisms pose a similar risk of opportunistic infections or allergies in astronauts as they do in people with compromised immunity on the ground and that treatment of fungal infections in space could be the same as on earth. © 2012 The Societies and Blackwell Publishing Asia Pty Ltd.

Characterization of microbial 'hot spots' in soils": Where are we, and where are we going?

NASA Astrophysics Data System (ADS)

Baveye, Philippe C.

2015-04-01

Fifty years ago, microbiologists realized that significant progress in our understanding of microbial processes in soils required being able to measure various physical, chemical, and microbial parameters at the scale of microorganisms, i.e., at micrometric or even submicrometric scales, and to identify areas of particularly high microbial activity. Back then, this was only a dream, severely hampered by the crudeness of our measuring instruments. In the intervening years, however, amazing technological progress has transformed that old dream into reality. We are now able to quantify the physical and (bio)chemical environment of soil microorganisms at spatial scales that are commensurate with bacterial cells. In this invited presentation, I will provide an overview of the significant progress achieved in this field over the last few years, and mention a number of further technological advances that are likely to profoundly influence the nature of the research over the next decade. Technology must however remain a means to an end, and therefore it is important to firmly keep in mind that the goal of the research on understanding better how soil processes work at the microscale is to be ultimately in a position to predict the behavior of soils at scales that matter to society at large, for example in terms of food security or global climate change. In that context, part of the research has to focus on how we can upscale information about soil microbial hotspots to macroscopic scales and beyond. I will discuss where we stand on this crucial question, which remains largely open at the moment.

Integrated Coupling of Surface and Subsurface Flow with HYDRUS-2D

NASA Astrophysics Data System (ADS)

Hartmann, Anne; Šimůnek, Jirka; Wöhling, Thomas; Schütze, Niels

2016-04-01

Describing interactions between surface and subsurface flow processes is important to adequately define water flow in natural systems. Since overland flow generation is highly influenced by rainfall and infiltration, both highly spatially heterogeneous processes, overland flow is unsteady and varies spatially. The prediction of overland flow needs to include an appropriate description of the interactions between the surface and subsurface flow. Coupling surface and subsurface water flow is a challenging task. Different approaches have been developed during the last few years, each having its own advantages and disadvantages. A new approach by Weill et al. (2009) to couple overland flow and subsurface flow based on a generalized Richards equation was implemented into the well-known subsurface flow model HYDRUS-2D (Šimůnek et al., 2011). This approach utilizes the one-dimensional diffusion wave equation to model overland flow. The diffusion wave model is integrated in HYDRUS-2D by replacing the terms of the Richards equation in a pre-defined runoff layer by terms defining the diffusion wave equation. Using this approach, pressure and flux continuity along the interface between both flow domains is provided. This direct coupling approach provides a strong coupling of both systems based on the definition of a single global system matrix to numerically solve the coupled flow problem. The advantage of the direct coupling approach, compared to the loosely coupled approach, is supposed to be a higher robustness, when many convergence problems can be avoided (Takizawa et al., 2014). The HYDRUS-2D implementation was verified using a) different test cases, including a direct comparison with the results of Weill et al. (2009), b) an analytical solution of the kinematic wave equation, and c) the results of a benchmark test of Maxwell et al. (2014), that included several known coupled surface subsurface flow models. Additionally, a sensitivity analysis evaluating the effects of various model parameters on simulated overland flow (while considering or neglecting the effects of subsurface flow) was carried out to verify the applicability of the model to different problems. The model produced reasonable results in describing the diffusion wave approximation and its interactions with subsurface flow processes. The model could handle coupled surface-subsurface processes for conditions involving runoff generated by infiltration excess, saturation excess, or run-on, as well as a combination of these runoff generating processes. Several standard features of the HYDRUS 2D model, such as root water uptake and evaporation from the soil surface, as well as evaporation from runoff layer, can still be considered by the new model. The code required relatively small time steps when overland flow was active, resulting in long simulation times, and sometimes produced poor mass balance. The model nevertheless showed potential to be a useful tool for addressing various issues related to irrigation research and to natural generation of overland flow at the hillslope scale. Maxwell, R., Putti, M., Meyerhoff, S., Delf, J., Ferguson, I., Ivanov, V., Kim, J., Kolditz, O., Kollet, S., Kumar, M., Lopez, S., Niu, J., Paniconi, C., Park, Y.-J., Phanikumar, M., Shen, C., Sudicky, E., and Sulis, M. (2014). Surface-subsurface model intercomparison: A first set of benchmark results to diagnose integrated hydrology and feedbacks. Water Resourc. Res., 50:1531-1549. Šimůnek, J., van Genuchten, M. T., and Šejna, M. (2011). The HYDRUS Software Package for Simulating Two- and Three-Dimensional Movement of Water, Heat, and Multiple Solutes in Variably-Saturated Media. Technical Manual, Version 2.0, PC Progress, Prague, Czech Republic. Takizawa, K., Bazilevs Y., Tezduyar, T. E., Long, C.C., Marsden, A. L. and Schjodt.K., Patient-Specific Cardiovascular Fluid Mechanics Analysis with the ST and ALE-VMS Method in Idelsohn, S. R. (2014). Numerical Simulations of Coupled Problems in Engineering. Springer. Weill, S., Mouche, E., and Patin, J. (2009). A generalized Richards equation for surface/subsurface flow modelling. Journal of Hydrology, 366:9-20.

The Center for Frontiers of Subsurface Energy Security (A "Life at the Frontiers of Energy Research" contest entry from the 2011 Energy Frontier Research Centers (EFRCs) Summit and Forum)

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

Pope, Gary A.

"The Center for Frontiers of Subsurface Energy Security (CFSES)" was submitted to the "Life at the Frontiers of Energy Research" video contest at the 2011 Science for Our Nation's Energy Future: Energy Frontier Research Centers (EFRCs) Summit and Forum. Twenty-six EFRCs created short videos to highlight their mission and their work. CFSES is directed by Gary A. Pope at the University of Texas at Austin and partners with Sandia National Laboratories. The Office of Basic Energy Sciences in the U.S. Department of Energy's Office of Science established the 46 Energy Frontier Research Centers (EFRCs) in 2009. These collaboratively-organized centers conductmore » fundamental research focused on 'grand challenges' and use-inspired 'basic research needs' recently identified in major strategic planning efforts by the scientific community. The overall purpose is to accelerate scientific progress toward meeting the nation's critical energy challenges.« less

The Center for Frontiers of Subsurface Energy Security (A "Life at the Frontiers of Energy Research" contest entry from the 2011 Energy Frontier Research Centers (EFRCs) Summit and Forum)

ScienceCinema

Pope, Gary A. (Director, Center for Frontiers of Subsurface Energy Security); CFSES Staff

2017-12-09

'The Center for Frontiers of Subsurface Energy Security (CFSES)' was submitted to the 'Life at the Frontiers of Energy Research' video contest at the 2011 Science for Our Nation's Energy Future: Energy Frontier Research Centers (EFRCs) Summit and Forum. Twenty-six EFRCs created short videos to highlight their mission and their work. CFSES is directed by Gary A. Pope at the University of Texas at Austin and partners with Sandia National Laboratories. The Office of Basic Energy Sciences in the U.S. Department of Energy's Office of Science established the 46 Energy Frontier Research Centers (EFRCs) in 2009. These collaboratively-organized centers conduct fundamental research focused on 'grand challenges' and use-inspired 'basic research needs' recently identified in major strategic planning efforts by the scientific community. The overall purpose is to accelerate scientific progress toward meeting the nation's critical energy challenges.

