Novel Pelagic Iron-Oxidizing Zetaproteobacteria from the Chesapeake Bay Oxic-Anoxic Transition Zone

Diversity and dynamics of bacteria from iron-rich microbial mats and colonizers in the Mediterranean Sea (EMSO-Western Ligurian Sea Observatory): Focus on Zetaproteobacteria

Autotrophic microaerophilic iron-oxidizing Zetaproteobacteria seem to play an important role in mineral weathering and metal corrosion in different environments. Here, we compare the bacterial and zetaproteobacterial communities of a mature iron-rich mat together with in situ incubations of different Fe-bearing materials at the EMSO-Ligure West seafloor observatory, which is located on the abyssal plain in the NW Mediterranean Sea. Our results on bacterial communities enable us to make a clear distinction between those growing on mild steel anthropic substrata and those developing on basaltic substrata. Moreover, on anthropic substrata we highlight an influence of mat age on the bacterial communities. Regarding zetaproteobacterial communities, our results point to an increase in ZetaOTUs abundance and diversification with the age of the mat. We corroborate the key role of the ZetaOTU 2 in mat construction, whatever the environment, the substrata on which they develop or the age of the mat. We also show that ZetaOTU 28 is specific to anthropogenic substrata. Finally, we demonstrate the advantage of using dPCR to precisely quantify very low abundant targets, as Zetaproteobacteria on our colonizers. Our study, also, allows to enrich our knowledge on the biogeography of Zetaproteobacteria, by adding new information on this class and their role in the Mediterranean Sea.

Comparative proteomics of a versatile, marine, iron-oxidizing chemolithoautotroph

This study conducted a comparative proteomic analysis to identify potential genetic markers for the biological function of chemolithoautotrophic iron oxidation in the marine bacterium Ghiorsea bivora. To date, this is the only characterized species in the class Zetaproteobacteria that is not an obligate iron-oxidizer, providing a unique opportunity to investigate differential protein expression to identify key genes involved in iron-oxidation at circumneutral pH. Over 1000 proteins were identified under both iron- and hydrogen-oxidizing conditions, with differentially expressed proteins found in both treatments. Notably, a gene cluster upregulated during iron oxidation was identified. This cluster contains genes encoding for cytochromes that share sequence similarity with the known iron-oxidase, Cyc2. Interestingly, these cytochromes, conserved in both Bacteria and Archaea, do not exhibit the typical β-barrel structure of Cyc2. This cluster potentially encodes a biological nanowire-like transmembrane complex containing multiple redox proteins spanning the inner membrane, periplasm, outer membrane, and extracellular space. The upregulation of key genes associated with this complex during iron-oxidizing conditions was confirmed by quantitative reverse transcription-PCR. These findings were further supported by electromicrobiological methods, which demonstrated negative current production by G. bivora in a three-electrode system poised at a cathodic potential. This research provides significant insights into the biological function of chemolithoautotrophic iron oxidation.

Ferriphaselus amnicola strain GF-20, a new iron- and thiosulfate-oxidizing bacterium isolated from a hard rock aquifer

Ferriphaselus amnicola GF-20 is the first Fe-oxidizing bacterium isolated from the continental subsurface. It was isolated from groundwater circulating at 20 m depth in the fractured-rock catchment observatory of Guidel-Ploemeur (France). Strain GF-20 is a neutrophilic, iron- and thiosulfate-oxidizer and grows autotrophically. The strain shows a preference for low oxygen concentrations, which suggests an adaptation to the limiting oxygen conditions of the subsurface. It produces extracellular stalks and dreads when grown with Fe(II) but does not secrete any structure when grown with thiosulfate. Phylogenetic analyses and genome comparisons revealed that strain GF-20 is affiliated with the species F. amnicola and is strikingly similar to F. amnicola strain OYT1, which was isolated from a groundwater seep in Japan. Based on the phenotypic and phylogenetic characteristics, we propose that GF-20 represents a new strain within the species F. amnicola.

Linking Zetaproteobacterial diversity and substratum type in iron-rich microbial mats from the Lucky Strike hydrothermal field (EMSO-Azores observatory)

Zetaproteobacteria have been reported in different marine and terrestrial environments all over the globe. They play an essential role in marine iron-rich microbial mats, as one of their autotrophic primary producers, oxidizing Fe(II) and producing Fe-oxyhydroxides with different morphologies. Here, we study and compare the Zetaproteobacterial communities of iron-rich microbial mats from six different sites of the Lucky Strike Hydrothermal Field through the use of the Zetaproteobacterial operational taxonomic unit (ZetaOTU) classification. We report for the first time the Zetaproteobacterial core microbiome of these iron-rich microbial mats, which is composed of four ZetaOTUs that are cosmopolitan and essential for the development of the mats. The study of the presence and abundance of different ZetaOTUs among sites reveals two clusters, which are related to the lithology and permeability of the substratum on which they develop. The Zetaproteobacterial communities of cluster 1 are characteristic of poorly permeable substrata, with little evidence of diffuse venting, while those of cluster 2 develop on hydrothermal slabs or deposits that allow the percolation and outflow of diffuse hydrothermal fluids. In addition, two NewZetaOTUs 1 and 2 were identified, which could be characteristic of anthropic iron and unsedimented basalt, respectively. We also report significant correlations between the abundance of certain ZetaOTUs and that of iron oxide morphologies, indicating that their formation could be taxonomically and/or environmentally driven. We identified a new morphology of Fe(III)-oxyhydroxides that we named "corals." Overall, our work contributes to the knowledge of the biogeography of this bacterial class by providing additional data from the Atlantic Ocean, a lesser-studied ocean in terms of Zetaproteobacterial diversity.IMPORTANCEUp until now, Zetaproteobacterial diversity studies have revealed possible links between Zetaproteobacteria taxa, habitats, and niches. Here, we report for the first time the Zetaproteobacterial core microbiome of iron-rich mats from the Lucky Strike Hydrothermal Field (LSHF), as well as two new Zetaproteobacterial operational taxonomic units (NewZetaOTUs) that could be substratum specific. We highlight that the substratum on which iron-rich microbial mats develop, especially because of its permeability to diffuse hydrothermal venting, has an influence on their Zetaproteobacterial communities. Moreover, our work adds to the knowledge of the biogeography of this bacterial class by providing additional data from the hydrothermal vent sites along the Mid-Atlantic Ridge. In addition to the already described iron oxide morphologies, we identify in our iron-rich mats a new morphology that we named corals. Finally, we argue for significant correlations between the relative abundance of certain ZetaOTUs and that of iron oxide morphologies, contributing to the understanding of the drivers of iron oxide production in iron-oxidizing bacteria.

