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 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 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.

The formation of marine red beds and iron cycling on the Mesoproterozoic North China Platform

2020 ◽  
Vol 105 (9) ◽  
pp. 1412-1423
Author(s):  
Dongjie Tang ◽  
Jianbai Ma ◽  
Xiaoying Shi ◽  
Maxwell Lechte ◽  
Xiqiang Zhou
Keyword(s):  
Water Column ◽  
Iron Reduction ◽  
North China ◽  
Iron Oxyhydroxide ◽  
Iron Cycling ◽  
Red Beds ◽  
Environmental Implications ◽  
North China Platform ◽  
The North ◽  
Dissimilatory Iron Reduction

Abstract Marine red beds (MRBs) are common in sedimentary records, but their genesis and environmental implications remain controversial. Genetic models proposed for MRBs variably invoke diagenetic or primary enrichments of iron, with vastly different implications for the redox state of the contemporaneous water column. The Xiamaling Formation (ca. 1.4 Ga) in the North China Platform hosts MRBs that offer insights into the iron cycling and redox conditions during the Mesoproterozoic Era. In the Xiamaling MRBs, well-preserved, nanometer-sized flaky hematite particles are randomly dispersed in the clay (illite) matrix, within the pressure shadow of rigid detrital grains. The presence of hematite flake aggregates with multiple face-to-edge (“cardhouse”) contacts indicates that the hematite particles were deposited as loosely bound, primary iron oxyhydroxide flocs. No greenalite or other ferrous iron precursor minerals have been identified in the MRBs. Early diagenetic ankerite concretions hosted in the MRBs show non-zero I/(Ca+Mg) values and positive Ce anomalies (>1.3), suggesting active redox cycling of iodine and manganese and therefore the presence of molecular oxygen in the porewater and likely in the water column during their formation. These observations support the hypothesis that iron oxyhydroxide precipitation occurred in moderately oxygenated marine waters above storm wave base (likely <100 m). Continentally sourced iron reactivated through microbial dissimilatory iron reduction, and distal hydrothermal fluids may have supplied Fe(II) for the iron oxyhydroxide precipitation. The accumulation of the Xiamaling MRBs may imply a slight increase of seawater oxygenation and the existence of long-lasting adjacent ferruginous water mass.

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.

scholarly journals A Systematic Review of Research Investigating the Combined Ecological Impact of Anthropogenic Noise and Artificial Light at Night

2021 ◽  
Vol 9 ◽  
Author(s):  
Wouter Halfwerk ◽  
Paul Jerem
Keyword(s):  
Systematic Review ◽  
Observational Studies ◽  
Ecological Impact ◽  
Experimental Studies ◽  
Ecological Impacts ◽  
Anthropogenic Noise ◽  
Light Pollution ◽  
Artificial Light ◽  
Light At Night ◽  
The Impact

Levels of anthropogenic noise and artificial light at night (ALAN) are rapidly rising on a global scale. Both sensory pollutants are well known to affect animal behavior and physiology, which can lead to substantial ecological impacts. Most studies on noise or light pollution to date have focused on single stressor impacts, studying both pollutants in isolation despite their high spatial and temporal co-occurrence. However, few studies have addressed their combined impact, known as multisensory pollution, with the specific aim to assess whether the interaction between noise and light pollution leads to predictable, additive effects, or less predictable, synergistic or antagonistic effects. We carried out a systematic review of research investigating multisensory pollution and found 28 studies that simultaneously assessed the impact of anthropogenic noise and ALAN on animal function (e.g., behavior, morphology or life-history), physiology (e.g., stress, oxidative, or immune status), or population demography (e.g., abundance or species richness). Only fifteen of these studies specifically tested for possible interactive effects when both sensory pollutants were combined. Four out of eight experimental studies revealed a significant interaction effect, in contrast to only three out seven observational studies. We discuss the benefits and limitations of experimental vs. observational studies addressing multisensory pollution and call for more specific testing of the diverse ways in which noise and light pollution can interact to affect wildlife.

scholarly journals Iron reduction from concentrates of hydrometallurgical dressing

2021 ◽  
Vol 64 (10) ◽  
pp. 728-735
Author(s):  
I. A. Rybenko ◽  
O. I. Nokhrina ◽  
I. D. Rozhikhina ◽  
M. A. Golodova ◽  
I. E. Khodosov
Keyword(s):  
Experimental Study ◽  
Thermal Decomposition ◽  
Thermodynamic Modeling ◽  
Iron Reduction ◽  
Solid Phase ◽  
Experimental Studies ◽  
Statistical Processing ◽  
Reducing Agent ◽  
Volatile Components ◽  
Software Complex

The article presents results of theoretical and experimental studies of the processes of iron solid-phase reduction from an iron-containing concentrate obtained as a result of hydrometallurgical dressing of ferromanganese and polymetallic manganese-containing ores with coals of grades D (long-flame) and 2B (brown). The method of thermodynamic modeling using TERRA software complex was used to study the reducing properties of hydrocarbons by calculating equilibrium compositions in the temperature range of 373 - 1873 K. The authors obtained the dependences of compositions and volume of the gas phase formed as a result of the release of volatile components during heating on the temperature for the coals of the grades under consideration. As a result of thermodynamic modeling, the optimal temperatures and consumption are determined, which ensure the complete iron reduction from an iron-containing concentrate. The results of experimental studies were obtained by modern research methods using laboratory and analytical equipment, as well as methods of statistical processing. Results of the coals analysis carried out using the Setaram LabSys Evo thermal analyzer showed that the process of thermal decomposition of coals of the studied grades proceeds according to general laws. The process of thermal decomposition of long-flame coal proceeds less intensively than of brown coal. The results of an experimental study of the processes of thermal decomposition of reducing agents have shown that volumes of the gas phases, formed when coals are heated to a temperature of 1173 K in an argon atmosphere, practically coincide with the calculated values. As a result of thermodynamic modeling and experimental study, the optimal consumption of D and 2B grades of coal is determined at a temperature of 1473 K. The best reducing agent with a minimum specific consumption is long-flame coal of D grade. When determining the optimal amount of reducing agent in charge mixtures during the study of metallization processes, it was found that with an excess of reducing agent, it is possible to achieve almost complete extraction (98 - 99 %) of iron from the concentrate.

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