Activity-dependent decrease in contact areas between subsurface cisterns and plasma membrane of hippocampal neurons.

PubMed

Tao-Cheng, Jung-Hwa

2018-04-16

Subsurface cistern (SSC) in neuronal soma and primary dendrites is a specialized compartment of endoplasmic reticulum (ER) that is in close apposition (10 nm) with the plasma membrane (PM). ER-PM contact areas are thought to be involved in intracellular calcium regulation. Here, structural changes of SSC in hippocampal neurons were examined by electron microscopy upon depolarization with high K + (90 mM) or application of NMDA (50 μM) in rat dissociated cultures as well as organotypic slice cultures. The number and average length of SSC-PM contact areas in neuronal somas significantly decreased within 30 s under excitatory condition. This decrease in SSC-PM contact area progressed with time and was reversible. These results demonstrate a structural decoupling between the SSC and the PM upon stimulation, suggesting that there may be a functional decoupling of the calcium regulation. Because SSC-PM contact areas may mediate calcium influx, the decrease in contact area may protect neurons from calcium overload upon heightened stimulation.

Deep-Focusing Time-Distance Helioseismology

NASA Technical Reports Server (NTRS)

Duvall, T. L., Jr.; Jensen, J. M.; Kosovichev, A. G.; Birch, A. C.; Fisher, Richard R. (Technical Monitor)

2001-01-01

Much progress has been made by measuring the travel times of solar acoustic waves from a central surface location to points at equal arc distance away. Depth information is obtained from the range of arc distances examined, with the larger distances revealing the deeper layers. This method we will call surface-focusing, as the common point, or focus, is at the surface. To obtain a clearer picture of the subsurface region, it would, no doubt, be better to focus on points below the surface. Our first attempt to do this used the ray theory to pick surface location pairs that would focus on a particular subsurface point. This is not the ideal procedure, as Born approximation kernels suggest that this focus should have zero sensitivity to sound speed inhomogeneities. However, the sensitivity is concentrated below the surface in a much better way than the old surface-focusing method, and so we expect the deep-focusing method to be more sensitive. A large sunspot group was studied by both methods. Inversions based on both methods will be compared.

Recrystallization texture in nickel heavily deformed by accumulative roll bonding

NASA Astrophysics Data System (ADS)

Mishin, O. V.; Zhang, Y. B.; Godfrey, A.

2017-07-01

The recrystallization behavior of Ni processed by accumulative roll bonding to a total accumulated von Mises strain of 4.8 has been examined, and analyzed with respect to heterogeneity in the deformation microstructure. The regions near the bonding interface are found to be more refined and contain particle deformation zones around fragments of the steel wire brush used to prepare the surface for bonding. Sample-scale gradients are also observed, manifested as differences between the subsurface, intermediate and central layers, where the distributions of texture components are different. These heterogeneities affect the progress of recrystallization. While the subsurface and near-interface regions typically contain lower frequencies of cube-oriented grains than anywhere else in the sample, a strong cube texture forms in the sample during recrystallization, attributed to both a high nucleation rate and fast growth rate of cube-oriented grains. The observations highlight the sensitivity of recrystallization to heterogeneity in the deformation microstructure and demonstrate the importance of characterizing this heterogeneity over several length scales.

Assessing Induced Seismicity Risk at CO 2 Storage Projects: Recent Progress and Remaining Challenges

DOE PAGES

White, Joshua A.; Foxall, William

2016-04-13

It is well established that fluid injection has the potential to induce earthquakes—from microseismicity to magnitude 5+ events—by altering state-of-stress conditions in the subsurface. This paper reviews recent lessons learned regarding induced seismicity at carbon storage sites. While similar to other subsurface injection practices, CO 2 injection has distinctive features that should be included in a discussion of its seismic hazard. Induced events have been observed at CO 2 injection projects, though to date it has not been a major operational issue. Nevertheless, the hazard exists and experience with this issue will likely grow as new storage operations come online.more » This review paper focuses on specific technical difficulties that can limit the effectiveness of current risk assessment and risk management approaches, and highlights recent research aimed at overcoming them. Finally, these challenges form the heart of the induced seismicity problem, and novel solutions to them will advance our ability to responsibly deploy large-scale CO 2 storage.« less

Predictability of Subsurface Temperature and the AMOC

NASA Astrophysics Data System (ADS)

Chang, Y.; Schubert, S. D.

2013-12-01

GEOS 5 coupled model is extensively used for experimental decadal climate prediction. Understanding the limits of decadal ocean predictability is critical for making progress in these efforts. Using this model, we study the subsurface temperature initial value predictability, the variability of the Atlantic meridional overturning circulation (AMOC) and its impacts on the global climate. Our approach is to utilize the idealized data assimilation technology developed at the GMAO. The technique 'replay' allows us to assess, for example, the impact of the surface wind stresses and/or precipitation on the ocean in a very well controlled environment. By running the coupled model in replay mode we can in fact constrain the model using any existing reanalysis data set. We replay the model constraining (nudging) it to the MERRA reanalysis in various fields from 1948-2012. The fields, u,v,T,q,ps, are adjusted towards the 6-hourly analyzed fields in atmosphere. The simulated AMOC variability is studied with a 400-year-long segment of replay integration. The 84 cases of 10-year hindcasts are initialized from 4 different replay cycles. Here, the variability and predictability are examined further by a measure to quantify how much the subsurface temperature and AMOC variability has been influenced by atmospheric forcing and by ocean internal variability. The simulated impact of the AMOC on the multi-decadal variability of the SST, sea surface height (SSH) and sea ice extent is also studied.

Advanced Development of the rF1V and rBV A/B Vaccines: Progress and Challenges

PubMed Central

Hart, Mary Kate; Saviolakis, George A.; Welkos, Susan L.; House, Robert V.

2012-01-01

The development of vaccines for microorganisms and bacterial toxins with the potential to be used as biowarfare and bioterrorism agents is an important component of the US biodefense program. DVC is developing two vaccines, one against inhalational exposure to botulinum neurotoxins A1 and B1 and a second for Yersinia pestis, with the ultimate goal of licensure by the FDA under the Animal Rule. Progress has been made in all technical areas, including manufacturing, nonclinical, and clinical development and testing of the vaccines, and in assay development. The current status of development of these vaccines, and remaining challenges are described in this chapter. PMID:22028978

The Effects of Subsurface Bioremediation on Soil Structure, Colloid Formation, and Contaminant Transport

NASA Astrophysics Data System (ADS)

Wang, Y.; Liang, X.; Zhuang, J.; Radosevich, M.

2016-12-01

Anaerobic bioremediation is widely applied to create anaerobic subsurface conditions designed to stimulate microorganisms that degrade organic contaminants and immobilize toxic metals in situ. Anaerobic conditions that accompany such techniques also promotes microbially mediated Fe(III)-oxide mineral reduction. The reduction of Fe(III) could potentially cause soil structure breakdown, formation of clay colloids, and alternation of soil surface chemical properties. These processes could then affect bioremediation and the migration of contaminants. Column experiments were conducted to investigate the impact of anaerobic bioreduction on soil structure, hydraulic properties, colloid formation, and transport of three tracers (bromide, DFBA, and silica shelled silver nanoparticles). Columns packed with inoculated water stable soil aggregates were placed in anaerobic glovebox, and artificial groundwater media was pumped into the columns to simulate anaerobic bioreduction process for four weeks. Decent amount of soluble Fe(II) accompanied by colloids were detected in the effluent from bioreduction columns a week after initiation of bioreduction treatment, which demonstrated bioreduction of Fe(III) and formation of colloids. Transport experiments were performed in the columns before and after bioreduction process to assess the changes of hydraulic and surface chemical properties through bioreduction treatment. Earlier breakthrough of bromide and DFBA after treatment indicated alterations in flow paths (formation of preferential flow paths). Less dispersion of bromide and DFBA, and less tailing of DFBA after treatment implied breakdown of soil aggregates. Dramatically enhanced transport and early breakthrough of silica shelled silver nanoparticles after treatment supported the above conclusion of alterations in flow paths, and indicated changes of soil surface chemical properties.