Seafloor incubation experiments at deep-sea hydrothermal vents reveal distinct biogeographic signatures of autotrophic communities

The discharge of hydrothermal vents on the seafloor provides energy sources for dynamic and productive ecosystems, which are supported by chemosynthetic microbial populations. These populations use the energy gained by oxidizing the reduced chemicals contained within the vent fluids to fix carbon and support multiple trophic levels. Hydrothermal discharge is ephemeral and chemical composition of such fluids varies over space and time, which can result in geographically distinct microbial communities. To investigate the foundational members of the community, microbial growth chambers were placed within the hydrothermal discharge at Axial Seamount (Juan de Fuca Ridge), Magic Mountain Seamount (Explorer Ridge), and Kama'ehuakanaloa Seamount (Hawai'i hotspot). Campylobacteria were identified within the nascent communities, but different amplicon sequence variants were present at Axial and Kama'ehuakanaloa Seamounts, indicating that geography in addition to the composition of the vent effluent influences microbial community development. Across these vent locations, dissolved iron concentration was the strongest driver of community structure. These results provide insights into nascent microbial community structure and shed light on the development of diverse lithotrophic communities at hydrothermal vents.

Putative novel hydrogen- and iron-oxidizing sheath-producing Zetaproteobacteria thrive at the Fåvne deep-sea hydrothermal vent field

IMPORTANCE

Knowledge on microbial iron oxidation is important for understanding the cycling of iron, carbon, nitrogen, nutrients, and metals. The current study yields important insights into the niche sharing, diversification, and Fe(III) oxyhydroxide morphology of Ghiorsea, an iron- and hydrogen-oxidizing Zetaproteobacteria representative belonging to Zetaproteobacteria operational taxonomic unit 9. The study proposes that Ghiorsea exhibits a more extensive morphology of Fe(III) oxyhydroxide than previously observed. Overall, the results increase our knowledge on potential drivers of Zetaproteobacteria diversity in iron microbial mats and can eventually be used to develop strategies for the cultivation of sheath-forming Zetaproteobacteria.

Gallionellaceae in rice root plaque: metabolic roles in iron oxidation, nutrient cycling, and plant interactions

IMPORTANCE

In waterlogged soils, iron plaque forms a reactive barrier between the root and soil, collecting phosphate and metals such as arsenic and cadmium. It is well established that iron-reducing bacteria solubilize iron, releasing these associated elements. In contrast, microbial roles in plaque formation have not been clear. Here, we show that there is a substantial population of iron oxidizers in plaque, and furthermore, that these organisms (Sideroxydans and Gallionella) are distinguished by genes for plant colonization and nutrient fixation. Our results suggest that iron-oxidizing and iron-reducing bacteria form and remodel iron plaque, making it a dynamic system that represents both a temporary sink for elements (P, As, Cd, C, etc.) as well as a source. In contrast to abiotic iron oxidation, microbial iron oxidation results in coupled Fe-C-N cycling, as well as microbe-microbe and microbe-plant ecological interactions that need to be considered in soil biogeochemistry, ecosystem dynamics, and crop management.

Aerobic iron-oxidizing bacteria secrete metabolites that markedly impede abiotic iron oxidation

Iron is one of the Earth's most abundant elements and is required for essentially all forms of life. Yet, iron's reactivity with oxygen and poor solubility in its oxidized form (Fe3+) mean that it is often a limiting nutrient in oxic, near-neutral pH environments like Earth's ocean. In addition to being a vital nutrient, there is a diversity of aerobic organisms that oxidize ferrous iron (Fe2+) to harness energy for growth and biosynthesis. Accordingly, these organisms rely on access to co-existing Fe2+ and O2 to survive. It is generally presumed that such aerobic iron-oxidizing bacteria (FeOB) are relegated to low-oxygen regimes where abiotic iron oxidation rates are slower, yet some FeOB live in higher oxygen environments where they cannot rely on lower oxygen concentrations to overcome abiotic competition. We hypothesized that FeOB chemically alter their environment to limit abiotic interactions between Fe2+ and O2. To test this, we incubated the secreted metabolites (collectively known as the exometabolome) of the deep-sea iron- and hydrogen-oxidizing bacterium Ghiorsea bivora TAG-1 with ferrous iron and oxygen. We found that this FeOB's iron-oxidizing exometabolome markedly impedes the abiotic oxidation of ferrous iron, increasing the half-life of Fe2+ 100-fold from ∼3 to ∼335 days in the presence of O2, while the exometabolome of TAG-1 grown on hydrogen had no effect. Moreover, the few precipitates that formed in the presence of TAG-1's iron-oxidizing exometabolome were poorly crystalline, compared with the abundant iron particles that mineralized in the absence of abiotic controls. We offer an initial exploration of TAG-1's iron-oxidizing exometabolome and discuss potential key contributors to this process. Overall, our findings demonstrate that the exometabolome as a whole leads to a sustained accumulation of ferrous iron in the presence of oxygen, consequently altering the redox equilibrium. This previously unknown adaptation likely enables these microorganisms to persist in an iron-oxidizing and iron-precipitating world and could have impacts on the bioavailability of iron to FeOB and other life in iron-limiting environments.

Mapping the microbial diversity associated with different geochemical regimes in the shallow-water hydrothermal vents of the Aeolian archipelago, Italy

Shallow-water hydrothermal vents are unique marine environments ubiquitous along the coast of volcanically active regions of the planet. In contrast to their deep-sea counterparts, primary production at shallow-water vents relies on both photoautotrophy and chemoautotrophy. Such processes are supported by a range of geochemical regimes driven by different geological settings. The Aeolian archipelago, located in the southern Tyrrhenian sea, is characterized by intense hydrothermal activity and harbors some of the best sampled shallow-water vents of the Mediterranean Sea. Despite this, the correlation between microbial diversity, geochemical regimes and geological settings of the different volcanic islands of the archipelago is largely unknown. Here, we report the microbial diversity associated with six distinct shallow-water hydrothermal vents of the Aeolian Islands using a combination of 16S rRNA amplicon sequencing along with physicochemical and geochemical measurements. Samples were collected from biofilms, fluids and sediments from shallow vents on the islands of Lipari, Panarea, Salina, and Vulcano. Two new shallow vent locations are described here for the first time. Our results show the presence of diverse microbial communities consistent in their composition with the local geochemical regimes. The shallow water vents of the Aeolian Islands harbor highly diverse microbial community and should be included in future conservation efforts.

Proximity to built structures on the seabed promotes biofilm development and diversity

The rapidly expanding built environment in the northern Gulf of Mexico includes thousands of human built structures (e.g. platforms, shipwrecks) on the seabed. Primary-colonizing microbial biofilms transform structures into artificial reefs capable of supporting biodiversity, yet little is known about formation and recruitment of biofilms. Short-term seafloor experiments containing steel surfaces were placed near six structures, including historic shipwrecks and modern decommissioned energy platforms. Biofilms were analyzed for changes in phylogenetic composition, richness, and diversity relative to proximity to the structures. The biofilm core microbiome was primarily composed of iron-oxidizing Mariprofundus, sulfur-oxidizing Sulfurimonas, and biofilm-forming Rhodobacteraceae. Alpha diversity and richness significantly declined as a function of distance from structures. This study explores how built structures influence marine biofilms and contributes knowledge on how anthropogenic activity impacts microbiomes on the seabed.

