The Architecture of Iron Microbial Mats Reflects the Adaptation of Chemolithotrophic Iron Oxidation in Freshwater and Marine Environments

Leptothrix ochracea genomes reveal potential for mixotrophic growth on Fe(II) and organic carbon

Leptothrix ochracea creates distinctive iron-mineralized mats that carpet streams and wetlands. Easily recognized by its iron-mineralized sheaths, L. ochracea was one of the first microorganisms described in the 1800s. Yet it has never been isolated and does not have a complete genome sequence available, so key questions about its physiology remain unresolved. It is debated whether iron oxidation can be used for energy or growth and if L. ochracea is an autotroph, heterotroph, or mixotroph. To address these issues, we sampled L. ochracea-rich mats from three of its typical environments (a stream, wetlands, and a drainage channel) and reconstructed nine high-quality genomes of L. ochracea from metagenomes. These genomes contain iron oxidase genes cyc2 and mtoA, showing that L. ochracea has the potential to conserve energy from iron oxidation. Sox genes confer potential to oxidize sulfur for energy. There are genes for both carbon fixation (RuBisCO) and utilization of sugars and organic acids (acetate, lactate, and formate). In silico stoichiometric metabolic models further demonstrated the potential for growth using sugars and organic acids. Metatranscriptomes showed a high expression of genes for iron oxidation; aerobic respiration; and utilization of lactate, acetate, and sugars, as well as RuBisCO, supporting mixotrophic growth in the environment. In summary, our results suggest that L. ochracea has substantial metabolic flexibility. It is adapted to iron-rich, organic carbon-containing wetland niches, where it can thrive as a mixotrophic iron oxidizer by utilizing both iron oxidation and organics for energy generation and both inorganic and organic carbon for cell and sheath production.

IMPORTANCE

Winogradsky's observations of L. ochracea led him to propose autotrophic iron oxidation as a new microbial metabolism, following his work on autotrophic sulfur-oxidizers. While much culture-based research has ensued, isolation proved elusive, so most work on L. ochracea has been based in the environment and in microcosms. Meanwhile, the autotrophic Gallionella became the model for freshwater microbial iron oxidation, while heterotrophic and mixotrophic iron oxidation is not well-studied. Ecological studies have shown that Leptothrix overtakes Gallionella when dissolved organic carbon content increases, demonstrating distinct niches. This study presents the first near-complete genomes of L. ochracea, which share some features with autotrophic iron oxidizers, while also incorporating heterotrophic metabolisms. These genome, metabolic modeling, and transcriptome results give us a detailed metabolic picture of how the organism may combine lithoautotrophy with organoheterotrophy to promote Fe oxidation and C cycling and drive many biogeochemical processes resulting from microbial growth and iron oxyhydroxide formation in wetlands.

Microbes as marine habitat formers and ecosystem engineers

Despite their small individual size, marine prokaryotic and eukaryotic microbes can form large 3D structures and complex habitats. These habitats contribute to seafloor heterogeneity, facilitating colonization by animals and protists. They also provide food and refuge for a variety of species and promote novel ecological interactions. Here we illustrate the role of microbes as ecosystem engineers and propose a classification based on five types of habitat: microbial mats, microbial forests, microbial-mineralized habitats, microbial outcrops and microbial nodules. We also describe the metabolic processes of microbial habitat formers and their ecological roles, highlighting current gaps in knowledge. Their biogeography indicates that these habitats are widespread in all oceans and are continuously being discovered across latitudes and depths. These habitats are also expected to expand under future global change owing to their ability to exploit extreme environmental conditions. Given their high ecological relevance and their role in supporting endemic species and high biodiversity levels, microbial habitats should be included in future spatial planning, conservation and management measures.

Shifting to biology promotes highly efficient iron removal in groundwater filters

Rapid sand filters are established and widely applied technologies for groundwater treatment. In these filters, main groundwater contaminants such as iron, manganese, and ammonium are oxidized and removed. Conventionally, intensive aeration is employed to provide oxygen for these redox reactions. While effective, intensive aeration promotes flocculent iron removal, which results in iron oxide flocs that rapidly clog the filter. In this study, we operated two parallel full-scale sand filters at different aeration intensities to resolve the relative contribution of homogeneous, heterogeneous and biological iron removal pathways, and identify their operational controls. Our results show that mild aeration in the LOW filter (5 mg/L O2, pH 6.9) promoted biological iron removal and enabled iron oxidation at twice the rate compared to the intensively aerated HIGH filter (>10 mg/L O2, pH 7.4). Microscopy images showed distinctive twisted stalk-like iron solids, the biosignatures of Gallionella ferruginea, both in the LOW filter sand coatings as well as in its backwash solids. In accordance, 10 times higher DNA copy numbers of G. ferruginea were found in the LOW filter effluent. Clogging by biogenic iron solids was slower than by chemical iron flocs, resulting in lower backwash frequencies and yielding four times more water per run. Ultimately, our results reveal that biological iron oxidation can be actively controlled and favoured over competing physico-chemical routes. The production of more compact and practically valuable iron oxide solids is of outmost interest. We conclude that, although counterintuitive, slowing down iron oxidation in the water before filtration enables rapid iron removal in the biofilter.

Chemosynthesis: a neglected foundation of marine ecology and biogeochemistry

Chemosynthesis is a metabolic process that transfers carbon to the biosphere using reduced compounds. It is well recognised that chemosynthesis occurs in much of the ocean, but it is often thought to be a negligible process compared to photosynthesis. Here we propose that chemosynthesis is the underlying process governing primary production in much of the ocean and suggest that it extends to a much wider range of compounds, microorganisms, and ecosystems than previously thought. In turn, this process has had a central role in controlling marine biogeochemistry, ecology, and carbon budgets across the vast realms of the ocean, from the dawn of life to contemporary times.

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.

Experimental Identification of Potential Martian Biosignatures in Open and Closed Systems

NASA's Perseverance and ESA's Rosalind Franklin rovers have the scientific goal of searching for evidence of ancient life on Mars. Geochemical biosignatures that form because of microbe-mineral interactions could play a key role in achieving this, as they can be preserved for millions of years on Earth, and the same could be true for Mars. Previous laboratory experiments have explored the formation of biosignatures under closed systems, but these do not represent the open systems that are found in natural martian environments, such as channels and lakes. In this study, we have conducted environmental simulation experiments using a global regolith simulant (OUCM-1), a thermochemically modelled groundwater, and an anaerobic microbial community to explore the formation of geochemical biosignatures within plausible open and closed systems on Mars. This initial investigation showed differences in the diversity of the microbial community developed after 28 days. In an open-system simulation (flow-through experiment), the acetogenic Acetobacterium (49% relative abundance) and the sulfate reducer Desulfosporomusa (43% relative abundance) were the dominant genera. Whereas in the batch experiment, the sulfate reducers Desulfovibrio, Desulfomicrobium, and Desulfuromonas (95% relative abundance in total) were dominant. We also found evidence of enhanced mineral dissolution within the flow-through experiment, but there was little evidence of secondary deposits in the presence of biota. In contrast, SiO2 and Fe deposits formed within the batch experiment with biota but not under abiotic conditions. The results from these initial experiments indicate that different geochemical biosignatures can be generated between open and closed systems, and therefore, biosignature formation in open systems warrants further investigation.

