Biogenic Mn-Oxides in Subseafloor Basalts

Environmentally persistent free radicals and other paramagnetic species in wildland-urban interface fire ashes

Wildland-urban interface (WUI) fires consume fuels, such as vegetation and structural materials, leaving behind ash composed primarily of pyrogenic carbon and metal oxides. However, there is currently limited understanding of the role of WUI fire ash from different sources as a source of paramagnetic species such as environmentally persistent free radicals (EPFRs) and transition metals in the environment. Electron paramagnetic resonance (EPR) was used to detect and quantify paramagnetic species, including organic persistent free radicals and transition metal spins, in fifty-three fire ash and soil samples collected following the North Complex Fire and the Sonoma-Lake-Napa Unit (LNU) Lightning Complex Fire, California, 2020. High concentrations of organic EPFRs (e.g., 1.4 × 1014 to 1.9 × 1017 spins g-1) were detected in the studied WUI fire ash along with other paramagnetic species such as iron and manganese oxides, as well as Fe3+ and Mn2+ ions. The mean concentrations of EPFRs in various ash types decreased following the order: vegetation ash (1.1 × 1017 ± 1.1 × 1017 spins g-1) > structural ash (1.6 × 1016 ± 3.7 × 1016 spins g-1) > vehicle ash (6.4 × 1015 ± 8.6 × 1015 spins g-1) > soil (3.2 × 1015 ± 3.7 × 1015 spins g-1). The mean concentrations of EPFRs decreased with increased combustion completeness indicated by ash color; black (1.1 × 1017 ± 1.1 × 1017 spins g-1) > white (2.5 × 1016 ± 4.4 × 1016 spins g-1) > gray (1.8 × 1016 ± 2.4 × 1016 spins g-1). In contrast, the relative amounts of reduced Mn2+ ions increased with increased combustion completeness. Thus, WUI fire ash is an important global source of EPFRs and reduced metal species (e.g., Mn2+). Further research is needed to underpin the formation, transformation, and environmental and human health impacts of these paramagnetic species in light of the projected increased frequency, size, and severity of WUI fires.

Microbiologically influenced corrosion of AISI 202 and 316L stainless steels under manganese-oxidizing biofilms

In this work, we study the microbiologically influenced corrosion (MIC) of AISI 316L (1-2% Mn) and AISI 202 (8-12% Mn) in the presence of manganese-oxidizing biofilms. Microbiological and 16S rRNA amplicon sequencing analysis on biofilms formed on the surfaces of both the SS materials after exposure to seawater for two months showed the presence of predominant Mn-oxidizing bacteria (MnOB) groups. The Mn contents in the biofilms formed on AISI 202 and 316L were 0.577 and 0.193 ppm, respectively. Mixed biofilms of 11 pure axenic cultures of MnOB isolated and identified from both the SS biofilms were used for MIC studies on SS. Electrochemical studies showed four orders of magnitude high icorr values (1.271 × 10-4 A.cm-2) and the onset of crevice corrosion potentials (502 mV) confirming the localized corrosion of AISI 202 and 316L, respectively, under MnOB biofilms. X-ray photoelectron spectroscopic (XPS) analysis on biotic surfaces showed a reduced Mn content from 10.1 to 7.9 atom.% confirming the Mn oxidation in AISI 202. This study confirms that MnOB biofilms on the SS surfaces can lead to MIC due to biogenic Mn oxidation, depletion of Fe and Mn content, and enrichment of Cr content.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03845-z.

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.

Chemical Gardens Mimic Electron Paramagnetic Resonance Spectra and Morphology of Biogenic Mn Oxides

Manganese (Mn) oxides are ubiquitous in nature and occur as both biological and abiotic minerals, but empirically distinguishing between the two remains a problem. Recently, electron paramagnetic resonance (EPR) spectroscopy has been proposed for this purpose. It has been reported that biogenic Mn oxides display a characteristic narrow linewidth in contrast to their pure abiotic counterparts, which is explained in part by the large number of cation vacancies that form within the layers of biogenic Mn oxides. It was, therefore, proposed that natural samples that display a narrow EPR linewidth, ΔHpp < 580G, could be assigned to a biogenic origin. However, in poorly crystalline or amorphous solids, both dipolar broadening and exchange narrowing simultaneously determine the linewidth. Considering that the spectral linewidth is governed by several mechanisms, this approach might be questioned. In this study, we report synthetic chemical garden Mn oxide biomorphs that exhibit both morphologically life-like structures and narrow EPR linewidths, suggesting that a narrow EPR line may be unsuitable as reliable evidence in assessment of biogenicity.