Bioconversion of Glycerol to 1,3-Propanediol Using Klebsiella pneumoniae L17 with the Microbially Influenced Corrosion of Zero-Valent Iron

The bacterial redox state is essential for controlling the titer and yield of the final metabolites in most bioconversion processes. Glycerol conversion to 1,3-propanediol (PDO) requires a large amount of reducing equivalent and the expression of reductive pathways. Zero-valent iron (ZVI) was used in the glycerol bioconversion of Klebsiella pneumoniae L17. The level of 1,3-PDO production increased with the oxidation of ZVI (31.8 ± 1.2 vs. 25.7 ± 0.5, ZVI vs. no ZVI) while the cellular NADH/NAD+ level increased (0.6 vs. 0.3, ZVI vs. no ZVI). X-ray diffraction showed that the iron oxide (Fe2O3) was formed during glycerol fermentation. L17 obtained electrons from ZVI and dissolved the iron continuously to form cracks on the surface, suggesting microbially influenced corrosion (MIC) was involved on the surface of ZVI. The ZVI-implemented fermentation shifted bioconversion to a more glycerol-reductive pathway. The qPCR-presented glycerol dehydratase (DhaB) with ZVI implementation was strongly expressed compared to the control. These results suggest that ZVI can contribute to the biotransformation of PDO by inducing intracellular metabolic shifts. This study could also suggest a novel microbial fermentation strategy with the application of MIC.

Diversity of Mixotrophic Neutrophilic Thiosulfate- and Iron-Oxidizing Bacteria from Deep-Sea Hydrothermal Vents

At deep-sea hydrothermal vents, sulfur oxidation and iron oxidation are of the highest importance to microbial metabolisms, which are thought to contribute mainly in chemolithoautotrophic groups. In this study, 17 mixotrophic neutrophilic thiosulfate- and iron-oxidizing bacteria were isolated from hydrothermal fields on the Carlsberg Ridge in the Indian Ocean, nine to the γ-proteobacteria (Halomonas (4), Pseudomonas (2), Marinobacter (2), and Rheinheimera (1)), seven to the α-proteobacteria (Thalassospira, Qipengyuania, Salipiger, Seohaeicola, Martelella, Citromicrobium, and Aurantimonas), and one to the Actinobacteria (Agromyces), as determined by their 16S rRNA and genome sequences. The physiological characterization of these isolates revealed wide versatility in electron donors (Fe(II) and Mn(II), or thiosulfate) and a variety of lifestyles as lithotrophic or heterotrophic, microaerobic, or anaerobic. As a representative strain, Pseudomonas sp. IOP_13 showed its autotrophic gowth from 10⁵ cells/ml to 10⁷ cells/ml;carbon dioxide fixation capacity with the δ13C_VPDB in the biomass increased from -27.42‱ to 3460.06‱; the thiosulfate-oxidizing ability with produced SO₄^2- increased from 60 mg/L to 287 mg/L; and the iron-oxidizing ability with Fe(II) decreased from 10 mM to 5.2 mM. In addition, iron-oxide crust formed outside the cells. Gene coding for energy metabolism involved in possible iron, manganese, and sulfur oxidation, and denitrification was identified by their genome analysis. This study sheds light on the function of the mixotrophic microbial community in the iron/manganese/sulfur cycles and the carbon fixation of the hydrothermal fields.

Biodeterioration of stone and metal - Fundamental microbial cycling processes with spatial and temporal scale differences

Fundamental processes for the biodeterioration of stone and metal involve many of the same microbially mediated reactions - oxidation, reduction, acid dissolution and elemental cycling - resulting from the activities of many of the same groups of environmental microorganisms. Differences depend on the nature of the substratum - stone vs. metal - and the composition of the surroundings, whether terrestrial (stone) or aquatic (stone and metal). Reactions within surface-related biofilms dominate the biodeterioration of metals and contribute greatly to the biodeterioration of stone. In the latter, phototrophic organisms, and especially cyanobacteria, are important first participants, while metal biodeterioration is almost entirely associated with bacteria, archaea and fungi. Biofilms on metal surfaces can produce chemical and electrochemical responses. While electrochemical responses are absent in stone, extracellular electron transfer can be a biodeterioration mechanism in some iron-rich rocks. Microorganisms in biofilms can penetrate and create fissures or cracks in stone and metals. However, the most obvious differences in the reactions of built stone and metal structures are related to the definition of failure, length of time required for a defined failure of the substratum, the area over which the failure occurs and the consequences of failure. Time and space are, similarly, quite distinct for biological breakdown and mineral cycling of metal and stone, with stone/rock cycling potentially occurring over thousands of years and kilometers.

Oligo-heterotrophic Activity of Marinobacter subterrani Creates an Indirect Fe(II) Oxidation Phenotype in Gradient Tubes

Autotrophic bacteria utilizing Fe(II) as their energy and electron sources for growth affect multiple biogeochemical cycles. Some chemoheterotrophic bacteria have also been considered to exhibit an Fe(II) oxidation phenotype. For example, several Marinobacter strains have been reported to oxidize Fe(II) based on formation of oxidized iron bands in semi-solid gradient tubes that produce opposing concentration gradients of Fe(II) and oxygen. While gradient tubes are a simple and visually compelling method to test for Fe(II) oxidation, this method alone cannot confirm if, and to what extent, Fe(II) oxidation is linked to metabolism in chemoheterotrophic bacteria. Here we probe the possibility of protein-mediated and metabolic by-product-mediated Fe(II) oxidation in Marinobacter subterrani JG233, a chemoheterotroph previously proposed to oxidize Fe(II). Results from conditional and mutant studies, along with measurements of Fe(II) oxidation rates, suggest M. subterrani is unlikely to facilitate Fe(II) oxidation under microaerobic conditions. We conclude that the Fe(II) oxidation phenotype observed in gradient tubes inoculated with M. subterrani JG233 is a result of oligo-heterotrophic activity, shifting the location where oxygen dependent chemical Fe(II) oxidation occurs, rather than a biologically mediated process. IMPORTANCE Gradient tubes are the most commonly used method to isolate and identify neutrophilic Fe(II)-oxidizing bacteria. The formation of oxidized iron bands in gradient tubes provides a compelling assay to ascribe the ability to oxidize Fe(II) to autotrophic bacteria whose growth is dependent on Fe(II) oxidation. However, the physiological significance of Fe(II) oxidation in chemoheterotrophic bacteria is less well understood. Our work suggests that oligo-heterotrophic activity of certain bacteria may create a false-positive phenotype in gradient tubes by altering the location of the abiotic, oxygen-mediated oxidized iron band. Based on the results and analysis presented here, we caution against utilizing gradient tubes as the sole evidence for the capability of a strain to oxidize Fe(II) and that additional experiments are necessary to ascribe this phenotype to new isolates.

