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Search Results: 1 - 10 of 144603 matches for " Jillian F. Banfield "
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Quantitative determination of elemental sulfur at the arsenopyrite surface after oxidation by ferric iron: mechanistic implications
Molly M McGuire, Jillian F Banfield, Robert J Hamers
Geochemical Transactions , 2001, DOI: 10.1186/1467-4866-2-25
Abstract: Arsenopyrite, FeAsS (a derivative of the marcasite structure), is the most common arsenic-bearing mineral. Under oxidizing conditions, either occurring naturally or as a result of mining processes, the mineral produces arsenite (AsO33-), arsenate (AsO43-), and sulfate (SO42-), [1-3] thus contributing to the acidification of water as well as the release of soluble arsenic species. Despite the potential environmental and health hazards posed by the oxidative dissolution of arsenopyrite, the mineral has received far less attention in the laboratory than pyrite (FeS2), the most studied of the sulfide minerals.In acidic environments, the rate of sulfide mineral dissolution is typically limited by the supply of ferric iron, Fe3+; however, in the presence of iron-oxidizing microorganisms, the supply of ferric iron is continuously replenished by microbial oxidation of the ferrous iron released from sulfide minerals.[4] Despite the importance of oxidation by ferric iron in natural systems, many of the fundamental details of the oxidation of arsenopyrite by Fe3+ under acidic conditions still remain unclear. One critical issue is the stoichiometry of the reaction with respect to the sulfur species. The literature is divided about whether the majority of the sulfur from the mineral is released into solution as sulfoxy anions[5,6] [in a scheme similar to eqn. (1)], or whether a substantial amount of the sulfur remains as insoluble elemental sulfur (S8) at the mineral surface[7,8] [as shown in eqn. (2)]:FeAsS + 11Fe(III) → 12Fe(II) + As(III) + S(VI) (1)FeAsS + 5Fe(III) → As(III) + 6Fe(II) + S(0) (2)Previous efforts to characterize the arsenopyrite surface by scanning electron microscopy (SEM) after leaching reactions with ferric iron found no evidence of elemental sulfur on the mineral surface.[5,7] Other studies, using X-ray photoelectron spectroscopy (XPS), did not detect elemental sulfur on arsenopyrite surfaces that were exposed to mine wastewaters.[1]In contrast, Raman spect
EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
Christopher S Miller, Brett J Baker, Brian C Thomas, Steven W Singer, Jillian F Banfield
Genome Biology , 2011, DOI: 10.1186/gb-2011-12-5-r44
Abstract: Characterization of microbial community composition is most often done with a phylogenetic marker gene, most commonly the small subunit ribosomal RNA (SSU rRNA) gene [1]. Traditionally, rRNA sequences were generated by amplification, cloning, and Sanger sequencing. More recently, technologies such as pyrotag sequencing of short hyper-variable regions [2,3], Illumina sequencing of variable tags [4-7], and hybridization to specialized high-density microarrays (for example, Phylochip) [8-10] have accelerated the throughput of SSU-based microbial community characterization. Although each method has limitations, these high-throughput approaches have been broadly adopted, and have provided new understanding of microbial community composition from a wide range of environments[8,11,12]. Complementing these approaches are growing databases of SSU sequences from both isolates and environmental samples [13-15] that provide a rich phylogenetic and ecological context.Searching for SSU genes directly in metagenomic data avoids PCR and primer biases [16,17]. For example, novel deeply branching archaea with unusual 16S rRNA gene sequences were recently detected through metagenomic sequencing [18]. These divergent sequences were not recovered by methods that relied on amplification with standard SSU primers.Most reported metagenomic sequencing has used Sanger or Roche 454 sequencing technologies. The rRNA gene sequences for closely related organisms in these datasets co-assemble. The result is a composite sequence that is not representative of any community member and obscures the real level of diversity. These problems are exacerbated when shorter sequencing reads are used. Typical reads from the Illumina platform currently range from 35 to 125 bp. Additionally, the k-mer-based methods used to assemble short read data can further confound de novo assembly near regions with high inter-species sequence identity, such as that found within the SSU gene. Because of these challenges, the
Special phase transformation and crystal growth pathways observed in nanoparticles?