Revealing the unexplored fungal communities in deep groundwater of crystalline bedrock fracture zones in Olkiluoto, Finland.

PubMed

Sohlberg, Elina; Bomberg, Malin; Miettinen, Hanna; Nyyssönen, Mari; Salavirta, Heikki; Vikman, Minna; Itävaara, Merja

2015-01-01

The diversity and functional role of fungi, one of the ecologically most important groups of eukaryotic microorganisms, remains largely unknown in deep biosphere environments. In this study we investigated fungal communities in packer-isolated bedrock fractures in Olkiluoto, Finland at depths ranging from 296 to 798 m below surface level. DNA- and cDNA-based high-throughput amplicon sequencing analysis of the fungal internal transcribed spacer (ITS) gene markers was used to examine the total fungal diversity and to identify the active members in deep fracture zones at different depths. Results showed that fungi were present in fracture zones at all depths and fungal diversity was higher than expected. Most of the observed fungal sequences belonged to the phylum Ascomycota. Phyla Basidiomycota and Chytridiomycota were only represented as a minor part of the fungal community. Dominating fungal classes in the deep bedrock aquifers were Sordariomycetes, Eurotiomycetes, and Dothideomycetes from the Ascomycota phylum and classes Microbotryomycetes and Tremellomycetes from the Basidiomycota phylum, which are the most frequently detected fungal taxa reported also from deep sea environments. In addition some fungal sequences represented potentially novel fungal species. Active fungi were detected in most of the fracture zones, which proves that fungi are able to maintain cellular activity in these oligotrophic conditions. Possible roles of fungi and their origin in deep bedrock groundwater can only be speculated in the light of current knowledge but some species may be specifically adapted to deep subsurface environment and may play important roles in the utilization and recycling of nutrients and thus sustaining the deep subsurface microbial community.

Ecogenomic characterization of a marine microorganism belonging to a Firmicutes lineage that is widespread in both terrestrial and oceanic subsurface environments

NASA Astrophysics Data System (ADS)

Jungbluth, S.; Glavina del Rio, T.; Tringe, S. G.; Stepanauskas, R.; Rappe, M. S.

2015-12-01

Large-volumes of basalt-hosted fluids from the sediment-covered subseafloor were collected in July 2011 from a horizon extending 29-117 meters below the sediment-rock interface at borehole 1362B, as well as from a deep horizon extending 193-292 meters below the sediment-rock interface at borehole 1362A, which are two of the latest generation of borehole observatories on the Juan de Fuca Ridge flank in the Northeast Pacific Ocean. Environmental DNA was sequenced from one fluid sample collected from each borehole, and a genomic bin related to the terrestrial Candidatus Desulforudis audaxviator lineage within the Firmicutes phylum of bacteria was identified. The near-complete bacterial genome, herein named Candidatus Desulfopertinax inferamarinus, is composed of six scaffolds totaling 1.78 Mbp in length. Despite vast differences in geography and environment of origin, phylogenomic analysis indicate that D. inferamarinus and D. audaxviator form a monophyletic clade to the exclusion of all other sequenced genomes. Similar to its terrestrial relative, the draft genome of the marine D. inferamarinus revealed a motile, sporulating, sulfate-reducing, chemoautotrophic thermophile that is capable of synthesizing all amino acids and fixing inorganic carbon via the Wood-Ljungdahl pathway. Unlike the terrestrial clade, relatively few integrases and transposases were identified. The marine genome described here provides evidence that a life-style adapted to the isolated deep subsurface environment is a general feature of the broader, globally-distributed Desulforudis/Desulfopertinax lineage and provides insight into the adaptations required for microbial life in the marine versus terrestrial deep biospheres.

Molecular analysis of phosphate limitation in Geobacteraceae during the bioremediation of a uranium-contaminated aquifer

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

N'Guessan, L.A.; Elifantz, H.; Nevin, K.P.

2009-09-01

Nutrient limitation is an environmental stress that may reduce the effectiveness of bioremediation strategies, especially when the contaminants are organic compounds or when organic compounds are added to promote microbial activities such as metal reduction. Genes indicative of phosphate-limitation were identified via microarray analysis of chemostat cultures of Geobacter sulfureducens. This analysis revealed that genes in the pst-pho operon, which is associated with a high affinity phosphate uptake system in other microorganisms, had significantly higher transcript abundance under phosphate-limiting conditions, with the genes pstB and phoU the most up-regulated. Quantitative PCR analysis of pstB and phoU transcript levels in G.more » sulfurreducens grown in chemostats demonstrated that the expression of these genes increased when phosphate was removed from the culture medium. Transcripts of pstB and phoU within the subsurface Geobacter species predominating during an in situ uranium bioremediation field experiment were more abundant than in chemostat cultures of G. sulfurreducens that were not limited for phosphate. Addition of phosphate to incubations of subsurface sediments did not stimulate dissimilatory metal reduction. The added phosphate was rapidly adsorbed onto the sediments. The results demonstrate that Geobacter species can effectively reduce U(VI) even when experiencing suboptimal phosphate concentrations and that increasing phosphate availability with phosphate additions is difficult to achieve due to the high reactivity of this compound. This transcript-based approach developed for diagnosing phosphate limitation should be applicable to assessing the potential need for additional phosphate in other bioremediation processes.« less

Molecular Analysis of Phosphate Limitation in Geobacteraceae During the Bioremediation of a Uranium-Contaminated Aquifer

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

N'Guessan, A. Lucie; Elifantz, H.; Nevin, Kelly P.

2010-02-01

Nutrient limitation is an environmental stress that may reduce the effectiveness of bioremediation strategies, especially when the contaminants are organic compounds or when organic compounds are added to promote microbial activities such as metal reduction. Genes indicative of phosphate-limitation were identified via microarray analysis of chemostat cultures of Geobacter sulfureducens. This analysis revealed that genes in the pst-pho operon, which is associated with a high affinity phosphate uptake system in other microorganisms, had significantly higher transcript abundance under phosphate-limiting conditions, with the genes pstB and phoU the most up-regulated. Quantitative PCR analysis of pstB and phoU transcript levels in G.more » sulfurreducens grown in chemostats demonstrated that the expression of these genes increased when phosphate was removed from the culture medium. Transcripts of pstB and phoU within the subsurface Geobacter species predominating during an in situ uranium bioremediation field experiment were more abundant than in chemostat cultures of G. sulfurreducens that were not limited for phosphate. Addition of phosphate to incubations of subsurface sediments did not stimulate dissimilatory metal reduction. The added phosphate was rapidly adsorbed onto the sediments. The results demonstrate that Geobacter species can effectively reduce U(VI) even when experiencing suboptimal phosphate concentrations and that increasing phosphate availability with phosphate additions is difficult to achieve due to the high reactivity of this compound. This transcript-based approach developed for diagnosing phosphate limitation should be applicable to assessing the potential need for additional phosphate in other bioremediation processes.« less

Molecular analysis of phosphate limitation in Geobacteraceae during the bioremediation of a uranium-contaminated aquifer

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

N'Guessan, A. Lucie; Elifantz, H.; Nevin, Kelly P.