Metagenomic Insights Into the Microbial Iron Cycle of Subseafloor Habitats

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.

Iron Oxidation by a Fused Cytochrome-Porin Common to Diverse Iron-Oxidizing Bacteria

Iron (Fe) oxidation is one of Earth’s major biogeochemical processes, key to weathering, soil formation, water quality, and corrosion. However, our understanding of microbial contribution is limited by incomplete knowledge of microbial iron oxidation mechanisms, particularly in neutrophilic iron oxidizers. The genomes of many diverse iron oxidizers encode a homolog to an outer membrane cytochrome (Cyc2) shown to oxidize iron in two acidophiles. Phylogenetic analyses show Cyc2 sequences from neutrophiles cluster together, suggesting a common function, though this function has not been verified in these organisms. Therefore, we investigated the iron oxidase function of heterologously expressed Cyc2 from a neutrophilic iron oxidizer Mariprofundus ferrooxydans PV-1. Cyc2_PV-1 is capable of oxidizing iron, and its redox potential is 208 ± 20 mV, consistent with the ability to accept electrons from Fe²⁺ at neutral pH. These results support the hypothesis that Cyc2 functions as an iron oxidase in neutrophilic iron-oxidizing organisms. The results of sequence analysis and modeling reveal that the entire Cyc2 family shares a unique fused cytochrome-porin structure, with a defining consensus motif in the cytochrome region. On the basis of results from structural analyses, we predict that the monoheme cytochrome Cyc2 specifically oxidizes dissolved Fe²⁺, in contrast to multiheme iron oxidases, which may oxidize solid Fe(II). With our results, there is now functional validation for diverse representatives of Cyc2 sequences. We present a comprehensive Cyc2 phylogenetic tree and offer a roadmap for identifying cyc2/Cyc2 homologs and interpreting their function. The occurrence of cyc2 in many genomes beyond known iron oxidizers presents the possibility that microbial iron oxidation may be a widespread metabolism.

Fe(II) Redox Chemistry in the Environment

Iron (Fe) is the fourth most abundant element in the earth's crust and plays important roles in both biological and chemical processes. The redox reactivity of various Fe(II) forms has gained increasing attention over recent decades in the areas of (bio) geochemistry, environmental chemistry and engineering, and material sciences. The goal of this paper is to review these recent advances and the current state of knowledge of Fe(II) redox chemistry in the environment. Specifically, this comprehensive review focuses on the redox reactivity of four types of Fe(II) species including aqueous Fe(II), Fe(II) complexed with ligands, minerals bearing structural Fe(II), and sorbed Fe(II) on mineral oxide surfaces. The formation pathways, factors governing the reactivity, insights into potential mechanisms, reactivity comparison, and characterization techniques are discussed with reference to the most recent breakthroughs in this field where possible. We also cover the roles of these Fe(II) species in environmental applications of zerovalent iron, microbial processes, biogeochemical cycling of carbon and nutrients, and their abiotic oxidation related processes in natural and engineered systems.

Zetaproteobacteria Pan-Genome Reveals Candidate Gene Cluster for Twisted Stalk Biosynthesis and Export

Twisted stalks are morphologically unique bacterial extracellular organo-metallic structures containing Fe(III) oxyhydroxides that are produced by microaerophilic Fe(II)-oxidizers belonging to the Betaproteobacteria and Zetaproteobacteria. Understanding the underlying genetic and physiological mechanisms of stalk formation is of great interest based on their potential as novel biogenic nanomaterials and their relevance as putative biomarkers for microbial Fe(II) oxidation on ancient Earth. Despite the recognition of these special biominerals for over 150 years, the genetic foundation for the stalk phenotype has remained unresolved. Here we present a candidate gene cluster for the biosynthesis and secretion of the stalk organic matrix that we identified with a trait-based analyses of a pan-genome comprising 16 Zetaproteobacteria isolate genomes. The “stalk formation in Zetaproteobacteria” (sfz) cluster comprises six genes (sfz1-sfz6), of which sfz1 and sfz2 were predicted with functions in exopolysaccharide synthesis, regulation, and export, sfz4 and sfz6 with functions in cell wall synthesis manipulation and carbohydrate hydrolysis, and sfz3 and sfz5 with unknown functions. The stalk-forming Betaproteobacteria Ferriphaselus R-1 and OYT-1, as well as dread-forming Zetaproteobacteria Mariprofundus aestuarium CP-5 and Mariprofundus ferrinatatus CP-8 contain distant sfz gene homologs, whereas stalk-less Zetaproteobacteria and Betaproteobacteria lack the entire gene cluster. Our pan-genome analysis further revealed a significant enrichment of clusters of orthologous groups (COGs) across all Zetaproteobacteria isolate genomes that are associated with the regulation of a switch between sessile and motile growth controlled by the intracellular signaling molecule c-di-GMP. Potential interactions between stalk-former unique transcription factor genes, sfz genes, and c-di-GMP point toward a c-di-GMP regulated surface attachment function of stalks during sessile growth.

Orange leads to black: evaluating the efficacy of co-culturing iron-oxidizing and sulfate-reducing bacteria to discern ecological relationships

Two global cycles, iron and sulfur, are critically interconnected in estuarine environments by microbiological actors. To this point, the methods of laboratory study of this interaction have been limited. Here we propose a methodology for co-culturing from numerous coastal environments, from the same source inocula, iron-oxidizing and sulfate-reducing bacteria. The use of same source inocula is largely beneficial to understand real-world interactions that are likely occurring in situ. Through the use of this methodology, the ecological interactions between these groups can be studied in a more controlled environment. Here, we characterize the oxygen and hydrogen sulfide concentrations using microelectrode depth profiling in the co-cultures of iron-oxidizing bacteria and sulfate-reducing bacteria. These results suggest that while oxygen drives the relationship between these organisms and sulfate-reducers are reliant on iron-oxidizers in this culture to create an anoxic environment, there is likely another environmental driver that also influences the interaction as the two remain spatially distinct, as trends in FeS precipitation changed within the anoxic zone relative to the presence of Fe(III) oxyhydroxides. Understanding the relationship between iron-oxidizing and sulfate-reducing bacteria will ultimately have implications for understanding microbial cycling in estuarine environments as well as in processes such as controlling microbially influenced corrosion.

