scholarly journals FeGenie: a comprehensive tool for the identification of iron genes and iron gene neighborhoods in genomes and metagenome assemblies

2019 ◽  
Author(s):  
Arkadiy I. Garber ◽  
Kenneth H. Nealson ◽  
Akihiro Okamoto ◽  
Sean M. McAllister ◽  
Clara S. Chan ◽  
...  
Keyword(s):  
Genetic Markers ◽  
Iron Reduction ◽  
Markov Models ◽  
Sequence Data ◽  
Iron Acquisition ◽  
Iron Oxidation ◽  
Gene Clusters ◽  
Dissimilatory Iron Reduction ◽  
And Function ◽  
Life On Earth

AbstractIron is a micronutrient for nearly all life on Earth. It can be used as an electron donor and electron acceptor by iron-oxidizing and iron-reducing microorganisms, and is used in a variety of biological processes, including photosynthesis and respiration. While it is the fourth most abundant metal in the Earth’s crust, iron is often limiting for growth in oxic environments because it is readily oxidized and precipitated. Much of our understanding of how microorganisms compete for and utilize iron is based on laboratory experiments. However, the advent of next-generation sequencing and the associated surge in publicly-available sequence data has now made it possible to probe the structure and function of microbial communities in the environment. To bridge the gap between our understanding of iron acquisition and utilization in model microorganisms and the plethora of sequence data available from environmental studies, we have created a comprehensive database of hidden Markov models (HMMs) that is based on genes related to iron acquisition, storage, and reduction/oxidation. Along with this database, we present FeGenie, a bioinformatics tool that accepts genome and metagenome assemblies as input and uses our comprehensive HMM database to annotate the provided datasets with respect to iron-related genes and gene clusters. An important contribution of this tool is the efficient identification of genes involved in iron oxidation and dissimilatory iron reduction, which have been largely overlooked by standard annotation pipelines. While this tool will not replace the reliability of culture-dependent analyses of microbial physiology, it provides reliable predictions derived from the most up-to-date genetic markers. FeGenie’s database will be maintained and continually-updated as new genetic markers are discovered. FeGenie is freely available: https://github.com/Arkadiy-Garber/FeGenie.

scholarly journals Ferric Iron Reduction in Extreme Acidophiles

2022 ◽  
Vol 12 ◽  
Author(s):  
Luise Malik ◽  
Sabrina Hedrich
Keyword(s):  
Iron Reduction ◽  
Ferric Iron ◽  
Hydrogen Oxidation ◽  
Iron Oxidation ◽  
Minor Role ◽  
Microbial Conversion ◽  
Dissimilatory Iron Reduction ◽  
Alternative Scenarios ◽  
A Minor ◽  
Life On Earth

Biochemical processes are a key element of natural cycles occurring in the environment and enabling life on earth. With regard to microbially catalyzed iron transformation, research predominantly has focused on iron oxidation in acidophiles, whereas iron reduction played a minor role. Microbial conversion of ferric to ferrous iron has however become more relevant in recent years. While there are several reviews on neutrophilic iron reducers, this article summarizes the research on extreme acidophilic iron reducers. After the first reports of dissimilatory iron reduction by acidophilic, chemolithoautotrophic Acidithiobacillus strains and heterotrophic Acidiphilium species, many other prokaryotes were shown to reduce iron as part of their metabolism. Still, little is known about the exact mechanisms of iron reduction in extreme acidophiles. Initially, hypotheses and postulations for the occurring mechanisms relied on observations of growth behavior or predictions based on the genome. By comparing genomes of well-studied neutrophilic with acidophilic iron reducers (e.g., Ferroglobus placidus and Sulfolobus spp.), it became clear that the electron transport for iron reduction proceeds differently in acidophiles. Moreover, transcriptomic investigations indicated an enzymatically-mediated process in Acidithiobacillus ferrooxidans using respiratory chain components of the iron oxidation in reverse. Depending on the strain of At. ferrooxidans, further mechanisms were postulated, e.g., indirect iron reduction by hydrogen sulfide, which may form by disproportionation of elemental sulfur. Alternative scenarios include Hip, a high potential iron-sulfur protein, and further cytochromes. Apart from the anaerobic iron reduction mechanisms, sulfur-oxidizing acidithiobacilli have been shown to mediate iron reduction at low pH (< 1.3) under aerobic conditions. This presumably non-enzymatic process may be attributed to intermediates formed during sulfur/tetrathionate and/or hydrogen oxidation and has already been successfully applied for the reductive bioleaching of laterites. The aim of this review is to provide an up-to-date overview on ferric iron reduction by acidophiles. The importance of this process in anaerobic habitats will be demonstrated as well as its potential for application.