2010-01-10

Nutrient limitation is an environmental stress that may reduce the effectiveness of bioremediation strategies, especially when the contaminants are organic compounds or when organic compounds are added to promote microbial activities such as metal reduction. Genes indicative of phosphatelimitation were identified by microarray analysis of chemostat cultures of Geobacter sulfureducens. This analysis revealed that genes in the pst-pho operon, which is associated with a high-affinity phosphate uptake system in other microorganisms, had significantly higher transcript abundance under phosphate-limiting conditions, with the genes pstB and phoU upregulated the most. Quantitative PCR analysis of pstB and phoU transcript levels in G. sulfurreducensmore » grown in chemostats demonstrated that the expression of these genes increased when phosphate was removed from the culture medium. Transcripts of pstB and phoU within the subsurface Geobacter species predominating during an in situ uranium-bioremediation field experiment were more abundant than in chemostat cultures of G. sulfurreducens that were not limited for phosphate. Addition of phosphate to incubations of subsurface sediments did not stimulate dissimilatory metal reduction. The added phosphate was rapidly adsorbed onto the sediments. The results demonstrate that Geobacter species can effectively reduce U(VI) even when experiencing suboptimal phosphate concentrations and that increasing phosphate availability with phosphate additions is difficult to achieve because of the high reactivity of this compound. This transcript-based approach developed for diagnosing phosphate limitation should be applicable to assessing the potential need for additional phosphate in other bioremediation processes.« less

Anaerobic biodegradation of partially hydrolyzed polyacrylamide in long-term methanogenic enrichment cultures from production water of oil reservoirs.

PubMed

Hu, Hao; Liu, Jin-Feng; Li, Cai-Yun; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

2018-06-01

The increasing usage of partially hydrolyzed polyacrylamide (HPAM) in oilfields as a flooding agent to enhance oil recovery at so large quantities is an ecological hazard to the subsurface ecosystem due to persistence and inertness. Biodegradation of HPAM is a potentially promising strategy for dealing with this problem among many other methods available. To understand the responsible microorganisms and mechanism of HPAM biodegradation under anaerobic conditions, an enrichment culture from production waters of oil reservoirs were established with HPAM as the sole source of carbon and nitrogen incubated for over 328 days, and analyzed using both molecular microbiology and chemical characterization methods. Gel permeation chromatography, High-pressure liquid chromatography and Fourier-transformed infrared spectroscopy results indicated that, after 328 days of anaerobic incubation, some of the amide groups on HPAM were removed and released as ammonia/ammonium and carboxylic groups, while the carbon backbone of HPAM was converted to smaller polymeric fragments, including oligomers and various fatty acids. Based on these results, the biochemical process of anaerobic biodegradation of HPAM was proposed. The phylogenetic analysis of 16S rRNA gene sequences retrieved from the enrichments showed that Proteobacteria and Planctomycetes were the dominant bacteria in the culture with HPAM as the source of carbon and nitrogen, respectively. For archaea, Methanofollis was more abundant in the anaerobic enrichment. These results are helpful for understanding the process of HPAM biodegradation and provide significant insights to the fate of HPAM in subsurface environment and for possible bioremediation.

ENVIRONMENTAL MANAGEMENT SCIENCE PROGRAM PROJECT NUMBER 87016 CO-PRECIPITATION OF TRACE METALS IN GROUNDWATER AND VADOSE ZONE CALCITE: IN SITU CONTAINMENT AND STABILIZATION OF STRONTIUM-90 AND OTHER DIVALENT METALS AND RADIONUCLIDES AT ARID WESTERN DOE SITES

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

Ferris, F. Grant; Fujita, Yoshiko; Smith, Robert W.

2004-06-15

Radionuclide and metal contaminants are present in the vadose zone and groundwater throughout the U.S. Department of Energy (DOE) weapons complex. In situ containment and stabilization of these contaminants in vadose zones or groundwater is a cost-effective treatment strategy. Our facilitated approach relies upon the hydrolysis of introduced urea to cause the acceleration of calcium carbonate precipitation (and trace metal coprecipitation) by increasing groundwater pH and alkalinity (Fujita et al., 2000; Warren et al., 2001). Subsurface urea hydrolysis is catalyzed by the urease enzyme, which may be either introduced with the urea or produced in situ by ubiquitous subsurface ureamore » hydrolyzing microorganisms. Because the precipitation processes are irreversible and many western aquifers are saturated with respect to calcite, the co-precipitated metals and radionuclides will be effectively removed from groundwater. The rate at which trace metals are incorporated into calcite is a function of calcite precipitation kinetics, adsorption interactions between the calcite surface and the trace metal in solution (Zachara et al., 1991), solid solution properties of the trace metal in calcite (Tesoriero and Pankow, 1996), and also the surfaces upon which the calcite is precipitating. A fundamental understanding of the coupling of calcite precipitation and trace metal partitioning, and how this occurs in aquifers and vadose environments is lacking. This report summarizes work undertaken during the second year of this project.« less

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.

Heterotrophic bacteria in soils of Larsemann Oasis of East Antarctica

NASA Astrophysics Data System (ADS)

Churilin, Nikita; Soina, Vera

2015-04-01

The study of diversity and functional state of microorganisms in subsurface rocks layers, their participation in the biochemical weathering and formation of organic horizons of soils is important for understanding ecology and microorganisms in Antarctic soils. The study of cultured forms of microorganisms and their potential viability is still relevant to characterize the physiological state, biological activity and resilience of microorganisms involved in the initial soil formation. Improvement of isolation techniques of viable bacteria from the extreme habitats has a particular importance for rising the efficiency of environmental monitoring. The aim of the study was to investigate the viable heterotrophic bacteria involved in the formation of soils from wet valleys Larsemann Oasis, which is one of the warmest ice-free space of East Antarctica. Soil samples were taken from the intermountain humid valleys, where silt-gravelly substrates formed moss, algae, lichen cover. We used nutrient solutions (trypticase soy, R2A and glucose-peptone) to isolate cultured bacteria and study their morphological types in the light microscope. The total number of microorganisms was determined by fluorescent microscopy with acridine orange. SEM was used for morphological studies of bacterial communities in situ. To activate the growth processes we added into nutrient solutions various regulatory metabolites that have dose-dependence and operate at the community level. Physiological and functional conditions were determined by the duration of the lag phase and specific growth rate of bacterial communities in nutrient solutions containing various organic substrates. Soils form under protection of «stone pavement» and organisms leave the surface, so the forming organo-mineral horizon occurs inside of rock, thus the microprofile can form on both sides of the organic horizons. UV radiation, lack of moisture and strong wind are main limiting factors for microorganisms' growth in Antarctic soils. Primitive soils and permafrost layer have a great unevenness in the number of cultivated and potentially viable cells in different horizons. This phenomenon is characteristic for habitats with stable and alternating negative temperatures that can be attributed to the irregular migration of cells during freezing and heterogeneity of microbial populations along the depth of dormancy. One of the identified features was the lack of correlation with the organic content. SEM study of microbial communities in native Antarctic soils revealed the presence of biofilms, which can play an important role in weathering of rocks and primary soil formation, by forming organic horizon and protecting cells from environmental impact. Biofilms can also influence on distribution of bacterial cells in forming soils. Growth regulators (indoleacetic acid, wheat germ agglutinin, alkylhydroxybenzenes, pyruvate Na and serotonin) were used in experiments on the growth reactivation using soil samples with low number of microorganisms. The results obtained by this analysis can be used for further research to develop methods of the most complete selection of viable bacteria from Antarctic soils. We also determined the physiological condition of bacterial populations and their maximum specific growth rate. This method determines the functional (trophic) diversity of microbial communities and the maximum specific growth rate that reflects the environmental strategy of bacterial growth. In spite of the extreme conditions, a variety of physiological and metabolic willingness to consume polymers hydrolytic bacterial associations of endolithic soil is highest in the surface horizon and sharply decreases in the mineral horizon.

