Biotic and abiotic oxidation and reduction of iron at circumneutral pH are inseparable processes under natural conditions

<div><p>Oxidation and reduction of iron can occur through abiotic (chemical) and biotic (microbial) processes. Abiotic iron oxidation is a function of pH and O₂ concentration. Biotic iron oxidation is carried out by a diverse group of bacteria, using O₂ or NO₃ as terminal electron acceptors. At circumneutral pH, both processes occur at similar rates and compete with each other. Abiotic iron reduction is catalyzed by iron-sulfur minerals or different types of organic compounds, whereas biotic iron reduction is carried out by a diverse group of microorganisms, often using chemical agents to dissolve solid iron minerals. We used iron oxidizing microbial mats to assess the potential impact of microbial activity on the deposition of banded iron formations (BIF). The mats were collected during several years from experimental tanks connected to groundwater aquifers with different Fe²⁺ concentrations. To separate between biotic and abiotic iron oxidation, live and killed mats were incubated with ⁵⁷Fe²⁺. Separate analyses of the water and solid phase revealed that the iron oxidation and reduction rates per mL of solid matter (biomass and iron precipitates) were 0.4-73 mmol L⁻¹ d⁻¹ and 30–280 mmol L⁻¹ d⁻¹, respectively. No significant differences in iron oxidation rates were observed between the live and killed samples. The iron reduction rates, however, were higher in the live samples in mats from 3 out of 4 environments. We suggest that in natural systems, in the presence of organic matter, biotic and abiotic iron oxidation and reduction are not separable processes. Fe²⁺ will be biotically and abiotically oxidized as well as bind to exposed charged groups of organic substances. Either way, this iron may serve as a nucleation matrix for further abiotic iron precipitation. The oxidized iron is then susceptible to iron reduction, which can likewise be a direct metabolic or an abiotic process. Nevertheless, it is important to note the significance of organic matter, since both the abiotic oxidation and reduction of iron are often mediated by substrates of biological origin.</p></div

Image_3_Comprehensive single cell analysis of pandemic influenza A virus infection in the human airways uncovers cell-type specific host transcriptional signatures relevant for disease progression and pathogenesis.tif

The respiratory epithelium constitutes the first line of defense against invading respiratory pathogens, such as the 2009 pandemic strain of influenza A virus (IAV, H1N1pdm09), and plays a crucial role in the host antiviral response to infection. Despite its importance, however, it remains unknown how individual cell types within the respiratory epithelium respond to IAV infection or how the latter may influence IAV disease progression and pathogenesis. Here, we used single cell RNA sequencing (scRNA-seq) to dissect the host response to IAV infection in its natural target cells. scRNA-seq was performed on human airway epithelial cell (hAEC) cultures infected with either wild-type pandemic IAV (WT) or with a mutant version of IAV (NS1R38A) that induced a robust innate immune response. We then characterized both the host and viral transcriptomes of more than 19,000 single cells across the 5 major cell types populating the human respiratory epithelium. For all cell types, we observed a wide spectrum of viral burden among single infected cells and a disparate host response between infected and bystander populations. Interestingly, we also identified multiple key differences in the host response to IAV among individual cell types, including high levels of pro-inflammatory cytokines and chemokines in secretory and basal cells and an important role for luminal cells in sensing and restricting incoming virus. Multiple infected cell types were shown to upregulate interferons (IFN), with type III IFNs clearly dominating the antiviral response. Transcriptional changes in genes related to cell differentiation, cell migration, and tissue repair were also identified. Strikingly, we also detected a shift in viral host cell tropism from non-ciliated cells to ciliated cells at later stages of infection and observed major changes in the cellular composition. Microscopic analysis of both WT and NS1R38A virus-infected hAECs at various stages of IAV infection revealed that the transcriptional changes we observed at 18 hpi were likely driving the downstream histopathological alterations in the airway epithelium. To our knowledge, this is the first study to provide a comprehensive analysis of the cell type-specific host antiviral response to influenza virus infection in its natural target cells – namely, the human respiratory epithelium.</p

Table_3_Comprehensive single cell analysis of pandemic influenza A virus infection in the human airways uncovers cell-type specific host transcriptional signatures relevant for disease progression and pathogenesis.xlsx