Benjamin Gilbert, Hengzhong Zhang, Feng Huang, Michael P Finnegan, Glenn A Waychunas, Jillian F Banfield
Geochemical Transactions , 2003, DOI: 10.1186/1467-4866-4-20
Abstract: The transformation of structure between stable or metastable phases reveals basic thermodynamical information about the state of matter. Consequently, investigations into the phase stability of nanoparticles have given some of the clearest demonstrations of the differences between nanoscale and bulk material of the same stoichiometry. For example, a reversal in phase stability at small particle size is observed in some systems; [1-4] melting temperatures are generally lower in nanoparticles;[5] transition temperatures to high temperature phases are often lower,[6] while transition pressures to high pressure phases can be higher [7-9] or lower.[10]By now, it is clear that the phase diagrams for materials can be size dependent.[11] Using the concepts of classical thermodynamics, observed size dependencies can be associated with the large surface area present in nanoscale materials. In particular, the excess energy of a nanoparticles relative to that of the bulk material (normalized by the surface area) is defined as the surface energy (usually in J m-2). Many of the observed data can be explained once surface energy contributions are considered. Yet, this quantity is difficult to measure accurately, and depends on the details of both surface and interior structure. The excess energy need not be confined to the surface: the effect of finite size on interior structure is currently a topic of interest.[12,13]In the field of nanoscience, it is generally difficult to translate specific experimental observations and thermodynamic principles into a precise quantitative theory of energy and structure. Structural and thermodynamic experiments are complicated by the fact that nanoparticles are metastable with respect to macroscopic crystals: ultimately, extremes of temperature or pressure, and aggregation, will lead to coarsening. An additional consideration is that conditions on both sides of the nanoparticle/environment interface are significant.In this review, we show how cl
Acid mine drainage biogeochemistry at Iron Mountain, California
Gregory K Druschel, Brett J Baker, Thomas M Gihring, Jillian F Banfield
Geochemical Transactions , 2004, DOI: 10.1186/1467-4866-5-13
Abstract: The enhanced oxidation of sulfide minerals principally pyrite (FeS2), by mining activities is a worldwide problem of significant environmental interest because it leads to the generation of acidic, metal-rich waters. The Richmond Mine, at Iron Mountain in northern California, USA, represents a rare opportunity to study the processes of acid mine drainage underground within an actively oxidizing pyritic body. Where many AMD sites are characterized by precipitation of iron oxyhydroxides, this site is characterized by the dissolved chemical species resulting from microbial pyrite oxidation. Specifically, this field site permits investigation of chemical and microbial factors important in the oxidation reactions that form acidic mine drainage isolated from the part of the system where precipitation of secondary oxyhydroxides occurs. An access tunnel intersects four mine tunnels within the Richmond ore deposit at a junction referred to as the "5-way" (Fig. 1). Essentially all solutions draining from the mine are collected at the 5-way, making it possible to determine and monitor the flux of metals and sulfur from the system. Previous studies of the geology, water chemistry, and microbial communities in the vicinity of the 5-way [1-5] provide the basis for ongoing work at the site.Iron Mountain is located approximately 9 miles northwest of the city of Redding, California (Fig. 1). Access to the Richmond Mine is provided by a 430 m long horizontal access tunnel that is maintained as part of the United States Government Superfund program remediation effort. The area of the 5-way is located at the edge of the main body of the Richmond deposit, a large, lenticular body that was originally over 800 m long, 60 m wide, and 60 m thick. The body contains approximately 90–95% pyrite (FeS2), locally enriched with ore minerals. The mine is within a Kuroko-type volcanogenic massive sulfide deposit that contains chalcopyrite (CuFeS2), sphalerite (ZnS), galena (PbS), bornite (Cu5FeS4),
Strainer: software for analysis of population variation in community genomic datasets
John M Eppley, Gene W Tyson, Wayne M Getz, Jillian F Banfield
BMC Bioinformatics , 2007, DOI: 10.1186/1471-2105-8-398