Reconstruction of paleoenvironmental changes based on the planktonic foraminiferal assemblages off Shimokita (Japan) in the northwestern North Pacific

NASA Astrophysics Data System (ADS)

Kuroyanagi, Azumi; Kawahata, Hodaka; Narita, Hisashi; Ohkushi, Ken'ichi; Aramaki, Takafumi

2006-08-01

Planktonic foraminifera live in the upper ocean, and their assemblages can record the surrounding environment. To reconstruct changes in water masses and the timing of flow of the Oyashio and Tsugaru currents through the Tsugaru Strait after the Last Glacial Maximum, when the Japan Sea had been almost isolated from the surrounding seas, we investigated at high resolution the planktonic foraminiferal fauna in seafloor sediments off the Shimokita (core MD01-2409: 41°33.9'N, 141°52.1'E), in the northwestern North Pacific, over the last 26,900 years. Factor analysis of the foraminiferal assemblage suggests that the water mass changed significantly as a result of the deglacial sea-level rise and opening of the straits into the Japan Sea. Mass accumulation rates of some selected foraminiferal species that inhabit characteristic environments (e.g., warm stratified water, Oyashio Current, Tsushima Current) corroborate these changes in water mass and water column structure. We also used the ratio of the dextral form to total Neogloboquadrina pachyderma as an indicator of subsurface (below the pycnocline) water temperature. We recognized five distinct periods of oceanographic change at the study site, which is just east of the Tsugaru Strait: (1) Oyashio Current affecting both surface and subsurface waters (26.9-15.7 thousand calendar years before present (cal. kyr BP)); (2) vertical mixing and subsurface warming as the Oyashio Current began to flow into the Japan Sea through the Tsugaru Strait (15.7-10.6 cal. kyr BP); (3) outflow of the Tsugaru Current from the Japan Sea into the Pacific, leading to baroclinic conditions, with the surface layer under the influence of the Tsugaru and the subsurface layers of the Oyashio Current (10.6-9.0 cal. kyr BP); (4) stratification of the water column developed as the flow of the Tsugaru Current increased (9.0-6.2 cal. kyr BP); and (5) warming of the subsurface layer, disruption of the stratification, and dominance of the Tsugaru Current in both surface and subsurface layers, similar to the present situation (6.2-1.5 cal. kyr BP). The timing of flow of the Oyashio and Tsugaru currents through the strait at the study site off Shimokita is generally compatible with the results of studies in the Japan Sea. The flow of the Tsugaru Current led to progressive warming of the waters, from the surface to the subsurface layers and from the Japan Sea side to the Pacific side of the Tsugaru Strait, beginning in 8.3-6.8 cal. kyr BP on the western side, and in 6.2 cal. kyr BP on the eastern side of the strait. By 4.8 cal. kyr BP on the western side, and by ˜ 3.4 cal. kyr BP on the eastern side of the strait, warm water prevailed in both surface and subsurface layers.

Viewing Marine Bacteria, Their Activity and Response to Environmental Drivers from Orbit

PubMed Central

Grimes, D. Jay; Ford, Tim E.; Colwell, Rita R.; Baker-Austin, Craig; Martinez-Urtaza, Jaime; Subramaniam, Ajit; Capone, Douglas G.

2014-01-01

Satellite-based remote sensing of marine microorganisms has become a useful tool in predicting human health risks associated with these microscopic targets. Early applications were focused on harmful algal blooms, but more recently methods have been developed to interrogate the ocean for bacteria. As satellite-based sensors have become more sophisticated and our ability to interpret information derived from these sensors has advanced, we have progressed from merely making fascinating pictures from space to developing process models with predictive capability. Our understanding of the role of marine microorganisms in primary production and global elemental cycles has been vastly improved as has our ability to use the combination of remote sensing data and models to provide early warning systems for disease outbreaks. This manuscript will discuss current approaches to monitoring cyanobacteria and vibrios, their activity and response to environmental drivers, and will also suggest future directions. PMID:24477922

Relating Anaerobic Digestion Microbial Community and Process Function.

PubMed

Venkiteshwaran, Kaushik; Bocher, Benjamin; Maki, James; Zitomer, Daniel

2015-01-01

Anaerobic digestion (AD) involves a consortium of microorganisms that convert substrates into biogas containing methane for renewable energy. The technology has suffered from the perception of being periodically unstable due to limited understanding of the relationship between microbial community structure and function. The emphasis of this review is to describe microbial communities in digesters and quantitative and qualitative relationships between community structure and digester function. Progress has been made in the past few decades to identify key microorganisms influencing AD. Yet, more work is required to realize robust, quantitative relationships between microbial community structure and functions such as methane production rate and resilience after perturbations. Other promising areas of research for improved AD may include methods to increase/control (1) hydrolysis rate, (2) direct interspecies electron transfer to methanogens, (3) community structure-function relationships of methanogens, (4) methanogenesis via acetate oxidation, and (5) bioaugmentation to study community-activity relationships or improve engineered bioprocesses.

Disruption of the Gut Ecosystem by Antibiotics

PubMed Central

2018-01-01

The intestinal microbiota is a complex ecosystem consisting of various microorganisms that expands human genetic repertoire and therefore affects human health and disease. The metabolic processes and signal transduction pathways of the host and intestinal microorganisms are intimately linked, and abnormal progression of each process leads to changes in the intestinal environment. Alterations in microbial communities lead to changes in functional structures based on the metabolites produced in the gut, and these environmental changes result in various bacterial infections and chronic enteric inflammatory diseases. Here, we illustrate how antibiotics are associated with an increased risk of antibiotic-associated diseases by driving intestinal environment changes that favor the proliferation and virulence of pathogens. Understanding the pathogenesis caused by antibiotics would be a crucial key to the treatment of antibiotic-associated diseases by mitigating changes in the intestinal environment and restoring it to its original state. PMID:29214770

Sugars en route to the roots. Transport, metabolism and storage within plant roots and towards microorganisms of the rhizosphere.

PubMed

Hennion, Nils; Durand, Mickael; Vriet, Cécile; Doidy, Joan; Maurousset, Laurence; Lemoine, Rémi; Pourtau, Nathalie

2018-04-28

In plants, root is a typical sink organ that relies exclusively on the import of sugar from the aerial parts. Sucrose is delivered by the phloem to the most distant root tips and, en route to the tip, is used by the different root tissues for metabolism and storage. Besides, a certain portion of this carbon is exuded in the rhizosphere, supplied to beneficial microorganisms and diverted by parasitic microbes. The transport of sugars towards these numerous sinks either occurs symplastically through cell connections (plasmodesmata) or is apoplastically mediated through membrane transporters (MST, SUT/SUC and SWEET) that control monosaccharide and sucrose fluxes. Here, we review recent progresses on carbon partitioning within and outside roots, discussing membrane transporters involved in plant responses to biotic and abiotic factors. This article is protected by copyright. All rights reserved.