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 pangenomic analysis reveals insight into phylogeny, metabolic flexibility, and iron oxidation mechanisms

IMPORTANCE

Neutrophilic iron-oxidizing bacteria (FeOB) produce copious iron (oxyhydr)oxides that can profoundly influence biogeochemical cycles, notably the fate of carbon and many metals. To fully understand environmental microbial iron oxidation, we need a thorough accounting of iron oxidation mechanisms. In this study, we show the Gallionellaceae FeOB genomes encode both characterized iron oxidases as well as uncharacterized multiheme cytochromes (MHCs). MHCs are predicted to transfer electrons from extracellular substrates and likely confer metabolic capabilities that help Gallionellaceae occupy a range of different iron- and mineral-rich niches. Gallionellaceae appear to specialize in iron oxidation, so it would be advantageous for them to have multiple mechanisms to oxidize various forms of iron, given the many iron minerals on Earth, as well as the physiological and kinetic challenges faced by FeOB. The multiple iron/mineral oxidation mechanisms may help drive the widespread ecological success of Gallionellaceae.

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.

Traces of Ancient Life in Oceanic Basalt Preserved as Iron-Mineralized Ultrastructures: Implications for Detecting Extraterrestrial Biosignatures

Benefiting from their adaptability to extreme environments, subsurface microorganisms have been discovered in sedimentary and igneous rock environments on Earth and have been advocated as candidates in the search for extraterrestrial life. In this article, we study iron-mineralized microstructures in calcite-filled veins within basaltic pillows of the late Ladinian Fernazza group (Middle Triassic, 239 Ma) in Italy. These microstructures represent diverse morphologies, including filaments, globules, nodules, and micro-digitate stromatolites, which are similar to extant iron-oxidizing bacterial communities. In situ analyses including Raman spectroscopy have been used to investigate the morphological, elemental, mineralogical, and bond-vibrational modes of the microstructures. According to the Raman spectral parameters, iron minerals preserve heterogeneous ultrastructures and crystallinities, coinciding with the morphologies and precursor microbial activities. The degree of crystallinity usually represents a microscale gradient decreasing toward previously existing microbial cells, revealing a decline of mineralization due to microbial activities. This study provides an analog of possible rock-dwelling subsurface life on Mars or icy moons and advocates Raman spectroscopy as an efficient tool for in situ analyses. We put forward the concept that ultrastructural characteristics of minerals described by Raman spectral parameters corresponding to microscale morphologies could be employed as carbon-lean biosignatures in future space missions.

Identification of lthB, a Gene Encoding a Putative Glycosyltransferase Family 8 Protein Required for Leptothrix Sheath Formation

The bacterium Leptothrix cholodnii generates cell chains encased in sheaths that are composed of woven nanofibrils. The nanofibrils are mainly composed of glycoconjugate repeats, and several glycosyltransferases (GTs) are required for its biosynthesis. However, only one GT (LthA) has been identified to date. In this study, we screened spontaneous variants of L. cholodnii SP6 to find those that form smooth colonies, which is one of the characteristics of sheathless variants. Genomic DNA sequencing of an isolated variant revealed an insertion in the locus Lcho_0972, which encodes a putative GT family 8 protein. We thus designated this protein LthB and characterized it using deletion mutants and antibodies. LthB localized adjacent to the cell envelope. ΔlthB cell chains were nanofibril free and thus sheathless, indicating that LthB is involved in nanofibril biosynthesis. Unlike the ΔlthA mutant and the wild-type strain, which often generate planktonic cells, most ΔlthB organisms presented as long cell chains under static conditions, resulting in deficient pellicle formation, which requires motile planktonic cells. These results imply that sheaths are not required for elongation of cell chains. Finally, calcium depletion, which induces cell chain breakage due to sheath loss, abrogated the expression of LthA, but not LthB, suggesting that these GTs cooperatively participate in glycoconjugate biosynthesis under different signaling controls. IMPORTANCE In recent years, the regulation of cell chain elongation of filamentous bacteria via extracellular signals has attracted attention as a potential strategy to prevent clogging of water distribution systems and filamentous bulking of activated sludge in industrial settings. However, a fundamental understanding of the ecology of filamentous bacteria remains elusive. Since sheath formation is associated with cell chain elongation in most of these bacteria, the molecular mechanisms underlying nanofibril sheath formation, including the intracellular signaling cascade in response to extracellular stimuli, must be elucidated. Here, we isolated a sheathless variant of L. cholodnii SP6 and thus identified a novel glycosyltransferase, LthB. Although mutants with deletions of lthA, encoding another GT, and lthB were both defective for nanofibril formation, they exhibited different phenotypes of cell chain elongation and pellicle formation. Moreover, LthA expression, but not LthB expression, was influenced by extracellular calcium, which is known to affect nanofibril formation, indicating the functional diversities of LthA and LthB. Such molecular insights are critical for a better understanding of ecology of filamentous bacteria, which, in turn, can be used to improve strategies to control filamentous bacteria in industrial facilities.

Gallionellaceae pangenomic analysis reveals insight into phylogeny, metabolic flexibility, and iron oxidation mechanisms

The iron-oxidizing Gallionellaceae drive a wide variety of biogeochemical cycles through their metabolisms and biominerals. To better understand the environmental impacts of Gallionellaceae, we need to improve our knowledge of their diversity and metabolisms, especially any novel iron oxidation mechanisms. Here, we used a pangenomic analysis of 103 genomes to resolve Gallionellaceae phylogeny and explore the range of genomic potential. Using a concatenated ribosomal protein tree and key gene patterns, we determined Gallionellaceae has four genera, divided into two groups-iron-oxidizing bacteria (FeOB) Gallionella, Sideroxydans, and Ferriphaselus with known iron oxidases (Cyc2, MtoA) and nitrite-oxidizing bacteria (NOB) Candidatus Nitrotoga with nitrite oxidase (Nxr). The FeOB and NOB have similar electron transport chains, including genes for reverse electron transport and carbon fixation. Auxiliary energy metabolisms including S oxidation, denitrification, and organotrophy were scattered throughout the Gallionellaceae FeOB. Within FeOB, we found genes that may represent adaptations for iron oxidation, including a variety of extracellular electron uptake (EEU) mechanisms. FeOB genomes encoded more predicted c-type cytochromes overall, notably more multiheme c-type cytochromes (MHCs) with >10 CXXCH motifs. These include homologs of several predicted outer membrane porin-MHC complexes, including MtoAB and Uet. MHCs are known to efficiently conduct electrons across longer distances and function across a wide range of redox potentials that overlap with mineral redox potentials, which can help expand the range of usable iron substrates. Overall, the results of pangenome analyses suggest that the Gallionellaceae genera Gallionella, Sideroxydans, and Ferriphaselus are primarily iron oxidizers, capable of oxidizing dissolved Fe2+ as well as a range of solid iron or other mineral substrates.