Dubiofossils from a Mars-analogue subsurface palaeoenvironment: The limits of biogenicity criteria

The search for a fossil record of Earth's deep biosphere, partly motivated by potential analogies with subsurface habitats on Mars, has uncovered numerous assemblages of inorganic microfilaments and tubules inside ancient pores and fractures. Although these enigmatic objects are morphologically similar to mineralized microorganisms (and some contain organic carbon), they also resemble some abiotic structures. Palaeobiologists have responded to this ambiguity by evaluating problematic filaments against checklists of "biogenicity criteria". Here, we describe material that tests the limits of this approach. We sampled Jurassic calcite veins formed through subseafloor serpentinization, a water-rock reaction that can fuel the deep biosphere and is known to have occurred widely on Mars. At two localities ~4 km apart, veins contained curving, branched microfilaments composed of Mg-silicate and Fe-oxide minerals. Using a wide range of analytical techniques including synchrotron X-ray microtomography and scanning transmission electron microscopy, we show that these features meet many published criteria for biogenicity and are comparable to fossilized cryptoendolithic fungi or bacteria. However, we argue that abiotic processes driven by serpentinization could account for the same set of lifelike features, and report a chemical garden experiment that supports this view. These filaments are, therefore, most objectively described as dubiofossils, a designation we here defend from criticism and recommend over alternative approaches, but which nevertheless signifies an impasse. Similar impasses can be anticipated in the future exploration of subsurface palaeo-habitats on Earth and Mars. To avoid them, further studies are required in biomimetic geochemical self-organization, microbial taphonomy and micro-analytical techniques, with a focus on subsurface habitats.

Deep-sea hydrothermal vent sediments reveal diverse fungi with antibacterial activities

Relatively little is known about the diversity of fungi in deep-sea, hydrothermal sediments. Less thoroughly explored environments are likely untapped reservoirs of unique biodiversity with the potential to augment our current arsenal of microbial compounds with biomedical and/or industrial applications. In this study, we applied traditional culture-based methods to examine a subset of the morphological and phylogenetic diversity of filamentous fungi and yeasts present in 11 hydrothermally influenced sediment samples collected from eight sites on the seafloor of Guaymas Basin, Mexico. A total of 12 unique isolates affiliating with Ascomycota and Basidiomycota were obtained and taxonomically identified on the basis of morphological features and analyses of marker genes including actin, β-tubulin, small subunit ribosomal DNA (18S rRNA), internal transcribed spacer (ITS) and large subunit ribosomal DNA (26S rRNA) D1/D2 domain sequences (depending on taxon). A total of 11 isolates possess congeners previously detected in, or recovered from, deep-sea environments. A total of seven isolates exhibited antibacterial activity against human bacterial pathogens Staphylococcus aureus ATCC-35556 and/or Escherichia coli ATCC-25922. This first investigation suggests that hydrothermal environments may serve as promising reservoirs of much greater fungal diversity, some of which may produce biomedically useful metabolites.

Forced Biomineralization: A Review

Biologically induced and controlled mineralization of metals promotes the development of protective structures to shield cells from thermal, chemical, and ultraviolet stresses. Metal biomineralization is widely considered to have been relevant for the survival of life in the environmental conditions of ancient terrestrial oceans. Similar behavior is seen among extremophilic biomineralizers today, which have evolved to inhabit a variety of industrial aqueous environments with elevated metal concentrations. As an example of extreme biomineralization, we introduce the category of "forced biomineralization", which we use to refer to the biologically mediated sequestration of dissolved metals and metalloids into minerals. We discuss forced mineralization as it is known to be carried out by a variety of organisms, including polyextremophiles in a range of psychrophilic, thermophilic, anaerobic, alkaliphilic, acidophilic, and halophilic conditions, as well as in environments with very high or toxic metal ion concentrations. While much additional work lies ahead to characterize the various pathways by which these biominerals form, forced biomineralization has been shown to provide insights for the progression of extreme biomimetics, allowing for promising new forays into creating the next generation of composites using organic-templating approaches under biologically extreme laboratory conditions relevant to a wide range of industrial conditions.