scholarly journals Millions of Boreal Shield Lakes can be used to Probe Archaean Ocean Biogeochemistry

2016 ◽  
Author(s):  
S. L. Schiff ◽  
J. M. Tsuji ◽  
L. Wu ◽  
J. J. Venkiteswaran ◽  
L. A. Molot ◽  
...  
Keyword(s):  
Water Column ◽  
Iron Reduction ◽  
Sequence Data ◽  
Iron Oxidation ◽  
Boreal Lakes ◽  
Early Earth ◽  
Banded Iron Formations ◽  
Stratified Lakes ◽  
Boreal Shield ◽  
Shield Lakes

AbstractLife originated in Archaean oceans, almost 4 billion years ago, in the absence of oxygen and the presence of high dissolved iron concentrations. Early Earth oxidation is marked globally by extensive banded iron formations but the contributing processes and timing remain controversial. Very few aquatic habitats have been discovered that match key physico-chemical parameters of the early Archaean Ocean. All previous whole ecosystem Archaean analogue studies have been confined to rare, low sulfur, and permanently stratified lakes. Here we provide first evidence that millions of Boreal Shield lakes with natural anoxia offer the opportunity to constrain biogeochemical and microbiological aspects of early Archaean life. Specifically, we combined novel isotopic signatures and nucleic acid sequence data to examine processes in the anoxic zone of stratified boreal lakes that are naturally low in sulfur and rich in ferrous iron, hallmark characteristics predicted for the Archaean Ocean. Anoxygenic photosynthesis was prominent in total water column biogeochemistry, marked by distinctive patterns in natural abundance isotopes of carbon, nitrogen, and iron. These processes are robust, returning reproducibly after water column re-oxygenation following lake turnover. Evidence of coupled iron oxidation, iron reduction, and methane oxidation affect current paradigms of both early Earth and modern aquatic ecosystems.

scholarly journals Metagenomic Insights Into the Microbial Iron Cycle of Subseafloor Habitats

2021 ◽  
Vol 12 ◽  
Author(s):  
Arkadiy I. Garber ◽  
Ashley B. Cohen ◽  
Kenneth H. Nealson ◽  
Gustavo A. Ramírez ◽  
Roman A. Barco ◽  
...  
Keyword(s):  
Iron Reduction ◽  
Gene Annotation ◽  
Ecological Impact ◽  
Iron Oxidation ◽  
Experimental Studies ◽  
Nutrient Status ◽  
Adsorptive Capacity ◽  
Iron Cycling ◽  
Iron Cycle ◽  
Dissimilatory Iron Reduction

Microbial iron cycling influences the flux of major nutrients in the environment (e.g., through the adsorptive capacity of iron oxides) and includes biotically induced iron oxidation and reduction processes. The ecological extent of microbial iron cycling is not well understood, even with increased sequencing efforts, in part due to limitations in gene annotation pipelines and limitations in experimental studies linking phenotype to genotype. This is particularly true for the marine subseafloor, which remains undersampled, but represents the largest contiguous habitat on Earth. To address this limitation, we used FeGenie, a database and bioinformatics tool that identifies microbial iron cycling genes and enables the development of testable hypotheses on the biogeochemical cycling of iron. Herein, we survey the microbial iron cycle in diverse subseafloor habitats, including sediment-buried crustal aquifers, as well as surficial and deep sediments. We inferred the genetic potential for iron redox cycling in 32 of the 46 metagenomes included in our analysis, demonstrating the prevalence of these activities across underexplored subseafloor ecosystems. We show that while some processes (e.g., iron uptake and storage, siderophore transport potential, and iron gene regulation) are near-universal, others (e.g., iron reduction/oxidation, siderophore synthesis, and magnetosome formation) are dependent on local redox and nutrient status. Additionally, we detected niche-specific differences in strategies used for dissimilatory iron reduction, suggesting that geochemical constraints likely play an important role in dictating the dominant mechanisms for iron cycling. Overall, our survey advances the known distribution, magnitude, and potential ecological impact of microbe-mediated iron cycling and utilization in sub-benthic ecosystems.

scholarly journals The Serratia marcescens Siderophore Serratiochelin Is Necessary for Full Virulence during Bloodstream Infection

2020 ◽  
Vol 88 (8) ◽  
Author(s):  
Danelle R. Weakland ◽  
Sara N. Smith ◽  
Bailey Bell ◽  
Ashootosh Tripathi ◽  
Harry L. T. Mobley
Keyword(s):  
Serratia Marcescens ◽  
Bloodstream Infection ◽  
Iron Acquisition ◽  
Gene Clusters ◽  
Clinical Isolates ◽  
Wild Type ◽  
Serratia Plymuthica ◽  
Content Type ◽  
Cas Assay ◽  
Essential Nutrient