Mixotrophy broadens the ecological niche range of the iron oxidizer Sideroxydans sp. CL21 isolated from an iron-rich peatland

Sideroxydans sp. CL21 is a microaerobic, acid-tolerant Fe(II)-oxidizer, isolated from the Schlöppnerbrunnen fen. Since the genome size of Sideroxydans sp. CL21 is 21% larger than that of the neutrophilic Sideroxydans lithotrophicus ES-1, we hypothesized that strain CL21 contains additional metabolic traits to thrive in the fen. The common genomic content of both strains contains homologs of the putative Fe(II) oxidation genes, mtoAB and cyc2. A large part of the accessory genome in strain CL21 contains genes linked to utilization of alternative electron donors, including NiFe uptake hydrogenases, and genes encoding lactate uptake and utilization proteins, motility and biofilm formation, transposable elements, and pH homeostasis mechanisms. Next, we incubated the strain in different combinations of electron donors and characterized the fen microbial communities. Sideroxydans spp. comprised 3.33% and 3.94% of the total relative abundance in the peatland soil and peatland water, respectively. Incubation results indicate Sideroxydans sp. CL21 uses H2 and thiosulfate, while lactate only enhances growth when combined with Fe, H2, or thiosulfate. Rates of H2 utilization were highest in combination with other substrates. Thus, Sideroxydans sp. CL21 is a mixotroph, growing best by simultaneously using substrate combinations, which helps to thrive in dynamic and complex habitats.

The biofilm life cycle: expanding the conceptual model of biofilm formation

Bacterial biofilms are often defined as communities of surface-attached bacteria and are typically depicted with a classic mushroom-shaped structure characteristic of Pseudomonas aeruginosa. However, it has become evident that this is not how all biofilms develop, especially in vivo, in clinical and industrial settings, and in the environment, where biofilms often are observed as non-surface-attached aggregates. In this Review, we describe the origin of the current five-step biofilm development model and why it fails to capture many aspects of bacterial biofilm physiology. We aim to present a simplistic developmental model for biofilm formation that is flexible enough to include all the diverse scenarios and microenvironments where biofilms are formed. With this new expanded, inclusive model, we hereby introduce a common platform for developing an understanding of biofilms and anti-biofilm strategies that can be tailored to the microenvironment under investigation.

Fe-Rich Fossil Vents as Mars Analog Samples: Identification of Extinct Chimneys in Miocene Marine Sediments Using Raman Spectroscopy, X-Ray Diffraction, and Scanning Electron Microscopy-Energy Dispersive X-Ray Spectroscopy

On Earth, the circulation of Fe-rich fluids in hydrothermal environments leads to characteristic iron mineral deposits, reflecting the pH and redox chemical conditions of the hydrothermal system, and is often associated with chemotroph microorganisms capable of deriving energy from chemical gradients. On Mars, iron-rich hydrothermal sites are considered to be potentially important astrobiological targets for searching evidence of life during exploration missions, such as the Mars 2020 and the ExoMars 2022 missions. In this study, an extinct hydrothermal chimney from the Jaroso hydrothermal system (SE Spain), considered an interesting geodynamic and mineralogical terrestrial analog for Mars, was analyzed using Raman spectroscopy, X-ray diffraction, and scanning electron microscopy coupled with energy dispersive X-ray spectroscopy. The sample consists of a fossil vent in a Miocene shallow-marine sedimentary deposit composed of a marl substrate, an iron-rich chimney pipe, and a central space filled with backfilling deposits and vent condensates. The iron crust is particularly striking due to the combined presence of molecular and morphological indications of a microbial colonization, including mineral microstructures (e.g., stalks, filaments), iron oxyhydroxide phases (altered goethite, ferrihydrite), and organic signatures (carotenoids, organopolymers). The clear identification of pigments by resonance Raman spectroscopy and the preservation of organics in association with iron oxyhydroxides by Raman microimaging demonstrate that the iron crust was indeed colonized by microbial communities. These analyses confirm that Raman spectroscopy is a powerful tool for documenting the habitability of such historical hydrothermal environments. Finally, based on the results obtained, we propose that the ancient iron-rich hydrothermal pipes should be recognized as singular terrestrial Mars analog specimens to support the preparatory work for robotic in situ exploration missions to Mars, as well as during the subsequent interpretation of data returned by those missions.

A critical review of mineral-microbe interaction and coevolution: mechanisms and applications

The mineral-microbe interactions play important roles in environmental change, biogeochemical cycling of elements, and formation of ore deposits. Minerals provide both beneficial (physical and chemical protection, nutrients, and energy) and detrimental (toxic substances and oxidative pressure) effects to microbes, resulting in mineral-specific microbial colonization. Microbes impact dissolution, transformation, and precipitation of minerals through their activity, resulting in either genetically-controlled or metabolism-induced biomineralization. Through these interactions minerals and microbes coevolve through Earth history. The mineral-microbe interactions typically occur at microscopic scale but the effect is often manifested at global scale. Despite advances achieved through decades of research, major questions remain. Four areas are identified for future research: integrating mineral and microbial ecology, establishing mineral biosignatures, linking laboratory mechanistic investigation to field observation, and manipulating mineral-microbe interactions for the benefit of humankind.

Metabolically diverse primordial microbial communities in Earth's oldest seafloor-hydrothermal jasper

The oldest putative fossils occur as hematite filaments and tubes in jasper-carbonate banded iron formations from the 4280- to 3750-Ma Nuvvuagittuq Supracrustal Belt, Québec. If biological in origin, these filaments might have affinities with modern descendants; however, if abiotic, they could indicate complex prebiotic forms on early Earth. Here, we report images of centimeter-size, autochthonous hematite filaments that are pectinate-branching, parallel-aligned, undulated, and containing Fe²⁺-oxides. These microstructures are considered microfossils because of their mineral associations and resemblance to younger microfossils, modern Fe-bacteria from hydrothermal environments, and the experimental products of heated Fe-oxidizing bacteria. Additional clusters of irregular hematite ellipsoids could reflect abiotic processes of silicification, producing similar structures and thus yielding an uncertain origin. Millimeter-sized chalcopyrite grains within the jasper-carbonate rocks have ³⁴S- and ³³S-enrichments consistent with microbial S-disproportionation and an O₂-poor atmosphere. Collectively, the observations suggest a diverse microbial ecosystem on the primordial Earth that may be common on other planetary bodies, including Mars.

