Mechanisms of iron reduction and phosphorus solubilization in an intermittently wet pasture soil

Microbial Fe-reduction in pasture soils may be of agronomic importance, because it has been shown to influence P cycling. The present study investigated the behavior of Fe and P in an intermittently wet, Appalachian pasture soil during a 42 day anaerobic incubation. Native humic acid (HA) extracted from the sampling location and anthraquinone-2,6-disulfonic acid (AQDS) were used in the experiment to determine their electron-mediating effects on Fe(III) reduction and P solubilization over time. Extracted HA and the International Humic Substance Society (IHSS) Elliott Soil HA standard were compared using 13C-NMR, FT-IR, SEM, and CHNS analysis. Soil samples treated with 1.24 g native HA/kg dry soil and 0.2 g AQDS/kg dry soil displayed the highest, most similar, solubilized P rates during the anaerobic incubation. However, the soil alone, without an added electron mediator, was able to release biologically significant concentrations of P to solution at Eh values between 0 and -200 mV. Total soluble P increases were strongly related to soluble Fe(II) increases over time. Field Eh measurements, relative to naturally occurring seasonal changes, are also reported. The purpose of this research was to further define the mechanisms of Fe and P cycling in temperate, pasture soils

Redox Heterogeneity Entangles Soil and Climate Interactions

Partial funding for Open Access provided by the UMD Libraries' Open Access Publishing Fund.Interactions between soils and climate impact wider environmental sustainability. Soil heterogeneity intricately regulates these interactions over short spatiotemporal scales and therefore needs to be more finely examined. This paper examines how redox heterogeneity at the level of minerals, microbial cells, organic matter, and the rhizosphere entangles biogeochemical cycles in soil with climate change. Redox heterogeneity is used to develop a conceptual framework that encompasses soil microsites (anaerobic and aerobic) and cryptic biogeochemical cycling, helping to explain poorly understood processes such as methanogenesis in oxygenated soils. This framework is further shown to disentangle global carbon (C) and nitrogen (N) pathways that include CO2, CH4, and N2O. Climate-driven redox perturbations are discussed using wetlands and tropical forests as model systems. Powerful analytical methods are proposed to be combined and used more extensively to study coupled abiotic and biotic reactions that are affected by redox heterogeneity. A core view is that emerging and future research will benefit substantially from developing multifaceted analyses of redox heterogeneity over short spatiotemporal scales in soil. Taking a leap in our understanding of soil and climate interactions and their evolving influence on environmental sustainability then depends on greater collaborative efforts to comprehensively investigate redox heterogeneity spanning the domain of microscopic soil interfaces.https://doi.org/10.3390/su13181008

Video frame prediction of microbial growth with a recurrent neural network

The recent explosion of interest and advances in machine learning technologies has opened the door to new analytical capabilities in microbiology. Using experimental data such as images or videos, machine learning, in particular deep learning with neural networks, can be harnessed to provide insights and predictions for microbial populations. This paper presents such an application in which a Recurrent Neural Network (RNN) was used to perform prediction of microbial growth for a population of two Pseudomonas aeruginosa mutants. The RNN was trained on videos that were acquired previously using fluorescence microscopy and microfluidics. Of the 20 frames that make up each video, 10 were used as inputs to the network which outputs a prediction for the next 10 frames of the video. The accuracy of the network was evaluated by comparing the predicted frames to the original frames, as well as population curves and the number and size of individual colonies extracted from these frames. Overall, the growth predictions are found to be accurate in metrics such as image comparison, colony size, and total population. Yet, limitations exist due to the scarcity of available and comparable data in the literature, indicating a need for more studies. Both the successes and challenges of our approach are discussed