Meta-omics highlights the diversity, activity and adaptations of fungi in deep oceanic crust

The lithified oceanic crust, lower crust gabbros in particular, has remained largely unexplored by microbiologists. Recently, evidence for heterogeneously distributed viable and transcriptionally active autotrophic and heterotrophic microbial populations within low-biomass communities was found down to 750 m below the seafloor at the Atlantis Bank Gabbro Massif, Indian Ocean. Here, we report on the diversity, activity and adaptations of fungal communities in the deep oceanic crust from ~10 to 780 mbsf by combining metabarcoding analyses with mid/high-throughput culturing approaches. Metabarcoding along with culturing indicate a low diversity of viable fungi, mostly affiliated to ubiquitous (terrestrial and aquatic environments) taxa. Ecophysiological analyses coupled with metatranscriptomics point to viable and transcriptionally active fungal populations engaged in cell division, translation, protein modifications and other vital cellular processes. Transcript data suggest possible adaptations for surviving in the nutrient-poor, lithified deep biosphere that include the recycling of organic matter. These active communities appear strongly influenced by the presence of cracks and veins in the rocks where fluids and resulting rock alteration create micro-niches.

Sequestration and Oxidation of Cr(III) by Fungal Mn Oxides with Mn(II) Oxidizing Activity

Biogenic manganese oxides (BMOs) have gained increasing attention for environmental application because of their sequestration and oxidizing abilities for various elements. Oxidation and sequestration of Cr(III) by BMOs, however, still remain unknown. We prepared BMOs in liquid cultures of Acremonium strictum strain KR21-2, and subsequently conducted single or repeated treatment experiments in Cr(NO3)3 at pH 6.0. Under aerobic conditions, newly formed BMOs exhibited a rapid production of Cr(VI) without a significant release of Mn(II), demonstrating that newly formed BMO mediates a catalytic oxidation of Cr(III) with a self-regeneration step of reduced Mn. In anaerobic solution, newly formed BMOs showed a cessation of Cr(III) oxidation in the early stage of the reaction, and subsequently had a much smaller Cr(VI) production with significant release of reduced Mn(II). Extraordinary sequestration of Cr(III) was observed during the repeated treatments under anaerobic conditions. Anaerobically sequestered Cr(III) was readily converted to Cr(VI) when the conditions became aerobic, which suggests that the surface passivation is responsible for the anaerobic cessation of Cr(III) oxidation. The results presented herein increase our understanding of the roles of BMO in Cr(III) oxidation and sequestration processes in potential application of BMOs towards the remediation of Cr(III)/Cr(VI) in contaminated sites.

Exceptional Preservation of Fungi as H2-Bearing Fluid Inclusions in an Early Quaternary Paleo-Hydrothermal System at Cape Vani, Milos, Greece

The production of H2 in hydrothermal systems and subsurface settings is almost exclusively assumed a result of abiotic processes, particularly serpentinization of ultramafic rocks. The origin of H2 in environments not hosted in ultramafic rocks is, as a rule, unjustifiably linked to abiotic processes. Additionally, multiple microbiological processes among both prokaryotes and eukaryotes are known to involve H2-production, of which anaerobic fungi have been put forward as a potential source of H2 in subsurface environments, which is still unconfirmed. Here, we report fungal remains exceptionally preserved as fluid inclusions in hydrothermal quartz from feeder quartz-barite veins from the Cape Vani Fe-Ba-Mn ore on the Greek island of Milos. The inclusions possess filamentous or near-spheroidal morphologies interpreted as remains of fungal hyphae and spores, respectively. They were characterized by microthermometry, Raman spectroscopy, and staining of exposed inclusions with WGA-FITC under fluorescence microscopy. The spheroidal aqueous inclusions interpreted as fungal spores are unique by their coating of Mn-oxide birnessite, and gas phase H2. A biological origin of the H2 resulting from anaerobic fungal respiration is suggested. We propose that biologically produced H2 by micro-eukaryotes is an unrecognized source of H2 in hydrothermal systems that may support communities of H2-dependent prokaryotes.

Instant Attraction: Clay Authigenesis in Fossil Fungal Biofilms

Clay authigenesis associated with the activity of microorganisms is an important process for biofilm preservation and may provide clues to the formation of biominerals on the ancient Earth. Fossilization of fungal biofilms attached to vesicles or cracks in igneous rock, is characterized by fungal-induced clay mineralization and can be tracked in deep rock and deep time, from late Paleoproterozoic (2.4 Ga), to the present. Here we briefly review the current data on clay mineralization by fossil fungal biofilms from oceanic and continental subsurface igneous rock. The aim of this study was to compare the nature of subsurface fungal clays from different igneous settings to evaluate the importance of host rock and ambient redox conditions for clay speciation related to fossil microorganisms. Our study suggests that the most common type of authigenic clay associated with pristine fossil fungal biofilms in both oxic (basaltic) and anoxic (granitic) settings are montmorillonite-like smectites and confirms a significant role of fungal biofilms in the cycling of elements between host rock, ocean and secondary precipitates. The presence of life in the deep subsurface may thus prove more significant than host rock geochemistry in directing the precipitation of authigenic clays in the igneous crust, the extent of which remains to be fully understood.