Precipitation of greigite and pyrite induced by Thermococcales: an advantage to live in Fe- and S-rich environments?

Thermococcales, a major order of archaea inhabiting the iron- and sulfur-rich anaerobic parts of hydrothermal deep-sea vents, have been shown to rapidly produce abundant quantities of pyrite FeS₂ in iron-sulfur-rich fluids at 85°C, suggesting that they may contribute to the formation of 'low temperature' FeS₂ in their ecosystem. We show that this process operates in Thermococcus kodakarensis only when zero-valent sulfur is directly available as intracellular sulfur vesicles. Whether in the presence or absence of zero-valent sulfur, significant amounts of Fe₃ S₄ greigite nanocrystals are formed extracellularly. We also show that mineralization of iron sulfides induces massive cell mortality but that concomitantly with the formation of greigite and/or pyrite, a new generation of cells can grow. This phenomenon is observed for Fe concentrations of 5 mM but not higher suggesting that above a threshold in the iron pulse all cells are lysed. We hypothesize that iron sulfides precipitation on former cell materials might induce the release of nutrients in the mineralization medium further used by a fraction of surviving non-mineralized cells allowing production of new alive cells. This suggests that biologically induced mineralization of iron-sulfides could be part of a survival strategy employed by Thermococcales to cope with mineralizing high-temperature hydrothermal environments.

Unraveling Fe(II)-Oxidizing Mechanisms in a Facultative Fe(II) Oxidizer, Sideroxydans lithotrophicus Strain ES-1, via Culturing, Transcriptomics, and Reverse Transcription-Quantitative PCR

Sideroxydans lithotrophicus ES-1 grows autotrophically either by Fe(II) oxidation or by thiosulfate oxidation, in contrast to most other isolates of neutrophilic Fe(II)-oxidizing bacteria (FeOB). This provides a unique opportunity to explore the physiology of a facultative FeOB and constrain the genes specific to Fe(II) oxidation. We compared the growth of S. lithotrophicus ES-1 on Fe(II), thiosulfate, and both substrates together. While initial growth rates were similar, thiosulfate-grown cultures had higher yield with or without Fe(II) present, which may give ES-1 an advantage over obligate FeOB. To investigate the Fe(II) and S oxidation pathways, we conducted transcriptomics experiments, validated with reverse transcription-quantitative PCR (RT-qPCR). We explored the long-term gene expression response at different growth phases (over days to a week) and expression changes during a short-term switch from thiosulfate to Fe(II) (90 min). The dsr and sox sulfur oxidation genes were upregulated in thiosulfate cultures. The Fe(II) oxidase gene cyc2 was among the top expressed genes during both Fe(II) and thiosulfate oxidation, and addition of Fe(II) to thiosulfate-grown cells caused an increase in cyc2 expression. These results support the role of Cyc2 as the Fe(II) oxidase and suggest that ES-1 maintains readiness to oxidize Fe(II), even in the absence of Fe(II). We used gene expression profiles to further constrain the ES-1 Fe(II) oxidation pathway. Notably, among the most highly upregulated genes during Fe(II) oxidation were genes for alternative complex III, reverse electron transport, and carbon fixation. This implies a direct connection between Fe(II) oxidation and carbon fixation, suggesting that CO2 is an important electron sink for Fe(II) oxidation. IMPORTANCE Neutrophilic FeOB are increasingly observed in various environments, but knowledge of their ecophysiology and Fe(II) oxidation mechanisms is still relatively limited. Sideroxydans isolates are widely observed in aquifers, wetlands, and sediments, and genome analysis suggests metabolic flexibility contributes to their success. The type strain ES-1 is unusual among neutrophilic FeOB isolates, as it can grow on either Fe(II) or a non-Fe(II) substrate, thiosulfate. Almost all our knowledge of neutrophilic Fe(II) oxidation pathways comes from genome analyses, with some work on metatranscriptomes. This study used culture-based experiments to test the genes specific to Fe(II) oxidation in a facultative FeOB and refine our model of the Fe(II) oxidation pathway. We gained insight into how facultative FeOB like ES-1 connect Fe, S, and C biogeochemical cycling in the environment and suggest a multigene indicator would improve understanding of Fe(II) oxidation activity in environments with facultative FeOB.

Green inhibitors reduce unwanted calcium carbonate precipitation: Implications for technical settings

Mineral scale deposits in water drainage and supply systems are a common and challenging issue, especially by clogging the water flow. The removal of such unwanted deposits is cost intensive arguing for case-specific and sustainable prevention strategies. In the present study, a novel on-site approach to prevent calcium carbonate (CaCO₃) scale formation was assessed in two road tunnel drainages: Application of the eco-friendly green inhibitor polyaspartate (PASP) caused (i) a significant inhibition of CaCO₃ precipitation, (ii) a more porous or even unconsolidated consistence of the deposits, and (iii) a shift from calcite to the metastable aragonite and vaterite polymorphs. Even relatively low PASP concentrations (1-33 mg/l) can significantly decrease CaCO₃ scale deposition, removing up to ∼7 t CaCO₃/year at an efficiency up to 84%. Application of PASP for water conditioning should also consider case-specific microbial activity effects, where consumption of PASP, e.g. by Leptothrix ochracea, can limit inhibition effects.

Organic Stabilization of Extracellular Elemental Sulfur in a Sulfurovum-Rich Biofilm: A New Role for Extracellular Polymeric Substances?

This work shines light on the role of extracellular polymeric substance (EPS) in the formation and preservation of elemental sulfur biominerals produced by sulfur-oxidizing bacteria. We characterized elemental sulfur particles produced within a Sulfurovum-rich biofilm in the Frasassi Cave System (Italy). The particles adopt spherical and bipyramidal morphologies, and display both stable (α-S8) and metastable (β-S8) crystal structures. Elemental sulfur is embedded within a dense matrix of EPS, and the particles are surrounded by organic envelopes rich in amide and carboxylic groups. Organic encapsulation and the presence of metastable crystal structures are consistent with elemental sulfur organomineralization, i.e., the formation and stabilization of elemental sulfur in the presence of organics, a mechanism that has previously been observed in laboratory studies. This research provides new evidence for the important role of microbial EPS in mineral formation in the environment. We hypothesize that the extracellular organics are used by sulfur-oxidizing bacteria for the stabilization of elemental sulfur minerals outside of the cell wall as a store of chemical energy. The stabilization of energy sources (in the form of a solid electron acceptor) in biofilms is a potential new role for microbial EPS that requires further investigation.