The Role of Oxygen in Stimulating Methane Production in Wetlands

Methane (CH4), a potent greenhouse gas, is the second most important greenhouse gas contributor to climate change after carbon dioxide (CO2). The biological emissions of CH4 from wetlands are a major uncertainty in CH4 budgets. Microbial methanogenesis by Archaea is an anaerobic process accounting for most biological CH4 production in nature, yet recent observations indicate that large emissions can originate from oxygenated or frequently oxygenated wetland soil layers. To determine how oxygen (O2) can stimulate CH4 emissions, we used incubations of Sphagnum peat to demonstrate that the temporary exposure of peat to O2 can increase CH4 yields up to 2000-fold during subsequent anoxic conditions relative to peat without O2 exposure. Geochemical (including ion cyclotron resonance mass spectrometry, X-ray absorbance spectroscopy) and microbiome (16S rDNA amplicons, metagenomics) analyses of peat showed that higher CH4 yields of redox-oscillated peat were due to functional shifts in the peat microbiome arising during redox oscillation that enhanced peat carbon (C) degradation. Novosphingobium species with O2-dependent aromatic oxygenase genes increased greatly in relative abundance during the oxygenation period in redox-oscillated peat compared to anoxic controls. Acidobacteria species were particularly important for anaerobic processing of peat C, including in the production of methanogenic substrates H2 and CO2. Higher CO2 production during the anoxic phase of redox-oscillated peat stimulated hydrogenotrophic CH4 production by Methanobacterium species. The persistence of reduced iron (Fe(II)) during prolonged oxygenation in redox-oscillated peat may further enhance C degradation through abiotic mechanisms (e.g., Fenton reactions). The results indicate that specific functional shifts in the peat microbiome underlie O2 enhancement of CH4 production in acidic, Sphagnum-rich wetland soils. They also imply that understanding microbial dynamics spanning temporal and spatial redox transitions in peatlands is critical for constraining CH4 budgets; predicting feedbacks between climate change, hydrologic variability, and wetland CH4 emissions; and guiding wetland C management strategies

A microfluidics and agent-based modeling framework for investigating spatial organization in bacterial colonies: The case of Pseudomonas Aeruginosa amd H1-type VI secretion interactions

The factors leading to changes in the organization of microbial assemblages at fine spatial scales are not well characterized or understood. However, they are expected to guide the succession of community development and function toward specific outcomes that could impact human health and the environment. In this study, we put forward a combined experimental and agent-based modeling framework and use it to interpret unique spatial organization patterns of H1-Type VI secretion system (T6SS) mutants of P. aeruginosa under spatial confinement. We find that key parameters, such as T6SS-mediated cell contact and lysis, spatial localization, relative species abundance, cell density and local concentrations of growth substrates and metabolites are influenced by spatial confinement. The model, written in the accessible programming language NetLogo, can be adapted to a variety of biological systems of interest and used to simulate experiments across a broad parameter space. It was implemented and run in a high-throughput mode by deploying it across multiple CPUs, with each simulation representing an individual well within a high-throughput microwell array experimental platform. The microfluidics and agent-based modeling framework we present in this paper provides an effective means by which to connect experimental studies in microbiology to model development. The work demonstrates progress in coupling experimental results to simulation while also highlighting potential sources of discrepancies between real-world experiments and idealized models

A Simple, Inexpensive Device for Nucleic Acid Amplification without Electricity—Toward Instrument-Free Molecular Diagnostics in Low-Resource Settings

Molecular assays targeted to nucleic acid (NA) markers are becoming increasingly important to medical diagnostics. However, these are typically confined to wealthy, developed countries; or, to the national reference laboratories of developing-world countries. There are many infectious diseases that are endemic in low-resource settings (LRS) where the lack of simple, instrument-free, NA diagnostic tests is a critical barrier to timely treatment. One of the primary barriers to the practicality and availability of NA assays in LRS has been the complexity and power requirements of polymerase chain reaction (PCR) instrumentation (another is sample preparation).In this article, we investigate the hypothesis that an electricity-free heater based on exothermic chemical reactions and engineered phase change materials can successfully incubate isothermal NA amplification assays. We assess the heater's equivalence to commercially available PCR instruments through the characterization of the temperature profiles produced, and a minimal method comparison. Versions of the prototype for several different isothermal techniques are presented.We demonstrate that an electricity-free heater based on exothermic chemical reactions and engineered phase change materials can successfully incubate isothermal NA amplification assays, and that the results of those assays are not significantly different from ones incubated in parallel in commercially available PCR instruments. These results clearly suggest the potential of the non-instrumented nucleic acid amplification (NINA) heater for molecular diagnostics in LRS. When combined with other innovations in development that eliminate power requirements for sample preparation, cold reagent storage, and readout, the NINA heater will comprise part of a kit that should enable electricity-free NA testing for many important analytes

Transient O2 pulses direct Fe crystallinity and Fe(III)-reducer gene expression within a soil microbiome