A late Paleoproterozoic (1.74 Ga) deep-sea, low-temperature, iron-oxidizing microbial hydrothermal vent community from Arizona, USA

Modern marine hydrothermal vents occur in a wide variety of tectonic settings and are characterized by seafloor emission of fluids rich in dissolved chemicals and rapid mineral precipitation. Some hydrothermal systems vent only low-temperature Fe-rich fluids, which precipitate deposits dominated by iron oxyhydroxides, in places together with Mn-oxyhydroxides and amorphous silica. While a proportion of this mineralization is abiogenic, most is the result of the metabolic activities of benthic, Fe-oxidizing bacteria (FeOB), principally belonging to the Zetaproteobacteria. These micro-organisms secrete micrometer-scale stalks, sheaths, and tubes with a variety of morphologies, composed largely of ferrihydrite that act as sacrificial structures, preventing encrustation of the cells that produce them. Cultivated marine FeOB generally require neutral pH and microaerobic conditions to grow. Here, we describe the morphology and mineralogy of filamentous microstructures from a late Paleoproterozoic (1.74 Ga) jasper (Fe-oxide-silica) deposit from the Jerome area of the Verde mining district in central Arizona, USA, that resemble the branching tubes formed by some modern marine FeOB. On the basis of this comparison, we interpret the Jerome area filaments as having formed by FeOB on the deep seafloor, at the interface of weakly oxygenated seawater and low-temperature Fe-rich hydrothermal fluids. We compare the Jerome area filaments with other purported examples of Precambrian FeOB and discuss the implications of their presence for existing redox models of Paleoproterozoic oceans during the "Boring Billion."

An evolving view on biogeochemical cycling of iron

Biogeochemical cycling of iron is crucial to many environmental processes, such as ocean productivity, carbon storage, greenhouse gas emissions and the fate of nutrients, toxic metals and metalloids. Knowledge of the underlying processes involved in iron cycling has accelerated in recent years along with appreciation of the complex network of biotic and abiotic reactions dictating the speciation, mobility and reactivity of iron in the environment. Recent studies have provided insights into novel processes in the biogeochemical iron cycle such as microbial ammonium oxidation and methane oxidation coupled to Fe(III) reduction. They have also revealed that processes in the biogeochemical iron cycle spatially overlap and may compete with each other, and that oxidation and reduction of iron occur cyclically or simultaneously in many environments. This Review discusses these advances with particular focus on their environmental consequences, including the formation of greenhouse gases and the fate of nutrients and contaminants.

Aerobic and anaerobic iron oxidizers together drive denitrification and carbon cycling at marine iron-rich hydrothermal vents

In principle, iron oxidation can fuel significant primary productivity and nutrient cycling in dark environments such as the deep sea. However, we have an extremely limited understanding of the ecology of iron-based ecosystems, and thus the linkages between iron oxidation, carbon cycling, and nitrate reduction. Here we investigate iron microbial mats from hydrothermal vents at Lōʻihi Seamount, Hawaiʻi, using genome-resolved metagenomics and metatranscriptomics to reconstruct potential microbial roles and interactions. Our results show that the aerobic iron-oxidizing Zetaproteobacteria are the primary producers, concentrated at the oxic mat surface. Their fixed carbon supports heterotrophs deeper in the mat, notably the second most abundant organism, Candidatus Ferristratum sp. (uncultivated gen. nov.) from the uncharacterized DTB120 phylum. Candidatus Ferristratum sp., described using nine high-quality metagenome-assembled genomes with similar distributions of genes, expressed nitrate reduction genes narGH and the iron oxidation gene cyc2 in situ and in response to Fe(II) in a shipboard incubation, suggesting it is an anaerobic nitrate-reducing iron oxidizer. Candidatus Ferristratum sp. lacks a full denitrification pathway, relying on Zetaproteobacteria to remove intermediates like nitrite. Thus, at Lōʻihi, anaerobic iron oxidizers coexist with and are dependent on aerobic iron oxidizers. In total, our work shows how key community members work together to connect iron oxidation with carbon and nitrogen cycling, thus driving the biogeochemistry of exported fluids.

Mixotrophic Iron-Oxidizing Thiomonas Isolates from an Acid Mine Drainage-Affected Creek

Natural attenuation of heavy metals occurs via coupled microbial iron cycling and metal precipitation in creeks impacted by acid mine drainage (AMD). Here, we describe the isolation, characterization, and genomic sequencing of two iron-oxidizing bacteria (FeOB) species: Thiomonas ferrovorans FB-6 and Thiomonas metallidurans FB-Cd, isolated from slightly acidic (pH 6.3), Fe-rich, AMD-impacted creek sediments. These strains precipitated amorphous iron oxides, lepidocrocite, goethite, and magnetite or maghemite and grew at a pH optimum of 5.5. While Thiomonas spp. are known as mixotrophic sulfur oxidizers and As oxidizers, the FB strains oxidized Fe, which suggests they can efficiently remove Fe and other metals via coprecipitation. Previous evidence for Thiomonas sp. Fe oxidation is largely ambiguous, possibly because of difficulty demonstrating Fe oxidation in heterotrophic/mixotrophic organisms. Therefore, we also conducted a genomic analysis to identify genetic mechanisms of Fe oxidation, other metal transformations, and additional adaptations, comparing the two FB strain genomes with 12 other Thiomonas genomes. The FB strains fall within a relatively novel group of Thiomonas strains that includes another strain (b6) with solid evidence of Fe oxidation. Most Thiomonas isolates, including the FB strains, have the putative iron oxidation gene cyc2, but only the two FB strains possess the putative Fe oxidase genes mtoAB The two FB strain genomes contain the highest numbers of strain-specific gene clusters, greatly increasing the known Thiomonas genetic potential. Our results revealed that the FB strains are two distinct novel species of Thiomonas with the genetic potential for bioremediation of AMD via iron oxidation.IMPORTANCE As AMD moves through the environment, it impacts aquatic ecosystems, but at the same time, these ecosystems can naturally attenuate contaminated waters via acid neutralization and catalyzing metal precipitation. This is the case in the former Ronneburg uranium-mining district, where AMD impacts creek sediments. We isolated and characterized two iron-oxidizing Thiomonas species that are mildly acidophilic to neutrophilic and that have two genetic pathways for iron oxidation. These Thiomonas species are well positioned to naturally attenuate AMD as it discharges across the landscape.

Using modern low-oxygen marine ecosystems to understand the nitrogen cycle of the Paleo- and Mesoproterozoic oceans

During the productive Paleoproterozoic (2.4-1.8 Ga) and less productive Mesoproterozoic (1.8-1.0 Ga), the ocean was suboxic to anoxic and multicellular organisms had not yet evolved. Here, we link geologic information about the Proterozoic ocean to microbial processes in modern low-oxygen systems. High iron concentrations and rates of Fe cycling in the Proterozoic are the largest differences from modern oxygen-deficient zones. In anoxic waters, which composed most of the Paleoproterozoic and ~40% of the Mesoproterozoic ocean, nitrogen cycling dominated. Rates of N₂ production by denitrification and anammox were likely linked to sinking organic matter fluxes and in situ primary productivity under anoxic conditions. Additionally autotrophic denitrifiers could have used reduced iron or methane. 50% of the Mesoproterozoic ocean may have been suboxic, promoting nitrification and metal oxidation in the suboxic water and N₂ O and N₂ production by partial and complete denitrification in anoxic zones in organic aggregates. Sulfidic conditions may have composed ~10% of the Mesoproterozoic ocean focused along continental margins. Due to low nitrate concentrations in offshore regions, anammox bacteria likely dominated N₂ production immediately above sulfidic zones, but in coastal regions, higher nitrate concentrations probably promoted complete S-oxidizing autotrophic denitrification at the sulfide interface.