ABSTRACT Serratia marcescens is a bacterium frequently found in the environment, but over the last several decades it has evolved into a concerning clinical pathogen, causing fatal bacteremia. To establish such infections, pathogens require specific nutrients; one very limited but essential nutrient is iron. We sought to characterize the iron acquisition systems in S. marcescens isolate UMH9, which was recovered from a clinical bloodstream infection. Using RNA sequencing (RNA-seq), we identified two predicted siderophore gene clusters (cbs and sch) that were regulated by iron. Mutants were constructed to delete each iron acquisition locus individually and in conjunction, generating both single and double mutants for the putative siderophore systems. Mutants lacking the sch gene cluster lost their iron-chelating ability as quantified by the chrome azurol S (CAS) assay, whereas the cbs mutant retained wild-type activity. Mass spectrometry-based analysis identified the chelating siderophore to be serratiochelin, a siderophore previously identified in Serratia plymuthica. Serratiochelin-producing mutants also displayed a decreased growth rate under iron-limited conditions created by dipyridyl added to LB medium. Additionally, mutants lacking serratiochelin were significantly outcompeted during cochallenge with wild-type UMH9 in the kidneys and spleen after inoculation via the tail vein in a bacteremia mouse model. This result was further confirmed by an independent challenge, suggesting that serratiochelin is required for full S. marcescens pathogenesis in the bloodstream. Nine other clinical isolates have at least 90% protein identity to the UMH9 serratiochelin system; therefore, our results are broadly applicable to emerging clinical isolates of S. marcescens causing bacteremia.

Biological iron oxidation-reduction and the effects on sulfur oxidation-reduction, denitrification and poly-P accumulation in an anaerobic-oxic activated sludge

2002 ◽  
Vol 46 (1-2) ◽  
pp. 55-60 ◽  
Author(s):  
R. Yamamoto-Ikemoto ◽  
T. Komori ◽  
S. Matsui
Keyword(s):  
Activated Sludge ◽  
Sulfate Reduction ◽  
Iron Reduction ◽  
Iron Oxidation ◽  
Sulfur Oxidation ◽  
Monod Equation ◽  
Oxidation Rates ◽  
Oxidation Reduction ◽  
Initial Iron ◽  
P Accumulation

Iron oxidation and reduction were examined using the activated sludge from a municipal plant. Iron contents of the activated sludge were 1–2%. Iron oxidation rates were correlated with the initial iron concentrations. Iron reducing rates could be described by the Monod equation. The effects of iron reducing bacteria on sulfate reduction, denitrification and poly-P accumulation were examined. Iron reduction suppressed sulfate reduction by competing with hydrogen produced from protein. Denitrification was outcompeted with iron reduction and sulfate reduction. These phenomena could be explained thermodynamically. Poly-P accumulation was also suppressed by denitrification. The activity of iron reduction was relatively high.

Fulvic Acid-Mediated Interfacial Reactions on Exposed Hematite Facets during Dissimilatory Iron Reduction

Langmuir ◽  
2021 ◽  
Author(s):  
Shiwen Hu ◽  
Yundang Wu ◽  
Fangbai Li ◽  
Zhenqing Shi ◽  
Chao Ma ◽  
...  
Keyword(s):  
Fulvic Acid ◽  
Iron Reduction ◽  
Interfacial Reactions ◽  
Dissimilatory Iron Reduction

scholarly journals Iron and Carbon Isotope Constraints on the Formation Pathway of Iron-Rich Carbonates within the Dagushan Iron Formation, North China Craton

Minerals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 94
Author(s):  
Xiaoxue Tong ◽  
Kaarel Mänd ◽  
Yuhao Li ◽  
Lianchang Zhang ◽  
Zidong Peng ◽  
...  
Keyword(s):  
Iron Reduction ◽  
Isotope Composition ◽  
Iron Formation ◽  
Banded Iron Formations ◽  
Organic C ◽  
Formation Pathway ◽  
Wide Range ◽  
Dissimilatory Iron Reduction ◽  
O Isotope ◽  
Iron Formations

Banded iron formations (BIFs) are enigmatic chemical sedimentary rocks that chronicle the geochemical and microbial cycling of iron and carbon in the Precambrian. However, the formation pathways of Fe carbonate, namely siderite, remain disputed. Here, we provide photomicrographs, Fe, C and O isotope of siderite, and organic C isotope of the whole rock from the ~2.52 Ga Dagushan BIF in the Anshan area, China, to discuss the origin of siderite. There are small magnetite grains that occur as inclusions within siderite, suggesting a diagenetic origin of the siderite. Moreover, the siderites have a wide range of iron isotope compositions (δ56FeSd) from −0.180‰ to +0.463‰, and a relatively negative C isotope composition (δ13CSd = −6.20‰ to −1.57‰). These results are compatible with the reduction of an Fe(III)-oxyhydroxide precursor to dissolved Fe(II) through microbial dissimilatory iron reduction (DIR) during early diagenesis. Partial reduction of the precursor and possible mixing with seawater Fe(II) could explain the presence of siderite with negative δ56Fe, while sustained reaction of residual Fe(III)-oxyhydroxide could have produced siderite with positive δ56Fe values. Bicarbonate derived from both DIR and seawater may have provided a C source for siderite formation. Our results suggest that microbial respiration played an important role in the formation of siderite in the late Archean Dagushan BIF.