Abstract: We have developed a software package for analysis and visualization of genetic variation in populations and reconstruction of strain variants from otherwise co-assembled sequences. Sequencing reads can be clustered by matching patterns of single nucleotide polymorphisms to generate predicted gene and protein variant sequences, identify conserved intergenic regulatory sequences, and determine the quantity and distribution of recombination events.The Strainer software, a first generation metagenomic bioinformatics tool, facilitates comprehension and analysis of heterogeneity intrinsic in natural communities. The program reveals the degree of clustering among closely related sequence variants and provides a rapid means to generate gene and protein sequences for functional, ecological, and evolutionary analyses.With increased computational power and refinements in methods for 'shotgun' sequencing, researchers are eschewing clonal cultures in favor of sequencing microbial genomes directly from environmental samples [1-4]. This approach has the potential to revolutionize microbiology by moving beyond cultivation-based studies. Emerging techniques enable analyses of genes from uncultivated microorganisms [5-7] and genomic studies of the diversity inherent in natural populations.The term "metagenomics" has been used broadly to encompass research ranging from cloning environmental DNA for functional screening and drug discovery [8,9] to random sampling of genes from a small subset of organisms present in an environment [3]. Some metagenomic studies aim to reconstruct the majority of genomes of the dominant organisms in microbial communities ("community genomics"). Due to current sequencing costs, near complete genome reconstruction is only possible for the dominant members of communities with a small number of organism types (e.g., AMD communities, [1]) and for a few highly abundant organisms from diverse communities (e.g., wastewater [10]). However, it is inevitable that de
Improved genome annotation through untargeted detection of pathway-specific metabolites
Bowen Benjamin P,Fischer Curt R,Baran Richard,Banfield Jillian F
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-s1-s6
Abstract: Background Mass spectrometry-based metabolomics analyses have the potential to complement sequence-based methods of genome annotation, but only if raw mass spectral data can be linked to specific metabolic pathways. In untargeted metabolomics, the measured mass of a detected compound is used to define the location of the compound in chemical space, but uncertainties in mass measurements lead to "degeneracies" in chemical space since multiple chemical formulae correspond to the same measured mass. We compare two methods to eliminate these degeneracies. One method relies on natural isotopic abundances, and the other relies on the use of stable-isotope labeling (SIL) to directly determine C and N atom counts. Both depend on combinatorial explorations of the "chemical space" comprised of all possible chemical formulae comprised of biologically relevant chemical elements. Results Of 1532 metabolic pathways curated in the MetaCyc database, 412 contain a metabolite having a chemical formula unique to that metabolic pathway. Thus, chemical formulae alone can suffice to infer the presence of some metabolic pathways. Of 248,928 unique chemical formulae selected from the PubChem database, more than 95% had at least one degeneracy on the basis of accurate mass information alone. Consideration of natural isotopic abundance reduced degeneracy to 64%, but mainly for formulae less than 500 Da in molecular weight, and only if the error in the relative isotopic peak intensity was less than 10%. Knowledge of exact C and N atom counts as determined by SIL enabled reduced degeneracy, allowing for determination of unique chemical formula for 55% of the PubChem formulae. Conclusions To facilitate the assignment of chemical formulae to unknown mass-spectral features, profiling can be performed on cultures uniformly labeled with stable isotopes of nitrogen (15N) or carbon (13C). This makes it possible to accurately count the number of carbon and nitrogen atoms in each molecule, providing a robust means for reducing the degeneracy of chemical space and thus obtaining unique chemical formulae for features measured in untargeted metabolomics having a mass greater than 500 Da, with relative errors in measured isotopic peak intensity greater than 10%, and without the use of a chemical formula generator dependent on heuristic filtering. These chemical formulae can serve as indicators for the presence of particular metabolic pathways.