Leptothrix cholodnii Response to Nutrient Limitation

Microorganisms are widely utilized for the treatment of wastewater in activated sludge systems. However, the uncontrolled growth of filamentous bacteria leads to bulking and adversely affects wastewater treatment efficiency. To clarify the nutrient requirements for filament formation, we track the growth of a filamentous bacterium, Leptothrix cholodnii SP-6 in different nutrient-limited conditions using a high aspect-ratio microfluidic chamber to follow cell-chain elongation and sheath formation. We find that limitations in Na⁺, K⁺, and Fe²⁺ yield no observable changes in the elongation of cell chains and sheath formation, whereas limitations of C, N, P, or vitamins lead to more pronounced changes in filament morphology; here we observe the appearance of partially empty filaments with wide intercellular gaps. We observe more dramatic differences when SP-6 cells are transferred to media lacking Mg²⁺ and Ca²⁺. Loss of Mg²⁺ results in cell autolysis, while removal of Ca²⁺ results in the catastrophic disintegration of the filaments. By simultaneously limiting both carbon and Ca²⁺ sources, we are able to stimulate planktonic cell generation. These findings paint a detailed picture of the ecophysiology of Leptothrix, which may lead to improved control over the unchecked growth of deleterious filamentous bacteria in water purification 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.

Acidophilic Iron- and Sulfur-Oxidizing Bacteria, Acidithiobacillus ferrooxidans, Drives Alkaline pH Neutralization and Mineral Weathering in Fe Ore Tailings

The neutralization of strongly alkaline pH conditions and acceleration of mineral weathering in alkaline Fe ore tailings have been identified as key prerequisites for eco-engineering tailings-soil formation for sustainable mine site rehabilitation. Acidithiobacillus ferrooxidans has great potential in neutralizing alkaline pH and accelerating primary mineral weathering in the tailings but little information is available. This study aimed to investigate the colonization of A. ferrooxidans in alkaline Fe ore tailings and its role in elemental sulfur (S⁰) oxidation, tailings neutralization, and Fe-bearing mineral weathering through a microcosm experiment. The effects of biological S⁰ oxidation on the weathering of alkaline Fe ore tailings were examined via various microspectroscopic analyses. It is found that (1) the A. ferrooxidans inoculum combined with the S⁰ amendment rapidly neutralized the alkaline Fe ore tailings; (2) A. ferrooxidans activities induced Fe-bearing primary mineral (e.g., biotite) weathering and secondary mineral (e.g., ferrihydrite and jarosite) formation; and (3) the association between bacterial cells and tailings minerals were likely facilitated by extracellular polymeric substances (EPS). The behavior and biogeochemical functionality of A. ferrooxidans in the tailings provide a fundamental basis for developing microbial-based technologies toward eco-engineering soil formation in Fe ore tailings.

Geographical Distribution of Iron Redox Cycling Bacterial Community in Peatlands: Distinct Assemble Mechanism Across Environmental Gradient

Microbial-mediated iron (Fe) oxidation and reduction greatly contribute to the biogeochemistry and mineralogy of ecosystems. However, knowledge regarding the composition and distribution patterns of iron redox cycling bacteria in peatlands remains limited. Here, using high-throughput sequencing, we compared biogeographic patterns and assemblies of the iron redox cycling bacterial community between soil and water samples obtained from different types of peatland across four regions in Northeast China. A total of 48 phylotypes were identified as potential iron redox bacteria, which had greater than 97% similarity with Fe(II)-oxidizing bacteria (FeOB) and Fe(III)-reducing bacteria (FeRB). Among them, Rhodoferax, Clostridium, Geothrix, Sideroxydans, Geobacter, Desulfovibrio, and Leptothrix could be used as bioindicators in peatlands for characterizing different hydrological conditions and nutrient demands. Across all samples, bacterial communities associated with iron redox cycling were mainly affected by pH, dissolved organic carbon (DOC), and Fe²⁺. Distance-decay relationship (DDR) analysis indicated that iron redox cycling bacterial communities in soil, but not in water, were highly correlated with geographic distance. Additionally, null model analysis revealed that stochastic processes substituted deterministic processes from minerotrophic fens to ombrotrophic bogs in soils, whereas deterministic processes were dominant in water. Overall, these observations suggest that bacteria involved in iron redox cycling are widespread in diverse habitats and exhibit distinct patterns of distribution and community assembly mechanisms between soil and water in peatlands.

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.

Quantifying Preservation Potential: Lipid Degradation in a Mars-Analog Circumneutral Iron Deposit

Comparisons between the preservation potential of Mars-analog environments have historically been qualitative rather than quantitative. Recently, however, laboratory-based artificial maturation combined with kinetic modeling techniques have emerged as a potential means by which the preservation potential of solvent-soluble organic matter can be quantified in various Mars-analog environments. These methods consider how elevated temperatures, pressures, and organic-inorganic interactions influence the degradation of organic biomarkers post-burial. We used these techniques to investigate the preservation potential of deposits from a circumneutral iron-rich groundwater system. These deposits are composed of ferrihydrite (Fe₅HO₈ · 4H₂O), an amorphous iron hydroxide mineral that is a common constituent of rocks found in ancient lacustrine environments on Mars, such as those observed in Gale Crater. Both natural and synthetic ferrihydrite samples were subjected to hydrous pyrolysis to observe the effects of long-term burial on the mineralogy and organic content of the samples. Our experiments revealed that organic-inorganic interactions in the samples are dominated by the transformation of iron minerals. As amorphous ferrihydrite transforms into more crystalline species, the decrease in surface area results in the desorption of organic matter, potentially rendering them more susceptible to degradation. We also find that circumneutral iron-rich deposits provide unfavorable conditions for the preservation of solvent-soluble organic matter. Quantitative comparisons between preservation potentials as calculated when using kinetic parameters show that circumneutral iron-rich deposits are ∼25 times less likely to preserve solvent-soluble organic matter compared with acidic, iron-rich environments. Our results suggest that circumneutral iron-rich deposits should be deprioritized in favor of acidic iron- and sulfur-rich deposits when searching for evidence of life with solvent extraction techniques.

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.

Iron Flocs and the Three Domains: Microbial Interactions in Freshwater Iron Mats

Freshwater iron mats are dynamic geochemical environments with broad ecological diversity, primarily formed by the iron-oxidizing bacteria. The community features functional groups involved in biogeochemical cycles for iron, sulfur, carbon, and nitrogen. Despite this complexity, iron mat communities provide an excellent model system for exploring microbial ecological interactions and ecological theories in situ Syntrophies and competition between the functional groups in iron mats, how they connect cycles, and the maintenance of these communities by taxons outside bacteria (the eukaryota, archaea, and viruses) have been largely unstudied. Here, we review what is currently known about freshwater iron mat communities, the taxa that reside there, and the interactions between these organisms, and we propose ways in which future studies may uncover exciting new discoveries. For example, the archaea in these mats may play a greater role than previously thought as they are diverse and widespread in iron mats based on 16S rRNA genes and include methanogenic taxa. Studies with a holistic view of the iron mat community members focusing on their diverse interactions will expand our understanding of community functions, such as those involved in pollution removal. To begin addressing questions regarding the fundamental interactions and to identify the conditions in which they occur, more laboratory culturing techniques and coculture studies, more network and keystone species analyses, and the expansion of studies to more freshwater iron mat systems are necessary. Increasingly accessible bioinformatic, geochemical, and culturing tools now open avenues to address the questions that we pose herein.