The respiratory epithelium constitutes the first line of defense against invading respiratory pathogens, such as the 2009 pandemic strain of influenza A virus (IAV, H1N1pdm09), and plays a crucial role in the host antiviral response to infection. Despite its importance, however, it remains unknown how individual cell types within the respiratory epithelium respond to IAV infection or how the latter may influence IAV disease progression and pathogenesis. Here, we used single cell RNA sequencing (scRNA-seq) to dissect the host response to IAV infection in its natural target cells. scRNA-seq was performed on human airway epithelial cell (hAEC) cultures infected with either wild-type pandemic IAV (WT) or with a mutant version of IAV (NS1R38A) that induced a robust innate immune response. We then characterized both the host and viral transcriptomes of more than 19,000 single cells across the 5 major cell types populating the human respiratory epithelium. For all cell types, we observed a wide spectrum of viral burden among single infected cells and a disparate host response between infected and bystander populations. Interestingly, we also identified multiple key differences in the host response to IAV among individual cell types, including high levels of pro-inflammatory cytokines and chemokines in secretory and basal cells and an important role for luminal cells in sensing and restricting incoming virus. Multiple infected cell types were shown to upregulate interferons (IFN), with type III IFNs clearly dominating the antiviral response. Transcriptional changes in genes related to cell differentiation, cell migration, and tissue repair were also identified. Strikingly, we also detected a shift in viral host cell tropism from non-ciliated cells to ciliated cells at later stages of infection and observed major changes in the cellular composition. Microscopic analysis of both WT and NS1R38A virus-infected hAECs at various stages of IAV infection revealed that the transcriptional changes we observed at 18 hpi were likely driving the downstream histopathological alterations in the airway epithelium. To our knowledge, this is the first study to provide a comprehensive analysis of the cell type-specific host antiviral response to influenza virus infection in its natural target cells – namely, the human respiratory epithelium.</p

Image_1_Comprehensive single cell analysis of pandemic influenza A virus infection in the human airways uncovers cell-type specific host transcriptional signatures relevant for disease progression and pathogenesis.tif

The respiratory epithelium constitutes the first line of defense against invading respiratory pathogens, such as the 2009 pandemic strain of influenza A virus (IAV, H1N1pdm09), and plays a crucial role in the host antiviral response to infection. Despite its importance, however, it remains unknown how individual cell types within the respiratory epithelium respond to IAV infection or how the latter may influence IAV disease progression and pathogenesis. Here, we used single cell RNA sequencing (scRNA-seq) to dissect the host response to IAV infection in its natural target cells. scRNA-seq was performed on human airway epithelial cell (hAEC) cultures infected with either wild-type pandemic IAV (WT) or with a mutant version of IAV (NS1R38A) that induced a robust innate immune response. We then characterized both the host and viral transcriptomes of more than 19,000 single cells across the 5 major cell types populating the human respiratory epithelium. For all cell types, we observed a wide spectrum of viral burden among single infected cells and a disparate host response between infected and bystander populations. Interestingly, we also identified multiple key differences in the host response to IAV among individual cell types, including high levels of pro-inflammatory cytokines and chemokines in secretory and basal cells and an important role for luminal cells in sensing and restricting incoming virus. Multiple infected cell types were shown to upregulate interferons (IFN), with type III IFNs clearly dominating the antiviral response. Transcriptional changes in genes related to cell differentiation, cell migration, and tissue repair were also identified. Strikingly, we also detected a shift in viral host cell tropism from non-ciliated cells to ciliated cells at later stages of infection and observed major changes in the cellular composition. Microscopic analysis of both WT and NS1R38A virus-infected hAECs at various stages of IAV infection revealed that the transcriptional changes we observed at 18 hpi were likely driving the downstream histopathological alterations in the airway epithelium. To our knowledge, this is the first study to provide a comprehensive analysis of the cell type-specific host antiviral response to influenza virus infection in its natural target cells – namely, the human respiratory epithelium.</p

Image_4_Comprehensive single cell analysis of pandemic influenza A virus infection in the human airways uncovers cell-type specific host transcriptional signatures relevant for disease progression and pathogenesis.tif