Abstract Background Many environments contain redox transition zones, where transient oxygenation events can modulate anaerobic reactions that influence the cycling of iron (Fe) and carbon (C) on a global scale. In predominantly anoxic soils, this biogeochemical cycling depends on Fe mineral composition and the activity of mixed Fe(III)-reducer populations that may be altered by periodic pulses of molecular oxygen (O2). Methods We repeatedly exposed anoxic (4% H2:96% N2) suspensions of soil from the Luquillo Critical Zone Observatory to 1.05 × 102, 1.05 × 103, and 1.05 × 104 mmol O2 kg−1 soil h−1 during pulsed oxygenation treatments. Metatranscriptomic analysis and 57Fe Mössbauer spectroscopy were used to investigate changes in Fe(III)-reducer gene expression and Fe(III) crystallinity, respectively. Results Slow oxygenation resulted in soil Fe-(oxyhydr)oxides of higher crystallinity (38.1 ± 1.1% of total Fe) compared to fast oxygenation (30.6 ± 1.5%, P < 0.001). Transcripts binning to the genomes of Fe(III)-reducers Anaeromyxobacter, Geobacter, and Pelosinus indicated significant differences in extracellular electron transport (e.g., multiheme cytochrome c, multicopper oxidase, and type-IV pilin gene expression), adhesion/contact (e.g., S-layer, adhesin, and flagellin gene expression), and selective microbial competition (e.g., bacteriocin gene expression) between the slow and fast oxygenation treatments during microbial Fe(III) reduction. These data also suggest that diverse Fe(III)-reducer functions, including cytochrome-dependent extracellular electron transport, are associated with type-III fibronectin domains. Additionally, the metatranscriptomic data indicate that Methanobacterium was significantly more active in the reduction of CO2 to CH4 and in the expression of class(III) signal peptide/type-IV pilin genes following repeated fast oxygenation compared to slow oxygenation. Conclusions This study demonstrates that specific Fe(III)-reduction mechanisms in mixed Fe(III)-reducer populations are uniquely sensitive to the rate of O2 influx, likely mediated by shifts in soil Fe(III)-(oxyhydr)oxide crystallinity. Overall, we provide evidence that transient oxygenation events play an important role in directing anaerobic pathways within soil microbiomes, which is expected to alter Fe and C cycling in redox-dynamic environments

Critical inundation level for methane emissions from wetlands

Global methane (CH4) emissions have reached approximately 600 Tg per year, 20%–40% of which are from wetlands. Of the primary factors affecting these emissions, the water table level is among the most uncertain. Here we conduct a global meta-analysis of chamber and flux-tower observations of CH4 emissions and employ a novel mechanistic model to show that wetlands have maximum emissions at a critical level of inundation and discuss its origin. This maximum arises from an interplay between methanogenesis, methanotrophy, and transport, whose rates vary differently with the inundation level. The specific location of the critical water level above the soil surface may differ depending on wetland characteristics, for example temperature or the presence of macrophytes with aerenchyma. However, data suggest that globally a water level of about 50 cm is the most favorable to CH4 emissions. Keeping the water level away from this critical value could reduce methane emissions in human-made wetlands, which comprise at least one fifth of the global wetland area

Molecular characterization of dissolved organic nitrogen and phosphorus in agricultural runoff and surface waters

Agricultural runoff is a significant contributor to nitrogen (N) and phosphorus (P) pollution in water bodies. Limited information is available about the molecular characteristics of the dissolved organic N (DON) and P (DOP) species in the agricultural runoff and surface waters. We employed Fourier Transform-Ion Cyclotron Resonance-Mass Spectrometry (FT-ICR-MS) to investigate the changes in the molecular characteristics of DON and DOP at three watershed positions (upstream water, runoff from agricultural fields, and downstream waters). Across three watershed locations, more-bioavailable compounds (such as amino sugars, carbohydrates, lipids, and proteins) accounted for 95% of DON and 69–96% of DOP. Of the dissolved organic matter, runoff waters from agricultural fields contained the greatest proportion of DON formulas (20–25%) than upstream (18%) and downstream (13–14%) waters, indicating the presence of a greater diversity of DON species in the runoff. Various nutrient sources present in agricultural fields such as crop residues, soil organic matter, and transformed fertilizers likely contributed to the diverse composition of DON and DOP in the runoff, which were likely altered as the surface water traversed along the flow pathways in the watershed. The presence of more-bioavailable molecules detected in upstream compared to agricultural runoff and downstream waters suggests that photochemical and/or microbial processes likely altered the characteristics of DON and DOP compounds. The findings of this study increase our understanding of DON and DOP compounds lability and transformations in runoff and surface waters, which may be useful in quantifying the contribution of organic N and P sources to water quality impairment in aquatic ecosystems.24 month embargo; available online 30 April 2022This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]