Portraying manganese biofilms via a merger of EPR spectroscopy and cathodic polarization

Microbial biofilms on stainless steel surfaces exposed to water from a freshwater pond were dominated by manganese-oxidizing bacteria, as initially diagnosed by microscopy and elemental analysis. The application of electron paramagnetic resonance (EPR) spectroscopy revealed conspicuous sextet (six-line) patterns that intensified with immersion time, implying the gradual accumulation of Mn(II) in the biofilms. Correspondingly, cathodic polarization designated the manganese oxide (MnO_x) reduction peak in the form of a distinctive 'nose', which grew increasingly more negative with biofilm growth. The progressive expansion of cathodic current densities and the concurrent area-under-the-curve also allowed the quantification of microbially mediated MnO_x deposition_. Furthermore, the merger of EPR and cathodic polarization techniques yielded key insights, in tandem with Mn speciation data, into the pathways of microbial manganese transformations in biofilms, besides providing meaningful interpretations of prevailing literature. Accordingly, the natural freshwater biofilm was inferred as one supporting a complete manganese cycle encompassing multiple redox states.

A New Frontier for Palaeobiology: Earth's Vast Deep Biosphere

Diverse micro-organisms populate a global deep biosphere hosted by rocks and sediments beneath land and sea, containing more biomass than any other biome except forests. This paper reviews an emerging palaeobiological archive of these dark habitats: microfossils preserved in ancient pores and fractures in the crust. This archive, seemingly dominated by mineralized filaments (although rods and coccoids are also reported), is presently far too sparsely sampled and poorly understood to reveal trends in the abundance, distribution, or diversity of deep life through time. New research is called for to establish the nature and extent of the fossil record of Earth's deep biosphere by combining systematic exploration, rigorous microanalysis, and experimental studies of both microbial preservation and the formation of abiotic pseudofossils within the crust. It is concluded that the fossil record of Earth's largest microbial habitat may still have much to tell us about the history of life, the evolution of biogeochemical cycles, and the search for life on Mars.

Manganese Oxides Resembling Microbial Fabrics and Their Implications for Recognizing Inorganically Preserved Microfossils

In the search for microfossils of early life on Earth, the demonstration of biogenicity is paramount. Traditionally, only syngenetic structures with cellular elaboration, hollow sheaths/cell walls, and indigenous kerogen have been considered bona fide fossils. Recent reports of inorganically preserved microfossils represent a shift from this practice. Such a shift, if accompanied by a robust set of biogenicity criteria, could have profound implications for the identification of biosignatures on early Earth and extraterrestrial bodies. Here, we reaffirm the conventional criteria by examining aggregates of inorganic filaments from the Pilbara region of Western Australia. These aggregates are preserved in bedded chert, and the filaments measure up to 1 μm in diameter and 100 μm in length. The aggregates superficially resemble kerogenous microbial fabrics and mycelial organisms. However, the filaments consist of manganese oxide, lack cellular elaboration, and show no evidence for hollow sheaths or cell walls. We conclude that the filaments are fibrous minerals of abiotic origin. The similarities between these pseudofossils and some filamentous fossils highlight the need for strict application of the conventional criteria for recognizing microfossils. In the absence of kerogen, morphologically simple structures should, at least, show evidence of cellular features to be considered bona fide fossils. Key Words: Fossil-Manganese oxide-Pilbara-Precambrian-Pseudofossil. Astrobiology 18, 249-258.

Fungi in Deep Subsurface Environments

The igneous crust of the oceans and the continents represents the major part of Earth's lithosphere and has recently been recognized as a substantial, yet underexplored, microbial habitat. While prokaryotes have been the focus of most investigations, microeukaryotes have been surprisingly neglected. However, recent work acknowledges eukaryotes, and in particular fungi, as common inhabitants of the deep biosphere, including the deep igneous provinces. The fossil record of the subseafloor igneous crust, and to some extent the continental bedrock, establishes fungi or fungus-like organisms as inhabitants of deep rock since at least the Paleoproterozoic, which challenges the present notion of early fungal evolution. Additionally, deep fungi have been shown to play an important ecological role engaging in symbiosis-like relationships with prokaryotes, decomposing organic matter, and being responsible for mineral weathering and formation, thus mediating mobilization of biogeochemically important elements. In this review, we aim at covering the abundance and diversity of fungi in the various igneous rock provinces on Earth as well as describing the ecological impact of deep fungi. We further discuss what consequences recent findings might have for the understanding of the fungal distribution in extensive anoxic environments and for early fungal evolution.