A Shallow Water Ferrous-Hulled Shipwreck Reveals a Distinct Microbial Community

Shipwrecks act as artificial reefs and provide a solid surface in aquatic systems for many different forms of life to attach to, especially microbial communities, making them a hotspot of biogeochemical cycling. Depending on the microbial community and surrounding environment, they may either contribute to the wreck’s preservation or deterioration. Even within a single wreck, preservation and deterioration processes may vary, suggesting that the microbial community may also vary. This study aimed to identify the differences through widespread sampling of the microbial communities associated with the Pappy Lane shipwreck (NC shipwreck site #PAS0001), a shallow water ferrous-hulled shipwreck in Pamlico Sound, North Carolina to determine if there are differences across the wreck as well as from its surrounding environment. Loose shipwreck debris, drilled shipcores, surrounding sediment, and seawater samples were collected from the Pappy Lane shipwreck to characterize the microbial communities on and around the shipwreck. Results indicated that the shipwreck samples were more similar to each other than the surrounding sediment and aquatic environments suggesting they have made a specialized niche associated with the shipwreck. There were differences between the microbial community across the shipwreck, including between visibly corroded and non-corroded shipwreck debris pieces. Relative abundance estimates for neutrophilic iron-oxidizing bacteria (FeOB), an organism that may contribute to deterioration through biocorrosion, revealed they are present across the shipwreck and at highest abundance on the samples containing visible corrosion products. Zetaproteobacteria, a known class of marine iron-oxidizers, were also found in higher abundance on shipwreck samples with visible corrosion. A novel Zetaproteobacteria strain, Mariprofundus ferrooxydans O1, was isolated from one of the shipwreck pieces and its genome analyzed to elucidate the functional potential of the organism. In addition to iron oxidation pathways, the isolate has the genomic potential to perform carbon fixation in both high and low oxygen environments, as well as perform nitrogen fixation, contributing to the overall biogeochemical cycling of nutrients and metals in the shipwreck ecosystem. By understanding the microbial communities associated with shallow water ferrous-hulled shipwrecks, better management strategies and preservation plans can be put into place to preserve these artificial reefs and non-renewable cultural resources.

Genomic Insights into Two Novel Fe(II)-Oxidizing Zetaproteobacteria Isolates Reveal Lifestyle Adaption to Coastal Marine Sediments

The discovery of the novel Zetaproteobacteria class greatly expanded our understanding of neutrophilic, microaerophilic microbial Fe(II) oxidation in marine environments. Despite molecular techniques demonstrating their global distribution, relatively few isolates exist, especially from low-Fe(II) environments. Furthermore, the Fe(II) oxidation pathways used by Zetaproteobacteria remain poorly understood. Here, we present the genomes (>99% genome completeness) of two Zetaproteobacteria, which are the only cultivated isolates originating from typical low-Fe [porewater Fe(II), 70 to 100 μM] coastal marine sediments. The two strains share <90% average nucleotide identity (ANI) with each other and <80% ANI with any other Zetaproteobacteria genome. The closest relatives were Mariprofundus aestuarium strain CP-5 and Mariprofundus ferrinatatus strain CP-8 (96 to 98% 16S rRNA gene sequence similarity). Fe(II) oxidation of strains KV and NF is most likely mediated by the putative Fe(II) oxidase Cyc2. Interestingly, the genome of strain KV also encodes a putative multicopper oxidase, PcoAB, which could play a role in Fe(II) oxidation, a pathway found only in two other Zetaproteobacteria genomes (Ghiorsea bivora TAG-1 and SCGC AB-602-C20). The strains show potential adaptations to fluctuating O₂ concentrations, indicated by the presence of both cbb ₃- and aa ₃-type cytochrome c oxidases, which are adapted to low and high O₂ concentrations, respectively. This is further supported by the presence of several oxidative-stress-related genes. In summary, our results reveal the potential Fe(II) oxidation pathways employed by these two novel chemolithoautotrophic Fe(II)-oxidizing species and the lifestyle adaptations which enable the Zetaproteobacteria to survive in coastal environments with low Fe(II) and regular redox fluctuations.IMPORTANCE Until recently, the importance and relevance of Zetaproteobacteria were mainly thought to be restricted to high-Fe(II) environments, such as deep-sea hydrothermal vents. The two novel Mariprofundus isolates presented here originate from typical low-Fe(II) coastal marine sediments. As well as being low in Fe(II), these environments are often subjected to fluctuating O₂ concentrations and regular mixing by wave action and bioturbation. The discovery of two novel isolates highlights the importance of these organisms in such environments, as Fe(II) oxidation has been shown to impact nutrients and trace metals. Genome analysis of these two strains further supported their lifestyle adaptation and therefore their potential preference for coastal marine sediments, as genes necessary for surviving dynamic O₂ concentrations and oxidative stress were identified. Furthermore, our analyses also expand our understanding of the poorly understood Fe(II) oxidation pathways used by neutrophilic, microaerophilic Fe(II) oxidizers.

FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies

Iron 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 surge in publicly available sequence data has 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, iron redox cycling, iron storage, and magnetosome formation in model microorganisms and the plethora of sequence data available from environmental studies, we have created a comprehensive database of hidden Markov models (HMMs) based on genes related to iron acquisition, storage, and reduction/oxidation in Bacteria and Archaea. 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 provided datasets with respect to iron-related genes and gene neighborhood. 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. We validated FeGenie against a selected set of 28 isolate genomes and showcase its utility in exploring iron genes present in 27 metagenomes, 4 isolate genomes from human oral biofilms, and 17 genomes from candidate organisms, including members of the candidate phyla radiation. We show that FeGenie accurately identifies iron genes in isolates. Furthermore, analysis of metagenomes using FeGenie demonstrates that the iron gene repertoire and abundance of each environment is correlated with iron richness. 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 genes are discovered. FeGenie is freely available: https://github.com/Arkadiy-Garber/FeGenie.