Genome reconstruction reveals distinct assemblages of Gallionellaceae in surface and subsurface redox transition zones

Fe-oxidizing bacteria of the family Gallionellaceae are major players in the Fe biogeochemical cycle in freshwater. These bacteria thrive in redox transition zones where they benefit from both high Fe concentrations and microaerobic conditions. We analysed the Gallionellaceae genomic diversity in an artesian hard-rock aquifer where redox transition zones develop (i) in the subsurface, where ancient, reduced groundwater mixes with recent oxygenated groundwater, and (ii) at the surface, where groundwater reaches the open air. A total of 15 new draft genomes of Gallionellaceae representing to 11 candidate genera were recovered from the two redox transition zones. Sulfur oxidation genes were encoded in most genomes while denitrification genes were much less represented. One genus dominated microbial communities belowground and we propose to name it 'Candidatus Houarnoksidobacter'. The two transition zones were populated by completely different assemblages of Gallionellaceae despite the almost constant upward circulation of groundwater between the two zones. The processes leading to redox transition zones, oxygen diffusion at the surface or groundwater mixing in subsurface, appear to be a major driver of the Gallionellaceae diversity.

Micro- and nano-scale mineralogical characterization of Fe(II)-oxidizing bacterial stalks

Neutrophilic, microaerobic Fe(II)-oxidizing bacteria (FeOB) from marine and freshwater environments are known to generate twisted ribbon-like organo-mineral stalks. These structures, which are extracellularly precipitated, are susceptible to chemical influences in the environment once synthesized. In this paper, we characterize the minerals associated with freshwater FeOB stalks in order to evaluate key organo-mineral mechanisms involved in biomineral formation. Micro-Raman spectroscopy and Field Emission Scanning Electron Microscopy revealed that FeOB isolated from drinking water wells in Sweden produced stalks with ferrihydrite, lepidocrocite and goethite as main mineral components. Based on our observations made by micro-Raman Spectroscopy, field emission scanning electron microscopy and scanning transmission electron microscope combined with electron energy-loss spectroscopy, we propose a model that describes the crystal-growth mechanism, the Fe-oxidation state, and the mineralogical state of the stalks, as well as the biogenic contribution to these features. Our study suggests that the main crystal-growth mechanism in stalks includes nanoparticle aggregation and dissolution/re-precipitation reactions, which are dominant near the organic exopolymeric material produced by the microorganism and in the peripheral region of the stalk, respectively.

Polyfunctional Nanofibril Appendages Mediate Attachment, Filamentation, and Filament Adaptability in Leptothrix cholodnii

Leptothrix is a species of Fe/Mn-oxidizing bacteria known to form long filaments composed of chains of cells that eventually produce a rigid tube surrounding the filament. Prior to the formation of this brittle microtube, Leptothrix cells secrete hair-like structures from the cell surface, called nanofibrils, which develop into a soft sheath that surrounds the filament. To clarify the role of nanofibrils in filament formation in L. cholodnii SP-6, we analyze the behavior of individual cells and multicellular filaments in high-aspect ratio microfluidic chambers using time-lapse and intermittent in situ fluorescent staining of nanofibrils, complemented with atmospheric scanning electron microscopy. We show that in SP-6 nanofibrils are important for attachment and their distribution on young filaments post-attachment is correlated to the directionality of filament elongation. Elongating filaments demonstrate a surprising ability to adapt to their physical environment by changing direction when they encounter obstacles: they bend or reverse direction depending on the angle of the collision. We show that the forces involved in the collision can be used to predict the behavior of filament. Finally, we show that as filaments grow in length, the older region becomes confined by the sheath, while the newly secreted nanofibrils at the leading edge of the filament form a loose, divergent, structure from which cells periodically escape.

Scale deposits in tunnel drainage systems - A study on fabrics and formation mechanisms

Rapid deposition of chemical sediments, particularly calcium carbonate, is a widespread phenomenon in tunnel constructions, which can significantly disturb water draining. The removal of the scale deposits in the drainage setting is labor and cost intensive. Prediction or prevention of these unwanted scale deposits are challenging and require detailed knowledge on their site-specific source, formation mechanisms and environmental dependencies. This case study combines a mineralogical, (micro)structural, isotopic, microbiological, and hydrochemical approach to understand the formation of scale deposits in an Austrian motorway tunnel. Chemical and isotopic results revealed that all investigated solutions originate from a distinct local aquifer. High pH (11), indicative high alkaline element concentrations (Na 26 mg/l; K 67 mg/l), originated from concrete leaching, and a strong supersaturation in respect to calcite (SI > 1) are representative for the environmental setting of scaling type 1. This type is characterized by the formation of calcite, aragonite, and rarely documented dypingite (Mg₅(CO₃)₄(OH)₂*5H₂O), and yields in a highly porous material showing minor indications of microbial presence. In contrast, scale deposits of type 2 are strongly microbially influenced, yielding dense and layered mineral deposits, typically consisting of calcite. The corresponding aqueous solution revealed elevated Mg concentration (38 mg/l) and a high molar Mg/Ca ratio (0.8). Scale deposits containing distinct aragonite precipitates next to calcite, mostly growing in pore spaces of the scale fabric, are accounted as type 3. Therein, dypingite is always growing on top of aragonite needles, indicative for prior CaCO₃ precipitation. The composition of corresponding solutions shows the highest Mg/Ca ratio (1.1). Scale type 4 is characterized as a compact deposit consisting entirely of calcite. Its corresponding solution exhibits a molar Mg/Ca ratio of 0.6. From the obtained data sets a conceptual model was developed describing the distinct operative and (micro)environmental conditions responsible for the distinct diversity of scale deposits.

Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of Zetaproteobacteria Iron Mats at Marine Hydrothermal Vents

Zetaproteobacteria create extensive iron (Fe) oxide mats at marine hydrothermal vents, making them an ideal model for microbial Fe oxidation at circumneutral pH. Comparison of neutrophilic Fe oxidizer isolate genomes has revealed a hypothetical Fe oxidation pathway, featuring a homolog of the Fe oxidase Cyc2 from Acidithiobacillus ferrooxidans However, Cyc2 function is not well verified in neutrophilic Fe oxidizers, particularly in Fe-oxidizing environments. Toward this, we analyzed genomes and metatranscriptomes of Zetaproteobacteria, using 53 new high-quality metagenome-assembled genomes reconstructed from Fe mats at Mid-Atlantic Ridge, Mariana Backarc, and Loihi Seamount (Hawaii) hydrothermal vents. Phylogenetic analysis demonstrated conservation of Cyc2 sequences among most neutrophilic Fe oxidizers, suggesting a common function. We confirmed the widespread distribution of cyc2 and other model Fe oxidation pathway genes across all represented Zetaproteobacteria lineages. High expression of these genes was observed in diverse Zetaproteobacteria under multiple environmental conditions and in incubations. The putative Fe oxidase gene cyc2 was highly expressed in situ, often as the top expressed gene. The cyc2 gene showed increased expression in Fe(II)-amended incubations, with corresponding increases in carbon fixation and central metabolism gene expression. These results substantiate the Cyc2-based Fe oxidation pathway in neutrophiles and demonstrate its significance in marine Fe-mineralizing environments.IMPORTANCE Iron oxides are important components of our soil, water supplies, and ecosystems, as they sequester nutrients, carbon, and metals. Microorganisms can form iron oxides, but it is unclear whether this is a significant mechanism in the environment. Unlike other major microbial energy metabolisms, there is no marker gene for iron oxidation, hindering our ability to track these microbes. Here, we investigate a promising possible iron oxidation gene, cyc2, in iron-rich hydrothermal vents, where iron-oxidizing microbes dominate. We pieced together diverse Zetaproteobacteria genomes, compared these genomes, and analyzed expression of cyc2 and other hypothetical iron oxidation genes. We show that cyc2 is widespread among iron oxidizers and is highly expressed and potentially regulated, making it a good marker for the capacity for iron oxidation and potentially a marker for activity. These findings will help us understand and potentially quantify the impacts of neutrophilic iron oxidizers in a wide variety of marine and terrestrial environments.

Peculiarities of biofilm formation by Paracoccus denitrificans

Most bacteria form biofilms, which are thick multicellular communities covered in extracellular matrix. Biofilms can become thick enough to be even observed by the naked eye, and biofilm formation is a tightly regulated process. Paracoccus denitrificans is a non-motile, Gram-negative bacterium that forms a very thin, unique biofilm. A key factor in the biofilm formed by this bacterium is a large surface protein named biofilm-associated protein A (BapA), which was recently reported to be regulated by cyclic diguanosine monophosphate (cyclic-di-GMP or c-di-GMP). Cyclic-di-GMP is a major second messenger involved in biofilm formation in many bacteria. Though cyclic-di-GMP is generally reported as a positive regulatory factor in biofilm formation, it represses biofilm formation in P. denitrificans. Furthermore, quorum sensing (QS) represses biofilm formation in this bacterium, which is also reported as a positive regulator of biofilm formation in most bacteria. The QS signal used in P. denitrificans is hydrophobic and is delivered through membrane vesicles. Studies on QS show that P. denitrificans can potentially form a thick biofilm but maintains a thin biofilm under normal growth conditions. In this review, we discuss the peculiarities of biofilm formation by P. denitrificans with the aim of deepening the overall understanding of bacterial biofilm formation and functions.

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.

Hunter-Gatherers Harvested and Heated Microbial Biogenic Iron Oxides to Produce Rock Art Pigment

Red mineral pigment use is recognized as a fundamental component of a series of traits associated with human evolutionary development, social interaction, and behavioral complexity. Iron-enriched mineral deposits have been collected and prepared as pigment for use in rock art, personal adornment, and mortuary practices for millennia, yet little is known about early developments in mineral processing techniques in North America. Microanalysis of rock art pigments from the North American Pacific Northwest reveals a sophisticated use of iron oxide produced by the biomineralizing bacterium Leptothrix ochracea; a keystone species of chemolithotroph recognized in recent advances in the development of thermostable, colorfast biomaterial pigments. Here we show evidence for human engagement with this bacterium, including nanostructural and magnetic properties evident of thermal enhancement, indicating that controlled use of pyrotechnology was a key feature of how biogenic iron oxides were prepared into paint. Our results demonstrate that hunter-gatherers in this area of study prepared pigments by harvesting aquatic microbial iron mats dominated by iron-oxidizing bacteria, which were subsequently heated in large open hearths at a controlled range of 750 °C to 850 °C. This technical gesture was performed to enhance color properties, and increase colorfastness and resistance to degradation. This skilled production of highly thermostable and long-lasting rock art paint represents a specialized technological innovation. Our results contribute to a growing body of knowledge on historical-ecological resource use practices in the Pacific Northwest during the Late Holocene.

Figshare link to figures: https://figshare.com/s/9392a0081632c20e9484.

Contribution of Microaerophilic Iron(II)-Oxidizers to Iron(III) Mineral Formation

Neutrophilic microbial aerobic oxidation of ferrous iron (Fe(II)) is restricted to pH-circumneutral environments characterized by low oxygen where microaerophilic Fe(II)-oxidizing microorganisms successfully compete with abiotic Fe(II) oxidation. However, accumulation of ferric (bio)minerals increases competition by stimulating abiotic surface-catalyzed heterogeneous Fe(II) oxidation. Here, we present an experimental approach that allows quantification of microbial and abiotic contribution to Fe(II) oxidation in the presence or initial absence of ferric (bio)minerals. We found that at 20 μM O₂ and the initial absence of Fe(III) minerals, an iron(II)-oxidizing enrichment culture (99.6% similarity to Sideroxydans spp.) contributed 40% to the overall Fe(II) oxidation within approximately 26 h and oxidized up to 3.6 × 10^-15 mol Fe(II) cell^-1 h^-1. Optimum O₂ concentrations at which enzymatic Fe(II) oxidation can compete with abiotic Fe(II) oxidation ranged from 5 to 20 μM. Lower O₂ levels limited biotic Fe(II) oxidation, while at higher O₂ levels abiotic Fe(II) oxidation dominated. The presence of ferric (bio)minerals induced surface-catalytic heterogeneous abiotic Fe(II) oxidation and reduced the microbial contribution to Fe(II) oxidation from 40% to 10% at 10 μM O₂. The obtained results will help to better assess the impact of microaerophilic Fe(II) oxidation on the biogeochemical iron cycle in a variety of environmental natural and anthropogenic settings.

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.