Assembly-Driven Community Genomics of a Hypersaline Microbial Ecosystem
Sheila Podell, Juan A. Ugalde, Priya Narasingarao, Jillian F. Banfield, Karla B. Heidelberg, Eric E. Allen
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0061692
Abstract: Microbial populations inhabiting a natural hypersaline lake ecosystem in Lake Tyrrell, Victoria, Australia, have been characterized using deep metagenomic sampling, iterative de novo assembly, and multidimensional phylogenetic binning. Composite genomes representing habitat-specific microbial populations were reconstructed for eleven different archaea and one bacterium, comprising between 0.6 and 14.1% of the planktonic community. Eight of the eleven archaeal genomes were from microbial species without previously cultured representatives. These new genomes provide habitat-specific reference sequences enabling detailed, lineage-specific compartmentalization of predicted functional capabilities and cellular properties associated with both dominant and less abundant community members, including organisms previously known only by their 16S rRNA sequences. Together, these data provide a comprehensive, culture-independent genomic blueprint for ecosystem-wide analysis of protein functions, population structure, and lifestyles of co-existing, co-evolving microbial groups within the same natural habitat. The “assembly-driven” community genomic approach demonstrated in this study advances our ability to push beyond single gene investigations, and promotes genome-scale reconstructions as a tangible goal in the quest to define the metabolic, ecological, and evolutionary dynamics that underpin environmental microbial diversity.
Population Genomic Analysis of Strain Variation in Leptospirillum Group II Bacteria Involved in Acid Mine Drainage Formation
Sheri L. Simmons,Genevieve DiBartolo,Vincent J. Denef,Daniela S. Aliaga Goltsman,Michael P. Thelen,Jillian F. Banfield
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.0060177
Abstract: Deeply sampled community genomic (metagenomic) datasets enable comprehensive analysis of heterogeneity in natural microbial populations. In this study, we used sequence data obtained from the dominant member of a low-diversity natural chemoautotrophic microbial community to determine how coexisting closely related individuals differ from each other in terms of gene sequence and gene content, and to uncover evidence of evolutionary processes that occur over short timescales. DNA sequence obtained from an acid mine drainage biofilm was reconstructed, taking into account the effects of strain variation, to generate a nearly complete genome tiling path for a Leptospirillum group II species closely related to L. ferriphilum (sampling depth ~20×). The population is dominated by one sequence type, yet we detected evidence for relatively abundant variants (>99.5% sequence identity to the dominant type) at multiple loci, and a few rare variants. Blocks of other Leptospirillum group II types (~94% sequence identity) have recombined into one or more variants. Variant blocks of both types are more numerous near the origin of replication. Heterogeneity in genetic potential within the population arises from localized variation in gene content, typically focused in integrated plasmid/phage-like regions. Some laterally transferred gene blocks encode physiologically important genes, including quorum-sensing genes of the LuxIR system. Overall, results suggest inter- and intrapopulation genetic exchange involving distinct parental genome types and implicate gain and loss of phage and plasmid genes in recent evolution of this Leptospirillum group II population. Population genetic analyses of single nucleotide polymorphisms indicate variation between closely related strains is not maintained by positive selection, suggesting that these regions do not represent adaptive differences between strains. Thus, the most likely explanation for the observed patterns of polymorphism is divergence of ancestral strains due to geographic isolation, followed by mixing and subsequent recombination.
Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments
Christopher S. Miller, Kim M. Handley, Kelly C. Wrighton, Kyle R. Frischkorn, Brian C. Thomas, Jillian F. Banfield
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0056018
Abstract: In microbial ecology, a fundamental question relates to how community diversity and composition change in response to perturbation. Most studies have had limited ability to deeply sample community structure (e.g. Sanger-sequenced 16S rRNA libraries), or have had limited taxonomic resolution (e.g. studies based on 16S rRNA hypervariable region sequencing). Here, we combine the higher taxonomic resolution of near-full-length 16S rRNA gene amplicons with the economics and sensitivity of short-read sequencing to assay the abundance and identity of organisms that represent as little as 0.01% of sediment bacterial communities. We used a new version of EMIRGE optimized for large data size to reconstruct near-full-length 16S rRNA genes from amplicons sheared and sequenced with Illumina technology. The approach allowed us to differentiate the community composition among samples acquired before perturbation, after acetate amendment shifted the predominant metabolism to iron reduction, and once sulfate reduction began. Results were highly reproducible across technical replicates, and identified specific taxa that responded to the perturbation. All samples contain very high alpha diversity and abundant organisms from phyla without cultivated representatives. Surprisingly, at the time points measured, there was no strong loss of evenness, despite the selective pressure of acetate amendment and change in the terminal electron accepting process. However, community membership was altered significantly. The method allows for sensitive, accurate profiling of the “long tail” of low abundance organisms that exist in many microbial communities, and can resolve population dynamics in response to environmental change.
Virus-Host and CRISPR Dynamics in Archaea-Dominated Hypersaline Lake Tyrrell, Victoria, Australia
Joanne B. Emerson,Karen Andrade,Brian C. Thomas,Anders Norman,Eric E. Allen,Karla B. Heidelberg,Jillian F. Banfield
Archaea , 2013, DOI: 10.1155/2013/370871
Abstract: The study of natural archaeal assemblages requires community context, namely, a concurrent assessment of the dynamics of archaeal, bacterial, and viral populations. Here, we use filter size-resolved metagenomic analyses to report the dynamics of 101 archaeal and bacterial OTUs and 140 viral populations across 17 samples collected over different timescales from 2007–2010 from Australian hypersaline Lake Tyrrell (LT). All samples were dominated by Archaea (75–95%). Archaeal, bacterial, and viral populations were found to be dynamic on timescales of months to years, and different viral assemblages were present in planktonic, relative to host-associated (active and provirus) size fractions. Analyses of clustered regularly interspaced short palindromic repeat (CRISPR) regions indicate that both rare and abundant viruses were targeted, primarily by lower abundance hosts. Although very few spacers had hits to the NCBI nr database or to the 140 LT viral populations, 21% had hits to unassembled LT viral concentrate reads. This suggests local adaptation to LT-specific viruses and/or undersampling of haloviral assemblages in public databases, along with successful CRISPR-mediated maintenance of viral populations at abundances low enough to preclude genomic assembly. This is the first metagenomic report evaluating widespread archaeal dynamics at the population level on short timescales in a hypersaline system. 1. Introduction As the most abundant and ubiquitous biological entities, viruses influence host mortality and community structure, food web dynamics, and geochemical cycles [1, 2]. In order to better characterize the potential influence that viruses have on archaeal evolution and ecology, it is important to understand the coupled dynamics of viruses and their archaeal hosts in natural systems. Although previous studies have demonstrated dynamics in virus-host populations, most of these studies have focused on bacterial hosts, often restricted to targeted groups of virus-host pairs, and little is known about archaeal virus-host dynamics in natural systems. Community-scale virus-host analyses have often been based on low-resolution measurements of the whole community, relying on techniques such as denaturing gradient gel electrophoresis (DGGE), pulsed-field gel electrophoresis (PFGE), and microscopic counts (e.g., [3–5]). One exception is a study that examined viral and microbial dynamics through single read-based metagenomic analyses in four aquatic environments, including an archaea-dominated hypersaline crystallizer pond [6]. In that work, it was proposed
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