Evaluation of anti-bacterial and wound healing activity of the fruits of Amorpha fruticosa L.

PubMed

Qu, Xueling; Diao, Yunpeng; Zhang, Zhen; Wang, Shouyu; Jia, Yujie

2013-01-01

As the traditional Chinese medicine, the fresh fruits of Amorpha fruticosa L. were applied for the treatment of carbuncle, eczema and burn (Das et al., 2007). However, little is known about the functional roles of the fruits of Amorpha fruticosa L. during wound healing progress. In the present study, we evaluated both antimicrobial potential against a wide range of microorganisms and wound healing activity of the seven compounds isolated from the fruits of Amorpha fruticosa L in vitro and in vivo. Our results showed that compounds I (6a,12a-dehydroamorphin), V (dehydrosermundone) and VI (tephrosin) isolated from the fruits of Amorpha fruticosa L. performed dominant antimicrobial potential against microorganisms. Moreover, these compounds significantly enhanced fibroblasts proliferation and migration, leading to promotion of wound healing. Thus, it could be possible for the therapeutic utilization of Amorpha fruticosa L. for wound healing in the future.

Toward RNA nanoparticle vaccines: synergizing RNA and inorganic nanoparticles to achieve immunopotentiation.

PubMed

DeLong, Robert K; Curtis, Chandler B

2017-03-01

Traditionally, vaccines have been composed of live attenuated or killed microorganisms. Alternatively, individual protein subunits or other molecular components of the microorganism can serve as the antigen and trigger an antibody response by the immune system. The immune system is a coordinated molecular and cellular response that works in concert to check the spread of infection. In the past decade, there has been much progress on DNA vaccines. DNA vaccination includes using the coding segments of a viral or bacterial genome to generate an immune response. However, the potential advantage of combining an RNA molecule with inorganic nanoparticle delivery should be considered, with the goal to achieve immuno-synergy between the two and to overcome some of the current limitations of DNA vaccines and traditional vaccines. WIREs Nanomed Nanobiotechnol 2017, 9:e1415. doi: 10.1002/wnan.1415 For further resources related to this article, please visit the WIREs website. © 2016 Wiley Periodicals, Inc.

Viewing marine bacteria, their activity and response to environmental drivers from orbit: satellite remote sensing of bacteria.

PubMed

Grimes, D Jay; Ford, Tim E; Colwell, Rita R; Baker-Austin, Craig; Martinez-Urtaza, Jaime; Subramaniam, Ajit; Capone, Douglas G

2014-04-01

Satellite-based remote sensing of marine microorganisms has become a useful tool in predicting human health risks associated with these microscopic targets. Early applications were focused on harmful algal blooms, but more recently methods have been developed to interrogate the ocean for bacteria. As satellite-based sensors have become more sophisticated and our ability to interpret information derived from these sensors has advanced, we have progressed from merely making fascinating pictures from space to developing process models with predictive capability. Our understanding of the role of marine microorganisms in primary production and global elemental cycles has been vastly improved as has our ability to use the combination of remote sensing data and models to provide early warning systems for disease outbreaks. This manuscript will discuss current approaches to monitoring cyanobacteria and vibrios, their activity and response to environmental drivers, and will also suggest future directions.

[Progress on biodegradation of polylactic acid--a review].

PubMed

Li, Fan; Wang, Sha; Liu, Weifeng; Chen, Guanjun

2008-02-01

Polylactic acid is a high molecular-weight polyester made from renewable resources such as corn or starch. It is a promising biodegradable plastic due to its mechanical properties, biocompatibility and biodegradability. To achieve natural recycling of polylactic acid, relative microorganisms and the underlying mechanisms in the biodegradation has become an important issue in biodegradable materials. Up to date, most isolated microbes capable of degrading polylactic acid belong to actinomycetes. Proteases secreted by these microorganisms are responsible for the degradation. However, subtle differences exist between these polylactic acid degrading enzymes and typical proteases with respect to substrate binding and catalysis. Amino acids relative to catalysis are postulated to be highly plastic allowing their catalytic hydrolysis of polylactic acid. In this paper we reviewed current studies on biodegradation of polylactic acid concerning its microbial, enzymatic reactions and the possible mechanisms. We also discussed the probability of biologically recycling PLA by applying highly efficient strains and enzymes.

Pathogenetic aspects of uncomplicated urinary tract infection: recent advances.

PubMed

Fünfstück, R; Smith, J W; Tschäpe, H; Stein, G

1997-01-01

Urinary tract infections mostly are caused by Enterobacteriaceae; E. coli dominating in 80-90% for uncomplicated diseases. Microorganisms possessing the ability to colonize the uroepithelium (fimbriae/pili) and to cytotoxically damage cells and tissue (hemolysin) may initiate acute infection. Properties such as serum resistance, iron sequesteration, hydroxamate production and the presence of K-antigen are found in strains which persist in the host without initiating clinical symptoms. The ability of bacteria to adhere to cells of the epithelial boundary layer of the host organisms is of initial importance in the origin and progress of an infection. A variety of specific factors, e.g. glycolipids on the surface of the uroepithelium as well as cellular and humoral disorders of immunoreactions in the host determine the course of a disease. The immune response may ameliorate clinical symptoms and select urovirulent characteristics of the causative microorganism in recurrent diseases.

Immobilization of U(VI) from Oxic Groundwater by Hanford 300 Area Sediments and Effects of Columbia River Water

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

Ahmed, B.; Cao, Bin; Mishra, Bhoopesh

2012-09-23

Regions within the U.S. Department of Energy Hanford 300 Area (300 A) site experience periodic hydrologic influences from the nearby Columbia River as a result of changing river stage, which causes changes in groundwater elevation, flow direction and water chemistry. An important question is the extent to which the mixing of Columbia River water and groundwater impacts the speciation and mobility of uranium (U). In this study, we designed experiments to mimic interactions among U, oxic groundwater or Columbia River water, and 300 A sediments in the subsurface environment of Hanford 300 A. The goals were to investigate mechanisms of:more » 1) U immobilization in 300 A sediments under bulk oxic conditions and 2) U remobilization from U-immobilized 300 A sediments exposed to oxic Columbia River water. Initially, 300 A sediments in column reactors were fed with U(VI)-containing oxic 1) synthetic groundwater (SGW), 2) organic-amended SGW (OA-SGW), and 3) de-ionized (DI) water to investigate U immobilization processes. After that, the sediments were exposed to oxic Columbia River water for U remobilization studies. The results reveal that U was immobilized by 300 A sediments predominantly through reduction (80-85%) when the column reactor was fed with oxic OA-SGW. However, U was immobilized by 300 A sediments through adsorption (100%) when the column reactors were fed with oxic SGW or DI water. The reduced U in the 300 A sediments fed with OA-SGW was relatively resistant to remobilization by oxic Columbia River water. Oxic Columbia River water resulted in U remobilization (~7%) through desorption, and most of the U that remained in the 300 A sediments fed with OA-SGW (~93%) was in the form of uraninite nanoparticles. These results reveal that: 1) the reductive immobilization of U through OA-SGW stimulation of indigenous 300 A sediment microorganisms may be viable in the relatively oxic Hanford 300 A subsurface environments and 2) with the intrusion of Columbia River water, desorption may be the primary process resulting in U remobilization from OA-SGW-stimulated 300 A sediments at the subsurface of the Hanford 300 A site.« less