Predicting Chromosome Flexibility from the Genomic Sequence Based on Deep Learning Neural Networks

2021 ◽  
Vol 16 ◽  
Author(s):  
Jinghao Peng ◽  
Jiajie Peng ◽  
Haiyin Piao ◽  
Zhang Luo ◽  
Kelin Xia ◽  
...  
Keyword(s):  
Deep Learning ◽  
High Performance ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Function Analysis ◽  
Double Helix ◽  
Gm12878 Cell ◽  
Genomic Sequence Analysis ◽  
And Function ◽  
Nuclear Processes

Background: The open and accessible regions of the chromosome are more likely to be bound by transcription factors which are important for nuclear processes and biological functions. Studying the change of chromosome flexibility can help to discover and analyze disease markers and improve the efficiency of clinical diagnosis. Current methods for predicting chromosome flexibility based on Hi-C data include the flexibility-rigidity index (FRI) and the Gaussian network model (GNM), which have been proposed to characterize chromosome flexibility. However, these methods require the chromosome structure data based on 3D biological experiments, which is time-consuming and expensive. Objective: Generally, the folding and curling of the double helix sequence of DNA have a great impact on chromosome flexibility and function. Motivated by the success of genomic sequence analysis in biomolecular function analysis, we hope to propose a method to predict chromosome flexibility only based on genomic sequence data. Method: We propose a new method (named "DeepCFP") using deep learning models to predict chromosome flexibility based on only genomic sequence features. The model has been tested in the GM12878 cell line. Results: The maximum accuracy of our model has reached 91%. The performance of DeepCFP is close to FRI and GNM. Conclusion: The DeepCFP can achieve high performance only based on genomic sequence.

scholarly journals Genomic and Functional Analysis of the IncP-9 Naphthalene-Catabolic Plasmid NAH7 and Its Transposon Tn4655 Suggests Catabolic Gene Spread by a Tyrosine Recombinase

2006 ◽  
Vol 188 (11) ◽  
pp. 4057-4067 ◽  
Author(s):  
Masahiro Sota ◽  
Hirokazu Yano ◽  
Akira Ono ◽  
Ryo Miyazaki ◽  
Hidenori Ishii ◽  
...  
Keyword(s):  
Sequence Data ◽  
Gene Clusters ◽  
Catabolic Gene ◽  
Genetic Determinants ◽  
Tyrosine Recombinase ◽  
Site Specific ◽  
Recombination System ◽  
Catabolic Plasmid ◽  
Transmissible Plasmid ◽  
Catabolic Plasmids

ABSTRACT The naphthalene-catabolic (nah) genes on the incompatibility group P-9 (IncP-9) self-transmissible plasmid NAH7 from Pseudomonas putida G7 are some of the most extensively characterized genetic determinants for bacterial aerobic catabolism of aromatic hydrocarbons. In contrast to the detailed studies of its catabolic cascade and enzymatic functions, the biological characteristics of plasmid NAH7 have remained unclear. Our sequence determination in this study together with the previously deposited sequences revealed the entire structure of NAH7 (82,232 bp). Comparison of NAH7 with two other completely sequenced IncP-9 catabolic plasmids, pDTG1 and pWW0, revealed that the three plasmids share very high nucleotide similarities in a 39-kb region encoding the basic plasmid functions (the IncP-9 backbone). The backbone of NAH7 is phylogenetically more related to that of pDTG1 than that of pWW0. These three plasmids carry their catabolic gene clusters at different positions on the IncP-9 backbone. All of the NAH7-specified nah genes are located on a class II transposon, Tn4655. Our analysis of the Tn4655-encoded site-specific recombination system revealed that (i) a novel tyrosine recombinase, TnpI, catalyzed both the intra- and intermolecular recombination between two copies of the attI site, (ii) the functional attI site was located within a 119-bp segment, and (iii) the site-specific strand exchange occurred within a 30-bp segment in the 41-bp CORE site. Our results and the sequence data of other naphthalene-catabolic plasmids, pDTG1 and pND6-1, suggest a potential role of the TnpI-attI recombination system in the establishment of these catabolic plasmids.

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