Long Range Correlation in Redox Potential Fluctuations Signals Energetic Efficiency of Bacterial Fe(II) Oxidation

Differentiating biotic and abiotic processes in nature remains a persistent challenge, specifically in evaluating microbial contributions to geochemical processes through time. Building on previous work reporting that biologically-influenced systems exhibit stronger long-range correlation than abiotic systems, this study evaluated the relationship between long-range correlation of redox potential and oxidation rates of circumneutral microaerophilic bacterial Fe(II) oxidation using a series of batch microcosms with bacteriogenic iron oxides (BIOS). Initial detrended fluctuation analysis (DFA) scaling exponents of the abiotic microcosms were lower (ca. 1.20) than those of the biotic microcosms (ca. 1.80). As Fe(II) oxidation proceeded, correlation strength decayed as a logistic function of elapsed reaction time, exhibiting direct dependence on the free energy of reaction. Correlation strength for all microcosms decayed sharply from strong correlation to uncorrelated fluctuations. The decay rates are greater for abiotic microcosms than biotic microcosms. The ΔG_m relaxation edges for biotic microcosms were lower, indicating less remaining free energy for Fe(II) oxidation than abiotic systems, with the implication that biologically-catalyzed reactions are likely more energetically efficient than abiotic reactions. These results strengthen the case for employing novel DFA techniques to distinguish in situ microbial metabolic activity from abiotic processes, as well as to potentially differentiate metabolisms among different chemoautotrophs.

Metabolic Processes Preserved as Biosignatures in Iron-Oxidizing Microorganisms: Implications for Biosignature Detection on Mars

Iron-oxidizing bacteria occupy a distinct environmental niche. These chemolithoautotrophic organisms require very little oxygen (when neutrophilic) or outcompete oxygen for access to Fe(II) (when acidophilic). The utilization of Fe(II) as an electron donor makes them strong analog organisms for any potential life that could be found on Mars. Despite their importance to the elucidation of early life on, and potentially beyond, Earth, many details of their metabolism remain unknown. By using on-line thermochemolysis and gas chromatography-mass spectrometry (GC-MS), a distinct signal for a low-molecular-weight molecule was discovered in multiple iron-oxidizing isolates as well as several iron-dominated environmental samples, from freshwater and marine environments and in both modern and older iron rock samples. This GC-MS signal was neither detected in organisms that did not use Fe(II) as an electron donor nor present in iron mats in which organic carbon was destroyed by heating. Mass spectral analysis indicates that the molecule bears the hallmarks of a pterin-bearing molecule. Genomic analysis has previously identified a molybdopterin that could be part of the electron transport chain in a number of lithotrophic iron-oxidizing bacteria, suggesting one possible source for this signal is the pterin component of this protein. The rock samples indicate the possibility that the molecule can be preserved within lithified sedimentary rocks. The specificity of the signal to organisms requiring iron in their metabolism makes this a novel biosignature with which to investigate both the evolution of life on ancient Earth and potential life on Mars.

Terraced Iron Formations: Biogeochemical Processes Contributing to Microbial Biomineralization and Microfossil Preservation

Terraced iron formations (TIFs) are laminated structures that cover square meter-size areas on the surface of weathered bench faces and tailings piles at the Mount Morgan mine, which is a non-operational open pit mine located in Queensland, Australia. Sampled TIFs were analyzed using molecular and microanalytical techniques to assess the bacterial communities that likely contributed to the development of these structures. The bacterial community from the TIFs was more diverse compared to the tailings on which the TIFs had formed. The detection of both chemolithotrophic iron-oxidizing bacteria, i.e., Acidithiobacillus ferrooxidans and Mariprofundus ferrooxydans, and iron-reducing bacteria, i.e., Acidobacterium capsulatum, suggests that iron oxidation/reduction are continuous processes occurring within the TIFs. Acidophilic, iron-oxidizing bacteria were enriched from the TIFs. High-resolution electron microscopy was used to characterize iron biomineralization, i.e., the association of cells with iron oxyhydroxide mineral precipitates, which served as an analog for identifying the structural microfossils of individual cells as well as biofilms within iron oxyhydroxide laminations—i.e., alternating layers containing schwertmannite (Fe16O16(OH)12(SO4)2) and goethite (FeO(OH)). Kinetic modeling estimated that it would take between 0.25–2.28 years to form approximately one gram of schwertmannite as a lamination over a one-m2 surface, thereby contributing to TIF development. This length of time could correspond with seasonable rainfall or greater than average annual rainfall. In either case, the presence of water is critical for sustaining microbial activity, and subsequently iron oxyhydroxide mineral precipitation. The TIFs from the Mount Morgan mine also contain laminations of gypsum (CaSO·2H2O) alternating with iron oxyhydroxide laminations. These gypsum laminations likely represented drier periods of the year, in which millimeter-size gypsum crystals presumably precipitated as water gradually evaporated. Interestingly, gypsum acted as a substrate for the attachment of cells and the growth of biofilms that eventually became mineralized within schwertmannite and goethite. The dissolution and reprecipitation of gypsum suggest that microenvironments with circumneutral pH conditions could exist within TIFs, thereby supporting iron oxidation under circumneutral pH conditions. In conclusion, this study highlights the relationship between microbes for the development of TIFs and also provides interpretations of biogeochemical processes contributing to the preservation of bacterial cells and entire biofilms under acidic conditions.

The role of iron-oxidizing bacteria in biocorrosion: a review

Lithotrophic iron-oxidizing bacteria depend on reduced iron, Fe(II), as their primary energy source, making them natural candidates for growing in association with steel infrastructure and potentially contributing to microbially influenced corrosion (MIC). This review summarizes recent work on the role of iron-oxidizing bacteria (FeOB) in MIC. By virtue of producing complex 3-dimensional biofilms that result from the accumulation of iron-oxides, FeOB may aid in the colonization of steel surfaces by other microbes involved in MIC. Evidence points to a successional pattern occurring whereby FeOB are early colonizers of mild steel (MS), followed by sulfate-reducing bacteria and other microbes, although studies of aged corrosion products indicate that FeOB do establish a long-term presence. There is evidence that only specific clades of FeOB, with unique adaptations for growing on steel surfaces are part of the MIC community. These are discussed in the context of the larger MIC microbiome.

Variation in electrode redox potential selects for different microorganisms under cathodic current flow from electrodes in marine sediments

Extracellular electron transport (EET) is a microbial process that allows microorganisms to transport electrons to and from insoluble substrates outside of the cell. Although progress has been made in understanding how microbes transfer electrons to insoluble substrates, the process of receiving electrons has largely remained unexplored. We investigated redox potentials favourable for donating electrons to dissolved and insoluble components in Catalina Harbor marine sediment by combining electrochemical techniques with geochemistry and molecular methods. Working electrodes buried in sediment microcosms were poised at seven redox potentials between -300 and -750 mV versus Ag/AgCl using a three-electrode system. In electrode biofilms recovered after 2-month incubations, overall community diversity increased with more negative redox potentials. Abundances of known EET-capable groups (e.g., Alteromonadales and Desulfuromonadales) varied with redox potential. Motility and chemotaxis genes were found in greater abundance in electrode communities, suggesting a possible selective advantage of these pathways for colonization and utilization of the electrode. Our enrichments demonstrated the validity of this approach in capturing groups known, as well as novel groups (e.g., Campylobacterales) that perform EET. The diverse nature of the enriched cathode communities suggest that insoluble substrate oxidation may be a critical, although poorly described microbial metabolic process in marine sediment.

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.