Impact of Ammonium on Syntrophic Organohalide-Respiring and Fermenting Microbial Communities

PubMed Central

Fajardo-Williams, Devyn; Kegerreis, Kylie L.; Parameswaran, Prathap

2016-01-01

ABSTRACT Syntrophic interactions between organohalide-respiring and fermentative microorganisms are critical for effective bioremediation of halogenated compounds. This work investigated the effect of ammonium concentration (up to 4 g liter−1 NH4+-N) on trichloroethene-reducing Dehalococcoides mccartyi and Geobacteraceae in microbial communities fed lactate and methanol. We found that production of ethene by D. mccartyi occurred in mineral medium containing ≤2 g liter−1 NH4+-N and in landfill leachate. For the partial reduction of trichloroethene (TCE) to cis-dichloroethene (cis-DCE) at ≥1 g liter−1 NH4+-N, organohalide-respiring dynamics shifted from D. mccartyi and Geobacteraceae to mainly D. mccartyi. An increasing concentration of ammonium was coupled to lower metabolic rates, longer lag times, and lower gene abundances for all microbial processes studied. The methanol fermentation pathway to acetate and H2 was conserved, regardless of the ammonium concentration provided. However, lactate fermentation shifted from propionic to acetogenic at concentrations of ≥2 g liter−1 NH4+-N. Our study findings strongly support a tolerance of D. mccartyi to high ammonium concentrations, highlighting the feasibility of organohalide respiration in ammonium-contaminated subsurface environments. IMPORTANCE Contamination with ammonium and chlorinated solvents has been reported in numerous subsurface environments, and these chemicals bring significant challenges for in situ bioremediation. Dehalococcoides mccartyi is able to reduce the chlorinated solvent trichloroethene to the nontoxic end product ethene. Fermentative bacteria are of central importance for organohalide respiration and bioremediation to provide D. mccartyi with H2, their electron donor, acetate, their carbon source, and other micronutrients. In this study, we found that high concentrations of ammonium negatively correlated with rates of trichloroethene reductive dehalogenation and fermentation. However, detoxification of trichloroethene to nontoxic ethene occurred even at ammonium concentrations typical of those found in animal waste (up to 2 g liter−1 NH4+-N). To date, hundreds of subsurface environments have been bioremediated through the unique metabolic capability of D. mccartyi. These findings extend our knowledge of D. mccartyi and provide insight for bioremediation of sites contaminated with chlorinated solvents and ammonium. PMID:27303735

Where microorganisms meet rocks in the Earth's Critical Zone

NASA Astrophysics Data System (ADS)

Akob, D. M.; Küsel, K.

2011-03-01

The Earth's Critical Zone (CZ) is the critical, outer shell of the Earth that provides an arena for the interplay of diverse physical, chemical, and biological processes that are fundamental for sustaining life. As microbes are the principle drivers of biogeochemical cycles, it is necessary to understand the biodiversity of the CZ unseen majority and their impact on life-sustaining processes. This review aims to summarize the factors controlling where microbes (prokaryotes and micro-eukaryotes) live within the CZ and what is known to date about their diversity and function. Microbes live in all regions of the CZ down to 5 km depth, but due to changing habitat complexity, e.g., variability in pore spaces, water, oxygen, and nutrients, their functional role changes with depth. The abundance of prokaryotes and micro-eukaryotes decreases from a maximum of 1010 or 107 cells g soil-1 up to eight orders of magnitude with depth. Symbiotic mycorrhizal fungi and free-living decomposers are best understood in soil habitats, where they are up to 103 cells g soil-1. However, little is known about their identity and impact on weathering in the deep subsurface. The relatively low abundance of micro-eukaryotes in the deep subsurface suggests that these organisms are either limited in space or nutrients or unable to cope with oxygen limitations. Since deep regions of the CZ are limited in the recent input of photosynthesis-derived carbon, microbes are dependent on deposited organic material or on chemolithoautotrophic metabolism that allows for the establishment of a complete food chain independent from the surface. However, the energy flux available might only allow cell growth over tens to thousands of years. The recent development of "omics" technologies has provided microbial ecologists with methods to link the composition and function of in situ microbial communities. We should expect new metabolic discoveries as we have a closer look utilizing a polyphasic approach into the microbial communities of the CZ. Thus, future work is still needed to link microbial biodiversity to the exact role of microbes in weathering and geochemical cycling in the CZ, especially in subsurface habitats.

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.

Research progress on the effect of microwave sterilization on agricultural products quality

NASA Astrophysics Data System (ADS)

Zhu, Xiang-hao; Yang, Yu-xia; Duan, Zhen-hua

2018-02-01

Different sterilization methods have different effects on the quality of agricultural products, microwave sterilization inhibited or eliminated microorganism by the use of microwave thermal effects and non-thermal. In this paper, the effects of microwave sterilization on the quality of fruits and vegetables, dairy, meat, grain, aquatic products and other agricultural products were introduced, and the possible development trends of microwave sterilization in agricultural products processing application were put forward.

Bioelectrochemical analysis of a hyperthermophilic microbial fuel cell generating electricity at temperatures above 80 °C.

PubMed

Fu, Qian; Fukushima, Naoya; Maeda, Haruo; Sato, Kozo; Kobayashi, Hajime

2015-01-01

We examined whether a hyperthermophilic microbial fuel cell (MFC) would be technically feasible. Two-chamber MFC reactors were inoculated with subsurface microorganisms indigenous to formation water from a petroleum reservoir and were started up at operating temperature 80 °C. The MFC generated a maximum current of 1.3 mA 45 h after the inoculation. Performance of the MFC improved with an increase in the operating temperature; the best performance was achieved at 95 °C with the maximum power density of 165 mWm(-2), which was approximately fourfold higher than that at 75 °C. Thus, to our knowledge, our study is the first to demonstrate generation of electricity in a hyperthermophilic MFC (operating temperature as high as 95 °C). Scanning electron microscopy showed that filamentous microbial cells were attached on the anode surface. The anodic microbial consortium showed limited phylogenetic diversity and primarily consisted of hyperthermophilic bacteria closely related to Caldanaerobacter subterraneus and Thermodesulfobacterium commune.

Alteration of Rock Fragments from Columbia River Basalt Microcosms

NASA Technical Reports Server (NTRS)

Wentworth, Susan J.; Thomas-Keprta, Kathie L.; Velbel, Michael A.; McKay, David S.; Stevens, Todd O.

1999-01-01

During an earlier study, microorganisms were grown microcosms consisting of sterilized chips of Columbia River Basalt (CRB) and natural CRB ground water with its natural microflora; environmental conditions simulated a deep subsurface, anaerobic, dark environment. Subsequent scanning and transmission electron microscope (SEM and TEM) studies revealed the presence of several types of bacteria and biofilm, some of which were mineralized. Some of these biological features are very similar to possible biogenic features found in two meteorites from Mars, ALH84001 (found in Antarctica) and Nakhla (observed to fall in Egypt). Both ALH84001 and Nakhla contain traces of low-temperature aqueous alteration of silicates, oxides, and sulfides. The goals of this study are to use high-resolution field-emission SEM (FE-SEM) to examine the CRB samples for evidence of alteration features similar to those in the martian meteorites, to determine the extent of alteration during the CRB microcosm experiments, and to determine whether effects of biological activity can be distinguished from inorganic effects.