On the biogenicity of Fe-oxyhydroxide filaments in silicified low-temperature hydrothermal deposits: Implications for the identification of Fe-oxidizing bacteria in the rock record

Microaerophilic Fe(II)-oxidizing bacteria produce biomineralized twisted and branched stalks, which are promising biosignatures of microbial Fe oxidation in ancient jaspers and iron formations. Extracellular Fe stalks retain their morphological characteristics under experimentally elevated temperatures, but the extent to which natural post-depositional processes affect fossil integrity remains to be resolved. We examined siliceous Fe deposits from laminated mounds and chimney structures from an extinct part of the Jan Mayen Vent Fields on the Arctic Mid-Ocean Ridge. Our aims were to determine how early seafloor diagenesis affects morphological and chemical signatures of Fe-oxyhydroxide biomineralization and how extracellular stalks differ from abiogenic features. Optical and scanning electron microscopy in combination with focused ion beam-transmission electron microscopy (FIB-TEM) was used to study the filamentous textures and cross sections of individual stalks. Our results revealed directional, dendritic, and radial arrangements of biogenic twisted stalks and randomly organized networks of hollow tubes. Stalks were encrusted by concentric Fe-oxyhydroxide laminae and silica casings. Element maps produced by energy dispersive X-ray spectroscopy (EDS) in TEM showed variations in the content of Si, P, and S within filaments, demonstrating that successive hydrothermal fluid pulses mediate early diagenetic alteration and modify the chemical composition and surface features of stalks through Fe-oxyhydroxide mineralization. The carbon content of the stalks was generally indistinguishable from background levels, suggesting that organic compounds were either scarce initially or lost due to percolating hydrothermal fluids. Dendrites and thicker abiotic filaments from a nearby chimney were composed of nanometer-sized microcrystalline iron particles and silica and showed Fe growth bands indicative of inorganic precipitation. Our study suggests that the identification of fossil stalks and sheaths of Fe-oxidizing bacteria in hydrothermal paleoenvironments may not rely on the detection of organic carbon and demonstrates that abiogenic filaments differ from stalks and sheaths of Fe-oxidizing bacteria with respect to width distribution, ultrastructure, and textural context.

Adaptive mechanism of Acidithiobacillus thiooxidans CCTCC M 2012104 under stress during bioleaching of low-grade chalcopyrite based on physiological and comparative transcriptomic analysis

Acidithiobacillus thiooxidans (A. thiooxidans) is often used for sulfur-bearing ores bioleaching, but its adaptive mechanism to harsh environments remains unclear. Here, we explored the adaptive mechanism of A. thiooxidans in the process of low-grade chalcopyrite bioleaching based on the physiology and comparative transcriptome analysis. It was indicated that A. thiooxidans maintains intracellular pH homeostasis by regulating unsaturated fatty acids, especially cyclopropane fatty acids, intracellular ATP, amino acid metabolism, and antioxidant factors. Comparative transcriptome analysis indicated that the key genes involved in sulfur oxidation, sor and soxABXYZ, were significantly up-regulated, generating more energy to resist extreme environmental stress by more active sulfur metabolism. Confocal laser scanning microscope analysis found that down-regulation of flagellar-related genes was likely to promote the biofilm formation. System-level understanding of leaching microorganisms under extreme stress can contribute to the evolution of these extremophiles via genetic engineering modification work, which further improves bioleaching in future.

Fine-Scale Biogeography and the Inference of Ecological Interactions Among Neutrophilic Iron-Oxidizing Zetaproteobacteria as Determined by a Rule-Based Microbial Network

Hydrothermal vents, such as those at Lō‘ihi Seamount and the Mariana Arc and back-arc, release iron required to support life from the Earth’s crust. In these ecosystems, bacteria and archaea can oxidize the released iron and therefore play an important role in the biogeochemical cycles of essential nutrients. These organisms often form microbial mats, and the primary producers in these communities can support diverse higher trophic levels. One such class of bacteria are the Zetaproteobacteria. This class of bacteria oxidize iron and commonly produce extracellular iron oxyhydroxide matrices that provide architecture to the microbial mats, so they are considered foundational members of the community and ecosystem engineers. Zetaproteobacteria are responsible for the majority of iron-oxidation in circumneutral, marine, low-oxygen environments. To study the composition of these communities, microbial mats were collected using a biomat sampler, which allows for fine-scale collection of microbial mats. DNA was then extracted and amplified for analysis of the SSU rRNA gene. After quality control and filtering, the SSU rRNA genes from Mariana Arc and Lō‘ihi Seamount microbial mat communities were compared pairwise to determine which site exhibits a greater microbial diversity and how much community overlap exists between the two sites. In-depth analysis was performed with the rule-based microbial network (RMN) algorithm, which identified a possible competitive relationship across oligotypes of a cosmopolitan Zetaproteobacteria operational taxonomic unit (OTU). This result demonstrated the ecological relevance of oligotypes, or fine-scale OTU variants. The oligotype distributions of the cosmopolitan ZetaOTUs varied greatly across the Pacific Ocean. The competitive relationship between dominant oligotypes at Lō‘ihi Seamount and the Mariana Arc and back-arc may be driving their differential distributions across the two regions and may result in species divergence within a cosmopolitan ZetaOTU. This implementation of the RMN algorithm can both predict directional relationships within a community and provide insight to the level at which evolution is occurring across ecosystems.

Environmental Evidence for and Genomic Insight into the Preference of Iron-Oxidizing Bacteria for More-Corrosion-Resistant Stainless Steel at Higher Salinities

Iron-oxidizing bacteria (FeOB) are some of the initial colonizing organisms during microbially influenced corrosion of steel infrastructure. To better understand the abiotic conditions under which FeOB colonize steel, an environmental study was conducted to determine the effects of salinity, temperature, dissolved oxygen levels, and steel type on FeOB colonization. Stainless steel (304 and 316 [i.e., 304SS and 316SS]) was used to determine the potential susceptibility of these specialized corrosion-resistant steels. Steel coupon deployments along salinity gradients in two river systems revealed attachment by FeOB at all sites, with greater abundance of FeOB at higher salinities and on 316SS, compared to 304SS. This may be due to the presence of molybdenum in 316SS, potentially providing a selective advantage for FeOB colonization. A novel Zetaproteobacteria species, Mariprofundus erugo, was isolated from these stainless steel samples. Genes for molybdenum utilization and uptake and reactive oxygen species protection were found within its genome, supporting the evidence from our FeOB abundance data; they may represent adaptations of FeOB for colonization of surfaces of anthropogenic iron sources such as stainless steel. These results reveal environmental conditions under which FeOB colonize steel surfaces most abundantly, and they provide the framework needed to develop biocorrosion prevention strategies for stainless steel infrastructure in coastal estuarine areas.IMPORTANCE Colonization of FeOB on corrosion-resistant stainless steel types (304SS and 316SS) has been quantified from environmental deployments along salinity gradients in estuarine environments. Greater FeOB abundance at higher salinities and on the more-corrosion-resistant 316SS suggests that there may be a higher risk of biocorrosion at higher salinities and there may be a selective advantage from certain stainless steel alloy metals, such as molybdenum, for FeOB colonization. A novel species of FeOB described here was isolated from our stainless steel coupon deployments, and its genome sequence supports our environmental data, as genes involved in the potential selectiveness toward surface colonization of stainless steel might lead to higher rates of biocorrosion of manmade aquatic infrastructure. These combined results provide environmental constraints for FeOB colonization on anthropogenic iron sources and build on previous frameworks for biocorrosion prevention strategies.