The respiratory epithelium constitutes the first line of defense against invading respiratory pathogens, such as the 2009 pandemic strain of influenza A virus (IAV, H1N1pdm09), and plays a crucial role in the host antiviral response to infection. Despite its importance, however, it remains unknown how individual cell types within the respiratory epithelium respond to IAV infection or how the latter may influence IAV disease progression and pathogenesis. Here, we used single cell RNA sequencing (scRNA-seq) to dissect the host response to IAV infection in its natural target cells. scRNA-seq was performed on human airway epithelial cell (hAEC) cultures infected with either wild-type pandemic IAV (WT) or with a mutant version of IAV (NS1R38A) that induced a robust innate immune response. We then characterized both the host and viral transcriptomes of more than 19,000 single cells across the 5 major cell types populating the human respiratory epithelium. For all cell types, we observed a wide spectrum of viral burden among single infected cells and a disparate host response between infected and bystander populations. Interestingly, we also identified multiple key differences in the host response to IAV among individual cell types, including high levels of pro-inflammatory cytokines and chemokines in secretory and basal cells and an important role for luminal cells in sensing and restricting incoming virus. Multiple infected cell types were shown to upregulate interferons (IFN), with type III IFNs clearly dominating the antiviral response. Transcriptional changes in genes related to cell differentiation, cell migration, and tissue repair were also identified. Strikingly, we also detected a shift in viral host cell tropism from non-ciliated cells to ciliated cells at later stages of infection and observed major changes in the cellular composition. Microscopic analysis of both WT and NS1R38A virus-infected hAECs at various stages of IAV infection revealed that the transcriptional changes we observed at 18 hpi were likely driving the downstream histopathological alterations in the airway epithelium. To our knowledge, this is the first study to provide a comprehensive analysis of the cell type-specific host antiviral response to influenza virus infection in its natural target cells – namely, the human respiratory epithelium.</p

RNA Synthesis Phenotype of the Alb <i>ts</i>16 and LA <i>ts</i>6 Mutants

<p>RNA synthesis (A) or negative-strand RNA synthesis (B) was determined using 20 or 30 min pulse labels with ³H-uridine in the presence of dactinomycin, with or without the addition of CH, after shifting the incubation temperature of MHV-A59-, Alb <i>ts</i>16-, and LA <i>ts</i>6-infected cells from 30 °C to 40 °C at 8 hpi: filled bar, 0–20 min pulse; grey bar, 20–40 min pulse; open bar, 40–60 min pulse; dark diagonal bar, 0–30 min pulse; light diagonal bar, 30–60 min pulse.</p

Petrographic observations on the black chert facies.

<p>(A-D) Thin sections (A, B, D: transmitted light; C: reflected light). (A) Layers are laterally not continuous in thickness but wavy. (B, C) Dark chert layers consist of a fine grained matrix that is enriched in organic matter and pyrite. Note that the organic material is laterally interwoven (B) and closely associated with pyrite (C). (B, D) Fenestrae are filled by blocky cements. (E, F) SEM photographs of the pyrite crystals. Note that the pyrite crystals are enriched in layers (E) and framboidal in shape (F). (G, H) Clusters of silicified acicular crystals, probably representing chert pseudomorphs after aragonite.</p

Stratigraphical context of the Strelley Pool Formation (representative sections; modified after [8], [35], [36], [43], [90]).

<p>The black chert facies corresponds to Member III.</p

CL overlay photographs of the black chert facies.

<p>Note that the calcite aggregates (red luminescence) appear to be linked to organic material (dark colors). (A) Finely laminated layers of organic matter containing CaCO₃ spheroids (red luminescence). (B) Close up view of (A). (C) Aggregated CaCO₃ spheroids (red luminescence) associated with organic matter. (D) Close up view of (C).</p

NanoSIMS isotope enrichment profile across a spheroid (see Fig 8 for orientation of the section).

<p>Organic matter (¹²C¹⁴N) and sulfur (³²S) are closely associated and preferentially enriched at the edges of the body, whereas carbon (¹²C) is also enriched in intermediate spaces due to the presence of carbonate phases.</p