Report of the COSPAR mars special regions colloquium

USGS Publications Warehouse

Kminek, G.; Rummel, J.D.; Cockell, C.S.; Atlas, R.; Barlow, N.; Beaty, D.; Boynton, W.; Carr, M.; Clifford, S.; Conley, C.A.; Davila, A.F.; Debus, A.; Doran, P.; Hecht, M.; Heldmann, J.; Helbert, J.; Hipkin, V.; Horneck, G.; Kieft, Thomas L.; Klingelhoefer, G.; Meyer, M.; Newsom, H.; Ori, G.G.; Parnell, J.; Prieur, D.; Raulin, F.; Schulze-Makuch, D.; Spry, J.A.; Stabekis, P.E.; Stackebrandt, E.; Vago, J.; Viso, M.; Voytek, M.; Wells, L.; Westall, F.

2010-01-01

In this paper we present the findings of a COSPAR Mars Special Regions Colloquium held in Rome in 2007. We review and discuss the definition of Mars Special Regions, the physical parameters used to define Mars Special Regions, and physical features on Mars that can be interpreted as Mars Special Regions. We conclude that any region experiencing temperatures > -25 ??C for a few hours a year and a water activity > 0.5 can potentially allow the replication of terrestrial microorganisms. Physical features on Mars that can be interpreted as meeting these conditions constitute a Mars Special Region. Based on current knowledge of the martian environment and the conservative nature of planetary protection, the following features constitute Mars Special regions: Gullies and bright streaks associated with them, pasted-on terrain, deep subsurface, dark streaks only on a case-by-case basis, others to be determined. The parameter definition and the associated list of physical features should be re-evaluated on a regular basis. ?? 2010 COSPAR. Published by Elsevier Ltd. All rights reserved.

Use of PRD1 bacteriophage in groundwater viral transport, inactivation, and attachment studies

USGS Publications Warehouse

Harvey, R.W.; Ryan, J.N.

2004-01-01

PRD1, an icosahedra-shaped, 62 nm (diameter), double-stranded DNA bacteriophage with an internal membrane, has emerged as an important model virus for studying the manner in which microorganisms are transported through a variety of groundwater environments. The popularity of this phage for use in transport studies involving geologic media is due, in part, to its relative stability over a range of temperatures and low degree of attachment in aquifer sediments. Laboratory and field investigations employing PRD1 are leading to a better understanding of viral attachment and transport behaviors in saturated geologic media and to improved methods for describing mathematically subsurface microbial transport at environmentally significant field scales. Radioisotopic labeling of PRD1 is facilitating additional information about the nature of viral interactions with solid surfaces in geologic media, the importance of iron oxide surfaces, and allowing differentiation between inactivation and attachment in field-scale tracer tests. ?? 2004 Published by Elsevier B.V. on behalf of the Federation of European Microbiological Societies.

Innovative Methods for Integrating Knowledge for Long-Term Monitoring of Contaminated Groundwater Sites: Understanding Microorganism Communities and their Associated Hydrochemical Environment

NASA Astrophysics Data System (ADS)

Mouser, P. J.; Rizzo, D. M.; Druschel, G.; O'Grady, P.; Stevens, L.

2005-12-01

This interdisciplinary study integrates hydrochemical and genome-based data to estimate the redox processes occurring at long-term monitoring sites. Groundwater samples have been collected from a well-characterized landfill-leachate contaminated aquifer in northeastern New York. Primers from the 16S rDNA gene were used to amplify Bacteria and Archaea in groundwater taken from monitoring wells located in clean, fringe, and contaminated locations within the aquifer. PCR-amplified rDNA were digested with restriction enzymes to evaluate terminal restriction fragment length polymorphism (T-RFLP) community profiles. The rDNA was cloned, sequenced, and partial sequences were matched against known organisms using the NCBI Blast database. Phylogenetic trees and bootstrapping were used to identify classifications of organisms and compare the communities from clean, fringe, and contaminated locations. We used Artificial Neural Network (ANN) models to incorporate microbial data with hydrochemical information for improving our understanding of subsurface processes.

Methane-producing microbial community in a coal bed of the Illinois basin.

PubMed

Strapoc, Dariusz; Picardal, Flynn W; Turich, Courtney; Schaperdoth, Irene; Macalady, Jennifer L; Lipp, Julius S; Lin, Yu-Shih; Ertefai, Tobias F; Schubotz, Florence; Hinrichs, Kai-Uwe; Mastalerz, Maria; Schimmelmann, Arndt

2008-04-01

A series of molecular and geochemical studies were performed to study microbial, coal bed methane formation in the eastern Illinois Basin. Results suggest that organic matter is biodegraded to simple molecules, such as H(2) and CO(2), which fuel methanogenesis and the generation of large coal bed methane reserves. Small-subunit rRNA analysis of both the in situ microbial community and highly purified, methanogenic enrichments indicated that Methanocorpusculum is the dominant genus. Additionally, we characterized this methanogenic microorganism using scanning electron microscopy and distribution of intact polar cell membrane lipids. Phylogenetic studies of coal water samples helped us develop a model of methanogenic biodegradation of macromolecular coal and coal-derived oil by a complex microbial community. Based on enrichments, phylogenetic analyses, and calculated free energies at in situ subsurface conditions for relevant metabolisms (H(2)-utilizing methanogenesis, acetoclastic methanogenesis, and homoacetogenesis), H(2)-utilizing methanogenesis appears to be the dominant terminal process of biodegradation of coal organic matter at this location.

Identification of subsurface microorganisms at Yucca Mountain. Quarterly report, July 1, 1995--September 30, 1995

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

Stetzenbach, L.D.

1995-12-01

More than 1100 bacterial isolates were obtained over a two year period from 31 springs in a region along the southern boarder of California and Nevada. Water samples were collected from 17 springs in Ash Meadows National Wildlife Refuge and 14 springs in Death Valley National Park. Bacteria isolated from these samples were subjected to extraction and gas chromatography to determine the cellular fatty acid profile of each isolate. Fatty acid methyl esters (FAME) extracted from cell membranes were separated and classified using the Hewlett Packard by gas chromatography. The FAME profiles of each isolate were then subjected to clustermore » analysis by the unweighted pair-group method using arithmetic averages. During this quarter the relatedness of FAME patterns of bacterial isolates were examined at the genus level by counting the number of clusters produced in a MIDI dendrogram at a Euclidian distance of 25. This information was then used to determine microbiological relationships among springs.« less

Biodegradation of aliphatic vs. aromatic hydrocarbons in fertilized arctic soils

USGS Publications Warehouse

Braddock, J.F.

1999-01-01

A study was carried out to test a simple bioremediation treatment strategy in the Arctic and analyze the influence of fertilization the degradation of aliphatic and aromatic hydrocarbons, e.g., pristine, n-tetradecane, n-pentadecane, 2-methylnaphthalene, naphthalene, and acenaphthalene. The site was a coarse sand pad that once supported fuel storage tanks. Diesel-range organics concentrations were 250-860 mg/kg soil at the beginning of the study. Replicate field plots treated with fertilizer yielded final concentrations of 0, 50, 100, or 200 mg N/kg soil. Soil pH and soil-water potentials decreased due to fertilizer application. The addition of fertilizer considerably increased soil respiration potentials, but not the populations of microorganisms measured. Fertilizer addition also led to ??? 50% loss of measured aliphatic and aromatic hydrocarbons in surface and subsurface soils. For fertilized plots, hydrocarbon loss was not associated with the quantity of fertilizer added. Losses of aliphatic hydrocarbons were ascribed to biotic processes, while losses of aromatic hydrocarbons were due to biotic and abiotic processes.