The Fe(II)-oxidizing Zetaproteobacteria: historical, ecological and genomic perspectives

The Zetaproteobacteria are a class of bacteria typically associated with marine Fe(II)-oxidizing environments. First discovered in the hydrothermal vents at Loihi Seamount, Hawaii, they have become model organisms for marine microbial Fe(II) oxidation. In addition to deep sea and shallow hydrothermal vents, Zetaproteobacteria are found in coastal sediments, other marine subsurface environments, steel corrosion biofilms and saline terrestrial springs. Isolates from a range of environments all grow by autotrophic Fe(II) oxidation. Their success lies partly in their microaerophily, which enables them to compete with abiotic Fe(II) oxidation at Fe(II)-rich oxic/anoxic transition zones. To determine the known diversity of the Zetaproteobacteria, we have used 16S rRNA gene sequences to define 59 operational taxonomic units (OTUs), at 97% similarity. While some Zetaproteobacteria taxa appear to be cosmopolitan, others are enriched by specific habitats. OTU networks show that certain Zetaproteobacteria co-exist, sharing compatible niches. These niches may correspond with adaptations to O2, H2 and nitrate availability, based on genomic analyses of metabolic potential. Also, a putative Fe(II) oxidation gene has been found in diverse Zetaproteobacteria taxa, suggesting that the Zetaproteobacteria evolved as Fe(II) oxidation specialists. In all, studies suggest that Zetaproteobacteria are widespread, and therefore may have a broad influence on marine and saline terrestrial Fe cycling.

Distribution Patterns of Iron-Oxidizing Zeta- and Beta-Proteobacteria From Different Environmental Settings at the Jan Mayen Vent Fields

Iron oxidizers are widespread in marine environments and play an important role in marine iron cycling. However, little is known about the overall distribution of iron oxidizers within hydrothermal systems, including settings with little hydrothermal activity. Moreover, the extent to which different phylogenetic groups of iron oxidizers exhibit niche specialization toward different environmental settings, remains largely unknown. Obtaining such knowledge is critical to unraveling the impact of the activity of iron oxidizers and how they are adapted. Here, we used 16S rRNA sequencing to characterize the distribution of iron oxidizers in different environmental settings within the Jan Mayen hydrothermal vent fields (JMVFs). Putative iron oxidizers affiliated to Zetaproteobacteria and Betaproteobacteria were detected within iron mounds, bottom seawater, basalt surfaces, and surface layers of sediments. The detected iron oxidizers were compared to sequence types previously observed in patchily distributed iron mats associated with diffuse venting at the JMVFs. Most OTUs of iron oxidizers reoccurred under different environmental settings, suggesting a limited degree of niche specialization. Consequently, most of the detected iron oxidizers seem to be generalists with a large habitat range. Our study highlights the importance of gathering information about the overall distribution of iron oxidizers in hydrothermal systems to fully understand the role of this metabolic group regarding cycling of iron. Furthermore, our results provide further evidence of the presence of iron-oxidizing members of Betaproteobacteria in marine environments.

Iron-oxidizing bacteria in marine environments: recent progresses and future directions

Iron-oxidizing bacteria (FeOB) refers to a group of bacteria with the ability to exchange and accumulate divalent iron dissolved in water as trivalent iron inside and outside the bacterial cell. Most FeOB belong the largest bacterial phylum, Proteobacteria. Within this phylum, FeOB with varying physiology with regards to their response to oxygen (obligate aerobes, facultative and obligate anaerobes) and pH optimum for proliferation (neutrophiles, moderate and extreme acidophiles) can be found. Although FeOB have been reported from a wide variety of environments, most of them have not been isolated and their biochemical characteristics remain largely unknown. This is especially true for those living in the marine realm, where the properties of FeOB was not known until the isolation of the Zetaproteobacteria Mariprofundus ferrooxydans, first reported in 2007. Since the proposal of Zetaproteobacteria by Emerson et al., the detection and isolation of those microorganisms from the marine environment has greatly escalated. Furthermore, FeOB have also recently been reported from works on ocean drilling and metal corrosion. This review aims to summarize the current state of phylogenetic and physiological diversity in marine FeOB, the significance of their roles in their environments (on both global and local scales), as well as their growing importance and applications in the industry.

Draft Genome Sequence of Mariprofundus micogutta Strain ET2

Mariprofundus micogutta strain ET2 was isolated in 2014 from a deep-sea hydrothermal field on the Bayonnaise Knoll of the Izu-Ogasawara arc. Here, we report its draft genome, which comprises 2,497,805 bp and contains 2,417 predicted coding sequences.

Insights into the Fundamental Physiology of the Uncultured Fe-Oxidizing Bacterium Leptothrix ochracea

Leptothrix ochracea is known for producing large volumes of iron oxyhydroxide sheaths that alter wetland biogeochemistry. For over a century, these delicate structures have fascinated microbiologists and geoscientists. Because L. ochracea still resists long-term in vitro culture, the debate regarding its metabolic classification dates back to 1885. We developed a novel culturing technique for L. ochracea using in situ natural waters and coupled this with single-cell genomics and nanoscale secondary-ion mass spectrophotometry (nanoSIMS) to probe L. ochracea's physiology. In microslide cultures L. ochracea doubled every 5.7 h and had an absolute growth requirement for ferrous iron, the genomic capacity for iron oxidation, and a branched electron transport chain with cytochromes putatively involved in lithotrophic iron oxidation. Additionally, its genome encoded several electron transport chain proteins, including a molybdopterin alternative complex III (ACIII), a cytochrome bd oxidase reductase, and several terminal oxidase genes. L. ochracea contained two key autotrophic proteins in the Calvin-Benson-Bassham cycle, a form II ribulose bisphosphate carboxylase, and a phosphoribulose kinase. L. ochracea also assimilated bicarbonate, although calculations suggest that bicarbonate assimilation is a small fraction of its total carbon assimilation. Finally, L. ochracea's fundamental physiology is a hybrid of those of the chemolithotrophic Gallionella-type iron-oxidizing bacteria and the sheathed, heterotrophic filamentous metal-oxidizing bacteria of the Leptothrix-Sphaerotilus genera. This allows L. ochracea to inhabit a unique niche within the neutrophilic iron seeps.IMPORTANCE Leptothrix ochracea was one of three groups of organisms that Sergei Winogradsky used in the 1880s to develop his hypothesis on chemolithotrophy. L. ochracea continues to resist cultivation and appears to have an absolute requirement for organic-rich waters, suggesting that its true physiology remains unknown. Further, L. ochracea is an ecological engineer; a few L. ochracea cells can generate prodigious volumes of iron oxyhydroxides, changing the ecosystem's geochemistry and ecology. Therefore, to determine L. ochracea's basic physiology, we employed new single-cell techniques to demonstrate that L. ochracea oxidizes iron to generate energy and, despite having predicted genes for autotrophic growth, assimilates a fraction of the total CO₂ that autotrophs do. Although not a true chemolithoautotroph, L. ochracea's physiological strategy allows it to be flexible and to extensively colonize iron-rich wetlands.