Exploring Fingerprints of the Extreme Thermoacidophile Metallosphaera sedula Grown on Synthetic Martian Regolith Materials as the Sole Energy Sources

The biology of metal transforming microorganisms is of a fundamental and applied importance for our understanding of past and present biogeochemical processes on Earth and in the Universe. The extreme thermoacidophile Metallosphaera sedula is a metal mobilizing archaeon, which thrives in hot acid environments (optimal growth at 74°C and pH 2.0) and utilizes energy from the oxidation of reduced metal inorganic sources. These characteristics of M. sedula make it an ideal organism to further our knowledge of the biogeochemical processes of possible life on extraterrestrial planetary bodies. Exploring the viability and metal extraction capacity of M. sedula living on and interacting with synthetic extraterrestrial minerals, we show that M. sedula utilizes metals trapped in the Martian regolith simulants (JSC Mars 1A; P-MRS; S-MRS; MRS07/52) as the sole energy sources. The obtained set of microbiological and mineralogical data suggests that M. sedula actively colonizes synthetic Martian regolith materials and releases free soluble metals. The surface of bioprocessed Martian regolith simulants is analyzed for specific mineralogical fingerprints left upon M. sedula growth. The obtained results provide insights of biomining of extraterrestrial material as well as of the detection of biosignatures implementing in life search missions.

Fungal and Prokaryotic Activities in the Marine Subsurface Biosphere at Peru Margin and Canterbury Basin Inferred from RNA-Based Analyses and Microscopy

The deep sedimentary biosphere, extending 100s of meters below the seafloor harbors unexpected diversity of Bacteria, Archaea, and microbial eukaryotes. Far less is known about microbial eukaryotes in subsurface habitats, albeit several studies have indicated that fungi dominate microbial eukaryotic communities and fungal molecular signatures (of both yeasts and filamentous forms) have been detected in samples as deep as 1740 mbsf. Here, we compare and contrast fungal ribosomal RNA gene signatures and whole community metatranscriptomes present in sediment core samples from 6 and 95 mbsf from Peru Margin site 1229A and from samples from 12 and 345 mbsf from Canterbury Basin site U1352. The metatranscriptome analyses reveal higher relative expression of amino acid and peptide transporters in the less nutrient rich Canterbury Basin sediments compared to the nutrient rich Peru Margin, and higher expression of motility genes in the Peru Margin samples. Higher expression of genes associated with metals transporters and antibiotic resistance and production was detected in Canterbury Basin sediments. A poly-A focused metatranscriptome produced for the Canterbury Basin sample from 345 mbsf provides further evidence for active fungal communities in the subsurface in the form of fungal-associated transcripts for metabolic and cellular processes, cell and membrane functions, and catalytic activities. Fungal communities at comparable depths at the two geographically separated locations appear dominated by distinct taxa. Differences in taxonomic composition and expression of genes associated with particular metabolic activities may be a function of sediment organic content as well as oceanic province. Microscopic analysis of Canterbury Basin sediment samples from 4 and 403 mbsf produced visualizations of septate fungal filaments, branching fungi, conidiogenesis, and spores. These images provide another important line of evidence supporting the occurrence and activity of fungi in the deep subseafloor biosphere.

Anaerobic Fungi: A Potential Source of Biological H2 in the Oceanic Crust

The recent recognition of fungi in the oceanic igneous crust challenges the understanding of this environment as being exclusively prokaryotic and forces reconsiderations of the ecology of the deep biosphere. Anoxic provinces in the igneous crust are abundant and increase with age and depth of the crust. The presence of anaerobic fungi in deep-sea sediments and on the seafloor introduces a type of organism with attributes of geobiological significance not previously accounted for. Anaerobic fungi are best known from the rumen of herbivores where they produce molecular hydrogen, which in turn stimulates the growth of methanogens. The symbiotic cooperation between anaerobic fungi and methanogens in the rumen enhance the metabolic rate and growth of both. Methanogens and other hydrogen-consuming anaerobic archaea are known from subseafloor basalt; however, the abiotic production of hydrogen is questioned to be sufficient to support such communities. Alternatively, biologically produced hydrogen could serve as a continuous source. Here, we propose anaerobic fungi as a source of bioavailable hydrogen in the oceanic crust, and a close interplay between anaerobic fungi and hydrogen-driven prokaryotes.